Query psy12853
Match_columns 137
No_of_seqs 120 out of 1273
Neff 8.2
Searched_HMMs 46136
Date Fri Aug 16 21:28:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12853.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12853hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1814|consensus 99.9 1E-24 2.2E-29 170.3 0.3 132 2-134 228-406 (445)
2 KOG1812|consensus 99.9 1.7E-23 3.6E-28 166.2 1.4 131 2-135 189-344 (384)
3 KOG0006|consensus 99.9 3.5E-22 7.5E-27 152.2 4.5 127 6-134 265-437 (446)
4 KOG1815|consensus 99.8 3.5E-20 7.6E-25 149.9 5.2 122 14-136 124-268 (444)
5 smart00647 IBR In Between Ring 99.3 2.7E-12 5.9E-17 77.3 3.7 57 32-88 2-62 (64)
6 PF01485 IBR: IBR domain; Int 99.2 2.3E-12 5E-17 77.5 1.6 57 32-88 2-62 (64)
7 PF01485 IBR: IBR domain; Int 98.7 1.1E-08 2.3E-13 61.3 2.0 43 94-136 16-62 (64)
8 smart00647 IBR In Between Ring 98.6 7E-08 1.5E-12 57.8 4.0 42 94-135 16-61 (64)
9 KOG0006|consensus 97.5 6.5E-05 1.4E-09 58.4 2.3 60 25-87 377-438 (446)
10 KOG1814|consensus 97.2 0.00018 4E-09 57.4 1.8 43 44-86 364-406 (445)
11 KOG1812|consensus 97.2 0.00018 4E-09 57.7 1.8 42 46-88 304-345 (384)
12 PF09297 zf-NADH-PPase: NADH p 96.4 0.0036 7.7E-08 32.4 2.4 29 47-75 2-30 (32)
13 PRK14890 putative Zn-ribbon RN 96.0 0.0087 1.9E-07 35.3 3.0 47 48-104 7-56 (59)
14 PF10571 UPF0547: Uncharacteri 96.0 0.0031 6.8E-08 31.2 1.0 24 97-124 1-24 (26)
15 PF07975 C1_4: TFIIH C1-like d 95.9 0.003 6.6E-08 36.3 0.6 45 51-103 2-50 (51)
16 PF13719 zinc_ribbon_5: zinc-r 95.8 0.0085 1.8E-07 32.1 2.2 29 48-76 2-35 (37)
17 smart00661 RPOL9 RNA polymeras 95.5 0.013 2.8E-07 33.4 2.3 27 49-75 1-29 (52)
18 PF13717 zinc_ribbon_4: zinc-r 95.5 0.012 2.7E-07 31.3 2.1 28 49-76 3-35 (36)
19 KOG1815|consensus 95.4 0.01 2.2E-07 48.6 2.3 44 44-87 222-267 (444)
20 PF14803 Nudix_N_2: Nudix N-te 95.0 0.019 4.2E-07 30.2 1.9 27 49-75 1-31 (34)
21 PF12773 DZR: Double zinc ribb 94.9 0.031 6.7E-07 31.6 2.6 14 46-59 10-23 (50)
22 PRK00398 rpoP DNA-directed RNA 94.9 0.03 6.5E-07 31.3 2.5 29 49-77 4-32 (46)
23 COG2888 Predicted Zn-ribbon RN 94.9 0.022 4.8E-07 33.6 2.0 50 48-104 9-58 (61)
24 PF12773 DZR: Double zinc ribb 94.7 0.019 4E-07 32.5 1.3 42 51-109 1-42 (50)
25 smart00661 RPOL9 RNA polymeras 94.7 0.038 8.3E-07 31.3 2.7 27 98-124 2-30 (52)
26 TIGR02098 MJ0042_CXXC MJ0042 f 94.3 0.058 1.3E-06 28.7 2.7 28 49-76 3-35 (38)
27 PRK14559 putative protein seri 94.0 0.031 6.8E-07 47.8 1.8 10 97-106 28-37 (645)
28 PF02150 RNA_POL_M_15KD: RNA p 93.6 0.045 9.8E-07 28.9 1.4 27 49-75 2-29 (35)
29 PRK00398 rpoP DNA-directed RNA 93.4 0.089 1.9E-06 29.3 2.5 28 98-125 5-32 (46)
30 PF14570 zf-RING_4: RING/Ubox 93.3 0.045 9.8E-07 31.1 1.1 47 51-106 1-47 (48)
31 PRK00432 30S ribosomal protein 93.2 0.06 1.3E-06 30.8 1.5 30 46-76 18-47 (50)
32 cd00162 RING RING-finger (Real 93.0 0.045 9.8E-07 29.2 0.8 32 68-106 14-45 (45)
33 PRK04023 DNA polymerase II lar 93.0 0.094 2E-06 46.8 3.1 48 44-107 622-674 (1121)
34 PF07191 zinc-ribbons_6: zinc- 92.9 0.12 2.6E-06 31.6 2.7 21 99-121 4-24 (70)
35 TIGR00622 ssl1 transcription f 92.8 0.13 2.9E-06 34.4 3.0 48 48-103 55-110 (112)
36 PRK14714 DNA polymerase II lar 92.8 0.1 2.2E-06 47.5 3.2 49 48-107 667-720 (1337)
37 PHA00626 hypothetical protein 92.7 0.11 2.4E-06 30.4 2.1 27 98-124 2-33 (59)
38 PF13248 zf-ribbon_3: zinc-rib 92.6 0.071 1.5E-06 26.2 1.2 11 97-107 3-13 (26)
39 PRK00432 30S ribosomal protein 92.2 0.15 3.2E-06 29.2 2.3 28 95-124 19-47 (50)
40 PF07191 zinc-ribbons_6: zinc- 91.6 0.17 3.6E-06 31.0 2.2 57 50-133 3-61 (70)
41 KOG0317|consensus 91.4 0.056 1.2E-06 41.6 -0.1 33 69-109 254-286 (293)
42 PF13240 zinc_ribbon_2: zinc-r 91.4 0.12 2.6E-06 24.6 1.1 11 98-108 1-11 (23)
43 PF13920 zf-C3HC4_3: Zinc fing 91.2 0.038 8.2E-07 31.2 -0.9 30 71-108 19-49 (50)
44 PHA02926 zinc finger-like prot 90.8 0.082 1.8E-06 39.5 0.3 59 48-108 170-231 (242)
45 PF07754 DUF1610: Domain of un 90.5 0.26 5.7E-06 23.8 1.9 21 53-73 3-23 (24)
46 COG1198 PriA Primosomal protei 90.4 0.34 7.3E-06 42.2 3.8 47 64-131 433-484 (730)
47 COG1594 RPB9 DNA-directed RNA 90.4 0.3 6.5E-06 32.7 2.8 30 48-77 2-33 (113)
48 PF08274 PhnA_Zn_Ribbon: PhnA 90.3 0.25 5.5E-06 25.2 1.8 26 98-124 4-29 (30)
49 PF09538 FYDLN_acid: Protein o 90.1 0.19 4E-06 33.5 1.6 31 47-78 8-38 (108)
50 TIGR01053 LSD1 zinc finger dom 90.0 0.43 9.2E-06 24.5 2.5 27 49-75 2-28 (31)
51 PF09297 zf-NADH-PPase: NADH p 90.0 0.5 1.1E-05 24.1 2.8 28 96-123 3-30 (32)
52 PLN03208 E3 ubiquitin-protein 89.8 0.094 2E-06 38.3 -0.1 58 45-108 15-80 (193)
53 PF14569 zf-UDP: Zinc-binding 89.5 0.14 2.9E-06 32.0 0.5 61 47-114 8-69 (80)
54 KOG2932|consensus 89.5 0.093 2E-06 41.0 -0.3 56 44-114 86-141 (389)
55 TIGR00570 cdk7 CDK-activating 89.1 0.21 4.6E-06 39.1 1.4 54 49-110 4-57 (309)
56 PRK00420 hypothetical protein; 89.1 0.47 1E-05 31.8 2.9 40 32-75 10-49 (112)
57 PRK14559 putative protein seri 89.0 0.34 7.3E-06 41.7 2.7 11 96-106 41-51 (645)
58 PF08271 TF_Zn_Ribbon: TFIIB z 89.0 0.53 1.1E-05 25.7 2.6 26 50-75 2-28 (43)
59 PF13923 zf-C3HC4_2: Zinc fing 88.8 0.18 3.9E-06 26.9 0.6 31 99-134 1-31 (39)
60 COG1998 RPS31 Ribosomal protei 88.7 0.31 6.6E-06 27.8 1.5 30 46-75 17-46 (51)
61 PF07282 OrfB_Zn_ribbon: Putat 88.1 0.54 1.2E-05 28.2 2.5 30 95-124 27-56 (69)
62 PF06677 Auto_anti-p27: Sjogre 87.8 0.57 1.2E-05 25.6 2.2 24 49-73 18-41 (41)
63 PF14369 zf-RING_3: zinc-finge 87.7 0.54 1.2E-05 24.8 2.0 29 48-76 2-31 (35)
64 COG1645 Uncharacterized Zn-fin 87.4 0.64 1.4E-05 31.9 2.8 35 35-74 18-52 (131)
65 PF07282 OrfB_Zn_ribbon: Putat 87.3 0.5 1.1E-05 28.3 2.0 33 44-76 24-56 (69)
66 KOG2906|consensus 87.1 0.55 1.2E-05 30.6 2.2 27 98-124 3-31 (105)
67 KOG0823|consensus 87.0 0.27 6E-06 36.8 0.9 48 53-108 49-96 (230)
68 PF06943 zf-LSD1: LSD1 zinc fi 87.0 0.84 1.8E-05 22.3 2.3 24 51-74 1-24 (25)
69 PF09538 FYDLN_acid: Protein o 87.0 0.41 8.8E-06 31.8 1.6 27 97-124 10-36 (108)
