Query psy12011
Match_columns 94
No_of_seqs 105 out of 1775
Neff 11.3
Searched_HMMs 46136
Date Fri Aug 16 16:24:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12011.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12011hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 9.4E-27 2E-31 131.6 4.9 88 6-94 159-249 (279)
2 KOG2462|consensus 99.8 6.2E-21 1.3E-25 108.2 3.2 78 4-82 183-265 (279)
3 KOG3623|consensus 99.7 3.3E-18 7.1E-23 107.6 0.5 78 3-81 889-971 (1007)
4 KOG3576|consensus 99.6 4.1E-17 8.8E-22 89.7 0.1 90 4-94 113-218 (267)
5 KOG3623|consensus 99.6 1E-15 2.2E-20 96.7 1.7 67 27-94 890-956 (1007)
6 KOG3576|consensus 99.4 1.1E-14 2.5E-19 80.2 -0.4 65 29-94 115-179 (267)
7 PHA00733 hypothetical protein 99.3 1.1E-12 2.4E-17 68.7 2.7 78 6-86 38-125 (128)
8 KOG3608|consensus 99.3 2.1E-12 4.5E-17 76.4 2.4 89 2-91 201-322 (467)
9 KOG1074|consensus 99.2 6.1E-12 1.3E-16 80.9 0.7 58 31-89 353-410 (958)
10 KOG3608|consensus 99.1 1.5E-11 3.3E-16 72.9 0.1 85 8-94 263-358 (467)
11 KOG1074|consensus 99.1 3.2E-11 6.8E-16 77.7 1.4 56 30-86 604-659 (958)
12 PHA02768 hypothetical protein; 99.1 3.7E-11 8.1E-16 53.5 1.1 43 31-76 5-47 (55)
13 PHA02768 hypothetical protein; 99.1 1.2E-10 2.7E-15 51.9 2.3 32 61-94 6-37 (55)
14 PHA00616 hypothetical protein 99.0 3.4E-10 7.4E-15 48.2 1.5 33 60-92 1-33 (44)
15 PLN03086 PRLI-interacting fact 98.9 3E-09 6.5E-14 67.2 4.4 84 6-94 451-547 (567)
16 PLN03086 PRLI-interacting fact 98.8 1.3E-08 2.8E-13 64.4 4.7 60 29-94 451-510 (567)
17 PF13465 zf-H2C2_2: Zinc-finge 98.8 5.2E-09 1.1E-13 40.2 1.9 24 47-71 2-25 (26)
18 PF13465 zf-H2C2_2: Zinc-finge 98.8 5E-09 1.1E-13 40.2 1.6 20 75-94 1-20 (26)
19 PHA00733 hypothetical protein 98.7 9E-09 2E-13 54.0 2.3 55 2-56 67-124 (128)
20 PHA00732 hypothetical protein 98.6 3.6E-08 7.7E-13 47.6 1.9 44 31-81 1-45 (79)
21 PHA00616 hypothetical protein 98.6 3.3E-08 7.2E-13 42.2 1.3 34 31-65 1-34 (44)
22 KOG3993|consensus 98.4 2.3E-08 5.1E-13 60.8 -1.1 79 7-85 266-381 (500)
23 PF00096 zf-C2H2: Zinc finger, 98.4 4.3E-07 9.4E-12 33.6 2.3 23 61-83 1-23 (23)
24 PF13894 zf-C2H2_4: C2H2-type 98.2 1.8E-06 4E-11 31.9 2.5 24 61-84 1-24 (24)
25 PF13912 zf-C2H2_6: C2H2-type 98.2 1.2E-06 2.5E-11 33.7 1.8 26 60-85 1-26 (27)
26 PHA00732 hypothetical protein 98.1 3.6E-06 7.7E-11 40.7 2.5 32 60-94 1-33 (79)
27 PF05605 zf-Di19: Drought indu 98.1 8.2E-06 1.8E-10 36.6 3.4 52 31-85 2-54 (54)
28 PF09237 GAGA: GAGA factor; I 98.1 4.9E-06 1.1E-10 36.4 2.5 35 54-88 18-52 (54)
29 PF00096 zf-C2H2: Zinc finger, 98.0 2.7E-06 5.9E-11 31.4 0.9 23 32-54 1-23 (23)
30 PF13912 zf-C2H2_6: C2H2-type 97.8 9E-06 1.9E-10 31.1 1.0 26 31-56 1-26 (27)
31 PF12756 zf-C2H2_2: C2H2 type 97.7 5.3E-05 1.2E-09 37.7 2.7 72 10-83 1-73 (100)
32 smart00355 ZnF_C2H2 zinc finge 97.7 5.6E-05 1.2E-09 28.1 2.1 24 61-84 1-24 (26)
33 PF13894 zf-C2H2_4: C2H2-type 97.6 3.4E-05 7.5E-10 28.3 1.2 23 32-54 1-23 (24)
34 PF13909 zf-H2C2_5: C2H2-type 97.6 0.0001 2.2E-09 27.3 2.3 24 61-85 1-24 (24)
35 COG5189 SFP1 Putative transcri 97.5 4E-05 8.7E-10 45.8 0.9 24 57-81 396-419 (423)
36 PRK04860 hypothetical protein; 97.4 0.00013 2.9E-09 39.8 2.5 31 60-94 119-149 (160)
37 PF05605 zf-Di19: Drought indu 97.2 0.00065 1.4E-08 30.4 3.0 33 61-94 3-37 (54)
38 smart00355 ZnF_C2H2 zinc finge 97.2 0.00028 6E-09 26.1 1.5 24 32-55 1-24 (26)
39 PF12874 zf-met: Zinc-finger o 97.1 0.00045 9.7E-09 25.7 1.8 22 61-82 1-22 (25)
40 PF09237 GAGA: GAGA factor; I 97.1 0.00041 8.9E-09 30.5 1.7 34 26-59 19-52 (54)
41 KOG3993|consensus 97.1 0.00015 3.2E-09 44.9 0.2 53 31-84 267-319 (500)
42 PF12874 zf-met: Zinc-finger o 96.9 0.00044 9.6E-09 25.7 0.8 23 32-54 1-23 (25)
43 PRK04860 hypothetical protein; 96.7 0.00082 1.8E-08 36.8 1.3 38 31-73 119-156 (160)
44 PF12171 zf-C2H2_jaz: Zinc-fin 96.7 0.0013 2.9E-08 25.0 1.5 21 32-52 2-22 (27)
45 COG5189 SFP1 Putative transcri 95.9 0.0055 1.2E-07 37.1 1.7 37 57-94 347-404 (423)
46 PF13913 zf-C2HC_2: zinc-finge 95.9 0.0098 2.1E-07 22.3 1.8 20 61-81 3-22 (25)
47 TIGR02098 MJ0042_CXXC MJ0042 f 95.1 0.017 3.6E-07 23.8 1.4 10 61-70 26-35 (38)
48 PF13717 zinc_ribbon_4: zinc-r 95.0 0.021 4.6E-07 23.3 1.5 10 61-70 26-35 (36)
49 smart00451 ZnF_U1 U1-like zinc 94.9 0.031 6.7E-07 22.3 2.0 22 61-82 4-25 (35)
50 PF13719 zinc_ribbon_5: zinc-r 94.6 0.027 5.8E-07 23.2 1.4 32 33-70 4-35 (37)
51 COG5048 FOG: Zn-finger [Genera 94.6 0.012 2.7E-07 36.2 0.5 61 30-91 288-354 (467)
52 PF09723 Zn-ribbon_8: Zinc rib 94.3 0.037 8E-07 23.4 1.5 28 9-38 6-33 (42)
53 COG2888 Predicted Zn-ribbon RN 94.0 0.051 1.1E-06 24.7 1.7 32 30-67 26-57 (61)
54 smart00834 CxxC_CXXC_SSSS Puta 93.0 0.085 1.8E-06 21.8 1.5 13 9-21 6-18 (41)
55 COG1592 Rubrerythrin [Energy p 92.5 0.14 3.1E-06 28.3 2.3 8 8-15 134-141 (166)
56 cd00350 rubredoxin_like Rubred 92.3 0.16 3.4E-06 20.2 1.8 24 32-68 2-25 (33)
57 smart00531 TFIIE Transcription 92.3 0.12 2.6E-06 28.0 1.9 39 28-71 96-134 (147)
58 TIGR02605 CxxC_CxxC_SSSS putat 92.1 0.13 2.7E-06 22.6 1.5 28 9-38 6-33 (52)
59 PRK00398 rpoP DNA-directed RNA 91.7 0.16 3.5E-06 21.8 1.6 28 8-40 3-30 (46)
60 KOG1146|consensus 91.7 0.21 4.6E-06 35.9 2.8 56 26-82 460-540 (1406)
61 cd00729 rubredoxin_SM Rubredox 91.6 0.2 4.3E-06 20.2 1.7 10 8-17 2-11 (34)
62 PF12756 zf-C2H2_2: C2H2 type 91.3 0.14 3E-06 25.3 1.4 25 31-55 50-74 (100)
63 smart00659 RPOLCX RNA polymera 90.7 0.19 4.1E-06 21.5 1.3 10 61-70 20-29 (44)
64 PF09538 FYDLN_acid: Protein o 90.2 0.2 4.4E-06 25.8 1.3 30 9-44 10-39 (108)
65 KOG2186|consensus 90.1 0.17 3.7E-06 29.9 1.1 38 32-72 4-41 (276)
66 TIGR00373 conserved hypothetic 89.9 0.22 4.7E-06 27.4 1.4 35 27-71 105-139 (158)
67 smart00614 ZnF_BED BED zinc fi 89.8 0.4 8.7E-06 20.9 2.0 22 61-82 19-45 (50)
68 PRK00464 nrdR transcriptional 89.7 0.17 3.7E-06 27.7 0.9 39 10-48 2-45 (154)
69 PF05443 ROS_MUCR: ROS/MUCR tr 89.4 0.27 5.9E-06 26.2 1.5 25 61-88 73-97 (132)
70 PRK14890 putative Zn-ribbon RN 89.2 0.4 8.8E-06 21.9 1.8 52 6-68 5-56 (59)
71 PF10571 UPF0547: Uncharacteri 89.1 0.28 6.1E-06 18.5 1.1 9 62-70 16-24 (26)
72 PRK06266 transcription initiat 89.0 0.3 6.4E-06 27.4 1.5 33 29-71 115-147 (178)
73 PF09986 DUF2225: Uncharacteri 88.8 0.15 3.2E-06 29.4 0.3 16 7-22 4-19 (214)
74 COG1997 RPL43A Ribosomal prote 88.2 0.28 6.1E-06 24.2 1.0 11 61-71 54-64 (89)
75 COG4049 Uncharacterized protei 88.1 0.36 7.7E-06 21.7 1.2 23 30-52 16-38 (65)
76 PF12013 DUF3505: Protein of u 87.9 0.65 1.4E-05 23.7 2.3 25 61-85 81-109 (109)
77 PF04959 ARS2: Arsenite-resist 87.5 0.35 7.5E-06 28.0 1.2 31 56-87 74-104 (214)
78 PF02892 zf-BED: BED zinc fing 87.5 0.74 1.6E-05 19.4 2.0 22 61-82 17-42 (45)
79 PF06524 NOA36: NOA36 protein; 85.8 0.41 9E-06 28.5 1.0 77 3-81 137-230 (314)
80 PHA00626 hypothetical protein 85.8 0.66 1.4E-05 20.9 1.4 11 31-41 23-33 (59)
81 KOG2893|consensus 85.5 0.2 4.4E-06 29.4 -0.4 28 37-69 16-43 (341)
82 PF05191 ADK_lid: Adenylate ki 85.0 0.82 1.8E-05 18.6 1.4 29 9-40 2-30 (36)
83 KOG2893|consensus 85.0 0.2 4.4E-06 29.4 -0.5 42 10-51 12-54 (341)
84 TIGR02300 FYDLN_acid conserved 84.3 0.82 1.8E-05 24.3 1.5 31 9-45 10-40 (129)
85 PF03604 DNA_RNApol_7kD: DNA d 84.0 0.45 9.8E-06 18.9 0.4 9 61-69 18-26 (32)
86 smart00734 ZnF_Rad18 Rad18-lik 83.9 1.3 2.9E-05 16.6 1.7 20 61-81 2-21 (26)
87 PF07754 DUF1610: Domain of un 81.2 1.7 3.8E-05 16.0 1.5 10 7-16 15-24 (24)
88 KOG4173|consensus 79.6 0.43 9.4E-06 27.5 -0.5 78 7-84 78-170 (253)
89 PTZ00255 60S ribosomal protein 79.6 0.71 1.5E-05 23.0 0.3 11 61-71 55-65 (90)
90 TIGR01206 lysW lysine biosynth 79.2 1.4 3E-05 19.8 1.2 30 9-41 3-32 (54)
91 PF10276 zf-CHCC: Zinc-finger 79.0 1.9 4E-05 18.1 1.4 12 7-18 28-39 (40)
92 PF14311 DUF4379: Domain of un 78.8 2.9 6.2E-05 18.5 2.1 15 61-75 29-43 (55)
93 KOG2593|consensus 78.6 1 2.2E-05 28.8 0.8 33 7-39 127-161 (436)
94 PF12760 Zn_Tnp_IS1595: Transp 77.9 1.6 3.6E-05 18.6 1.2 8 9-16 19-26 (46)
95 COG1996 RPC10 DNA-directed RNA 77.6 1.5 3.3E-05 19.2 1.0 11 31-41 6-16 (49)
96 PF13451 zf-trcl: Probable zin 77.6 0.81 1.8E-05 20.1 0.1 15 30-44 3-17 (49)
97 KOG4167|consensus 75.6 0.69 1.5E-05 31.6 -0.5 24 61-84 793-816 (907)
98 COG0068 HypF Hydrogenase matur 75.0 2.2 4.9E-05 29.2 1.6 52 11-69 126-182 (750)
99 COG4957 Predicted transcriptio 75.0 1.8 4E-05 23.2 1.1 25 61-88 77-101 (148)
100 PF01780 Ribosomal_L37ae: Ribo 74.7 0.95 2.1E-05 22.6 -0.0 11 61-71 54-64 (90)
101 PF10083 DUF2321: Uncharacteri 74.6 2.4 5.1E-05 23.4 1.4 36 10-45 41-82 (158)
102 KOG1146|consensus 73.6 2.3 5E-05 31.2 1.5 76 9-85 1261-1353(1406)
103 COG3364 Zn-ribbon containing p 73.5 1.2 2.7E-05 22.7 0.2 16 8-23 2-17 (112)
104 KOG3408|consensus 72.9 2.6 5.6E-05 22.3 1.3 26 56-82 54-79 (129)
105 COG4888 Uncharacterized Zn rib 72.6 2.1 4.6E-05 21.8 0.9 38 6-43 20-58 (104)
106 TIGR00280 L37a ribosomal prote 72.3 1.2 2.7E-05 22.2 0.0 11 61-71 54-64 (91)
107 COG3677 Transposase and inacti 72.1 2.8 6E-05 22.4 1.3 16 29-44 51-66 (129)
108 COG3357 Predicted transcriptio 71.6 3 6.4E-05 20.9 1.3 13 31-43 58-70 (97)
109 PRK04023 DNA polymerase II lar 69.9 7.3 0.00016 28.1 3.1 10 8-17 626-635 (1121)
110 PF08274 PhnA_Zn_Ribbon: PhnA 68.5 3.6 7.9E-05 16.0 1.0 8 61-68 20-27 (30)
111 PF05129 Elf1: Transcription e 68.0 1.8 3.9E-05 21.1 0.1 9 7-15 21-29 (81)
112 PF09845 DUF2072: Zn-ribbon co 66.2 3 6.6E-05 22.3 0.7 15 8-22 1-15 (131)
113 smart00154 ZnF_AN1 AN1-like Zi 66.2 3.9 8.4E-05 16.9 0.9 16 8-23 12-27 (39)
114 PF00301 Rubredoxin: Rubredoxi 64.3 8.1 0.00018 16.8 1.8 9 9-17 2-10 (47)
115 PRK03976 rpl37ae 50S ribosomal 63.5 2.2 4.8E-05 21.3 -0.1 11 61-71 55-65 (90)
116 PRK09678 DNA-binding transcrip 63.4 3.4 7.4E-05 19.7 0.5 37 9-45 2-43 (72)
117 PF13453 zf-TFIIB: Transcripti 63.2 4.7 0.0001 16.7 0.9 15 33-47 21-35 (41)
118 PF07975 C1_4: TFIIH C1-like d 62.9 3.8 8.2E-05 18.2 0.6 26 29-54 19-44 (51)
119 smart00731 SprT SprT homologue 62.4 7.3 0.00016 21.0 1.8 32 31-70 112-143 (146)
120 PF15269 zf-C2H2_7: Zinc-finge 62.3 7.3 0.00016 16.8 1.4 21 61-81 21-41 (54)
121 PF14446 Prok-RING_1: Prokaryo 61.6 4.5 9.7E-05 18.2 0.7 14 10-23 7-20 (54)
122 KOG0782|consensus 61.6 1.8 3.9E-05 29.1 -0.7 36 10-45 255-290 (1004)
123 PF08271 TF_Zn_Ribbon: TFIIB z 61.0 5.3 0.00012 16.7 0.9 28 9-40 1-28 (43)
124 COG1571 Predicted DNA-binding 61.0 6.1 0.00013 25.5 1.5 30 10-45 352-381 (421)
125 PF05290 Baculo_IE-1: Baculovi 60.5 8.7 0.00019 20.7 1.8 57 5-75 77-136 (140)
126 PF10263 SprT-like: SprT-like 60.4 5.8 0.00012 21.4 1.2 31 31-70 123-153 (157)
127 PF01428 zf-AN1: AN1-like Zinc 59.8 4.5 9.7E-05 17.0 0.5 17 7-23 12-28 (43)
128 COG3091 SprT Zn-dependent meta 59.3 4.3 9.4E-05 22.3 0.6 29 61-94 118-146 (156)
129 PF01363 FYVE: FYVE zinc finge 58.8 5.8 0.00013 18.3 0.9 30 8-44 9-38 (69)
130 COG5048 FOG: Zn-finger [Genera 58.4 9.5 0.00021 23.7 2.0 59 29-88 31-91 (467)
131 PF08790 zf-LYAR: LYAR-type C2 58.0 4.5 9.7E-05 15.6 0.4 9 33-41 2-10 (28)
132 PRK12380 hydrogenase nickel in 57.8 8.3 0.00018 20.0 1.4 11 31-41 70-80 (113)
133 PF07295 DUF1451: Protein of u 57.4 6.8 0.00015 21.4 1.1 9 31-39 112-120 (146)
134 PF01155 HypA: Hydrogenase exp 56.6 7.4 0.00016 20.1 1.1 11 32-42 71-81 (113)
135 COG1198 PriA Primosomal protei 55.6 9.6 0.00021 26.5 1.8 11 29-39 473-483 (730)
136 PLN02294 cytochrome c oxidase 55.2 7.5 0.00016 21.9 1.0 15 6-20 139-153 (174)
137 PF04423 Rad50_zn_hook: Rad50 54.6 5.8 0.00013 17.5 0.5 12 10-21 22-33 (54)
138 PF02748 PyrI_C: Aspartate car 54.0 4.9 0.00011 17.8 0.2 15 5-19 32-46 (52)
139 KOG4167|consensus 53.5 3.5 7.5E-05 28.5 -0.4 26 30-55 791-816 (907)
140 PF14353 CpXC: CpXC protein 53.4 8.8 0.00019 20.1 1.1 19 7-25 37-55 (128)
141 COG1675 TFA1 Transcription ini 53.0 8.7 0.00019 21.8 1.1 9 61-69 133-141 (176)
142 PF05180 zf-DNL: DNL zinc fing 52.7 5.8 0.00013 18.6 0.3 34 32-69 5-38 (66)
143 PRK03824 hypA hydrogenase nick 52.7 12 0.00026 20.1 1.6 15 7-21 69-83 (135)
144 smart00440 ZnF_C2C2 C2C2 Zinc 51.9 13 0.00028 15.4 1.3 9 61-69 29-37 (40)
145 TIGR00100 hypA hydrogenase nic 51.5 13 0.00027 19.4 1.5 13 31-43 70-82 (115)
146 PF08394 Arc_trans_TRASH: Arch 51.4 5 0.00011 16.5 0.0 9 11-19 1-9 (37)
147 PRK04351 hypothetical protein; 51.2 14 0.0003 20.3 1.7 32 31-71 112-143 (149)
148 PF01286 XPA_N: XPA protein N- 51.1 9.4 0.0002 15.4 0.8 16 10-25 5-20 (34)
149 PRK14892 putative transcriptio 51.0 18 0.00039 18.5 1.9 34 7-42 20-53 (99)
150 KOG3507|consensus 50.7 19 0.00042 16.5 1.8 12 61-72 38-49 (62)
151 PF06397 Desulfoferrod_N: Desu 49.5 11 0.00025 15.4 0.9 12 7-18 5-16 (36)
152 PF12773 DZR: Double zinc ribb 49.4 17 0.00036 15.5 1.5 9 61-69 30-38 (50)
153 PF11789 zf-Nse: Zinc-finger o 49.2 9.5 0.00021 17.2 0.7 15 31-45 24-38 (57)
154 COG2879 Uncharacterized small 49.1 21 0.00045 16.6 1.8 19 72-90 24-42 (65)
155 cd00065 FYVE FYVE domain; Zinc 48.5 12 0.00026 16.3 1.1 27 10-43 4-30 (57)
156 COG4391 Uncharacterized protei 48.4 8.9 0.00019 17.7 0.6 12 8-19 48-59 (62)
157 cd00924 Cyt_c_Oxidase_Vb Cytoc 47.7 9.1 0.0002 19.4 0.6 22 48-71 69-90 (97)
158 PRK00432 30S ribosomal protein 47.1 13 0.00029 16.3 1.0 9 61-69 38-46 (50)
159 PF09963 DUF2197: Uncharacteri 46.6 5.4 0.00012 18.1 -0.3 6 61-66 32-37 (56)
160 PF01927 Mut7-C: Mut7-C RNAse 46.4 12 0.00026 20.3 1.0 16 61-76 125-140 (147)
161 smart00661 RPOL9 RNA polymeras 46.2 18 0.00039 15.5 1.4 11 31-41 20-30 (52)
162 PF10013 DUF2256: Uncharacteri 45.0 18 0.00038 15.4 1.2 12 10-21 10-21 (42)
163 PRK00564 hypA hydrogenase nick 44.4 17 0.00036 19.0 1.3 12 31-42 71-82 (117)
164 TIGR00622 ssl1 transcription f 44.4 26 0.00057 18.3 2.0 74 8-84 15-105 (112)
165 TIGR03831 YgiT_finger YgiT-typ 44.0 14 0.0003 15.2 0.9 12 8-19 32-43 (46)
166 PF07282 OrfB_Zn_ribbon: Putat 43.9 17 0.00037 16.7 1.2 11 61-71 47-57 (69)
167 smart00064 FYVE Protein presen 43.5 17 0.00038 16.6 1.2 29 8-43 10-38 (68)
168 PRK03681 hypA hydrogenase nick 43.1 19 0.00041 18.7 1.4 11 31-41 70-80 (114)
169 COG4530 Uncharacterized protei 42.9 13 0.00027 19.4 0.7 29 9-43 10-38 (129)
170 KOG2482|consensus 41.4 17 0.00037 23.0 1.2 22 61-82 196-217 (423)
171 PTZ00043 cytochrome c oxidase 40.5 15 0.00032 21.8 0.8 18 5-22 178-195 (268)
172 PF07649 C1_3: C1-like domain; 40.4 18 0.00038 13.7 0.8 6 61-66 16-21 (30)
173 PF10537 WAC_Acf1_DNA_bd: ATP- 40.0 36 0.00078 17.4 2.1 33 7-39 2-38 (102)
174 smart00132 LIM Zinc-binding do 39.6 22 0.00047 13.7 1.1 7 61-67 28-34 (39)
175 COG1773 Rubredoxin [Energy pro 39.4 16 0.00036 16.5 0.7 12 8-19 3-14 (55)
176 PRK12496 hypothetical protein; 39.2 27 0.00059 19.4 1.7 10 32-41 128-137 (164)
177 PF13878 zf-C2H2_3: zinc-finge 39.1 35 0.00075 14.2 2.1 23 61-83 14-38 (41)
178 COG1655 Uncharacterized protei 37.7 7.2 0.00016 23.1 -0.7 9 61-69 63-71 (267)
179 KOG2932|consensus 37.7 50 0.0011 20.8 2.7 73 4-84 86-171 (389)
180 PRK05978 hypothetical protein; 37.2 29 0.00062 19.1 1.5 6 11-16 36-41 (148)
181 PF12907 zf-met2: Zinc-binding 37.2 17 0.00036 15.3 0.5 22 61-82 2-26 (40)
182 TIGR00319 desulf_FeS4 desulfof 36.6 27 0.00059 13.6 1.1 13 6-18 5-17 (34)
183 cd00974 DSRD Desulforedoxin (D 36.6 27 0.00059 13.6 1.1 12 7-18 3-14 (34)
184 PF02176 zf-TRAF: TRAF-type zi 36.3 24 0.00053 15.5 1.1 27 44-71 23-53 (60)
185 KOG2071|consensus 35.9 27 0.00059 23.7 1.5 24 61-84 419-442 (579)
186 TIGR00143 hypF [NiFe] hydrogen 35.5 29 0.00063 24.2 1.7 53 11-70 93-150 (711)
187 PF11494 Ta0938: Ta0938; Inte 35.4 24 0.00052 18.0 1.0 38 5-42 11-48 (105)
188 PF01215 COX5B: Cytochrome c o 35.1 19 0.00042 19.5 0.7 13 7-19 111-123 (136)
189 PF09151 DUF1936: Domain of un 35.0 14 0.0003 14.5 0.1 9 9-17 2-10 (36)
190 KOG2636|consensus 34.3 25 0.00055 23.1 1.2 27 26-52 396-423 (497)
191 PRK03564 formate dehydrogenase 34.1 45 0.00098 20.8 2.2 11 7-17 186-196 (309)
192 PRK11823 DNA repair protein Ra 33.9 44 0.00096 21.8 2.2 15 6-20 5-19 (446)
193 PF13240 zinc_ribbon_2: zinc-r 33.8 28 0.0006 12.5 0.8 7 11-17 2-8 (23)
194 PRK11032 hypothetical protein; 33.4 43 0.00092 18.8 1.8 8 31-38 124-131 (160)
195 PF04641 Rtf2: Rtf2 RING-finge 33.4 32 0.00069 20.7 1.5 18 5-22 110-127 (260)
196 PF14255 Cys_rich_CPXG: Cystei 32.6 23 0.0005 15.8 0.6 13 10-22 2-14 (52)
197 PF06689 zf-C4_ClpX: ClpX C4-t 32.4 11 0.00023 15.7 -0.4 28 10-37 3-30 (41)
198 KOG2785|consensus 32.3 68 0.0015 20.7 2.7 51 31-82 166-242 (390)
199 PF03811 Zn_Tnp_IS1: InsA N-te 32.3 45 0.00098 13.5 1.6 6 61-66 30-35 (36)
200 KOG0978|consensus 32.3 13 0.00027 25.8 -0.3 16 61-76 679-694 (698)
201 PF04810 zf-Sec23_Sec24: Sec23 32.1 42 0.00092 13.7 1.4 8 31-38 24-31 (40)
202 PF15135 UPF0515: Uncharacteri 32.1 37 0.0008 20.6 1.5 11 5-15 109-119 (278)
203 PRK05452 anaerobic nitric oxid 31.8 55 0.0012 21.7 2.4 14 29-42 423-436 (479)
204 TIGR00627 tfb4 transcription f 31.8 37 0.0008 20.8 1.6 12 30-41 254-265 (279)
205 PF04780 DUF629: Protein of un 31.3 52 0.0011 21.9 2.2 23 61-83 58-80 (466)
206 PF00412 LIM: LIM domain; Int 30.9 28 0.00061 15.0 0.8 13 30-42 25-37 (58)
207 PTZ00448 hypothetical protein; 30.6 40 0.00087 21.6 1.6 22 61-82 315-336 (373)
208 PF05741 zf-nanos: Nanos RNA b 30.5 21 0.00047 16.1 0.3 11 7-17 32-42 (55)
209 PF08209 Sgf11: Sgf11 (transcr 30.5 36 0.00079 13.5 1.0 22 60-82 4-25 (33)
210 TIGR03829 YokU_near_AblA uncha 30.3 25 0.00055 17.6 0.6 16 9-24 36-51 (89)
211 cd01121 Sms Sms (bacterial rad 30.3 30 0.00066 22.0 1.1 9 9-17 1-9 (372)
212 PHA02998 RNA polymerase subuni 30.0 40 0.00086 19.3 1.4 38 32-73 144-184 (195)
213 PRK12722 transcriptional activ 29.8 52 0.0011 19.0 1.8 10 33-42 136-145 (187)
214 PRK00420 hypothetical protein; 29.7 37 0.0008 17.8 1.2 8 32-39 41-48 (112)
215 KOG1842|consensus 29.4 32 0.0007 22.7 1.1 21 61-81 16-36 (505)
216 TIGR01562 FdhE formate dehydro 29.3 59 0.0013 20.3 2.1 10 8-17 184-193 (305)
