Query psy4407
Match_columns 130
No_of_seqs 122 out of 1720
Neff 10.4
Searched_HMMs 46136
Date Sat Aug 17 00:44:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4407.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4407hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 1.3E-23 2.7E-28 137.9 4.8 97 29-130 127-247 (279)
2 KOG2462|consensus 99.9 1.9E-22 4.1E-27 132.4 3.4 100 15-115 142-263 (279)
3 KOG3623|consensus 99.7 1.6E-17 3.4E-22 121.3 0.7 82 27-115 889-970 (1007)
4 KOG1074|consensus 99.6 5.5E-17 1.2E-21 119.8 2.7 54 67-121 605-658 (958)
5 KOG1074|consensus 99.6 9.2E-16 2E-20 113.4 5.0 57 68-127 880-936 (958)
6 KOG3576|consensus 99.6 2.4E-16 5.2E-21 99.9 -1.0 89 26-121 111-199 (267)
7 KOG3608|consensus 99.5 2.4E-15 5.2E-20 102.3 2.3 115 13-129 189-355 (467)
8 KOG3623|consensus 99.4 5.5E-14 1.2E-18 103.1 1.3 65 63-130 890-954 (1007)
9 KOG3576|consensus 99.3 4.2E-13 9.1E-18 85.3 -0.7 94 19-120 133-237 (267)
10 PHA00733 hypothetical protein 99.2 1.6E-11 3.4E-16 74.4 2.4 90 26-121 34-125 (128)
11 KOG3608|consensus 99.1 4.5E-11 9.7E-16 81.8 2.6 108 6-121 266-378 (467)
12 PHA02768 hypothetical protein; 99.0 2.4E-10 5.1E-15 58.3 1.7 44 67-112 5-48 (55)
13 PF13465 zf-H2C2_2: Zinc-finge 98.8 5E-09 1.1E-13 45.9 2.0 26 82-107 1-26 (26)
14 PLN03086 PRLI-interacting fact 98.6 2.2E-08 4.7E-13 73.5 3.4 59 66-130 477-545 (567)
15 PHA02768 hypothetical protein; 98.6 5.4E-09 1.2E-13 53.4 -0.3 44 32-84 5-48 (55)
16 PLN03086 PRLI-interacting fact 98.6 3.8E-08 8.2E-13 72.3 3.4 93 14-120 463-565 (567)
17 KOG3993|consensus 98.6 1.2E-08 2.6E-13 71.5 0.3 80 33-120 268-380 (500)
18 PHA00733 hypothetical protein 98.5 4.9E-08 1.1E-12 59.2 2.0 57 27-92 68-124 (128)
19 PHA00616 hypothetical protein 98.5 4.1E-08 8.9E-13 47.8 1.1 31 68-98 2-32 (44)
20 PF13465 zf-H2C2_2: Zinc-finge 98.5 3.8E-08 8.2E-13 43.0 0.7 24 19-43 2-25 (26)
21 PHA00616 hypothetical protein 98.4 1.2E-07 2.6E-12 46.2 1.0 33 95-130 1-33 (44)
22 PHA00732 hypothetical protein 98.1 2.9E-06 6.3E-11 47.1 2.4 47 32-91 1-48 (79)
23 PHA00732 hypothetical protein 97.9 6.9E-06 1.5E-10 45.6 1.7 43 67-115 1-44 (79)
24 PF00096 zf-C2H2: Zinc finger, 97.8 1.6E-05 3.5E-10 33.4 1.8 22 68-89 1-22 (23)
25 PF05605 zf-Di19: Drought indu 97.6 0.00011 2.3E-09 37.8 3.7 48 68-118 3-52 (54)
26 PF13912 zf-C2H2_6: C2H2-type 97.5 6.7E-05 1.5E-09 32.7 1.4 23 68-90 2-24 (27)
27 KOG3993|consensus 97.5 3.6E-05 7.8E-10 54.6 0.6 76 15-91 279-380 (500)
28 PF05605 zf-Di19: Drought indu 97.4 9.1E-05 2E-09 38.1 1.5 51 32-91 2-53 (54)
29 PF13894 zf-C2H2_4: C2H2-type 97.4 0.00018 3.8E-09 30.1 2.2 23 68-90 1-23 (24)
30 PF00096 zf-C2H2: Zinc finger, 97.4 4.3E-05 9.3E-10 32.1 0.0 21 96-116 1-21 (23)
31 COG5189 SFP1 Putative transcri 97.3 0.00016 3.5E-09 49.7 2.2 51 65-115 347-418 (423)
32 PF13912 zf-C2H2_6: C2H2-type 97.2 0.00017 3.6E-09 31.5 1.2 25 95-120 1-25 (27)
33 PF09237 GAGA: GAGA factor; I 97.1 0.00089 1.9E-08 33.5 3.0 33 63-95 20-52 (54)
34 PF13894 zf-C2H2_4: C2H2-type 97.0 0.00033 7.2E-09 29.3 1.0 23 96-118 1-23 (24)
35 PRK04860 hypothetical protein; 97.0 0.00084 1.8E-08 42.3 2.9 39 66-108 118-156 (160)
36 COG5189 SFP1 Putative transcri 96.9 0.00033 7.2E-09 48.2 0.7 59 30-88 347-419 (423)
37 PF12756 zf-C2H2_2: C2H2 type 96.8 0.0012 2.5E-08 37.9 2.2 18 34-51 1-18 (100)
38 smart00355 ZnF_C2H2 zinc finge 96.7 0.0014 3E-08 27.7 1.9 22 69-90 2-23 (26)
39 PF12756 zf-C2H2_2: C2H2 type 96.6 0.0015 3.3E-08 37.3 2.1 23 95-117 50-72 (100)
40 PF12874 zf-met: Zinc-finger o 96.3 0.0025 5.4E-08 27.0 1.4 22 68-89 1-22 (25)
41 smart00355 ZnF_C2H2 zinc finge 96.3 0.002 4.3E-08 27.1 1.0 25 96-121 1-25 (26)
42 PF09237 GAGA: GAGA factor; I 95.9 0.0039 8.4E-08 31.3 1.0 33 91-126 20-52 (54)
43 PF13909 zf-H2C2_5: C2H2-type 95.6 0.013 2.9E-07 24.5 1.9 22 68-90 1-22 (24)
44 COG2888 Predicted Zn-ribbon RN 95.5 0.013 2.8E-07 30.3 2.0 26 34-59 11-36 (61)
45 PF12171 zf-C2H2_jaz: Zinc-fin 95.3 0.0035 7.6E-08 27.2 -0.4 20 68-87 2-21 (27)
46 PRK14890 putative Zn-ribbon RN 95.1 0.027 5.8E-07 29.2 2.4 26 33-58 8-33 (59)
47 PRK04860 hypothetical protein; 94.4 0.017 3.6E-07 36.5 0.8 39 31-80 118-156 (160)
48 PF13913 zf-C2HC_2: zinc-finge 94.2 0.048 1E-06 23.2 1.8 21 68-89 3-23 (25)
49 PRK00398 rpoP DNA-directed RNA 93.3 0.061 1.3E-06 26.5 1.5 27 32-58 3-29 (46)
50 smart00451 ZnF_U1 U1-like zinc 92.9 0.094 2E-06 23.9 1.8 22 67-88 3-24 (35)
51 cd00350 rubredoxin_like Rubred 91.9 0.16 3.4E-06 23.1 1.8 9 94-102 16-24 (33)
52 KOG2186|consensus 91.3 0.12 2.7E-06 34.8 1.4 45 68-115 4-48 (276)
53 PF09538 FYDLN_acid: Protein o 91.2 0.2 4.3E-06 29.5 2.1 17 64-80 23-39 (108)
54 PF13719 zinc_ribbon_5: zinc-r 91.2 0.26 5.7E-06 23.0 2.2 11 67-77 25-35 (37)
55 PF09723 Zn-ribbon_8: Zinc rib 91.1 0.17 3.6E-06 24.4 1.5 16 32-47 5-20 (42)
56 COG5048 FOG: Zn-finger [Genera 90.8 0.087 1.9E-06 37.6 0.4 54 67-121 289-348 (467)
57 PF09986 DUF2225: Uncharacteri 90.8 0.17 3.6E-06 33.6 1.7 48 30-80 3-61 (214)
58 COG5048 FOG: Zn-finger [Genera 90.7 0.15 3.2E-06 36.5 1.5 62 31-99 288-355 (467)
59 COG1996 RPC10 DNA-directed RNA 90.4 0.16 3.4E-06 25.4 1.0 30 30-59 4-33 (49)
60 PHA00626 hypothetical protein 90.2 0.35 7.6E-06 24.8 2.2 13 66-78 22-34 (59)
61 TIGR02098 MJ0042_CXXC MJ0042 f 90.1 0.36 7.9E-06 22.5 2.2 13 33-45 3-15 (38)
62 PF13717 zinc_ribbon_4: zinc-r 90.1 0.47 1E-05 22.0 2.5 14 34-47 4-17 (36)
63 smart00834 CxxC_CXXC_SSSS Puta 90.1 0.22 4.7E-06 23.5 1.4 14 32-45 5-18 (41)
64 COG1198 PriA Primosomal protei 89.7 0.39 8.4E-06 37.6 3.1 9 35-43 438-446 (730)
65 COG1997 RPL43A Ribosomal prote 88.3 0.5 1.1E-05 26.6 2.1 29 51-79 36-65 (89)
66 smart00659 RPOLCX RNA polymera 88.3 0.37 8.1E-06 23.5 1.5 26 32-58 2-27 (44)
67 PF09845 DUF2072: Zn-ribbon co 88.2 0.28 6.1E-06 29.8 1.2 28 32-59 1-28 (131)
68 PF10571 UPF0547: Uncharacteri 88.0 0.52 1.1E-05 20.2 1.7 9 69-77 16-24 (26)
69 PF03604 DNA_RNApol_7kD: DNA d 87.6 0.59 1.3E-05 21.2 1.8 11 33-43 1-11 (32)
70 TIGR02605 CxxC_CxxC_SSSS putat 87.2 0.43 9.4E-06 23.9 1.4 14 32-45 5-18 (52)
71 COG3364 Zn-ribbon containing p 87.1 0.3 6.4E-06 28.3 0.8 28 32-59 2-29 (112)
72 PF07754 DUF1610: Domain of un 86.4 1.1 2.4E-05 18.9 2.2 7 68-74 17-23 (24)
73 COG4049 Uncharacterized protei 85.7 0.46 9.9E-06 24.3 1.0 28 62-89 12-39 (65)
74 cd00729 rubredoxin_SM Rubredox 83.9 1 2.2E-05 20.6 1.7 10 33-42 3-12 (34)
75 KOG2893|consensus 82.6 0.51 1.1E-05 31.7 0.5 42 34-86 12-53 (341)
76 TIGR02300 FYDLN_acid conserved 82.0 1.2 2.6E-05 27.0 1.8 28 53-80 12-39 (129)
77 TIGR00595 priA primosomal prot 81.9 1.6 3.5E-05 32.8 3.0 9 34-42 215-223 (505)
78 smart00531 TFIIE Transcription 81.7 0.8 1.7E-05 28.5 1.1 40 27-77 94-133 (147)
79 KOG2893|consensus 80.0 0.4 8.7E-06 32.2 -0.7 45 65-114 9-53 (341)
80 PRK14873 primosome assembly pr 78.8 2.2 4.7E-05 33.3 2.8 9 34-42 385-393 (665)
81 TIGR00622 ssl1 transcription f 78.3 3.1 6.7E-05 24.7 2.7 87 31-120 14-105 (112)
82 KOG2907|consensus 77.9 1.2 2.6E-05 26.3 1.0 38 68-106 75-113 (116)
83 KOG4173|consensus 77.0 0.61 1.3E-05 30.6 -0.5 82 30-121 77-172 (253)
84 PF12773 DZR: Double zinc ribb 76.7 2.4 5.2E-05 20.9 1.8 8 68-75 30-37 (50)
85 KOG1146|consensus 76.4 1.5 3.3E-05 36.4 1.4 55 62-116 460-539 (1406)
86 PTZ00255 60S ribosomal protein 76.3 2.2 4.8E-05 24.3 1.7 15 65-79 52-66 (90)
87 TIGR00373 conserved hypothetic 76.3 1.6 3.5E-05 27.5 1.3 23 26-48 103-125 (158)
88 PRK00464 nrdR transcriptional 75.6 1.9 4.1E-05 27.2 1.4 19 67-85 28-46 (154)
89 smart00661 RPOL9 RNA polymeras 75.5 4.4 9.6E-05 20.0 2.6 12 67-78 20-31 (52)
90 COG1592 Rubrerythrin [Energy p 74.4 2.3 5E-05 27.1 1.6 10 93-102 147-156 (166)
91 COG1773 Rubredoxin [Energy pro 74.4 3 6.6E-05 21.4 1.7 43 31-75 2-44 (55)
92 PRK06266 transcription initiat 74.2 1.9 4.1E-05 27.8 1.2 21 28-48 113-133 (178)
93 TIGR00280 L37a ribosomal prote 74.2 2.3 5E-05 24.2 1.4 15 65-79 51-65 (91)
94 PF00301 Rubredoxin: Rubredoxi 74.1 4.2 9.1E-05 20.1 2.2 14 33-46 2-15 (47)
95 PF08790 zf-LYAR: LYAR-type C2 74.0 1 2.2E-05 19.7 -0.0 19 96-115 1-19 (28)
96 PF14446 Prok-RING_1: Prokaryo 73.7 2.1 4.6E-05 21.9 1.1 24 33-58 6-29 (54)
97 KOG3408|consensus 73.7 2.3 5E-05 25.5 1.4 27 63-89 53-79 (129)
98 PF06524 NOA36: NOA36 protein; 73.0 1.6 3.4E-05 29.9 0.6 21 29-49 139-159 (314)
99 KOG1146|consensus 72.8 1.7 3.7E-05 36.2 0.9 66 24-89 457-540 (1406)
100 PRK04023 DNA polymerase II lar 71.1 5.3 0.00012 32.7 3.2 35 30-74 624-658 (1121)
101 PRK00432 30S ribosomal protein 71.1 4.4 9.6E-05 20.3 1.9 9 68-76 38-46 (50)
102 PF02892 zf-BED: BED zinc fing 70.7 3.6 7.9E-05 19.7 1.6 11 68-78 17-27 (45)
103 COG1198 PriA Primosomal protei 70.4 3.2 7E-05 32.7 1.9 41 32-76 444-484 (730)
104 PRK05580 primosome assembly pr 70.2 5 0.00011 31.4 2.9 21 52-76 410-430 (679)
105 PF14353 CpXC: CpXC protein 69.9 2.6 5.6E-05 25.4 1.1 12 34-45 3-14 (128)
106 PF09082 DUF1922: Domain of un 69.9 1.6 3.4E-05 23.4 0.1 25 33-59 4-28 (68)
107 smart00154 ZnF_AN1 AN1-like Zi 69.3 4.1 8.9E-05 19.2 1.5 15 32-46 12-26 (39)
108 PRK03564 formate dehydrogenase 69.1 6.6 0.00014 27.7 3.0 43 30-75 185-234 (309)
109 PF08274 PhnA_Zn_Ribbon: PhnA 69.0 2.3 5.1E-05 18.9 0.6 7 68-74 20-26 (30)
110 KOG2186|consensus 68.5 2.1 4.6E-05 29.1 0.5 51 33-93 4-54 (276)
111 PF01286 XPA_N: XPA protein N- 68.4 4 8.7E-05 18.7 1.3 17 34-50 5-21 (34)
112 PRK03976 rpl37ae 50S ribosomal 68.4 3.5 7.7E-05 23.4 1.3 15 65-79 52-66 (90)
113 PF01780 Ribosomal_L37ae: Ribo 67.7 1.9 4.1E-05 24.5 0.1 12 67-78 53-64 (90)
114 PF05290 Baculo_IE-1: Baculovi 67.4 6.1 0.00013 24.2 2.3 26 28-53 76-101 (140)
115 PF05191 ADK_lid: Adenylate ki 66.8 5.9 0.00013 18.3 1.7 11 34-44 3-13 (36)
116 TIGR01206 lysW lysine biosynth 66.5 4.7 0.0001 20.6 1.5 11 33-43 3-13 (54)
117 PF01428 zf-AN1: AN1-like Zinc 66.5 4.2 9E-05 19.5 1.2 23 31-53 12-35 (43)
118 cd00730 rubredoxin Rubredoxin; 66.1 5.3 0.00011 20.1 1.6 13 33-45 2-14 (50)
119 PF04216 FdhE: Protein involve 66.0 3.1 6.7E-05 28.9 1.0 48 52-103 199-246 (290)
120 PF14803 Nudix_N_2: Nudix N-te 64.6 5.8 0.00013 18.2 1.4 8 68-75 23-30 (34)
121 PRK12380 hydrogenase nickel in 64.5 4.6 9.9E-05 24.0 1.4 27 30-58 68-94 (113)
122 PRK12496 hypothetical protein; 64.3 5.5 0.00012 25.3 1.8 25 33-59 128-152 (164)
123 PF11781 RRN7: RNA polymerase 64.1 5.7 0.00012 18.4 1.4 10 65-74 23-32 (36)
124 smart00734 ZnF_Rad18 Rad18-lik 63.7 8 0.00017 16.4 1.7 19 69-88 3-21 (26)
125 PF07282 OrfB_Zn_ribbon: Putat 62.6 8.6 0.00019 20.3 2.1 27 52-78 30-57 (69)
126 PF13451 zf-trcl: Probable zin 62.2 8.7 0.00019 19.2 1.9 39 65-103 2-41 (49)
127 PRK00420 hypothetical protein; 61.8 8.6 0.00019 22.9 2.2 27 53-79 26-52 (112)
128 COG1571 Predicted DNA-binding 61.7 5.9 0.00013 29.1 1.7 30 52-81 352-381 (421)
129 smart00614 ZnF_BED BED zinc fi 61.1 6.1 0.00013 19.5 1.3 21 68-88 19-44 (50)
130 PF12013 DUF3505: Protein of u 61.0 8.8 0.00019 22.4 2.2 24 68-91 81-108 (109)
131 COG2331 Uncharacterized protei 61.0 2.4 5.3E-05 23.2 -0.2 13 32-44 12-24 (82)
132 PRK09678 DNA-binding transcrip 61.0 2.9 6.2E-05 22.8 0.1 19 65-83 25-45 (72)
133 COG3357 Predicted transcriptio 60.9 5.6 0.00012 22.6 1.2 14 31-44 57-70 (97)
134 KOG4167|consensus 59.6 2.4 5.3E-05 33.2 -0.5 25 95-120 792-816 (907)
135 PF08271 TF_Zn_Ribbon: TFIIB z 59.4 9.1 0.0002 18.2 1.7 8 68-75 20-27 (43)
136 PF13248 zf-ribbon_3: zinc-rib 59.3 5.4 0.00012 16.9 0.8 6 35-40 5-10 (26)
137 PF07295 DUF1451: Protein of u 59.2 8.2 0.00018 24.1 1.9 13 30-42 110-122 (146)
138 COG4888 Uncharacterized Zn rib 59.0 9.2 0.0002 22.2 1.9 20 29-48 19-38 (104)
139 KOG3183|consensus 58.7 9.2 0.0002 25.9 2.1 25 29-53 20-45 (250)
140 PF15269 zf-C2H2_7: Zinc-finge 58.6 7.7 0.00017 19.0 1.3 24 67-90 20-43 (54)
141 PRK00564 hypA hydrogenase nick 57.6 7.3 0.00016 23.3 1.4 30 29-59 68-97 (117)
142 PF01155 HypA: Hydrogenase exp 57.0 5.4 0.00012 23.6 0.8 29 29-59 67-95 (113)
143 KOG2593|consensus 56.1 7.2 0.00016 28.7 1.4 25 25-49 121-145 (436)
144 KOG4167|consensus 55.4 2.1 4.5E-05 33.6 -1.4 28 65-92 790-817 (907)
145 PRK10220 hypothetical protein; 54.8 12 0.00026 22.1 1.9 12 67-78 20-31 (111)
146 PF04959 ARS2: Arsenite-resist 54.1 12 0.00027 24.9 2.1 28 63-90 73-100 (214)
147 TIGR00686 phnA alkylphosphonat 54.0 9.5 0.00021 22.5 1.4 11 67-77 19-29 (109)
148 PF07649 C1_3: C1-like domain; 53.7 13 0.00028 16.1 1.6 11 66-76 14-24 (30)
149 PF07503 zf-HYPF: HypF finger; 53.2 3.4 7.3E-05 19.1 -0.4 13 35-47 2-14 (35)
150 PF12760 Zn_Tnp_IS1595: Transp 53.1 19 0.00042 17.4 2.3 7 68-74 38-44 (46)
151 COG5112 UFD2 U1-like Zn-finger 51.5 6.2 0.00013 23.1 0.4 28 61-88 49-76 (126)
152 PF01096 TFIIS_C: Transcriptio 51.1 12 0.00027 17.5 1.4 9 68-76 29-37 (39)
153 COG5236 Uncharacterized conser 51.1 7.5 0.00016 27.9 0.8 38 13-51 198-239 (493)
154 TIGR00100 hypA hydrogenase nic 50.0 11 0.00025 22.3 1.4 28 29-58 67-94 (115)
155 cd00924 Cyt_c_Oxidase_Vb Cytoc 50.0 9 0.00019 22.2 0.9 19 25-44 73-91 (97)
156 COG1645 Uncharacterized Zn-fin 49.9 14 0.0003 22.7 1.7 23 52-76 30-53 (131)
157 PLN02294 cytochrome c oxidase 49.6 9 0.0002 24.5 0.9 15 30-44 139-153 (174)
158 PF08792 A2L_zn_ribbon: A2L zi 49.2 17 0.00038 16.4 1.6 10 68-77 22-31 (33)
159 KOG2231|consensus 48.8 15 0.00032 28.8 2.1 48 68-119 183-236 (669)
160 COG4530 Uncharacterized protei 48.7 10 0.00023 22.4 1.0 16 63-78 22-37 (129)
161 PF01363 FYVE: FYVE zinc finge 48.7 9.7 0.00021 20.0 0.9 25 32-58 9-33 (69)
162 KOG1280|consensus 48.4 28 0.00061 25.0 3.2 37 66-102 78-116 (381)
163 TIGR01562 FdhE formate dehydro 48.2 29 0.00062 24.6 3.3 41 33-76 185-233 (305)
164 COG1439 Predicted nucleic acid 47.8 13 0.00027 24.1 1.4 23 33-59 140-162 (177)
165 COG0068 HypF Hydrogenase matur 47.7 4 8.6E-05 32.0 -1.0 66 34-105 103-183 (750)
166 KOG2785|consensus 47.6 19 0.0004 26.2 2.3 51 66-116 165-241 (390)
167 PF15135 UPF0515: Uncharacteri 47.4 19 0.00041 24.7 2.2 53 27-79 107-167 (278)
168 smart00440 ZnF_C2C2 C2C2 Zinc 47.4 26 0.00056 16.5 2.2 9 68-76 29-37 (40)
169 PRK14714 DNA polymerase II lar 46.8 21 0.00044 30.3 2.7 35 33-77 668-702 (1337)
170 PF05443 ROS_MUCR: ROS/MUCR tr 45.8 13 0.00028 22.8 1.2 24 67-93 72-95 (132)
171 COG3677 Transposase and inacti 45.3 17 0.00037 22.2 1.7 16 65-80 51-66 (129)
172 PF13453 zf-TFIIB: Transcripti 44.4 36 0.00078 15.9 2.5 18 67-84 19-36 (41)
173 PRK05978 hypothetical protein; 44.1 14 0.00031 23.1 1.2 27 33-59 34-61 (148)
174 cd00065 FYVE FYVE domain; Zinc 44.0 18 0.00038 18.1 1.4 24 34-59 4-27 (57)
175 PF09855 DUF2082: Nucleic-acid 43.7 16 0.00034 19.4 1.2 9 33-41 1-9 (64)
176 PF14599 zinc_ribbon_6: Zinc-r 43.5 12 0.00025 19.7 0.7 25 34-58 32-56 (61)
177 PF07191 zinc-ribbons_6: zinc- 43.2 20 0.00043 19.4 1.5 39 31-74 16-57 (70)
178 PRK11823 DNA repair protein Ra 43.1 19 0.0004 26.8 1.9 26 30-59 5-30 (446)
179 PF05495 zf-CHY: CHY zinc fing 43.0 26 0.00056 18.8 2.0 57 32-103 10-69 (71)
180 PF02148 zf-UBP: Zn-finger in 42.3 17 0.00037 18.9 1.2 25 64-88 8-35 (63)
181 PF14206 Cys_rich_CPCC: Cystei 42.2 19 0.0004 20.0 1.3 27 33-59 2-29 (78)
182 PF10083 DUF2321: Uncharacteri 42.1 20 0.00044 22.6 1.6 19 65-83 66-84 (158)
183 PRK14559 putative protein seri 42.1 23 0.0005 27.8 2.3 36 34-78 17-52 (645)
184 TIGR00416 sms DNA repair prote 41.9 17 0.00037 27.1 1.6 25 31-59 6-30 (454)
185 PF13878 zf-C2H2_3: zinc-finge 41.7 30 0.00064 16.4 1.9 23 68-90 14-38 (41)
186 PF07975 C1_4: TFIIH C1-like d 41.6 14 0.00029 18.7 0.7 22 30-51 19-40 (51)
187 PRK03824 hypA hydrogenase nick 40.7 13 0.00029 22.8 0.7 10 68-77 71-80 (135)
188 PRK00762 hypA hydrogenase nick 40.6 20 0.00043 21.7 1.4 16 29-45 67-82 (124)
189 PHA02942 putative transposase; 40.6 32 0.0007 25.1 2.7 29 51-79 326-354 (383)
190 PF02150 RNA_POL_M_15KD: RNA p 40.6 17 0.00037 16.6 0.9 9 69-77 22-30 (35)
191 TIGR00244 transcriptional regu 39.8 21 0.00045 22.4 1.4 17 68-84 29-45 (147)
192 cd01121 Sms Sms (bacterial rad 39.8 18 0.00039 26.3 1.3 23 33-59 1-23 (372)
193 PF02591 DUF164: Putative zinc 39.5 23 0.00051 17.9 1.4 9 94-102 45-53 (56)
194 COG1655 Uncharacterized protei 39.5 8.1 0.00018 26.1 -0.4 17 30-46 17-33 (267)
195 PF14205 Cys_rich_KTR: Cystein 38.9 26 0.00056 17.9 1.5 9 66-74 27-35 (55)
196 PF06677 Auto_anti-p27: Sjogre 38.7 29 0.00063 16.6 1.6 22 53-74 20-41 (41)
197 COG5216 Uncharacterized conser 38.5 24 0.00053 18.3 1.3 29 33-74 23-51 (67)
198 PRK03681 hypA hydrogenase nick 38.3 22 0.00047 21.1 1.3 13 31-43 69-81 (114)
199 PF09297 zf-NADH-PPase: NADH p 38.3 25 0.00053 15.5 1.2 10 66-75 20-29 (32)
200 PF12647 RNHCP: RNHCP domain; 37.6 56 0.0012 18.7 2.8 29 30-59 2-33 (92)
201 PF05766 NinG: Bacteriophage L 37.0 11 0.00024 24.6 -0.0 30 30-59 4-33 (189)
202 KOG3507|consensus 36.6 27 0.00059 18.2 1.3 14 94-107 36-49 (62)
203 TIGR03830 CxxCG_CxxCG_HTH puta 36.5 38 0.00083 20.0 2.3 23 65-87 29-51 (127)
204 COG5152 Uncharacterized conser 36.5 6.3 0.00014 25.9 -1.2 18 28-45 192-209 (259)
205 COG1066 Sms Predicted ATP-depe 36.4 26 0.00056 26.1 1.7 25 31-59 6-30 (456)
206 PF01215 COX5B: Cytochrome c o 35.3 18 0.00039 22.3 0.7 18 26-44 107-124 (136)
207 PF00628 PHD: PHD-finger; Int 34.7 56 0.0012 15.7 2.4 15 64-78 11-25 (51)
208 PF03811 Zn_Tnp_IS1: InsA N-te 34.5 32 0.00069 15.9 1.3 11 63-73 25-35 (36)
209 TIGR03826 YvyF flagellar opero 34.5 21 0.00045 22.1 0.8 23 34-59 5-27 (137)
210 PRK11032 hypothetical protein; 33.9 35 0.00076 21.7 1.8 12 31-42 123-134 (160)
211 PF09332 Mcm10: Mcm10 replicat 33.7 11 0.00024 27.0 -0.5 9 33-41 253-261 (344)
212 TIGR01384 TFS_arch transcripti 33.4 46 0.00099 19.1 2.2 10 95-104 62-71 (104)
213 PF10276 zf-CHCC: Zinc-finger 33.2 25 0.00054 16.7 0.8 12 31-42 28-39 (40)
214 PF02318 FYVE_2: FYVE-type zin 32.0 12 0.00027 22.2 -0.4 14 31-44 53-66 (118)
215 KOG2906|consensus 31.6 43 0.00094 19.4 1.8 15 66-80 20-34 (105)
216 PRK12286 rpmF 50S ribosomal pr 31.3 34 0.00074 17.6 1.2 9 33-41 28-36 (57)
217 PF05129 Elf1: Transcription e 30.9 23 0.00051 19.6 0.6 42 28-80 18-59 (81)
218 PF00130 C1_1: Phorbol esters/ 30.9 30 0.00065 17.0 1.0 13 30-42 9-21 (53)
219 PF07800 DUF1644: Protein of u 30.9 1.5E+02 0.0032 19.0 4.2 57 67-128 80-139 (162)
220 PF04810 zf-Sec23_Sec24: Sec23 30.6 39 0.00084 15.8 1.3 12 64-75 21-32 (40)
221 PF14149 YhfH: YhfH-like prote 30.5 8 0.00017 18.1 -1.1 11 34-44 15-25 (37)
222 PF14369 zf-RING_3: zinc-finge 30.5 48 0.001 15.1 1.5 10 69-78 23-32 (35)
223 PRK14892 putative transcriptio 30.4 68 0.0015 18.6 2.5 11 30-40 19-29 (99)
224 COG1327 Predicted transcriptio 30.2 31 0.00068 21.7 1.1 14 69-82 30-43 (156)
225 PF12907 zf-met2: Zinc-binding 29.9 29 0.00063 16.5 0.8 9 97-105 3-11 (40)
226 COG3091 SprT Zn-dependent meta 29.7 46 0.001 21.0 1.8 34 65-103 115-148 (156)
227 PF09416 UPF1_Zn_bind: RNA hel 29.5 95 0.0021 19.6 3.2 12 93-104 58-69 (152)
228 PHA02998 RNA polymerase subuni 29.3 62 0.0013 21.1 2.3 12 96-107 172-183 (195)
229 PF11672 DUF3268: Protein of u 29.0 83 0.0018 18.4 2.7 9 32-40 2-10 (102)
230 PRK09710 lar restriction allev 28.7 64 0.0014 17.1 2.0 10 67-76 27-36 (64)
231 PF14319 Zn_Tnp_IS91: Transpos 28.3 51 0.0011 19.5 1.8 13 29-41 39-51 (111)
232 smart00778 Prim_Zn_Ribbon Zinc 28.0 76 0.0016 14.8 2.1 9 66-74 24-32 (37)
233 PTZ00043 cytochrome c oxidase 27.9 30 0.00064 23.4 0.8 16 29-44 178-193 (268)
234 PF02176 zf-TRAF: TRAF-type zi 27.5 64 0.0014 16.2 1.9 34 67-100 9-43 (60)
235 KOG0782|consensus 26.9 15 0.00032 28.4 -0.8 31 17-48 239-269 (1004)
236 PF10263 SprT-like: SprT-like 26.7 53 0.0011 20.2 1.8 11 67-77 123-133 (157)
237 PRK05452 anaerobic nitric oxid 26.6 55 0.0012 24.7 2.1 18 28-45 421-438 (479)
238 KOG0978|consensus 26.4 6.7 0.00014 30.8 -2.7 17 94-110 677-693 (698)
239 PF03107 C1_2: C1 domain; Int 26.3 70 0.0015 13.8 2.0 8 67-74 15-22 (30)
240 COG0375 HybF Zn finger protein 26.3 45 0.00097 20.0 1.3 25 32-58 70-94 (115)
241 PF10122 Mu-like_Com: Mu-like 26.3 33 0.00071 17.3 0.6 13 32-44 4-16 (51)
242 COG2051 RPS27A Ribosomal prote 26.0 63 0.0014 17.3 1.7 10 68-77 39-48 (67)
243 TIGR01031 rpmF_bact ribosomal 25.8 43 0.00094 17.1 1.0 9 33-41 27-35 (55)
244 CHL00174 accD acetyl-CoA carbo 25.6 37 0.00079 24.0 1.0 35 52-86 40-76 (296)
245 smart00064 FYVE Protein presen 25.6 60 0.0013 16.9 1.6 25 33-59 11-35 (68)
246 PF06827 zf-FPG_IleRS: Zinc fi 25.5 44 0.00096 14.3 0.9 9 65-73 19-27 (30)
247 COG1545 Predicted nucleic-acid 25.3 51 0.0011 20.3 1.5 23 33-59 30-52 (140)
248 PF06397 Desulfoferrod_N: Desu 24.9 35 0.00076 15.8 0.5 12 31-42 5-16 (36)
249 smart00249 PHD PHD zinc finger 24.8 85 0.0018 14.2 2.3 13 65-77 12-24 (47)
250 PF13824 zf-Mss51: Zinc-finger 24.7 62 0.0013 16.6 1.5 13 65-77 12-24 (55)