70 PRK05654 acetyl-CoA carboxylas 86.5 0.13 2.9E-06 39.9 -1.1 30 95-124 26-56 (292)
71 PLN02189 cellulose synthase 86.5 0.64 1.4E-05 41.8 2.9 63 46-115 32-95 (1040)
72 COG1645 Uncharacterized Zn-fin 86.4 0.65 1.4E-05 31.9 2.3 25 96-122 28-52 (131)
73 PF12861 zf-Apc11: Anaphase-pr 86.1 0.78 1.7E-05 29.2 2.5 50 50-108 34-83 (85)
74 PF14353 CpXC: CpXC protein 85.9 0.72 1.6E-05 31.1 2.4 39 50-88 3-60 (128)
75 KOG0317|consensus 85.5 0.15 3.3E-06 39.3 -1.2 36 94-135 237-272 (293)
76 TIGR03655 anti_R_Lar restricti 85.3 0.99 2.1E-05 25.8 2.5 30 96-125 1-37 (53)
77 PF15227 zf-C3HC4_4: zinc fing 85.2 0.29 6.2E-06 26.8 0.1 28 71-102 15-42 (42)
78 smart00834 CxxC_CXXC_SSSS Puta 85.1 0.5 1.1E-05 25.2 1.1 13 96-108 26-38 (41)
79 TIGR01384 TFS_arch transcripti 85.1 0.69 1.5E-05 30.1 1.9 27 49-77 1-27 (104)
80 PF08792 A2L_zn_ribbon: A2L zi 85.1 1.2 2.5E-05 23.2 2.4 29 48-76 3-31 (33)
81 TIGR00686 phnA alkylphosphonat 84.9 0.78 1.7E-05 30.4 2.1 28 49-77 3-30 (109)
82 PRK00241 nudC NADH pyrophospha 84.8 0.72 1.6E-05 35.1 2.2 31 45-75 96-126 (256)
83 PRK08665 ribonucleotide-diphos 84.8 0.58 1.3E-05 41.0 1.9 27 97-125 725-751 (752)
84 KOG0320|consensus 84.8 0.26 5.6E-06 35.6 -0.2 49 48-108 131-179 (187)
85 KOG2906|consensus 84.7 0.84 1.8E-05 29.8 2.1 31 49-79 2-34 (105)
86 PF14835 zf-RING_6: zf-RING of 84.4 0.52 1.1E-05 28.4 1.0 37 95-131 6-49 (65)
87 TIGR01206 lysW lysine biosynth 84.4 1.1 2.5E-05 25.9 2.4 27 50-76 4-32 (54)
88 PF14634 zf-RING_5: zinc-RING 84.3 0.85 1.8E-05 24.9 1.8 26 71-104 19-44 (44)
89 KOG0823|consensus 84.3 0.33 7.1E-06 36.3 0.2 20 115-136 62-81 (230)
90 PHA02929 N1R/p28-like protein; 84.3 0.95 2.1E-05 34.2 2.6 53 47-107 173-227 (238)
91 COG2816 NPY1 NTP pyrophosphohy 84.3 0.62 1.3E-05 36.0 1.6 32 44-75 107-138 (279)
92 PF14952 zf-tcix: Putative tre 84.2 0.59 1.3E-05 25.9 1.1 22 93-118 8-29 (44)
93 TIGR00515 accD acetyl-CoA carb 84.2 0.19 4.1E-06 39.0 -1.2 30 95-124 25-55 (285)
94 CHL00174 accD acetyl-CoA carbo 84.0 0.18 3.9E-06 39.3 -1.4 30 95-124 37-67 (296)
95 PF00097 zf-C3HC4: Zinc finger 83.8 0.3 6.4E-06 26.0 -0.2 31 99-134 1-31 (41)
96 TIGR01384 TFS_arch transcripti 83.7 0.91 2E-05 29.5 2.0 25 98-124 2-26 (104)
97 PF10122 Mu-like_Com: Mu-like 83.6 0.53 1.2E-05 26.9 0.8 25 98-122 6-32 (51)
98 PF14354 Lar_restr_allev: Rest 83.5 1.1 2.4E-05 26.1 2.2 28 95-122 2-37 (61)
99 KOG0978|consensus 83.4 0.26 5.7E-06 42.5 -0.8 49 45-106 640-688 (698)
100 PRK14892 putative transcriptio 83.3 1.1 2.4E-05 29.3 2.3 14 111-124 39-52 (99)
101 smart00659 RPOLCX RNA polymera 82.8 1.3 2.9E-05 24.5 2.2 8 51-58 5-12 (44)
102 PRK10220 hypothetical protein; 82.8 1.2 2.6E-05 29.6 2.3 27 49-76 4-30 (111)
103 PLN02638 cellulose synthase A 82.7 1 2.2E-05 40.7 2.6 63 46-115 15-78 (1079)
104 PRK12495 hypothetical protein; 82.6 0.52 1.1E-05 35.1 0.6 27 45-73 39-65 (226)
105 PF03119 DNA_ligase_ZBD: NAD-d 81.3 1.6 3.5E-05 21.7 2.0 21 50-70 1-21 (28)
106 PF15135 UPF0515: Uncharacteri 81.2 1.7 3.7E-05 33.1 2.9 62 64-135 110-187 (278)
107 PRK00420 hypothetical protein; 81.2 1.6 3.5E-05 29.2 2.5 25 96-122 23-48 (112)
108 PLN02436 cellulose synthase A 81.2 1.5 3.3E-05 39.7 3.0 63 46-115 34-97 (1094)
109 PRK09710 lar restriction allev 81.0 1.8 3.9E-05 26.0 2.4 31 94-124 4-37 (64)
110 PRK11827 hypothetical protein; 80.8 2 4.3E-05 25.5 2.5 28 48-75 8-35 (60)
111 PLN03208 E3 ubiquitin-protein 80.4 0.81 1.8E-05 33.5 0.9 35 93-133 15-49 (193)
112 COG0777 AccD Acetyl-CoA carbox 80.2 0.54 1.2E-05 36.3 -0.0 31 94-124 26-57 (294)
113 PF13453 zf-TFIIB: Transcripti 80.0 1.4 3E-05 23.8 1.6 24 50-73 1-26 (41)
114 PF01363 FYVE: FYVE zinc finge 79.7 2.5 5.5E-05 25.1 2.9 38 94-133 7-44 (69)
115 TIGR00686 phnA alkylphosphonat 79.5 1.6 3.6E-05 28.9 2.1 27 97-124 3-29 (109)
116 PF04216 FdhE: Protein involve 79.4 0.91 2E-05 35.0 1.0 65 48-124 172-248 (290)
117 COG1997 RPL43A Ribosomal prote 79.2 2.1 4.5E-05 27.3 2.4 29 96-124 35-63 (89)
118 PF13639 zf-RING_2: Ring finge 78.8 0.86 1.9E-05 24.7 0.5 34 98-134 2-35 (44)
119 PF03604 DNA_RNApol_7kD: DNA d 78.7 1.2 2.6E-05 23.0 1.0 6 68-73 19-24 (32)
120 TIGR02300 FYDLN_acid conserved 78.3 1.4 3.1E-05 30.1 1.6 29 47-76 8-36 (129)
121 PRK11827 hypothetical protein; 78.2 2.2 4.8E-05 25.3 2.2 30 95-124 7-36 (60)
122 PLN03086 PRLI-interacting fact 78.2 1.2 2.6E-05 37.8 1.4 22 102-123 441-462 (567)
123 COG2051 RPS27A Ribosomal prote 77.4 2.3 5E-05 25.7 2.1 30 48-77 19-49 (67)
124 PLN02400 cellulose synthase 77.1 2.6 5.7E-05 38.3 3.3 62 47-115 35-97 (1085)
125 KOG2164|consensus 76.4 0.88 1.9E-05 37.8 0.2 52 48-108 186-237 (513)
126 PF01599 Ribosomal_S27: Riboso 76.3 1.8 3.9E-05 24.4 1.3 28 95-122 17-46 (47)
127 COG1656 Uncharacterized conser 75.9 2.8 6E-05 30.0 2.5 33 45-77 94-141 (165)
128 COG5175 MOT2 Transcriptional r 75.6 0.64 1.4E-05 37.0 -0.8 51 48-107 14-64 (480)
129 COG1198 PriA Primosomal protei 75.5 2.7 5.8E-05 36.8 2.8 36 48-83 444-484 (730)
130 PF05129 Elf1: Transcription e 75.4 1.9 4.1E-05 27.1 1.5 17 108-124 40-56 (81)
131 PF01873 eIF-5_eIF-2B: Domain 75.1 5.7 0.00012 27.0 3.9 46 22-75 75-123 (125)
132 TIGR00595 priA primosomal prot 75.0 3.1 6.8E-05 34.7 3.1 35 97-131 223-262 (505)
133 PLN02915 cellulose synthase A 74.0 2.6 5.5E-05 38.2 2.4 61 48-115 15-76 (1044)
134 COG1996 RPC10 DNA-directed RNA 73.9 2.1 4.5E-05 24.4 1.2 7 98-104 26-32 (49)
135 PRK10220 hypothetical protein; 73.7 3.1 6.6E-05 27.7 2.1 27 97-124 4-30 (111)
136 PF15616 TerY-C: TerY-C metal 73.5 3 6.5E-05 28.7 2.2 25 95-126 76-100 (131)
137 COG1594 RPB9 DNA-directed RNA 72.1 3.9 8.4E-05 27.3 2.4 29 96-124 2-32 (113)
138 PF03966 Trm112p: Trm112p-like 71.6 5.1 0.00011 24.0 2.7 11 114-124 53-63 (68)
139 PRK00415 rps27e 30S ribosomal 71.6 4.7 0.0001 23.8 2.4 30 48-77 11-41 (59)
140 COG1997 RPL43A Ribosomal prote 71.2 4 8.7E-05 26.1 2.2 32 46-77 33-64 (89)
141 KOG1039|consensus 71.1 1.8 3.9E-05 34.5 0.7 38 70-108 185-222 (344)