217 PRK00762 hypA hydrogenase nick 29.3 50 0.0011 17.5 1.7 14 30-44 69-82 (124)
218 COG4338 Uncharacterized protei 29.2 15 0.00033 16.1 -0.3 13 10-22 14-26 (54)
219 TIGR00416 sms DNA repair prote 29.0 40 0.00087 22.1 1.5 23 7-38 6-28 (454)
220 COG4306 Uncharacterized protei 28.9 46 0.001 17.9 1.4 15 30-44 67-81 (160)
221 COG5112 UFD2 U1-like Zn-finger 28.9 20 0.00044 18.6 0.1 21 61-81 56-76 (126)
222 KOG0562|consensus 28.8 52 0.0011 18.7 1.7 24 61-84 154-177 (184)
223 PF02150 RNA_POL_M_15KD: RNA p 28.7 17 0.00038 14.5 -0.1 8 33-40 22-29 (35)
224 COG2331 Uncharacterized protei 28.4 25 0.00055 17.1 0.4 28 9-39 13-41 (82)
225 PF14690 zf-ISL3: zinc-finger 27.7 28 0.00061 14.5 0.5 9 8-16 2-10 (47)
226 COG4847 Uncharacterized protei 27.7 24 0.00053 17.9 0.3 30 5-34 3-34 (103)
227 PF08792 A2L_zn_ribbon: A2L zi 27.6 53 0.0012 13.0 1.2 7 9-15 4-10 (33)
228 PF11672 DUF3268: Protein of u 27.6 27 0.00059 17.9 0.5 12 30-41 1-12 (102)
229 KOG3214|consensus 27.3 43 0.00093 17.2 1.1 11 33-43 49-59 (109)
230 PF01096 TFIIS_C: Transcriptio 26.8 33 0.00071 14.0 0.6 11 8-18 28-38 (39)
231 PRK01343 zinc-binding protein; 26.6 57 0.0012 14.9 1.3 13 7-19 8-20 (57)
232 COG1066 Sms Predicted ATP-depe 26.4 71 0.0015 21.1 2.1 16 7-22 6-21 (456)
233 PRK12860 transcriptional activ 25.9 82 0.0018 18.2 2.2 9 33-41 136-144 (189)
234 TIGR00595 priA primosomal prot 25.8 56 0.0012 21.8 1.7 12 28-39 250-261 (505)
235 PF11023 DUF2614: Protein of u 25.8 56 0.0012 17.2 1.4 8 31-38 69-76 (114)
236 KOG4124|consensus 25.8 23 0.00049 22.6 -0.0 19 7-25 348-368 (442)
237 KOG4477|consensus 25.8 36 0.00077 19.6 0.7 10 5-14 21-30 (228)
238 PF04606 Ogr_Delta: Ogr/Delta- 25.4 16 0.00035 15.6 -0.5 6 66-71 33-38 (47)
239 PF13639 zf-RING_2: Ring finge 24.7 68 0.0015 13.1 1.8 27 61-94 17-43 (44)
240 PF02591 DUF164: Putative zinc 24.7 32 0.0007 15.2 0.4 32 33-69 24-55 (56)
241 PF12156 ATPase-cat_bd: Putati 24.5 49 0.0011 16.3 1.0 33 10-42 2-37 (88)
242 PF14369 zf-RING_3: zinc-finge 24.2 41 0.00089 13.5 0.6 10 10-19 23-32 (35)
243 KOG0320|consensus 24.2 23 0.0005 20.2 -0.2 11 61-71 168-178 (187)
244 TIGR00686 phnA alkylphosphonat 24.2 49 0.0011 17.3 1.0 12 31-42 19-30 (109)
245 PLN02748 tRNA dimethylallyltra 23.7 46 0.00099 22.1 1.0 24 30-53 417-441 (468)
246 KOG0717|consensus 23.7 48 0.001 22.1 1.1 22 61-82 293-314 (508)
247 PRK14873 primosome assembly pr 23.5 75 0.0016 22.2 2.0 10 9-18 393-402 (665)
248 cd00730 rubredoxin Rubredoxin; 23.3 40 0.00087 14.8 0.5 11 9-19 2-12 (50)
249 KOG2231|consensus 23.3 90 0.002 21.9 2.3 23 33-55 184-206 (669)
250 COG5236 Uncharacterized conser 23.0 66 0.0014 20.6 1.6 23 33-55 222-244 (493)
251 PRK10220 hypothetical protein; 23.0 59 0.0013 17.0 1.2 12 31-42 20-31 (111)
252 PF14803 Nudix_N_2: Nudix N-te 22.9 67 0.0014 12.8 1.1 13 5-17 19-31 (34)
253 COG1779 C4-type Zn-finger prot 22.6 35 0.00076 19.8 0.3 34 9-42 15-54 (201)
254 PF13824 zf-Mss51: Zinc-finger 22.4 49 0.0011 15.0 0.7 12 6-17 12-23 (55)
255 PF11331 DUF3133: Protein of u 22.0 46 0.001 14.4 0.6 6 33-38 33-38 (46)
256 KOG0402|consensus 22.0 26 0.00055 17.3 -0.2 34 27-71 32-65 (92)
257 KOG1280|consensus 21.8 1E+02 0.0022 19.8 2.1 29 61-89 80-108 (381)
258 KOG3352|consensus 21.8 34 0.00073 19.0 0.2 22 49-72 124-145 (153)
259 PRK05580 primosome assembly pr 21.7 73 0.0016 22.2 1.7 13 28-40 418-430 (679)
260 PF10915 DUF2709: Protein of u 21.7 83 0.0018 18.4 1.7 20 4-23 83-102 (238)
261 PF14447 Prok-RING_4: Prokaryo 21.3 60 0.0013 14.7 0.9 8 11-18 42-49 (55)
262 PF14787 zf-CCHC_5: GAG-polypr 20.9 69 0.0015 13.1 0.9 14 10-23 4-17 (36)
263 PF00130 C1_1: Phorbol esters/ 20.6 94 0.002 13.2 1.8 12 7-18 10-21 (53)
264 PF13248 zf-ribbon_3: zinc-rib 20.4 62 0.0013 11.8 0.7 7 10-16 4-10 (26)
265 KOG4602|consensus 20.3 41 0.00089 20.5 0.3 11 7-17 267-277 (318)
No 1
>KOG2462|consensus
Probab=99.93 E-value=9.4e-27 Score=131.56 Aligned_cols=88 Identities=20% Similarity=0.503 Sum_probs=79.6
Q ss_pred CceeecCCCCccccchhccC-C--CCCCccccccchhhccChHHHHcchhhhcCCCCceeCCCCcccccchhHHHHHHHH
Q psy12011 6 LQVHFCGLFPESFLTWSNLK-P--NLNGMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKRKGNLKSHLAI 82 (94)
Q Consensus 6 ~~~~~c~~c~~~~~~~~~l~-~--~~~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~ 82 (94)
.+.+.|++|||.|...-.|+ | +..-+++|.+||+.|..+..|+.|+++|+||+| |.|..|+++|.-++||+.|++|
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKP-F~C~hC~kAFADRSNLRAHmQT 237 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKP-FSCPHCGKAFADRSNLRAHMQT 237 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCC-ccCCcccchhcchHHHHHHHHh
Confidence 56677888888887777776 2 444689999999999999999999999999999 9999999999999999999999
Q ss_pred hcCcccCCCCCC
Q psy12011 83 RHECYLDDSANC 94 (94)
Q Consensus 83 ~~~~~~~~c~~C 94 (94)
|.+.|.|+|..|
T Consensus 238 HS~~K~~qC~~C 249 (279)
T KOG2462|consen 238 HSDVKKHQCPRC 249 (279)
T ss_pred hcCCccccCcch
Confidence 999999999987
No 2
>KOG2462|consensus
Probab=99.82 E-value=6.2e-21 Score=108.22 Aligned_cols=78 Identities=23% Similarity=0.384 Sum_probs=73.2
Q ss_pred CCCceeecCCCCccccchhccC-----CCCCCccccccchhhccChHHHHcchhhhcCCCCceeCCCCcccccchhHHHH
Q psy12011 4 QNLQVHFCGLFPESFLTWSNLK-----PNLNGMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKRKGNLKS 78 (94)
Q Consensus 4 ~~~~~~~c~~c~~~~~~~~~l~-----~~~~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~ 78 (94)
+..-+++|..|||.|...+-|+ |+|||||.|..|++.|.+.++|..||++|.+.++ |+|..|+|.|...+-|.+
T Consensus 183 TH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~-~qC~~C~KsFsl~SyLnK 261 (279)
T KOG2462|consen 183 THTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKK-HQCPRCGKSFALKSYLNK 261 (279)
T ss_pred ccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCcc-ccCcchhhHHHHHHHHHH
Confidence 4456899999999999999887 8999999999999999999999999999999998 999999999999999999
Q ss_pred HHHH
Q psy12011 79 HLAI 82 (94)
Q Consensus 79 h~~~ 82 (94)
|...
T Consensus 262 H~ES 265 (279)
T KOG2462|consen 262 HSES 265 (279)
T ss_pred hhhh
Confidence 9864
No 3
>KOG3623|consensus
Probab=99.69 E-value=3.3e-18 Score=107.65 Aligned_cols=78 Identities=27% Similarity=0.533 Sum_probs=69.1
Q ss_pred CCCCceeecCCCCccccchhccC-----CCCCCccccccchhhccChHHHHcchhhhcCCCCceeCCCCcccccchhHHH
Q psy12011 3 SQNLQVHFCGLFPESFLTWSNLK-----PNLNGMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKRKGNLK 77 (94)
Q Consensus 3 ~~~~~~~~c~~c~~~~~~~~~l~-----~~~~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~ 77 (94)
.+...+|.|..|+|.|...+.|. |+|.+||+|.+|.+.|..+..|..|.+.|.|++| |+|..|++.|..+++..
T Consensus 889 kte~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKP-fQCdKClKRFSHSGSYS 967 (1007)
T KOG3623|consen 889 KTEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKP-FQCDKCLKRFSHSGSYS 967 (1007)
T ss_pred cCccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCc-chhhhhhhhcccccchH
Confidence 45667899999999998877776 8999999999999999999999999999999888 99999999999999888
Q ss_pred HHHH
Q psy12011 78 SHLA 81 (94)
Q Consensus 78 ~h~~ 81 (94)
.||-
T Consensus 968 QHMN 971 (1007)
T KOG3623|consen 968 QHMN 971 (1007)
T ss_pred hhhc
Confidence 8875
No 4
>KOG3576|consensus
Probab=99.63 E-value=4.1e-17 Score=89.67 Aligned_cols=90 Identities=21% Similarity=0.404 Sum_probs=76.8
Q ss_pred CCCceeecCCCCccccchhccC-----CCCCCccccccchhhccChHHHHcchhhhcCCCCceeCCCCcccccchhHHHH
Q psy12011 4 QNLQVHFCGLFPESFLTWSNLK-----PNLNGMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKRKGNLKS 78 (94)
Q Consensus 4 ~~~~~~~c~~c~~~~~~~~~l~-----~~~~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~ 78 (94)
.+...|.|..|+|.|....-|. |...+-+-|..||+.|.+.-+|.+|+++|+|.+| |+|..|+++|+..-+|..
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrp-ykc~~c~kaftqrcsles 191 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRP-YKCSLCEKAFTQRCSLES 191 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccc-cchhhhhHHHHhhccHHH
Confidence 3456799999999998777665 6777889999999999999999999999999887 999999999999999999
Q ss_pred HHHHhcC-----------cccCCCCCC
Q psy12011 79 HLAIRHE-----------CYLDDSANC 94 (94)
Q Consensus 79 h~~~~~~-----------~~~~~c~~C 94 (94)
|++.-|+ .|.|.|..|
T Consensus 192 hl~kvhgv~~~yaykerr~kl~vcedc 218 (267)
T KOG3576|consen 192 HLKKVHGVQHQYAYKERRAKLYVCEDC 218 (267)
T ss_pred HHHHHcCchHHHHHHHhhhheeeeccc
Confidence 9986554 455666655
No 5
>KOG3623|consensus
Probab=99.56 E-value=1e-15 Score=96.70 Aligned_cols=67 Identities=33% Similarity=0.635 Sum_probs=63.8
Q ss_pred CCCCccccccchhhccChHHHHcchhhhcCCCCceeCCCCcccccchhHHHHHHHHhcCcccCCCCCC
Q psy12011 27 NLNGMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKRKGNLKSHLAIRHECYLDDSANC 94 (94)
Q Consensus 27 ~~~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~~C 94 (94)
+.+.+|.|+.|++.|.-.+.|.+|..-|.|.+| |+|.+|.++|..+..|..|+|.|.|||||+|.+|
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRP-yqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKC 956 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSGQRP-YQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKC 956 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcCCCC-cccchhhHhhhhhhhhhhhhhhccCCCcchhhhh
Confidence 556789999999999999999999999999888 9999999999999999999999999999999988
No 6
>KOG3576|consensus
Probab=99.44 E-value=1.1e-14 Score=80.16 Aligned_cols=65 Identities=22% Similarity=0.383 Sum_probs=61.6
Q ss_pred CCccccccchhhccChHHHHcchhhhcCCCCceeCCCCcccccchhHHHHHHHHhcCcccCCCCCC
Q psy12011 29 NGMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKRKGNLKSHLAIRHECYLDDSANC 94 (94)
Q Consensus 29 ~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~~C 94 (94)
...+.|.+|++.|.....|.+|++.|...+. +.|.-||+.|.-.-+|++|+++|+|..||+|..|
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr-~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c 179 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKR-HLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLC 179 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHH-HHHhhccCcccchhhhhhhhccccCccccchhhh
Confidence 4568999999999999999999999999888 9999999999999999999999999999999887
No 7
>PHA00733 hypothetical protein
Probab=99.32 E-value=1.1e-12 Score=68.66 Aligned_cols=78 Identities=14% Similarity=0.264 Sum_probs=65.2
Q ss_pred CceeecCCCCccccchhccC----------CCCCCccccccchhhccChHHHHcchhhhcCCCCceeCCCCcccccchhH
Q psy12011 6 LQVHFCGLFPESFLTWSNLK----------PNLNGMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKRKGN 75 (94)
Q Consensus 6 ~~~~~c~~c~~~~~~~~~l~----------~~~~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~ 75 (94)
.+++.|..|.+.|.....|. +.++++|.|..|++.|.....|..|++.+ ..+ +.|.+|++.|.....
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~-~~C~~CgK~F~~~~s 114 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHS-KVCPVCGKEFRNTDS 114 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcC-ccCCCCCCccCCHHH
Confidence 46678888888777666555 35578999999999999999999999876 345 999999999999999
Q ss_pred HHHHHHHhcCc
Q psy12011 76 LKSHLAIRHEC 86 (94)
Q Consensus 76 l~~h~~~~~~~ 86 (94)
|..|+...|+.
T Consensus 115 L~~H~~~~h~~ 125 (128)
T PHA00733 115 TLDHVCKKHNI 125 (128)
T ss_pred HHHHHHHhcCc
Confidence 99999987764
No 8
>KOG3608|consensus
Probab=99.28 E-value=2.1e-12 Score=76.44 Aligned_cols=89 Identities=24% Similarity=0.396 Sum_probs=48.5
Q ss_pred CCCCCceeecCCCCccccchhccC-C------CCCCcc--------------------------ccccchhhccChHHHH
Q psy12011 2 SSQNLQVHFCGLFPESFLTWSNLK-P------NLNGMF--------------------------ACDLCDKEYKYKRNLY 48 (94)
Q Consensus 2 ~~~~~~~~~c~~c~~~~~~~~~l~-~------~~~k~~--------------------------~c~~c~~~~~~~~~l~ 48 (94)
.|+++|.-.|+.||.-|.+...|- | ....+| +|+.|+-+....+.|.
T Consensus 201 ~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~ 280 (467)
T KOG3608|consen 201 THSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLT 280 (467)
T ss_pred hcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHH
Confidence 467777778888887777666543 1 112244 4444444444555555
Q ss_pred cchhhhcCCCCceeCCCCcccccchhHHHHHHHHhcCcccCCC
Q psy12011 49 SHKKDECGQEPRFQCPQCSYRTKRKGNLKSHLAIRHECYLDDS 91 (94)
Q Consensus 49 ~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c 91 (94)
.|++..+.+..||+|..|++.+...+.|.+|..+|. +..|.|
T Consensus 281 ~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C 322 (467)
T KOG3608|consen 281 THIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQC 322 (467)
T ss_pred HHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceec
Confidence 555442222222666666666666666666655554 445555
No 9
>KOG1074|consensus
Probab=99.17 E-value=6.1e-12 Score=80.87 Aligned_cols=58 Identities=34% Similarity=0.658 Sum_probs=54.0
Q ss_pred ccccccchhhccChHHHHcchhhhcCCCCceeCCCCcccccchhHHHHHHHHhcCcccC
Q psy12011 31 MFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKRKGNLKSHLAIRHECYLD 89 (94)
Q Consensus 31 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~ 89 (94)
.++|..|.+.|...+.|+.|++.|+|++| |+|++||..|..+++|+.|...|+...|+
T Consensus 353 khkCr~CakvfgS~SaLqiHlRSHTGERP-fqCnvCG~~FSTkGNLKvH~~rH~e~~p~ 410 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRSHTGERP-FQCNVCGNRFSTKGNLKVHFQRHREKYPH 410 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhccCCCCC-eeecccccccccccceeeeeeeccccCCc
Confidence 46899999999999999999999999998 99999999999999999999998877653
No 10
>KOG3608|consensus
Probab=99.09 E-value=1.5e-11 Score=72.88 Aligned_cols=85 Identities=22% Similarity=0.413 Sum_probs=71.0
Q ss_pred eeecCCCCccccchhccC------CCCCCccccccchhhccChHHHHcchhhhcCCCCceeCCC--CcccccchhHHHHH
Q psy12011 8 VHFCGLFPESFLTWSNLK------PNLNGMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQ--CSYRTKRKGNLKSH 79 (94)
Q Consensus 8 ~~~c~~c~~~~~~~~~l~------~~~~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~--c~~~f~~~~~l~~h 79 (94)
-|.|+.|+.+....+.|. |..+||++|+.|+..+...++|.+|...|. +.. |+|.. |...|.....+++|
T Consensus 263 ~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~-y~C~h~~C~~s~r~~~q~~~H 340 (467)
T KOG3608|consen 263 CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTV-YQCEHPDCHYSVRTYTQMRRH 340 (467)
T ss_pred cccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccc-eecCCCCCcHHHHHHHHHHHH
Confidence 367888887777777665 788999999999999999999999999887 354 99987 88889999999999
Q ss_pred HHHhc---CcccCCCCCC
Q psy12011 80 LAIRH---ECYLDDSANC 94 (94)
Q Consensus 80 ~~~~~---~~~~~~c~~C 94 (94)
.+.++ ...+|.|..|
T Consensus 341 ~~evhEg~np~~Y~CH~C 358 (467)
T KOG3608|consen 341 FLEVHEGNNPILYACHCC 358 (467)
T ss_pred HHHhccCCCCCceeeecc
Confidence 99877 3456888766
No 11
>KOG1074|consensus
Probab=99.09 E-value=3.2e-11 Score=77.73 Aligned_cols=56 Identities=27% Similarity=0.557 Sum_probs=51.1
Q ss_pred CccccccchhhccChHHHHcchhhhcCCCCceeCCCCcccccchhHHHHHHHHhcCc
Q psy12011 30 GMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKRKGNLKSHLAIRHEC 86 (94)
Q Consensus 30 k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~ 86 (94)
.|.+|.+|.+...-.+.|+.|.++|+|++| |+|.+||++|+.++||+.|+..|-..
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGERP-FkCKiCgRAFtTkGNLkaH~~vHka~ 659 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGERP-FKCKICGRAFTTKGNLKAHMSVHKAK 659 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCcCc-cccccccchhccccchhhcccccccC
Confidence 478999999999999999999999999888 99999999999999999999887543
No 12
>PHA02768 hypothetical protein; Provisional
Probab=99.08 E-value=3.7e-11 Score=53.52 Aligned_cols=43 Identities=16% Similarity=0.510 Sum_probs=35.1
Q ss_pred ccccccchhhccChHHHHcchhhhcCCCCceeCCCCcccccchhHH
Q psy12011 31 MFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKRKGNL 76 (94)
Q Consensus 31 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l 76 (94)
.|+|++||+.|...+.|..|++.|. ++ ++|..|++.|...++|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~-~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TN-LKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--Cc-ccCCcccceeccccee
Confidence 4688888888888888888988887 45 8888888888876655
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.06 E-value=1.2e-10 Score=51.85 Aligned_cols=32 Identities=22% Similarity=0.513 Sum_probs=29.2
Q ss_pred eeCCCCcccccchhHHHHHHHHhcCcccCCCCCC
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAIRHECYLDDSANC 94 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~~C 94 (94)
|.|+.||+.|...++|..|+++|+ ++++|.+|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C 37 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNC 37 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcc
Confidence 899999999999999999999999 67777766
No 14
>PHA00616 hypothetical protein
Probab=98.96 E-value=3.4e-10 Score=48.21 Aligned_cols=33 Identities=21% Similarity=0.290 Sum_probs=24.7
Q ss_pred ceeCCCCcccccchhHHHHHHHHhcCcccCCCC
Q psy12011 60 RFQCPQCSYRTKRKGNLKSHLAIRHECYLDDSA 92 (94)
Q Consensus 60 ~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~ 92 (94)
||+|..||+.|...++|..|++.||+++++.+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 377777777777777777777777777777653
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.88 E-value=3e-09 Score=67.15 Aligned_cols=84 Identities=14% Similarity=0.309 Sum_probs=63.4
Q ss_pred CceeecCCCCccccchhccC-C--CCCCccccccchhhccChHHHHcchhhhcCCCCceeCCCCcccccc----------
Q psy12011 6 LQVHFCGLFPESFLTWSNLK-P--NLNGMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKR---------- 72 (94)
Q Consensus 6 ~~~~~c~~c~~~~~~~~~l~-~--~~~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~---------- 72 (94)
+..+.|+.|++.|. ...|. | .-.+++.|. |++.+ ....|..|+..+...++ +.|..|+..|..