251 PRK05654 acetyl-CoA carboxylas 24.6 38 0.00083 23.8 0.9 23 68-90 47-69 (292)
252 KOG2071|consensus 24.4 56 0.0012 25.3 1.8 27 65-91 416-442 (579)
253 TIGR03831 YgiT_finger YgiT-typ 24.1 38 0.00082 15.9 0.6 14 31-44 31-44 (46)
254 PF15199 DAOA: D-amino acid ox 24.0 25 0.00055 18.6 -0.0 7 2-8 15-21 (82)
255 COG0333 RpmF Ribosomal protein 24.0 55 0.0012 16.9 1.2 21 33-58 28-48 (57)
256 COG1998 RPS31 Ribosomal protei 24.0 74 0.0016 16.0 1.6 7 68-74 38-44 (51)
257 PF06221 zf-C2HC5: Putative zi 24.0 58 0.0013 16.8 1.3 11 35-45 21-31 (57)
258 PF04981 NMD3: NMD3 family ; 23.7 67 0.0015 21.6 1.9 12 68-79 36-47 (236)
259 TIGR00515 accD acetyl-CoA carb 23.7 35 0.00076 23.9 0.6 15 68-82 46-60 (285)
260 PF04423 Rad50_zn_hook: Rad50 23.6 36 0.00078 17.0 0.5 11 69-79 22-32 (54)
261 KOG1994|consensus 23.5 29 0.00063 23.4 0.2 26 26-51 233-258 (268)
262 PF04780 DUF629: Protein of un 23.2 65 0.0014 24.4 1.9 32 61-92 51-83 (466)
263 KOG2807|consensus 23.1 85 0.0018 22.6 2.3 25 94-119 344-368 (378)
264 PF01783 Ribosomal_L32p: Ribos 22.6 73 0.0016 16.2 1.5 9 33-41 27-35 (56)
265 KOG4602|consensus 22.3 1.2E+02 0.0026 21.1 2.8 7 52-58 270-276 (318)
266 COG4957 Predicted transcriptio 22.1 65 0.0014 20.0 1.4 22 69-93 78-99 (148)
267 PF10058 DUF2296: Predicted in 21.9 1E+02 0.0022 15.6 2.0 7 68-74 45-51 (54)
268 PF06044 DRP: Dam-replacing fa 21.8 44 0.00094 22.9 0.7 16 65-80 51-66 (254)
269 KOG1813|consensus 21.7 84 0.0018 22.2 2.1 18 28-45 237-254 (313)
270 PRK00415 rps27e 30S ribosomal 21.6 1.2E+02 0.0025 15.9 2.1 11 67-77 30-40 (59)
271 PRK04351 hypothetical protein; 21.5 84 0.0018 19.7 1.9 33 66-106 111-143 (149)
272 KOG2923|consensus 21.3 52 0.0011 17.5 0.8 11 33-44 23-33 (67)
273 PF10013 DUF2256: Uncharacteri 21.1 51 0.0011 15.9 0.7 11 69-79 10-20 (42)
274 KOG4727|consensus 21.1 55 0.0012 21.1 1.0 23 66-88 74-96 (193)
275 PF14311 DUF4379: Domain of un 20.8 98 0.0021 15.4 1.8 11 68-78 29-39 (55)
276 PF13821 DUF4187: Domain of un 20.8 39 0.00085 17.2 0.3 25 27-51 22-46 (55)
277 PF14445 Prok-RING_2: Prokaryo 20.7 5.4 0.00012 20.0 -2.8 11 33-43 8-18 (57)
278 KOG0957|consensus 20.7 1E+02 0.0022 23.7 2.4 46 28-76 540-598 (707)
279 COG0675 Transposase and inacti 20.6 1.3E+02 0.0028 20.8 3.0 24 52-79 311-334 (364)
280 cd00029 C1 Protein kinase C co 20.5 59 0.0013 15.4 0.9 12 32-43 11-22 (50)
281 PF14354 Lar_restr_allev: Rest 20.5 1.3E+02 0.0027 15.2 2.2 8 68-75 30-37 (61)
282 COG1326 Uncharacterized archae 20.4 1.2E+02 0.0027 20.0 2.5 13 66-78 29-41 (201)
283 PF08646 Rep_fac-A_C: Replicat 20.3 56 0.0012 20.0 1.0 10 67-76 37-46 (146)
284 smart00109 C1 Protein kinase C 20.2 80 0.0017 14.7 1.4 12 32-43 11-22 (49)
285 PF14569 zf-UDP: Zinc-binding 20.0 83 0.0018 17.5 1.4 55 46-105 5-61 (80)
No 1
>KOG2462|consensus
Probab=99.89 E-value=1.3e-23 Score=137.93 Aligned_cols=97 Identities=28% Similarity=0.501 Sum_probs=80.5
Q ss_pred cCcceecccccccccCccccccc-------------cCCCCCCc-----------ccCCCCceeeCCCCCCcccCchhHH
Q psy4407 29 ETEMLTCKYCYEFLPNDAEIIAD-------------HCKFCSYK-----------LRPDKTYIFTCFACEYHSAKRSHIK 84 (130)
Q Consensus 29 ~~~~~~C~~C~~~~~~~~~l~~h-------------~c~~C~~~-----------~~h~~~~~~~C~~C~~~f~~~~~l~ 84 (130)
....|.|+.||+.+.+.++|.+| .|+.||+. ++|+ -++.|.+||+.|...=-|+
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQ 204 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQ 204 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhh
Confidence 44568888888888888888777 58888887 4443 6688899999998888888
Q ss_pred HHHHhhcCCCCeecccChhhhcCcchHHHhhhhcCCCCCCCCccCC
Q psy4407 85 EHIRQHTGEKPFSCLLCEYKAAKKSNLTKHMSKKHPSSYEDPFFVS 130 (130)
Q Consensus 85 ~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~~h~g~~e~~~~C~ 130 (130)
.|+++|||||||.|..|++.|..+++|+.|+ ++|.+ .|+|+|.
T Consensus 205 GHiRTHTGEKPF~C~hC~kAFADRSNLRAHm-QTHS~--~K~~qC~ 247 (279)
T KOG2462|consen 205 GHIRTHTGEKPFSCPHCGKAFADRSNLRAHM-QTHSD--VKKHQCP 247 (279)
T ss_pred cccccccCCCCccCCcccchhcchHHHHHHH-HhhcC--CccccCc
Confidence 9999999999999999999999999999999 88888 8888884
No 2
>KOG2462|consensus
Probab=99.86 E-value=1.9e-22 Score=132.41 Aligned_cols=100 Identities=26% Similarity=0.440 Sum_probs=77.5
Q ss_pred ccccceehhhhhcc---cCcceecccccccccCccccccc--------cCCCCCCc-----------ccCCCCceeeCCC
Q psy4407 15 YSSGLKVSEVDFRF---ETEMLTCKYCYEFLPNDAEIIAD--------HCKFCSYK-----------LRPDKTYIFTCFA 72 (130)
Q Consensus 15 ~~~~~~~~~~~~~~---~~~~~~C~~C~~~~~~~~~l~~h--------~c~~C~~~-----------~~h~~~~~~~C~~ 72 (130)
..++|.+|. ++|- ..+.+.|..||+.|.+...|..| .|.+||+. ++|+|||||.|..
T Consensus 142 T~snLsrHk-Q~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~h 220 (279)
T KOG2462|consen 142 TSSNLSRHK-QTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPH 220 (279)
T ss_pred cccccchhh-cccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCCc
Confidence 444455552 3332 23445555566555555555444 45555555 9999999999999
Q ss_pred CCCcccCchhHHHHHHhhcCCCCeecccChhhhcCcchHHHhh
Q psy4407 73 CEYHSAKRSHIKEHIRQHTGEKPFSCLLCEYKAAKKSNLTKHM 115 (130)
Q Consensus 73 C~~~f~~~~~l~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~ 115 (130)
|++.|...++|+.|+++|.+.|+|.|..|++.|...+.|++|.
T Consensus 221 C~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ 263 (279)
T KOG2462|consen 221 CGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHS 263 (279)
T ss_pred ccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhh
Confidence 9999999999999999999999999999999999999999998
No 3
>KOG3623|consensus
Probab=99.66 E-value=1.6e-17 Score=121.30 Aligned_cols=82 Identities=24% Similarity=0.562 Sum_probs=79.1
Q ss_pred cccCcceecccccccccCccccccccCCCCCCcccCCCCceeeCCCCCCcccCchhHHHHHHhhcCCCCeecccChhhhc
Q psy4407 27 RFETEMLTCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLLCEYKAA 106 (130)
Q Consensus 27 ~~~~~~~~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~C~~~f~ 106 (130)
.+++..|.|+.|+|.|...+.|.+|. -.|+|.+||+|.+|.+.|..+-+|..|++.|.|+|||.|..|+++|.
T Consensus 889 kte~gmyaCDqCDK~FqKqSSLaRHK-------YEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFS 961 (1007)
T KOG3623|consen 889 KTEDGMYACDQCDKAFQKQSSLARHK-------YEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFS 961 (1007)
T ss_pred cCccccchHHHHHHHHHhhHHHHHhh-------hhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcc
Confidence 45778899999999999999999998 89999999999999999999999999999999999999999999999
Q ss_pred CcchHHHhh
Q psy4407 107 KKSNLTKHM 115 (130)
Q Consensus 107 ~~~~l~~h~ 115 (130)
...++..||
T Consensus 962 HSGSYSQHM 970 (1007)
T KOG3623|consen 962 HSGSYSQHM 970 (1007)
T ss_pred cccchHhhh
Confidence 999999999
No 4
>KOG1074|consensus
Probab=99.65 E-value=5.5e-17 Score=119.79 Aligned_cols=54 Identities=35% Similarity=0.626 Sum_probs=51.7
Q ss_pred eeeCCCCCCcccCchhHHHHHHhhcCCCCeecccChhhhcCcchHHHhhhhcCCC
Q psy4407 67 IFTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLLCEYKAAKKSNLTKHMSKKHPS 121 (130)
Q Consensus 67 ~~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~~h~g 121 (130)
|..|.+|-++..-.+.|+.|.++|+|++||+|.+||+.|..+..|+.|+ .+|..
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~-~vHka 658 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHM-SVHKA 658 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcc-ccccc
Confidence 5789999999999999999999999999999999999999999999999 88886
No 5
>KOG1074|consensus
Probab=99.60 E-value=9.2e-16 Score=113.44 Aligned_cols=57 Identities=33% Similarity=0.611 Sum_probs=52.9
Q ss_pred eeCCCCCCcccCchhHHHHHHhhcCCCCeecccChhhhcCcchHHHhhhhcCCCCCCCCc
Q psy4407 68 FTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLLCEYKAAKKSNLTKHMSKKHPSSYEDPF 127 (130)
Q Consensus 68 ~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~~h~g~~e~~~ 127 (130)
..|.+||+.|.+.+.|..|+++|+++|||.|..|++.|.....|+.|| ..|.+ ..|+
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHM-gtH~w--~q~~ 936 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHM-GTHMW--VQPP 936 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhh-ccccc--cCCC
Confidence 689999999999999999999999999999999999999999999999 68877 5543
No 6
>KOG3576|consensus
Probab=99.56 E-value=2.4e-16 Score=99.89 Aligned_cols=89 Identities=22% Similarity=0.398 Sum_probs=81.4
Q ss_pred hcccCcceecccccccccCccccccccCCCCCCcccCCCCceeeCCCCCCcccCchhHHHHHHhhcCCCCeecccChhhh
Q psy4407 26 FRFETEMLTCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLLCEYKA 105 (130)
Q Consensus 26 ~~~~~~~~~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~C~~~f 105 (130)
.-.+.-.|.|..|++.|.-..-|.+|. .-|+..+.+.|..||++|...-.|.+|+++|+|.+||+|..|++.|
T Consensus 111 sssd~d~ftCrvCgK~F~lQRmlnrh~-------kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaf 183 (267)
T KOG3576|consen 111 SSSDQDSFTCRVCGKKFGLQRMLNRHL-------KCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAF 183 (267)
T ss_pred CCCCCCeeeeehhhhhhhHHHHHHHHh-------hhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHH
Confidence 344566799999999999889999998 7888899999999999999999999999999999999999999999
Q ss_pred cCcchHHHhhhhcCCC
Q psy4407 106 AKKSNLTKHMSKKHPS 121 (130)
Q Consensus 106 ~~~~~l~~h~~~~h~g 121 (130)
.+..+|..|++++|..
T Consensus 184 tqrcsleshl~kvhgv 199 (267)
T KOG3576|consen 184 TQRCSLESHLKKVHGV 199 (267)
T ss_pred HhhccHHHHHHHHcCc
Confidence 9999999999888863
No 7
>KOG3608|consensus
Probab=99.54 E-value=2.4e-15 Score=102.29 Aligned_cols=115 Identities=17% Similarity=0.453 Sum_probs=89.5
Q ss_pred eeccccceehhhhhcccCcceecccccccccCccccccc--------------------------------------cCC
Q psy4407 13 LFYSSGLKVSEVDFRFETEMLTCKYCYEFLPNDAEIIAD--------------------------------------HCK 54 (130)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~h--------------------------------------~c~ 54 (130)
+..+..|+.| +++|+++|.-.|+.||..|.++..|..| .|+
T Consensus 189 ~~~k~~LreH-~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCp 267 (467)
T KOG3608|consen 189 MGNKYRLREH-IRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCP 267 (467)
T ss_pred hccHHHHHHH-HHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhccccc
Confidence 3466677777 6999999999999999999988887777 577
Q ss_pred CCCCc------------ccCCCCceeeCCCCCCcccCchhHHHHHHhhcCCCCeeccc--ChhhhcCcchHHHhhhhcCC
Q psy4407 55 FCSYK------------LRPDKTYIFTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLL--CEYKAAKKSNLTKHMSKKHP 120 (130)
Q Consensus 55 ~C~~~------------~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~--C~~~f~~~~~l~~h~~~~h~ 120 (130)
.|.++ ..|+.++||+|+.|+..+...+.|++|...|. +-.|.|.- |...+.....++.|.+.+|.
T Consensus 268 lCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhE 346 (467)
T KOG3608|consen 268 LCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHE 346 (467)
T ss_pred ccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhcc
Confidence 77666 55677888888888888888888888888776 56678855 88888888888888877787
Q ss_pred CCCCCCccC
Q psy4407 121 SSYEDPFFV 129 (130)
Q Consensus 121 g~~e~~~~C 129 (130)
|..+-+|.|
T Consensus 347 g~np~~Y~C 355 (467)
T KOG3608|consen 347 GNNPILYAC 355 (467)
T ss_pred CCCCCceee
Confidence 744555765
No 8
>KOG3623|consensus
Probab=99.41 E-value=5.5e-14 Score=103.15 Aligned_cols=65 Identities=28% Similarity=0.671 Sum_probs=62.1
Q ss_pred CCCceeeCCCCCCcccCchhHHHHHHhhcCCCCeecccChhhhcCcchHHHhhhhcCCCCCCCCccCC
Q psy4407 63 DKTYIFTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLLCEYKAAKKSNLTKHMSKKHPSSYEDPFFVS 130 (130)
Q Consensus 63 ~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~~h~g~~e~~~~C~ 130 (130)
+.+.+|.|+.|++.|...+.|.+|.-.|+|.+||.|.+|.+.|..+.+|..|+ +.|.| ||||.|+
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHk-RLHSG--EKPfQCd 954 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHK-RLHSG--EKPFQCD 954 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhh-hhccC--CCcchhh
Confidence 45668999999999999999999999999999999999999999999999999 99999 9999996
No 9
>KOG3576|consensus
Probab=99.27 E-value=4.2e-13 Score=85.33 Aligned_cols=94 Identities=17% Similarity=0.389 Sum_probs=80.5
Q ss_pred ceehhhhhcccCcceecccccccccCccccccccCCCCCCcccCCCCceeeCCCCCCcccCchhHHHHHH-hhc------
Q psy4407 19 LKVSEVDFRFETEMLTCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACEYHSAKRSHIKEHIR-QHT------ 91 (130)
Q Consensus 19 ~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~-~h~------ 91 (130)
|.+| ++-|...+.+.|..||+.|....+|++|. ++|+|.+||+|..|++.|...-.|..|++ .|.
T Consensus 133 lnrh-~kch~~vkr~lct~cgkgfndtfdlkrh~-------rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~ya 204 (267)
T KOG3576|consen 133 LNRH-LKCHSDVKRHLCTFCGKGFNDTFDLKRHT-------RTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYA 204 (267)
T ss_pred HHHH-hhhccHHHHHHHhhccCcccchhhhhhhh-------ccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHH
Confidence 4444 68899999999999999999999999999 99999999999999999999999999976 342
Q ss_pred ----CCCCeecccChhhhcCcchHHHhhhhcCC
Q psy4407 92 ----GEKPFSCLLCEYKAAKKSNLTKHMSKKHP 120 (130)
Q Consensus 92 ----~~k~~~C~~C~~~f~~~~~l~~h~~~~h~ 120 (130)
.++.|.|.+||..-.....+-.|++..|.
T Consensus 205 ykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 205 YKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred HHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 25779999999988888788888844333
No 10
>PHA00733 hypothetical protein
Probab=99.16 E-value=1.6e-11 Score=74.35 Aligned_cols=90 Identities=20% Similarity=0.278 Sum_probs=72.1
Q ss_pred hcccCcceecccccccccCccccccc--cCCCCCCcccCCCCceeeCCCCCCcccCchhHHHHHHhhcCCCCeecccChh
Q psy4407 26 FRFETEMLTCKYCYEFLPNDAEIIAD--HCKFCSYKLRPDKTYIFTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLLCEY 103 (130)
Q Consensus 26 ~~~~~~~~~C~~C~~~~~~~~~l~~h--~c~~C~~~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~C~~ 103 (130)
.-.+.+++.|..|+..|.....|..+ .-.. ..+.+++||.|..||+.|.+...|..|++.+ +.++.|..|++
T Consensus 34 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~----~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK 107 (128)
T PHA00733 34 LTPEQKRLIRAVVKTLIYNPQLLDESSYLYKL----LTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGK 107 (128)
T ss_pred CChhhhhHHHHHHhhhccChhhhcchHHHHhh----cccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCC
Confidence 44567889999999988877766655 0000 2334588999999999999999999999876 35799999999
Q ss_pred hhcCcchHHHhhhhcCCC
Q psy4407 104 KAAKKSNLTKHMSKKHPS 121 (130)
Q Consensus 104 ~f~~~~~l~~h~~~~h~g 121 (130)
.|.....|..|+.+.|+.
T Consensus 108 ~F~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 108 EFRNTDSTLDHVCKKHNI 125 (128)
T ss_pred ccCCHHHHHHHHHHhcCc
Confidence 999999999999777764
No 11
>KOG3608|consensus
Probab=99.10 E-value=4.5e-11 Score=81.81 Aligned_cols=108 Identities=15% Similarity=0.266 Sum_probs=91.1
Q ss_pred cceeeeeeeccccceehhhhhcccCcceecccccccccCccccccccCCCCCCcccCCCCceeeCCC--CCCcccCchhH
Q psy4407 6 RSYYVLFLFYSSGLKVSEVDFRFETEMLTCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFA--CEYHSAKRSHI 83 (130)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~--C~~~f~~~~~l 83 (130)
.|..-+-....+.|..|.+..|..++||+|+.|++.+...++|..|. .+|+ +..|.|.. |...+.+..++
T Consensus 266 CplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~-------~~HS-~~~y~C~h~~C~~s~r~~~q~ 337 (467)
T KOG3608|consen 266 CPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHV-------QVHS-KTVYQCEHPDCHYSVRTYTQM 337 (467)
T ss_pred ccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHH-------Hhcc-ccceecCCCCCcHHHHHHHHH
Confidence 34444556678889999777799999999999999999999999997 7776 66799987 99999999999
Q ss_pred HHHHHhhc-C--CCCeecccChhhhcCcchHHHhhhhcCCC
Q psy4407 84 KEHIRQHT-G--EKPFSCLLCEYKAAKKSNLTKHMSKKHPS 121 (130)
Q Consensus 84 ~~h~~~h~-~--~k~~~C~~C~~~f~~~~~l~~h~~~~h~g 121 (130)
..|++.+. | ..+|.|..|++-|..-..|..|+.+-|.-
T Consensus 338 ~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f 378 (467)
T KOG3608|consen 338 RRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGF 378 (467)
T ss_pred HHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcc
Confidence 99988654 4 35699999999999999999999776653
No 12
>PHA02768 hypothetical protein; Provisional
Probab=98.98 E-value=2.4e-10 Score=58.33 Aligned_cols=44 Identities=18% Similarity=0.357 Sum_probs=39.0
Q ss_pred eeeCCCCCCcccCchhHHHHHHhhcCCCCeecccChhhhcCcchHH
Q psy4407 67 IFTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLLCEYKAAKKSNLT 112 (130)
Q Consensus 67 ~~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~C~~~f~~~~~l~ 112 (130)
.|.|++||+.|...++|..|+++|+ ++++|..|++.|.+.+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 3789999999999999999999998 7899999999998776664
No 13
>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=5e-09 Score=45.87 Aligned_cols=26 Identities=38% Similarity=0.929 Sum_probs=23.2
Q ss_pred hHHHHHHhhcCCCCeecccChhhhcC
Q psy4407 82 HIKEHIRQHTGEKPFSCLLCEYKAAK 107 (130)
Q Consensus 82 ~l~~h~~~h~~~k~~~C~~C~~~f~~ 107 (130)
+|..|+++|++++||.|..|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 47899999999999999999998863
No 14
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.65 E-value=2.2e-08 Score=73.50 Aligned_cols=59 Identities=10% Similarity=0.202 Sum_probs=41.2
Q ss_pred ceeeCCCCCCcccCchhHHHHHHhhcCCCCeecccChhhhcC----------cchHHHhhhhcCCCCCCCCccCC
Q psy4407 66 YIFTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLLCEYKAAK----------KSNLTKHMSKKHPSSYEDPFFVS 130 (130)
Q Consensus 66 ~~~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~C~~~f~~----------~~~l~~h~~~~h~g~~e~~~~C~ 130 (130)
+++.|+ ||..+ ....|..|+.+|...+++.|..|++.+.. ...|..|. .++ | .+++.|+
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE-~~C-G--~rt~~C~ 545 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHE-SIC-G--SRTAPCD 545 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHH-Hhc-C--CcceEcc
Confidence 567787 87644 55777788777777788888888877742 23677777 543 6 7777773
No 15
>PHA02768 hypothetical protein; Provisional
Probab=98.62 E-value=5.4e-09 Score=53.36 Aligned_cols=44 Identities=14% Similarity=0.203 Sum_probs=38.6
Q ss_pred ceecccccccccCccccccccCCCCCCcccCCCCceeeCCCCCCcccCchhHH
Q psy4407 32 MLTCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACEYHSAKRSHIK 84 (130)
Q Consensus 32 ~~~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~~f~~~~~l~ 84 (130)
.|+|+.||+.|...++|..|+ ++|+ ++++|..|++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~-------r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHL-------RKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHH-------HhcC--CcccCCcccceecccceeE
Confidence 489999999999999999999 8988 6899999999998666543
No 16
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.59 E-value=3.8e-08 Score=72.29 Aligned_cols=93 Identities=17% Similarity=0.280 Sum_probs=69.7
Q ss_pred eccccceehhhhhcccCcceecccccccccCccccccccCCCCCCcccCCCCceeeCCCCCCcccC----------chhH
Q psy4407 14 FYSSGLKVSEVDFRFETEMLTCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACEYHSAK----------RSHI 83 (130)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~~f~~----------~~~l 83 (130)
+....|..|. +.+. +++.|+ ||+.+ ....|..|. .++.+.+++.|..|+..+.. ...|
T Consensus 463 f~~s~LekH~-~~~H--kpv~Cp-Cg~~~-~R~~L~~H~-------~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~L 530 (567)
T PLN03086 463 FQQGEMEKHM-KVFH--EPLQCP-CGVVL-EKEQMVQHQ-------ASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGM 530 (567)
T ss_pred cchHHHHHHH-HhcC--CCccCC-CCCCc-chhHHHhhh-------hccCCCCceeCCCCCCccccCccccchhhhhhhH
Confidence 4455666663 4543 778888 88655 457788887 77888999999999998842 3478
Q ss_pred HHHHHhhcCCCCeecccChhhhcCcchHHHhhhhcCC
Q psy4407 84 KEHIRQHTGEKPFSCLLCEYKAAKKSNLTKHMSKKHP 120 (130)
Q Consensus 84 ~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~~h~ 120 (130)
..|...+ |.+++.|..|++.+. ...+..|+..+|.
T Consensus 531 t~HE~~C-G~rt~~C~~Cgk~Vr-lrdm~~H~~~~h~ 565 (567)
T PLN03086 531 SEHESIC-GSRTAPCDSCGRSVM-LKEMDIHQIAVHQ 565 (567)
T ss_pred HHHHHhc-CCcceEccccCCeee-ehhHHHHHHHhhc
Confidence 9998886 889999999998764 4567778756664
No 17
>KOG3993|consensus
Probab=98.57 E-value=1.2e-08 Score=71.53 Aligned_cols=80 Identities=24% Similarity=0.468 Sum_probs=65.9
Q ss_pred eecccccccccCccccccccCCCCCCcccCCCCceeeCCCCCCcccCchhHHHHHHhhc--------CC-----------
Q psy4407 33 LTCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACEYHSAKRSHIKEHIRQHT--------GE----------- 93 (130)
Q Consensus 33 ~~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~h~--------~~----------- 93 (130)
|.|..|...|.+...|.+|.|+- .+ . .-|.|++|+++|.-..+|..|.++|- +.