142 PF09526 DUF2387: Probable met 70.5 4.1 8.9E-05 25.0 2.1 27 97-123 9-39 (71)
143 TIGR00595 priA primosomal prot 70.4 4.4 9.5E-05 33.9 2.9 34 49-82 223-261 (505)
144 smart00531 TFIIE Transcription 70.2 2.6 5.7E-05 29.3 1.3 31 45-75 96-132 (147)
145 PF03833 PolC_DP2: DNA polymer 70.1 1.4 3.1E-05 38.9 0.0 10 48-57 655-664 (900)
146 PRK12380 hydrogenase nickel in 70.0 4.3 9.4E-05 27.0 2.3 16 45-60 67-82 (113)
147 PLN03086 PRLI-interacting fact 69.8 1.7 3.7E-05 36.9 0.4 17 45-61 404-420 (567)
148 PF04981 NMD3: NMD3 family ; 69.6 2.9 6.2E-05 31.4 1.5 34 75-108 14-47 (236)
149 TIGR02443 conserved hypothetic 69.4 4.6 9.9E-05 23.9 2.0 27 97-123 10-40 (59)
150 PF02318 FYVE_2: FYVE-type zin 69.0 4 8.7E-05 27.2 2.0 36 47-83 53-88 (118)
151 PRK05580 primosome assembly pr 68.8 4.9 0.00011 34.9 2.9 35 97-131 391-430 (679)
152 PF01927 Mut7-C: Mut7-C RNAse 68.8 6.2 0.00013 27.3 3.0 34 44-77 87-135 (147)
153 smart00653 eIF2B_5 domain pres 68.5 6.3 0.00014 26.2 2.8 27 48-74 80-109 (110)
154 PRK14873 primosome assembly pr 68.5 6.5 0.00014 34.1 3.6 27 48-74 392-418 (665)
155 TIGR00515 accD acetyl-CoA carb 68.5 1.5 3.3E-05 34.0 -0.2 33 44-76 22-55 (285)
156 cd00065 FYVE FYVE domain; Zinc 68.4 4.4 9.4E-05 23.0 1.8 33 49-83 3-35 (57)
157 COG0777 AccD Acetyl-CoA carbox 68.3 1.9 4.2E-05 33.3 0.4 33 45-77 25-58 (294)
158 KOG2807|consensus 68.2 2.7 5.8E-05 33.3 1.1 49 44-103 326-374 (378)
159 PRK14714 DNA polymerase II lar 68.1 3.2 7E-05 38.3 1.7 16 67-82 668-687 (1337)
160 PRK05654 acetyl-CoA carboxylas 67.9 1.7 3.7E-05 33.8 0.0 33 44-76 23-56 (292)
161 TIGR00311 aIF-2beta translatio 67.9 6.5 0.00014 27.1 2.9 29 48-76 97-128 (133)
162 PF09723 Zn-ribbon_8: Zinc rib 67.8 3.1 6.6E-05 22.6 1.0 13 96-108 26-39 (42)
163 CHL00174 accD acetyl-CoA carbo 67.8 1.5 3.2E-05 34.2 -0.3 33 44-76 34-67 (296)
164 smart00184 RING Ring finger. E 67.6 1.2 2.6E-05 22.4 -0.7 16 71-86 15-30 (39)
165 PRK03988 translation initiatio 67.6 6.7 0.00015 27.2 2.9 29 48-76 102-133 (138)
166 COG1096 Predicted RNA-binding 67.5 5 0.00011 29.3 2.3 27 48-76 149-175 (188)
167 PF05715 zf-piccolo: Piccolo Z 67.0 1.8 3.8E-05 25.6 -0.1 35 97-131 3-39 (61)
168 COG5574 PEX10 RING-finger-cont 66.9 1.5 3.3E-05 33.6 -0.5 29 97-131 216-244 (271)
169 PRK14873 primosome assembly pr 66.5 5 0.00011 34.8 2.6 34 98-131 394-431 (665)
170 PF11793 FANCL_C: FANCL C-term 65.3 3.5 7.6E-05 25.0 1.0 59 50-108 4-67 (70)
171 COG2824 PhnA Uncharacterized Z 65.3 6.1 0.00013 26.2 2.2 26 48-74 3-28 (112)
172 PF01667 Ribosomal_S27e: Ribos 65.0 7 0.00015 22.8 2.2 30 48-77 7-37 (55)
173 PF06044 DRP: Dam-replacing fa 64.4 4.4 9.6E-05 30.8 1.6 35 48-82 31-69 (254)
174 PRK03681 hypA hydrogenase nick 64.4 4.6 9.9E-05 26.9 1.5 13 46-58 68-80 (114)
175 PLN02195 cellulose synthase A 64.1 6.4 0.00014 35.5 2.8 53 48-107 6-59 (977)
176 TIGR00100 hypA hydrogenase nic 62.6 5.1 0.00011 26.7 1.5 14 46-59 68-81 (115)
177 COG0266 Nei Formamidopyrimidin 62.6 6.7 0.00015 30.3 2.4 27 95-121 244-272 (273)
178 smart00064 FYVE Protein presen 62.4 3.9 8.5E-05 24.2 0.9 34 48-83 10-43 (68)
179 PF06827 zf-FPG_IleRS: Zinc fi 62.4 5.9 0.00013 19.6 1.4 25 97-121 2-28 (30)
180 PF10083 DUF2321: Uncharacteri 62.3 1.4 3.1E-05 31.1 -1.2 26 73-109 27-52 (158)
181 PF12760 Zn_Tnp_IS1595: Transp 61.8 13 0.00028 20.4 2.8 29 46-74 16-45 (46)
182 PRK12286 rpmF 50S ribosomal pr 61.8 6.2 0.00013 23.1 1.6 24 94-122 25-48 (57)
183 COG2835 Uncharacterized conser 61.5 9.2 0.0002 22.7 2.3 27 48-74 8-34 (60)
184 PRK14810 formamidopyrimidine-D 61.2 7.6 0.00017 29.8 2.5 26 96-121 244-271 (272)
185 PRK01103 formamidopyrimidine/5 61.1 7.9 0.00017 29.7 2.5 26 96-121 245-272 (274)
186 PRK14811 formamidopyrimidine-D 61.1 7.5 0.00016 29.8 2.4 26 96-121 235-262 (269)
187 KOG2907|consensus 61.0 3.5 7.7E-05 27.5 0.5 27 47-73 6-32 (116)
188 KOG2177|consensus 61.0 7.3 0.00016 28.8 2.3 68 48-129 13-112 (386)
189 PRK09521 exosome complex RNA-b 61.0 8.6 0.00019 27.7 2.6 26 98-124 151-176 (189)
190 PRK03824 hypA hydrogenase nick 60.7 6.1 0.00013 27.2 1.7 16 96-111 107-123 (135)
191 PRK00423 tfb transcription ini 60.6 8.8 0.00019 30.0 2.7 31 46-76 9-40 (310)
192 TIGR00599 rad18 DNA repair pro 60.4 5.7 0.00012 32.3 1.7 49 46-108 24-72 (397)
193 PRK10445 endonuclease VIII; Pr 60.1 8.4 0.00018 29.4 2.5 26 96-121 235-262 (263)
194 PF14205 Cys_rich_KTR: Cystein 59.7 7.2 0.00016 22.6 1.6 28 48-75 4-37 (55)
195 PRK06266 transcription initiat 59.7 6.4 0.00014 28.3 1.7 31 45-75 114-145 (178)
196 KOG0320|consensus 59.6 2.3 5E-05 30.8 -0.6 28 93-120 128-159 (187)
197 KOG2879|consensus 59.6 5.9 0.00013 30.6 1.6 51 46-107 237-287 (298)
198 PLN00209 ribosomal protein S27 59.3 9.5 0.00021 24.3 2.2 30 48-77 36-66 (86)
199 PRK13945 formamidopyrimidine-D 59.2 8.7 0.00019 29.6 2.5 26 96-121 254-281 (282)
200 PTZ00083 40S ribosomal protein 59.0 9.8 0.00021 24.1 2.2 30 48-77 35-65 (85)
201 TIGR00373 conserved hypothetic 59.0 3.6 7.7E-05 29.0 0.3 32 44-75 105-137 (158)
202 PRK04023 DNA polymerase II lar 58.8 7 0.00015 35.5 2.1 7 98-104 628-634 (1121)
203 PRK05580 primosome assembly pr 58.8 9.6 0.00021 33.1 2.9 34 49-82 391-429 (679)
204 TIGR00577 fpg formamidopyrimid 58.6 9 0.0002 29.4 2.5 25 96-120 245-271 (272)
205 cd00350 rubredoxin_like Rubred 58.0 7 0.00015 20.0 1.2 8 51-58 4-11 (33)
206 PRK08665 ribonucleotide-diphos 57.6 8 0.00017 34.1 2.3 27 49-77 725-751 (752)
207 TIGR02605 CxxC_CxxC_SSSS putat 57.6 8.5 0.00018 21.5 1.7 8 97-104 27-34 (52)
208 PF14446 Prok-RING_1: Prokaryo 56.7 14 0.0003 21.5 2.4 23 49-73 6-28 (54)
209 KOG2691|consensus 56.0 12 0.00025 24.9 2.3 31 47-77 3-37 (113)
210 COG2995 PqiA Uncharacterized p 55.3 9.4 0.0002 31.1 2.1 34 44-77 14-49 (418)
211 COG3809 Uncharacterized protei 55.0 10 0.00023 23.7 1.8 32 49-88 2-35 (88)
212 PF01155 HypA: Hydrogenase exp 53.9 3.6 7.7E-05 27.3 -0.4 15 46-60 68-82 (113)
213 TIGR00155 pqiA_fam integral me 52.8 17 0.00036 29.6 3.2 43 31-76 197-240 (403)