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kp-i~C~fC~~~v~~g~~~~d~~d~ 526 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFHEPLQCP-CGVVL-EKEQMVQHQASTCPLRL-ITCRFCGDMVQAGGSAMDVRDR 526 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcCCCccCC-CCCCc-chhHHHhhhhccCCCCc-eeCCCCCCccccCccccchhhh
Confidence 34567999998885 34454 2 113788898 98655 56788889888888777 999999988842
Q ss_pred hhHHHHHHHHhcCcccCCCCCC
Q psy12011 73 KGNLKSHLAIRHECYLDDSANC 94 (94)
Q Consensus 73 ~~~l~~h~~~~~~~~~~~c~~C 94 (94)
...|..|..+. +.+++.|..|
T Consensus 527 ~s~Lt~HE~~C-G~rt~~C~~C 547 (567)
T PLN03086 527 LRGMSEHESIC-GSRTAPCDSC 547 (567)
T ss_pred hhhHHHHHHhc-CCcceEcccc
Confidence 35788888874 8899999887
No 16
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.78 E-value=1.3e-08 Score=64.36 Aligned_cols=60 Identities=25% Similarity=0.486 Sum_probs=51.3
Q ss_pred CCccccccchhhccChHHHHcchhhhcCCCCceeCCCCcccccchhHHHHHHHHhcCcccCCCCCC
Q psy12011 29 NGMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKRKGNLKSHLAIRHECYLDDSANC 94 (94)
Q Consensus 29 ~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~~C 94 (94)
++++.|..|++.|. ...+..|+..++ .+ +.|+ |+..+ ....|..|+.+|.+.+++.|..|
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kp-v~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC 510 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EP-LQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFC 510 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CC-ccCC-CCCCc-chhHHHhhhhccCCCCceeCCCC
Confidence 45678999999996 577899999874 56 9999 99755 66899999999999999999987
No 17
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.77 E-value=5.2e-09 Score=40.16 Aligned_cols=24 Identities=29% Similarity=0.802 Sum_probs=18.7
Q ss_pred HHcchhhhcCCCCceeCCCCccccc
Q psy12011 47 LYSHKKDECGQEPRFQCPQCSYRTK 71 (94)
Q Consensus 47 l~~h~~~~~~~~~~~~c~~c~~~f~ 71 (94)
|..|++.|.++++ |.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k~-~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKP-YKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSS-EEESSSSEEES
T ss_pred HHHHhhhcCCCCC-CCCCCCcCeeC
Confidence 6678888888777 88888887775
No 18
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.76 E-value=5e-09 Score=40.19 Aligned_cols=20 Identities=20% Similarity=0.305 Sum_probs=18.8
Q ss_pred HHHHHHHHhcCcccCCCCCC
Q psy12011 75 NLKSHLAIRHECYLDDSANC 94 (94)
Q Consensus 75 ~l~~h~~~~~~~~~~~c~~C 94 (94)
+|.+|+++|++++||.|+.|
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C 20 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYC 20 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSS
T ss_pred CHHHHhhhcCCCCCCCCCCC
Confidence 58899999999999999998
No 19
>PHA00733 hypothetical protein
Probab=98.72 E-value=9e-09 Score=54.03 Aligned_cols=55 Identities=20% Similarity=0.309 Sum_probs=46.1
Q ss_pred CCCCCceeecCCCCccccchhccC-CCC--CCccccccchhhccChHHHHcchhhhcC
Q psy12011 2 SSQNLQVHFCGLFPESFLTWSNLK-PNL--NGMFACDLCDKEYKYKRNLYSHKKDECG 56 (94)
Q Consensus 2 ~~~~~~~~~c~~c~~~~~~~~~l~-~~~--~k~~~c~~c~~~~~~~~~l~~h~~~~~~ 56 (94)
.+.+.++|.|+.|++.|...+.|. |.. +.++.|..|++.|.....|..|+...++
T Consensus 67 ~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 67 TSKAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred ccCCCCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 345678999999999999999987 322 5689999999999999999999876654
No 20
>PHA00732 hypothetical protein
Probab=98.58 E-value=3.6e-08 Score=47.59 Aligned_cols=44 Identities=25% Similarity=0.517 Sum_probs=24.2
Q ss_pred ccccccchhhccChHHHHcchhh-hcCCCCceeCCCCcccccchhHHHHHHH
Q psy12011 31 MFACDLCDKEYKYKRNLYSHKKD-ECGQEPRFQCPQCSYRTKRKGNLKSHLA 81 (94)
Q Consensus 31 ~~~c~~c~~~~~~~~~l~~h~~~-~~~~~~~~~c~~c~~~f~~~~~l~~h~~ 81 (94)
||.|..|++.|.....|..|++. |. + +.|..|++.|. .+..|.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~-~~C~~CgKsF~---~l~~H~~ 45 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---L-TKCPVCNKSYR---RLNQHFY 45 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---C-CccCCCCCEeC---Chhhhhc
Confidence 35566666666666666666553 32 2 45666666665 2344544
No 21
>PHA00616 hypothetical protein
Probab=98.56 E-value=3.3e-08 Score=42.15 Aligned_cols=34 Identities=18% Similarity=0.348 Sum_probs=30.8
Q ss_pred ccccccchhhccChHHHHcchhhhcCCCCceeCCC
Q psy12011 31 MFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQ 65 (94)
Q Consensus 31 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~ 65 (94)
||+|..||+.|...+.+..|++.++++++ +.+..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~-~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK-LTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc-cceeE
Confidence 68999999999999999999999999888 87754
No 22
>KOG3993|consensus
Probab=98.42 E-value=2.3e-08 Score=60.79 Aligned_cols=79 Identities=24% Similarity=0.426 Sum_probs=64.2
Q ss_pred ceeecCCCCccccchhccC-C----CCCCccccccchhhccChHHHHcchhhhcC--------CCC--------------
Q psy12011 7 QVHFCGLFPESFLTWSNLK-P----NLNGMFACDLCDKEYKYKRNLYSHKKDECG--------QEP-------------- 59 (94)
Q Consensus 7 ~~~~c~~c~~~~~~~~~l~-~----~~~k~~~c~~c~~~~~~~~~l~~h~~~~~~--------~~~-------------- 59 (94)
..|+|..|...|.+...|. | .....|+|.+|++.|.-+.+|..|.++|.- ..+
T Consensus 266 GdyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea 345 (500)
T KOG3993|consen 266 GDYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEA 345 (500)
T ss_pred HHHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhc
Confidence 3478888888888877776 3 344579999999999999999999998841 111
Q ss_pred ----------ceeCCCCcccccchhHHHHHHHHhcC
Q psy12011 60 ----------RFQCPQCSYRTKRKGNLKSHLAIRHE 85 (94)
Q Consensus 60 ----------~~~c~~c~~~f~~~~~l~~h~~~~~~ 85 (94)
.|.|..|++.|....-|+.|+.+|+.
T Consensus 346 ~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 346 ERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred cccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 38999999999999999999988874
No 23
>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=98.38 E-value=4.3e-07 Score=33.60 Aligned_cols=23 Identities=35% Similarity=0.752 Sum_probs=18.1
Q ss_pred eeCCCCcccccchhHHHHHHHHh
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAIR 83 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~~ 83 (94)
|.|..|++.|....+|..|++.|
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 57888888888888888888763
No 24
>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=98.22 E-value=1.8e-06 Score=31.94 Aligned_cols=24 Identities=38% Similarity=0.866 Sum_probs=18.1
Q ss_pred eeCCCCcccccchhHHHHHHHHhc
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAIRH 84 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~~~ 84 (94)
|.|..|++.|.....|..|+++++
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 578888888888888888888764
No 25
>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=98.21 E-value=1.2e-06 Score=33.71 Aligned_cols=26 Identities=19% Similarity=0.431 Sum_probs=20.9
Q ss_pred ceeCCCCcccccchhHHHHHHHHhcC
Q psy12011 60 RFQCPQCSYRTKRKGNLKSHLAIRHE 85 (94)
Q Consensus 60 ~~~c~~c~~~f~~~~~l~~h~~~~~~ 85 (94)
||.|..|++.|....+|..|++.|..
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 47888888888888888888877653
No 26
>PHA00732 hypothetical protein
Probab=98.09 E-value=3.6e-06 Score=40.68 Aligned_cols=32 Identities=28% Similarity=0.529 Sum_probs=27.2
Q ss_pred ceeCCCCcccccchhHHHHHHHH-hcCcccCCCCCC
Q psy12011 60 RFQCPQCSYRTKRKGNLKSHLAI-RHECYLDDSANC 94 (94)
Q Consensus 60 ~~~c~~c~~~f~~~~~l~~h~~~-~~~~~~~~c~~C 94 (94)
||.|..|++.|....+|..|++. |.+ +.|..|
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~C 33 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVC 33 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCC
Confidence 48999999999999999999985 553 578777
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=98.08 E-value=8.2e-06 Score=36.61 Aligned_cols=52 Identities=33% Similarity=0.602 Sum_probs=35.9
Q ss_pred ccccccchhhccChHHHHcchhh-hcCCCCceeCCCCcccccchhHHHHHHHHhcC
Q psy12011 31 MFACDLCDKEYKYKRNLYSHKKD-ECGQEPRFQCPQCSYRTKRKGNLKSHLAIRHE 85 (94)
Q Consensus 31 ~~~c~~c~~~~~~~~~l~~h~~~-~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~ 85 (94)
.|.|+.|++. .....|..|... |..+...+.|+.|...+. .+|..|+...|+
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 4678888884 455678888665 444333489999987544 488889887763
No 28
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=98.07 E-value=4.9e-06 Score=36.39 Aligned_cols=35 Identities=31% Similarity=0.498 Sum_probs=23.9
Q ss_pred hcCCCCceeCCCCcccccchhHHHHHHHHhcCccc
Q psy12011 54 ECGQEPRFQCPQCSYRTKRKGNLKSHLAIRHECYL 88 (94)
Q Consensus 54 ~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~ 88 (94)
+.....|-.|++|+..+...-+|++|+.+.|+.||
T Consensus 18 ~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 18 KSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 33334448999999999999999999999888876
No 29
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.00 E-value=2.7e-06 Score=31.36 Aligned_cols=23 Identities=30% Similarity=0.761 Sum_probs=19.2
Q ss_pred cccccchhhccChHHHHcchhhh
Q psy12011 32 FACDLCDKEYKYKRNLYSHKKDE 54 (94)
Q Consensus 32 ~~c~~c~~~~~~~~~l~~h~~~~ 54 (94)
|+|..|++.|.....|..|++.|
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 57888999999999999888763
No 30
>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=97.82 E-value=9e-06 Score=31.14 Aligned_cols=26 Identities=35% Similarity=0.775 Sum_probs=22.1
Q ss_pred ccccccchhhccChHHHHcchhhhcC
Q psy12011 31 MFACDLCDKEYKYKRNLYSHKKDECG 56 (94)
Q Consensus 31 ~~~c~~c~~~~~~~~~l~~h~~~~~~ 56 (94)
+|+|..|++.|.....|..|++.|..
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 57899999999999999999887643
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.66 E-value=5.3e-05 Score=37.75 Aligned_cols=72 Identities=21% Similarity=0.384 Sum_probs=21.5
Q ss_pred ecCCCCccccchhccCCCCCCcccccc-chhhccChHHHHcchhhhcCCCCceeCCCCcccccchhHHHHHHHHh
Q psy12011 10 FCGLFPESFLTWSNLKPNLNGMFACDL-CDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKRKGNLKSHLAIR 83 (94)
Q Consensus 10 ~c~~c~~~~~~~~~l~~~~~k~~~c~~-c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~ 83 (94)
.|..|+..|.....|..+-...+.-.. ....+.....+..+...... .. +.|..|++.|.....|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~-~~-~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVK-ES-FRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -------------------------------------------------SS-EEBSSSS-EESSHHHHHHHHHHT
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccC-CC-CCCCccCCCCcCHHHHHHHHcCc
Confidence 377888888887777622222221111 11112222333333332222 34 99999999999999999999975
No 32
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.66 E-value=5.6e-05 Score=28.15 Aligned_cols=24 Identities=33% Similarity=0.751 Sum_probs=16.2
Q ss_pred eeCCCCcccccchhHHHHHHHHhc
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAIRH 84 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~~~ 84 (94)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 356777777777777777776543
No 33
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.60 E-value=3.4e-05 Score=28.31 Aligned_cols=23 Identities=30% Similarity=0.801 Sum_probs=17.7
Q ss_pred cccccchhhccChHHHHcchhhh
Q psy12011 32 FACDLCDKEYKYKRNLYSHKKDE 54 (94)
Q Consensus 32 ~~c~~c~~~~~~~~~l~~h~~~~ 54 (94)
|.|+.|++.|.....|..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 57888999999999999888765
No 34
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.58 E-value=0.0001 Score=27.34 Aligned_cols=24 Identities=54% Similarity=1.089 Sum_probs=17.9
Q ss_pred eeCCCCcccccchhHHHHHHHHhcC
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAIRHE 85 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~~~~ 85 (94)
|+|+.|+.... ...|..|++.+++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 67888987777 7789999988764
No 35
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.48 E-value=4e-05 Score=45.76 Aligned_cols=24 Identities=33% Similarity=0.686 Sum_probs=19.4
Q ss_pred CCCceeCCCCcccccchhHHHHHHH
Q psy12011 57 QEPRFQCPQCSYRTKRKGNLKSHLA 81 (94)
Q Consensus 57 ~~~~~~c~~c~~~f~~~~~l~~h~~ 81 (94)
.+| |+|.+|++.+.....|+.|..
T Consensus 396 ~KP-YrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 396 DKP-YRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CCc-eeccccchhhccCccceeccc
Confidence 366 999999999988888877754
No 36
>PRK04860 hypothetical protein; Provisional
Probab=97.44 E-value=0.00013 Score=39.83 Aligned_cols=31 Identities=13% Similarity=0.390 Sum_probs=24.8
Q ss_pred ceeCCCCcccccchhHHHHHHHHhcCcccCCCCCC
Q psy12011 60 RFQCPQCSYRTKRKGNLKSHLAIRHECYLDDSANC 94 (94)
Q Consensus 60 ~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~~C 94 (94)
+|.|. |+. ....+++|.+++.++++|.|..|
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C 149 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRC 149 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCC
Confidence 38887 876 66677888888888888888877
No 37
>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=97.22 E-value=0.00065 Score=30.38 Aligned_cols=33 Identities=24% Similarity=0.410 Sum_probs=26.3
Q ss_pred eeCCCCcccccchhHHHHHHHHhcC--cccCCCCCC
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAIRHE--CYLDDSANC 94 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~~~~--~~~~~c~~C 94 (94)
|.|+.|++. .....|..|....|. .+.+.|++|
T Consensus 3 f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC 37 (54)
T PF05605_consen 3 FTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPIC 37 (54)
T ss_pred cCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCc
Confidence 899999994 556789999887654 357899987
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.18 E-value=0.00028 Score=26.12 Aligned_cols=24 Identities=29% Similarity=0.613 Sum_probs=20.2
Q ss_pred cccccchhhccChHHHHcchhhhc
Q psy12011 32 FACDLCDKEYKYKRNLYSHKKDEC 55 (94)
Q Consensus 32 ~~c~~c~~~~~~~~~l~~h~~~~~ 55 (94)
++|..|++.|.....+..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 478899999999999999988654
No 39
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.14 E-value=0.00045 Score=25.72 Aligned_cols=22 Identities=27% Similarity=0.591 Sum_probs=15.3
Q ss_pred eeCCCCcccccchhHHHHHHHH
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAI 82 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~ 82 (94)
|.|..|++.|.....+..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 4567777777777777777664
No 40
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.11 E-value=0.00041 Score=30.46 Aligned_cols=34 Identities=21% Similarity=0.336 Sum_probs=24.3
Q ss_pred CCCCCccccccchhhccChHHHHcchhhhcCCCC
Q psy12011 26 PNLNGMFACDLCDKEYKYKRNLYSHKKDECGQEP 59 (94)
Q Consensus 26 ~~~~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~ 59 (94)
...+.|..|++|+..+....+|..|+...++.++
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 4556788999999999999999999988887665
No 41
>KOG3993|consensus
Probab=97.07 E-value=0.00015 Score=44.90 Aligned_cols=53 Identities=25% Similarity=0.501 Sum_probs=46.3
Q ss_pred ccccccchhhccChHHHHcchhhhcCCCCceeCCCCcccccchhHHHHHHHHhc
Q psy12011 31 MFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKRKGNLKSHLAIRH 84 (94)
Q Consensus 31 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 84 (94)
-|.|.+|...|.+.-.|.+|.-..+.... |+|++|+|.|+=..||-.|.|=|-
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vE-YrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVE-YRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEee-ecCCcccccccCchhhhhhhcccC
Confidence 47899999999999999999877666666 999999999999999999987553
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.90 E-value=0.00044 Score=25.73 Aligned_cols=23 Identities=30% Similarity=0.830 Sum_probs=19.1
Q ss_pred cccccchhhccChHHHHcchhhh
Q psy12011 32 FACDLCDKEYKYKRNLYSHKKDE 54 (94)
Q Consensus 32 ~~c~~c~~~~~~~~~l~~h~~~~ 54 (94)
|.|.+|++.|.....+..|++.+
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 56889999999999998887654
No 43
>PRK04860 hypothetical protein; Provisional
Probab=96.73 E-value=0.00082 Score=36.78 Aligned_cols=38 Identities=18% Similarity=0.516 Sum_probs=32.0
Q ss_pred ccccccchhhccChHHHHcchhhhcCCCCceeCCCCcccccch
Q psy12011 31 MFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKRK 73 (94)
Q Consensus 31 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~ 73 (94)
+|.|. |+. ....+..|.+++.++++ |.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~-YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAV-YRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCcc-EECCCCCceeEEe
Confidence 68897 886 56667899999999888 9999999888654
No 44
>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=96.72 E-value=0.0013 Score=25.00 Aligned_cols=21 Identities=43% Similarity=0.823 Sum_probs=12.5
Q ss_pred cccccchhhccChHHHHcchh
Q psy12011 32 FACDLCDKEYKYKRNLYSHKK 52 (94)
Q Consensus 32 ~~c~~c~~~~~~~~~l~~h~~ 52 (94)
|.|..|++.|.....+..|+.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 446666666666666666554
No 45
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=95.90 E-value=0.0055 Score=37.06 Aligned_cols=37 Identities=24% Similarity=0.521 Sum_probs=26.9
Q ss_pred CCCceeCCC--CcccccchhHHHHHHHHh-------------------cCcccCCCCCC
Q psy12011 57 QEPRFQCPQ--CSYRTKRKGNLKSHLAIR-------------------HECYLDDSANC 94 (94)
Q Consensus 57 ~~~~~~c~~--c~~~f~~~~~l~~h~~~~-------------------~~~~~~~c~~C 94 (94)
++| |+|++ |.+.+.....|+.|+..- ..+|||.|..|
T Consensus 347 ~Kp-ykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC 404 (423)
T COG5189 347 GKP-YKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVC 404 (423)
T ss_pred Cce-ecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceecccc
Confidence 355 88876 778888877787777532 24599999887
No 46
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.87 E-value=0.0098 Score=22.26 Aligned_cols=20 Identities=25% Similarity=0.599 Sum_probs=12.5
Q ss_pred eeCCCCcccccchhHHHHHHH
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLA 81 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~ 81 (94)
..|+.||+.| ....|..|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4677777777 4445566654
No 47
>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=95.13 E-value=0.017 Score=23.75 Aligned_cols=10 Identities=20% Similarity=0.574 Sum_probs=5.0
Q ss_pred eeCCCCcccc
Q psy12011 61 FQCPQCSYRT 70 (94)
Q Consensus 61 ~~c~~c~~~f 70 (94)
+.|+.|+..|
T Consensus 26 v~C~~C~~~~ 35 (38)
T TIGR02098 26 VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEE
Confidence 4555555443
No 48
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=95.01 E-value=0.021 Score=23.34 Aligned_cols=10 Identities=20% Similarity=0.683 Sum_probs=5.3
Q ss_pred eeCCCCcccc
Q psy12011 61 FQCPQCSYRT 70 (94)
Q Consensus 61 ~~c~~c~~~f 70 (94)
.+|+.|+..|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 5555555444
No 49
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=94.93 E-value=0.031 Score=22.29 Aligned_cols=22 Identities=23% Similarity=0.457 Sum_probs=17.7
Q ss_pred eeCCCCcccccchhHHHHHHHH
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAI 82 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~ 82 (94)
|.|..|+..|.....+..|+..
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred eEccccCCccCCHHHHHHHHCh
Confidence 7888888888888888877764
No 50
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=94.60 E-value=0.027 Score=23.15 Aligned_cols=32 Identities=19% Similarity=0.587 Sum_probs=16.6
Q ss_pred ccccchhhccChHHHHcchhhhcCCCCceeCCCCcccc
Q psy12011 33 ACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRT 70 (94)
Q Consensus 33 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 70 (94)
+|+.|+..|..+..- ...+... .+|+.|+..|
T Consensus 4 ~CP~C~~~f~v~~~~-----l~~~~~~-vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDK-----LPAGGRK-VRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHH-----cccCCcE-EECCCCCcEe
Confidence 456666666555431 1122234 6677666555
No 51
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.58 E-value=0.012 Score=36.19 Aligned_cols=61 Identities=21% Similarity=0.459 Sum_probs=53.3
Q ss_pred CccccccchhhccChHHHHcchh--hhcCC--CCceeCC--CCcccccchhHHHHHHHHhcCcccCCC
Q psy12011 30 GMFACDLCDKEYKYKRNLYSHKK--DECGQ--EPRFQCP--QCSYRTKRKGNLKSHLAIRHECYLDDS 91 (94)
Q Consensus 30 k~~~c~~c~~~~~~~~~l~~h~~--~~~~~--~~~~~c~--~c~~~f~~~~~l~~h~~~~~~~~~~~c 91 (94)
.++.+..|...|.....+..|.+ .|.++ ++ +.|+ .|++.|.....+.+|..+|.+..+..+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~-~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKP-FSCPYSLCGKLFSRNDALKRHILLHTSISPAKE 354 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCc-eeeeccCCCccccccccccCCcccccCCCcccc
Confidence 36788899999999999999999 78888 67 9999 799999999999999999988877665
No 52
>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=94.28 E-value=0.037 Score=23.39 Aligned_cols=28 Identities=14% Similarity=0.330 Sum_probs=13.3
Q ss_pred eecCCCCccccchhccCCCCCCccccccch
Q psy12011 9 HFCGLFPESFLTWSNLKPNLNGMFACDLCD 38 (94)
Q Consensus 9 ~~c~~c~~~~~~~~~l~~~~~k~~~c~~c~ 38 (94)
|.|..||..|.....+.. .....|+.||
T Consensus 6 y~C~~Cg~~fe~~~~~~~--~~~~~CP~Cg 33 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE--DDPVPCPECG 33 (42)
T ss_pred EEeCCCCCEEEEEEEcCC--CCCCcCCCCC
Confidence 555666655554433222 3344455554
No 53
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=93.98 E-value=0.051 Score=24.71 Aligned_cols=32 Identities=28% Similarity=0.670 Sum_probs=17.8
Q ss_pred CccccccchhhccChHHHHcchhhhcCCCCceeCCCCc
Q psy12011 30 GMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCS 67 (94)
Q Consensus 30 k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~ 67 (94)
..|.|+.||+....... +...-..+ |.|+.||
T Consensus 26 v~F~CPnCGe~~I~Rc~-----~CRk~g~~-Y~Cp~CG 57 (61)
T COG2888 26 VKFPCPNCGEVEIYRCA-----KCRKLGNP-YRCPKCG 57 (61)
T ss_pred eEeeCCCCCceeeehhh-----hHHHcCCc-eECCCcC
Confidence 35678888755433321 12222355 8888887
No 54
>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=93.02 E-value=0.085 Score=21.81 Aligned_cols=13 Identities=15% Similarity=0.112 Sum_probs=7.0
Q ss_pred eecCCCCccccch
Q psy12011 9 HFCGLFPESFLTW 21 (94)
Q Consensus 9 ~~c~~c~~~~~~~ 21 (94)
|.|+.||..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (41)
T smart00834 6 YRCEDCGHTFEVL 18 (41)
T ss_pred EEcCCCCCEEEEE
Confidence 5566666555443
No 55
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=92.51 E-value=0.14 Score=28.34 Aligned_cols=8 Identities=25% Similarity=0.501 Sum_probs=3.9
Q ss_pred eeecCCCC
Q psy12011 8 VHFCGLFP 15 (94)
Q Consensus 8 ~~~c~~c~ 15 (94)
.|+|++||
T Consensus 134 ~~vC~vCG 141 (166)
T COG1592 134 VWVCPVCG 141 (166)
T ss_pred EEEcCCCC
Confidence 45555554
No 56
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=92.34 E-value=0.16 Score=20.22 Aligned_cols=24 Identities=29% Similarity=0.937 Sum_probs=14.8
Q ss_pred cccccchhhccChHHHHcchhhhcCCCCceeCCCCcc
Q psy12011 32 FACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSY 68 (94)
Q Consensus 32 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 68 (94)
|.|..||..+.... .+ +.|+.|+.
T Consensus 2 ~~C~~CGy~y~~~~------------~~-~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------AP-WVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CC-CcCcCCCC
Confidence 56778874442211 34 88888874
No 57
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=92.30 E-value=0.12 Score=27.97 Aligned_cols=39 Identities=21% Similarity=0.586 Sum_probs=20.5
Q ss_pred CCCccccccchhhccChHHHHcchhhhcCCCCceeCCCCccccc
Q psy12011 28 LNGMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTK 71 (94)
Q Consensus 28 ~~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 71 (94)
+...|.|+.|+..|.....+.. . .. ... |.|+.||....
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~-~--d~-~~~-f~Cp~Cg~~l~ 134 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL-L--DM-DGT-FTCPRCGEELE 134 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh-c--CC-CCc-EECCCCCCEEE
Confidence 3445677777766665433221 0 11 233 77777776543
No 58
>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=92.12 E-value=0.13 Score=22.61 Aligned_cols=28 Identities=14% Similarity=0.354 Sum_probs=13.3
Q ss_pred eecCCCCccccchhccCCCCCCccccccch
Q psy12011 9 HFCGLFPESFLTWSNLKPNLNGMFACDLCD 38 (94)
Q Consensus 9 ~~c~~c~~~~~~~~~l~~~~~k~~~c~~c~ 38 (94)
|.|..||..|.....+.. +..-.|+.||
T Consensus 6 y~C~~Cg~~fe~~~~~~~--~~~~~CP~Cg 33 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSD--DPLATCPECG 33 (52)
T ss_pred EEeCCCCCEeEEEEecCC--CCCCCCCCCC
Confidence 556666665554322211 2333455555
No 59
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=91.69 E-value=0.16 Score=21.78 Aligned_cols=28 Identities=11% Similarity=0.019 Sum_probs=13.3
Q ss_pred eeecCCCCccccchhccCCCCCCccccccchhh
Q psy12011 8 VHFCGLFPESFLTWSNLKPNLNGMFACDLCDKE 40 (94)
Q Consensus 8 ~~~c~~c~~~~~~~~~l~~~~~k~~~c~~c~~~ 40 (94)
.|.|+.||..|...... ....|+.||..