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~R----IV-~--vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~ra 340 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPR----IV-H--VEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRA 340 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCe----eE-E--eeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhh
Confidence 88999999999999999997643 22 2 23899999999999999999999872 11
Q ss_pred --------------CCeecccChhhhcCcchHHHhhhhcCC
Q psy4407 94 --------------KPFSCLLCEYKAAKKSNLTKHMSKKHP 120 (130)
Q Consensus 94 --------------k~~~C~~C~~~f~~~~~l~~h~~~~h~ 120 (130)
-.|.|..|++.|.....|+.|+ ..|.
T Consensus 341 e~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHq-lthq 380 (500)
T KOG3993|consen 341 EVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQ-LTHQ 380 (500)
T ss_pred hhhhccccCCcccCceeecHHhhhhhHHHHHHHHhH-Hhhh
Confidence 1389999999999999999997 4443
No 18
>PHA00733 hypothetical protein
Probab=98.53 E-value=4.9e-08 Score=59.17 Aligned_cols=57 Identities=9% Similarity=0.153 Sum_probs=48.5
Q ss_pred cccCcceecccccccccCccccccccCCCCCCcccCCCCceeeCCCCCCcccCchhHHHHHHhhcC
Q psy4407 27 RFETEMLTCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACEYHSAKRSHIKEHIRQHTG 92 (130)
Q Consensus 27 ~~~~~~~~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~ 92 (130)
+.+++||.|+.||+.|.+...|..|. ..+ +.++.|..|++.|.....|..|+....+
T Consensus 68 ~~~~kPy~C~~Cgk~Fss~s~L~~H~-------r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 68 SKAVSPYVCPLCLMPFSSSVSLKQHI-------RYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred cCCCCCccCCCCCCcCCCHHHHHHHH-------hcC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 34588999999999999999999996 554 4569999999999999999999876543
No 19
>PHA00616 hypothetical protein
Probab=98.51 E-value=4.1e-08 Score=47.81 Aligned_cols=31 Identities=16% Similarity=0.403 Sum_probs=17.6
Q ss_pred eeCCCCCCcccCchhHHHHHHhhcCCCCeec
Q psy4407 68 FTCFACEYHSAKRSHIKEHIRQHTGEKPFSC 98 (130)
Q Consensus 68 ~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C 98 (130)
|+|..||..|.....+..|++.|++++++.|
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 4555555555555555555555555555544
No 20
>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=98.49 E-value=3.8e-08 Score=43.04 Aligned_cols=24 Identities=17% Similarity=0.376 Sum_probs=20.5
Q ss_pred ceehhhhhcccCcceeccccccccc
Q psy4407 19 LKVSEVDFRFETEMLTCKYCYEFLP 43 (130)
Q Consensus 19 ~~~~~~~~~~~~~~~~C~~C~~~~~ 43 (130)
|..| +++|++++||.|+.|++.|.
T Consensus 2 l~~H-~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRH-MRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHH-HHHHSSSSSEEESSSSEEES
T ss_pred HHHH-hhhcCCCCCCCCCCCcCeeC
Confidence 5566 58999999999999999885
No 21
>PHA00616 hypothetical protein
Probab=98.38 E-value=1.2e-07 Score=46.20 Aligned_cols=33 Identities=18% Similarity=0.371 Sum_probs=28.8
Q ss_pred CeecccChhhhcCcchHHHhhhhcCCCCCCCCccCC
Q psy4407 95 PFSCLLCEYKAAKKSNLTKHMSKKHPSSYEDPFFVS 130 (130)
Q Consensus 95 ~~~C~~C~~~f~~~~~l~~h~~~~h~g~~e~~~~C~ 130 (130)
||.|..||+.|.+.+.|+.|+ +.|+| ++|+.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~-r~~hg--~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHL-LSVHK--QNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHH-HHhcC--CCcccee
Confidence 588999999999999999999 77888 8988774
No 22
>PHA00732 hypothetical protein
Probab=98.08 E-value=2.9e-06 Score=47.08 Aligned_cols=47 Identities=15% Similarity=0.231 Sum_probs=29.4
Q ss_pred ceecccccccccCccccccccCCCCCCccc-CCCCceeeCCCCCCcccCchhHHHHHHhhc
Q psy4407 32 MLTCKYCYEFLPNDAEIIADHCKFCSYKLR-PDKTYIFTCFACEYHSAKRSHIKEHIRQHT 91 (130)
Q Consensus 32 ~~~C~~C~~~~~~~~~l~~h~c~~C~~~~~-h~~~~~~~C~~C~~~f~~~~~l~~h~~~h~ 91 (130)
||.|..||+.|.+...|..|. .. |.+ +.|..||+.|. .+..|..+..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~-------r~~H~~---~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHA-------RRNHTL---TKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHh-------hcccCC---CccCCCCCEeC---ChhhhhcccC
Confidence 466777777777777777775 42 332 36777777775 3566665443
No 23
>PHA00732 hypothetical protein
Probab=97.89 E-value=6.9e-06 Score=45.56 Aligned_cols=43 Identities=28% Similarity=0.632 Sum_probs=36.5
Q ss_pred eeeCCCCCCcccCchhHHHHHHh-hcCCCCeecccChhhhcCcchHHHhh
Q psy4407 67 IFTCFACEYHSAKRSHIKEHIRQ-HTGEKPFSCLLCEYKAAKKSNLTKHM 115 (130)
Q Consensus 67 ~~~C~~C~~~f~~~~~l~~h~~~-h~~~k~~~C~~C~~~f~~~~~l~~h~ 115 (130)
||.|..|++.|.+...|..|++. |++ +.|..|++.|. .+..|.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~---~l~~H~ 44 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR---RLNQHF 44 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC---Chhhhh
Confidence 57899999999999999999984 653 58999999997 467777
No 24
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.80 E-value=1.6e-05 Score=33.41 Aligned_cols=22 Identities=27% Similarity=0.699 Sum_probs=13.3
Q ss_pred eeCCCCCCcccCchhHHHHHHh
Q psy4407 68 FTCFACEYHSAKRSHIKEHIRQ 89 (130)
Q Consensus 68 ~~C~~C~~~f~~~~~l~~h~~~ 89 (130)
|.|..|++.|.+...|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4566666666666666666554
No 25
>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=97.64 E-value=0.00011 Score=37.79 Aligned_cols=48 Identities=29% Similarity=0.624 Sum_probs=33.1
Q ss_pred eeCCCCCCcccCchhHHHHHHh-hcC-CCCeecccChhhhcCcchHHHhhhhc
Q psy4407 68 FTCFACEYHSAKRSHIKEHIRQ-HTG-EKPFSCLLCEYKAAKKSNLTKHMSKK 118 (130)
Q Consensus 68 ~~C~~C~~~f~~~~~l~~h~~~-h~~-~k~~~C~~C~~~f~~~~~l~~h~~~~ 118 (130)
|.|+.|++ ..+...|..|... |.. .+.+.|++|...+. ..|..|+...
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHh
Confidence 67888888 4566788888664 544 35688888887544 3777887433
No 26
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.47 E-value=6.7e-05 Score=32.74 Aligned_cols=23 Identities=35% Similarity=0.634 Sum_probs=12.1
Q ss_pred eeCCCCCCcccCchhHHHHHHhh
Q psy4407 68 FTCFACEYHSAKRSHIKEHIRQH 90 (130)
Q Consensus 68 ~~C~~C~~~f~~~~~l~~h~~~h 90 (130)
|.|..|+..|.+...|..|++.|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCccCCccCChhHHHHHhHHh
Confidence 45555555555555555555443
No 27
>KOG3993|consensus
Probab=97.46 E-value=3.6e-05 Score=54.56 Aligned_cols=76 Identities=14% Similarity=0.210 Sum_probs=52.8
Q ss_pred ccccceehhhhhcccCcceecccccccccCcccccccc-----CCCCC-------C--------------cccCCCCcee
Q psy4407 15 YSSGLKVSEVDFRFETEMLTCKYCYEFLPNDAEIIADH-----CKFCS-------Y--------------KLRPDKTYIF 68 (130)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l~~h~-----c~~C~-------~--------------~~~h~~~~~~ 68 (130)
+...|..| .-...--..|+|++|+|.|....+|..|. =++-+ + ....+.+..|
T Consensus 279 D~F~LAQH-rC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~ 357 (500)
T KOG3993|consen 279 DAFALAQH-RCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIF 357 (500)
T ss_pred hHHHHhhc-cCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCcee
Confidence 44455555 34444556799999999999999999881 00000 0 0111334579
Q ss_pred eCCCCCCcccCchhHHHHHHhhc
Q psy4407 69 TCFACEYHSAKRSHIKEHIRQHT 91 (130)
Q Consensus 69 ~C~~C~~~f~~~~~l~~h~~~h~ 91 (130)
.|..|++.|.....|+.|+.+|.
T Consensus 358 ~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 358 SCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred ecHHhhhhhHHHHHHHHhHHhhh
Confidence 99999999999999999987774
No 28
>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=97.40 E-value=9.1e-05 Score=38.06 Aligned_cols=51 Identities=14% Similarity=0.329 Sum_probs=36.3
Q ss_pred ceecccccccccCccccccccCCCCCCcccCCC-CceeeCCCCCCcccCchhHHHHHHhhc
Q psy4407 32 MLTCKYCYEFLPNDAEIIADHCKFCSYKLRPDK-TYIFTCFACEYHSAKRSHIKEHIRQHT 91 (130)
Q Consensus 32 ~~~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~-~~~~~C~~C~~~f~~~~~l~~h~~~h~ 91 (130)
.|.|+.|++. .+...|..|.= ..|.. .+.+.|++|...+. .+|..|+....
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~------~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCE------DEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHH------hHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 5899999994 55678888820 34443 35689999998644 48888887543
No 29
>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=97.39 E-value=0.00018 Score=30.14 Aligned_cols=23 Identities=30% Similarity=0.735 Sum_probs=13.3
Q ss_pred eeCCCCCCcccCchhHHHHHHhh
Q psy4407 68 FTCFACEYHSAKRSHIKEHIRQH 90 (130)
Q Consensus 68 ~~C~~C~~~f~~~~~l~~h~~~h 90 (130)
|.|+.|+..|.+...+..|+..+
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 45666666666666666666544
No 30
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.37 E-value=4.3e-05 Score=32.05 Aligned_cols=21 Identities=38% Similarity=0.808 Sum_probs=19.5
Q ss_pred eecccChhhhcCcchHHHhhh
Q psy4407 96 FSCLLCEYKAAKKSNLTKHMS 116 (130)
Q Consensus 96 ~~C~~C~~~f~~~~~l~~h~~ 116 (130)
|.|..|++.|.....|..|++
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHh
Confidence 689999999999999999993
No 31
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.30 E-value=0.00016 Score=49.68 Aligned_cols=51 Identities=20% Similarity=0.484 Sum_probs=36.7
Q ss_pred CceeeCCC--CCCcccCchhHHHHHHhh-------------------cCCCCeecccChhhhcCcchHHHhh
Q psy4407 65 TYIFTCFA--CEYHSAKRSHIKEHIRQH-------------------TGEKPFSCLLCEYKAAKKSNLTKHM 115 (130)
Q Consensus 65 ~~~~~C~~--C~~~f~~~~~l~~h~~~h-------------------~~~k~~~C~~C~~~f~~~~~l~~h~ 115 (130)
+|||+|++ |.+.+.....|.-|+... ..+|||+|.+|++++.....|+.|+
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 36666655 666666666666665421 2358999999999999999998887
No 32
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.24 E-value=0.00017 Score=31.45 Aligned_cols=25 Identities=32% Similarity=0.563 Sum_probs=22.5
Q ss_pred CeecccChhhhcCcchHHHhhhhcCC
Q psy4407 95 PFSCLLCEYKAAKKSNLTKHMSKKHP 120 (130)
Q Consensus 95 ~~~C~~C~~~f~~~~~l~~h~~~~h~ 120 (130)
+|.|..|++.|.....|..|+ +.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~-~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHK-RSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHH-CTTT
T ss_pred CCCCCccCCccCChhHHHHHh-HHhc
Confidence 689999999999999999999 6654
No 33
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.08 E-value=0.00089 Score=33.53 Aligned_cols=33 Identities=18% Similarity=0.308 Sum_probs=18.3
Q ss_pred CCCceeeCCCCCCcccCchhHHHHHHhhcCCCC
Q psy4407 63 DKTYIFTCFACEYHSAKRSHIKEHIRQHTGEKP 95 (130)
Q Consensus 63 ~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~k~ 95 (130)
.++.|..|++|+..+....+|..|+....+.||
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 346667777777777777777777766555444
No 34
>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=97.02 E-value=0.00033 Score=29.25 Aligned_cols=23 Identities=35% Similarity=0.688 Sum_probs=18.4
Q ss_pred eecccChhhhcCcchHHHhhhhc
Q psy4407 96 FSCLLCEYKAAKKSNLTKHMSKK 118 (130)
Q Consensus 96 ~~C~~C~~~f~~~~~l~~h~~~~ 118 (130)
|.|..|++.|.....|..|++..
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 68999999999999999999443
No 35
>PRK04860 hypothetical protein; Provisional
Probab=96.97 E-value=0.00084 Score=42.27 Aligned_cols=39 Identities=23% Similarity=0.540 Sum_probs=33.6
Q ss_pred ceeeCCCCCCcccCchhHHHHHHhhcCCCCeecccChhhhcCc
Q psy4407 66 YIFTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLLCEYKAAKK 108 (130)
Q Consensus 66 ~~~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~C~~~f~~~ 108 (130)
-+|.|. |+. ....+..|.++++++++|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 579997 987 567789999999999999999999987654
No 36
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.89 E-value=0.00033 Score=48.20 Aligned_cols=59 Identities=14% Similarity=0.197 Sum_probs=43.1
Q ss_pred Ccceeccc--ccccccCcccccccc----CCCCCC--------cccCCCCceeeCCCCCCcccCchhHHHHHH
Q psy4407 30 TEMLTCKY--CYEFLPNDAEIIADH----CKFCSY--------KLRPDKTYIFTCFACEYHSAKRSHIKEHIR 88 (130)
Q Consensus 30 ~~~~~C~~--C~~~~~~~~~l~~h~----c~~C~~--------~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~ 88 (130)
++||+|+. |.|.|.....|+-|+ |..--. .......|||.|.+|++.+.....|.-|..
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 59999986 999999999998882 111000 011234689999999999999888887754
No 37
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.76 E-value=0.0012 Score=37.86 Aligned_cols=18 Identities=17% Similarity=0.604 Sum_probs=0.0
Q ss_pred ecccccccccCccccccc
Q psy4407 34 TCKYCYEFLPNDAEIIAD 51 (130)
Q Consensus 34 ~C~~C~~~~~~~~~l~~h 51 (130)
+|..|+..|.+...|..|
T Consensus 1 ~C~~C~~~f~~~~~l~~H 18 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQH 18 (100)
T ss_dssp ------------------
T ss_pred Cccccccccccccccccc
Confidence 477777777777777777
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.74 E-value=0.0014 Score=27.68 Aligned_cols=22 Identities=36% Similarity=0.665 Sum_probs=12.3
Q ss_pred eCCCCCCcccCchhHHHHHHhh
Q psy4407 69 TCFACEYHSAKRSHIKEHIRQH 90 (130)
Q Consensus 69 ~C~~C~~~f~~~~~l~~h~~~h 90 (130)
.|..|+..|.....+..|++.|
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHHh
Confidence 4555555555555555555543
No 39
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.62 E-value=0.0015 Score=37.34 Aligned_cols=23 Identities=26% Similarity=0.609 Sum_probs=18.5
Q ss_pred CeecccChhhhcCcchHHHhhhh
Q psy4407 95 PFSCLLCEYKAAKKSNLTKHMSK 117 (130)
Q Consensus 95 ~~~C~~C~~~f~~~~~l~~h~~~ 117 (130)
.+.|..|+..|.....|..|++.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCCccCCCCcCHHHHHHHHcC
Confidence 47899999999999999999953
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.34 E-value=0.0025 Score=27.02 Aligned_cols=22 Identities=23% Similarity=0.634 Sum_probs=13.8
Q ss_pred eeCCCCCCcccCchhHHHHHHh
Q psy4407 68 FTCFACEYHSAKRSHIKEHIRQ 89 (130)
Q Consensus 68 ~~C~~C~~~f~~~~~l~~h~~~ 89 (130)
|.|..|+..|.+...+..|++.
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 4566666666666666666553
No 41
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.30 E-value=0.002 Score=27.14 Aligned_cols=25 Identities=32% Similarity=0.624 Sum_probs=21.4
Q ss_pred eecccChhhhcCcchHHHhhhhcCCC
Q psy4407 96 FSCLLCEYKAAKKSNLTKHMSKKHPS 121 (130)
Q Consensus 96 ~~C~~C~~~f~~~~~l~~h~~~~h~g 121 (130)
|.|..|++.|.....|..|+ ..|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~-~~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHM-RTHXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHH-HHhcc
Confidence 57999999999999999999 56653
No 42
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.92 E-value=0.0039 Score=31.27 Aligned_cols=33 Identities=24% Similarity=0.559 Sum_probs=22.4
Q ss_pred cCCCCeecccChhhhcCcchHHHhhhhcCCCCCCCC
Q psy4407 91 TGEKPFSCLLCEYKAAKKSNLTKHMSKKHPSSYEDP 126 (130)
Q Consensus 91 ~~~k~~~C~~C~~~f~~~~~l~~h~~~~h~g~~e~~ 126 (130)
..+.|-.|++|+..+.+..+|+.|+ .++.+ -||
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHl-e~~H~--~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHL-EIRHF--KKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHH-HHHTT--TS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHH-HHHhc--ccC
Confidence 3567899999999999999999999 65555 565
No 43
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.58 E-value=0.013 Score=24.49 Aligned_cols=22 Identities=32% Similarity=0.991 Sum_probs=12.4
Q ss_pred eeCCCCCCcccCchhHHHHHHhh
Q psy4407 68 FTCFACEYHSAKRSHIKEHIRQH 90 (130)
Q Consensus 68 ~~C~~C~~~f~~~~~l~~h~~~h 90 (130)
|.|..|+.... ...|..|++.+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 45666666665 66666666653
No 44
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=95.51 E-value=0.013 Score=30.33 Aligned_cols=26 Identities=15% Similarity=0.354 Sum_probs=13.7
Q ss_pred ecccccccccCccccccccCCCCCCc
Q psy4407 34 TCKYCYEFLPNDAEIIADHCKFCSYK 59 (130)
Q Consensus 34 ~C~~C~~~~~~~~~l~~h~c~~C~~~ 59 (130)
.|..||...........+.|+.||..
T Consensus 11 ~CtSCg~~i~p~e~~v~F~CPnCGe~ 36 (61)
T COG2888 11 VCTSCGREIAPGETAVKFPCPNCGEV 36 (61)
T ss_pred eeccCCCEeccCCceeEeeCCCCCce
Confidence 46666666544444444455555533
No 45
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.28 E-value=0.0035 Score=27.21 Aligned_cols=20 Identities=30% Similarity=0.692 Sum_probs=9.8
Q ss_pred eeCCCCCCcccCchhHHHHH
Q psy4407 68 FTCFACEYHSAKRSHIKEHI 87 (130)
Q Consensus 68 ~~C~~C~~~f~~~~~l~~h~ 87 (130)
|.|..|++.|.+...+..|+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~ 21 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHM 21 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCT
T ss_pred CCcccCCCCcCCHHHHHHHH
Confidence 34555555555555544443
No 46
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=95.11 E-value=0.027 Score=29.19 Aligned_cols=26 Identities=15% Similarity=0.309 Sum_probs=10.7
Q ss_pred eecccccccccCccccccccCCCCCC
Q psy4407 33 LTCKYCYEFLPNDAEIIADHCKFCSY 58 (130)
Q Consensus 33 ~~C~~C~~~~~~~~~l~~h~c~~C~~ 58 (130)
..|..||....-...-....|+.||.
T Consensus 8 ~~CtSCg~~i~~~~~~~~F~CPnCG~ 33 (59)
T PRK14890 8 PKCTSCGIEIAPREKAVKFLCPNCGE 33 (59)
T ss_pred ccccCCCCcccCCCccCEeeCCCCCC
Confidence 34555555543323223333444433
No 47
>PRK04860 hypothetical protein; Provisional
Probab=94.40 E-value=0.017 Score=36.48 Aligned_cols=39 Identities=15% Similarity=0.302 Sum_probs=30.8
Q ss_pred cceecccccccccCccccccccCCCCCCcccCCCCceeeCCCCCCcccCc
Q psy4407 31 EMLTCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACEYHSAKR 80 (130)
Q Consensus 31 ~~~~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~~f~~~ 80 (130)
-+|.|. |+. ....+..|. ++++++++|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~-------ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHN-------RVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHH-------HHhcCCccEECCCCCceeEEe
Confidence 468897 987 456777787 888999999999999877543
No 48
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.19 E-value=0.048 Score=23.20 Aligned_cols=21 Identities=14% Similarity=0.384 Sum_probs=14.0
Q ss_pred eeCCCCCCcccCchhHHHHHHh
Q psy4407 68 FTCFACEYHSAKRSHIKEHIRQ 89 (130)
Q Consensus 68 ~~C~~C~~~f~~~~~l~~h~~~ 89 (130)
..|+.||+.| ....|..|+..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3577788777 56667777653
No 49
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=93.29 E-value=0.061 Score=26.45 Aligned_cols=27 Identities=22% Similarity=0.501 Sum_probs=15.3
Q ss_pred ceecccccccccCccccccccCCCCCC
Q psy4407 32 MLTCKYCYEFLPNDAEIIADHCKFCSY 58 (130)
Q Consensus 32 ~~~C~~C~~~~~~~~~l~~h~c~~C~~ 58 (130)
.|.|+.||..+........-.|+.||.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~ 29 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGY 29 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCC
Confidence 578888888775433322233444444
No 50
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=92.91 E-value=0.094 Score=23.86 Aligned_cols=22 Identities=18% Similarity=0.472 Sum_probs=17.2
Q ss_pred eeeCCCCCCcccCchhHHHHHH
Q psy4407 67 IFTCFACEYHSAKRSHIKEHIR 88 (130)
Q Consensus 67 ~~~C~~C~~~f~~~~~l~~h~~ 88 (130)
+|.|..|+..|.+...+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4778888888887777777765
No 51
>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=91.86 E-value=0.16 Score=23.12 Aligned_cols=9 Identities=33% Similarity=1.165 Sum_probs=4.4
Q ss_pred CCeecccCh
Q psy4407 94 KPFSCLLCE 102 (130)
Q Consensus 94 k~~~C~~C~ 102 (130)
.++.|++|+
T Consensus 16 ~~~~CP~Cg 24 (33)
T cd00350 16 APWVCPVCG 24 (33)
T ss_pred CCCcCcCCC
Confidence 344555554
No 52
>KOG2186|consensus
Probab=91.28 E-value=0.12 Score=34.78 Aligned_cols=45 Identities=22% Similarity=0.550 Sum_probs=19.7
Q ss_pred eeCCCCCCcccCchhHHHHHHhhcCCCCeecccChhhhcCcchHHHhh
Q psy4407 68 FTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLLCEYKAAKKSNLTKHM 115 (130)
Q Consensus 68 ~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h~ 115 (130)
|.|..||.... ...+..|+...++ .-|.|..|+..|.. .++..|.
T Consensus 4 FtCnvCgEsvK-Kp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVK-KPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhcc-ccchHHHHHhccC-CeeEEeeccccccc-chhhhhh
Confidence 34444444332 2333444444443 34555555555544 3344444
No 53
>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=91.16 E-value=0.2 Score=29.53 Aligned_cols=17 Identities=12% Similarity=0.204 Sum_probs=10.5
Q ss_pred CCceeeCCCCCCcccCc
Q psy4407 64 KTYIFTCFACEYHSAKR 80 (130)
Q Consensus 64 ~~~~~~C~~C~~~f~~~ 80 (130)
+..|..|+.||..|...
T Consensus 23 nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 23 NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCCCccCCCCCCccCcc
Confidence 34556677777666544
No 54
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=91.16 E-value=0.26 Score=23.03 Aligned_cols=11 Identities=18% Similarity=0.268 Sum_probs=6.1
Q ss_pred eeeCCCCCCcc
Q psy4407 67 IFTCFACEYHS 77 (130)
Q Consensus 67 ~~~C~~C~~~f 77 (130)
...|+.|+..|
T Consensus 25 ~vrC~~C~~~f 35 (37)
T PF13719_consen 25 KVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCcEe
Confidence 45566665544
No 55
>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=91.10 E-value=0.17 Score=24.41 Aligned_cols=16 Identities=13% Similarity=0.150 Sum_probs=11.6
Q ss_pred ceecccccccccCccc
Q psy4407 32 MLTCKYCYEFLPNDAE 47 (130)
Q Consensus 32 ~~~C~~C~~~~~~~~~ 47 (130)
.|.|..||..|.....
T Consensus 5 ey~C~~Cg~~fe~~~~ 20 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQS 20 (42)
T ss_pred EEEeCCCCCEEEEEEE
Confidence 4889999988865433
No 56
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.79 E-value=0.087 Score=37.62 Aligned_cols=54 Identities=33% Similarity=0.650 Sum_probs=34.4
Q ss_pred eeeCCCCCCcccCchhHHHHHH--hhcCC--CCeecc--cChhhhcCcchHHHhhhhcCCC
Q psy4407 67 IFTCFACEYHSAKRSHIKEHIR--QHTGE--KPFSCL--LCEYKAAKKSNLTKHMSKKHPS 121 (130)
Q Consensus 67 ~~~C~~C~~~f~~~~~l~~h~~--~h~~~--k~~~C~--~C~~~f~~~~~l~~h~~~~h~g 121 (130)
++.|..|...|.....+..|.+ .|+++ +++.|. .|++.|.....+..|. .+|.+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~-~~~~~ 348 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHI-LLHTS 348 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCc-ccccC
Confidence 4556666666666666666666 56666 666666 5666666666666666 55555
No 57
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=90.76 E-value=0.17 Score=33.56 Aligned_cols=48 Identities=19% Similarity=0.414 Sum_probs=29.5
Q ss_pred CcceecccccccccCccccccc------cCCCCCCcccCCCCce-----eeCCCCCCcccCc
Q psy4407 30 TEMLTCKYCYEFLPNDAEIIAD------HCKFCSYKLRPDKTYI-----FTCFACEYHSAKR 80 (130)
Q Consensus 30 ~~~~~C~~C~~~~~~~~~l~~h------~c~~C~~~~~h~~~~~-----~~C~~C~~~f~~~ 80 (130)
++...|+.|++.|.++.-+... .-+.| ....+..| +.|+.||.++...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~---~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFC---PRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCc---cccCCCCCeeeeEEECCCCCCccccc
Confidence 4678999999999876544333 12222 11123333 6899999877644
No 58
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.66 E-value=0.15 Score=36.47 Aligned_cols=62 Identities=18% Similarity=0.224 Sum_probs=51.0
Q ss_pred cceecccccccccCccccccccCCCCCCcc--cCCCC--ceeeCC--CCCCcccCchhHHHHHHhhcCCCCeecc
Q psy4407 31 EMLTCKYCYEFLPNDAEIIADHCKFCSYKL--RPDKT--YIFTCF--ACEYHSAKRSHIKEHIRQHTGEKPFSCL 99 (130)
Q Consensus 31 ~~~~C~~C~~~~~~~~~l~~h~c~~C~~~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~h~~~h~~~k~~~C~ 99 (130)
.++.|..|...|.....|..|. + .|.++ +++.|+ .|+..|.....+..|...|++..++.+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~-------~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHL-------RSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred cCCCCccccCCccccccccccc-------cccccccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 4678888888888888888887 6 68888 899998 7999999888888888888877666553
No 59
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=90.36 E-value=0.16 Score=25.40 Aligned_cols=30 Identities=20% Similarity=0.425 Sum_probs=20.4
Q ss_pred CcceecccccccccCccccccccCCCCCCc
Q psy4407 30 TEMLTCKYCYEFLPNDAEIIADHCKFCSYK 59 (130)
Q Consensus 30 ~~~~~C~~C~~~~~~~~~l~~h~c~~C~~~ 59 (130)
...|.|..||+.+........-.|+.||..
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 456999999999854444444467777654
No 60
>PHA00626 hypothetical protein
Probab=90.23 E-value=0.35 Score=24.77 Aligned_cols=13 Identities=23% Similarity=0.774 Sum_probs=8.8
Q ss_pred ceeeCCCCCCccc
Q psy4407 66 YIFTCFACEYHSA 78 (130)
Q Consensus 66 ~~~~C~~C~~~f~ 78 (130)
..|.|..||..|.
T Consensus 22 nrYkCkdCGY~ft 34 (59)
T PHA00626 22 DDYVCCDCGYNDS 34 (59)
T ss_pred cceEcCCCCCeec
Confidence 4577777777664
No 61
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=90.14 E-value=0.36 Score=22.48 Aligned_cols=13 Identities=15% Similarity=0.381 Sum_probs=7.2
Q ss_pred eecccccccccCc
Q psy4407 33 LTCKYCYEFLPND 45 (130)
Q Consensus 33 ~~C~~C~~~~~~~ 45 (130)
..|+.|+..|.-.
T Consensus 3 ~~CP~C~~~~~v~ 15 (38)
T TIGR02098 3 IQCPNCKTSFRVV 15 (38)
T ss_pred EECCCCCCEEEeC
Confidence 4566666665443
No 62
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=90.12 E-value=0.47 Score=22.04 Aligned_cols=14 Identities=36% Similarity=0.553 Sum_probs=7.7
Q ss_pred ecccccccccCccc
Q psy4407 34 TCKYCYEFLPNDAE 47 (130)
Q Consensus 34 ~C~~C~~~~~~~~~ 47 (130)
.|+.|+..|.-...