214 PF14319 Zn_Tnp_IS91: Transpos 52.7 26 0.00056 23.2 3.6 30 45-82 39-68 (111)
215 PRK12336 translation initiatio 52.7 16 0.00035 26.8 2.9 35 48-82 98-135 (201)
216 PRK02935 hypothetical protein; 52.6 10 0.00022 25.1 1.6 11 98-108 88-98 (110)
217 PF11023 DUF2614: Protein of u 52.6 6.5 0.00014 26.3 0.7 11 98-108 87-97 (114)
218 COG0675 Transposase and inacti 52.3 15 0.00032 28.0 2.8 12 45-56 306-317 (364)
219 COG1096 Predicted RNA-binding 51.9 12 0.00026 27.3 2.0 25 97-123 150-174 (188)
220 COG0375 HybF Zn finger protein 51.4 8.1 0.00018 26.0 1.0 15 46-60 68-82 (115)
221 PF04216 FdhE: Protein involve 50.5 8.9 0.00019 29.6 1.3 36 97-132 173-221 (290)
222 PF09862 DUF2089: Protein of u 50.2 14 0.0003 24.8 2.0 22 51-76 1-22 (113)
223 PF02318 FYVE_2: FYVE-type zin 50.1 20 0.00043 23.8 2.8 34 97-131 55-88 (118)
224 PF03833 PolC_DP2: DNA polymer 49.7 5.5 0.00012 35.4 0.0 31 96-132 655-690 (900)
225 PF00643 zf-B_box: B-box zinc 49.2 7.9 0.00017 20.5 0.6 23 65-87 14-36 (42)
226 PRK08115 ribonucleotide-diphos 48.9 9.6 0.00021 34.1 1.4 27 96-124 827-854 (858)
227 PF04606 Ogr_Delta: Ogr/Delta- 48.6 13 0.00029 20.5 1.5 11 50-60 1-11 (47)
228 smart00154 ZnF_AN1 AN1-like Zi 48.5 14 0.0003 19.7 1.5 13 114-126 12-24 (39)
229 PRK00241 nudC NADH pyrophospha 48.0 18 0.00039 27.5 2.6 30 95-124 98-127 (256)
230 KOG3002|consensus 47.9 13 0.00028 29.2 1.8 49 43-107 43-91 (299)
231 COG3677 Transposase and inacti 47.7 15 0.00032 25.1 1.9 37 46-82 28-69 (129)
232 PF14447 Prok-RING_4: Prokaryo 47.6 14 0.0003 21.5 1.5 28 72-109 25-52 (55)
233 cd00729 rubredoxin_SM Rubredox 47.3 15 0.00032 19.0 1.4 8 51-58 5-12 (34)
234 PRK00564 hypA hydrogenase nick 46.8 10 0.00023 25.3 1.0 8 98-105 90-97 (117)
235 TIGR00155 pqiA_fam integral me 46.6 17 0.00037 29.6 2.4 30 47-76 12-43 (403)
236 KOG4537|consensus 46.5 4.4 9.6E-05 28.7 -0.8 44 25-72 20-63 (178)
237 COG5151 SSL1 RNA polymerase II 46.5 7.9 0.00017 30.6 0.4 53 44-104 358-418 (421)
238 PF01428 zf-AN1: AN1-like Zinc 46.4 12 0.00026 20.3 1.1 18 65-82 12-29 (43)
239 PRK00464 nrdR transcriptional 45.8 14 0.0003 26.1 1.5 28 50-77 2-39 (154)
240 PRK00762 hypA hydrogenase nick 45.7 18 0.00039 24.4 2.0 6 98-103 94-99 (124)
241 TIGR01031 rpmF_bact ribosomal 44.8 22 0.00047 20.5 2.0 24 94-122 24-47 (55)
242 PF13465 zf-H2C2_2: Zinc-finge 44.5 13 0.00028 17.7 0.9 14 63-76 11-24 (26)
243 PF13913 zf-C2HC_2: zinc-finge 44.4 9.4 0.0002 18.2 0.4 9 68-76 4-12 (25)
244 KOG3183|consensus 44.0 20 0.00042 27.3 2.2 46 62-107 19-66 (250)
245 COG2816 NPY1 NTP pyrophosphohy 43.6 19 0.00041 27.9 2.1 30 95-124 110-139 (279)
246 PF14149 YhfH: YhfH-like prote 43.6 1.2 2.6E-05 23.8 -3.1 27 94-120 11-37 (37)
247 PRK10445 endonuclease VIII; Pr 43.4 21 0.00045 27.2 2.3 26 48-73 235-262 (263)
248 PF07503 zf-HYPF: HypF finger; 42.8 11 0.00024 19.7 0.6 30 77-106 2-31 (35)
249 smart00249 PHD PHD zinc finger 42.6 48 0.001 17.0 3.2 29 51-82 2-30 (47)
250 PRK14810 formamidopyrimidine-D 42.4 22 0.00047 27.3 2.3 26 48-73 244-271 (272)
251 KOG2324|consensus 42.3 25 0.00055 28.6 2.6 37 63-109 224-261 (457)
252 COG1571 Predicted DNA-binding 41.4 14 0.00031 30.3 1.2 26 50-76 352-377 (421)
253 PHA02942 putative transposase; 41.2 28 0.00061 28.1 2.9 31 45-76 322-352 (383)
254 PRK15103 paraquat-inducible me 41.1 25 0.00054 28.8 2.6 30 47-76 9-40 (419)
255 COG0266 Nei Formamidopyrimidin 40.0 24 0.00051 27.4 2.1 27 47-73 244-272 (273)
256 PRK12496 hypothetical protein; 39.9 15 0.00034 26.0 1.1 12 97-108 128-139 (164)
257 PRK13130 H/ACA RNA-protein com 39.8 17 0.00037 21.2 1.0 11 96-106 5-15 (56)
258 PF08646 Rep_fac-A_C: Replicat 39.4 31 0.00068 23.5 2.5 27 96-123 18-46 (146)
259 PRK01103 formamidopyrimidine/5 39.0 28 0.0006 26.7 2.4 27 48-74 245-273 (274)
260 PRK08332 ribonucleotide-diphos 38.2 22 0.00048 34.3 2.0 27 98-126 1706-1738(1740)
261 PF11781 RRN7: RNA polymerase 38.2 32 0.0007 18.0 1.9 25 50-75 10-34 (36)
262 PRK14811 formamidopyrimidine-D 38.0 35 0.00076 26.1 2.8 26 49-74 236-263 (269)
263 PF13445 zf-RING_UBOX: RING-ty 37.0 20 0.00043 19.6 1.0 33 99-134 1-33 (43)
264 PF03811 Zn_Tnp_IS1: InsA N-te 36.9 38 0.00082 17.8 2.0 26 48-73 5-36 (36)
265 COG4888 Uncharacterized Zn rib 36.8 34 0.00073 22.5 2.2 18 64-81 20-37 (104)
266 KOG4739|consensus 36.7 17 0.00037 27.5 0.9 27 71-107 22-48 (233)
267 PF13451 zf-trcl: Probable zin 36.5 24 0.00053 20.0 1.3 15 114-128 4-18 (49)
268 PF10238 Eapp_C: E2F-associate 36.3 40 0.00086 23.3 2.6 20 63-82 26-45 (136)
269 PF00628 PHD: PHD-finger; Int 35.8 41 0.0009 18.3 2.3 23 51-76 2-24 (51)
270 PF06221 zf-C2HC5: Putative zi 35.6 27 0.00059 20.4 1.5 12 96-107 35-46 (57)
271 PF01780 Ribosomal_L37ae: Ribo 35.5 25 0.00054 22.6 1.4 29 96-124 35-63 (90)
272 PTZ00255 60S ribosomal protein 35.1 21 0.00045 23.0 1.0 34 44-77 32-65 (90)
273 PF00096 zf-C2H2: Zinc finger, 34.8 19 0.00041 16.1 0.6 9 68-76 2-10 (23)
274 COG1326 Uncharacterized archae 34.5 21 0.00045 26.3 1.0 29 48-76 6-40 (201)
275 COG3024 Uncharacterized protei 34.2 24 0.00051 21.2 1.1 21 94-114 5-25 (65)
276 cd04476 RPA1_DBD_C RPA1_DBD_C: 33.5 34 0.00073 23.9 2.0 26 96-122 34-59 (166)
277 KOG3084|consensus 33.2 30 0.00064 27.5 1.7 35 46-83 148-182 (345)
278 COG3529 Predicted nucleic-acid 32.5 17 0.00038 21.6 0.3 26 98-123 12-41 (66)
279 PRK03564 formate dehydrogenase 32.1 36 0.00077 26.8 2.1 35 96-130 187-234 (309)
280 smart00440 ZnF_C2C2 C2C2 Zinc 32.0 53 0.0011 17.5 2.2 8 50-57 2-9 (40)
281 cd00021 BBOX B-Box-type zinc f 32.0 28 0.00062 17.6 1.1 24 64-87 10-33 (39)
282 PF08882 Acetone_carb_G: Aceto 31.9 25 0.00054 23.5 1.0 12 114-126 24-35 (112)
283 PF01396 zf-C4_Topoisom: Topoi 31.3 32 0.00069 18.2 1.2 21 97-118 2-25 (39)
284 PF03884 DUF329: Domain of unk 31.2 21 0.00045 20.9 0.5 19 96-114 2-20 (57)
285 PRK03976 rpl37ae 50S ribosomal 31.2 22 0.00047 22.8 0.6 33 45-77 33-65 (90)