T Consensus 3 ~y~C~~CG~~~~~~~~~-----~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVELDEYG-----TGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEEECCCC-----CceECCCCCCe
Confidence 45666666554432211 14455555543
No 60
>KOG1146|consensus
Probab=91.68 E-value=0.21 Score=35.87 Aligned_cols=56 Identities=29% Similarity=0.611 Sum_probs=43.6
Q ss_pred CCCCCccccccchhhccChHHHHcchhhhc-------------------------CCCCceeCCCCcccccchhHHHHHH
Q psy12011 26 PNLNGMFACDLCDKEYKYKRNLYSHKKDEC-------------------------GQEPRFQCPQCSYRTKRKGNLKSHL 80 (94)
Q Consensus 26 ~~~~k~~~c~~c~~~~~~~~~l~~h~~~~~-------------------------~~~~~~~c~~c~~~f~~~~~l~~h~ 80 (94)
+.-.+-+.|..|+..|.+...|..|++..+ +.++ |.|..|...+....+|..|+
T Consensus 460 ~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p-~~C~~C~~stttng~Lsihl 538 (1406)
T KOG1146|consen 460 HSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKP-YPCRACNYSTTTNGNLSIHL 538 (1406)
T ss_pred ecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCc-ccceeeeeeeecchHHHHHH
Confidence 344467788888888888888888887611 2244 89999999999999999999
Q ss_pred HH
Q psy12011 81 AI 82 (94)
Q Consensus 81 ~~ 82 (94)
+.
T Consensus 539 qS 540 (1406)
T KOG1146|consen 539 QS 540 (1406)
T ss_pred HH
Confidence 75
No 61
>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=91.65 E-value=0.2 Score=20.15 Aligned_cols=10 Identities=20% Similarity=0.252 Sum_probs=5.5
Q ss_pred eeecCCCCcc
Q psy12011 8 VHFCGLFPES 17 (94)
Q Consensus 8 ~~~c~~c~~~ 17 (94)
.|+|..||-.
T Consensus 2 ~~~C~~CG~i 11 (34)
T cd00729 2 VWVCPVCGYI 11 (34)
T ss_pred eEECCCCCCE
Confidence 3556666644
No 62
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=91.33 E-value=0.14 Score=25.25 Aligned_cols=25 Identities=24% Similarity=0.687 Sum_probs=21.6
Q ss_pred ccccccchhhccChHHHHcchhhhc
Q psy12011 31 MFACDLCDKEYKYKRNLYSHKKDEC 55 (94)
Q Consensus 31 ~~~c~~c~~~~~~~~~l~~h~~~~~ 55 (94)
.+.|..|++.|.....|..|++.+.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCcc
Confidence 6899999999999999999998653
No 63
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=90.69 E-value=0.19 Score=21.52 Aligned_cols=10 Identities=40% Similarity=1.255 Sum_probs=5.6
Q ss_pred eeCCCCcccc
Q psy12011 61 FQCPQCSYRT 70 (94)
Q Consensus 61 ~~c~~c~~~f 70 (94)
..|+.||...
T Consensus 20 irC~~CG~rI 29 (44)
T smart00659 20 VRCRECGYRI 29 (44)
T ss_pred eECCCCCceE
Confidence 5666666443
No 64
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=90.15 E-value=0.2 Score=25.78 Aligned_cols=30 Identities=17% Similarity=0.415 Sum_probs=20.7
Q ss_pred eecCCCCccccchhccCCCCCCccccccchhhccCh
Q psy12011 9 HFCGLFPESFLTWSNLKPNLNGMFACDLCDKEYKYK 44 (94)
Q Consensus 9 ~~c~~c~~~~~~~~~l~~~~~k~~~c~~c~~~~~~~ 44 (94)
.+|+.||+.|.... ..|..|+.||..|...
T Consensus 10 R~Cp~CG~kFYDLn------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLN------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCC------CCCccCCCCCCccCcc
Confidence 56888888776533 2466788888777666
No 65
>KOG2186|consensus
Probab=90.08 E-value=0.17 Score=29.88 Aligned_cols=38 Identities=24% Similarity=0.553 Sum_probs=16.4
Q ss_pred cccccchhhccChHHHHcchhhhcCCCCceeCCCCcccccc
Q psy12011 32 FACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKR 72 (94)
Q Consensus 32 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~ 72 (94)
|.|..||....-+. +.+|+....+ .- |.|..|++.|..
T Consensus 4 FtCnvCgEsvKKp~-vekH~srCrn-~~-fSCIDC~k~F~~ 41 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQ-VEKHMSRCRN-AY-FSCIDCGKTFER 41 (276)
T ss_pred Eehhhhhhhccccc-hHHHHHhccC-Ce-eEEeeccccccc
Confidence 34444444443332 2334444433 22 555555555544
No 66
>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=89.91 E-value=0.22 Score=27.38 Aligned_cols=35 Identities=20% Similarity=0.481 Sum_probs=21.9
Q ss_pred CCCCccccccchhhccChHHHHcchhhhcCCCCceeCCCCccccc
Q psy12011 27 NLNGMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTK 71 (94)
Q Consensus 27 ~~~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 71 (94)
.+..-|.|+.|+..|.....+. .. |.|+.||....
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~---------~~-F~Cp~Cg~~L~ 139 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME---------LN-FTCPRCGAMLD 139 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH---------cC-CcCCCCCCEee
Confidence 3445577777777776665543 13 78888876544
No 67
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=89.77 E-value=0.4 Score=20.90 Aligned_cols=22 Identities=32% Similarity=0.640 Sum_probs=16.8
Q ss_pred eeCCCCcccccc-----hhHHHHHHHH
Q psy12011 61 FQCPQCSYRTKR-----KGNLKSHLAI 82 (94)
Q Consensus 61 ~~c~~c~~~f~~-----~~~l~~h~~~ 82 (94)
..|..|++.+.. .++|.+|++.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 688888877754 3689999884
No 68
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=89.74 E-value=0.17 Score=27.72 Aligned_cols=39 Identities=13% Similarity=0.138 Sum_probs=22.7
Q ss_pred ecCCCCccccc--hhc-cCC--CCCCccccccchhhccChHHHH
Q psy12011 10 FCGLFPESFLT--WSN-LKP--NLNGMFACDLCDKEYKYKRNLY 48 (94)
Q Consensus 10 ~c~~c~~~~~~--~~~-l~~--~~~k~~~c~~c~~~~~~~~~l~ 48 (94)
.||+||..... .+. +.. ...+.++|..||..|..-..+.
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~ 45 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVE 45 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEecc
Confidence 68999865421 111 112 2233488999999887654443
No 69
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=89.35 E-value=0.27 Score=26.23 Aligned_cols=25 Identities=28% Similarity=0.442 Sum_probs=16.5
Q ss_pred eeCCCCcccccchhHHHHHHHHhcCccc
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAIRHECYL 88 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~ 88 (94)
..|.+||+.|..- .+|+++|+|..|
T Consensus 73 i~clecGk~~k~L---krHL~~~~gltp 97 (132)
T PF05443_consen 73 IICLECGKKFKTL---KRHLRTHHGLTP 97 (132)
T ss_dssp EE-TBT--EESBH---HHHHHHTT-S-H
T ss_pred eEEccCCcccchH---HHHHHHccCCCH
Confidence 8999999988765 799999987654
No 70
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=89.22 E-value=0.4 Score=21.85 Aligned_cols=52 Identities=19% Similarity=0.469 Sum_probs=27.1
Q ss_pred CceeecCCCCccccchhccCCCCCCccccccchhhccChHHHHcchhhhcCCCCceeCCCCcc
Q psy12011 6 LQVHFCGLFPESFLTWSNLKPNLNGMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSY 68 (94)
Q Consensus 6 ~~~~~c~~c~~~~~~~~~l~~~~~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~ 68 (94)
..+.+|..|+...... ..-..|.|+.||+.....- .+......+ |.|+.||.
T Consensus 5 ~~~~~CtSCg~~i~~~-----~~~~~F~CPnCG~~~I~RC-----~~CRk~~~~-Y~CP~CGF 56 (59)
T PRK14890 5 MEPPKCTSCGIEIAPR-----EKAVKFLCPNCGEVIIYRC-----EKCRKQSNP-YTCPKCGF 56 (59)
T ss_pred ccCccccCCCCcccCC-----CccCEeeCCCCCCeeEeec-----hhHHhcCCc-eECCCCCC
Confidence 3455677777543211 1134577888886522221 111122255 99999873
No 71
>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=89.08 E-value=0.28 Score=18.49 Aligned_cols=9 Identities=44% Similarity=1.291 Sum_probs=4.0
Q ss_pred eCCCCcccc
Q psy12011 62 QCPQCSYRT 70 (94)
Q Consensus 62 ~c~~c~~~f 70 (94)
.|+.||..|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 344444444
No 72
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=88.99 E-value=0.3 Score=27.43 Aligned_cols=33 Identities=27% Similarity=0.697 Sum_probs=19.4
Q ss_pred CCccccccchhhccChHHHHcchhhhcCCCCceeCCCCccccc
Q psy12011 29 NGMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTK 71 (94)
Q Consensus 29 ~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 71 (94)
..-|.|+.|+..|.....+. .. |.|+.||....
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~---------~~-F~Cp~Cg~~L~ 147 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME---------YG-FRCPQCGEMLE 147 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh---------cC-CcCCCCCCCCe
Confidence 34566777776666654432 23 77777775543
No 73
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=88.83 E-value=0.15 Score=29.45 Aligned_cols=16 Identities=19% Similarity=0.212 Sum_probs=11.0
Q ss_pred ceeecCCCCccccchh
Q psy12011 7 QVHFCGLFPESFLTWS 22 (94)
Q Consensus 7 ~~~~c~~c~~~~~~~~ 22 (94)
+...||+|++.|....
T Consensus 4 k~~~CPvC~~~F~~~~ 19 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKK 19 (214)
T ss_pred CceECCCCCCeeeeeE
Confidence 4567888887777654
No 74
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=88.16 E-value=0.28 Score=24.17 Aligned_cols=11 Identities=18% Similarity=0.818 Sum_probs=6.6
Q ss_pred eeCCCCccccc
Q psy12011 61 FQCPQCSYRTK 71 (94)
Q Consensus 61 ~~c~~c~~~f~ 71 (94)
|.|..|+..|.
T Consensus 54 W~C~kCg~~fA 64 (89)
T COG1997 54 WKCRKCGAKFA 64 (89)
T ss_pred EEcCCCCCeec
Confidence 66666665554
No 75
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=88.14 E-value=0.36 Score=21.74 Aligned_cols=23 Identities=13% Similarity=0.535 Sum_probs=10.8
Q ss_pred CccccccchhhccChHHHHcchh
Q psy12011 30 GMFACDLCDKEYKYKRNLYSHKK 52 (94)
Q Consensus 30 k~~~c~~c~~~~~~~~~l~~h~~ 52 (94)
.-++|+-|+..|....++..|..
T Consensus 16 ~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 16 EFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred eeeeCCchhHHHHHhHHHHHHhh
Confidence 33445555555554444444443
No 76
>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=87.92 E-value=0.65 Score=23.72 Aligned_cols=25 Identities=32% Similarity=0.874 Sum_probs=23.1
Q ss_pred eeC----CCCcccccchhHHHHHHHHhcC
Q psy12011 61 FQC----PQCSYRTKRKGNLKSHLAIRHE 85 (94)
Q Consensus 61 ~~c----~~c~~~f~~~~~l~~h~~~~~~ 85 (94)
|.| ..|+....+...++.|.+.+|+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 899 9999999999999999998875
No 77
>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=87.55 E-value=0.35 Score=28.00 Aligned_cols=31 Identities=19% Similarity=0.442 Sum_probs=23.1
Q ss_pred CCCCceeCCCCcccccchhHHHHHHHHhcCcc
Q psy12011 56 GQEPRFQCPQCSYRTKRKGNLKSHLAIRHECY 87 (94)
Q Consensus 56 ~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~ 87 (94)
.+.. |.|..|+|.|....-+..|+..-|+++
T Consensus 74 ~~~K-~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 74 DEDK-WRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SSEE-EEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred cCCE-ECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 4455 999999999999999999998877654
No 78
>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=87.49 E-value=0.74 Score=19.35 Aligned_cols=22 Identities=36% Similarity=0.543 Sum_probs=15.3
Q ss_pred eeCCCCcccccc----hhHHHHHHHH
Q psy12011 61 FQCPQCSYRTKR----KGNLKSHLAI 82 (94)
Q Consensus 61 ~~c~~c~~~f~~----~~~l~~h~~~ 82 (94)
..|..|++.+.. .++|.+|++.
T Consensus 17 a~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 17 AKCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp EEETTTTEE-----SSTHHHHHHHHH
T ss_pred EEeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 789999987765 4788888854
No 79
>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=85.84 E-value=0.41 Score=28.51 Aligned_cols=77 Identities=16% Similarity=0.321 Sum_probs=37.5
Q ss_pred CCCCceeecCCCCccccchhccCC------CCCCccccccchhh-----------ccChHHHHcchhhhcCCCCceeCCC
Q psy12011 3 SQNLQVHFCGLFPESFLTWSNLKP------NLNGMFACDLCDKE-----------YKYKRNLYSHKKDECGQEPRFQCPQ 65 (94)
Q Consensus 3 ~~~~~~~~c~~c~~~~~~~~~l~~------~~~k~~~c~~c~~~-----------~~~~~~l~~h~~~~~~~~~~~~c~~ 65 (94)
..|-++|.|..|....-....+.| .....|+|..|++. |........-.. ....++ +.|+.
T Consensus 137 ~hGGrif~CsfC~~flCEDDQFEHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~k-y~k~k~-~PCPK 214 (314)
T PF06524_consen 137 DHGGRIFKCSFCDNFLCEDDQFEHQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFK-YEKGKP-IPCPK 214 (314)
T ss_pred cCCCeEEEeecCCCeeeccchhhhhhhhhhhhcccccccccccccchhhhheeeeehhhhhhhcccc-cccCCC-CCCCC
Confidence 356778888888764444444443 22234555555543 222211111111 112255 78888
Q ss_pred CcccccchhHHHHHHH
Q psy12011 66 CSYRTKRKGNLKSHLA 81 (94)
Q Consensus 66 c~~~f~~~~~l~~h~~ 81 (94)
|+........|..-.|
T Consensus 215 Cg~et~eTkdLSmStR 230 (314)
T PF06524_consen 215 CGYETQETKDLSMSTR 230 (314)
T ss_pred CCCcccccccceeeee
Confidence 8876555544443333
No 80
>PHA00626 hypothetical protein
Probab=85.76 E-value=0.66 Score=20.93 Aligned_cols=11 Identities=18% Similarity=0.428 Sum_probs=5.0
Q ss_pred ccccccchhhc
Q psy12011 31 MFACDLCDKEY 41 (94)
Q Consensus 31 ~~~c~~c~~~~ 41 (94)
.|.|..||..|
T Consensus 23 rYkCkdCGY~f 33 (59)
T PHA00626 23 DYVCCDCGYND 33 (59)
T ss_pred ceEcCCCCCee
Confidence 34455554333
No 81
>KOG2893|consensus
Probab=85.50 E-value=0.2 Score=29.42 Aligned_cols=28 Identities=29% Similarity=0.796 Sum_probs=14.8
Q ss_pred chhhccChHHHHcchhhhcCCCCceeCCCCccc
Q psy12011 37 CDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYR 69 (94)
Q Consensus 37 c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 69 (94)
|++.|..+..|.+|++ .+. |+|..|-+-
T Consensus 16 cnrefddekiliqhqk----akh-fkchichkk 43 (341)
T KOG2893|consen 16 CNREFDDEKILIQHQK----AKH-FKCHICHKK 43 (341)
T ss_pred cccccchhhhhhhhhh----hcc-ceeeeehhh
Confidence 5556666655555544 233 555555543
No 82
>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=85.03 E-value=0.82 Score=18.63 Aligned_cols=29 Identities=21% Similarity=0.225 Sum_probs=15.6
Q ss_pred eecCCCCccccchhccCCCCCCccccccchhh
Q psy12011 9 HFCGLFPESFLTWSNLKPNLNGMFACDLCDKE 40 (94)
Q Consensus 9 ~~c~~c~~~~~~~~~l~~~~~k~~~c~~c~~~ 40 (94)
..|+.||+.|....+ .-...-.|+.||..
T Consensus 2 r~C~~Cg~~Yh~~~~---pP~~~~~Cd~cg~~ 30 (36)
T PF05191_consen 2 RICPKCGRIYHIEFN---PPKVEGVCDNCGGE 30 (36)
T ss_dssp EEETTTTEEEETTTB-----SSTTBCTTTTEB
T ss_pred cCcCCCCCccccccC---CCCCCCccCCCCCe
Confidence 467778877655443 22223456666653
No 83
>KOG2893|consensus
Probab=84.98 E-value=0.2 Score=29.40 Aligned_cols=42 Identities=21% Similarity=0.295 Sum_probs=32.4
Q ss_pred ecCCCCccccchhccC-CCCCCccccccchhhccChHHHHcch
Q psy12011 10 FCGLFPESFLTWSNLK-PNLNGMFACDLCDKEYKYKRNLYSHK 51 (94)
Q Consensus 10 ~c~~c~~~~~~~~~l~-~~~~k~~~c~~c~~~~~~~~~l~~h~ 51 (94)
+|=+|++.|-+..-|. |...|.|+|.+|.+.+-.--.|..|-
T Consensus 12 wcwycnrefddekiliqhqkakhfkchichkkl~sgpglsihc 54 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKAKHFKCHICHKKLFSGPGLSIHC 54 (341)
T ss_pred eeeecccccchhhhhhhhhhhccceeeeehhhhccCCCceeeh
Confidence 4778999999988877 78889999999988765544455553
No 84
>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=84.34 E-value=0.82 Score=24.25 Aligned_cols=31 Identities=6% Similarity=0.129 Sum_probs=21.5
Q ss_pred eecCCCCccccchhccCCCCCCccccccchhhccChH
Q psy12011 9 HFCGLFPESFLTWSNLKPNLNGMFACDLCDKEYKYKR 45 (94)
Q Consensus 9 ~~c~~c~~~~~~~~~l~~~~~k~~~c~~c~~~~~~~~ 45 (94)
..|+.||+.|.... ..|..|+.||..|....
T Consensus 10 r~Cp~cg~kFYDLn------k~p~vcP~cg~~~~~~~ 40 (129)
T TIGR02300 10 RICPNTGSKFYDLN------RRPAVSPYTGEQFPPEE 40 (129)
T ss_pred ccCCCcCccccccC------CCCccCCCcCCccCcch
Confidence 67888888876533 24667888888776653
No 85
>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=84.04 E-value=0.45 Score=18.90 Aligned_cols=9 Identities=44% Similarity=1.394 Sum_probs=4.5
Q ss_pred eeCCCCccc
Q psy12011 61 FQCPQCSYR 69 (94)
Q Consensus 61 ~~c~~c~~~ 69 (94)
.+|..||..
T Consensus 18 irC~~CG~R 26 (32)
T PF03604_consen 18 IRCPECGHR 26 (32)
T ss_dssp SSBSSSS-S
T ss_pred EECCcCCCe
Confidence 556666544
No 86
>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=83.92 E-value=1.3 Score=16.56 Aligned_cols=20 Identities=35% Similarity=0.682 Sum_probs=13.6
Q ss_pred eeCCCCcccccchhHHHHHHH
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLA 81 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~ 81 (94)
..|+.|++.+ ....+..|+.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 4678888777 4556667765
No 87
>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=81.18 E-value=1.7 Score=16.04 Aligned_cols=10 Identities=10% Similarity=-0.217 Sum_probs=6.3
Q ss_pred ceeecCCCCc
Q psy12011 7 QVHFCGLFPE 16 (94)
Q Consensus 7 ~~~~c~~c~~ 16 (94)
..|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4577777763
No 88
>KOG4173|consensus
Probab=79.61 E-value=0.43 Score=27.46 Aligned_cols=78 Identities=17% Similarity=0.303 Sum_probs=50.7
Q ss_pred ceeecCC--CCccccchhccCC--CCCCccccccchhhccChHHHHcchhhhc---------CCCCceeCCC--Cccccc
Q psy12011 7 QVHFCGL--FPESFLTWSNLKP--NLNGMFACDLCDKEYKYKRNLYSHKKDEC---------GQEPRFQCPQ--CSYRTK 71 (94)
Q Consensus 7 ~~~~c~~--c~~~~~~~~~l~~--~~~k~~~c~~c~~~~~~~~~l~~h~~~~~---------~~~~~~~c~~--c~~~f~ 71 (94)
+.+.|+. |.+.|....++.+ +..-...|..|.+.|.....|..|+.--+ .+.++|+|.+ |+--|.
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFk 157 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHGNSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFK 157 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhcccchhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhh
Confidence 4466776 6566666665542 11122379999999999888888765221 2356688854 777788
Q ss_pred chhHHHHHHHHhc
Q psy12011 72 RKGNLKSHLAIRH 84 (94)
Q Consensus 72 ~~~~l~~h~~~~~ 84 (94)
..-....|+..-|
T Consensus 158 T~r~RkdH~I~~H 170 (253)
T KOG4173|consen 158 TSRDRKDHMIRMH 170 (253)
T ss_pred hhhhhhhHHHHhc
Confidence 7777777776443
No 89
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=79.57 E-value=0.71 Score=22.99 Aligned_cols=11 Identities=18% Similarity=0.724 Sum_probs=6.5
Q ss_pred eeCCCCccccc
Q psy12011 61 FQCPQCSYRTK 71 (94)
Q Consensus 61 ~~c~~c~~~f~ 71 (94)
|.|..|++.|.
T Consensus 55 W~C~~C~~~~A 65 (90)
T PTZ00255 55 WRCKGCKKTVA 65 (90)
T ss_pred EEcCCCCCEEe
Confidence 66666665554
No 90
>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=79.21 E-value=1.4 Score=19.76 Aligned_cols=30 Identities=17% Similarity=0.160 Sum_probs=14.8
Q ss_pred eecCCCCccccchhccCCCCCCccccccchhhc
Q psy12011 9 HFCGLFPESFLTWSNLKPNLNGMFACDLCDKEY 41 (94)
Q Consensus 9 ~~c~~c~~~~~~~~~l~~~~~k~~~c~~c~~~~ 41 (94)
+.|+.||..+....... ++ ...|+.||..+
T Consensus 3 ~~CP~CG~~iev~~~~~--Ge-iV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPEL--GE-LVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCcc--CC-EEeCCCCCCEE
Confidence 56666666554433222 22 33566666444
No 91
>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=78.95 E-value=1.9 Score=18.09 Aligned_cols=12 Identities=8% Similarity=0.213 Sum_probs=9.6
Q ss_pred ceeecCCCCccc
Q psy12011 7 QVHFCGLFPESF 18 (94)
Q Consensus 7 ~~~~c~~c~~~~ 18 (94)
++..|++|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 478899998776
No 92
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=78.82 E-value=2.9 Score=18.54 Aligned_cols=15 Identities=33% Similarity=0.789 Sum_probs=10.1
Q ss_pred eeCCCCcccccchhH
Q psy12011 61 FQCPQCSYRTKRKGN 75 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~ 75 (94)
+.|..|+..+....+
T Consensus 29 W~C~~Cgh~w~~~v~ 43 (55)
T PF14311_consen 29 WKCPKCGHEWKASVN 43 (55)
T ss_pred EECCCCCCeeEccHh
Confidence 777777776665544
No 93
>KOG2593|consensus
Probab=78.56 E-value=1 Score=28.76 Aligned_cols=33 Identities=21% Similarity=0.455 Sum_probs=17.1
Q ss_pred ceeecCCCCccccchhccC--CCCCCccccccchh
Q psy12011 7 QVHFCGLFPESFLTWSNLK--PNLNGMFACDLCDK 39 (94)
Q Consensus 7 ~~~~c~~c~~~~~~~~~l~--~~~~k~~~c~~c~~ 39 (94)
.-|+|+.|.+.|.....++ ....-.|.|..|+.
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGG 161 (436)
T ss_pred ccccCCccccchhhhHHHHhhcccCceEEEecCCC
Confidence 3466666666665555444 22234455555553
No 94
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=77.87 E-value=1.6 Score=18.60 Aligned_cols=8 Identities=13% Similarity=0.243 Sum_probs=4.0
Q ss_pred eecCCCCc
Q psy12011 9 HFCGLFPE 16 (94)
Q Consensus 9 ~~c~~c~~ 16 (94)
++|+.||.
T Consensus 19 ~~CP~Cg~ 26 (46)
T PF12760_consen 19 FVCPHCGS 26 (46)
T ss_pred CCCCCCCC
Confidence 44555553
No 95
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=77.63 E-value=1.5 Score=19.23 Aligned_cols=11 Identities=27% Similarity=0.863 Sum_probs=6.6
Q ss_pred ccccccchhhc
Q psy12011 31 MFACDLCDKEY 41 (94)
Q Consensus 31 ~~~c~~c~~~~ 41 (94)
.|.|..||+.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 45666666555
No 96
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=77.55 E-value=0.81 Score=20.09 Aligned_cols=15 Identities=20% Similarity=0.718 Sum_probs=7.1
Q ss_pred CccccccchhhccCh
Q psy12011 30 GMFACDLCDKEYKYK 44 (94)
Q Consensus 30 k~~~c~~c~~~~~~~ 44 (94)
+.+.|..||..|...