T Consensus 4 ~Cp~C~~~y~i~d~ 17 (36)
T PF13717_consen 4 TCPNCQAKYEIDDE 17 (36)
T ss_pred ECCCCCCEEeCCHH
Confidence 46666666654433
No 63
>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=90.10 E-value=0.22 Score=23.55 Aligned_cols=14 Identities=14% Similarity=0.209 Sum_probs=10.5
Q ss_pred ceecccccccccCc
Q psy4407 32 MLTCKYCYEFLPND 45 (130)
Q Consensus 32 ~~~C~~C~~~~~~~ 45 (130)
.|+|..||..|...
T Consensus 5 ~y~C~~Cg~~fe~~ 18 (41)
T smart00834 5 EYRCEDCGHTFEVL 18 (41)
T ss_pred EEEcCCCCCEEEEE
Confidence 47899999887543
No 64
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=89.73 E-value=0.39 Score=37.55 Aligned_cols=9 Identities=22% Similarity=0.575 Sum_probs=5.6
Q ss_pred ccccccccc
Q psy4407 35 CKYCYEFLP 43 (130)
Q Consensus 35 C~~C~~~~~ 43 (130)
|..||..+.
T Consensus 438 C~~Cg~v~~ 446 (730)
T COG1198 438 CRDCGYIAE 446 (730)
T ss_pred cccCCCccc
Confidence 666666653
No 65
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=88.29 E-value=0.5 Score=26.56 Aligned_cols=29 Identities=28% Similarity=0.512 Sum_probs=16.0
Q ss_pred ccCCCCCCcc-cCCCCceeeCCCCCCcccC
Q psy4407 51 DHCKFCSYKL-RPDKTYIFTCFACEYHSAK 79 (130)
Q Consensus 51 h~c~~C~~~~-~h~~~~~~~C~~C~~~f~~ 79 (130)
|.|+.|+... ...+...|.|..||..|.-
T Consensus 36 ~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 36 HVCPFCGRTTVKRIATGIWKCRKCGAKFAG 65 (89)
T ss_pred CcCCCCCCcceeeeccCeEEcCCCCCeecc
Confidence 3455555441 1123445888888877753
No 66
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=88.26 E-value=0.37 Score=23.53 Aligned_cols=26 Identities=19% Similarity=0.384 Sum_probs=15.0
Q ss_pred ceecccccccccCccccccccCCCCCC
Q psy4407 32 MLTCKYCYEFLPNDAEIIADHCKFCSY 58 (130)
Q Consensus 32 ~~~C~~C~~~~~~~~~l~~h~c~~C~~ 58 (130)
.|.|..||..+... ....-.|+.||.
T Consensus 2 ~Y~C~~Cg~~~~~~-~~~~irC~~CG~ 27 (44)
T smart00659 2 IYICGECGRENEIK-SKDVVRCRECGY 27 (44)
T ss_pred EEECCCCCCEeecC-CCCceECCCCCc
Confidence 47888888877543 222224555554
No 67
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=88.20 E-value=0.28 Score=29.79 Aligned_cols=28 Identities=18% Similarity=0.408 Sum_probs=22.1
Q ss_pred ceecccccccccCccccccccCCCCCCc
Q psy4407 32 MLTCKYCYEFLPNDAEIIADHCKFCSYK 59 (130)
Q Consensus 32 ~~~C~~C~~~~~~~~~l~~h~c~~C~~~ 59 (130)
|++|..||+.|.+-+.-..--|+.||..
T Consensus 1 PH~Ct~Cg~~f~dgs~eil~GCP~CGg~ 28 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKEILSGCPECGGN 28 (131)
T ss_pred CcccCcCCCCcCCCcHHHHccCcccCCc
Confidence 5789999999987664444569999887
No 68
>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=88.04 E-value=0.52 Score=20.23 Aligned_cols=9 Identities=33% Similarity=0.770 Sum_probs=4.8
Q ss_pred eCCCCCCcc
Q psy4407 69 TCFACEYHS 77 (130)
Q Consensus 69 ~C~~C~~~f 77 (130)
.|+.||..|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 455555554
No 69
>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=87.58 E-value=0.59 Score=21.16 Aligned_cols=11 Identities=18% Similarity=0.365 Sum_probs=7.2
Q ss_pred eeccccccccc
Q psy4407 33 LTCKYCYEFLP 43 (130)
Q Consensus 33 ~~C~~C~~~~~ 43 (130)
|.|..||..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 56777777765
No 70
>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=87.24 E-value=0.43 Score=23.91 Aligned_cols=14 Identities=14% Similarity=0.173 Sum_probs=10.9
Q ss_pred ceecccccccccCc
Q psy4407 32 MLTCKYCYEFLPND 45 (130)
Q Consensus 32 ~~~C~~C~~~~~~~ 45 (130)
.|+|..||..|...
T Consensus 5 ey~C~~Cg~~fe~~ 18 (52)
T TIGR02605 5 EYRCTACGHRFEVL 18 (52)
T ss_pred EEEeCCCCCEeEEE
Confidence 48899999988643
No 71
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=87.13 E-value=0.3 Score=28.27 Aligned_cols=28 Identities=25% Similarity=0.524 Sum_probs=23.5
Q ss_pred ceecccccccccCccccccccCCCCCCc
Q psy4407 32 MLTCKYCYEFLPNDAEIIADHCKFCSYK 59 (130)
Q Consensus 32 ~~~C~~C~~~~~~~~~l~~h~c~~C~~~ 59 (130)
|+.|..||..|.+-+.+...-|+.||..
T Consensus 2 pH~CtrCG~vf~~g~~~il~GCp~CG~n 29 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEILSGCPKCGCN 29 (112)
T ss_pred CceecccccccccccHHHHccCccccch
Confidence 6789999999988666666779999887
No 72
>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=86.45 E-value=1.1 Score=18.87 Aligned_cols=7 Identities=43% Similarity=1.198 Sum_probs=3.2
Q ss_pred eeCCCCC
Q psy4407 68 FTCFACE 74 (130)
Q Consensus 68 ~~C~~C~ 74 (130)
|.|+.||
T Consensus 17 f~CPnCG 23 (24)
T PF07754_consen 17 FPCPNCG 23 (24)
T ss_pred EeCCCCC
Confidence 4444444
No 73
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=85.69 E-value=0.46 Score=24.34 Aligned_cols=28 Identities=18% Similarity=0.374 Sum_probs=16.7
Q ss_pred CCCCceeeCCCCCCcccCchhHHHHHHh
Q psy4407 62 PDKTYIFTCFACEYHSAKRSHIKEHIRQ 89 (130)
Q Consensus 62 h~~~~~~~C~~C~~~f~~~~~l~~h~~~ 89 (130)
..|+..+.|+.||..|.....+..|...
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 3455566666666666666666665543
No 74
>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=83.90 E-value=1 Score=20.60 Aligned_cols=10 Identities=20% Similarity=0.434 Sum_probs=5.8
Q ss_pred eecccccccc
Q psy4407 33 LTCKYCYEFL 42 (130)
Q Consensus 33 ~~C~~C~~~~ 42 (130)
|.|..||..+
T Consensus 3 ~~C~~CG~i~ 12 (34)
T cd00729 3 WVCPVCGYIH 12 (34)
T ss_pred EECCCCCCEe
Confidence 5566666554
No 75
>KOG2893|consensus
Probab=82.59 E-value=0.51 Score=31.72 Aligned_cols=42 Identities=21% Similarity=0.459 Sum_probs=24.7
Q ss_pred ecccccccccCccccccccCCCCCCcccCCCCceeeCCCCCCcccCchhHHHH
Q psy4407 34 TCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACEYHSAKRSHIKEH 86 (130)
Q Consensus 34 ~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~~f~~~~~l~~h 86 (130)
.|..|.+.|....-|.+|+ ..|.|+|.+|-+-..+-..|..|
T Consensus 12 wcwycnrefddekiliqhq-----------kakhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQ-----------KAKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhhh-----------hhccceeeeehhhhccCCCceee
Confidence 3556777776666665552 34556777776555555555555
No 76
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=82.00 E-value=1.2 Score=26.97 Aligned_cols=28 Identities=7% Similarity=-0.152 Sum_probs=14.9
Q ss_pred CCCCCCcccCCCCceeeCCCCCCcccCc
Q psy4407 53 CKFCSYKLRPDKTYIFTCFACEYHSAKR 80 (130)
Q Consensus 53 c~~C~~~~~h~~~~~~~C~~C~~~f~~~ 80 (130)
|+.||..+--.+..|..|+.||..+...
T Consensus 12 Cp~cg~kFYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 12 CPNTGSKFYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred CCCcCccccccCCCCccCCCcCCccCcc
Confidence 3333333333344566777777776544
No 77
>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=81.90 E-value=1.6 Score=32.76 Aligned_cols=9 Identities=33% Similarity=0.770 Sum_probs=5.2
Q ss_pred ecccccccc
Q psy4407 34 TCKYCYEFL 42 (130)
Q Consensus 34 ~C~~C~~~~ 42 (130)
.|..||...
T Consensus 215 ~C~~Cg~~~ 223 (505)
T TIGR00595 215 LCRSCGYIL 223 (505)
T ss_pred EhhhCcCcc
Confidence 466666554
No 78
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=81.74 E-value=0.8 Score=28.46 Aligned_cols=40 Identities=15% Similarity=0.114 Sum_probs=26.2
Q ss_pred cccCcceecccccccccCccccccccCCCCCCcccCCCCceeeCCCCCCcc
Q psy4407 27 RFETEMLTCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACEYHS 77 (130)
Q Consensus 27 ~~~~~~~~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~~f 77 (130)
-.+...|.|+.|+..|.....+..- .. ...|.|+.||...
T Consensus 94 e~~~~~Y~Cp~C~~~y~~~ea~~~~----------d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 94 ETNNAYYKCPNCQSKYTFLEANQLL----------DM-DGTFTCPRCGEEL 133 (147)
T ss_pred ccCCcEEECcCCCCEeeHHHHHHhc----------CC-CCcEECCCCCCEE
Confidence 3455679999999998765543321 11 3338898888655
No 79
>KOG2893|consensus
Probab=80.02 E-value=0.4 Score=32.22 Aligned_cols=45 Identities=22% Similarity=0.505 Sum_probs=28.4
Q ss_pred CceeeCCCCCCcccCchhHHHHHHhhcCCCCeecccChhhhcCcchHHHh
Q psy4407 65 TYIFTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLLCEYKAAKKSNLTKH 114 (130)
Q Consensus 65 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~C~~~f~~~~~l~~h 114 (130)
.|+| |=.|++.|....-|.+|++ .|.|+|.+|-+...+-..|..|
T Consensus 9 ~kpw-cwycnrefddekiliqhqk----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred CCce-eeecccccchhhhhhhhhh----hccceeeeehhhhccCCCceee
Confidence 4454 4467788887777777765 3557888877765554444433
No 80
>PRK14873 primosome assembly protein PriA; Provisional
Probab=78.77 E-value=2.2 Score=33.31 Aligned_cols=9 Identities=22% Similarity=0.538 Sum_probs=5.3
Q ss_pred ecccccccc
Q psy4407 34 TCKYCYEFL 42 (130)
Q Consensus 34 ~C~~C~~~~ 42 (130)
.|..||..+
T Consensus 385 ~C~~Cg~~~ 393 (665)
T PRK14873 385 ACARCRTPA 393 (665)
T ss_pred EhhhCcCee
Confidence 466666554
No 81
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=78.26 E-value=3.1 Score=24.70 Aligned_cols=87 Identities=14% Similarity=0.190 Sum_probs=45.8
Q ss_pred cceecccccccccCccccccccC---CCCCCcccCCC--CceeeCCCCCCcccCchhHHHHHHhhcCCCCeecccChhhh
Q psy4407 31 EMLTCKYCYEFLPNDAEIIADHC---KFCSYKLRPDK--TYIFTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLLCEYKA 105 (130)
Q Consensus 31 ~~~~C~~C~~~~~~~~~l~~h~c---~~C~~~~~h~~--~~~~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~C~~~f 105 (130)
-|-.|+.||-.......|.+..- +.-........ ...-.|..|...|........ ..-.....|.|..|...|
T Consensus 14 LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~F 91 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNVF 91 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccccceeCCCCCCcc
Confidence 35566777766666555554410 00000001000 011248888887765431110 001223468999999988
Q ss_pred cCcchHHHhhhhcCC
Q psy4407 106 AKKSNLTKHMSKKHP 120 (130)
Q Consensus 106 ~~~~~l~~h~~~~h~ 120 (130)
--.-+.-.|. .+|+
T Consensus 92 C~dCD~fiHe-~Lh~ 105 (112)
T TIGR00622 92 CVDCDVFVHE-SLHC 105 (112)
T ss_pred ccccchhhhh-hccC
Confidence 8777777787 6665
No 82
>KOG2907|consensus
Probab=77.92 E-value=1.2 Score=26.30 Aligned_cols=38 Identities=18% Similarity=0.459 Sum_probs=19.4
Q ss_pred eeCCCCCCcccCchhHHHHHHhhcC-CCCeecccChhhhc
Q psy4407 68 FTCFACEYHSAKRSHIKEHIRQHTG-EKPFSCLLCEYKAA 106 (130)
Q Consensus 68 ~~C~~C~~~f~~~~~l~~h~~~h~~-~k~~~C~~C~~~f~ 106 (130)
..|+.||..-.+-..++.- ..+-| ..-|.|..|++.|.
T Consensus 75 ~kCpkCghe~m~Y~T~QlR-SADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQLR-SADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred ccCcccCCchhhhhhhhcc-cccCCceEEEEcCccceeee
Confidence 5788887533222222211 01222 23488888887765
No 83
>KOG4173|consensus
Probab=76.98 E-value=0.61 Score=30.64 Aligned_cols=82 Identities=18% Similarity=0.372 Sum_probs=56.2
Q ss_pred Ccceeccc--ccccccCccccccccCCCCCCcccCCCCceeeCCCCCCcccCchhHHHHHHh-h---------cCCCCee
Q psy4407 30 TEMLTCKY--CYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACEYHSAKRSHIKEHIRQ-H---------TGEKPFS 97 (130)
Q Consensus 30 ~~~~~C~~--C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~-h---------~~~k~~~ 97 (130)
...+.|.. |-..|.+......|. .+-. ...|..|.+.|.+.--|..|+.. | .|.--|.
T Consensus 77 ~~~~~cqvagc~~~~d~lD~~E~hY-------~~~h---~~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ 146 (253)
T KOG4173|consen 77 VPAFACQVAGCCQVFDALDDYEHHY-------HTLH---GNSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQ 146 (253)
T ss_pred cccccccccchHHHHhhhhhHHHhh-------hhcc---cchhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHH
Confidence 34466765 667776666555553 2211 13799999999999888888753 3 2334588
Q ss_pred ccc--ChhhhcCcchHHHhhhhcCCC
Q psy4407 98 CLL--CEYKAAKKSNLTKHMSKKHPS 121 (130)
Q Consensus 98 C~~--C~~~f~~~~~l~~h~~~~h~g 121 (130)
|.+ |+..|........|+-.+|.-
T Consensus 147 ClvEgCt~KFkT~r~RkdH~I~~Hk~ 172 (253)
T KOG4173|consen 147 CLVEGCTEKFKTSRDRKDHMIRMHKY 172 (253)
T ss_pred HHHHhhhhhhhhhhhhhhHHHHhccC
Confidence 854 999999888888888666653
No 84
>PF12773 DZR: Double zinc ribbon
Probab=76.72 E-value=2.4 Score=20.89 Aligned_cols=8 Identities=25% Similarity=0.501 Sum_probs=3.4
Q ss_pred eeCCCCCC
Q psy4407 68 FTCFACEY 75 (130)
Q Consensus 68 ~~C~~C~~ 75 (130)
..|+.|+.
T Consensus 30 ~~C~~Cg~ 37 (50)
T PF12773_consen 30 KICPNCGA 37 (50)
T ss_pred CCCcCCcC
Confidence 34444443
No 85
>KOG1146|consensus
Probab=76.38 E-value=1.5 Score=36.42 Aligned_cols=55 Identities=25% Similarity=0.596 Sum_probs=42.4
Q ss_pred CCCCceeeCCCCCCcccCchhHHHHHHh-hc------------------------CCCCeecccChhhhcCcchHHHhhh
Q psy4407 62 PDKTYIFTCFACEYHSAKRSHIKEHIRQ-HT------------------------GEKPFSCLLCEYKAAKKSNLTKHMS 116 (130)
Q Consensus 62 h~~~~~~~C~~C~~~f~~~~~l~~h~~~-h~------------------------~~k~~~C~~C~~~f~~~~~l~~h~~ 116 (130)
++..+.+.|+.|+..|.....|..|++. |. +.++|.|..|...+.....|..|+.
T Consensus 460 ~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 460 HSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred ecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHH
Confidence 3344678888888888888888888876 11 1367899999999999899988884
No 86
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=76.34 E-value=2.2 Score=24.26 Aligned_cols=15 Identities=27% Similarity=0.505 Sum_probs=10.4
Q ss_pred CceeeCCCCCCcccC
Q psy4407 65 TYIFTCFACEYHSAK 79 (130)
Q Consensus 65 ~~~~~C~~C~~~f~~ 79 (130)
...|.|..|++.|.-
T Consensus 52 ~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 52 VGIWRCKGCKKTVAG 66 (90)
T ss_pred eEEEEcCCCCCEEeC
Confidence 455788888877654
No 87
>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=76.31 E-value=1.6 Score=27.49 Aligned_cols=23 Identities=9% Similarity=0.209 Sum_probs=17.1
Q ss_pred hcccCcceecccccccccCcccc
Q psy4407 26 FRFETEMLTCKYCYEFLPNDAEI 48 (130)
Q Consensus 26 ~~~~~~~~~C~~C~~~~~~~~~l 48 (130)
......-|.|+.|+..|.....+
T Consensus 103 ~e~~~~~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 103 FETNNMFFICPNMCVRFTFNEAM 125 (158)
T ss_pred hccCCCeEECCCCCcEeeHHHHH
Confidence 34556779999999888766654
No 88
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=75.63 E-value=1.9 Score=27.15 Aligned_cols=19 Identities=16% Similarity=0.289 Sum_probs=13.0
Q ss_pred eeeCCCCCCcccCchhHHH
Q psy4407 67 IFTCFACEYHSAKRSHIKE 85 (130)
Q Consensus 67 ~~~C~~C~~~f~~~~~l~~ 85 (130)
.+.|+.||..|.+...+..
T Consensus 28 ~~~c~~c~~~f~~~e~~~~ 46 (154)
T PRK00464 28 RRECLACGKRFTTFERVEL 46 (154)
T ss_pred eeeccccCCcceEeEeccC
Confidence 3778888888876655443
No 89
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=75.49 E-value=4.4 Score=20.02 Aligned_cols=12 Identities=33% Similarity=0.885 Sum_probs=6.7
Q ss_pred eeeCCCCCCccc
Q psy4407 67 IFTCFACEYHSA 78 (130)
Q Consensus 67 ~~~C~~C~~~f~ 78 (130)
.+.|+.||..+.
T Consensus 20 ~~vC~~Cg~~~~ 31 (52)
T smart00661 20 RFVCRKCGYEEP 31 (52)
T ss_pred EEECCcCCCeEE
Confidence 456666665443
No 90
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=74.36 E-value=2.3 Score=27.12 Aligned_cols=10 Identities=40% Similarity=0.952 Sum_probs=5.6
Q ss_pred CCCeecccCh
Q psy4407 93 EKPFSCLLCE 102 (130)
Q Consensus 93 ~k~~~C~~C~ 102 (130)
+-|-+|++||
T Consensus 147 e~P~~CPiCg 156 (166)
T COG1592 147 EAPEVCPICG 156 (166)
T ss_pred CCCCcCCCCC
Confidence 4455565555
No 91
>COG1773 Rubredoxin [Energy production and conversion]
Probab=74.36 E-value=3 Score=21.38 Aligned_cols=43 Identities=14% Similarity=0.215 Sum_probs=23.1
Q ss_pred cceecccccccccCccccccccCCCCCCcccCCCCceeeCCCCCC
Q psy4407 31 EMLTCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACEY 75 (130)
Q Consensus 31 ~~~~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~ 75 (130)
+.|+|..||-.|.-...-- .+.+++-+..-.-.-.+.|++||.
T Consensus 2 ~~~~C~~CG~vYd~e~Gdp--~~gi~pgT~fedlPd~w~CP~Cg~ 44 (55)
T COG1773 2 KRWRCSVCGYVYDPEKGDP--RCGIAPGTPFEDLPDDWVCPECGV 44 (55)
T ss_pred CceEecCCceEeccccCCc--cCCCCCCCchhhCCCccCCCCCCC
Confidence 3588999999886543322 233333221111112378888884
No 92
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=74.23 E-value=1.9 Score=27.81 Aligned_cols=21 Identities=14% Similarity=0.256 Sum_probs=15.4
Q ss_pred ccCcceecccccccccCcccc
Q psy4407 28 FETEMLTCKYCYEFLPNDAEI 48 (130)
Q Consensus 28 ~~~~~~~C~~C~~~~~~~~~l 48 (130)
....-|.|+.|+..|.....+
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA~ 133 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEAM 133 (178)
T ss_pred cCCCEEECCCCCcEEeHHHHh
Confidence 345678999999888766554
No 93
>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=74.15 E-value=2.3 Score=24.24 Aligned_cols=15 Identities=40% Similarity=0.536 Sum_probs=10.0
Q ss_pred CceeeCCCCCCcccC
Q psy4407 65 TYIFTCFACEYHSAK 79 (130)
Q Consensus 65 ~~~~~C~~C~~~f~~ 79 (130)
...|.|..|+..|.-
T Consensus 51 ~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 51 TGIWTCRKCGAKFAG 65 (91)
T ss_pred eEEEEcCCCCCEEeC
Confidence 445778888777653
No 94
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=74.13 E-value=4.2 Score=20.13 Aligned_cols=14 Identities=14% Similarity=0.368 Sum_probs=10.3
Q ss_pred eecccccccccCcc
Q psy4407 33 LTCKYCYEFLPNDA 46 (130)
Q Consensus 33 ~~C~~C~~~~~~~~ 46 (130)
|+|..||..|....
T Consensus 2 y~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 2 YQCPVCGYVYDPEK 15 (47)
T ss_dssp EEETTTSBEEETTT
T ss_pred cCCCCCCEEEcCCc
Confidence 78888888776543
No 95
>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=74.00 E-value=1 Score=19.71 Aligned_cols=19 Identities=26% Similarity=0.592 Sum_probs=8.7
Q ss_pred eecccChhhhcCcchHHHhh
Q psy4407 96 FSCLLCEYKAAKKSNLTKHM 115 (130)
Q Consensus 96 ~~C~~C~~~f~~~~~l~~h~ 115 (130)
|.|..|++.| ....++.|.
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHT 19 (28)
T ss_dssp EEETTTTEEE-EGGGTTT--
T ss_pred CeeecCCCCc-CcCCcCCCC
Confidence 3566666666 333444444
No 96
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=73.72 E-value=2.1 Score=21.86 Aligned_cols=24 Identities=21% Similarity=0.580 Sum_probs=13.3
Q ss_pred eecccccccccCccccccccCCCCCC
Q psy4407 33 LTCKYCYEFLPNDAEIIADHCKFCSY 58 (130)
Q Consensus 33 ~~C~~C~~~~~~~~~l~~h~c~~C~~ 58 (130)
..|..||+.|....++. .|+.|+.
T Consensus 6 ~~C~~Cg~~~~~~dDiV--vCp~Cga 29 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIV--VCPECGA 29 (54)
T ss_pred ccChhhCCcccCCCCEE--ECCCCCC
Confidence 45777777775443332 3555554
No 97
>KOG3408|consensus
Probab=73.67 E-value=2.3 Score=25.52 Aligned_cols=27 Identities=19% Similarity=0.341 Sum_probs=23.6
Q ss_pred CCCceeeCCCCCCcccCchhHHHHHHh
Q psy4407 63 DKTYIFTCFACEYHSAKRSHIKEHIRQ 89 (130)
Q Consensus 63 ~~~~~~~C~~C~~~f~~~~~l~~h~~~ 89 (130)
.|-..|.|..|.+.|.+...+..|.++
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 456679999999999999999999874
No 98
>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=73.01 E-value=1.6 Score=29.87 Aligned_cols=21 Identities=24% Similarity=0.676 Sum_probs=13.6
Q ss_pred cCcceecccccccccCccccc
Q psy4407 29 ETEMLTCKYCYEFLPNDAEII 49 (130)
Q Consensus 29 ~~~~~~C~~C~~~~~~~~~l~ 49 (130)
|-+.|+|..|...+.....+.
T Consensus 139 GGrif~CsfC~~flCEDDQFE 159 (314)
T PF06524_consen 139 GGRIFKCSFCDNFLCEDDQFE 159 (314)
T ss_pred CCeEEEeecCCCeeeccchhh
Confidence 456678888877766554443
No 99
>KOG1146|consensus
Probab=72.83 E-value=1.7 Score=36.15 Aligned_cols=66 Identities=15% Similarity=0.295 Sum_probs=48.4
Q ss_pred hhhcccCcceecccccccccCccccccccCC--------CCCCc----------ccCCCCceeeCCCCCCcccCchhHHH
Q psy4407 24 VDFRFETEMLTCKYCYEFLPNDAEIIADHCK--------FCSYK----------LRPDKTYIFTCFACEYHSAKRSHIKE 85 (130)
Q Consensus 24 ~~~~~~~~~~~C~~C~~~~~~~~~l~~h~c~--------~C~~~----------~~h~~~~~~~C~~C~~~f~~~~~l~~ 85 (130)
.-.+...+.+.|+.|+..|.....|..|+=. .|-.. ....+.++|.|..|...+.....|..
T Consensus 457 ~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsi 536 (1406)
T KOG1146|consen 457 VVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSI 536 (1406)
T ss_pred eeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHH
Confidence 3456677999999999999998999888411 22111 11123568999999999999999999
Q ss_pred HHHh
Q psy4407 86 HIRQ 89 (130)
Q Consensus 86 h~~~ 89 (130)
|+..
T Consensus 537 hlqS 540 (1406)
T KOG1146|consen 537 HLQS 540 (1406)
T ss_pred HHHH
Confidence 9864
No 100
>PRK04023 DNA polymerase II large subunit; Validated
Probab=71.13 E-value=5.3 Score=32.65 Aligned_cols=35 Identities=20% Similarity=0.549 Sum_probs=21.6
Q ss_pred CcceecccccccccCccccccccCCCCCCcccCCCCceeeCCCCC
Q psy4407 30 TEMLTCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACE 74 (130)
Q Consensus 30 ~~~~~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~ 74 (130)
.....|+.||... ....|+.||.. .+..+.|+.|+
T Consensus 624 Vg~RfCpsCG~~t------~~frCP~CG~~----Te~i~fCP~CG 658 (1121)
T PRK04023 624 IGRRKCPSCGKET------FYRRCPFCGTH----TEPVYRCPRCG 658 (1121)
T ss_pred ccCccCCCCCCcC------CcccCCCCCCC----CCcceeCcccc
Confidence 3456799999873 23468888764 12335566664
No 101
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=71.06 E-value=4.4 Score=20.30 Aligned_cols=9 Identities=33% Similarity=1.014 Sum_probs=4.6
Q ss_pred eeCCCCCCc
Q psy4407 68 FTCFACEYH 76 (130)
Q Consensus 68 ~~C~~C~~~ 76 (130)
+.|..||..
T Consensus 38 ~~C~~Cgyt 46 (50)
T PRK00432 38 WHCGKCGYT 46 (50)
T ss_pred EECCCcCCE
Confidence 455555543
No 102
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=70.74 E-value=3.6 Score=19.67 Aligned_cols=11 Identities=18% Similarity=0.250 Sum_probs=4.3
Q ss_pred eeCCCCCCccc
Q psy4407 68 FTCFACEYHSA 78 (130)
Q Consensus 68 ~~C~~C~~~f~ 78 (130)
..|..|+..+.
T Consensus 17 a~C~~C~~~~~ 27 (45)
T PF02892_consen 17 AKCKYCGKVIK 27 (45)
T ss_dssp EEETTTTEE--
T ss_pred EEeCCCCeEEe
Confidence 44555554433
No 103
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=70.39 E-value=3.2 Score=32.71 Aligned_cols=41 Identities=20% Similarity=0.492 Sum_probs=23.1
Q ss_pred ceecccccccccCccccccccCCCCCCcccCCCCceeeCCCCCCc
Q psy4407 32 MLTCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACEYH 76 (130)
Q Consensus 32 ~~~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~~ 76 (130)
..+|+.|+..+.-...-..-.|-.||.. ...|..|+.||..
T Consensus 444 v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~----~~~p~~Cp~Cgs~ 484 (730)
T COG1198 444 IAECPNCDSPLTLHKATGQLRCHYCGYQ----EPIPQSCPECGSE 484 (730)
T ss_pred cccCCCCCcceEEecCCCeeEeCCCCCC----CCCCCCCCCCCCC
Confidence 3668888876543222222246666442 4566778888755
No 104
>PRK05580 primosome assembly protein PriA; Validated
Probab=70.16 E-value=5 Score=31.44 Aligned_cols=21 Identities=24% Similarity=0.719 Sum_probs=10.8
Q ss_pred cCCCCCCcccCCCCceeeCCCCCCc
Q psy4407 52 HCKFCSYKLRPDKTYIFTCFACEYH 76 (130)
Q Consensus 52 ~c~~C~~~~~h~~~~~~~C~~C~~~ 76 (130)
.|..||.. ...+..|+.||..