286 PF10058 DUF2296: Predicted in 31.0 25 0.00054 20.2 0.8 9 96-104 44-52 (54)
287 COG5222 Uncharacterized conser 31.0 21 0.00046 28.1 0.6 44 49-104 275-318 (427)
288 TIGR00280 L37a ribosomal prote 30.8 22 0.00048 22.9 0.6 33 45-77 32-64 (91)
289 PF01783 Ribosomal_L32p: Ribos 30.8 38 0.00082 19.5 1.6 25 44-73 22-46 (56)
290 COG1545 Predicted nucleic-acid 30.7 42 0.0009 23.1 2.0 24 48-75 29-52 (140)
291 PRK09678 DNA-binding transcrip 30.6 45 0.00097 20.4 1.9 10 49-58 2-11 (72)
292 COG5432 RAD18 RING-finger-cont 30.6 12 0.00025 29.4 -0.8 30 96-132 25-55 (391)
293 COG5082 AIR1 Arginine methyltr 29.8 48 0.001 24.3 2.2 55 48-113 60-114 (190)
294 COG4416 Com Mu-like prophage p 29.7 9.3 0.0002 22.2 -1.1 13 96-108 24-36 (60)
295 PRK07218 replication factor A; 29.1 26 0.00056 28.8 0.9 13 96-108 297-309 (423)
296 PF07295 DUF1451: Protein of u 28.7 46 0.001 23.2 2.0 32 63-106 109-140 (146)
297 TIGR01562 FdhE formate dehydro 28.5 44 0.00096 26.3 2.0 35 97-131 185-233 (305)
298 COG1571 Predicted DNA-binding 28.4 32 0.00069 28.3 1.2 27 97-124 351-377 (421)
299 COG1592 Rubrerythrin [Energy p 28.3 32 0.0007 24.6 1.2 24 48-74 134-157 (166)
300 PF07227 DUF1423: Protein of u 28.3 42 0.00091 27.8 1.9 55 49-122 98-154 (446)
301 COG1499 NMD3 NMD protein affec 28.1 40 0.00087 27.1 1.8 47 46-103 4-50 (355)
302 PF13894 zf-C2H2_4: C2H2-type 28.0 31 0.00067 15.0 0.7 7 69-75 3-9 (24)
303 COG4306 Uncharacterized protei 27.9 19 0.0004 24.8 -0.1 15 94-108 37-51 (160)
304 smart00778 Prim_Zn_Ribbon Zinc 27.5 78 0.0017 16.7 2.3 7 97-103 4-10 (37)
305 PF09889 DUF2116: Uncharacteri 27.4 31 0.00068 20.3 0.8 13 96-108 3-15 (59)
306 PF09082 DUF1922: Domain of un 27.1 49 0.0011 20.1 1.6 26 50-77 5-30 (68)
307 PF04161 Arv1: Arv1-like famil 27.0 26 0.00056 25.7 0.5 18 96-113 24-41 (208)
308 PF12675 DUF3795: Protein of u 26.9 50 0.0011 20.2 1.7 35 96-130 34-71 (78)
309 PF11682 DUF3279: Protein of u 26.9 35 0.00076 23.4 1.1 28 74-110 97-124 (128)
310 PRK05978 hypothetical protein; 26.9 39 0.00085 23.7 1.3 12 48-59 33-44 (148)
311 PRK06386 replication factor A; 26.9 30 0.00065 27.8 0.8 13 96-108 236-248 (358)
312 TIGR01623 put_zinc_LRP1 putati 26.8 16 0.00034 20.1 -0.5 24 108-131 9-32 (43)
313 KOG1842|consensus 26.8 15 0.00032 30.4 -0.9 40 44-85 176-215 (505)
314 cd02340 ZZ_NBR1_like Zinc fing 26.7 57 0.0012 17.6 1.7 29 50-82 2-31 (43)
315 COG4640 Predicted membrane pro 26.7 37 0.0008 27.8 1.3 7 49-55 2-8 (465)
316 PLN02248 cellulose synthase-li 26.5 41 0.00089 31.1 1.7 50 49-107 125-177 (1135)
317 COG2023 RPR2 RNase P subunit R 26.5 38 0.00083 22.4 1.2 30 46-75 54-91 (105)
318 PF12172 DUF35_N: Rubredoxin-l 26.1 35 0.00076 17.6 0.8 22 48-73 11-32 (37)
319 KOG4367|consensus 25.9 25 0.00055 29.2 0.3 63 65-134 175-255 (699)
320 COG0068 HypF Hydrogenase matur 25.7 26 0.00057 30.8 0.3 64 45-108 98-185 (750)
321 cd01412 SIRT5_Af1_CobB SIRT5_A 25.5 91 0.002 22.8 3.2 44 54-106 97-140 (224)
322 PF12678 zf-rbx1: RING-H2 zinc 25.5 19 0.00042 21.8 -0.4 45 51-103 22-73 (73)
323 PF10497 zf-4CXXC_R1: Zinc-fin 25.4 47 0.001 21.8 1.5 36 92-131 3-47 (105)
324 PF05605 zf-Di19: Drought indu 25.3 41 0.00088 18.9 1.0 6 51-56 5-10 (54)
325 PF13821 DUF4187: Domain of un 25.2 37 0.0008 19.6 0.8 14 121-134 26-39 (55)
326 KOG1952|consensus 24.7 29 0.00063 31.1 0.4 69 48-122 191-259 (950)
327 COG4049 Uncharacterized protei 24.5 42 0.00091 19.7 0.9 12 48-59 17-28 (65)
328 PF02591 DUF164: Putative zinc 24.5 42 0.0009 19.1 1.0 13 46-58 44-56 (56)
329 COG3357 Predicted transcriptio 24.5 41 0.00088 21.7 1.0 22 51-72 61-82 (97)
330 PTZ00303 phosphatidylinositol 24.4 53 0.0011 29.6 1.9 37 96-132 460-499 (1374)
331 PF09151 DUF1936: Domain of un 24.4 39 0.00085 17.3 0.7 9 98-106 3-11 (36)
332 COG3634 AhpF Alkyl hydroperoxi 24.4 31 0.00067 28.2 0.5 30 31-60 323-353 (520)
333 KOG1356|consensus 23.9 52 0.0011 29.5 1.8 33 98-134 231-263 (889)
334 KOG2462|consensus 23.6 43 0.00093 26.0 1.1 31 46-76 159-197 (279)
335 smart00336 BBOX B-Box-type zin 23.4 62 0.0013 16.5 1.5 23 65-87 14-36 (42)
336 PRK00418 DNA gyrase inhibitor; 23.2 47 0.001 19.8 1.0 16 95-110 5-20 (62)
337 COG0551 TopA Zn-finger domain 23.0 1.7E+02 0.0036 19.8 3.9 26 45-70 14-41 (140)
338 PF05495 zf-CHY: CHY zinc fing 22.9 68 0.0015 19.3 1.7 42 67-108 11-53 (71)
339 PHA02325 hypothetical protein 22.7 44 0.00095 20.1 0.8 12 95-106 2-13 (72)
340 PRK08332 ribonucleotide-diphos 22.5 75 0.0016 31.0 2.6 29 48-78 1704-1738(1740)
341 PF08209 Sgf11: Sgf11 (transcr 22.3 45 0.00097 17.2 0.7 12 97-108 5-16 (33)
342 PF04032 Rpr2: RNAse P Rpr2/Rp 22.2 49 0.0011 20.1 1.0 17 44-60 42-58 (85)
343 PF08772 NOB1_Zn_bind: Nin one 22.2 42 0.0009 20.6 0.7 15 44-58 20-34 (73)
344 PF04810 zf-Sec23_Sec24: Sec23 22.1 72 0.0016 16.9 1.6 25 50-74 4-32 (40)
345 KOG3800|consensus 21.9 43 0.00093 26.2 0.8 52 50-109 2-53 (300)
346 PF10276 zf-CHCC: Zinc-finger 21.7 79 0.0017 17.0 1.6 13 64-76 27-39 (40)
347 COG1579 Zn-ribbon protein, pos 21.4 32 0.0007 26.1 0.1 28 48-75 197-230 (239)
348 PF14206 Cys_rich_CPCC: Cystei 21.2 1E+02 0.0022 19.2 2.2 26 98-123 3-29 (78)
349 TIGR00143 hypF [NiFe] hydrogen 21.2 24 0.00051 31.0 -0.8 43 44-86 64-110 (711)
350 PF05876 Terminase_GpA: Phage 21.1 61 0.0013 27.6 1.7 41 65-107 199-240 (557)
351 COG1327 Predicted transcriptio 21.0 60 0.0013 23.0 1.3 28 50-77 2-39 (156)
352 KOG1002|consensus 20.9 22 0.00047 30.4 -1.0 34 71-107 553-586 (791)
No 1
>KOG1814|consensus
Probab=99.89 E-value=1e-24 Score=170.31 Aligned_cols=132 Identities=27% Similarity=0.556 Sum_probs=111.5
Q ss_pred ccccchHHHHhhcCCCcccccccccchhhhHHHHhhccccccCCCCcccCCC--CCCceeecCCCCeeeccccccccccc
Q psy12853 2 TSLVSLDDFLLRHYDKGPCKNKLGHSRASVIWHRTQVSGATFDSELIKCCPM--CSVPIEKDEGCAQMLCKRCKHVFCWY 79 (137)
Q Consensus 2 ~~l~~~~~f~~~~~~~~~c~~~l~~~~~~~~~~r~~~~~a~~~~~~~~~CP~--C~~~i~~~~~~~~~~C~~C~~~fC~~ 79 (137)
++|.+|+.-..+...++..++.+..+ +.++|.+..+++++....+.+|||+ |..+...+++...+.|.+|+..||+.