T Consensus 3 k~l~C~dCg~~FvfT 17 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFT 17 (49)
T ss_pred eeEEcccCCCeEEEe
Confidence 344455555554443
No 97
>KOG4167|consensus
Probab=75.61 E-value=0.69 Score=31.58 Aligned_cols=24 Identities=17% Similarity=0.425 Sum_probs=22.1
Q ss_pred eeCCCCcccccchhHHHHHHHHhc
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAIRH 84 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~~~ 84 (94)
|.|.+|++.|..--++..||++|.
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHH
Confidence 899999999999989999999884
No 98
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=74.99 E-value=2.2 Score=29.18 Aligned_cols=52 Identities=31% Similarity=0.618 Sum_probs=36.1
Q ss_pred cCCCCccccchhccC----CCCCCcc-ccccchhhccChHHHHcchhhhcCCCCceeCCCCccc
Q psy12011 11 CGLFPESFLTWSNLK----PNLNGMF-ACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYR 69 (94)
Q Consensus 11 c~~c~~~~~~~~~l~----~~~~k~~-~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 69 (94)
|..||-.|+-...|. ++.=+.| -|+.|.+.+..+.+ ++.|+ .+ ..|+.||..
T Consensus 126 CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~n----RRfHA--Qp-~aCp~CGP~ 182 (750)
T COG0068 126 CTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLN----RRFHA--QP-IACPKCGPH 182 (750)
T ss_pred cCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccc----ccccc--cc-ccCcccCCC
Confidence 888998888877776 3333333 58999888877655 34443 35 899999963
No 99
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=74.96 E-value=1.8 Score=23.23 Aligned_cols=25 Identities=24% Similarity=0.235 Sum_probs=19.1
Q ss_pred eeCCCCcccccchhHHHHHHHHhcCccc
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAIRHECYL 88 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~ 88 (94)
+.|.++|+.|.+ |++|+.+|.+-.|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCH
Confidence 688888887764 5899998877654
No 100
>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=74.73 E-value=0.95 Score=22.56 Aligned_cols=11 Identities=18% Similarity=0.830 Sum_probs=6.7
Q ss_pred eeCCCCccccc
Q psy12011 61 FQCPQCSYRTK 71 (94)
Q Consensus 61 ~~c~~c~~~f~ 71 (94)
|.|..|++.|.
T Consensus 54 W~C~~C~~~~A 64 (90)
T PF01780_consen 54 WKCKKCGKKFA 64 (90)
T ss_dssp EEETTTTEEEE
T ss_pred eecCCCCCEEe
Confidence 66666666554
No 101
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=74.62 E-value=2.4 Score=23.39 Aligned_cols=36 Identities=14% Similarity=0.255 Sum_probs=23.6
Q ss_pred ecCCCCccccchhccC------CCCCCccccccchhhccChH
Q psy12011 10 FCGLFPESFLTWSNLK------PNLNGMFACDLCDKEYKYKR 45 (94)
Q Consensus 10 ~c~~c~~~~~~~~~l~------~~~~k~~~c~~c~~~~~~~~ 45 (94)
.|+.|+........+. .+-+.|.-|..||+.|+...
T Consensus 41 ~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyPWt~ 82 (158)
T PF10083_consen 41 SCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYPWTE 82 (158)
T ss_pred HCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCchHH
Confidence 3666666555554443 35557888999998887753
No 102
>KOG1146|consensus
Probab=73.56 E-value=2.3 Score=31.16 Aligned_cols=76 Identities=16% Similarity=0.351 Sum_probs=52.1
Q ss_pred eecCCCCccccchhccCC-CCCCccccccchhhccChHHHHcchhhhc----------------CCCCceeCCCCccccc
Q psy12011 9 HFCGLFPESFLTWSNLKP-NLNGMFACDLCDKEYKYKRNLYSHKKDEC----------------GQEPRFQCPQCSYRTK 71 (94)
Q Consensus 9 ~~c~~c~~~~~~~~~l~~-~~~k~~~c~~c~~~~~~~~~l~~h~~~~~----------------~~~~~~~c~~c~~~f~ 71 (94)
+.|..|++.+.....+.+ -...+|.|..|...|.....|..|++... -...+| |..|...|.
T Consensus 1261 ~~c~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~ 1339 (1406)
T KOG1146|consen 1261 GECGAVDELLTPSFGISTLDVTHRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLS 1339 (1406)
T ss_pred chhhhccccccCccceeecccchhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHHhhcc
Confidence 345566665555554442 22346888999999998888888875321 113336 999999999
Q ss_pred chhHHHHHHHHhcC
Q psy12011 72 RKGNLKSHLAIRHE 85 (94)
Q Consensus 72 ~~~~l~~h~~~~~~ 85 (94)
....|..|+++.++
T Consensus 1340 ~~~alqihm~~~~~ 1353 (1406)
T KOG1146|consen 1340 GREALQIHMRSSAH 1353 (1406)
T ss_pred hhHHHHHHHHHhhh
Confidence 99999999997543
No 103
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=73.48 E-value=1.2 Score=22.65 Aligned_cols=16 Identities=31% Similarity=0.254 Sum_probs=12.0
Q ss_pred eeecCCCCccccchhc
Q psy12011 8 VHFCGLFPESFLTWSN 23 (94)
Q Consensus 8 ~~~c~~c~~~~~~~~~ 23 (94)
||.|.-||..|..-+.
T Consensus 2 pH~CtrCG~vf~~g~~ 17 (112)
T COG3364 2 PHQCTRCGEVFDDGSE 17 (112)
T ss_pred CceecccccccccccH
Confidence 6788888888877543
No 104
>KOG3408|consensus
Probab=72.88 E-value=2.6 Score=22.26 Aligned_cols=26 Identities=27% Similarity=0.498 Sum_probs=20.7
Q ss_pred CCCCceeCCCCcccccchhHHHHHHHH
Q psy12011 56 GQEPRFQCPQCSYRTKRKGNLKSHLAI 82 (94)
Q Consensus 56 ~~~~~~~c~~c~~~f~~~~~l~~h~~~ 82 (94)
|.-. |-|..|.+.|.....|..|.++
T Consensus 54 G~Gq-fyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQ-FYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCce-eehhhhhhhhcchHHHHHHHhc
Confidence 3344 8888999999988888888875
No 105
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=72.63 E-value=2.1 Score=21.77 Aligned_cols=38 Identities=13% Similarity=0.216 Sum_probs=21.5
Q ss_pred CceeecCCCCccccchhccCC-CCCCccccccchhhccC
Q psy12011 6 LQVHFCGLFPESFLTWSNLKP-NLNGMFACDLCDKEYKY 43 (94)
Q Consensus 6 ~~~~~c~~c~~~~~~~~~l~~-~~~k~~~c~~c~~~~~~ 43 (94)
.+.|.|+.|+..-...-.++. .+.....|..||.+|..
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ 58 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFEC 58 (104)
T ss_pred CceEecCccCCeeeeEEEEEecCceeEEEcccCcceEEE
Confidence 456888888865444333442 22233467777766543
No 106
>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=72.26 E-value=1.2 Score=22.20 Aligned_cols=11 Identities=18% Similarity=0.773 Sum_probs=6.5
Q ss_pred eeCCCCccccc
Q psy12011 61 FQCPQCSYRTK 71 (94)
Q Consensus 61 ~~c~~c~~~f~ 71 (94)
|.|..|++.|.
T Consensus 54 W~C~~C~~~~A 64 (91)
T TIGR00280 54 WTCRKCGAKFA 64 (91)
T ss_pred EEcCCCCCEEe
Confidence 66666665554
No 107
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=72.07 E-value=2.8 Score=22.35 Aligned_cols=16 Identities=13% Similarity=0.625 Sum_probs=9.2
Q ss_pred CCccccccchhhccCh
Q psy12011 29 NGMFACDLCDKEYKYK 44 (94)
Q Consensus 29 ~k~~~c~~c~~~~~~~ 44 (94)
.--|.|..|++.|...
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 3346666666666543
No 108
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=71.63 E-value=3 Score=20.86 Aligned_cols=13 Identities=23% Similarity=0.552 Sum_probs=6.6
Q ss_pred ccccccchhhccC
Q psy12011 31 MFACDLCDKEYKY 43 (94)
Q Consensus 31 ~~~c~~c~~~~~~ 43 (94)
|-+|..||..|..
T Consensus 58 Pa~CkkCGfef~~ 70 (97)
T COG3357 58 PARCKKCGFEFRD 70 (97)
T ss_pred ChhhcccCccccc
Confidence 4455556555433
No 109
>PRK04023 DNA polymerase II large subunit; Validated
Probab=69.89 E-value=7.3 Score=28.12 Aligned_cols=10 Identities=10% Similarity=0.072 Sum_probs=6.4
Q ss_pred eeecCCCCcc
Q psy12011 8 VHFCGLFPES 17 (94)
Q Consensus 8 ~~~c~~c~~~ 17 (94)
...|+.||..
T Consensus 626 ~RfCpsCG~~ 635 (1121)
T PRK04023 626 RRKCPSCGKE 635 (1121)
T ss_pred CccCCCCCCc
Confidence 4567777765
No 110
>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=68.48 E-value=3.6 Score=16.04 Aligned_cols=8 Identities=38% Similarity=1.290 Sum_probs=5.1
Q ss_pred eeCCCCcc
Q psy12011 61 FQCPQCSY 68 (94)
Q Consensus 61 ~~c~~c~~ 68 (94)
+.|+.|+.
T Consensus 20 ~vCp~C~~ 27 (30)
T PF08274_consen 20 LVCPECGH 27 (30)
T ss_dssp EEETTTTE
T ss_pred EeCCcccc
Confidence 66666654
No 111
>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=67.96 E-value=1.8 Score=21.11 Aligned_cols=9 Identities=22% Similarity=0.390 Sum_probs=2.4
Q ss_pred ceeecCCCC
Q psy12011 7 QVHFCGLFP 15 (94)
Q Consensus 7 ~~~~c~~c~ 15 (94)
+.|.|+.|+
T Consensus 21 ~~F~CPfC~ 29 (81)
T PF05129_consen 21 KVFDCPFCN 29 (81)
T ss_dssp S----TTT-
T ss_pred ceEcCCcCC
Confidence 456666666
No 112
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=66.25 E-value=3 Score=22.31 Aligned_cols=15 Identities=27% Similarity=0.208 Sum_probs=12.3
Q ss_pred eeecCCCCccccchh
Q psy12011 8 VHFCGLFPESFLTWS 22 (94)
Q Consensus 8 ~~~c~~c~~~~~~~~ 22 (94)
||.|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 688999999888765
No 113
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=66.18 E-value=3.9 Score=16.91 Aligned_cols=16 Identities=13% Similarity=-0.029 Sum_probs=12.0
Q ss_pred eeecCCCCccccchhc
Q psy12011 8 VHFCGLFPESFLTWSN 23 (94)
Q Consensus 8 ~~~c~~c~~~~~~~~~ 23 (94)
++.|..|++.|-....
T Consensus 12 ~f~C~~C~~~FC~~HR 27 (39)
T smart00154 12 GFKCRHCGNLFCGEHR 27 (39)
T ss_pred CeECCccCCccccccC
Confidence 7889999888766543
No 114
>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=64.32 E-value=8.1 Score=16.76 Aligned_cols=9 Identities=11% Similarity=0.032 Sum_probs=5.0
Q ss_pred eecCCCCcc
Q psy12011 9 HFCGLFPES 17 (94)
Q Consensus 9 ~~c~~c~~~ 17 (94)
|+|..|+-.
T Consensus 2 y~C~~Cgyv 10 (47)
T PF00301_consen 2 YQCPVCGYV 10 (47)
T ss_dssp EEETTTSBE
T ss_pred cCCCCCCEE
Confidence 556666544
No 115
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=63.51 E-value=2.2 Score=21.29 Aligned_cols=11 Identities=18% Similarity=0.824 Sum_probs=6.9
Q ss_pred eeCCCCccccc
Q psy12011 61 FQCPQCSYRTK 71 (94)
Q Consensus 61 ~~c~~c~~~f~ 71 (94)
|.|..|++.|.
T Consensus 55 W~C~~C~~~~A 65 (90)
T PRK03976 55 WECRKCGAKFA 65 (90)
T ss_pred EEcCCCCCEEe
Confidence 66666666554
No 116
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=63.38 E-value=3.4 Score=19.72 Aligned_cols=37 Identities=11% Similarity=0.244 Sum_probs=16.6
Q ss_pred eecCCCCccccchh-ccC--CCCCCccccc--cchhhccChH
Q psy12011 9 HFCGLFPESFLTWS-NLK--PNLNGMFACD--LCDKEYKYKR 45 (94)
Q Consensus 9 ~~c~~c~~~~~~~~-~l~--~~~~k~~~c~--~c~~~~~~~~ 45 (94)
+.|+.||....... ... ...+.-++|. +||..|....
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFITYE 43 (72)
T ss_pred ccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEEEE
Confidence 35677765432111 111 2333345565 6666665433
No 117
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=63.17 E-value=4.7 Score=16.68 Aligned_cols=15 Identities=20% Similarity=0.403 Sum_probs=6.5
Q ss_pred ccccchhhccChHHH
Q psy12011 33 ACDLCDKEYKYKRNL 47 (94)
Q Consensus 33 ~c~~c~~~~~~~~~l 47 (94)
.|..|+..+.....|
T Consensus 21 ~C~~C~G~W~d~~el 35 (41)
T PF13453_consen 21 VCPSCGGIWFDAGEL 35 (41)
T ss_pred ECCCCCeEEccHHHH
Confidence 344444444444333
No 118
>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=62.94 E-value=3.8 Score=18.17 Aligned_cols=26 Identities=12% Similarity=0.474 Sum_probs=14.3
Q ss_pred CCccccccchhhccChHHHHcchhhh
Q psy12011 29 NGMFACDLCDKEYKYKRNLYSHKKDE 54 (94)
Q Consensus 29 ~k~~~c~~c~~~~~~~~~l~~h~~~~ 54 (94)
...|+|+.|+..|-..-++-.|...|
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CCeEECCCCCCccccCcChhhhcccc
Confidence 34688889988888887777665555
No 119
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=62.41 E-value=7.3 Score=21.03 Aligned_cols=32 Identities=16% Similarity=0.610 Sum_probs=15.5
Q ss_pred ccccccchhhccChHHHHcchhhhcCCCCceeCCCCcccc
Q psy12011 31 MFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRT 70 (94)
Q Consensus 31 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 70 (94)
.|+|..|+..+. .+.+.. .... |.|..|+..+
T Consensus 112 ~y~C~~C~~~~~------~~rr~~-~~~~-y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYL------RVRRSN-NVSR-YRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCc------eEcccc-Ccce-EEcCCCCCEE
Confidence 466766765542 111111 1134 7777776543
No 120
>PF15269 zf-C2H2_7: Zinc-finger
Probab=62.30 E-value=7.3 Score=16.76 Aligned_cols=21 Identities=29% Similarity=0.782 Sum_probs=14.8
Q ss_pred eeCCCCcccccchhHHHHHHH
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLA 81 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~ 81 (94)
|+|-+|.....-.+.|-.|++
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 577777766667777777765
No 121
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=61.61 E-value=4.5 Score=18.18 Aligned_cols=14 Identities=14% Similarity=0.261 Sum_probs=7.6
Q ss_pred ecCCCCccccchhc
Q psy12011 10 FCGLFPESFLTWSN 23 (94)
Q Consensus 10 ~c~~c~~~~~~~~~ 23 (94)
.|+.|++.|....+
T Consensus 7 ~C~~Cg~~~~~~dD 20 (54)
T PF14446_consen 7 KCPVCGKKFKDGDD 20 (54)
T ss_pred cChhhCCcccCCCC
Confidence 46666666554433
No 122
>KOG0782|consensus
Probab=61.59 E-value=1.8 Score=29.07 Aligned_cols=36 Identities=17% Similarity=0.309 Sum_probs=21.5
Q ss_pred ecCCCCccccchhccCCCCCCccccccchhhccChH
Q psy12011 10 FCGLFPESFLTWSNLKPNLNGMFACDLCDKEYKYKR 45 (94)
Q Consensus 10 ~c~~c~~~~~~~~~l~~~~~k~~~c~~c~~~~~~~~ 45 (94)
+|..|+|.|.++..+..-......|+.|...|..+.
T Consensus 255 kC~~CgKgFQQKf~FhsKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 255 KCNTCGKGFQQKFFFHSKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred ccchhhhhhhhheeeccccEEEEEehHHHHHhhcch
Confidence 477777777776654433333456777776665553
No 123
>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=60.98 E-value=5.3 Score=16.68 Aligned_cols=28 Identities=14% Similarity=0.187 Sum_probs=12.1
Q ss_pred eecCCCCccccchhccCCCCCCccccccchhh
Q psy12011 9 HFCGLFPESFLTWSNLKPNLNGMFACDLCDKE 40 (94)
Q Consensus 9 ~~c~~c~~~~~~~~~l~~~~~k~~~c~~c~~~ 40 (94)
+.|+.|+.... +.......+.|..||..
T Consensus 1 m~Cp~Cg~~~~----~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 1 MKCPNCGSKEI----VFDPERGELVCPNCGLV 28 (43)
T ss_dssp ESBTTTSSSEE----EEETTTTEEEETTT-BB
T ss_pred CCCcCCcCCce----EEcCCCCeEECCCCCCE
Confidence 35666665321 11223334456666543
No 124
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=60.97 E-value=6.1 Score=25.47 Aligned_cols=30 Identities=13% Similarity=0.210 Sum_probs=18.1
Q ss_pred ecCCCCccccchhccCCCCCCccccccchhhccChH
Q psy12011 10 FCGLFPESFLTWSNLKPNLNGMFACDLCDKEYKYKR 45 (94)
Q Consensus 10 ~c~~c~~~~~~~~~l~~~~~k~~~c~~c~~~~~~~~ 45 (94)
+|+.||..+... |.+-|+|..||..+....
T Consensus 352 ~Cp~Cg~~m~S~------G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRMKSA------GRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCchhhc------CCCCcccccccccCCccc
Confidence 477777654332 233677888877665543
No 125
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=60.49 E-value=8.7 Score=20.74 Aligned_cols=57 Identities=25% Similarity=0.448 Sum_probs=32.9
Q ss_pred CCceeecCCCCccccchhccCCCCCCcccc---ccchhhccChHHHHcchhhhcCCCCceeCCCCcccccchhH
Q psy12011 5 NLQVHFCGLFPESFLTWSNLKPNLNGMFAC---DLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKRKGN 75 (94)
Q Consensus 5 ~~~~~~c~~c~~~~~~~~~l~~~~~k~~~c---~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~~~~~ 75 (94)
+.+.|.|..|..++....-|+ |-+| .+|+.-+ ..|+++-..+ | .|++|..+|.+++.
T Consensus 77 d~~lYeCnIC~etS~ee~FLK-----PneCCgY~iCn~Cy---a~LWK~~~~y----p--vCPvCkTSFKss~~ 136 (140)
T PF05290_consen 77 DPKLYECNICKETSAEERFLK-----PNECCGYSICNACY---ANLWKFCNLY----P--VCPVCKTSFKSSSS 136 (140)
T ss_pred CCCceeccCcccccchhhcCC-----cccccchHHHHHHH---HHHHHHcccC----C--CCCccccccccccc
Confidence 347889999988766555443 3233 3333222 3344443322 2 78899888877643
No 126
>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=60.37 E-value=5.8 Score=21.45 Aligned_cols=31 Identities=26% Similarity=0.840 Sum_probs=15.3
Q ss_pred ccccccchhhccChHHHHcchhhhcCCCCceeCCCCcccc
Q psy12011 31 MFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRT 70 (94)
Q Consensus 31 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 70 (94)
.|.|..|+..+.. +.+. .... +.|..|+..+
T Consensus 123 ~~~C~~C~~~~~r------~~~~--~~~~-~~C~~C~~~l 153 (157)
T PF10263_consen 123 VYRCPSCGREYKR------HRRS--KRKR-YRCGRCGGPL 153 (157)
T ss_pred EEEcCCCCCEeee------eccc--chhh-EECCCCCCEE
Confidence 3567777655422 2222 1233 6777776443
No 127
>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=59.78 E-value=4.5 Score=16.99 Aligned_cols=17 Identities=18% Similarity=0.071 Sum_probs=9.8
Q ss_pred ceeecCCCCccccchhc
Q psy12011 7 QVHFCGLFPESFLTWSN 23 (94)
Q Consensus 7 ~~~~c~~c~~~~~~~~~ 23 (94)
-++.|+.|++.|-..-.
T Consensus 12 ~~~~C~~C~~~FC~~Hr 28 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHR 28 (43)
T ss_dssp SHEE-TTTS-EE-TTTH
T ss_pred CCeECCCCCcccCcccc
Confidence 47888888888765443
No 128
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=59.33 E-value=4.3 Score=22.34 Aligned_cols=29 Identities=21% Similarity=0.568 Sum_probs=14.7
Q ss_pred eeCCCCcccccchhHHHHHHHHhcCcccCCCCCC
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAIRHECYLDDSANC 94 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~~C 94 (94)
|.|. |+..+... ++|-..-.|+ .|.|-.|
T Consensus 118 Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C 146 (156)
T COG3091 118 YRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKC 146 (156)
T ss_pred EEee-cCCccchh---hhcccccccc-eEEeccC
Confidence 6666 65544333 3444444444 5666554
No 129
>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=58.78 E-value=5.8 Score=18.27 Aligned_cols=30 Identities=13% Similarity=0.283 Sum_probs=11.7
Q ss_pred eeecCCCCccccchhccCCCCCCccccccchhhccCh
Q psy12011 8 VHFCGLFPESFLTWSNLKPNLNGMFACDLCDKEYKYK 44 (94)
Q Consensus 8 ~~~c~~c~~~~~~~~~l~~~~~k~~~c~~c~~~~~~~ 44 (94)
.-.|..|++.|... .+.+.|..||..|-..
T Consensus 9 ~~~C~~C~~~F~~~-------~rrhhCr~CG~~vC~~ 38 (69)
T PF01363_consen 9 ASNCMICGKKFSLF-------RRRHHCRNCGRVVCSS 38 (69)
T ss_dssp -SB-TTT--B-BSS-------S-EEE-TTT--EEECC
T ss_pred CCcCcCcCCcCCCc-------eeeEccCCCCCEECCc
Confidence 45577777777432 3355666666665543
No 130
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=58.39 E-value=9.5 Score=23.67 Aligned_cols=59 Identities=22% Similarity=0.348 Sum_probs=43.9
Q ss_pred CCccccccchhhccChHHHHcchhhhcCCCCceeCCCC--cccccchhHHHHHHHHhcCccc
Q psy12011 29 NGMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQC--SYRTKRKGNLKSHLAIRHECYL 88 (94)
Q Consensus 29 ~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c--~~~f~~~~~l~~h~~~~~~~~~ 88 (94)
...+.|..|...|........|...+.++++ +.|... ...+.....+.+|.+.++....
T Consensus 31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 91 (467)
T COG5048 31 PRPDSCPNCTDSFSRLEHLTRHIRSHTGEKP-SQCSYSGCDKSFSRPLELSRHLRTHHNNPS 91 (467)
T ss_pred CchhhcccccccccccchhhhhcccccccCC-ccccccccccccCCcchhhhhccccccccc
Confidence 3567788888888888888888888988877 888664 4566667777777776665443
No 131
>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=57.95 E-value=4.5 Score=15.56 Aligned_cols=9 Identities=33% Similarity=1.029 Sum_probs=4.5
Q ss_pred ccccchhhc
Q psy12011 33 ACDLCDKEY 41 (94)
Q Consensus 33 ~c~~c~~~~ 41 (94)
.|..|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 344555555
No 132
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=57.76 E-value=8.3 Score=20.02 Aligned_cols=11 Identities=18% Similarity=0.181 Sum_probs=6.1
Q ss_pred ccccccchhhc
Q psy12011 31 MFACDLCDKEY 41 (94)
Q Consensus 31 ~~~c~~c~~~~ 41 (94)
...|..|+..|
T Consensus 70 ~~~C~~Cg~~~ 80 (113)
T PRK12380 70 QAWCWDCSQVV 80 (113)
T ss_pred EEEcccCCCEE
Confidence 35566666444
No 133
>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=57.36 E-value=6.8 Score=21.42 Aligned_cols=9 Identities=22% Similarity=0.922 Sum_probs=5.1
Q ss_pred ccccccchh
Q psy12011 31 MFACDLCDK 39 (94)
Q Consensus 31 ~~~c~~c~~ 39 (94)
.+.|..||.
T Consensus 112 ~l~C~~Cg~ 120 (146)
T PF07295_consen 112 TLVCENCGH 120 (146)
T ss_pred eEecccCCC
Confidence 456666653
No 134
>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=56.59 E-value=7.4 Score=20.15 Aligned_cols=11 Identities=27% Similarity=0.800 Sum_probs=4.7
Q ss_pred cccccchhhcc
Q psy12011 32 FACDLCDKEYK 42 (94)
Q Consensus 32 ~~c~~c~~~~~ 42 (94)
..|..||..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PF01155_consen 71 ARCRDCGHEFE 81 (113)
T ss_dssp EEETTTS-EEE
T ss_pred EECCCCCCEEe
Confidence 34555554443
No 135
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=55.57 E-value=9.6 Score=26.52 Aligned_cols=11 Identities=18% Similarity=0.317 Sum_probs=5.3
Q ss_pred CCccccccchh
Q psy12011 29 NGMFACDLCDK 39 (94)
Q Consensus 29 ~k~~~c~~c~~ 39 (94)
..|..|+.||.
T Consensus 473 ~~p~~Cp~Cgs 483 (730)
T COG1198 473 PIPQSCPECGS 483 (730)
T ss_pred CCCCCCCCCCC
Confidence 34455555543
No 136
>PLN02294 cytochrome c oxidase subunit Vb
Probab=55.23 E-value=7.5 Score=21.88 Aligned_cols=15 Identities=13% Similarity=0.131 Sum_probs=9.5
Q ss_pred CceeecCCCCccccc
Q psy12011 6 LQVHFCGLFPESFLT 20 (94)
Q Consensus 6 ~~~~~c~~c~~~~~~ 20 (94)
.+++.|+.||..|.-
T Consensus 139 Gkp~RCpeCG~~fkL 153 (174)
T PLN02294 139 GKSFECPVCTQYFEL 153 (174)
T ss_pred CCceeCCCCCCEEEE
Confidence 356777777766543
No 137
>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=54.57 E-value=5.8 Score=17.46 Aligned_cols=12 Identities=17% Similarity=0.144 Sum_probs=5.5
Q ss_pred ecCCCCccccch
Q psy12011 10 FCGLFPESFLTW 21 (94)
Q Consensus 10 ~c~~c~~~~~~~ 21 (94)
.||.|+..|...