T Consensus 410 ~Ch~Cg~~----~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 410 RCHHCGYQ----EPIPKACPECGST 430 (679)
T ss_pred ECCCCcCC----CCCCCCCCCCcCC
Confidence 35555432 2334567777654
No 105
>PF14353 CpXC: CpXC protein
Probab=69.93 E-value=2.6 Score=25.40 Aligned_cols=12 Identities=25% Similarity=0.454 Sum_probs=8.0
Q ss_pred ecccccccccCc
Q psy4407 34 TCKYCYEFLPND 45 (130)
Q Consensus 34 ~C~~C~~~~~~~ 45 (130)
.|+.|+..|...
T Consensus 3 tCP~C~~~~~~~ 14 (128)
T PF14353_consen 3 TCPHCGHEFEFE 14 (128)
T ss_pred CCCCCCCeeEEE
Confidence 577788776543
No 106
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=69.89 E-value=1.6 Score=23.42 Aligned_cols=25 Identities=20% Similarity=0.588 Sum_probs=16.1
Q ss_pred eecccccccccCccccccccCCCCCCc
Q psy4407 33 LTCKYCYEFLPNDAEIIADHCKFCSYK 59 (130)
Q Consensus 33 ~~C~~C~~~~~~~~~l~~h~c~~C~~~ 59 (130)
|.| .||.....+..-..+.| .||..
T Consensus 4 frC-~Cgr~lya~e~~kTkkC-~CG~~ 28 (68)
T PF09082_consen 4 FRC-DCGRYLYAKEGAKTKKC-VCGKT 28 (68)
T ss_dssp EEE-TTS--EEEETT-SEEEE-TTTEE
T ss_pred EEe-cCCCEEEecCCcceeEe-cCCCe
Confidence 678 58887777777777777 77775
No 107
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=69.26 E-value=4.1 Score=19.22 Aligned_cols=15 Identities=13% Similarity=0.494 Sum_probs=12.6
Q ss_pred ceecccccccccCcc
Q psy4407 32 MLTCKYCYEFLPNDA 46 (130)
Q Consensus 32 ~~~C~~C~~~~~~~~ 46 (130)
||.|..|+..|....
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 789999999998764
No 108
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=69.14 E-value=6.6 Score=27.71 Aligned_cols=43 Identities=19% Similarity=0.389 Sum_probs=21.5
Q ss_pred Ccceeccccccccc-------CccccccccCCCCCCcccCCCCceeeCCCCCC
Q psy4407 30 TEMLTCKYCYEFLP-------NDAEIIADHCKFCSYKLRPDKTYIFTCFACEY 75 (130)
Q Consensus 30 ~~~~~C~~C~~~~~-------~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~ 75 (130)
+..-.|+.||..=. ....++.-.|..|+.. +.-....|+.||.
T Consensus 185 ~~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~te---W~~~R~~C~~Cg~ 234 (309)
T PRK03564 185 EQRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESE---WHVVRVKCSNCEQ 234 (309)
T ss_pred cCCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCc---ccccCccCCCCCC
Confidence 34456888885421 1122222257777442 2233356777775
No 109
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=69.05 E-value=2.3 Score=18.89 Aligned_cols=7 Identities=29% Similarity=0.970 Sum_probs=2.9
Q ss_pred eeCCCCC
Q psy4407 68 FTCFACE 74 (130)
Q Consensus 68 ~~C~~C~ 74 (130)
+.|+.|+
T Consensus 20 ~vCp~C~ 26 (30)
T PF08274_consen 20 LVCPECG 26 (30)
T ss_dssp EEETTTT
T ss_pred EeCCccc
Confidence 4444443
No 110
>KOG2186|consensus
Probab=68.45 E-value=2.1 Score=29.09 Aligned_cols=51 Identities=22% Similarity=0.397 Sum_probs=33.9
Q ss_pred eecccccccccCccccccccCCCCCCcccCCCCceeeCCCCCCcccCchhHHHHHHhhcCC
Q psy4407 33 LTCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACEYHSAKRSHIKEHIRQHTGE 93 (130)
Q Consensus 33 ~~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~ 93 (130)
|.|..||..... -.+..|+ ..-.+ .-|.|..|+..|-. ..+..|...-+..
T Consensus 4 FtCnvCgEsvKK-p~vekH~-------srCrn-~~fSCIDC~k~F~~-~sYknH~kCITEa 54 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHM-------SRCRN-AYFSCIDCGKTFER-VSYKNHTKCITEA 54 (276)
T ss_pred Eehhhhhhhccc-cchHHHH-------HhccC-CeeEEeeccccccc-chhhhhhhhcchH
Confidence 678888887754 4455563 22233 45889999999887 6677787655443
No 111
>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=68.42 E-value=4 Score=18.73 Aligned_cols=17 Identities=12% Similarity=0.223 Sum_probs=8.3
Q ss_pred ecccccccccCcccccc
Q psy4407 34 TCKYCYEFLPNDAEIIA 50 (130)
Q Consensus 34 ~C~~C~~~~~~~~~l~~ 50 (130)
.|..|++.|..+.-+..
T Consensus 5 ~C~eC~~~f~dSyL~~~ 21 (34)
T PF01286_consen 5 KCDECGKPFMDSYLLNN 21 (34)
T ss_dssp E-TTT--EES-SSCCCC
T ss_pred hHhHhCCHHHHHHHHHh
Confidence 68899999876444333
No 112
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=68.38 E-value=3.5 Score=23.45 Aligned_cols=15 Identities=33% Similarity=0.479 Sum_probs=9.8
Q ss_pred CceeeCCCCCCcccC
Q psy4407 65 TYIFTCFACEYHSAK 79 (130)
Q Consensus 65 ~~~~~C~~C~~~f~~ 79 (130)
...|.|..|+..|.-
T Consensus 52 ~GIW~C~~C~~~~AG 66 (90)
T PRK03976 52 TGIWECRKCGAKFAG 66 (90)
T ss_pred EEEEEcCCCCCEEeC
Confidence 345777777776653
No 113
>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=67.70 E-value=1.9 Score=24.54 Aligned_cols=12 Identities=33% Similarity=0.675 Sum_probs=8.5
Q ss_pred eeeCCCCCCccc
Q psy4407 67 IFTCFACEYHSA 78 (130)
Q Consensus 67 ~~~C~~C~~~f~ 78 (130)
.|.|..|+..|.
T Consensus 53 IW~C~~C~~~~A 64 (90)
T PF01780_consen 53 IWKCKKCGKKFA 64 (90)
T ss_dssp EEEETTTTEEEE
T ss_pred EeecCCCCCEEe
Confidence 377888877665
No 114
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=67.37 E-value=6.1 Score=24.22 Aligned_cols=26 Identities=15% Similarity=0.558 Sum_probs=20.2
Q ss_pred ccCcceecccccccccCccccccccC
Q psy4407 28 FETEMLTCKYCYEFLPNDAEIIADHC 53 (130)
Q Consensus 28 ~~~~~~~C~~C~~~~~~~~~l~~h~c 53 (130)
.+.+-|+|..|.+....+..|+.-.|
T Consensus 76 ~d~~lYeCnIC~etS~ee~FLKPneC 101 (140)
T PF05290_consen 76 LDPKLYECNICKETSAEERFLKPNEC 101 (140)
T ss_pred cCCCceeccCcccccchhhcCCcccc
Confidence 34578999999999888777776643
No 115
>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=66.83 E-value=5.9 Score=18.34 Aligned_cols=11 Identities=18% Similarity=0.401 Sum_probs=7.4
Q ss_pred ecccccccccC
Q psy4407 34 TCKYCYEFLPN 44 (130)
Q Consensus 34 ~C~~C~~~~~~ 44 (130)
.|+.||..|..
T Consensus 3 ~C~~Cg~~Yh~ 13 (36)
T PF05191_consen 3 ICPKCGRIYHI 13 (36)
T ss_dssp EETTTTEEEET
T ss_pred CcCCCCCcccc
Confidence 57777777753
No 116
>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=66.54 E-value=4.7 Score=20.60 Aligned_cols=11 Identities=18% Similarity=0.483 Sum_probs=7.8
Q ss_pred eeccccccccc
Q psy4407 33 LTCKYCYEFLP 43 (130)
Q Consensus 33 ~~C~~C~~~~~ 43 (130)
|.|+.||..+.
T Consensus 3 ~~CP~CG~~ie 13 (54)
T TIGR01206 3 FECPDCGAEIE 13 (54)
T ss_pred cCCCCCCCEEe
Confidence 57888887654
No 117
>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=66.49 E-value=4.2 Score=19.53 Aligned_cols=23 Identities=17% Similarity=0.228 Sum_probs=13.7
Q ss_pred cceecccccccccCcc-ccccccC
Q psy4407 31 EMLTCKYCYEFLPNDA-EIIADHC 53 (130)
Q Consensus 31 ~~~~C~~C~~~~~~~~-~l~~h~c 53 (130)
-++.|..|++.|.... ....|.|
T Consensus 12 ~~~~C~~C~~~FC~~Hr~~e~H~C 35 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHRLPEDHNC 35 (43)
T ss_dssp SHEE-TTTS-EE-TTTHSTTTCT-
T ss_pred CCeECCCCCcccCccccCccccCC
Confidence 5899999999998764 3444544
No 118
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=66.07 E-value=5.3 Score=20.06 Aligned_cols=13 Identities=15% Similarity=0.444 Sum_probs=9.6
Q ss_pred eecccccccccCc
Q psy4407 33 LTCKYCYEFLPND 45 (130)
Q Consensus 33 ~~C~~C~~~~~~~ 45 (130)
|+|..||..|...
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 6788888877643
No 119
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=65.99 E-value=3.1 Score=28.90 Aligned_cols=48 Identities=15% Similarity=0.336 Sum_probs=15.5
Q ss_pred cCCCCCCcccCCCCceeeCCCCCCcccCchhHHHHHHhhcCCCCeecccChh
Q psy4407 52 HCKFCSYKLRPDKTYIFTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLLCEY 103 (130)
Q Consensus 52 ~c~~C~~~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~C~~ 103 (130)
.|..|+.. +.-....|+.||..-.....+.. .....+.+...|..|+.
T Consensus 199 ~Cs~C~t~---W~~~R~~Cp~Cg~~~~~~l~~~~-~e~~~~~rve~C~~C~~ 246 (290)
T PF04216_consen 199 HCSLCGTE---WRFVRIKCPYCGNTDHEKLEYFT-VEGEPAYRVEVCESCGS 246 (290)
T ss_dssp EETTT--E---EE--TTS-TTT---SS-EEE---------SEEEEEETTTTE
T ss_pred EcCCCCCe---eeecCCCCcCCCCCCCcceeeEe-cCCCCcEEEEECCcccc
Confidence 46666543 11112356666655443333211 11122344566666654
No 120
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=64.60 E-value=5.8 Score=18.16 Aligned_cols=8 Identities=38% Similarity=1.161 Sum_probs=4.2
Q ss_pred eeCCCCCC
Q psy4407 68 FTCFACEY 75 (130)
Q Consensus 68 ~~C~~C~~ 75 (130)
+.|+.||.
T Consensus 23 ~vC~~Cg~ 30 (34)
T PF14803_consen 23 LVCPACGF 30 (34)
T ss_dssp EEETTTTE
T ss_pred eECCCCCC
Confidence 45555553
No 121
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=64.46 E-value=4.6 Score=23.97 Aligned_cols=27 Identities=15% Similarity=0.314 Sum_probs=15.0
Q ss_pred CcceecccccccccCccccccccCCCCCC
Q psy4407 30 TEMLTCKYCYEFLPNDAEIIADHCKFCSY 58 (130)
Q Consensus 30 ~~~~~C~~C~~~~~~~~~l~~h~c~~C~~ 58 (130)
.....|..||..|...... ..|+.||.
T Consensus 68 p~~~~C~~Cg~~~~~~~~~--~~CP~Cgs 94 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQHD--AQCPHCHG 94 (113)
T ss_pred CcEEEcccCCCEEecCCcC--ccCcCCCC
Confidence 3456788888776543211 12666654
No 122
>PRK12496 hypothetical protein; Provisional
Probab=64.30 E-value=5.5 Score=25.33 Aligned_cols=25 Identities=32% Similarity=0.664 Sum_probs=15.3
Q ss_pred eecccccccccCccccccccCCCCCCc
Q psy4407 33 LTCKYCYEFLPNDAEIIADHCKFCSYK 59 (130)
Q Consensus 33 ~~C~~C~~~~~~~~~l~~h~c~~C~~~ 59 (130)
|.|.-|++.|.... ..-.|+.||..
T Consensus 128 ~~C~gC~~~~~~~~--~~~~C~~CG~~ 152 (164)
T PRK12496 128 KVCKGCKKKYPEDY--PDDVCEICGSP 152 (164)
T ss_pred EECCCCCccccCCC--CCCcCCCCCCh
Confidence 66888888885321 12247777654
No 123
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=64.05 E-value=5.7 Score=18.40 Aligned_cols=10 Identities=20% Similarity=0.577 Sum_probs=5.2
Q ss_pred CceeeCCCCC
Q psy4407 65 TYIFTCFACE 74 (130)
Q Consensus 65 ~~~~~C~~C~ 74 (130)
+..+.|..||
T Consensus 23 dG~~yC~~cG 32 (36)
T PF11781_consen 23 DGFYYCDRCG 32 (36)
T ss_pred CCEEEhhhCc
Confidence 3445565555
No 124
>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=63.73 E-value=8 Score=16.41 Aligned_cols=19 Identities=21% Similarity=0.445 Sum_probs=10.9
Q ss_pred eCCCCCCcccCchhHHHHHH
Q psy4407 69 TCFACEYHSAKRSHIKEHIR 88 (130)
Q Consensus 69 ~C~~C~~~f~~~~~l~~h~~ 88 (130)
.|++|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 466666665 4455555554
No 125
>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=62.59 E-value=8.6 Score=20.29 Aligned_cols=27 Identities=22% Similarity=0.621 Sum_probs=15.4
Q ss_pred cCCCCCCcccC-CCCceeeCCCCCCccc
Q psy4407 52 HCKFCSYKLRP-DKTYIFTCFACEYHSA 78 (130)
Q Consensus 52 ~c~~C~~~~~h-~~~~~~~C~~C~~~f~ 78 (130)
.|+.||..... .....+.|+.||....
T Consensus 30 ~C~~CG~~~~~~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CccCcccccccccccceEEcCCCCCEEC
Confidence 46666654222 3455677777776543
No 126
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=62.16 E-value=8.7 Score=19.22 Aligned_cols=39 Identities=15% Similarity=0.305 Sum_probs=22.5
Q ss_pred CceeeCCCCCCcccCchhHHHHHHhhc-CCCCeecccChh
Q psy4407 65 TYIFTCFACEYHSAKRSHIKEHIRQHT-GEKPFSCLLCEY 103 (130)
Q Consensus 65 ~~~~~C~~C~~~f~~~~~l~~h~~~h~-~~k~~~C~~C~~ 103 (130)
++.+.|..||..|.-...-+..-..-. ...|-.|..|-.
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR~ 41 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCRQ 41 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHHH
Confidence 456788888877776655444433211 124566766643
No 127
>PRK00420 hypothetical protein; Validated
Probab=61.76 E-value=8.6 Score=22.87 Aligned_cols=27 Identities=19% Similarity=0.155 Sum_probs=14.9
Q ss_pred CCCCCCcccCCCCceeeCCCCCCcccC
Q psy4407 53 CKFCSYKLRPDKTYIFTCFACEYHSAK 79 (130)
Q Consensus 53 c~~C~~~~~h~~~~~~~C~~C~~~f~~ 79 (130)
|+.||............|+.||....-
T Consensus 26 CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 26 CPVCGLPLFELKDGEVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCcceecCCCceECCCCCCeeee
Confidence 555655433222334678888875553
No 128
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=61.71 E-value=5.9 Score=29.13 Aligned_cols=30 Identities=17% Similarity=0.424 Sum_probs=20.5
Q ss_pred cCCCCCCcccCCCCceeeCCCCCCcccCch
Q psy4407 52 HCKFCSYKLRPDKTYIFTCFACEYHSAKRS 81 (130)
Q Consensus 52 ~c~~C~~~~~h~~~~~~~C~~C~~~f~~~~ 81 (130)
.|+.||......|.+-|.|..||..+....
T Consensus 352 ~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRMKSAGRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCchhhcCCCCcccccccccCCccc
Confidence 577777765555555788888887776543
No 129
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=61.13 E-value=6.1 Score=19.54 Aligned_cols=21 Identities=24% Similarity=0.592 Sum_probs=10.7
Q ss_pred eeCCCCCCcccCc-----hhHHHHHH
Q psy4407 68 FTCFACEYHSAKR-----SHIKEHIR 88 (130)
Q Consensus 68 ~~C~~C~~~f~~~-----~~l~~h~~ 88 (130)
-.|..|++.+... ++|..|+.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 4566666555332 34555544
No 130
>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=61.04 E-value=8.8 Score=22.39 Aligned_cols=24 Identities=21% Similarity=0.674 Sum_probs=19.7
Q ss_pred eeC----CCCCCcccCchhHHHHHHhhc
Q psy4407 68 FTC----FACEYHSAKRSHIKEHIRQHT 91 (130)
Q Consensus 68 ~~C----~~C~~~f~~~~~l~~h~~~h~ 91 (130)
|.| ..|+....+...+..|.+.+.
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 788 888888888888888887654
No 131
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.98 E-value=2.4 Score=23.21 Aligned_cols=13 Identities=15% Similarity=0.301 Sum_probs=10.0
Q ss_pred ceecccccccccC
Q psy4407 32 MLTCKYCYEFLPN 44 (130)
Q Consensus 32 ~~~C~~C~~~~~~ 44 (130)
.|+|..||..|.-
T Consensus 12 ~Y~c~~cg~~~dv 24 (82)
T COG2331 12 SYECTECGNRFDV 24 (82)
T ss_pred EEeecccchHHHH
Confidence 4889999988743
No 132
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=60.95 E-value=2.9 Score=22.77 Aligned_cols=19 Identities=11% Similarity=0.228 Sum_probs=10.2
Q ss_pred CceeeCC--CCCCcccCchhH
Q psy4407 65 TYIFTCF--ACEYHSAKRSHI 83 (130)
Q Consensus 65 ~~~~~C~--~C~~~f~~~~~l 83 (130)
+.-+.|. +||..|.+...+
T Consensus 25 ~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 25 ERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred eeeeecCCCCCCCEEEEEEEE
Confidence 3345565 666666554443
No 133
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=60.88 E-value=5.6 Score=22.65 Aligned_cols=14 Identities=21% Similarity=0.292 Sum_probs=9.8
Q ss_pred cceecccccccccC
Q psy4407 31 EMLTCKYCYEFLPN 44 (130)
Q Consensus 31 ~~~~C~~C~~~~~~ 44 (130)
.|-.|..||..|.+
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 45667778877754
No 134
>KOG4167|consensus
Probab=59.64 E-value=2.4 Score=33.18 Aligned_cols=25 Identities=32% Similarity=0.432 Sum_probs=21.4
Q ss_pred CeecccChhhhcCcchHHHhhhhcCC
Q psy4407 95 PFSCLLCEYKAAKKSNLTKHMSKKHP 120 (130)
Q Consensus 95 ~~~C~~C~~~f~~~~~l~~h~~~~h~ 120 (130)
-|.|.+|++.|....+++.|| +.|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHM-K~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHM-KTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHH-HHHH
Confidence 489999999999999999999 5553
No 135
>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=59.43 E-value=9.1 Score=18.24 Aligned_cols=8 Identities=25% Similarity=0.837 Sum_probs=3.6
Q ss_pred eeCCCCCC
Q psy4407 68 FTCFACEY 75 (130)
Q Consensus 68 ~~C~~C~~ 75 (130)
+.|..||.
T Consensus 20 ~vC~~CG~ 27 (43)
T PF08271_consen 20 LVCPNCGL 27 (43)
T ss_dssp EEETTT-B
T ss_pred EECCCCCC
Confidence 45555553
No 136
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=59.31 E-value=5.4 Score=16.85 Aligned_cols=6 Identities=33% Similarity=0.944 Sum_probs=3.1
Q ss_pred cccccc
Q psy4407 35 CKYCYE 40 (130)
Q Consensus 35 C~~C~~ 40 (130)
|+.||.
T Consensus 5 Cp~Cg~ 10 (26)
T PF13248_consen 5 CPNCGA 10 (26)
T ss_pred CcccCC
Confidence 555554
No 137
>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=59.25 E-value=8.2 Score=24.09 Aligned_cols=13 Identities=23% Similarity=0.508 Sum_probs=8.9
Q ss_pred Ccceecccccccc
Q psy4407 30 TEMLTCKYCYEFL 42 (130)
Q Consensus 30 ~~~~~C~~C~~~~ 42 (130)
...|.|..||...
T Consensus 110 ~G~l~C~~Cg~~~ 122 (146)
T PF07295_consen 110 PGTLVCENCGHEV 122 (146)
T ss_pred CceEecccCCCEE
Confidence 3457788888654
No 138
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=58.98 E-value=9.2 Score=22.21 Aligned_cols=20 Identities=15% Similarity=0.276 Sum_probs=13.5
Q ss_pred cCcceecccccccccCcccc
Q psy4407 29 ETEMLTCKYCYEFLPNDAEI 48 (130)
Q Consensus 29 ~~~~~~C~~C~~~~~~~~~l 48 (130)
-++.|.|+.||..-...-.+
T Consensus 19 L~k~FtCp~Cghe~vs~ctv 38 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTV 38 (104)
T ss_pred CCceEecCccCCeeeeEEEE
Confidence 56779999999765443333
No 139
>KOG3183|consensus
Probab=58.67 E-value=9.2 Score=25.88 Aligned_cols=25 Identities=16% Similarity=0.385 Sum_probs=18.6
Q ss_pred cCcceecccccccccCcc-ccccccC
Q psy4407 29 ETEMLTCKYCYEFLPNDA-EIIADHC 53 (130)
Q Consensus 29 ~~~~~~C~~C~~~~~~~~-~l~~h~c 53 (130)
.--||.|..|+..|.... ....|.|
T Consensus 20 DFLPf~Cd~C~~~FC~eHrsye~H~C 45 (250)
T KOG3183|consen 20 DFLPFKCDGCSGIFCLEHRSYESHHC 45 (250)
T ss_pred cccceeeCCccchhhhccchHhhcCC
Confidence 456899999999998774 4566643
No 140
>PF15269 zf-C2H2_7: Zinc-finger
Probab=58.61 E-value=7.7 Score=18.96 Aligned_cols=24 Identities=25% Similarity=0.816 Sum_probs=19.4
Q ss_pred eeeCCCCCCcccCchhHHHHHHhh
Q psy4407 67 IFTCFACEYHSAKRSHIKEHIRQH 90 (130)
Q Consensus 67 ~~~C~~C~~~f~~~~~l~~h~~~h 90 (130)
.|+|-+|.....-+++|-.|++..
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred cceeecCCcccchHHHHHHHHHHH
Confidence 378888988888888888888754
No 141
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=57.56 E-value=7.3 Score=23.27 Aligned_cols=30 Identities=30% Similarity=0.485 Sum_probs=16.2
Q ss_pred cCcceecccccccccCccccccccCCCCCCc
Q psy4407 29 ETEMLTCKYCYEFLPNDAEIIADHCKFCSYK 59 (130)
Q Consensus 29 ~~~~~~C~~C~~~~~~~~~l~~h~c~~C~~~ 59 (130)
..-.+.|..||..|....... -.|+.||..
T Consensus 68 vp~~~~C~~Cg~~~~~~~~~~-~~CP~Cgs~ 97 (117)
T PRK00564 68 EKVELECKDCSHVFKPNALDY-GVCEKCHSK 97 (117)
T ss_pred cCCEEEhhhCCCccccCCccC-CcCcCCCCC
Confidence 344577888887765432211 126666543
No 142
>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=56.97 E-value=5.4 Score=23.61 Aligned_cols=29 Identities=17% Similarity=0.237 Sum_probs=15.5
Q ss_pred cCcceecccccccccCccccccccCCCCCCc
Q psy4407 29 ETEMLTCKYCYEFLPNDAEIIADHCKFCSYK 59 (130)
Q Consensus 29 ~~~~~~C~~C~~~~~~~~~l~~h~c~~C~~~ 59 (130)
..-.+.|..||..|...... -.|+.||..
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~--~~CP~Cgs~ 95 (113)
T PF01155_consen 67 VPARARCRDCGHEFEPDEFD--FSCPRCGSP 95 (113)
T ss_dssp E--EEEETTTS-EEECHHCC--HH-SSSSSS
T ss_pred cCCcEECCCCCCEEecCCCC--CCCcCCcCC
Confidence 34457788899888654332 247777654
No 143
>KOG2593|consensus
Probab=56.11 E-value=7.2 Score=28.68 Aligned_cols=25 Identities=8% Similarity=0.071 Sum_probs=18.7
Q ss_pred hhcccCcceecccccccccCccccc
Q psy4407 25 DFRFETEMLTCKYCYEFLPNDAEII 49 (130)
Q Consensus 25 ~~~~~~~~~~C~~C~~~~~~~~~l~ 49 (130)
+..+....|.|+.|.+.|.....+.
T Consensus 121 ~d~t~~~~Y~Cp~C~kkyt~Lea~~ 145 (436)
T KOG2593|consen 121 RDDTNVAGYVCPNCQKKYTSLEALQ 145 (436)
T ss_pred hhccccccccCCccccchhhhHHHH
Confidence 3455567799999999998776654
No 144
>KOG4167|consensus
Probab=55.35 E-value=2.1 Score=33.55 Aligned_cols=28 Identities=29% Similarity=0.412 Sum_probs=24.6
Q ss_pred CceeeCCCCCCcccCchhHHHHHHhhcC
Q psy4407 65 TYIFTCFACEYHSAKRSHIKEHIRQHTG 92 (130)
Q Consensus 65 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~ 92 (130)
...|.|.+|++.|.....+..||++|..
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 3459999999999999999999999864
No 145
>PRK10220 hypothetical protein; Provisional
Probab=54.79 E-value=12 Score=22.10 Aligned_cols=12 Identities=17% Similarity=0.578 Sum_probs=6.6
Q ss_pred eeeCCCCCCccc
Q psy4407 67 IFTCFACEYHSA 78 (130)
Q Consensus 67 ~~~C~~C~~~f~ 78 (130)
.|.|++|+.-..
T Consensus 20 ~~vCpeC~hEW~ 31 (111)
T PRK10220 20 MYICPECAHEWN 31 (111)
T ss_pred eEECCcccCcCC
Confidence 466666664443
No 146
>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=54.15 E-value=12 Score=24.93 Aligned_cols=28 Identities=14% Similarity=0.297 Sum_probs=21.7
Q ss_pred CCCceeeCCCCCCcccCchhHHHHHHhh
Q psy4407 63 DKTYIFTCFACEYHSAKRSHIKEHIRQH 90 (130)
Q Consensus 63 ~~~~~~~C~~C~~~f~~~~~l~~h~~~h 90 (130)
..+..|.|..|++.|.......+|+..-
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nK 100 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNK 100 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhc
Confidence 3456699999999999999999998753
No 147
>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=54.02 E-value=9.5 Score=22.47 Aligned_cols=11 Identities=27% Similarity=0.664 Sum_probs=5.9
Q ss_pred eeeCCCCCCcc
Q psy4407 67 IFTCFACEYHS 77 (130)
Q Consensus 67 ~~~C~~C~~~f 77 (130)
.|.|++|+...
T Consensus 19 ~~iCpeC~~EW 29 (109)
T TIGR00686 19 QLICPSCLYEW 29 (109)
T ss_pred eeECccccccc
Confidence 35666665444
No 148
>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=53.69 E-value=13 Score=16.12 Aligned_cols=11 Identities=18% Similarity=1.162 Sum_probs=3.9
Q ss_pred ceeeCCCCCCc
Q psy4407 66 YIFTCFACEYH 76 (130)
Q Consensus 66 ~~~~C~~C~~~ 76 (130)
..|.|.+|+..
T Consensus 14 ~~Y~C~~Cdf~ 24 (30)
T PF07649_consen 14 WFYRCSECDFD 24 (30)
T ss_dssp -EEE-TTT---
T ss_pred ceEECccCCCc
Confidence 45666666543
No 149
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=53.22 E-value=3.4 Score=19.08 Aligned_cols=13 Identities=15% Similarity=0.455 Sum_probs=5.9
Q ss_pred cccccccccCccc
Q psy4407 35 CKYCYEFLPNDAE 47 (130)
Q Consensus 35 C~~C~~~~~~~~~ 47 (130)
|+.|.+.+....+
T Consensus 2 C~~C~~Ey~~p~~ 14 (35)
T PF07503_consen 2 CDDCLKEYFDPSN 14 (35)
T ss_dssp -HHHHHHHCSTTS
T ss_pred CHHHHHHHcCCCC
Confidence 4455555544444
No 150
>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=53.06 E-value=19 Score=17.40 Aligned_cols=7 Identities=43% Similarity=1.303 Sum_probs=3.0
Q ss_pred eeCCCCC
Q psy4407 68 FTCFACE 74 (130)
Q Consensus 68 ~~C~~C~ 74 (130)
|.|..|+
T Consensus 38 ~~C~~C~ 44 (46)
T PF12760_consen 38 YRCKACR 44 (46)
T ss_pred EECCCCC
Confidence 4444443
No 151
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=51.52 E-value=6.2 Score=23.14 Aligned_cols=28 Identities=14% Similarity=0.179 Sum_probs=23.3
Q ss_pred cCCCCceeeCCCCCCcccCchhHHHHHH
Q psy4407 61 RPDKTYIFTCFACEYHSAKRSHIKEHIR 88 (130)
Q Consensus 61 ~h~~~~~~~C~~C~~~f~~~~~l~~h~~ 88 (130)
.-.|-..+.|.+|.+.|.+...|..|.+
T Consensus 49 ~lPGlGqhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 49 ELPGLGQHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred CCCCCceeeeehhHHHHHHHHHHHHHhc
Confidence 3355667899999999999999999976
No 152
>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=51.14 E-value=12 Score=17.49 Aligned_cols=9 Identities=22% Similarity=0.910 Sum_probs=5.2
Q ss_pred eeCCCCCCc
Q psy4407 68 FTCFACEYH 76 (130)
Q Consensus 68 ~~C~~C~~~ 76 (130)
|.|..|+..