T Consensus 228 ~~l~Cp~~~C~~~a~~g~vKelvg~E-L~arYe~l~lqk~l~~msdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtl 306 (445)
T KOG1814|consen 228 SCLKCPDPKCGSVAPPGQVKELVGDE-LFARYEKLMLQKTLELMSDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTL 306 (445)
T ss_pred eeecCCCCCCcccCCchHHHHHHHHH-HHHHHHHHHHHHHHHhhcccccCChhhccCccccCchhhhhhhccCccHHHHH
Confidence 45666776666666777666666554 4579999999988888899999994 99999777899999999999999999
Q ss_pred ccccccCCC---------------------------------------------CcccccccCCCCCCCcceeecCCCCe
Q psy12853 80 CLASRDYGG---------------------------------------------ATFDSELIKCCPMCSVPIEKDEGCAQ 114 (137)
Q Consensus 80 C~~~~h~~~---------------------------------------------~~~~~~~~~~CP~C~~~iek~~gC~h 114 (137)
|+..||+.. +.|...+.++||+|++.|||++|||+
T Consensus 307 Ck~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnK 386 (445)
T KOG1814|consen 307 CKLTWHGVSPCKVKAEKLIELYLEYLEADEARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNK 386 (445)
T ss_pred HHHhhcCCCcccCchHHHHHHHHHHhhcCHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccc
Confidence 999999983 02334578999999999999999999
Q ss_pred EEeccCcceeeccccccccc
Q psy12853 115 MLCKRCKHVFCWYCLASLDV 134 (137)
Q Consensus 115 m~C~~C~~~fC~~C~~~~~~ 134 (137)
|+|.+||+.|||.|+..+.+
T Consensus 387 M~C~~c~~~fc~~c~~~l~~ 406 (445)
T KOG1814|consen 387 MHCTKCGTYFCWICAELLYP 406 (445)
T ss_pred eeeccccccceeehhhhcCC
Confidence 99999999999999998874
No 2
>KOG1812|consensus
Probab=99.87 E-value=1.7e-23 Score=166.21 Aligned_cols=131 Identities=24% Similarity=0.547 Sum_probs=106.1
Q ss_pred ccccchHHHHhhcCCCcccccccccchhhhHHHHhhccccccCCCCcccCC--CCCCceeecC-----CCCeeecccccc
Q psy12853 2 TSLVSLDDFLLRHYDKGPCKNKLGHSRASVIWHRTQVSGATFDSELIKCCP--MCSVPIEKDE-----GCAQMLCKRCKH 74 (137)
Q Consensus 2 ~~l~~~~~f~~~~~~~~~c~~~l~~~~~~~~~~r~~~~~a~~~~~~~~~CP--~C~~~i~~~~-----~~~~~~C~~C~~ 74 (137)
+.+.+|+.-....++.+.|...|+. .+.+.|.++..+..+...+.. ||| +|...+.... ......|+.|+.
T Consensus 189 ~~~~C~~~~C~~~l~~~~c~~llt~-kl~e~~e~~~~e~~i~~~~~~-ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~ 266 (384)
T KOG1812|consen 189 TVIRCPHDGCESRLTLESCRKLLTP-KLREMWEQRLKEEVIPSLDRV-YCPYPRCSSLMSKTELSSEVKSKRRPCVKCHE 266 (384)
T ss_pred CCccCCCCCCCccCCHHHHhhhcCH-HHHHHHHHHHHHHhhhhhhcc-cCCCCCchHhhhhhhhccchhhcccccccCCC
Confidence 4556677777788888889999988 566799988776665555555 998 8988877543 345677999999
Q ss_pred cccccccccccCCCC------------------cccccccCCCCCCCcceeecCCCCeEEeccCcceeecccccccccC
Q psy12853 75 VFCWYCLASRDYGGA------------------TFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDVS 135 (137)
Q Consensus 75 ~fC~~C~~~~h~~~~------------------~~~~~~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~~~ 135 (137)
.||.+|+.+||.+.. .+.++.|++||+|+..||+++|||||+|+ ||++|||.|+.+|..+
T Consensus 267 ~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~~la~~wr~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~~~ 344 (384)
T KOG1812|consen 267 LFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLKYLAKRWRQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDWKTH 344 (384)
T ss_pred ceeecCCCcCCCCCCHHHHHHhCCcccccHHHHHHHHHhcCcCcccceeeeecCCcceEEee-ccccchhhcCcchhhC
Confidence 999999999999841 11136799999999999999999999999 9999999999988654
No 3
>KOG0006|consensus
Probab=99.85 E-value=3.5e-22 Score=152.22 Aligned_cols=127 Identities=24% Similarity=0.552 Sum_probs=100.9
Q ss_pred chHHHHhhcCCCccccccc----------ccchhhhHHHHhhccccccCCCCcccCC--CCCCceeecCCCCeeeccc-c
Q psy12853 6 SLDDFLLRHYDKGPCKNKL----------GHSRASVIWHRTQVSGATFDSELIKCCP--MCSVPIEKDEGCAQMLCKR-C 72 (137)
Q Consensus 6 ~~~~f~~~~~~~~~c~~~l----------~~~~~~~~~~r~~~~~a~~~~~~~~~CP--~C~~~i~~~~~~~~~~C~~-C 72 (137)
..++|-.++-.+++|.+.| .++.+ .+|+|+..++.++... .+.|| +|++.+...+++..++|+. |
T Consensus 265 ~~p~~gyslpc~agc~~s~i~e~HHF~ilg~e~Y-~rYQr~atEe~vlq~g-GVlCP~pgCG~gll~EPD~rkvtC~~gC 342 (446)
T KOG0006|consen 265 HDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQY-NRYQRYATEECVLQMG-GVLCPRPGCGAGLLPEPDQRKVTCEGGC 342 (446)
T ss_pred cCccccccccccCCCchHHHHhhhhheecchhHH-HHHHHhhhhhheeecC-CEecCCCCCCcccccCCCCCcccCCCCc
Confidence 3444555555566666444 33334 4788887777666555 78998 8999999999999999995 9
Q ss_pred cccccccccccccCCCC------------------------ccc-------ccccCCCCCCCcceeecCCCCeEEecc--
Q psy12853 73 KHVFCWYCLASRDYGGA------------------------TFD-------SELIKCCPMCSVPIEKDEGCAQMLCKR-- 119 (137)
Q Consensus 73 ~~~fC~~C~~~~h~~~~------------------------~~~-------~~~~~~CP~C~~~iek~~gC~hm~C~~-- 119 (137)
++.||..|...||.+.. .|+ ...+|+||+|++++||+|||.||.|++
T Consensus 343 gf~FCR~C~e~yh~geC~~~~~as~t~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~ 422 (446)
T KOG0006|consen 343 GFAFCRECKEAYHEGECSAVFEASGTTTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQ 422 (446)
T ss_pred hhHhHHHHHhhhccccceeeeccccccceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCC
Confidence 99999999999999941 122 336899999999999999999999995
Q ss_pred Ccceeeccccccccc
Q psy12853 120 CKHVFCWYCLASLDV 134 (137)
Q Consensus 120 C~~~fC~~C~~~~~~ 134 (137)
||.+|||.|+..|..