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 788888776543
No 138
>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=54.02 E-value=4.9 Score=17.83 Aligned_cols=15 Identities=7% Similarity=-0.064 Sum_probs=7.7
Q ss_pred CCceeecCCCCcccc
Q psy12011 5 NLQVHFCGLFPESFL 19 (94)
Q Consensus 5 ~~~~~~c~~c~~~~~ 19 (94)
+...++|.+|++.+.
T Consensus 32 ~~~~~rC~YCe~~~~ 46 (52)
T PF02748_consen 32 EPIKLRCHYCERIIT 46 (52)
T ss_dssp TTCEEEETTT--EEE
T ss_pred CCCEEEeeCCCCEec
Confidence 344566777776554
No 139
>KOG4167|consensus
Probab=53.46 E-value=3.5 Score=28.50 Aligned_cols=26 Identities=27% Similarity=0.544 Sum_probs=22.4
Q ss_pred CccccccchhhccChHHHHcchhhhc
Q psy12011 30 GMFACDLCDKEYKYKRNLYSHKKDEC 55 (94)
Q Consensus 30 k~~~c~~c~~~~~~~~~l~~h~~~~~ 55 (94)
.-|.|.+|++.|.--.++..||+.|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 35789999999988888899998885
No 140
>PF14353 CpXC: CpXC protein
Probab=53.40 E-value=8.8 Score=20.15 Aligned_cols=19 Identities=16% Similarity=-0.027 Sum_probs=14.6
Q ss_pred ceeecCCCCccccchhccC
Q psy12011 7 QVHFCGLFPESFLTWSNLK 25 (94)
Q Consensus 7 ~~~~c~~c~~~~~~~~~l~ 25 (94)
-.+.|+.||..|.-...+.
T Consensus 37 ~~~~CP~Cg~~~~~~~p~l 55 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLL 55 (128)
T ss_pred CEEECCCCCCceecCCCEE
Confidence 3588999999887666555
No 141
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=52.99 E-value=8.7 Score=21.75 Aligned_cols=9 Identities=44% Similarity=1.350 Sum_probs=5.1
Q ss_pred eeCCCCccc
Q psy12011 61 FQCPQCSYR 69 (94)
Q Consensus 61 ~~c~~c~~~ 69 (94)
|.|+.||-.
T Consensus 133 F~Cp~Cg~~ 141 (176)
T COG1675 133 FTCPKCGED 141 (176)
T ss_pred CCCCCCCch
Confidence 566666643
No 142
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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 DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=52.70 E-value=5.8 Score=18.61 Aligned_cols=34 Identities=29% Similarity=0.606 Sum_probs=14.5
Q ss_pred cccccchhhccChHHHHcchhhhcCCCCceeCCCCccc
Q psy12011 32 FACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYR 69 (94)
Q Consensus 32 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 69 (94)
|.|..|+..-.. .+ ..+.-+.|..- .+|+.|...
T Consensus 5 FTC~~C~~Rs~~--~~-sk~aY~~GvVi-v~C~gC~~~ 38 (66)
T PF05180_consen 5 FTCNKCGTRSAK--MF-SKQAYHKGVVI-VQCPGCKNR 38 (66)
T ss_dssp EEETTTTEEEEE--EE-EHHHHHTSEEE-EE-TTS--E
T ss_pred EEcCCCCCccce--ee-CHHHHhCCeEE-EECCCCcce
Confidence 667777632211 11 11223445333 788888643
No 143
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=52.65 E-value=12 Score=20.09 Aligned_cols=15 Identities=13% Similarity=0.023 Sum_probs=10.2
Q ss_pred ceeecCCCCccccch
Q psy12011 7 QVHFCGLFPESFLTW 21 (94)
Q Consensus 7 ~~~~c~~c~~~~~~~ 21 (94)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 457788888766553
No 144
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=51.90 E-value=13 Score=15.37 Aligned_cols=9 Identities=33% Similarity=1.150 Sum_probs=4.3
Q ss_pred eeCCCCccc
Q psy12011 61 FQCPQCSYR 69 (94)
Q Consensus 61 ~~c~~c~~~ 69 (94)
|.|..|+..
T Consensus 29 y~C~~C~~~ 37 (40)
T smart00440 29 YVCTKCGHR 37 (40)
T ss_pred EEeCCCCCE
Confidence 455555443
No 145
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=51.50 E-value=13 Score=19.40 Aligned_cols=13 Identities=23% Similarity=0.516 Sum_probs=7.3
Q ss_pred ccccccchhhccC
Q psy12011 31 MFACDLCDKEYKY 43 (94)
Q Consensus 31 ~~~c~~c~~~~~~ 43 (94)
...|..|+..|..
T Consensus 70 ~~~C~~Cg~~~~~ 82 (115)
T TIGR00100 70 ECECEDCSEEVSP 82 (115)
T ss_pred EEEcccCCCEEec
Confidence 3566666655433
No 146
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=51.36 E-value=5 Score=16.51 Aligned_cols=9 Identities=11% Similarity=0.309 Sum_probs=4.2
Q ss_pred cCCCCcccc
Q psy12011 11 CGLFPESFL 19 (94)
Q Consensus 11 c~~c~~~~~ 19 (94)
|.+||....
T Consensus 1 Cd~CG~~I~ 9 (37)
T PF08394_consen 1 CDYCGGEIT 9 (37)
T ss_pred CCccCCccc
Confidence 445555433
No 147
>PRK04351 hypothetical protein; Provisional
Probab=51.25 E-value=14 Score=20.30 Aligned_cols=32 Identities=19% Similarity=0.706 Sum_probs=18.2
Q ss_pred ccccccchhhccChHHHHcchhhhcCCCCceeCCCCccccc
Q psy12011 31 MFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTK 71 (94)
Q Consensus 31 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 71 (94)
.|+|..|+..+.. + +.+ .... |.|..|+..+.
T Consensus 112 ~Y~C~~Cg~~~~r------~-Rr~-n~~~-yrCg~C~g~L~ 143 (149)
T PRK04351 112 LYECQSCGQQYLR------K-RRI-NTKR-YRCGKCRGKLK 143 (149)
T ss_pred EEECCCCCCEeee------e-eec-CCCc-EEeCCCCcEee
Confidence 3678778755422 1 122 2255 88888876554
No 148
>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=51.11 E-value=9.4 Score=15.39 Aligned_cols=16 Identities=19% Similarity=0.233 Sum_probs=7.4
Q ss_pred ecCCCCccccchhccC
Q psy12011 10 FCGLFPESFLTWSNLK 25 (94)
Q Consensus 10 ~c~~c~~~~~~~~~l~ 25 (94)
.|..|++.|....-+.
T Consensus 5 ~C~eC~~~f~dSyL~~ 20 (34)
T PF01286_consen 5 KCDECGKPFMDSYLLN 20 (34)
T ss_dssp E-TTT--EES-SSCCC
T ss_pred hHhHhCCHHHHHHHHH
Confidence 5777777777655443
No 149
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=50.96 E-value=18 Score=18.45 Aligned_cols=34 Identities=9% Similarity=0.163 Sum_probs=15.4
Q ss_pred ceeecCCCCccccchhccCCCCCCccccccchhhcc
Q psy12011 7 QVHFCGLFPESFLTWSNLKPNLNGMFACDLCDKEYK 42 (94)
Q Consensus 7 ~~~~c~~c~~~~~~~~~l~~~~~k~~~c~~c~~~~~ 42 (94)
..|.|+.|+.. ...-.+ ..+.....|..||..+.
T Consensus 20 t~f~CP~Cge~-~v~v~~-~k~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 20 KIFECPRCGKV-SISVKI-KKNIAIITCGNCGLYTE 53 (99)
T ss_pred cEeECCCCCCe-Eeeeec-CCCcceEECCCCCCccC
Confidence 45667777731 111111 11333445666665443
No 150
>KOG3507|consensus
Probab=50.74 E-value=19 Score=16.47 Aligned_cols=12 Identities=33% Similarity=0.963 Sum_probs=7.0
Q ss_pred eeCCCCcccccc
Q psy12011 61 FQCPQCSYRTKR 72 (94)
Q Consensus 61 ~~c~~c~~~f~~ 72 (94)
++|.+||.....
T Consensus 38 irCReCG~RIly 49 (62)
T KOG3507|consen 38 IRCRECGYRILY 49 (62)
T ss_pred EehhhcchHHHH
Confidence 666666655443
No 151
>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=49.46 E-value=11 Score=15.36 Aligned_cols=12 Identities=8% Similarity=0.055 Sum_probs=6.1
Q ss_pred ceeecCCCCccc
Q psy12011 7 QVHFCGLFPESF 18 (94)
Q Consensus 7 ~~~~c~~c~~~~ 18 (94)
+.|+|..||...
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 567888887653
No 152
>PF12773 DZR: Double zinc ribbon
Probab=49.42 E-value=17 Score=15.50 Aligned_cols=9 Identities=33% Similarity=0.914 Sum_probs=4.9
Q ss_pred eeCCCCccc
Q psy12011 61 FQCPQCSYR 69 (94)
Q Consensus 61 ~~c~~c~~~ 69 (94)
..|+.|+..
T Consensus 30 ~~C~~Cg~~ 38 (50)
T PF12773_consen 30 KICPNCGAE 38 (50)
T ss_pred CCCcCCcCC
Confidence 455666544
No 153
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=49.18 E-value=9.5 Score=17.20 Aligned_cols=15 Identities=7% Similarity=0.284 Sum_probs=6.1
Q ss_pred ccccccchhhccChH
Q psy12011 31 MFACDLCDKEYKYKR 45 (94)
Q Consensus 31 ~~~c~~c~~~~~~~~ 45 (94)
|.....|+-.|...+
T Consensus 24 PV~s~~C~H~fek~a 38 (57)
T PF11789_consen 24 PVKSKKCGHTFEKEA 38 (57)
T ss_dssp EEEESSS--EEEHHH
T ss_pred CcCcCCCCCeecHHH
Confidence 444445555554443
No 154
>COG2879 Uncharacterized small protein [Function unknown]
Probab=49.13 E-value=21 Score=16.61 Aligned_cols=19 Identities=16% Similarity=0.055 Sum_probs=14.0
Q ss_pred chhHHHHHHHHhcCcccCC
Q psy12011 72 RKGNLKSHLAIRHECYLDD 90 (94)
Q Consensus 72 ~~~~l~~h~~~~~~~~~~~ 90 (94)
.-.+.-.|++.+|+++|.-
T Consensus 24 dYdnYVehmr~~hPd~p~m 42 (65)
T COG2879 24 DYDNYVEHMRKKHPDKPPM 42 (65)
T ss_pred cHHHHHHHHHHhCcCCCcc
Confidence 3455668999999988853
No 155
>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=48.55 E-value=12 Score=16.34 Aligned_cols=27 Identities=15% Similarity=0.221 Sum_probs=14.8
Q ss_pred ecCCCCccccchhccCCCCCCccccccchhhccC
Q psy12011 10 FCGLFPESFLTWSNLKPNLNGMFACDLCDKEYKY 43 (94)
Q Consensus 10 ~c~~c~~~~~~~~~l~~~~~k~~~c~~c~~~~~~ 43 (94)
.|..|++.|... .+.+.|..||+.|-.
T Consensus 4 ~C~~C~~~F~~~-------~rk~~Cr~Cg~~~C~ 30 (57)
T cd00065 4 SCMGCGKPFTLT-------RRRHHCRNCGRIFCS 30 (57)
T ss_pred cCcccCccccCC-------ccccccCcCcCCcCh
Confidence 466666666552 224556666666544
No 156
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.43 E-value=8.9 Score=17.71 Aligned_cols=12 Identities=8% Similarity=0.232 Sum_probs=8.8
Q ss_pred eeecCCCCcccc
Q psy12011 8 VHFCGLFPESFL 19 (94)
Q Consensus 8 ~~~c~~c~~~~~ 19 (94)
--.|++|+..|.
T Consensus 48 ev~CPYC~t~y~ 59 (62)
T COG4391 48 EVVCPYCSTRYR 59 (62)
T ss_pred cEecCccccEEE
Confidence 346899988765
No 157
>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=47.72 E-value=9.1 Score=19.42 Aligned_cols=22 Identities=32% Similarity=0.475 Sum_probs=16.2
Q ss_pred HcchhhhcCCCCceeCCCCccccc
Q psy12011 48 YSHKKDECGQEPRFQCPQCSYRTK 71 (94)
Q Consensus 48 ~~h~~~~~~~~~~~~c~~c~~~f~ 71 (94)
..++..+.+ ++ .+|.+||..|.
T Consensus 69 v~W~~l~~g-~~-~rC~eCG~~fk 90 (97)
T cd00924 69 VIWMWLEKG-KP-KRCPECGHVFK 90 (97)
T ss_pred EEEEEEeCC-Cc-eeCCCCCcEEE
Confidence 345566666 56 99999998875
No 158
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=47.09 E-value=13 Score=16.26 Aligned_cols=9 Identities=33% Similarity=1.320 Sum_probs=5.7
Q ss_pred eeCCCCccc
Q psy12011 61 FQCPQCSYR 69 (94)
Q Consensus 61 ~~c~~c~~~ 69 (94)
+.|..||..
T Consensus 38 ~~C~~Cgyt 46 (50)
T PRK00432 38 WHCGKCGYT 46 (50)
T ss_pred EECCCcCCE
Confidence 667766644
No 159
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=46.64 E-value=5.4 Score=18.08 Aligned_cols=6 Identities=33% Similarity=1.558 Sum_probs=3.2
Q ss_pred eeCCCC
Q psy12011 61 FQCPQC 66 (94)
Q Consensus 61 ~~c~~c 66 (94)
|-|..|
T Consensus 32 YmC~eC 37 (56)
T PF09963_consen 32 YMCDEC 37 (56)
T ss_pred eeChhH
Confidence 555555
No 160
>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=46.38 E-value=12 Score=20.26 Aligned_cols=16 Identities=19% Similarity=0.530 Sum_probs=11.2
Q ss_pred eeCCCCcccccchhHH
Q psy12011 61 FQCPQCSYRTKRKGNL 76 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l 76 (94)
+.|+.|++.|=..+.+
T Consensus 125 ~~C~~C~kiyW~GsH~ 140 (147)
T PF01927_consen 125 WRCPGCGKIYWEGSHW 140 (147)
T ss_pred EECCCCCCEecccccH
Confidence 7888888877554443
No 161
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=46.25 E-value=18 Score=15.46 Aligned_cols=11 Identities=36% Similarity=0.754 Sum_probs=5.7
Q ss_pred ccccccchhhc
Q psy12011 31 MFACDLCDKEY 41 (94)
Q Consensus 31 ~~~c~~c~~~~ 41 (94)
.+.|+.||..+
T Consensus 20 ~~vC~~Cg~~~ 30 (52)
T smart00661 20 RFVCRKCGYEE 30 (52)
T ss_pred EEECCcCCCeE
Confidence 44555565443
No 162
>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=45.01 E-value=18 Score=15.37 Aligned_cols=12 Identities=17% Similarity=0.327 Sum_probs=6.3
Q ss_pred ecCCCCccccch
Q psy12011 10 FCGLFPESFLTW 21 (94)
Q Consensus 10 ~c~~c~~~~~~~ 21 (94)
.|.+|+..|...
T Consensus 10 ~C~~C~rpf~WR 21 (42)
T PF10013_consen 10 ICPVCGRPFTWR 21 (42)
T ss_pred cCcccCCcchHH
Confidence 355555555543
No 163
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=44.38 E-value=17 Score=19.02 Aligned_cols=12 Identities=25% Similarity=0.750 Sum_probs=6.7
Q ss_pred ccccccchhhcc
Q psy12011 31 MFACDLCDKEYK 42 (94)
Q Consensus 31 ~~~c~~c~~~~~ 42 (94)
...|..||..|.
T Consensus 71 ~~~C~~Cg~~~~ 82 (117)
T PRK00564 71 ELECKDCSHVFK 82 (117)
T ss_pred EEEhhhCCCccc
Confidence 456666664443
No 164
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=44.37 E-value=26 Score=18.33 Aligned_cols=74 Identities=9% Similarity=0.059 Sum_probs=42.5
Q ss_pred eeecCCCCccccchhccC---C-------CCCC-------ccccccchhhccChHHHHcchhhhcCCCCceeCCCCcccc
Q psy12011 8 VHFCGLFPESFLTWSNLK---P-------NLNG-------MFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRT 70 (94)
Q Consensus 8 ~~~c~~c~~~~~~~~~l~---~-------~~~k-------~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 70 (94)
|-.|+.|+=......+|. | -.+. ...|-.|...|........ ........ |.|..|...|
T Consensus 15 P~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~-y~C~~C~~~F 91 (112)
T TIGR00622 15 PVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDSHR-YVCAVCKNVF 91 (112)
T ss_pred CCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccccc-eeCCCCCCcc
Confidence 567888887665555554 1 1111 1237778777765421110 00122245 9999999888
Q ss_pred cchhHHHHHHHHhc
Q psy12011 71 KRKGNLKSHLAIRH 84 (94)
Q Consensus 71 ~~~~~l~~h~~~~~ 84 (94)
=..-+.-.|...|.
T Consensus 92 C~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 92 CVDCDVFVHESLHC 105 (112)
T ss_pred ccccchhhhhhccC
Confidence 77777667766554
No 165
>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=43.95 E-value=14 Score=15.20 Aligned_cols=12 Identities=25% Similarity=0.476 Sum_probs=7.1
Q ss_pred eeecCCCCcccc
Q psy12011 8 VHFCGLFPESFL 19 (94)
Q Consensus 8 ~~~c~~c~~~~~ 19 (94)
.+.|+.||..+.
T Consensus 32 ~~~C~~CGE~~~ 43 (46)
T TIGR03831 32 ALVCPQCGEEYL 43 (46)
T ss_pred ccccccCCCEee
Confidence 355777776543
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=43.86 E-value=17 Score=16.69 Aligned_cols=11 Identities=36% Similarity=1.334 Sum_probs=7.6
Q ss_pred eeCCCCccccc
Q psy12011 61 FQCPQCSYRTK 71 (94)
Q Consensus 61 ~~c~~c~~~f~ 71 (94)
|.|+.||..+.
T Consensus 47 ~~C~~Cg~~~~ 57 (69)
T PF07282_consen 47 FTCPNCGFEMD 57 (69)
T ss_pred EEcCCCCCEEC
Confidence 77877776544
No 167
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=43.14 E-value=19 Score=18.74 Aligned_cols=11 Identities=18% Similarity=0.504 Sum_probs=6.0
Q ss_pred ccccccchhhc
Q psy12011 31 MFACDLCDKEY 41 (94)
Q Consensus 31 ~~~c~~c~~~~ 41 (94)
...|..|+..|
T Consensus 70 ~~~C~~Cg~~~ 80 (114)
T PRK03681 70 ECWCETCQQYV 80 (114)
T ss_pred EEEcccCCCee
Confidence 35566666443
No 169
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.90 E-value=13 Score=19.42 Aligned_cols=29 Identities=10% Similarity=0.067 Sum_probs=17.1
Q ss_pred eecCCCCccccchhccCCCCCCccccccchhhccC
Q psy12011 9 HFCGLFPESFLTWSNLKPNLNGMFACDLCDKEYKY 43 (94)
Q Consensus 9 ~~c~~c~~~~~~~~~l~~~~~k~~~c~~c~~~~~~ 43 (94)
..|+.|++.|..... .|..|+.||++|..
T Consensus 10 ridPetg~KFYDLNr------dPiVsPytG~s~P~ 38 (129)
T COG4530 10 RIDPETGKKFYDLNR------DPIVSPYTGKSYPR 38 (129)
T ss_pred ccCccccchhhccCC------CccccCcccccchH
Confidence 356677777766552 35556666666633
No 170
>KOG2482|consensus
Probab=41.43 E-value=17 Score=23.04 Aligned_cols=22 Identities=27% Similarity=0.546 Sum_probs=20.7
Q ss_pred eeCCCCcccccchhHHHHHHHH
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAI 82 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~ 82 (94)
+.|..|.+.|.-+..|+.||+.
T Consensus 196 ~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred heeeeeccccCCcHHHHHHHHh
Confidence 7999999999999999999985
No 171
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=40.55 E-value=15 Score=21.81 Aligned_cols=18 Identities=17% Similarity=0.182 Sum_probs=13.6
Q ss_pred CCceeecCCCCccccchh
Q psy12011 5 NLQVHFCGLFPESFLTWS 22 (94)
Q Consensus 5 ~~~~~~c~~c~~~~~~~~ 22 (94)
..++++|+.||..|.-..
T Consensus 178 EGkpqRCpECGqVFKLVr 195 (268)
T PTZ00043 178 EGFLYRCGECDQIFMLVR 195 (268)
T ss_pred CCCCccCCCCCcEEEEEE
Confidence 345889999998877644
No 172
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=40.43 E-value=18 Score=13.69 Aligned_cols=6 Identities=33% Similarity=1.758 Sum_probs=2.2
Q ss_pred eeCCCC
Q psy12011 61 FQCPQC 66 (94)
Q Consensus 61 ~~c~~c 66 (94)
|.|..|
T Consensus 16 Y~C~~C 21 (30)
T PF07649_consen 16 YRCSEC 21 (30)
T ss_dssp EE-TTT
T ss_pred EECccC
Confidence 444444
No 173
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=40.02 E-value=36 Score=17.44 Aligned_cols=33 Identities=15% Similarity=0.344 Sum_probs=16.9
Q ss_pred ceeecCCCCccccchhccC----CCCCCccccccchh
Q psy12011 7 QVHFCGLFPESFLTWSNLK----PNLNGMFACDLCDK 39 (94)
Q Consensus 7 ~~~~c~~c~~~~~~~~~l~----~~~~k~~~c~~c~~ 39 (94)
.+|.|+.-|..|.+...+. --..+-|.|...|+
T Consensus 2 eVf~i~~T~EiF~dYe~Y~~R~~~y~~~vwtC~~TGk 38 (102)
T PF10537_consen 2 EVFYIPFTGEIFRDYEEYLKRMILYNQRVWTCEITGK 38 (102)
T ss_pred ceEEeCCCCcccCCHHHHHHHHHHHhCCeeEEecCCC
Confidence 3566666666666555543 12334455555444
No 174
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=39.65 E-value=22 Score=13.66 Aligned_cols=7 Identities=43% Similarity=1.606 Sum_probs=2.8
Q ss_pred eeCCCCc
Q psy12011 61 FQCPQCS 67 (94)
Q Consensus 61 ~~c~~c~ 67 (94)
|.|..|+
T Consensus 28 f~C~~C~ 34 (39)
T smart00132 28 FKCSKCG 34 (39)
T ss_pred CCCcccC
Confidence 3444443
No 175
>COG1773 Rubredoxin [Energy production and conversion]
Probab=39.37 E-value=16 Score=16.46 Aligned_cols=12 Identities=8% Similarity=0.077 Sum_probs=7.5
Q ss_pred eeecCCCCcccc
Q psy12011 8 VHFCGLFPESFL 19 (94)
Q Consensus 8 ~~~c~~c~~~~~ 19 (94)
.|+|..||-.|.
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 467777775544
No 176
>PRK12496 hypothetical protein; Provisional
Probab=39.21 E-value=27 Score=19.45 Aligned_cols=10 Identities=40% Similarity=0.953 Sum_probs=5.6
Q ss_pred cccccchhhc
Q psy12011 32 FACDLCDKEY 41 (94)
Q Consensus 32 ~~c~~c~~~~ 41 (94)
+.|..|++.|
T Consensus 128 ~~C~gC~~~~ 137 (164)
T PRK12496 128 KVCKGCKKKY 137 (164)
T ss_pred EECCCCCccc
Confidence 4466666555
No 177
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=39.08 E-value=35 Score=14.18 Aligned_cols=23 Identities=22% Similarity=0.391 Sum_probs=13.2
Q ss_pred eeCCCCccccc--chhHHHHHHHHh
Q psy12011 61 FQCPQCSYRTK--RKGNLKSHLAIR 83 (94)
Q Consensus 61 ~~c~~c~~~f~--~~~~l~~h~~~~ 83 (94)
..|+.||-.+. ...+-..|.+-|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 57777775554 344455565544
No 178
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.73 E-value=7.2 Score=23.14 Aligned_cols=9 Identities=44% Similarity=1.206 Sum_probs=6.2
Q ss_pred eeCCCCccc
Q psy12011 61 FQCPQCSYR 69 (94)
Q Consensus 61 ~~c~~c~~~ 69 (94)
+.|+.|+.+
T Consensus 63 vvCP~C~yA 71 (267)
T COG1655 63 VVCPICYYA 71 (267)
T ss_pred EEcchhhHH
Confidence 578888743
No 179
>KOG2932|consensus
Probab=37.71 E-value=50 Score=20.80 Aligned_cols=73 Identities=21% Similarity=0.382 Sum_probs=41.6
Q ss_pred CCCceeecCCCCccccchhccC---C-------CCCCccccccchhhccChHHHHcchhhhcCCCCceeCCC---Ccccc
Q psy12011 4 QNLQVHFCGLFPESFLTWSNLK---P-------NLNGMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQ---CSYRT 70 (94)
Q Consensus 4 ~~~~~~~c~~c~~~~~~~~~l~---~-------~~~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~---c~~~f 70 (94)
.+.++|-|..|+....-...|. | ..+.--.|..|... +++ +..-..+-- |.|.. |.++|
T Consensus 86 l~p~VHfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~------Vqr-Ieq~~~g~i-FmC~~~~GC~RTy 157 (389)
T KOG2932|consen 86 LGPRVHFCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDR------VQR-IEQIMMGGI-FMCAAPHGCLRTY 157 (389)
T ss_pred cCcceEeecccCCcceeeecccccchhhhhhhhhcCccccCcCcccH------HHH-HHHhcccce-EEeecchhHHHHH
Confidence 3557899999998777766665 1 11111134444322 111 111122234 77754 77888
Q ss_pred cchhHHHHHHHHhc
Q psy12011 71 KRKGNLKSHLAIRH 84 (94)
Q Consensus 71 ~~~~~l~~h~~~~~ 84 (94)
.+.-+|..|+-.-|
T Consensus 158 LsqrDlqAHInhrH 171 (389)
T KOG2932|consen 158 LSQRDLQAHINHRH 171 (389)
T ss_pred hhHHHHHHHhhhhh
Confidence 88888888876433
No 180
>PRK05978 hypothetical protein; Provisional
Probab=37.20 E-value=29 Score=19.14 Aligned_cols=6 Identities=33% Similarity=0.551 Sum_probs=2.7
Q ss_pred cCCCCc
Q psy12011 11 CGLFPE 16 (94)
Q Consensus 11 c~~c~~ 16 (94)
|+.||+
T Consensus 36 CP~CG~ 41 (148)
T PRK05978 36 CPACGE 41 (148)
T ss_pred CCCCCC
Confidence 444443
No 181
>PF12907 zf-met2: Zinc-binding
Probab=37.16 E-value=17 Score=15.26 Aligned_cols=22 Identities=23% Similarity=0.363 Sum_probs=11.0
Q ss_pred eeCCCCccccc---chhHHHHHHHH
Q psy12011 61 FQCPQCSYRTK---RKGNLKSHLAI 82 (94)
Q Consensus 61 ~~c~~c~~~f~---~~~~l~~h~~~ 82 (94)
+.|.+|...|. ....|..|...