T Consensus 29 y~C~~C~~~ 37 (39)
T PF01096_consen 29 YVCCNCGHR 37 (39)
T ss_dssp EEESSSTEE
T ss_pred EEeCCCCCe
Confidence 566666543
No 153
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=51.06 E-value=7.5 Score=27.90 Aligned_cols=38 Identities=29% Similarity=0.497 Sum_probs=27.2
Q ss_pred eeccccceehhhhhcccCccee----cccccccccCccccccc
Q psy4407 13 LFYSSGLKVSEVDFRFETEMLT----CKYCYEFLPNDAEIIAD 51 (130)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~----C~~C~~~~~~~~~l~~h 51 (130)
+|++..|..|. ..-..+..|+ |..|...|.+...|..|
T Consensus 198 lF~~~~Lr~H~-~~G~~e~GFKGHP~C~FC~~~FYdDDEL~~H 239 (493)
T COG5236 198 LFRSSTLRDHK-NGGLEEEGFKGHPLCIFCKIYFYDDDELRRH 239 (493)
T ss_pred eeecccccccc-cCCccccCcCCCchhhhccceecChHHHHHH
Confidence 46778888884 3333332343 99999999999999888
No 154
>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=49.99 E-value=11 Score=22.34 Aligned_cols=28 Identities=21% Similarity=0.415 Sum_probs=15.3
Q ss_pred cCcceecccccccccCccccccccCCCCCC
Q psy4407 29 ETEMLTCKYCYEFLPNDAEIIADHCKFCSY 58 (130)
Q Consensus 29 ~~~~~~C~~C~~~~~~~~~l~~h~c~~C~~ 58 (130)
..-...|..||..|..... .-.|+.||.
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs 94 (115)
T TIGR00100 67 EPVECECEDCSEEVSPEID--LYRCPKCHG 94 (115)
T ss_pred eCcEEEcccCCCEEecCCc--CccCcCCcC
Confidence 3444678888877654322 123666654
No 155
>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=49.98 E-value=9 Score=22.16 Aligned_cols=19 Identities=11% Similarity=0.076 Sum_probs=14.2
Q ss_pred hhcccCcceecccccccccC
Q psy4407 25 DFRFETEMLTCKYCYEFLPN 44 (130)
Q Consensus 25 ~~~~~~~~~~C~~C~~~~~~ 44 (130)
..+.+ ++++|.+||..|.-
T Consensus 73 ~l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 73 WLEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred EEeCC-CceeCCCCCcEEEE
Confidence 34455 79999999998853
No 156
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=49.91 E-value=14 Score=22.66 Aligned_cols=23 Identities=35% Similarity=0.831 Sum_probs=12.4
Q ss_pred cCCCCCCc-ccCCCCceeeCCCCCCc
Q psy4407 52 HCKFCSYK-LRPDKTYIFTCFACEYH 76 (130)
Q Consensus 52 ~c~~C~~~-~~h~~~~~~~C~~C~~~ 76 (130)
.|+.||.. +.++|+ ..|+.|+..
T Consensus 30 hCp~Cg~PLF~KdG~--v~CPvC~~~ 53 (131)
T COG1645 30 HCPKCGTPLFRKDGE--VFCPVCGYR 53 (131)
T ss_pred hCcccCCcceeeCCe--EECCCCCce
Confidence 36666655 223333 567777743
No 157
>PLN02294 cytochrome c oxidase subunit Vb
Probab=49.61 E-value=9 Score=24.53 Aligned_cols=15 Identities=13% Similarity=0.563 Sum_probs=11.5
Q ss_pred CcceecccccccccC
Q psy4407 30 TEMLTCKYCYEFLPN 44 (130)
Q Consensus 30 ~~~~~C~~C~~~~~~ 44 (130)
.++++|++||..|.-
T Consensus 139 Gkp~RCpeCG~~fkL 153 (174)
T PLN02294 139 GKSFECPVCTQYFEL 153 (174)
T ss_pred CCceeCCCCCCEEEE
Confidence 368889889988853
No 158
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=49.19 E-value=17 Score=16.41 Aligned_cols=10 Identities=20% Similarity=0.404 Sum_probs=4.9
Q ss_pred eeCCCCCCcc
Q psy4407 68 FTCFACEYHS 77 (130)
Q Consensus 68 ~~C~~C~~~f 77 (130)
+.|..|+..|
T Consensus 22 ~~C~~Cg~~~ 31 (33)
T PF08792_consen 22 EVCIFCGSSF 31 (33)
T ss_pred EEcccCCcEe
Confidence 4455555443
No 159
>KOG2231|consensus
Probab=48.82 E-value=15 Score=28.83 Aligned_cols=48 Identities=21% Similarity=0.359 Sum_probs=26.3
Q ss_pred eeCCCCCCcccCchhHHHHHHhhcCCCCeecccC------hhhhcCcchHHHhhhhcC
Q psy4407 68 FTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLLC------EYKAAKKSNLTKHMSKKH 119 (130)
Q Consensus 68 ~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~C------~~~f~~~~~l~~h~~~~h 119 (130)
-.|..|...|.....+..|++.+. |-|..| +..|.....|..|-|.-|
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 356667777777777777766433 233333 223444556666664433
No 160
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.72 E-value=10 Score=22.38 Aligned_cols=16 Identities=0% Similarity=-0.390 Sum_probs=10.0
Q ss_pred CCCceeeCCCCCCccc
Q psy4407 63 DKTYIFTCFACEYHSA 78 (130)
Q Consensus 63 ~~~~~~~C~~C~~~f~ 78 (130)
....|..|+.||+.|.
T Consensus 22 LNrdPiVsPytG~s~P 37 (129)
T COG4530 22 LNRDPIVSPYTGKSYP 37 (129)
T ss_pred cCCCccccCcccccch
Confidence 3445567777777763
No 161
>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=48.68 E-value=9.7 Score=20.05 Aligned_cols=25 Identities=20% Similarity=0.404 Sum_probs=9.2
Q ss_pred ceecccccccccCccccccccCCCCCC
Q psy4407 32 MLTCKYCYEFLPNDAEIIADHCKFCSY 58 (130)
Q Consensus 32 ~~~C~~C~~~~~~~~~l~~h~c~~C~~ 58 (130)
.-.|..|++.|.- ...+|.|..||.
T Consensus 9 ~~~C~~C~~~F~~--~~rrhhCr~CG~ 33 (69)
T PF01363_consen 9 ASNCMICGKKFSL--FRRRHHCRNCGR 33 (69)
T ss_dssp -SB-TTT--B-BS--SS-EEE-TTT--
T ss_pred CCcCcCcCCcCCC--ceeeEccCCCCC
Confidence 3457788888832 345555666655
No 162
>KOG1280|consensus
Probab=48.37 E-value=28 Score=25.04 Aligned_cols=37 Identities=24% Similarity=0.501 Sum_probs=25.4
Q ss_pred ceeeCCCCCCcccCchhHHHHHHh-hcCCC-CeecccCh
Q psy4407 66 YIFTCFACEYHSAKRSHIKEHIRQ-HTGEK-PFSCLLCE 102 (130)
Q Consensus 66 ~~~~C~~C~~~f~~~~~l~~h~~~-h~~~k-~~~C~~C~ 102 (130)
.-|.|+.|+..-.+...+..|... |.... ...|..|.
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 458999999888889999999763 44322 13455554
No 163
>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=48.22 E-value=29 Score=24.58 Aligned_cols=41 Identities=17% Similarity=0.310 Sum_probs=21.3
Q ss_pred eecccccccccC--------ccccccccCCCCCCcccCCCCceeeCCCCCCc
Q psy4407 33 LTCKYCYEFLPN--------DAEIIADHCKFCSYKLRPDKTYIFTCFACEYH 76 (130)
Q Consensus 33 ~~C~~C~~~~~~--------~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~~ 76 (130)
-.|+.||..=.. ...++.-.|..|+.. +.-....|+.||..
T Consensus 185 ~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~te---W~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 185 TLCPACGSPPVASMVRQGGKETGLRYLSCSLCATE---WHYVRVKCSHCEES 233 (305)
T ss_pred CcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCc---ccccCccCCCCCCC
Confidence 468888854211 122222357777442 33334577777753
No 164
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=47.77 E-value=13 Score=24.07 Aligned_cols=23 Identities=30% Similarity=0.761 Sum_probs=16.8
Q ss_pred eecccccccccCccccccccCCCCCCc
Q psy4407 33 LTCKYCYEFLPNDAEIIADHCKFCSYK 59 (130)
Q Consensus 33 ~~C~~C~~~~~~~~~l~~h~c~~C~~~ 59 (130)
+.|.-|++.|. ...+.|+.||..
T Consensus 140 ~rC~GC~~~f~----~~~~~Cp~CG~~ 162 (177)
T COG1439 140 LRCHGCKRIFP----EPKDFCPICGSP 162 (177)
T ss_pred EEEecCceecC----CCCCcCCCCCCc
Confidence 66888999997 233468888765
No 165
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=47.67 E-value=4 Score=31.97 Aligned_cols=66 Identities=18% Similarity=0.314 Sum_probs=38.6
Q ss_pred ecccccccccCccccccc----cCCCCCCc----------ccCCCCce-eeCCCCCCcccCchhHHHHHHhhcCCCCeec
Q psy4407 34 TCKYCYEFLPNDAEIIAD----HCKFCSYK----------LRPDKTYI-FTCFACEYHSAKRSHIKEHIRQHTGEKPFSC 98 (130)
Q Consensus 34 ~C~~C~~~~~~~~~l~~h----~c~~C~~~----------~~h~~~~~-~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C 98 (130)
.|+.|-+.+.++.+..-+ .|..||-. +.++.=+. -.|+.|.+-+....+-+-| .+|..|
T Consensus 103 ~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRfH------AQp~aC 176 (750)
T COG0068 103 TCEDCLEEIFDPNSRRYLYPFINCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRFH------AQPIAC 176 (750)
T ss_pred hhHHHHHHhcCCCCcceeccccccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccccccc------cccccC
Confidence 477777666655554433 57777765 33332222 2577787777666554433 356788
Q ss_pred ccChhhh
Q psy4407 99 LLCEYKA 105 (130)
Q Consensus 99 ~~C~~~f 105 (130)
+.||...
T Consensus 177 p~CGP~~ 183 (750)
T COG0068 177 PKCGPHL 183 (750)
T ss_pred cccCCCe
Confidence 8888743
No 166
>KOG2785|consensus
Probab=47.62 E-value=19 Score=26.20 Aligned_cols=51 Identities=22% Similarity=0.404 Sum_probs=41.3
Q ss_pred ceeeCCCCCCcccCchhHHHHHHhhcCC-----------------------CCeecccCh---hhhcCcchHHHhhh
Q psy4407 66 YIFTCFACEYHSAKRSHIKEHIRQHTGE-----------------------KPFSCLLCE---YKAAKKSNLTKHMS 116 (130)
Q Consensus 66 ~~~~C~~C~~~f~~~~~l~~h~~~h~~~-----------------------k~~~C~~C~---~~f~~~~~l~~h~~ 116 (130)
.|-.|..|+..+.+......||..++|- +.+.|..|. +.|.+....+.||.
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 3567888999999988888998876652 346888888 89999999999994
No 167
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=47.43 E-value=19 Score=24.66 Aligned_cols=53 Identities=13% Similarity=0.221 Sum_probs=29.9
Q ss_pred cccCcceecccccccccCcccccc--ccCCCCCCc------ccCCCCceeeCCCCCCcccC
Q psy4407 27 RFETEMLTCKYCYEFLPNDAEIIA--DHCKFCSYK------LRPDKTYIFTCFACEYHSAK 79 (130)
Q Consensus 27 ~~~~~~~~C~~C~~~~~~~~~l~~--h~c~~C~~~------~~h~~~~~~~C~~C~~~f~~ 79 (130)
-..++.|.|..|+..+-..-.-.. ..|..|.+. ..-.|-.-|.|+.|+..|..
T Consensus 107 p~~drqFaC~~Cd~~WwRrvp~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 107 PSVDRQFACSSCDHMWWRRVPQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred cccceeeeccccchHHHhccCcccccccccccccccCCCccccccceeeeecccccccchh
Confidence 344578999999865432211111 156666554 12234445888888887764
No 168
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=47.38 E-value=26 Score=16.51 Aligned_cols=9 Identities=22% Similarity=0.855 Sum_probs=4.9
Q ss_pred eeCCCCCCc
Q psy4407 68 FTCFACEYH 76 (130)
Q Consensus 68 ~~C~~C~~~ 76 (130)
|.|..|+..
T Consensus 29 y~C~~C~~~ 37 (40)
T smart00440 29 YVCTKCGHR 37 (40)
T ss_pred EEeCCCCCE
Confidence 555555543
No 169
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=46.84 E-value=21 Score=30.28 Aligned_cols=35 Identities=17% Similarity=0.433 Sum_probs=23.4
Q ss_pred eecccccccccCccccccccCCCCCCcccCCCCceeeCCCCCCcc
Q psy4407 33 LTCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACEYHS 77 (130)
Q Consensus 33 ~~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~~f 77 (130)
+.|+.||..-.. ..|+.||... +.++.|+.||...
T Consensus 668 rkCPkCG~~t~~------~fCP~CGs~t----e~vy~CPsCGaev 702 (1337)
T PRK14714 668 RRCPSCGTETYE------NRCPDCGTHT----EPVYVCPDCGAEV 702 (1337)
T ss_pred EECCCCCCcccc------ccCcccCCcC----CCceeCccCCCcc
Confidence 789999985321 1688887743 2246888888653
No 170
>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=45.85 E-value=13 Score=22.80 Aligned_cols=24 Identities=29% Similarity=0.677 Sum_probs=15.4
Q ss_pred eeeCCCCCCcccCchhHHHHHHhhcCC
Q psy4407 67 IFTCFACEYHSAKRSHIKEHIRQHTGE 93 (130)
Q Consensus 67 ~~~C~~C~~~f~~~~~l~~h~~~h~~~ 93 (130)
-..|-+||+.|.. |..|++.|.|-
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~gl 95 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGL 95 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S
T ss_pred eeEEccCCcccch---HHHHHHHccCC
Confidence 3689999998865 58999998664
No 171
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.32 E-value=17 Score=22.16 Aligned_cols=16 Identities=13% Similarity=0.316 Sum_probs=11.0
Q ss_pred CceeeCCCCCCcccCc
Q psy4407 65 TYIFTCFACEYHSAKR 80 (130)
Q Consensus 65 ~~~~~C~~C~~~f~~~ 80 (130)
...|.|..|++.|...
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 4557788888777644
No 172
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=44.41 E-value=36 Score=15.92 Aligned_cols=18 Identities=17% Similarity=0.222 Sum_probs=9.6
Q ss_pred eeeCCCCCCcccCchhHH
Q psy4407 67 IFTCFACEYHSAKRSHIK 84 (130)
Q Consensus 67 ~~~C~~C~~~f~~~~~l~ 84 (130)
...|..|+-.+.....|.
T Consensus 19 id~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 19 IDVCPSCGGIWFDAGELE 36 (41)
T ss_pred EEECCCCCeEEccHHHHH
Confidence 355666665555544443
No 173
>PRK05978 hypothetical protein; Provisional
Probab=44.05 E-value=14 Score=23.09 Aligned_cols=27 Identities=26% Similarity=0.289 Sum_probs=14.5
Q ss_pred eecccccccccCccccccc-cCCCCCCc
Q psy4407 33 LTCKYCYEFLPNDAEIIAD-HCKFCSYK 59 (130)
Q Consensus 33 ~~C~~C~~~~~~~~~l~~h-~c~~C~~~ 59 (130)
-+|+.||+.---...|+-+ .|+.||..
T Consensus 34 grCP~CG~G~LF~g~Lkv~~~C~~CG~~ 61 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPVDHCAACGED 61 (148)
T ss_pred CcCCCCCCCcccccccccCCCccccCCc
Confidence 3577887543223344333 46777665
No 174
>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=43.97 E-value=18 Score=18.12 Aligned_cols=24 Identities=21% Similarity=0.440 Sum_probs=12.3
Q ss_pred ecccccccccCccccccccCCCCCCc
Q psy4407 34 TCKYCYEFLPNDAEIIADHCKFCSYK 59 (130)
Q Consensus 34 ~C~~C~~~~~~~~~l~~h~c~~C~~~ 59 (130)
.|..|++.|.. ....|.|..||..
T Consensus 4 ~C~~C~~~F~~--~~rk~~Cr~Cg~~ 27 (57)
T cd00065 4 SCMGCGKPFTL--TRRRHHCRNCGRI 27 (57)
T ss_pred cCcccCccccC--CccccccCcCcCC
Confidence 35666666653 3334445555443
No 175
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=43.70 E-value=16 Score=19.39 Aligned_cols=9 Identities=22% Similarity=0.497 Sum_probs=4.9
Q ss_pred eeccccccc
Q psy4407 33 LTCKYCYEF 41 (130)
Q Consensus 33 ~~C~~C~~~ 41 (130)
|.|+.||..
T Consensus 1 y~C~KCg~~ 9 (64)
T PF09855_consen 1 YKCPKCGNE 9 (64)
T ss_pred CCCCCCCCc
Confidence 456666643
No 176
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=43.54 E-value=12 Score=19.68 Aligned_cols=25 Identities=16% Similarity=0.460 Sum_probs=10.9
Q ss_pred ecccccccccCccccccccCCCCCC
Q psy4407 34 TCKYCYEFLPNDAEIIADHCKFCSY 58 (130)
Q Consensus 34 ~C~~C~~~~~~~~~l~~h~c~~C~~ 58 (130)
.|.-|++.......+..|.|..|+.
T Consensus 32 lCNDC~~~s~v~fH~lg~KC~~C~S 56 (61)
T PF14599_consen 32 LCNDCNAKSEVPFHFLGHKCSHCGS 56 (61)
T ss_dssp EESSS--EEEEE--TT----TTTS-
T ss_pred ECCCCCCccceeeeHhhhcCCCCCC
Confidence 3777888766666666667777753
No 177
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=43.23 E-value=20 Score=19.42 Aligned_cols=39 Identities=21% Similarity=0.484 Sum_probs=18.8
Q ss_pred cceecccccccccCccccccccCCCCCCc---ccCCCCceeeCCCCC
Q psy4407 31 EMLTCKYCYEFLPNDAEIIADHCKFCSYK---LRPDKTYIFTCFACE 74 (130)
Q Consensus 31 ~~~~C~~C~~~~~~~~~l~~h~c~~C~~~---~~h~~~~~~~C~~C~ 74 (130)
..|.|..|++.|.... .|+.|+.. ...-|...|.|..|.
T Consensus 16 ~~~~C~~C~~~~~~~a-----~CPdC~~~Le~LkACGAvdYFC~~c~ 57 (70)
T PF07191_consen 16 GHYHCEACQKDYKKEA-----FCPDCGQPLEVLKACGAVDYFCNHCH 57 (70)
T ss_dssp TEEEETTT--EEEEEE-----E-TTT-SB-EEEEETTEEEEE-TTTT
T ss_pred CEEECccccccceecc-----cCCCcccHHHHHHHhcccceeeccCC
Confidence 4677888887764322 37777766 112234456666554
No 178
>PRK11823 DNA repair protein RadA; Provisional
Probab=43.13 E-value=19 Score=26.83 Aligned_cols=26 Identities=19% Similarity=0.336 Sum_probs=19.3
Q ss_pred CcceecccccccccCccccccccCCCCCCc
Q psy4407 30 TEMLTCKYCYEFLPNDAEIIADHCKFCSYK 59 (130)
Q Consensus 30 ~~~~~C~~C~~~~~~~~~l~~h~c~~C~~~ 59 (130)
...|.|..||........ .|+.|+..
T Consensus 5 ~~~y~C~~Cg~~~~~~~g----~Cp~C~~w 30 (446)
T PRK11823 5 KTAYVCQECGAESPKWLG----RCPECGAW 30 (446)
T ss_pred CCeEECCcCCCCCcccCe----eCcCCCCc
Confidence 346999999988765443 58888776
No 179
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=43.01 E-value=26 Score=18.83 Aligned_cols=57 Identities=14% Similarity=0.317 Sum_probs=26.4
Q ss_pred ceecccccccccCc---cccccccCCCCCCcccCCCCceeeCCCCCCcccCchhHHHHHHhhcCCCCeecccChh
Q psy4407 32 MLTCKYCYEFLPND---AEIIADHCKFCSYKLRPDKTYIFTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLLCEY 103 (130)
Q Consensus 32 ~~~C~~C~~~~~~~---~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~C~~ 103 (130)
..+++-|++.|.-. ..+..|. ..........|..|+........ ..+ ..+.|+.|+.
T Consensus 10 ~~~~~cC~~~y~C~~CHde~~~H~-------~~~~~~~~v~Cg~C~~~~~~~~~-------~c~-~~~~C~~C~~ 69 (71)
T PF05495_consen 10 AIRFPCCGKYYPCRFCHDELEDHP-------FDRWPVKRVICGKCRTEQPIDEY-------SCG-ADYFCPICGL 69 (71)
T ss_dssp EEEETTTTEEESSHHHHHHCSSS----------TTT--EEEETTT--EEES-SB-------TT---SEEETTTTE
T ss_pred EEECCcccCeecHHHHHHHhccCc-------cccccccCeECCCCCCccChhhh-------hcC-CCccCcCcCC
Confidence 45566677766533 2334443 33334446778888766554433 111 4567777764
No 180
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=42.31 E-value=17 Score=18.91 Aligned_cols=25 Identities=24% Similarity=0.717 Sum_probs=15.2
Q ss_pred CCceeeCCCCCCcccCc---hhHHHHHH
Q psy4407 64 KTYIFTCFACEYHSAKR---SHIKEHIR 88 (130)
Q Consensus 64 ~~~~~~C~~C~~~f~~~---~~l~~h~~ 88 (130)
....|.|..||..+-.. .+...|.+
T Consensus 8 ~~~lw~CL~Cg~~~C~~~~~~Ha~~H~~ 35 (63)
T PF02148_consen 8 NSNLWLCLTCGYVGCGRYSNGHALKHYK 35 (63)
T ss_dssp SSSEEEETTTS-EEETTTSTSHHHHHHH
T ss_pred CCceEEeCCCCcccccCCcCcHHHHhhc
Confidence 35578888888777664 34444543
No 181
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=42.18 E-value=19 Score=19.98 Aligned_cols=27 Identities=26% Similarity=0.603 Sum_probs=16.1
Q ss_pred eeccccccc-ccCccccccccCCCCCCc
Q psy4407 33 LTCKYCYEF-LPNDAEIIADHCKFCSYK 59 (130)
Q Consensus 33 ~~C~~C~~~-~~~~~~l~~h~c~~C~~~ 59 (130)
|.|+-||.. |.....-.-.+|+.|.+.
T Consensus 2 ~~CPCCg~~Tl~~~~~~~ydIC~VC~WE 29 (78)
T PF14206_consen 2 YPCPCCGYYTLEERGEGTYDICPVCFWE 29 (78)
T ss_pred ccCCCCCcEEeccCCCcCceECCCCCcc
Confidence 578888854 333333224478888776
No 182
>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=42.10 E-value=20 Score=22.63 Aligned_cols=19 Identities=11% Similarity=0.078 Sum_probs=12.6
Q ss_pred CceeeCCCCCCcccCchhH
Q psy4407 65 TYIFTCFACEYHSAKRSHI 83 (130)
Q Consensus 65 ~~~~~C~~C~~~f~~~~~l 83 (130)
+.|..|..||+.|......
T Consensus 66 ~~PsYC~~CGkpyPWt~~~ 84 (158)
T PF10083_consen 66 EAPSYCHNCGKPYPWTENA 84 (158)
T ss_pred CCChhHHhCCCCCchHHHH
Confidence 4667777777777765443
No 183
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=42.09 E-value=23 Score=27.80 Aligned_cols=36 Identities=22% Similarity=0.523 Sum_probs=20.3
Q ss_pred ecccccccccCccccccccCCCCCCcccCCCCceeeCCCCCCccc
Q psy4407 34 TCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACEYHSA 78 (130)
Q Consensus 34 ~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~~f~ 78 (130)
-|..||..+.. -.|+.||.. ...+.+ .|+.||....
T Consensus 17 FC~~CG~~l~~------~~Cp~CG~~-~~~~~~--fC~~CG~~~~ 52 (645)
T PRK14559 17 FCQKCGTSLTH------KPCPQCGTE-VPVDEA--HCPNCGAETG 52 (645)
T ss_pred cccccCCCCCC------CcCCCCCCC-CCcccc--cccccCCccc
Confidence 36677666532 247777763 333332 6777775543
No 184
>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=41.92 E-value=17 Score=27.09 Aligned_cols=25 Identities=20% Similarity=0.395 Sum_probs=18.2
Q ss_pred cceecccccccccCccccccccCCCCCCc
Q psy4407 31 EMLTCKYCYEFLPNDAEIIADHCKFCSYK 59 (130)
Q Consensus 31 ~~~~C~~C~~~~~~~~~l~~h~c~~C~~~ 59 (130)
..|.|..||........ +|+.|+..
T Consensus 6 ~~y~C~~Cg~~~~~~~g----~Cp~C~~w 30 (454)
T TIGR00416 6 SKFVCQHCGADSPKWQG----KCPACHAW 30 (454)
T ss_pred CeEECCcCCCCCccccE----ECcCCCCc
Confidence 35999999988755433 58888766
No 185
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=41.71 E-value=30 Score=16.42 Aligned_cols=23 Identities=26% Similarity=0.349 Sum_probs=12.5
Q ss_pred eeCCCCCCcccCc--hhHHHHHHhh
Q psy4407 68 FTCFACEYHSAKR--SHIKEHIRQH 90 (130)
Q Consensus 68 ~~C~~C~~~f~~~--~~l~~h~~~h 90 (130)
-.|+.||..+... .....|.+.|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 4677777555432 3445555544
No 186
>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=41.57 E-value=14 Score=18.70 Aligned_cols=22 Identities=14% Similarity=0.403 Sum_probs=11.5
Q ss_pred CcceecccccccccCccccccc
Q psy4407 30 TEMLTCKYCYEFLPNDAEIIAD 51 (130)
Q Consensus 30 ~~~~~C~~C~~~~~~~~~l~~h 51 (130)
...|+|+.|+..|...-++-.|
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiH 40 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIH 40 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTT
T ss_pred CCeEECCCCCCccccCcChhhh
Confidence 4679999999999876555444
No 187
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=40.74 E-value=13 Score=22.77 Aligned_cols=10 Identities=20% Similarity=0.550 Sum_probs=4.7
Q ss_pred eeCCCCCCcc
Q psy4407 68 FTCFACEYHS 77 (130)
Q Consensus 68 ~~C~~C~~~f 77 (130)
+.|..||..|
T Consensus 71 ~~C~~CG~~~ 80 (135)
T PRK03824 71 LKCRNCGNEW 80 (135)
T ss_pred EECCCCCCEE
Confidence 4455554444
No 188
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=40.62 E-value=20 Score=21.65 Aligned_cols=16 Identities=19% Similarity=0.048 Sum_probs=10.4
Q ss_pred cCcceecccccccccCc
Q psy4407 29 ETEMLTCKYCYEFLPND 45 (130)
Q Consensus 29 ~~~~~~C~~C~~~~~~~ 45 (130)
-...+.| .||..|...
T Consensus 67 vp~~~~C-~Cg~~~~~~ 82 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVD 82 (124)
T ss_pred cCeeEEe-eCcCccccc
Confidence 3445778 888776543
No 189
>PHA02942 putative transposase; Provisional
Probab=40.61 E-value=32 Score=25.08 Aligned_cols=29 Identities=24% Similarity=0.557 Sum_probs=16.8
Q ss_pred ccCCCCCCcccCCCCceeeCCCCCCcccC
Q psy4407 51 DHCKFCSYKLRPDKTYIFTCFACEYHSAK 79 (130)
Q Consensus 51 h~c~~C~~~~~h~~~~~~~C~~C~~~f~~ 79 (130)
..|+.||......+.+.|.|..||.....