T Consensus 423 Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 423 CGLEWCWNCGTEWNR 437 (446)
T ss_pred CCceeEeccCChhhh
Confidence 999999999999975
No 4
>KOG1815|consensus
Probab=99.80 E-value=3.5e-20 Score=149.92 Aligned_cols=122 Identities=31% Similarity=0.647 Sum_probs=100.2
Q ss_pred cCCCcccccccccchhhhHHHHhhccccccCCCCcccCC--CCCCceee-cCCCCeeecccccccccccccccccCCCC-
Q psy12853 14 HYDKGPCKNKLGHSRASVIWHRTQVSGATFDSELIKCCP--MCSVPIEK-DEGCAQMLCKRCKHVFCWYCLASRDYGGA- 89 (137)
Q Consensus 14 ~~~~~~c~~~l~~~~~~~~~~r~~~~~a~~~~~~~~~CP--~C~~~i~~-~~~~~~~~C~~C~~~fC~~C~~~~h~~~~- 89 (137)
..+...+..........++|.++.+.+++......+||| +|+.++.. ......+.| .|++.|||.|+.+||.+..
T Consensus 124 ~v~~~~i~~~~s~~~~~~ky~~~i~~syve~~~~lkwCP~~~C~~av~~~~~~~~~v~C-~~g~~FC~~C~~~~H~p~~C 202 (444)
T KOG1815|consen 124 LVGEDTVEKLVSDKEDKEKYQRYILRSYVEDNVPLKWCPAPGCGLAVKFGSLESVEVDC-GCGHEFCFACGEESHSPVSC 202 (444)
T ss_pred cCCCceeeeecCCHHHHHHHHHHHHHHHHhcCCccccCCCCCCCceeeccCCCccceeC-CCCchhHhhccccccCCCcc
Confidence 333344444444434567999999998888888899998 89999886 566788999 5788999999999999951
Q ss_pred -----------------cccccccCCCCCCCcceeecCCCCeEEecc--CcceeecccccccccCC
Q psy12853 90 -----------------TFDSELIKCCPMCSVPIEKDEGCAQMLCKR--CKHVFCWYCLASLDVSR 136 (137)
Q Consensus 90 -----------------~~~~~~~~~CP~C~~~iek~~gC~hm~C~~--C~~~fC~~C~~~~~~~~ 136 (137)
.|+..++++||+|..+|||++|||||+|.. |+++|||+|.++|.++.
T Consensus 203 ~~~~~wl~k~~~~se~~~wi~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h~ 268 (444)
T KOG1815|consen 203 PGAKKWLKKCRDDSETINWILANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDHG 268 (444)
T ss_pred cchHHHHHhhhhhhhhhhhhhccCccCCCcccchhccCCccccccccCCcCCeeceeeeccccccc
Confidence 245678999999999999999999999997 99999999999998874
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.29 E-value=2.7e-12 Score=77.29 Aligned_cols=57 Identities=26% Similarity=0.588 Sum_probs=49.2
Q ss_pred HHHHhhccccccCCCCcccCC--CCCCceeecC--CCCeeecccccccccccccccccCCC
Q psy12853 32 IWHRTQVSGATFDSELIKCCP--MCSVPIEKDE--GCAQMLCKRCKHVFCWYCLASRDYGG 88 (137)
Q Consensus 32 ~~~r~~~~~a~~~~~~~~~CP--~C~~~i~~~~--~~~~~~C~~C~~~fC~~C~~~~h~~~ 88 (137)
+|++++++.++..+++.+||| +|..++...+ +...+.|+.|+..||+.|+.+||.+.
T Consensus 2 ~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~ 62 (64)
T smart00647 2 KYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPV 62 (64)
T ss_pred hHHHHHHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCC
Confidence 566776766666678899999 9999998864 78899999999999999999999874
No 6
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=99.24 E-value=2.3e-12 Score=77.53 Aligned_cols=57 Identities=28% Similarity=0.616 Sum_probs=38.7
Q ss_pred HHHHhhccccccCCCCcccCC--CCCCceeecCCCCe--eecccccccccccccccccCCC
Q psy12853 32 IWHRTQVSGATFDSELIKCCP--MCSVPIEKDEGCAQ--MLCKRCKHVFCWYCLASRDYGG 88 (137)
Q Consensus 32 ~~~r~~~~~a~~~~~~~~~CP--~C~~~i~~~~~~~~--~~C~~C~~~fC~~C~~~~h~~~ 88 (137)
+|+++.++.++..+++.+||| +|+.++..+++... ++|+.|++.||+.|+.+||.+.
T Consensus 2 ky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~ 62 (64)
T PF01485_consen 2 KYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGV 62 (64)
T ss_dssp CHHHCCCHS---S---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS
T ss_pred hHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCC
Confidence 567777777777888889998 59999999887666 9999999999999999999974
No 7
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=98.67 E-value=1.1e-08 Score=61.32 Aligned_cols=43 Identities=35% Similarity=0.823 Sum_probs=32.1
Q ss_pred cccCCCCC--CCcceeecCCCCe--EEeccCcceeecccccccccCC
Q psy12853 94 ELIKCCPM--CSVPIEKDEGCAQ--MLCKRCKHVFCWYCLASLDVSR 136 (137)
Q Consensus 94 ~~~~~CP~--C~~~iek~~gC~h--m~C~~C~~~fC~~C~~~~~~~~ 136 (137)
.+.+.||+ |...+++.++.++ |+|..|++.|||.|+.+|+...
T Consensus 16 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~ 62 (64)
T PF01485_consen 16 PNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGV 62 (64)
T ss_dssp --CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS
T ss_pred CCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCC
Confidence 45679988 9999999999999 9999999999999999997653
No 8
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.59 E-value=7e-08 Score=57.78 Aligned_cols=42 Identities=33% Similarity=0.838 Sum_probs=37.5
Q ss_pred cccCCCC--CCCcceeecC--CCCeEEeccCcceeecccccccccC
Q psy12853 94 ELIKCCP--MCSVPIEKDE--GCAQMLCKRCKHVFCWYCLASLDVS 135 (137)
Q Consensus 94 ~~~~~CP--~C~~~iek~~--gC~hm~C~~C~~~fC~~C~~~~~~~ 135 (137)
.+++.|| +|...|+..+ +..+|+|..||+.|||.|+.+|+..
T Consensus 16 ~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~ 61 (64)
T smart00647 16 PDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSP 61 (64)
T ss_pred CCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCC
Confidence 4678899 9999999974 8999999779999999999999764
No 9
>KOG0006|consensus
Probab=97.48 E-value=6.5e-05 Score=58.36 Aligned_cols=60 Identities=27% Similarity=0.689 Sum_probs=47.9
Q ss_pred ccchhhhHHHHhhccccccCCCCcccCCCCCCceeecCCCCeeeccc--ccccccccccccccCC
Q psy12853 25 GHSRASVIWHRTQVSGATFDSELIKCCPMCSVPIEKDEGCAQMLCKR--CKHVFCWYCLASRDYG 87 (137)
Q Consensus 25 ~~~~~~~~~~r~~~~~a~~~~~~~~~CP~C~~~i~~~~~~~~~~C~~--C~~~fC~~C~~~~h~~ 87 (137)
++.+++++|....-. ......+.||+|..+.++++|+..|.|+. |+...||.|+.+|...
T Consensus 377 e~~a~~arwd~as~~---TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r~ 438 (446)
T KOG0006|consen 377 ERAAEQARWDAASKE---TIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNRV 438 (446)
T ss_pred hhhhhhhhhhhhhhh---hhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhhh
Confidence 334456677665322 25667899999999999999999999985 9999999999999764
No 10
>KOG1814|consensus
Probab=97.19 E-value=0.00018 Score=57.44 Aligned_cols=43 Identities=40% Similarity=0.891 Sum_probs=38.5
Q ss_pred CCCCcccCCCCCCceeecCCCCeeecccccccccccccccccC
Q psy12853 44 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDY 86 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~ 86 (137)
...+.+.||.|..+|++.+|++.|.|..|++.|||.|.....+
T Consensus 364 l~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~ 406 (445)
T KOG1814|consen 364 LESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLYP 406 (445)
T ss_pred HHhcCCCCCcccceeecCCCccceeeccccccceeehhhhcCC
Confidence 3467899999999999999999999999999999999986553
No 11
>KOG1812|consensus
Probab=97.18 E-value=0.00018 Score=57.71 Aligned_cols=42 Identities=36% Similarity=0.886 Sum_probs=38.7
Q ss_pred CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCC
Q psy12853 46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGG 88 (137)
Q Consensus 46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~ 88 (137)
...+.||.|...|+...|++.|+|. |++.||+.|+.+|..+.
T Consensus 304 ~~wr~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~~~~ 345 (384)
T KOG1812|consen 304 KRWRQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDWKTHN 345 (384)
T ss_pred HhcCcCcccceeeeecCCcceEEee-ccccchhhcCcchhhCC
Confidence 6689999999999999999999997 99999999999987764
No 12
>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=96.39 E-value=0.0036 Score=32.40 Aligned_cols=29 Identities=24% Similarity=0.527 Sum_probs=19.7
Q ss_pred CcccCCCCCCceeecCCCCeeeccccccc
Q psy12853 47 LIKCCPMCSVPIEKDEGCAQMLCKRCKHV 75 (137)
Q Consensus 47 ~~~~CP~C~~~i~~~~~~~~~~C~~C~~~ 75 (137)
+.+|||.|+.+.....+....+|+.|+..