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~en 26 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAEN 26 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHc
Confidence 45556654443 33445566553
No 182
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=36.58 E-value=27 Score=13.61 Aligned_cols=13 Identities=23% Similarity=0.143 Sum_probs=9.2
Q ss_pred CceeecCCCCccc
Q psy12011 6 LQVHFCGLFPESF 18 (94)
Q Consensus 6 ~~~~~c~~c~~~~ 18 (94)
.+.|+|..||...
T Consensus 5 ~~~ykC~~Cgniv 17 (34)
T TIGR00319 5 GQVYKCEVCGNIV 17 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 3478888888654
No 183
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=36.56 E-value=27 Score=13.64 Aligned_cols=12 Identities=17% Similarity=0.276 Sum_probs=7.8
Q ss_pred ceeecCCCCccc
Q psy12011 7 QVHFCGLFPESF 18 (94)
Q Consensus 7 ~~~~c~~c~~~~ 18 (94)
+.|+|..||...
T Consensus 3 ~~ykC~~CGniv 14 (34)
T cd00974 3 EVYKCEICGNIV 14 (34)
T ss_pred cEEEcCCCCcEE
Confidence 467777777554
No 184
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=36.33 E-value=24 Score=15.50 Aligned_cols=27 Identities=33% Similarity=0.847 Sum_probs=12.8
Q ss_pred hHHHHcchhhhcCCCCceeCCC----Cccccc
Q psy12011 44 KRNLYSHKKDECGQEPRFQCPQ----CSYRTK 71 (94)
Q Consensus 44 ~~~l~~h~~~~~~~~~~~~c~~----c~~~f~ 71 (94)
...|..|....-...+ ..|.. |...+.
T Consensus 23 r~~l~~H~~~~C~~~~-v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 23 RKELDDHLENECPKRP-VPCPYSPYGCKERVP 53 (60)
T ss_dssp CCCHHHHHHTTSTTSE-EE-SS----S--EEE
T ss_pred HHHHHHHHHccCCCCc-EECCCCCCCCCCccc
Confidence 3446666664434344 67776 654443
No 185
>KOG2071|consensus
Probab=35.90 E-value=27 Score=23.72 Aligned_cols=24 Identities=25% Similarity=0.515 Sum_probs=20.3
Q ss_pred eeCCCCcccccchhHHHHHHHHhc
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAIRH 84 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~~~ 84 (94)
-+|..||..|........||..|-
T Consensus 419 nqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 419 NQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred chhcccccccccchhhhhHhhhhh
Confidence 799999999998888887877664
No 186
>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=35.46 E-value=29 Score=24.23 Aligned_cols=53 Identities=26% Similarity=0.532 Sum_probs=32.5
Q ss_pred cCCCCccccchhccC----CCCCCcc-ccccchhhccChHHHHcchhhhcCCCCceeCCCCcccc
Q psy12011 11 CGLFPESFLTWSNLK----PNLNGMF-ACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRT 70 (94)
Q Consensus 11 c~~c~~~~~~~~~l~----~~~~k~~-~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f 70 (94)
|..||-.|.-...|. ++.-+.+ -|+.|.+.+..+.+ .+.|. .+ ..|..||...
T Consensus 93 Ct~CGPr~~i~~~lpydr~~t~m~~f~~C~~C~~ey~~p~~----rr~h~--~~-~~C~~Cgp~l 150 (711)
T TIGR00143 93 CTHCGPRFTIIEALPYDRENTSMADFPLCPDCAKEYKDPLD----RRFHA--QP-IACPRCGPQL 150 (711)
T ss_pred ccCCCCCeEEeecCCCCCCCcCCCCCcCCHHHHHHhcCCcc----ccCCC--CC-ccCCCCCcEE
Confidence 778888777666665 2222222 48888877766543 23332 34 8999999654
No 187
>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=35.36 E-value=24 Score=17.96 Aligned_cols=38 Identities=24% Similarity=0.400 Sum_probs=10.6
Q ss_pred CCceeecCCCCccccchhccCCCCCCccccccchhhcc
Q psy12011 5 NLQVHFCGLFPESFLTWSNLKPNLNGMFACDLCDKEYK 42 (94)
Q Consensus 5 ~~~~~~c~~c~~~~~~~~~l~~~~~k~~~c~~c~~~~~ 42 (94)
|.+.-.|..||+++.....=.....--|-|..|.+.|.
T Consensus 11 g~ke~~CalCG~tWg~~y~Ev~G~rLfFCCd~ca~EF~ 48 (105)
T PF11494_consen 11 GTKEMGCALCGATWGDYYEEVDGERLFFCCDDCAKEFK 48 (105)
T ss_dssp -SGGGS-SS---S---SS-B-TT--BSSS--SSSS-TT
T ss_pred ccccccccccCCcHHHHHHhhcCCEEEEEcHHHHHHHH
Confidence 34444566666655533321122223345566655553
No 188
>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=35.15 E-value=19 Score=19.52 Aligned_cols=13 Identities=15% Similarity=0.207 Sum_probs=7.6
Q ss_pred ceeecCCCCcccc
Q psy12011 7 QVHFCGLFPESFL 19 (94)
Q Consensus 7 ~~~~c~~c~~~~~ 19 (94)
++..|+.||..|.
T Consensus 111 ~~~RCpeCG~~fk 123 (136)
T PF01215_consen 111 KPQRCPECGQVFK 123 (136)
T ss_dssp SEEEETTTEEEEE
T ss_pred CccCCCCCCeEEE
Confidence 4566666665543
No 189
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=35.00 E-value=14 Score=14.50 Aligned_cols=9 Identities=22% Similarity=0.442 Sum_probs=3.7
Q ss_pred eecCCCCcc
Q psy12011 9 HFCGLFPES 17 (94)
Q Consensus 9 ~~c~~c~~~ 17 (94)
+.|+.||..
T Consensus 2 hlcpkcgvg 10 (36)
T PF09151_consen 2 HLCPKCGVG 10 (36)
T ss_dssp -B-TTTSSS
T ss_pred ccCCccCce
Confidence 345556543
No 190
>KOG2636|consensus
Probab=34.33 E-value=25 Score=23.10 Aligned_cols=27 Identities=22% Similarity=0.532 Sum_probs=21.5
Q ss_pred CCCCCccccccch-hhccChHHHHcchh
Q psy12011 26 PNLNGMFACDLCD-KEYKYKRNLYSHKK 52 (94)
Q Consensus 26 ~~~~k~~~c~~c~-~~~~~~~~l~~h~~ 52 (94)
|.-...|.|.+|| .++..+..+.+|-.
T Consensus 396 HGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 396 HGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred cCCCcccceeeccCccccCcHHHHHHhH
Confidence 6667789999999 67777888887754
No 191
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=34.15 E-value=45 Score=20.82 Aligned_cols=11 Identities=27% Similarity=0.516 Sum_probs=8.0
Q ss_pred ceeecCCCCcc
Q psy12011 7 QVHFCGLFPES 17 (94)
Q Consensus 7 ~~~~c~~c~~~ 17 (94)
....|++||..
T Consensus 186 ~~~~CPvCGs~ 196 (309)
T PRK03564 186 QRQFCPVCGSM 196 (309)
T ss_pred CCCCCCCCCCc
Confidence 45679999864
No 192
>PRK11823 DNA repair protein RadA; Provisional
Probab=33.89 E-value=44 Score=21.85 Aligned_cols=15 Identities=7% Similarity=-0.077 Sum_probs=10.3
Q ss_pred CceeecCCCCccccc
Q psy12011 6 LQVHFCGLFPESFLT 20 (94)
Q Consensus 6 ~~~~~c~~c~~~~~~ 20 (94)
...|+|..||-.+..
T Consensus 5 ~~~y~C~~Cg~~~~~ 19 (446)
T PRK11823 5 KTAYVCQECGAESPK 19 (446)
T ss_pred CCeEECCcCCCCCcc
Confidence 346999999865443
No 193
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=33.79 E-value=28 Score=12.46 Aligned_cols=7 Identities=14% Similarity=0.225 Sum_probs=3.2
Q ss_pred cCCCCcc
Q psy12011 11 CGLFPES 17 (94)
Q Consensus 11 c~~c~~~ 17 (94)
|+.||..
T Consensus 2 Cp~CG~~ 8 (23)
T PF13240_consen 2 CPNCGAE 8 (23)
T ss_pred CcccCCC
Confidence 4444443
No 194
>PRK11032 hypothetical protein; Provisional
Probab=33.44 E-value=43 Score=18.77 Aligned_cols=8 Identities=25% Similarity=0.995 Sum_probs=4.8
Q ss_pred ccccccch
Q psy12011 31 MFACDLCD 38 (94)
Q Consensus 31 ~~~c~~c~ 38 (94)
...|..||
T Consensus 124 ~LvC~~Cg 131 (160)
T PRK11032 124 NLVCEKCH 131 (160)
T ss_pred eEEecCCC
Confidence 45666665
No 195
>PF04641 Rtf2: Rtf2 RING-finger
Probab=33.40 E-value=32 Score=20.65 Aligned_cols=18 Identities=11% Similarity=0.086 Sum_probs=13.1
Q ss_pred CCceeecCCCCccccchh
Q psy12011 5 NLQVHFCGLFPESFLTWS 22 (94)
Q Consensus 5 ~~~~~~c~~c~~~~~~~~ 22 (94)
....|.|+..++.|....
T Consensus 110 ~~~~~~CPvt~~~~~~~~ 127 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKH 127 (260)
T ss_pred CCceeECCCCCcccCCce
Confidence 456799999888775443
No 196
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=32.65 E-value=23 Score=15.75 Aligned_cols=13 Identities=15% Similarity=0.105 Sum_probs=8.8
Q ss_pred ecCCCCccccchh
Q psy12011 10 FCGLFPESFLTWS 22 (94)
Q Consensus 10 ~c~~c~~~~~~~~ 22 (94)
.|++||..+...-
T Consensus 2 ~CPyCge~~~~~i 14 (52)
T PF14255_consen 2 QCPYCGEPIEILI 14 (52)
T ss_pred CCCCCCCeeEEEE
Confidence 5888888765433
No 197
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=32.43 E-value=11 Score=15.72 Aligned_cols=28 Identities=25% Similarity=0.482 Sum_probs=10.9
Q ss_pred ecCCCCccccchhccCCCCCCccccccc
Q psy12011 10 FCGLFPESFLTWSNLKPNLNGMFACDLC 37 (94)
Q Consensus 10 ~c~~c~~~~~~~~~l~~~~~k~~~c~~c 37 (94)
.|..||+.-.....|.......+-|+.|
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~C 30 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDEC 30 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHH
Confidence 4666666544444333222135555554
No 198
>KOG2785|consensus
Probab=32.32 E-value=68 Score=20.74 Aligned_cols=51 Identities=24% Similarity=0.332 Sum_probs=33.5
Q ss_pred ccccccchhhccChHHHHcchhhhcCC-----------------------CCceeCCCCc---ccccchhHHHHHHHH
Q psy12011 31 MFACDLCDKEYKYKRNLYSHKKDECGQ-----------------------EPRFQCPQCS---YRTKRKGNLKSHLAI 82 (94)
Q Consensus 31 ~~~c~~c~~~~~~~~~l~~h~~~~~~~-----------------------~~~~~c~~c~---~~f~~~~~l~~h~~~ 82 (94)
|-.|..|++.+..-..-..||..++|- .. +.|..|. +.|.+..+.+.||..
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~-~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIG-FICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccC-ceEEEeccccCcccccHHHHHHHhh
Confidence 345666666666555555566554432 22 6676666 889999999999975
No 199
>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=32.29 E-value=45 Score=13.51 Aligned_cols=6 Identities=33% Similarity=1.658 Sum_probs=2.5
Q ss_pred eeCCCC
Q psy12011 61 FQCPQC 66 (94)
Q Consensus 61 ~~c~~c 66 (94)
|.|..|
T Consensus 30 yrC~~C 35 (36)
T PF03811_consen 30 YRCKDC 35 (36)
T ss_pred EecCcC
Confidence 444433
No 200
>KOG0978|consensus
Probab=32.26 E-value=13 Score=25.79 Aligned_cols=16 Identities=19% Similarity=0.447 Sum_probs=11.6
Q ss_pred eeCCCCcccccchhHH
Q psy12011 61 FQCPQCSYRTKRKGNL 76 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l 76 (94)
-+||.|+.+|.....+
T Consensus 679 RKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 679 RKCPKCNAAFGANDVH 694 (698)
T ss_pred CCCCCCCCCCCccccc
Confidence 5788888888766443
No 201
>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=32.12 E-value=42 Score=13.74 Aligned_cols=8 Identities=25% Similarity=1.227 Sum_probs=3.2
Q ss_pred ccccccch
Q psy12011 31 MFACDLCD 38 (94)
Q Consensus 31 ~~~c~~c~ 38 (94)
.+.|..|+
T Consensus 24 ~w~C~~C~ 31 (40)
T PF04810_consen 24 TWICNFCG 31 (40)
T ss_dssp EEEETTT-
T ss_pred EEECcCCC
Confidence 34444444
No 202
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=32.10 E-value=37 Score=20.57 Aligned_cols=11 Identities=9% Similarity=-0.007 Sum_probs=7.8
Q ss_pred CCceeecCCCC
Q psy12011 5 NLQVHFCGLFP 15 (94)
Q Consensus 5 ~~~~~~c~~c~ 15 (94)
..+.|.|..|+
T Consensus 109 ~drqFaC~~Cd 119 (278)
T PF15135_consen 109 VDRQFACSSCD 119 (278)
T ss_pred cceeeeccccc
Confidence 34678888885
No 203
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=31.82 E-value=55 Score=21.66 Aligned_cols=14 Identities=21% Similarity=0.639 Sum_probs=7.7
Q ss_pred CCccccccchhhcc
Q psy12011 29 NGMFACDLCDKEYK 42 (94)
Q Consensus 29 ~k~~~c~~c~~~~~ 42 (94)
.+.|+|..|+..+.
T Consensus 423 ~~~~~c~~c~~~yd 436 (479)
T PRK05452 423 GPRMQCSVCQWIYD 436 (479)
T ss_pred CCeEEECCCCeEEC
Confidence 34566666664443
No 204
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.80 E-value=37 Score=20.81 Aligned_cols=12 Identities=25% Similarity=0.517 Sum_probs=7.3
Q ss_pred Cccccccchhhc
Q psy12011 30 GMFACDLCDKEY 41 (94)
Q Consensus 30 k~~~c~~c~~~~ 41 (94)
..|.|+.|...|
T Consensus 254 ~GyvCs~Clsi~ 265 (279)
T TIGR00627 254 IGFVCSVCLSVL 265 (279)
T ss_pred ceEECCCccCCc
Confidence 347777775444
No 205
>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=31.27 E-value=52 Score=21.87 Aligned_cols=23 Identities=26% Similarity=0.577 Sum_probs=17.4
Q ss_pred eeCCCCcccccchhHHHHHHHHh
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAIR 83 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~~ 83 (94)
+.|+.|.+-|.....+..|+..-
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~e 80 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQE 80 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHh
Confidence 67777887788888888887643
No 206
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=30.86 E-value=28 Score=15.04 Aligned_cols=13 Identities=31% Similarity=0.766 Sum_probs=6.9
Q ss_pred Cccccccchhhcc
Q psy12011 30 GMFACDLCDKEYK 42 (94)
Q Consensus 30 k~~~c~~c~~~~~ 42 (94)
.-+.|..|++.+.
T Consensus 25 ~Cf~C~~C~~~l~ 37 (58)
T PF00412_consen 25 ECFKCSKCGKPLN 37 (58)
T ss_dssp TTSBETTTTCBTT
T ss_pred cccccCCCCCccC
Confidence 3455666665443
No 207
>PTZ00448 hypothetical protein; Provisional
Probab=30.58 E-value=40 Score=21.61 Aligned_cols=22 Identities=18% Similarity=0.492 Sum_probs=19.2
Q ss_pred eeCCCCcccccchhHHHHHHHH
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAI 82 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~ 82 (94)
|.|..|+-.|......+.|.++
T Consensus 315 ~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 315 LLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred ccccccccccCCHHHHHHHhhh
Confidence 7899999999888888888876
No 208
>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=30.54 E-value=21 Score=16.09 Aligned_cols=11 Identities=9% Similarity=0.289 Sum_probs=3.2
Q ss_pred ceeecCCCCcc
Q psy12011 7 QVHFCGLFPES 17 (94)
Q Consensus 7 ~~~~c~~c~~~ 17 (94)
+.++|+.||.+
T Consensus 32 r~y~Cp~CgAt 42 (55)
T PF05741_consen 32 RKYVCPICGAT 42 (55)
T ss_dssp GG---TTT---
T ss_pred hcCcCCCCcCc
Confidence 45667777653
No 209
>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=30.49 E-value=36 Score=13.54 Aligned_cols=22 Identities=23% Similarity=0.581 Sum_probs=13.3
Q ss_pred ceeCCCCcccccchhHHHHHHHH
Q psy12011 60 RFQCPQCSYRTKRKGNLKSHLAI 82 (94)
Q Consensus 60 ~~~c~~c~~~f~~~~~l~~h~~~ 82 (94)
.+.|+.|++.+... -+..|+..
T Consensus 4 ~~~C~nC~R~v~a~-RfA~HLek 25 (33)
T PF08209_consen 4 YVECPNCGRPVAAS-RFAPHLEK 25 (33)
T ss_dssp EEE-TTTSSEEEGG-GHHHHHHH
T ss_pred eEECCCCcCCcchh-hhHHHHHH
Confidence 38899999876543 34556553
No 210
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=30.28 E-value=25 Score=17.59 Aligned_cols=16 Identities=6% Similarity=0.063 Sum_probs=11.1
Q ss_pred eecCCCCccccchhcc
Q psy12011 9 HFCGLFPESFLTWSNL 24 (94)
Q Consensus 9 ~~c~~c~~~~~~~~~l 24 (94)
.+|+.||..+....-+
T Consensus 36 ~~C~~CGe~y~~dev~ 51 (89)
T TIGR03829 36 ISCSHCGMEYQDDTTV 51 (89)
T ss_pred ccccCCCcEeecHHHH
Confidence 5688888877765543
No 211
>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=30.25 E-value=30 Score=22.02 Aligned_cols=9 Identities=11% Similarity=0.036 Sum_probs=4.8
Q ss_pred eecCCCCcc
Q psy12011 9 HFCGLFPES 17 (94)
Q Consensus 9 ~~c~~c~~~ 17 (94)
|+|..||..
T Consensus 1 ~~c~~cg~~ 9 (372)
T cd01121 1 YVCSECGYV 9 (372)
T ss_pred CCCCCCCCC
Confidence 456666543
No 212
>PHA02998 RNA polymerase subunit; Provisional
Probab=30.04 E-value=40 Score=19.34 Aligned_cols=38 Identities=18% Similarity=0.414 Sum_probs=19.8
Q ss_pred cccccchhhccChHHHHcchhhhcCCCCc---eeCCCCcccccch
Q psy12011 32 FACDLCDKEYKYKRNLYSHKKDECGQEPR---FQCPQCSYRTKRK 73 (94)
Q Consensus 32 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~---~~c~~c~~~f~~~ 73 (94)
-+|+.|+..- ..+. .+++..+++|+ |.|..||+.|...
T Consensus 144 v~CPkCg~~~---A~f~-qlQTRSADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 144 TPCPNCKSKN---TTPM-MIQTRAADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCCc---eEEE-EEeeccCCCCceEEEEcCCCCCccCCc
Confidence 4677776321 1111 12233344443 6888888877543
No 213
>PRK12722 transcriptional activator FlhC; Provisional
Probab=29.82 E-value=52 Score=18.96 Aligned_cols=10 Identities=20% Similarity=0.919 Sum_probs=5.2
Q ss_pred ccccchhhcc
Q psy12011 33 ACDLCDKEYK 42 (94)
Q Consensus 33 ~c~~c~~~~~ 42 (94)
.|..||..|.
T Consensus 136 ~C~~Cgg~fv 145 (187)
T PRK12722 136 SCNCCGGHFV 145 (187)
T ss_pred cCCCCCCCee
Confidence 4555555543
No 214
>PRK00420 hypothetical protein; Validated
Probab=29.67 E-value=37 Score=17.79 Aligned_cols=8 Identities=25% Similarity=0.617 Sum_probs=3.8
Q ss_pred cccccchh
Q psy12011 32 FACDLCDK 39 (94)
Q Consensus 32 ~~c~~c~~ 39 (94)
..|+.||.
T Consensus 41 ~~Cp~Cg~ 48 (112)
T PRK00420 41 VVCPVHGK 48 (112)
T ss_pred eECCCCCC
Confidence 34555544
No 215
>KOG1842|consensus
Probab=29.42 E-value=32 Score=22.67 Aligned_cols=21 Identities=33% Similarity=0.684 Sum_probs=10.0
Q ss_pred eeCCCCcccccchhHHHHHHH
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLA 81 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~ 81 (94)
|.|+.|...|.+...|..|..
T Consensus 16 flCPiC~~dl~~~~~L~~H~d 36 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLD 36 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHh
Confidence 444444444444444444443
No 216
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=29.35 E-value=59 Score=20.28 Aligned_cols=10 Identities=10% Similarity=0.222 Sum_probs=7.2
Q ss_pred eeecCCCCcc
Q psy12011 8 VHFCGLFPES 17 (94)
Q Consensus 8 ~~~c~~c~~~ 17 (94)
...|++||..
T Consensus 184 ~~~CPvCGs~ 193 (305)
T TIGR01562 184 RTLCPACGSP 193 (305)
T ss_pred CCcCCCCCCh
Confidence 3479999864
No 217
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.30 E-value=50 Score=17.46 Aligned_cols=14 Identities=21% Similarity=0.268 Sum_probs=8.2
Q ss_pred CccccccchhhccCh
Q psy12011 30 GMFACDLCDKEYKYK 44 (94)
Q Consensus 30 k~~~c~~c~~~~~~~ 44 (94)
....| .|+..|...
T Consensus 69 ~~~~C-~Cg~~~~~~ 82 (124)
T PRK00762 69 VEIEC-ECGYEGVVD 82 (124)
T ss_pred eeEEe-eCcCccccc
Confidence 34567 777665543
No 218
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.16 E-value=15 Score=16.08 Aligned_cols=13 Identities=15% Similarity=0.320 Sum_probs=8.9
Q ss_pred ecCCCCccccchh
Q psy12011 10 FCGLFPESFLTWS 22 (94)
Q Consensus 10 ~c~~c~~~~~~~~ 22 (94)
.|+.|+..|....
T Consensus 14 ICpvCqRPFsWRk 26 (54)
T COG4338 14 ICPVCQRPFSWRK 26 (54)
T ss_pred hhhhhcCchHHHH
Confidence 5778887776543
No 219
>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=29.02 E-value=40 Score=22.12 Aligned_cols=23 Identities=17% Similarity=0.426 Sum_probs=14.6
Q ss_pred ceeecCCCCccccchhccCCCCCCccccccch
Q psy12011 7 QVHFCGLFPESFLTWSNLKPNLNGMFACDLCD 38 (94)
Q Consensus 7 ~~~~c~~c~~~~~~~~~l~~~~~k~~~c~~c~ 38 (94)
..|+|..||-.+... .++|+.|+
T Consensus 6 ~~y~C~~Cg~~~~~~---------~g~Cp~C~ 28 (454)
T TIGR00416 6 SKFVCQHCGADSPKW---------QGKCPACH 28 (454)
T ss_pred CeEECCcCCCCCccc---------cEECcCCC
Confidence 369999998654332 24666664
No 220
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.90 E-value=46 Score=17.87 Aligned_cols=15 Identities=13% Similarity=0.459 Sum_probs=9.2
Q ss_pred CccccccchhhccCh
Q psy12011 30 GMFACDLCDKEYKYK 44 (94)
Q Consensus 30 k~~~c~~c~~~~~~~ 44 (94)
-|.-|..||+.|+..