T Consensus 326 q~Cs~CG~~~~~l~~r~f~C~~CG~~~dr 354 (383)
T PHA02942 326 VSCPKCGHKMVEIAHRYFHCPSCGYENDR 354 (383)
T ss_pred ccCCCCCCccCcCCCCEEECCCCCCEeCc
Confidence 35777776432223456777777765543
No 190
>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=40.57 E-value=17 Score=16.59 Aligned_cols=9 Identities=33% Similarity=1.058 Sum_probs=4.2
Q ss_pred eCCCCCCcc
Q psy4407 69 TCFACEYHS 77 (130)
Q Consensus 69 ~C~~C~~~f 77 (130)
.|..|+..+
T Consensus 22 ~C~~C~Y~~ 30 (35)
T PF02150_consen 22 ACRTCGYEE 30 (35)
T ss_dssp EESSSS-EE
T ss_pred CCCCCCCcc
Confidence 455555443
No 191
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=39.84 E-value=21 Score=22.36 Aligned_cols=17 Identities=12% Similarity=0.313 Sum_probs=11.3
Q ss_pred eeCCCCCCcccCchhHH
Q psy4407 68 FTCFACEYHSAKRSHIK 84 (130)
Q Consensus 68 ~~C~~C~~~f~~~~~l~ 84 (130)
=.|..|++.|.+...+.
T Consensus 29 ReC~~C~~RFTTyErve 45 (147)
T TIGR00244 29 RECLECHERFTTFERAE 45 (147)
T ss_pred ccCCccCCccceeeecc
Confidence 36778888877665543
No 192
>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=39.83 E-value=18 Score=26.26 Aligned_cols=23 Identities=22% Similarity=0.381 Sum_probs=14.9
Q ss_pred eecccccccccCccccccccCCCCCCc
Q psy4407 33 LTCKYCYEFLPNDAEIIADHCKFCSYK 59 (130)
Q Consensus 33 ~~C~~C~~~~~~~~~l~~h~c~~C~~~ 59 (130)
|.|..||.....+.. +|+.|+..
T Consensus 1 ~~c~~cg~~~~~~~g----~cp~c~~w 23 (372)
T cd01121 1 YVCSECGYVSPKWLG----KCPECGEW 23 (372)
T ss_pred CCCCCCCCCCCCccE----ECcCCCCc
Confidence 567888877654333 57777665
No 193
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=39.52 E-value=23 Score=17.86 Aligned_cols=9 Identities=22% Similarity=0.475 Sum_probs=3.9
Q ss_pred CCeecccCh
Q psy4407 94 KPFSCLLCE 102 (130)
Q Consensus 94 k~~~C~~C~ 102 (130)
....|+.||
T Consensus 45 ~i~~Cp~Cg 53 (56)
T PF02591_consen 45 EIVFCPNCG 53 (56)
T ss_pred CeEECcCCC
Confidence 334444444
No 194
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.48 E-value=8.1 Score=26.07 Aligned_cols=17 Identities=12% Similarity=0.487 Sum_probs=9.1
Q ss_pred CcceecccccccccCcc
Q psy4407 30 TEMLTCKYCYEFLPNDA 46 (130)
Q Consensus 30 ~~~~~C~~C~~~~~~~~ 46 (130)
++...|++|+-.|....
T Consensus 17 kk~ieCPvC~tkFkkee 33 (267)
T COG1655 17 KKTIECPVCNTKFKKEE 33 (267)
T ss_pred hceeccCcccchhhhhh
Confidence 44555666666555433
No 195
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=38.88 E-value=26 Score=17.94 Aligned_cols=9 Identities=22% Similarity=0.837 Sum_probs=4.7
Q ss_pred ceeeCCCCC
Q psy4407 66 YIFTCFACE 74 (130)
Q Consensus 66 ~~~~C~~C~ 74 (130)
-|..|+.|-
T Consensus 27 fPlyCpKCK 35 (55)
T PF14205_consen 27 FPLYCPKCK 35 (55)
T ss_pred ccccCCCCC
Confidence 345555554
No 196
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=38.70 E-value=29 Score=16.57 Aligned_cols=22 Identities=32% Similarity=0.629 Sum_probs=9.4
Q ss_pred CCCCCCcccCCCCceeeCCCCC
Q psy4407 53 CKFCSYKLRPDKTYIFTCFACE 74 (130)
Q Consensus 53 c~~C~~~~~h~~~~~~~C~~C~ 74 (130)
|+.|+.......+....|..|+
T Consensus 20 Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 20 CPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred cCCCCCeeEEecCCCEECCCCC
Confidence 5555544222222234566553
No 197
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=38.53 E-value=24 Score=18.34 Aligned_cols=29 Identities=14% Similarity=0.360 Sum_probs=15.3
Q ss_pred eecccccccccCccccccccCCCCCCcccCCCCceeeCCCCC
Q psy4407 33 LTCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACE 74 (130)
Q Consensus 33 ~~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~ 74 (130)
|.|+ ||..|... |. ....|+..-.|+.|.
T Consensus 23 yPCP-CGDRFeIs--Le----------Dl~~GE~VArCPSCS 51 (67)
T COG5216 23 YPCP-CGDRFEIS--LE----------DLRNGEVVARCPSCS 51 (67)
T ss_pred ecCC-CCCEeEEE--HH----------HhhCCceEEEcCCce
Confidence 5564 77777432 21 223455555666654
No 198
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=38.28 E-value=22 Score=21.12 Aligned_cols=13 Identities=15% Similarity=0.572 Sum_probs=6.9
Q ss_pred cceeccccccccc
Q psy4407 31 EMLTCKYCYEFLP 43 (130)
Q Consensus 31 ~~~~C~~C~~~~~ 43 (130)
..+.|..||..|.
T Consensus 69 ~~~~C~~Cg~~~~ 81 (114)
T PRK03681 69 AECWCETCQQYVT 81 (114)
T ss_pred cEEEcccCCCeee
Confidence 3355666665543
No 199
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=38.25 E-value=25 Score=15.50 Aligned_cols=10 Identities=20% Similarity=0.574 Sum_probs=4.1
Q ss_pred ceeeCCCCCC
Q psy4407 66 YIFTCFACEY 75 (130)
Q Consensus 66 ~~~~C~~C~~ 75 (130)
..-.|+.|+.
T Consensus 20 ~~r~C~~Cg~ 29 (32)
T PF09297_consen 20 WARRCPSCGH 29 (32)
T ss_dssp S-EEESSSS-
T ss_pred CEeECCCCcC
Confidence 3345555553
No 200
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=37.58 E-value=56 Score=18.74 Aligned_cols=29 Identities=21% Similarity=0.311 Sum_probs=18.4
Q ss_pred CcceecccccccccCc---cccccccCCCCCCc
Q psy4407 30 TEMLTCKYCYEFLPND---AEIIADHCKFCSYK 59 (130)
Q Consensus 30 ~~~~~C~~C~~~~~~~---~~l~~h~c~~C~~~ 59 (130)
...|.|..||...... +....| |+.|-..
T Consensus 2 ~~~F~C~~CG~~V~p~~~g~~~RNH-CP~CL~S 33 (92)
T PF12647_consen 2 NESFTCVHCGLTVSPLAAGSAHRNH-CPSCLSS 33 (92)
T ss_pred CcccCccccCCCcccCCCCCCccCc-Ccccccc
Confidence 3568999999866432 223444 7777665
No 201
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=36.98 E-value=11 Score=24.59 Aligned_cols=30 Identities=17% Similarity=0.248 Sum_probs=23.2
Q ss_pred CcceecccccccccCccccccccCCCCCCc
Q psy4407 30 TEMLTCKYCYEFLPNDAEIIADHCKFCSYK 59 (130)
Q Consensus 30 ~~~~~C~~C~~~~~~~~~l~~h~c~~C~~~ 59 (130)
.++-+|..||..|.....+...-++.|+..
T Consensus 4 ~k~rKCKvCg~~F~P~~s~q~vCSpeCa~a 33 (189)
T PF05766_consen 4 PKRRKCKVCGEWFVPARSNQKVCSPECAIA 33 (189)
T ss_pred CCCCcCcccCCccccCCCceeeeCHHHHhH
Confidence 356789999999987777776667888853
No 202
>KOG3507|consensus
Probab=36.60 E-value=27 Score=18.16 Aligned_cols=14 Identities=21% Similarity=0.551 Sum_probs=8.7
Q ss_pred CCeecccChhhhcC
Q psy4407 94 KPFSCLLCEYKAAK 107 (130)
Q Consensus 94 k~~~C~~C~~~f~~ 107 (130)
-.+.|.+||....+
T Consensus 36 D~irCReCG~RIly 49 (62)
T KOG3507|consen 36 DVIRCRECGYRILY 49 (62)
T ss_pred CcEehhhcchHHHH
Confidence 35677777765543
No 203
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=36.52 E-value=38 Score=19.96 Aligned_cols=23 Identities=17% Similarity=0.157 Sum_probs=15.9
Q ss_pred CceeeCCCCCCcccCchhHHHHH
Q psy4407 65 TYIFTCFACEYHSAKRSHIKEHI 87 (130)
Q Consensus 65 ~~~~~C~~C~~~f~~~~~l~~h~ 87 (130)
..-+.|..||..+.+........
T Consensus 29 ~~~~~C~~CGe~~~~~e~~~~~~ 51 (127)
T TIGR03830 29 VPGWYCPACGEELLDPEESKRNS 51 (127)
T ss_pred eeeeECCCCCCEEEcHHHHHHHH
Confidence 34478999998888776655443
No 204
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=36.48 E-value=6.3 Score=25.92 Aligned_cols=18 Identities=17% Similarity=0.179 Sum_probs=12.8
Q ss_pred ccCcceecccccccccCc
Q psy4407 28 FETEMLTCKYCYEFLPND 45 (130)
Q Consensus 28 ~~~~~~~C~~C~~~~~~~ 45 (130)
.++-||.|..|.+.|.+.
T Consensus 192 ~e~IPF~C~iCKkdy~sp 209 (259)
T COG5152 192 GEKIPFLCGICKKDYESP 209 (259)
T ss_pred CCCCceeehhchhhccch
Confidence 345678888888887654
No 205
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=36.38 E-value=26 Score=26.09 Aligned_cols=25 Identities=20% Similarity=0.413 Sum_probs=19.4
Q ss_pred cceecccccccccCccccccccCCCCCCc
Q psy4407 31 EMLTCKYCYEFLPNDAEIIADHCKFCSYK 59 (130)
Q Consensus 31 ~~~~C~~C~~~~~~~~~l~~h~c~~C~~~ 59 (130)
..|.|..||.....+.. +|+.|+..
T Consensus 6 t~f~C~~CG~~s~KW~G----kCp~Cg~W 30 (456)
T COG1066 6 TAFVCQECGYVSPKWLG----KCPACGAW 30 (456)
T ss_pred cEEEcccCCCCCccccc----cCCCCCCc
Confidence 56999999988765444 69999876
No 206
>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=35.26 E-value=18 Score=22.34 Aligned_cols=18 Identities=11% Similarity=0.213 Sum_probs=13.4
Q ss_pred hcccCcceecccccccccC
Q psy4407 26 FRFETEMLTCKYCYEFLPN 44 (130)
Q Consensus 26 ~~~~~~~~~C~~C~~~~~~ 44 (130)
.+.+ ++.+|+.||..|.-
T Consensus 107 l~~g-~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 107 LHKG-KPQRCPECGQVFKL 124 (136)
T ss_dssp EETT-SEEEETTTEEEEEE
T ss_pred EeCC-CccCCCCCCeEEEE
Confidence 3444 58899999998863
No 207
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=34.70 E-value=56 Score=15.75 Aligned_cols=15 Identities=13% Similarity=0.341 Sum_probs=8.9
Q ss_pred CCceeeCCCCCCccc
Q psy4407 64 KTYIFTCFACEYHSA 78 (130)
Q Consensus 64 ~~~~~~C~~C~~~f~ 78 (130)
......|..|+..|.
T Consensus 11 ~~~~i~C~~C~~~~H 25 (51)
T PF00628_consen 11 DGDMIQCDSCNRWYH 25 (51)
T ss_dssp TSSEEEBSTTSCEEE
T ss_pred CCCeEEcCCCChhhC
Confidence 344566777776654
No 208
>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=34.51 E-value=32 Score=15.90 Aligned_cols=11 Identities=18% Similarity=0.585 Sum_probs=5.0
Q ss_pred CCCceeeCCCC
Q psy4407 63 DKTYIFTCFAC 73 (130)
Q Consensus 63 ~~~~~~~C~~C 73 (130)
.|...|.|..|
T Consensus 25 ~G~qryrC~~C 35 (36)
T PF03811_consen 25 SGHQRYRCKDC 35 (36)
T ss_pred CCCEeEecCcC
Confidence 34444555444
No 209
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=34.46 E-value=21 Score=22.10 Aligned_cols=23 Identities=22% Similarity=0.493 Sum_probs=15.9
Q ss_pred ecccccccccCccccccccCCCCCCc
Q psy4407 34 TCKYCYEFLPNDAEIIADHCKFCSYK 59 (130)
Q Consensus 34 ~C~~C~~~~~~~~~l~~h~c~~C~~~ 59 (130)
-|+.||+.|... ..-.|+.|...
T Consensus 5 nC~~CgklF~~~---~~~iCp~C~~~ 27 (137)
T TIGR03826 5 NCPKCGRLFVKT---GRDVCPSCYEE 27 (137)
T ss_pred cccccchhhhhc---CCccCHHHhHH
Confidence 488899988762 22358888765
No 210
>PRK11032 hypothetical protein; Provisional
Probab=33.94 E-value=35 Score=21.70 Aligned_cols=12 Identities=33% Similarity=0.700 Sum_probs=6.5
Q ss_pred cceecccccccc
Q psy4407 31 EMLTCKYCYEFL 42 (130)
Q Consensus 31 ~~~~C~~C~~~~ 42 (130)
....|..||...
T Consensus 123 G~LvC~~Cg~~~ 134 (160)
T PRK11032 123 GNLVCEKCHHHL 134 (160)
T ss_pred ceEEecCCCCEE
Confidence 335566666543
No 211
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=33.69 E-value=11 Score=27.04 Aligned_cols=9 Identities=44% Similarity=0.807 Sum_probs=3.6
Q ss_pred eeccccccc
Q psy4407 33 LTCKYCYEF 41 (130)
Q Consensus 33 ~~C~~C~~~ 41 (130)
+.|..|...
T Consensus 253 v~C~~C~yt 261 (344)
T PF09332_consen 253 VTCKQCKYT 261 (344)
T ss_dssp EEETTT--E
T ss_pred EEcCCCCCc
Confidence 445555543
No 212
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=33.38 E-value=46 Score=19.11 Aligned_cols=10 Identities=30% Similarity=0.607 Sum_probs=7.2
Q ss_pred CeecccChhh
Q psy4407 95 PFSCLLCEYK 104 (130)
Q Consensus 95 ~~~C~~C~~~ 104 (130)
...|..||..
T Consensus 62 ~~~Cp~Cg~~ 71 (104)
T TIGR01384 62 RVECPKCGHK 71 (104)
T ss_pred cCCCCCCCCC
Confidence 3688888864
No 213
>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=33.19 E-value=25 Score=16.74 Aligned_cols=12 Identities=25% Similarity=0.597 Sum_probs=8.3
Q ss_pred cceecccccccc
Q psy4407 31 EMLTCKYCYEFL 42 (130)
Q Consensus 31 ~~~~C~~C~~~~ 42 (130)
++-.|+.||..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 456788887765
No 214
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=31.96 E-value=12 Score=22.23 Aligned_cols=14 Identities=14% Similarity=0.150 Sum_probs=7.8
Q ss_pred cceecccccccccC
Q psy4407 31 EMLTCKYCYEFLPN 44 (130)
Q Consensus 31 ~~~~C~~C~~~~~~ 44 (130)
....|..|+..|..
T Consensus 53 ~~~~C~~C~~~fg~ 66 (118)
T PF02318_consen 53 GERHCARCGKPFGF 66 (118)
T ss_dssp CCSB-TTTS-BCSC
T ss_pred CCcchhhhCCcccc
Confidence 34568888887653
No 215
>KOG2906|consensus
Probab=31.61 E-value=43 Score=19.44 Aligned_cols=15 Identities=27% Similarity=0.569 Sum_probs=10.2
Q ss_pred ceeeCCCCCCcccCc
Q psy4407 66 YIFTCFACEYHSAKR 80 (130)
Q Consensus 66 ~~~~C~~C~~~f~~~ 80 (130)
..+.|..|+..|.-+
T Consensus 20 ~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 20 NRFSCRTCPYVFPIS 34 (105)
T ss_pred eeEEcCCCCceeeEe
Confidence 457788888776644
No 216
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=31.29 E-value=34 Score=17.62 Aligned_cols=9 Identities=33% Similarity=0.685 Sum_probs=5.3
Q ss_pred eeccccccc
Q psy4407 33 LTCKYCYEF 41 (130)
Q Consensus 33 ~~C~~C~~~ 41 (130)
..|+.||..
T Consensus 28 ~~C~~CG~~ 36 (57)
T PRK12286 28 VECPNCGEP 36 (57)
T ss_pred eECCCCCCc
Confidence 446666654
No 217
>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=30.94 E-value=23 Score=19.65 Aligned_cols=42 Identities=14% Similarity=0.334 Sum_probs=14.5
Q ss_pred ccCcceecccccccccCccccccccCCCCCCcccCCCCceeeCCCCCCcccCc
Q psy4407 28 FETEMLTCKYCYEFLPNDAEIIADHCKFCSYKLRPDKTYIFTCFACEYHSAKR 80 (130)
Q Consensus 28 ~~~~~~~C~~C~~~~~~~~~l~~h~c~~C~~~~~h~~~~~~~C~~C~~~f~~~ 80 (130)
.-++.|.|+.|+-.-.-.-.+ ....+.....|..|+..|...
T Consensus 18 ~l~~~F~CPfC~~~~sV~v~i-----------dkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 18 KLPKVFDCPFCNHEKSVSVKI-----------DKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp --SS----TTT--SS-EEEEE-----------ETTTTEEEEEESSS--EEEEE
T ss_pred CCCceEcCCcCCCCCeEEEEE-----------EccCCEEEEEecCCCCeEEEc
Confidence 344668888887321111111 112333446777777666543
No 218
>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=30.91 E-value=30 Score=16.98 Aligned_cols=13 Identities=23% Similarity=0.679 Sum_probs=7.6
Q ss_pred Ccceecccccccc
Q psy4407 30 TEMLTCKYCYEFL 42 (130)
Q Consensus 30 ~~~~~C~~C~~~~ 42 (130)
..+-.|..|++..
T Consensus 9 ~~~~~C~~C~~~i 21 (53)
T PF00130_consen 9 SKPTYCDVCGKFI 21 (53)
T ss_dssp SSTEB-TTSSSBE
T ss_pred CCCCCCcccCccc
Confidence 4555677777665
No 219
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=30.89 E-value=1.5e+02 Score=18.98 Aligned_cols=57 Identities=26% Similarity=0.402 Sum_probs=34.6
Q ss_pred eeeCCCCCCcccCchhHHHHHHhhcCCCCeeccc--Chhhhc-CcchHHHhhhhcCCCCCCCCcc
Q psy4407 67 IFTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLL--CEYKAA-KKSNLTKHMSKKHPSSYEDPFF 128 (130)
Q Consensus 67 ~~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~--C~~~f~-~~~~l~~h~~~~h~g~~e~~~~ 128 (130)
...|+.|--......... --+.+-..|+-.|.. |. |. .-..|++|.|..|.. -+|-+
T Consensus 80 ~L~CPLCRG~V~GWtvve-~AR~~LN~K~RsC~~e~C~--F~GtY~eLrKHar~~HP~--~rP~~ 139 (162)
T PF07800_consen 80 ELACPLCRGEVKGWTVVE-PARRFLNAKKRSCSQESCS--FSGTYSELRKHARSEHPS--ARPSE 139 (162)
T ss_pred cccCccccCceeceEEch-HHHHHhccCCccCcccccc--cccCHHHHHHHHHhhCCC--CCCcc
Confidence 456777754433333332 244555567777754 54 44 455788999888888 77744
No 220
>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=30.62 E-value=39 Score=15.83 Aligned_cols=12 Identities=17% Similarity=0.362 Sum_probs=5.6
Q ss_pred CCceeeCCCCCC
Q psy4407 64 KTYIFTCFACEY 75 (130)
Q Consensus 64 ~~~~~~C~~C~~ 75 (130)
+.+.|.|..|+.
T Consensus 21 ~~~~w~C~~C~~ 32 (40)
T PF04810_consen 21 GGKTWICNFCGT 32 (40)
T ss_dssp TTTEEEETTT--
T ss_pred CCCEEECcCCCC
Confidence 344566666654
No 221
>PF14149 YhfH: YhfH-like protein
Probab=30.47 E-value=8 Score=18.11 Aligned_cols=11 Identities=18% Similarity=0.516 Sum_probs=7.2
Q ss_pred ecccccccccC
Q psy4407 34 TCKYCYEFLPN 44 (130)
Q Consensus 34 ~C~~C~~~~~~ 44 (130)
.|..||+....
T Consensus 15 ~C~~CG~~i~E 25 (37)
T PF14149_consen 15 KCTECGKEIEE 25 (37)
T ss_pred ccHHHHHHHHH
Confidence 47778876543
No 222
>PF14369 zf-RING_3: zinc-finger
Probab=30.46 E-value=48 Score=15.13 Aligned_cols=10 Identities=20% Similarity=0.384 Sum_probs=6.1
Q ss_pred eCCCCCCccc
Q psy4407 69 TCFACEYHSA 78 (130)
Q Consensus 69 ~C~~C~~~f~ 78 (130)
.|+.|+.+|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 4666666653
No 223
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=30.40 E-value=68 Score=18.63 Aligned_cols=11 Identities=18% Similarity=0.712 Sum_probs=7.6
Q ss_pred Ccceecccccc
Q psy4407 30 TEMLTCKYCYE 40 (130)
Q Consensus 30 ~~~~~C~~C~~ 40 (130)
...|.|+.|+.
T Consensus 19 pt~f~CP~Cge 29 (99)
T PRK14892 19 PKIFECPRCGK 29 (99)
T ss_pred CcEeECCCCCC
Confidence 34577888883
No 224
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=30.15 E-value=31 Score=21.73 Aligned_cols=14 Identities=14% Similarity=0.418 Sum_probs=8.7
Q ss_pred eCCCCCCcccCchh
Q psy4407 69 TCFACEYHSAKRSH 82 (130)
Q Consensus 69 ~C~~C~~~f~~~~~ 82 (130)
.|..|+..|.+...
T Consensus 30 eC~~C~~RFTTfE~ 43 (156)
T COG1327 30 ECLECGERFTTFER 43 (156)
T ss_pred cccccccccchhhe
Confidence 56777766665543
No 225
>PF12907 zf-met2: Zinc-binding
Probab=29.89 E-value=29 Score=16.54 Aligned_cols=9 Identities=22% Similarity=0.681 Sum_probs=3.7
Q ss_pred ecccChhhh
Q psy4407 97 SCLLCEYKA 105 (130)
Q Consensus 97 ~C~~C~~~f 105 (130)
.|.+|...|
T Consensus 3 ~C~iC~qtF 11 (40)
T PF12907_consen 3 ICKICRQTF 11 (40)
T ss_pred CcHHhhHHH
Confidence 344444333
No 226
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=29.73 E-value=46 Score=21.02 Aligned_cols=34 Identities=29% Similarity=0.649 Sum_probs=17.5
Q ss_pred CceeeCCCCCCcccCchhHHHHHHhhcCCCCeecccChh
Q psy4407 65 TYIFTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLLCEY 103 (130)
Q Consensus 65 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~C~~ 103 (130)
..+|.|. |+..+.+. +.|-..-.|+ .|.|..|+.
T Consensus 115 ~~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~g 148 (156)
T COG3091 115 TYPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGG 148 (156)
T ss_pred ceeEEee-cCCccchh---hhcccccccc-eEEeccCCc
Confidence 3456666 66655443 3333333444 566666654
No 227
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=29.47 E-value=95 Score=19.63 Aligned_cols=12 Identities=17% Similarity=0.645 Sum_probs=3.1
Q ss_pred CCCeecccChhh
Q psy4407 93 EKPFSCLLCEYK 104 (130)
Q Consensus 93 ~k~~~C~~C~~~ 104 (130)
+-...|-.||-.
T Consensus 58 dt~leCy~Cg~~ 69 (152)
T PF09416_consen 58 DTVLECYNCGSR 69 (152)
T ss_dssp S-B---TTT---
T ss_pred CcEEEEEecCCC
Confidence 344677777653
No 228
>PHA02998 RNA polymerase subunit; Provisional
Probab=29.26 E-value=62 Score=21.07 Aligned_cols=12 Identities=17% Similarity=0.395 Sum_probs=8.0
Q ss_pred eecccChhhhcC
Q psy4407 96 FSCLLCEYKAAK 107 (130)
Q Consensus 96 ~~C~~C~~~f~~ 107 (130)
|.|..|+..|..
T Consensus 172 YkC~~CG~~wkp 183 (195)
T PHA02998 172 HACRDCKKHFKP 183 (195)
T ss_pred EEcCCCCCccCC
Confidence 677777776643
No 229
>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=29.01 E-value=83 Score=18.42 Aligned_cols=9 Identities=33% Similarity=0.932 Sum_probs=5.1
Q ss_pred ceecccccc
Q psy4407 32 MLTCKYCYE 40 (130)
Q Consensus 32 ~~~C~~C~~ 40 (130)
|-.|+.||.
T Consensus 2 p~~CpYCg~ 10 (102)
T PF11672_consen 2 PIICPYCGG 10 (102)
T ss_pred CcccCCCCC
Confidence 445666664
No 230
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=28.67 E-value=64 Score=17.14 Aligned_cols=10 Identities=30% Similarity=0.604 Sum_probs=6.2
Q ss_pred eeeCCCCCCc
Q psy4407 67 IFTCFACEYH 76 (130)
Q Consensus 67 ~~~C~~C~~~ 76 (130)
.+.|..|+..
T Consensus 27 ~v~C~~CgA~ 36 (64)
T PRK09710 27 RAKCNGCESR 36 (64)
T ss_pred EEEcCCCCcC
Confidence 3567777653
No 231
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=28.28 E-value=51 Score=19.47 Aligned_cols=13 Identities=15% Similarity=0.243 Sum_probs=7.2
Q ss_pred cCcceeccccccc
Q psy4407 29 ETEMLTCKYCYEF 41 (130)
Q Consensus 29 ~~~~~~C~~C~~~ 41 (130)
|-..+.|+.||..
T Consensus 39 G~~~~~C~~Cg~~ 51 (111)
T PF14319_consen 39 GFHRYRCEDCGHE 51 (111)
T ss_pred CcceeecCCCCce
Confidence 4445666666654
No 232
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=28.04 E-value=76 Score=14.77 Aligned_cols=9 Identities=22% Similarity=0.604 Sum_probs=4.9
Q ss_pred ceeeCCCCC
Q psy4407 66 YIFTCFACE 74 (130)
Q Consensus 66 ~~~~C~~C~ 74 (130)
..+.|..|+
T Consensus 24 G~~~C~~Cg 32 (37)
T smart00778 24 GTWFCSVCG 32 (37)
T ss_pred cCEEeCCCC
Confidence 345666554
No 233
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=27.94 E-value=30 Score=23.40 Aligned_cols=16 Identities=19% Similarity=0.353 Sum_probs=12.7
Q ss_pred cCcceecccccccccC
Q psy4407 29 ETEMLTCKYCYEFLPN 44 (130)
Q Consensus 29 ~~~~~~C~~C~~~~~~ 44 (130)
+.++.+|++||..|.-
T Consensus 178 EGkpqRCpECGqVFKL 193 (268)
T PTZ00043 178 EGFLYRCGECDQIFML 193 (268)
T ss_pred CCCCccCCCCCcEEEE
Confidence 4458899999999864
No 234
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=27.48 E-value=64 Score=16.15 Aligned_cols=34 Identities=18% Similarity=0.494 Sum_probs=15.1
Q ss_pred eeeCCC-CCCcccCchhHHHHHHhhcCCCCeeccc
Q psy4407 67 IFTCFA-CEYHSAKRSHIKEHIRQHTGEKPFSCLL 100 (130)
Q Consensus 67 ~~~C~~-C~~~f~~~~~l~~h~~~h~~~k~~~C~~ 100 (130)
+..|+. |+..-.....|..|+...=..++..|..
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPY 43 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS
T ss_pred EeeCCCCCcccceeHHHHHHHHHccCCCCcEECCC
Confidence 345555 3322223456666766433345556665
No 235
>KOG0782|consensus
Probab=26.87 E-value=15 Score=28.43 Aligned_cols=31 Identities=13% Similarity=0.076 Sum_probs=20.6
Q ss_pred ccceehhhhhcccCcceecccccccccCcccc
Q psy4407 17 SGLKVSEVDFRFETEMLTCKYCYEFLPNDAEI 48 (130)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~l 48 (130)
+++..|| =.|.....-+|..||+.|..+..+
T Consensus 239 ~~fvrHH-WVHrrRqeGkC~~CgKgFQQKf~F 269 (1004)
T KOG0782|consen 239 SGFVRHH-WVHRRRQEGKCNTCGKGFQQKFFF 269 (1004)
T ss_pred ccchHHh-HhhHhhhccccchhhhhhhhheee
Confidence 3566665 355555666788999888766543
No 236
>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=26.72 E-value=53 Score=20.23 Aligned_cols=11 Identities=18% Similarity=0.733 Sum_probs=5.4
Q ss_pred eeeCCCCCCcc
Q psy4407 67 IFTCFACEYHS 77 (130)
Q Consensus 67 ~~~C~~C~~~f 77 (130)
.|.|..|+..+
T Consensus 123 ~~~C~~C~~~~ 133 (157)
T PF10263_consen 123 VYRCPSCGREY 133 (157)
T ss_pred EEEcCCCCCEe
Confidence 34555555444
No 237
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=26.61 E-value=55 Score=24.69 Aligned_cols=18 Identities=11% Similarity=0.137 Sum_probs=13.1
Q ss_pred ccCcceecccccccccCc
Q psy4407 28 FETEMLTCKYCYEFLPND 45 (130)
Q Consensus 28 ~~~~~~~C~~C~~~~~~~ 45 (130)
.....|+|..||..|...