T Consensus 67 ~psfchncgs~fpwt 81 (160)
T COG4306 67 PPSFCHNCGSRFPWT 81 (160)
T ss_pred CcchhhcCCCCCCcH
Confidence 455567777766553
No 221
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=28.87 E-value=20 Score=18.57 Aligned_cols=21 Identities=19% Similarity=0.309 Sum_probs=17.6
Q ss_pred eeCCCCcccccchhHHHHHHH
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLA 81 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~ 81 (94)
+=|.+|.+.|...-.|..|++
T Consensus 56 hYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 56 HYCIECARYFITEKALMEHKK 76 (126)
T ss_pred eeeehhHHHHHHHHHHHHHhc
Confidence 678889999988888888875
No 222
>KOG0562|consensus
Probab=28.79 E-value=52 Score=18.69 Aligned_cols=24 Identities=25% Similarity=0.364 Sum_probs=20.0
Q ss_pred eeCCCCcccccchhHHHHHHHHhc
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAIRH 84 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~~~ 84 (94)
..|-.|+..-...+.|+.|++.+.
T Consensus 154 LrC~~Cq~~~~~~~kLK~Hl~~~~ 177 (184)
T KOG0562|consen 154 LRCWRCQTFGPHFPKLKAHLREEY 177 (184)
T ss_pred eeehhhhhcccccHHHHHHHHHHH
Confidence 899999955568899999999764
No 223
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=28.72 E-value=17 Score=14.53 Aligned_cols=8 Identities=50% Similarity=1.057 Sum_probs=3.5
Q ss_pred ccccchhh
Q psy12011 33 ACDLCDKE 40 (94)
Q Consensus 33 ~c~~c~~~ 40 (94)
.|..|+..
T Consensus 22 ~C~~C~Y~ 29 (35)
T PF02150_consen 22 ACRTCGYE 29 (35)
T ss_dssp EESSSS-E
T ss_pred CCCCCCCc
Confidence 45555533
No 224
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.42 E-value=25 Score=17.06 Aligned_cols=28 Identities=14% Similarity=0.267 Sum_probs=13.4
Q ss_pred eecCCCCccccchhccCCCCCCcc-ccccchh
Q psy12011 9 HFCGLFPESFLTWSNLKPNLNGMF-ACDLCDK 39 (94)
Q Consensus 9 ~~c~~c~~~~~~~~~l~~~~~k~~-~c~~c~~ 39 (94)
|+|..|+..|.... +-.+.|+ .|++|+.
T Consensus 13 Y~c~~cg~~~dvvq---~~~ddplt~ce~c~a 41 (82)
T COG2331 13 YECTECGNRFDVVQ---AMTDDPLTTCEECGA 41 (82)
T ss_pred EeecccchHHHHHH---hcccCccccChhhCh
Confidence 56666665543322 2223332 4666654
No 225
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=27.69 E-value=28 Score=14.47 Aligned_cols=9 Identities=11% Similarity=-0.009 Sum_probs=5.8
Q ss_pred eeecCCCCc
Q psy12011 8 VHFCGLFPE 16 (94)
Q Consensus 8 ~~~c~~c~~ 16 (94)
+..|+.||.
T Consensus 2 ~~~Cp~Cg~ 10 (47)
T PF14690_consen 2 PPRCPHCGS 10 (47)
T ss_pred CccCCCcCC
Confidence 456777774
No 226
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.68 E-value=24 Score=17.87 Aligned_cols=30 Identities=10% Similarity=0.213 Sum_probs=16.2
Q ss_pred CCceeecCCCCccccchhccC--CCCCCcccc
Q psy12011 5 NLQVHFCGLFPESFLTWSNLK--PNLNGMFAC 34 (94)
Q Consensus 5 ~~~~~~c~~c~~~~~~~~~l~--~~~~k~~~c 34 (94)
+-+.|.|..|+.......... .-|...|.|
T Consensus 3 ~lkewkC~VCg~~iieGqkFTF~~kGsVH~eC 34 (103)
T COG4847 3 GLKEWKCYVCGGTIIEGQKFTFTKKGSVHYEC 34 (103)
T ss_pred ccceeeEeeeCCEeeeccEEEEeeCCcchHHH
Confidence 446788888886544332222 234445555
No 227
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=27.60 E-value=53 Score=12.97 Aligned_cols=7 Identities=14% Similarity=0.225 Sum_probs=3.1
Q ss_pred eecCCCC
Q psy12011 9 HFCGLFP 15 (94)
Q Consensus 9 ~~c~~c~ 15 (94)
..|..|+
T Consensus 4 ~~C~~C~ 10 (33)
T PF08792_consen 4 KKCSKCG 10 (33)
T ss_pred eEcCCCC
Confidence 3444444
No 228
>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=27.56 E-value=27 Score=17.94 Aligned_cols=12 Identities=17% Similarity=0.426 Sum_probs=7.5
Q ss_pred Cccccccchhhc
Q psy12011 30 GMFACDLCDKEY 41 (94)
Q Consensus 30 k~~~c~~c~~~~ 41 (94)
||-.|+-||..-
T Consensus 1 ~p~~CpYCg~~~ 12 (102)
T PF11672_consen 1 KPIICPYCGGPA 12 (102)
T ss_pred CCcccCCCCCee
Confidence 455677777543
No 229
>KOG3214|consensus
Probab=27.25 E-value=43 Score=17.21 Aligned_cols=11 Identities=18% Similarity=1.072 Sum_probs=6.0
Q ss_pred ccccchhhccC
Q psy12011 33 ACDLCDKEYKY 43 (94)
Q Consensus 33 ~c~~c~~~~~~ 43 (94)
.|.+|+.+|..
T Consensus 49 sC~iC~esFqt 59 (109)
T KOG3214|consen 49 SCRICEESFQT 59 (109)
T ss_pred eeeehhhhhcc
Confidence 45556555544
No 230
>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=26.76 E-value=33 Score=14.02 Aligned_cols=11 Identities=9% Similarity=0.181 Sum_probs=7.4
Q ss_pred eeecCCCCccc
Q psy12011 8 VHFCGLFPESF 18 (94)
Q Consensus 8 ~~~c~~c~~~~ 18 (94)
.|+|..|+..|
T Consensus 28 fy~C~~C~~~w 38 (39)
T PF01096_consen 28 FYVCCNCGHRW 38 (39)
T ss_dssp EEEESSSTEEE
T ss_pred EEEeCCCCCee
Confidence 47777777654
No 231
>PRK01343 zinc-binding protein; Provisional
Probab=26.56 E-value=57 Score=14.88 Aligned_cols=13 Identities=8% Similarity=-0.028 Sum_probs=8.8
Q ss_pred ceeecCCCCcccc
Q psy12011 7 QVHFCGLFPESFL 19 (94)
Q Consensus 7 ~~~~c~~c~~~~~ 19 (94)
..-.|+.|++.+.
T Consensus 8 p~~~CP~C~k~~~ 20 (57)
T PRK01343 8 PTRPCPECGKPST 20 (57)
T ss_pred CCCcCCCCCCcCc
Confidence 3456888888754
No 232
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=26.36 E-value=71 Score=21.13 Aligned_cols=16 Identities=13% Similarity=0.185 Sum_probs=11.1
Q ss_pred ceeecCCCCccccchh
Q psy12011 7 QVHFCGLFPESFLTWS 22 (94)
Q Consensus 7 ~~~~c~~c~~~~~~~~ 22 (94)
..|.|..||-.+....
T Consensus 6 t~f~C~~CG~~s~KW~ 21 (456)
T COG1066 6 TAFVCQECGYVSPKWL 21 (456)
T ss_pred cEEEcccCCCCCcccc
Confidence 5699999986644433
No 233
>PRK12860 transcriptional activator FlhC; Provisional
Probab=25.88 E-value=82 Score=18.25 Aligned_cols=9 Identities=22% Similarity=0.825 Sum_probs=4.4
Q ss_pred ccccchhhc
Q psy12011 33 ACDLCDKEY 41 (94)
Q Consensus 33 ~c~~c~~~~ 41 (94)
.|..||..|
T Consensus 136 ~C~~Cgg~f 144 (189)
T PRK12860 136 RCCRCGGKF 144 (189)
T ss_pred cCCCCCCCe
Confidence 455555444
No 234
>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=25.84 E-value=56 Score=21.80 Aligned_cols=12 Identities=17% Similarity=0.213 Sum_probs=6.9
Q ss_pred CCCccccccchh
Q psy12011 28 LNGMFACDLCDK 39 (94)
Q Consensus 28 ~~k~~~c~~c~~ 39 (94)
...+..|+.|+.
T Consensus 250 ~~~~~~Cp~C~s 261 (505)
T TIGR00595 250 EPIPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCCCC
Confidence 334566777664
No 235
>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=25.83 E-value=56 Score=17.18 Aligned_cols=8 Identities=25% Similarity=0.771 Sum_probs=3.9
Q ss_pred ccccccch
Q psy12011 31 MFACDLCD 38 (94)
Q Consensus 31 ~~~c~~c~ 38 (94)
..+|+.|+
T Consensus 69 ~V~CP~C~ 76 (114)
T PF11023_consen 69 QVECPNCG 76 (114)
T ss_pred eeECCCCC
Confidence 34455554
No 236
>KOG4124|consensus
Probab=25.80 E-value=23 Score=22.58 Aligned_cols=19 Identities=16% Similarity=0.282 Sum_probs=12.2
Q ss_pred ceeecCC--CCccccchhccC
Q psy12011 7 QVHFCGL--FPESFLTWSNLK 25 (94)
Q Consensus 7 ~~~~c~~--c~~~~~~~~~l~ 25 (94)
+++.|++ |++.+...-.|+
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~ 368 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLK 368 (442)
T ss_pred CCCCCCCCcchhhcccCccee
Confidence 5667765 777766655555
No 237
>KOG4477|consensus
Probab=25.80 E-value=36 Score=19.59 Aligned_cols=10 Identities=10% Similarity=0.145 Sum_probs=5.0
Q ss_pred CCceeecCCC
Q psy12011 5 NLQVHFCGLF 14 (94)
Q Consensus 5 ~~~~~~c~~c 14 (94)
++..|-|..|
T Consensus 21 Deg~WdCsvC 30 (228)
T KOG4477|consen 21 DEGKWDCSVC 30 (228)
T ss_pred ccCceeeeee
Confidence 3444555555
No 238
>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=25.37 E-value=16 Score=15.60 Aligned_cols=6 Identities=17% Similarity=0.312 Sum_probs=2.8
Q ss_pred Cccccc
Q psy12011 66 CSYRTK 71 (94)
Q Consensus 66 c~~~f~ 71 (94)
||..|.
T Consensus 33 Cg~tfv 38 (47)
T PF04606_consen 33 CGHTFV 38 (47)
T ss_pred CCCEEE
Confidence 554443
No 239
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=24.71 E-value=68 Score=13.06 Aligned_cols=27 Identities=22% Similarity=0.444 Sum_probs=13.8
Q ss_pred eeCCCCcccccchhHHHHHHHHhcCcccCCCCCC
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAIRHECYLDDSANC 94 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~c~~C 94 (94)
+..+ |+..|-..- +...++.. ..|+.|
T Consensus 17 ~~l~-C~H~fh~~C-i~~~~~~~-----~~CP~C 43 (44)
T PF13639_consen 17 VKLP-CGHVFHRSC-IKEWLKRN-----NSCPVC 43 (44)
T ss_dssp EEET-TSEEEEHHH-HHHHHHHS-----SB-TTT
T ss_pred EEcc-CCCeeCHHH-HHHHHHhC-----CcCCcc
Confidence 4444 777776654 34444432 266665
No 240
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=24.65 E-value=32 Score=15.17 Aligned_cols=32 Identities=25% Similarity=0.478 Sum_probs=16.2
Q ss_pred ccccchhhccChHHHHcchhhhcCCCCceeCCCCccc
Q psy12011 33 ACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYR 69 (94)
Q Consensus 33 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 69 (94)
.|..|+-.... ... .....++.- ..|+.||+.
T Consensus 24 ~C~gC~~~l~~--~~~--~~i~~~~~i-~~Cp~CgRi 55 (56)
T PF02591_consen 24 TCSGCHMELPP--QEL--NEIRKGDEI-VFCPNCGRI 55 (56)
T ss_pred ccCCCCEEcCH--HHH--HHHHcCCCe-EECcCCCcc
Confidence 56666533322 222 123334445 788888764
No 241
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=24.46 E-value=49 Score=16.32 Aligned_cols=33 Identities=15% Similarity=0.241 Sum_probs=22.3
Q ss_pred ecCCCCccccchhccC---CCCCCccccccchhhcc
Q psy12011 10 FCGLFPESFLTWSNLK---PNLNGMFACDLCDKEYK 42 (94)
Q Consensus 10 ~c~~c~~~~~~~~~l~---~~~~k~~~c~~c~~~~~ 42 (94)
.|-+||..+.....+. ...++.|-|..|...+.
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~~ 37 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVYQ 37 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHHH
Confidence 4778888876444444 34567889988876653
No 242
>PF14369 zf-RING_3: zinc-finger
Probab=24.25 E-value=41 Score=13.46 Aligned_cols=10 Identities=20% Similarity=0.398 Sum_probs=7.6
Q ss_pred ecCCCCcccc
Q psy12011 10 FCGLFPESFL 19 (94)
Q Consensus 10 ~c~~c~~~~~ 19 (94)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 4888887775
No 243
>KOG0320|consensus
Probab=24.24 E-value=23 Score=20.23 Aligned_cols=11 Identities=27% Similarity=0.875 Sum_probs=6.9
Q ss_pred eeCCCCccccc
Q psy12011 61 FQCPQCSYRTK 71 (94)
Q Consensus 61 ~~c~~c~~~f~ 71 (94)
-.|+.|++-..
T Consensus 168 ~~CP~C~kkIt 178 (187)
T KOG0320|consen 168 NKCPTCRKKIT 178 (187)
T ss_pred CCCCCcccccc
Confidence 56777776433
No 244
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=24.16 E-value=49 Score=17.26 Aligned_cols=12 Identities=25% Similarity=0.634 Sum_probs=6.5
Q ss_pred ccccccchhhcc
Q psy12011 31 MFACDLCDKEYK 42 (94)
Q Consensus 31 ~~~c~~c~~~~~ 42 (94)
.+-|++|+..|.
T Consensus 19 ~~iCpeC~~EW~ 30 (109)
T TIGR00686 19 QLICPSCLYEWN 30 (109)
T ss_pred eeECcccccccc
Confidence 355666655543
No 245
>PLN02748 tRNA dimethylallyltransferase
Probab=23.70 E-value=46 Score=22.08 Aligned_cols=24 Identities=17% Similarity=0.473 Sum_probs=16.6
Q ss_pred Cccccccchh-hccChHHHHcchhh
Q psy12011 30 GMFACDLCDK-EYKYKRNLYSHKKD 53 (94)
Q Consensus 30 k~~~c~~c~~-~~~~~~~l~~h~~~ 53 (94)
+.|.|+.|++ .+.....+..|+..
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 5667888886 67777777766653
No 246
>KOG0717|consensus
Probab=23.68 E-value=48 Score=22.05 Aligned_cols=22 Identities=27% Similarity=0.446 Sum_probs=18.3
Q ss_pred eeCCCCcccccchhHHHHHHHH
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAI 82 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~ 82 (94)
+-|.+|.+.|.+.-.|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7889999999988888887754
No 247
>PRK14873 primosome assembly protein PriA; Provisional
Probab=23.48 E-value=75 Score=22.17 Aligned_cols=10 Identities=10% Similarity=0.185 Sum_probs=4.7
Q ss_pred eecCCCCccc
Q psy12011 9 HFCGLFPESF 18 (94)
Q Consensus 9 ~~c~~c~~~~ 18 (94)
..|+.|+-.+
T Consensus 393 ~~C~~C~~~L 402 (665)
T PRK14873 393 ARCRHCTGPL 402 (665)
T ss_pred eECCCCCCce
Confidence 3455555443
No 248
>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=23.28 E-value=40 Score=14.80 Aligned_cols=11 Identities=9% Similarity=0.045 Sum_probs=6.0
Q ss_pred eecCCCCcccc
Q psy12011 9 HFCGLFPESFL 19 (94)
Q Consensus 9 ~~c~~c~~~~~ 19 (94)
|+|..||-.+.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 55666664433
No 249
>KOG2231|consensus
Probab=23.27 E-value=90 Score=21.91 Aligned_cols=23 Identities=22% Similarity=0.619 Sum_probs=13.3
Q ss_pred ccccchhhccChHHHHcchhhhc
Q psy12011 33 ACDLCDKEYKYKRNLYSHKKDEC 55 (94)
Q Consensus 33 ~c~~c~~~~~~~~~l~~h~~~~~ 55 (94)
.|..|...|.....+..|++.++
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h 206 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH 206 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce
Confidence 35556666666666666655443
No 250
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=23.02 E-value=66 Score=20.65 Aligned_cols=23 Identities=17% Similarity=0.291 Sum_probs=16.9
Q ss_pred ccccchhhccChHHHHcchhhhc
Q psy12011 33 ACDLCDKEYKYKRNLYSHKKDEC 55 (94)
Q Consensus 33 ~c~~c~~~~~~~~~l~~h~~~~~ 55 (94)
.|..|...|-....|..|++..+
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~H 244 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRH 244 (493)
T ss_pred hhhhccceecChHHHHHHHHhhh
Confidence 47778877777777877777544
No 251
>PRK10220 hypothetical protein; Provisional
Probab=22.99 E-value=59 Score=17.01 Aligned_cols=12 Identities=33% Similarity=1.024 Sum_probs=6.2
Q ss_pred ccccccchhhcc
Q psy12011 31 MFACDLCDKEYK 42 (94)
Q Consensus 31 ~~~c~~c~~~~~ 42 (94)
.|.|++|+.-|.
T Consensus 20 ~~vCpeC~hEW~ 31 (111)
T PRK10220 20 MYICPECAHEWN 31 (111)
T ss_pred eEECCcccCcCC
Confidence 355555554443
No 252
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=22.89 E-value=67 Score=12.83 Aligned_cols=13 Identities=8% Similarity=-0.036 Sum_probs=8.0
Q ss_pred CCceeecCCCCcc
Q psy12011 5 NLQVHFCGLFPES 17 (94)
Q Consensus 5 ~~~~~~c~~c~~~ 17 (94)
+...++|+.|+..
T Consensus 19 ~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 19 DRERLVCPACGFI 31 (34)
T ss_dssp SS-EEEETTTTEE
T ss_pred CccceECCCCCCE
Confidence 3345778888754
No 253
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=22.65 E-value=35 Score=19.84 Aligned_cols=34 Identities=12% Similarity=0.037 Sum_probs=18.9
Q ss_pred eecCCCCccccchhccC---CCCCC---ccccccchhhcc
Q psy12011 9 HFCGLFPESFLTWSNLK---PNLNG---MFACDLCDKEYK 42 (94)
Q Consensus 9 ~~c~~c~~~~~~~~~l~---~~~~k---~~~c~~c~~~~~ 42 (94)
-.||.||..+.....+- +-++. .+.|..||..+.
T Consensus 15 ~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 15 IDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred ecCCcccceeeEEEeeecCCccceEEEEEEEccccCCccc
Confidence 35888887555433332 44443 346777775543
No 254
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=22.38 E-value=49 Score=14.97 Aligned_cols=12 Identities=8% Similarity=-0.230 Sum_probs=7.3
Q ss_pred CceeecCCCCcc
Q psy12011 6 LQVHFCGLFPES 17 (94)
Q Consensus 6 ~~~~~c~~c~~~ 17 (94)
...|.|+.||-.
T Consensus 12 ~v~~~Cp~cGip 23 (55)
T PF13824_consen 12 HVNFECPDCGIP 23 (55)
T ss_pred ccCCcCCCCCCc
Confidence 345677777753
No 255
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=22.00 E-value=46 Score=14.41 Aligned_cols=6 Identities=33% Similarity=1.209 Sum_probs=2.4
Q ss_pred ccccch
Q psy12011 33 ACDLCD 38 (94)
Q Consensus 33 ~c~~c~ 38 (94)
+|..|.
T Consensus 33 rCGaCs 38 (46)
T PF11331_consen 33 RCGACS 38 (46)
T ss_pred eCCCCc
Confidence 344443
No 256
>KOG0402|consensus
Probab=21.97 E-value=26 Score=17.34 Aligned_cols=34 Identities=18% Similarity=0.580 Sum_probs=17.8
Q ss_pred CCCCccccccchhhccChHHHHcchhhhcCCCCceeCCCCccccc
Q psy12011 27 NLNGMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTK 71 (94)
Q Consensus 27 ~~~k~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~c~~~f~ 71 (94)
+....|.|+.||+.-.- +...| .|.|..|.+.+.
T Consensus 32 ~Qhaky~CsfCGK~~vK--------R~AvG---iW~C~~C~kv~a 65 (92)
T KOG0402|consen 32 QQHAKYTCSFCGKKTVK--------RKAVG---IWKCGSCKKVVA 65 (92)
T ss_pred HHhhhhhhhhcchhhhh--------hhcee---EEecCCccceec
Confidence 33446778888754211 11111 277777776554
No 257
>KOG1280|consensus
Probab=21.84 E-value=1e+02 Score=19.84 Aligned_cols=29 Identities=21% Similarity=0.427 Sum_probs=19.2
Q ss_pred eeCCCCcccccchhHHHHHHHHhcCcccC
Q psy12011 61 FQCPQCSYRTKRKGNLKSHLAIRHECYLD 89 (94)
Q Consensus 61 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~~ 89 (94)
|.|++|+..=..-..|..|...-|.+.++
T Consensus 80 ftCPyC~~~Gfte~~f~~Hv~s~Hpda~~ 108 (381)
T KOG1280|consen 80 FTCPYCGIMGFTERQFGTHVLSQHPEAST 108 (381)
T ss_pred ccCCcccccccchhHHHHHhhhcCcccCc
Confidence 77777776655666667777666655543
No 258
>KOG3352|consensus
Probab=21.79 E-value=34 Score=18.96 Aligned_cols=22 Identities=32% Similarity=0.407 Sum_probs=15.2
Q ss_pred cchhhhcCCCCceeCCCCcccccc
Q psy12011 49 SHKKDECGQEPRFQCPQCSYRTKR 72 (94)
Q Consensus 49 ~h~~~~~~~~~~~~c~~c~~~f~~ 72 (94)
.++-.+.| +. .+|.+||..|.-
T Consensus 124 ~Wmwl~Kg-e~-~rc~eCG~~fkL 145 (153)
T KOG3352|consen 124 VWMWLEKG-ET-QRCPECGHYFKL 145 (153)
T ss_pred EEEEEEcC-Cc-ccCCcccceEEe
Confidence 44555556 55 789999988753
No 259
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.75 E-value=73 Score=22.17 Aligned_cols=13 Identities=23% Similarity=0.209 Sum_probs=7.7
Q ss_pred CCCccccccchhh
Q psy12011 28 LNGMFACDLCDKE 40 (94)
Q Consensus 28 ~~k~~~c~~c~~~ 40 (94)
...+..|+.|+..
T Consensus 418 ~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 418 EPIPKACPECGST 430 (679)
T ss_pred CCCCCCCCCCcCC
Confidence 3446677777653
No 260
>PF10915 DUF2709: Protein of unknown function (DUF2709); InterPro: IPR024484 Members of this family appear restricted to Chlamydiales. Their function is unknown.
Probab=21.67 E-value=83 Score=18.38 Aligned_cols=20 Identities=15% Similarity=0.243 Sum_probs=15.8
Q ss_pred CCCceeecCCCCccccchhc
Q psy12011 4 QNLQVHFCGLFPESFLTWSN 23 (94)
Q Consensus 4 ~~~~~~~c~~c~~~~~~~~~ 23 (94)
...+.|.|+.-|+.|.+...
T Consensus 83 ~TkkIYICPFTGKVF~DNt~ 102 (238)
T PF10915_consen 83 QTKKIYICPFTGKVFGDNTH 102 (238)
T ss_pred ccceEEEcCCcCccccCCCC
Confidence 34688999999999987553
No 261
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=21.27 E-value=60 Score=14.69 Aligned_cols=8 Identities=25% Similarity=0.700 Sum_probs=3.4
Q ss_pred cCCCCccc
Q psy12011 11 CGLFPESF 18 (94)
Q Consensus 11 c~~c~~~~ 18 (94)
|+.|++.|
T Consensus 42 CPfC~~~~ 49 (55)
T PF14447_consen 42 CPFCGTPF 49 (55)
T ss_pred CCCCCCcc
Confidence 44444433
No 262
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=20.88 E-value=69 Score=13.10 Aligned_cols=14 Identities=21% Similarity=0.240 Sum_probs=7.5
Q ss_pred ecCCCCccccchhc
Q psy12011 10 FCGLFPESFLTWSN 23 (94)
Q Consensus 10 ~c~~c~~~~~~~~~ 23 (94)
.|+-|++.|...++
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 56777777665543
No 263
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=20.62 E-value=94 Score=13.18 Aligned_cols=12 Identities=8% Similarity=0.415 Sum_probs=5.5
Q ss_pred ceeecCCCCccc
Q psy12011 7 QVHFCGLFPESF 18 (94)
Q Consensus 7 ~~~~c~~c~~~~ 18 (94)
++-.|..|++..
T Consensus 10 ~~~~C~~C~~~i 21 (53)
T PF00130_consen 10 KPTYCDVCGKFI 21 (53)
T ss_dssp STEB-TTSSSBE
T ss_pred CCCCCcccCccc
Confidence 344555555543
No 264
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=20.40 E-value=62 Score=11.75 Aligned_cols=7 Identities=29% Similarity=0.548 Sum_probs=3.9
Q ss_pred ecCCCCc
Q psy12011 10 FCGLFPE 16 (94)
Q Consensus 10 ~c~~c~~ 16 (94)
.|+.||.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 4556655
No 265
>KOG4602|consensus
Probab=20.25 E-value=41 Score=20.49 Aligned_cols=11 Identities=9% Similarity=0.310 Sum_probs=8.6
Q ss_pred ceeecCCCCcc
Q psy12011 7 QVHFCGLFPES 17 (94)
Q Consensus 7 ~~~~c~~c~~~ 17 (94)
+.|+|+.||.+
T Consensus 267 R~YVCPiCGAT 277 (318)
T KOG4602|consen 267 RSYVCPICGAT 277 (318)
T ss_pred hhhcCcccccc
Confidence 56889999864
Done!