T Consensus 421 ~~~~~~~c~~c~~~yd~~ 438 (479)
T PRK05452 421 DLGPRMQCSVCQWIYDPA 438 (479)
T ss_pred CCCCeEEECCCCeEECCC
Confidence 355678899999887643
No 238
>KOG0978|consensus
Probab=26.41 E-value=6.7 Score=30.78 Aligned_cols=17 Identities=12% Similarity=0.260 Sum_probs=9.9
Q ss_pred CCeecccChhhhcCcch
Q psy4407 94 KPFSCLLCEYKAAKKSN 110 (130)
Q Consensus 94 k~~~C~~C~~~f~~~~~ 110 (130)
+.-+|+.|+.+|.....
T Consensus 677 RqRKCP~Cn~aFganDv 693 (698)
T KOG0978|consen 677 RQRKCPKCNAAFGANDV 693 (698)
T ss_pred hcCCCCCCCCCCCcccc
Confidence 34466777776665443
No 239
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=26.32 E-value=70 Score=13.79 Aligned_cols=8 Identities=25% Similarity=0.957 Sum_probs=4.8
Q ss_pred eeeCCCCC
Q psy4407 67 IFTCFACE 74 (130)
Q Consensus 67 ~~~C~~C~ 74 (130)
.|.|..|+
T Consensus 15 ~Y~C~~c~ 22 (30)
T PF03107_consen 15 FYHCSECC 22 (30)
T ss_pred eEEeCCCC
Confidence 56666655
No 240
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=26.31 E-value=45 Score=19.99 Aligned_cols=25 Identities=16% Similarity=0.226 Sum_probs=13.1
Q ss_pred ceecccccccccCccccccccCCCCCC
Q psy4407 32 MLTCKYCYEFLPNDAEIIADHCKFCSY 58 (130)
Q Consensus 32 ~~~C~~C~~~~~~~~~l~~h~c~~C~~ 58 (130)
..+|..|+..+....... .|+.||.
T Consensus 70 ~~~C~~C~~~~~~e~~~~--~CP~C~s 94 (115)
T COG0375 70 ECWCLDCGQEVELEELDY--RCPKCGS 94 (115)
T ss_pred EEEeccCCCeecchhhee--ECCCCCC
Confidence 366777866664432222 2555553
No 241
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=26.29 E-value=33 Score=17.31 Aligned_cols=13 Identities=23% Similarity=0.698 Sum_probs=8.9
Q ss_pred ceecccccccccC
Q psy4407 32 MLTCKYCYEFLPN 44 (130)
Q Consensus 32 ~~~C~~C~~~~~~ 44 (130)
.++|..|++....
T Consensus 4 eiRC~~CnklLa~ 16 (51)
T PF10122_consen 4 EIRCGHCNKLLAK 16 (51)
T ss_pred ceeccchhHHHhh
Confidence 4678888877654
No 242
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=25.99 E-value=63 Score=17.29 Aligned_cols=10 Identities=30% Similarity=0.723 Sum_probs=5.9
Q ss_pred eeCCCCCCcc
Q psy4407 68 FTCFACEYHS 77 (130)
Q Consensus 68 ~~C~~C~~~f 77 (130)
..|..||...
T Consensus 39 V~C~~CG~~l 48 (67)
T COG2051 39 VTCLICGTTL 48 (67)
T ss_pred EEecccccEE
Confidence 4666666544
No 243
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=25.76 E-value=43 Score=17.07 Aligned_cols=9 Identities=44% Similarity=1.087 Sum_probs=5.6
Q ss_pred eeccccccc
Q psy4407 33 LTCKYCYEF 41 (130)
Q Consensus 33 ~~C~~C~~~ 41 (130)
..|+.||+.
T Consensus 27 ~~C~~cG~~ 35 (55)
T TIGR01031 27 VVCPNCGEF 35 (55)
T ss_pred eECCCCCCc
Confidence 447777764
No 244
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=25.64 E-value=37 Score=23.96 Aligned_cols=35 Identities=23% Similarity=0.334 Sum_probs=19.0
Q ss_pred cCCCCCCc--ccCCCCceeeCCCCCCcccCchhHHHH
Q psy4407 52 HCKFCSYK--LRPDKTYIFTCFACEYHSAKRSHIKEH 86 (130)
Q Consensus 52 ~c~~C~~~--~~h~~~~~~~C~~C~~~f~~~~~l~~h 86 (130)
.|+.|+.. .....+..+.|+.|+..|.....-+..
T Consensus 40 kc~~C~~~~~~~~l~~~~~vcp~c~~h~rltAreRI~ 76 (296)
T CHL00174 40 QCENCYGLNYKKFLKSKMNICEQCGYHLKMSSSDRIE 76 (296)
T ss_pred ECCCccchhhHHHHHHcCCCCCCCCCCcCCCHHHHHH
Confidence 46666554 111223446788888877665443333
No 245
>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 PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=25.46 E-value=44 Score=14.31 Aligned_cols=9 Identities=22% Similarity=0.729 Sum_probs=3.6
Q ss_pred CceeeCCCC
Q psy4407 65 TYIFTCFAC 73 (130)
Q Consensus 65 ~~~~~C~~C 73 (130)
..++.|+.|
T Consensus 19 r~~~~C~rC 27 (30)
T PF06827_consen 19 RSTYLCPRC 27 (30)
T ss_dssp EEEEE-TTT
T ss_pred CCCeECcCC
Confidence 334555544
No 247
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=25.27 E-value=51 Score=20.33 Aligned_cols=23 Identities=22% Similarity=0.436 Sum_probs=15.5
Q ss_pred eecccccccccCccccccccCCCCCCc
Q psy4407 33 LTCKYCYEFLPNDAEIIADHCKFCSYK 59 (130)
Q Consensus 33 ~~C~~C~~~~~~~~~l~~h~c~~C~~~ 59 (130)
-+|..||..|.-... .|+.|+..
T Consensus 30 ~kC~~CG~v~~PPr~----~Cp~C~~~ 52 (140)
T COG1545 30 TKCKKCGRVYFPPRA----YCPKCGSE 52 (140)
T ss_pred EEcCCCCeEEcCCcc----cCCCCCCC
Confidence 458888887765544 47777664
No 248
>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=24.89 E-value=35 Score=15.83 Aligned_cols=12 Identities=25% Similarity=0.750 Sum_probs=6.2
Q ss_pred cceecccccccc
Q psy4407 31 EMLTCKYCYEFL 42 (130)
Q Consensus 31 ~~~~C~~C~~~~ 42 (130)
+-|+|..||...
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 457888888664
No 249
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=24.71 E-value=62 Score=16.62 Aligned_cols=13 Identities=23% Similarity=0.526 Sum_probs=7.9
Q ss_pred CceeeCCCCCCcc
Q psy4407 65 TYIFTCFACEYHS 77 (130)
Q Consensus 65 ~~~~~C~~C~~~f 77 (130)
...|.|+.||..+
T Consensus 12 ~v~~~Cp~cGipt 24 (55)
T PF13824_consen 12 HVNFECPDCGIPT 24 (55)
T ss_pred ccCCcCCCCCCcC
Confidence 4456777777544
No 251
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=24.64 E-value=38 Score=23.78 Aligned_cols=23 Identities=13% Similarity=0.192 Sum_probs=12.9
Q ss_pred eeCCCCCCcccCchhHHHHHHhh
Q psy4407 68 FTCFACEYHSAKRSHIKEHIRQH 90 (130)
Q Consensus 68 ~~C~~C~~~f~~~~~l~~h~~~h 90 (130)
+.|+.|+..|.....-+...-.+
T Consensus 47 ~vc~~c~~h~rl~areRi~~L~D 69 (292)
T PRK05654 47 NVCPKCGHHMRISARERLDLLLD 69 (292)
T ss_pred CCCCCCCCCeeCCHHHHHHHHcc
Confidence 56777777776554433333333
No 252
>KOG2071|consensus
Probab=24.35 E-value=56 Score=25.30 Aligned_cols=27 Identities=15% Similarity=0.273 Sum_probs=21.2
Q ss_pred CceeeCCCCCCcccCchhHHHHHHhhc
Q psy4407 65 TYIFTCFACEYHSAKRSHIKEHIRQHT 91 (130)
Q Consensus 65 ~~~~~C~~C~~~f~~~~~l~~h~~~h~ 91 (130)
..+..|..||..|........|+..|.
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 456889999999998888777776663
No 253
>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=24.14 E-value=38 Score=15.87 Aligned_cols=14 Identities=29% Similarity=0.456 Sum_probs=10.3
Q ss_pred cceecccccccccC
Q psy4407 31 EMLTCKYCYEFLPN 44 (130)
Q Consensus 31 ~~~~C~~C~~~~~~ 44 (130)
..+.|+.||+.+.+
T Consensus 31 p~~~C~~CGE~~~~ 44 (46)
T TIGR03831 31 PALVCPQCGEEYLD 44 (46)
T ss_pred CccccccCCCEeeC
Confidence 44679999987754
No 254
>PF15199 DAOA: D-amino acid oxidase activator
Probab=24.04 E-value=25 Score=18.59 Aligned_cols=7 Identities=43% Similarity=0.923 Sum_probs=5.7
Q ss_pred CCCCcce
Q psy4407 2 SSVPRSY 8 (130)
Q Consensus 2 ~~~~~~~ 8 (130)
|.+||||
T Consensus 15 sylpqpy 21 (82)
T PF15199_consen 15 SYLPQPY 21 (82)
T ss_pred hhCCchH
Confidence 6788888
No 255
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=24.03 E-value=55 Score=16.94 Aligned_cols=21 Identities=29% Similarity=0.705 Sum_probs=11.8
Q ss_pred eecccccccccCccccccccCCCCCC
Q psy4407 33 LTCKYCYEFLPNDAEIIADHCKFCSY 58 (130)
Q Consensus 33 ~~C~~C~~~~~~~~~l~~h~c~~C~~ 58 (130)
-.|+.||+.- |..+.|..||.
T Consensus 28 ~~c~~cG~~~-----l~Hrvc~~cg~ 48 (57)
T COG0333 28 SVCPNCGEYK-----LPHRVCLKCGY 48 (57)
T ss_pred eeccCCCCcc-----cCceEcCCCCC
Confidence 4577777652 33345666654
No 256
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=24.02 E-value=74 Score=15.98 Aligned_cols=7 Identities=29% Similarity=0.989 Sum_probs=3.1
Q ss_pred eeCCCCC
Q psy4407 68 FTCFACE 74 (130)
Q Consensus 68 ~~C~~C~ 74 (130)
+.|..||
T Consensus 38 ~~CGkCg 44 (51)
T COG1998 38 WACGKCG 44 (51)
T ss_pred eEecccc
Confidence 4444444
No 257
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. 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, 0005634 nucleus
Probab=24.01 E-value=58 Score=16.83 Aligned_cols=11 Identities=18% Similarity=0.582 Sum_probs=5.9
Q ss_pred cccccccccCc
Q psy4407 35 CKYCYEFLPND 45 (130)
Q Consensus 35 C~~C~~~~~~~ 45 (130)
|..||+.....
T Consensus 21 Cl~CGkIiC~~ 31 (57)
T PF06221_consen 21 CLNCGKIICEQ 31 (57)
T ss_pred ccccChhhccc
Confidence 55566555443
No 258
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=23.72 E-value=67 Score=21.63 Aligned_cols=12 Identities=17% Similarity=0.254 Sum_probs=7.2
Q ss_pred eeCCCCCCcccC
Q psy4407 68 FTCFACEYHSAK 79 (130)
Q Consensus 68 ~~C~~C~~~f~~ 79 (130)
..|+.||+.+..
T Consensus 36 ~~C~~Cg~~~~~ 47 (236)
T PF04981_consen 36 TICPKCGRYRIG 47 (236)
T ss_pred eECCCCCCEECC
Confidence 466777665543
No 259
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=23.71 E-value=35 Score=23.87 Aligned_cols=15 Identities=20% Similarity=0.432 Sum_probs=8.5
Q ss_pred eeCCCCCCcccCchh
Q psy4407 68 FTCFACEYHSAKRSH 82 (130)
Q Consensus 68 ~~C~~C~~~f~~~~~ 82 (130)
+.|+.|+..|.....
T Consensus 46 ~vc~~c~~h~rl~ar 60 (285)
T TIGR00515 46 EVCPKCDHHMRMDAR 60 (285)
T ss_pred CCCCCCCCcCcCCHH
Confidence 456666666554433
No 260
>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=23.59 E-value=36 Score=17.00 Aligned_cols=11 Identities=18% Similarity=0.383 Sum_probs=5.1
Q ss_pred eCCCCCCcccC
Q psy4407 69 TCFACEYHSAK 79 (130)
Q Consensus 69 ~C~~C~~~f~~ 79 (130)
.|+.|++.|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 78888877754
No 261
>KOG1994|consensus
Probab=23.53 E-value=29 Score=23.44 Aligned_cols=26 Identities=12% Similarity=0.340 Sum_probs=21.3
Q ss_pred hcccCcceecccccccccCccccccc
Q psy4407 26 FRFETEMLTCKYCYEFLPNDAEIIAD 51 (130)
Q Consensus 26 ~~~~~~~~~C~~C~~~~~~~~~l~~h 51 (130)
......-|-|-+||..|.+...|..|
T Consensus 233 ~~LR~eh~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 233 IFLRSEHYYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred HHHhccceEEEEeccccCCHHHHHHh
Confidence 34456668899999999999999887
No 262
>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=23.24 E-value=65 Score=24.35 Aligned_cols=32 Identities=13% Similarity=0.298 Sum_probs=26.0
Q ss_pred cCCCCceeeCCCCCCcccCchhHHHHHH-hhcC
Q psy4407 61 RPDKTYIFTCFACEYHSAKRSHIKEHIR-QHTG 92 (130)
Q Consensus 61 ~h~~~~~~~C~~C~~~f~~~~~l~~h~~-~h~~ 92 (130)
.+...+-+.|+.|.+.|.....+..|+. .|.+
T Consensus 51 ~n~sWrFWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 51 ENKSWRFWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred hcCceeEeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 3445567899999999999999999987 4654
No 263
>KOG2807|consensus
Probab=23.05 E-value=85 Score=22.61 Aligned_cols=25 Identities=16% Similarity=0.315 Sum_probs=15.8
Q ss_pred CCeecccChhhhcCcchHHHhhhhcC
Q psy4407 94 KPFSCLLCEYKAAKKSNLTKHMSKKH 119 (130)
Q Consensus 94 k~~~C~~C~~~f~~~~~l~~h~~~~h 119 (130)
..|.|..|...|-...+.-.|. ..|
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHe-sLh 368 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHE-SLH 368 (378)
T ss_pred CcEEchhccceeeccchHHHHh-hhh
Confidence 4577777777776655555555 444
No 264
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=22.55 E-value=73 Score=16.20 Aligned_cols=9 Identities=33% Similarity=0.693 Sum_probs=5.4
Q ss_pred eeccccccc
Q psy4407 33 LTCKYCYEF 41 (130)
Q Consensus 33 ~~C~~C~~~ 41 (130)
-.|+.||..
T Consensus 27 ~~c~~cg~~ 35 (56)
T PF01783_consen 27 VKCPNCGEP 35 (56)
T ss_dssp EESSSSSSE
T ss_pred eeeccCCCE
Confidence 456777744
No 265
>KOG4602|consensus
Probab=22.29 E-value=1.2e+02 Score=21.09 Aligned_cols=7 Identities=29% Similarity=0.933 Sum_probs=3.2
Q ss_pred cCCCCCC
Q psy4407 52 HCKFCSY 58 (130)
Q Consensus 52 ~c~~C~~ 58 (130)
.|++||.
T Consensus 270 VCPiCGA 276 (318)
T KOG4602|consen 270 VCPICGA 276 (318)
T ss_pred cCccccc
Confidence 3444444
No 266
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=22.07 E-value=65 Score=19.96 Aligned_cols=22 Identities=23% Similarity=0.409 Sum_probs=11.5
Q ss_pred eCCCCCCcccCchhHHHHHHhhcCC
Q psy4407 69 TCFACEYHSAKRSHIKEHIRQHTGE 93 (130)
Q Consensus 69 ~C~~C~~~f~~~~~l~~h~~~h~~~ 93 (130)
.|-++|+.|. .|.+|+.+|.+.
T Consensus 78 icLEDGkkfK---SLKRHL~t~~gm 99 (148)
T COG4957 78 ICLEDGKKFK---SLKRHLTTHYGL 99 (148)
T ss_pred EEeccCcchH---HHHHHHhcccCC
Confidence 4555555553 355555555543
No 267
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=21.87 E-value=1e+02 Score=15.64 Aligned_cols=7 Identities=29% Similarity=1.004 Sum_probs=3.5
Q ss_pred eeCCCCC
Q psy4407 68 FTCFACE 74 (130)
Q Consensus 68 ~~C~~C~ 74 (130)
|.|+.|+
T Consensus 45 y~C~~Cg 51 (54)
T PF10058_consen 45 YRCPYCG 51 (54)
T ss_pred EEcCCCC
Confidence 4555544
No 268
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=21.80 E-value=44 Score=22.89 Aligned_cols=16 Identities=19% Similarity=0.320 Sum_probs=6.7
Q ss_pred CceeeCCCCCCcccCc
Q psy4407 65 TYIFTCFACEYHSAKR 80 (130)
Q Consensus 65 ~~~~~C~~C~~~f~~~ 80 (130)
..-|.|..|+..|..+
T Consensus 51 VaDF~C~~C~eeyELK 66 (254)
T PF06044_consen 51 VADFYCPNCNEEYELK 66 (254)
T ss_dssp --EEE-TTT--EEEEE
T ss_pred cceeECCCCchHHhhh
Confidence 4447777777666543
No 269
>KOG1813|consensus
Probab=21.65 E-value=84 Score=22.24 Aligned_cols=18 Identities=17% Similarity=0.412 Sum_probs=13.6
Q ss_pred ccCcceecccccccccCc
Q psy4407 28 FETEMLTCKYCYEFLPND 45 (130)
Q Consensus 28 ~~~~~~~C~~C~~~~~~~ 45 (130)
.+.-||.|..|.+.|...
T Consensus 237 ~~~~Pf~c~icr~~f~~p 254 (313)
T KOG1813|consen 237 IELLPFKCFICRKYFYRP 254 (313)
T ss_pred cccCCccccccccccccc
Confidence 355678899999888764
No 270
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=21.56 E-value=1.2e+02 Score=15.87 Aligned_cols=11 Identities=18% Similarity=0.691 Sum_probs=6.4
Q ss_pred eeeCCCCCCcc
Q psy4407 67 IFTCFACEYHS 77 (130)
Q Consensus 67 ~~~C~~C~~~f 77 (130)
...|..||...
T Consensus 30 ~V~C~~Cg~~L 40 (59)
T PRK00415 30 VVRCLVCGKTL 40 (59)
T ss_pred EEECcccCCCc
Confidence 35666666554
No 271
>PRK04351 hypothetical protein; Provisional
Probab=21.54 E-value=84 Score=19.70 Aligned_cols=33 Identities=24% Similarity=0.631 Sum_probs=21.3
Q ss_pred ceeeCCCCCCcccCchhHHHHHHhhcCCCCeecccChhhhc
Q psy4407 66 YIFTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLLCEYKAA 106 (130)
Q Consensus 66 ~~~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~C~~~f~ 106 (130)
..|.|..||..+.... + + ....|.|..|+..+.
T Consensus 111 y~Y~C~~Cg~~~~r~R------r-~-n~~~yrCg~C~g~L~ 143 (149)
T PRK04351 111 YLYECQSCGQQYLRKR------R-I-NTKRYRCGKCRGKLK 143 (149)
T ss_pred EEEECCCCCCEeeeee------e-c-CCCcEEeCCCCcEee
Confidence 4588888887665431 1 1 236688888886654
No 272
>KOG2923|consensus
Probab=21.33 E-value=52 Score=17.45 Aligned_cols=11 Identities=18% Similarity=0.516 Sum_probs=6.6
Q ss_pred eecccccccccC
Q psy4407 33 LTCKYCYEFLPN 44 (130)
Q Consensus 33 ~~C~~C~~~~~~ 44 (130)
|.|+ ||..|.-
T Consensus 23 yPCp-CGDrf~I 33 (67)
T KOG2923|consen 23 YPCP-CGDRFQI 33 (67)
T ss_pred cCCC-CCCeeee
Confidence 4454 7777653
No 273
>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=21.12 E-value=51 Score=15.90 Aligned_cols=11 Identities=18% Similarity=0.283 Sum_probs=8.1
Q ss_pred eCCCCCCcccC
Q psy4407 69 TCFACEYHSAK 79 (130)
Q Consensus 69 ~C~~C~~~f~~ 79 (130)
.|..|++.|.-
T Consensus 10 ~C~~C~rpf~W 20 (42)
T PF10013_consen 10 ICPVCGRPFTW 20 (42)
T ss_pred cCcccCCcchH
Confidence 58888887754
No 274
>KOG4727|consensus
Probab=21.07 E-value=55 Score=21.13 Aligned_cols=23 Identities=17% Similarity=0.345 Sum_probs=19.7
Q ss_pred ceeeCCCCCCcccCchhHHHHHH
Q psy4407 66 YIFTCFACEYHSAKRSHIKEHIR 88 (130)
Q Consensus 66 ~~~~C~~C~~~f~~~~~l~~h~~ 88 (130)
..|.|.+|+-++..+.++..|+.
T Consensus 74 ~GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 74 GGYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred CceeeeecceeehhhHHHHHHhc
Confidence 34999999999999999888864
No 275
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=20.84 E-value=98 Score=15.42 Aligned_cols=11 Identities=18% Similarity=0.491 Sum_probs=5.6
Q ss_pred eeCCCCCCccc
Q psy4407 68 FTCFACEYHSA 78 (130)
Q Consensus 68 ~~C~~C~~~f~ 78 (130)
+.|..||..+.
T Consensus 29 W~C~~Cgh~w~ 39 (55)
T PF14311_consen 29 WKCPKCGHEWK 39 (55)
T ss_pred EECCCCCCeeE
Confidence 45555554443
No 276
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=20.76 E-value=39 Score=17.25 Aligned_cols=25 Identities=12% Similarity=0.307 Sum_probs=19.1
Q ss_pred cccCcceecccccccccCccccccc
Q psy4407 27 RFETEMLTCKYCYEFLPNDAEIIAD 51 (130)
Q Consensus 27 ~~~~~~~~C~~C~~~~~~~~~l~~h 51 (130)
....+-+-|-.||..|.+...|..+
T Consensus 22 YLR~~~~YC~~Cg~~Y~d~~dL~~~ 46 (55)
T PF13821_consen 22 YLREEHNYCFWCGTKYDDEEDLERN 46 (55)
T ss_pred HHHhhCceeeeeCCccCCHHHHHhC
Confidence 3445557799999999998888665
No 277
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=20.74 E-value=5.4 Score=20.03 Aligned_cols=11 Identities=27% Similarity=0.809 Sum_probs=6.3
Q ss_pred eeccccccccc
Q psy4407 33 LTCKYCYEFLP 43 (130)
Q Consensus 33 ~~C~~C~~~~~ 43 (130)
|.|..|...+.
T Consensus 8 y~CDLCn~~~p 18 (57)
T PF14445_consen 8 YSCDLCNSSHP 18 (57)
T ss_pred HhHHhhcccCc
Confidence 55666665553
No 278
>KOG0957|consensus
Probab=20.74 E-value=1e+02 Score=23.70 Aligned_cols=46 Identities=17% Similarity=0.553 Sum_probs=26.2
Q ss_pred ccCcceecccccccccCccccccccCCCCCCc-----------ccC--CCCceeeCCCCCCc
Q psy4407 28 FETEMLTCKYCYEFLPNDAEIIADHCKFCSYK-----------LRP--DKTYIFTCFACEYH 76 (130)
Q Consensus 28 ~~~~~~~C~~C~~~~~~~~~l~~h~c~~C~~~-----------~~h--~~~~~~~C~~C~~~ 76 (130)
.....|.|..|.+.-.. .|.. .|+.|... +.. +...-|+|.+|++.
T Consensus 540 ~~a~~ysCgiCkks~dQ--Hll~-~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECdk~ 598 (707)
T KOG0957|consen 540 PKAMNYSCGICKKSTDQ--HLLT-QCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECDKN 598 (707)
T ss_pred ccccceeeeeeccchhh--HHHh-hcchhhceeeccccCCccccCcccccCcceeecccccc
Confidence 34566999999887422 2221 46666554 111 12234889999643
No 279
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.65 E-value=1.3e+02 Score=20.83 Aligned_cols=24 Identities=21% Similarity=0.635 Sum_probs=14.2
Q ss_pred cCCCCCCcccCCCCceeeCCCCCCcccC
Q psy4407 52 HCKFCSYKLRPDKTYIFTCFACEYHSAK 79 (130)
Q Consensus 52 ~c~~C~~~~~h~~~~~~~C~~C~~~f~~ 79 (130)
.|+.||. .....+.|+.||.....
T Consensus 311 ~C~~cg~----~~~r~~~C~~cg~~~~r 334 (364)
T COG0675 311 TCPCCGH----LSGRLFKCPRCGFVHDR 334 (364)
T ss_pred cccccCC----ccceeEECCCCCCeehh
Confidence 4666665 33445777777765443
No 280
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=20.50 E-value=59 Score=15.39 Aligned_cols=12 Identities=17% Similarity=0.304 Sum_probs=7.0
Q ss_pred ceeccccccccc
Q psy4407 32 MLTCKYCYEFLP 43 (130)
Q Consensus 32 ~~~C~~C~~~~~ 43 (130)
+-.|..|++.+.
T Consensus 11 ~~~C~~C~~~i~ 22 (50)
T cd00029 11 PTFCDVCRKSIW 22 (50)
T ss_pred CCChhhcchhhh
Confidence 445666666553
No 281
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=20.50 E-value=1.3e+02 Score=15.21 Aligned_cols=8 Identities=25% Similarity=0.729 Sum_probs=4.8
Q ss_pred eeCCCCCC
Q psy4407 68 FTCFACEY 75 (130)
Q Consensus 68 ~~C~~C~~ 75 (130)
..|..||.
T Consensus 30 V~C~~Cga 37 (61)
T PF14354_consen 30 VECTDCGA 37 (61)
T ss_pred EEcCCCCC
Confidence 44666764
No 282
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=20.38 E-value=1.2e+02 Score=20.03 Aligned_cols=13 Identities=15% Similarity=0.363 Sum_probs=8.3
Q ss_pred ceeeCCCCCCccc
Q psy4407 66 YIFTCFACEYHSA 78 (130)
Q Consensus 66 ~~~~C~~C~~~f~ 78 (130)
....|..||..+.
T Consensus 29 ~lvrC~eCG~V~~ 41 (201)
T COG1326 29 PLVRCEECGTVHP 41 (201)
T ss_pred eEEEccCCCcEee
Confidence 4567777776653
No 283
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=20.31 E-value=56 Score=20.01 Aligned_cols=10 Identities=20% Similarity=0.677 Sum_probs=4.9
Q ss_pred eeeCCCCCCc
Q psy4407 67 IFTCFACEYH 76 (130)
Q Consensus 67 ~~~C~~C~~~ 76 (130)
.|.|..|+..
T Consensus 37 ~y~C~~C~~~ 46 (146)
T PF08646_consen 37 SYRCEKCNKT 46 (146)
T ss_dssp EEEETTTTEE
T ss_pred EEECCCCCCc
Confidence 3555555543
No 284
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=20.25 E-value=80 Score=14.71 Aligned_cols=12 Identities=17% Similarity=0.276 Sum_probs=7.1
Q ss_pred ceeccccccccc
Q psy4407 32 MLTCKYCYEFLP 43 (130)
Q Consensus 32 ~~~C~~C~~~~~ 43 (130)
+-.|..|++.+.
T Consensus 11 ~~~C~~C~~~i~ 22 (49)
T smart00109 11 PTKCCVCRKSIW 22 (49)
T ss_pred CCCccccccccC
Confidence 445666766653
No 285
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=20.04 E-value=83 Score=17.47 Aligned_cols=55 Identities=18% Similarity=0.454 Sum_probs=17.9
Q ss_pred cccccccCCCCCCc--ccCCCCceeeCCCCCCcccCchhHHHHHHhhcCCCCeecccChhhh
Q psy4407 46 AEIIADHCKFCSYK--LRPDKTYIFTCFACEYHSAKRSHIKEHIRQHTGEKPFSCLLCEYKA 105 (130)
Q Consensus 46 ~~l~~h~c~~C~~~--~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~k~~~C~~C~~~f 105 (130)
.+|..+.|.+||.. .+..|+.-.-|.+|++-.-. ......+. +-.-.|..|+-.|
T Consensus 5 k~~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr--~CyEYErk---eg~q~CpqCkt~y 61 (80)
T PF14569_consen 5 KNLNGQICQICGDDVGLTENGEVFVACHECAFPVCR--PCYEYERK---EGNQVCPQCKTRY 61 (80)
T ss_dssp S--SS-B-SSS--B--B-SSSSB--S-SSS-----H--HHHHHHHH---TS-SB-TTT--B-
T ss_pred hhcCCcccccccCccccCCCCCEEEEEcccCCccch--hHHHHHhh---cCcccccccCCCc
Confidence 34555677777776 44456655567777643321 12222222 2223677776444
Done!