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred CCcccCcCCccccCCCCcCEeECCCCcCE
Confidence 46799999999999888889999998864
No 13
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=96.04 E-value=0.0087 Score=35.34 Aligned_cols=47 Identities=28% Similarity=0.639 Sum_probs=33.1
Q ss_pred cccCCCCCCceeecCCCCeeeccccccc---ccccccccccCCCCcccccccCCCCCCCc
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCKHV---FCWYCLASRDYGGATFDSELIKCCPMCSV 104 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~---fC~~C~~~~h~~~~~~~~~~~~~CP~C~~ 104 (137)
...|-.|+..|...+....+.||.||.. -|..|++. .+.-.||+|+.
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~----------~~~Y~CP~CGF 56 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQ----------SNPYTCPKCGF 56 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhc----------CCceECCCCCC
Confidence 4467789988876666788999999876 45666543 23447888875
No 14
>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=96.01 E-value=0.0031 Score=31.20 Aligned_cols=24 Identities=29% Similarity=0.830 Sum_probs=15.8
Q ss_pred CCCCCCCcceeecCCCCeEEeccCccee
Q psy12853 97 KCCPMCSVPIEKDEGCAQMLCKRCKHVF 124 (137)
Q Consensus 97 ~~CP~C~~~iek~~gC~hm~C~~C~~~f 124 (137)
|.||.|+..|..+ -..|..||+.|
T Consensus 1 K~CP~C~~~V~~~----~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPES----AKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhh----cCcCCCCCCCC
Confidence 5788888888442 24455577776
No 15
>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=95.89 E-value=0.003 Score=36.33 Aligned_cols=45 Identities=29% Similarity=0.727 Sum_probs=24.4
Q ss_pred CCCCCCceeecC----CCCeeecccccccccccccccccCCCCcccccccCCCCCCC
Q psy12853 51 CPMCSVPIEKDE----GCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCS 103 (137)
Q Consensus 51 CP~C~~~i~~~~----~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~ 103 (137)
|-+|..++.... +.....|++|+..||..|-.=.| +....||.|.
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiH--------E~LH~CPGC~ 50 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIH--------ETLHNCPGCE 50 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTT--------TTS-SSSTT-
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhh--------ccccCCcCCC
Confidence 445666554432 24679999999999999976444 4577899985
No 16
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=95.81 E-value=0.0085 Score=32.09 Aligned_cols=29 Identities=34% Similarity=0.874 Sum_probs=22.8
Q ss_pred cccCCCCCCceeecC-----CCCeeecccccccc
Q psy12853 48 IKCCPMCSVPIEKDE-----GCAQMLCKRCKHVF 76 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~-----~~~~~~C~~C~~~f 76 (137)
...||+|+..+..++ +...+.|++|++.|
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 357999999988754 36689999998876
No 17
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=95.50 E-value=0.013 Score=33.36 Aligned_cols=27 Identities=30% Similarity=0.769 Sum_probs=20.2
Q ss_pred ccCCCCCCceeecCC--CCeeeccccccc
Q psy12853 49 KCCPMCSVPIEKDEG--CAQMLCKRCKHV 75 (137)
Q Consensus 49 ~~CP~C~~~i~~~~~--~~~~~C~~C~~~ 75 (137)
++||.|+..+....+ .+...|+.|++.
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCe
Confidence 489999998876543 247889988865
No 18
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=95.49 E-value=0.012 Score=31.27 Aligned_cols=28 Identities=36% Similarity=0.857 Sum_probs=22.2
Q ss_pred ccCCCCCCceeecC-----CCCeeecccccccc
Q psy12853 49 KCCPMCSVPIEKDE-----GCAQMLCKRCKHVF 76 (137)
Q Consensus 49 ~~CP~C~~~i~~~~-----~~~~~~C~~C~~~f 76 (137)
..||+|+..+..++ ....++|++|++.|
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 57999999888754 35689999998875
No 19
>KOG1815|consensus
Probab=95.42 E-value=0.01 Score=48.62 Aligned_cols=44 Identities=57% Similarity=1.111 Sum_probs=38.3
Q ss_pred CCCCcccCCCCCCceeecCCCCeeeccc--ccccccccccccccCC
Q psy12853 44 DSELIKCCPMCSVPIEKDEGCAQMLCKR--CKHVFCWYCLASRDYG 87 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~~~~~~~~~C~~--C~~~fC~~C~~~~h~~ 87 (137)
...+.+.||.|..+++++.|.+.+.|.. |++.|||.|...|...
T Consensus 222 i~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h 267 (444)
T KOG1815|consen 222 ILANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDH 267 (444)
T ss_pred hhccCccCCCcccchhccCCccccccccCCcCCeeceeeecccccc
Confidence 3677888999999999999999999976 9999999997776555
No 20
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=95.04 E-value=0.019 Score=30.19 Aligned_cols=27 Identities=30% Similarity=0.936 Sum_probs=15.6
Q ss_pred ccCCCCCCceeec----CCCCeeeccccccc
Q psy12853 49 KCCPMCSVPIEKD----EGCAQMLCKRCKHV 75 (137)
Q Consensus 49 ~~CP~C~~~i~~~----~~~~~~~C~~C~~~ 75 (137)
+|||.|+.+++.. ++-.+..|+.|+..
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCCE
Confidence 5899999998763 24567889998864
No 21
>PF12773 DZR: Double zinc ribbon
Probab=94.86 E-value=0.031 Score=31.57 Aligned_cols=14 Identities=36% Similarity=0.949 Sum_probs=7.7
Q ss_pred CCcccCCCCCCcee
Q psy12853 46 ELIKCCPMCSVPIE 59 (137)
Q Consensus 46 ~~~~~CP~C~~~i~ 59 (137)
++.++||.|+..+.
T Consensus 10 ~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 10 DDAKFCPHCGTPLP 23 (50)
T ss_pred ccccCChhhcCChh
Confidence 34555666655554
No 22
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=94.86 E-value=0.03 Score=31.26 Aligned_cols=29 Identities=24% Similarity=0.407 Sum_probs=20.3
Q ss_pred ccCCCCCCceeecCCCCeeeccccccccc
Q psy12853 49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFC 77 (137)
Q Consensus 49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC 77 (137)
..||+|+..+..++....+.||.||..+=
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 46888888887766544777887776543
No 23
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=94.85 E-value=0.022 Score=33.61 Aligned_cols=50 Identities=22% Similarity=0.472 Sum_probs=33.8
Q ss_pred cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCc
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSV 104 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~ 104 (137)
...|-.|+..|........+.||+||...=+.|..- -...+.-+||+|+.
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~C-------Rk~g~~Y~Cp~CGF 58 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKC-------RKLGNPYRCPKCGF 58 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceeeehhhhH-------HHcCCceECCCcCc
Confidence 456778999887777788899999995554444321 01234557999875
No 24
>PF12773 DZR: Double zinc ribbon
Probab=94.67 E-value=0.019 Score=32.50 Aligned_cols=42 Identities=26% Similarity=0.566 Sum_probs=25.4
Q ss_pred CCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853 51 CPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD 109 (137)
Q Consensus 51 CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~ 109 (137)
||.|+..+.. +..||..|+.... ......+.||+|+..+...
T Consensus 1 Cp~Cg~~~~~------------~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 1 CPHCGTPNPD------------DAKFCPHCGTPLP-----PPDQSKKICPNCGAENPPN 42 (50)
T ss_pred CCCcCCcCCc------------cccCChhhcCChh-----hccCCCCCCcCCcCCCcCC
Confidence 6777777543 2556666665322 1133466788888887654
No 25
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=94.66 E-value=0.038 Score=31.34 Aligned_cols=27 Identities=26% Similarity=0.682 Sum_probs=21.0
Q ss_pred CCCCCCcceeecCC--CCeEEeccCccee
Q psy12853 98 CCPMCSVPIEKDEG--CAQMLCKRCKHVF 124 (137)
Q Consensus 98 ~CP~C~~~iek~~g--C~hm~C~~C~~~f 124 (137)
-||.|+.++...++ -++..|+.||+.+
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 58999988877543 4688999999875
No 26
>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=94.31 E-value=0.058 Score=28.68 Aligned_cols=28 Identities=25% Similarity=0.717 Sum_probs=19.4
Q ss_pred ccCCCCCCceeecC-----CCCeeecccccccc
Q psy12853 49 KCCPMCSVPIEKDE-----GCAQMLCKRCKHVF 76 (137)
Q Consensus 49 ~~CP~C~~~i~~~~-----~~~~~~C~~C~~~f 76 (137)
..||+|+..+..++ ....+.|++|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 46888888777653 23468888887654
No 27
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=93.97 E-value=0.031 Score=47.83 Aligned_cols=10 Identities=40% Similarity=1.089 Sum_probs=6.1
Q ss_pred CCCCCCCcce
Q psy12853 97 KCCPMCSVPI 106 (137)
Q Consensus 97 ~~CP~C~~~i 106 (137)
+.||+|+..+
T Consensus 28 ~~Cp~CG~~~ 37 (645)
T PRK14559 28 KPCPQCGTEV 37 (645)
T ss_pred CcCCCCCCCC
Confidence 3566666665
No 28
>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=93.64 E-value=0.045 Score=28.92 Aligned_cols=27 Identities=22% Similarity=0.589 Sum_probs=17.5
Q ss_pred ccCCCCCCceeecC-CCCeeeccccccc
Q psy12853 49 KCCPMCSVPIEKDE-GCAQMLCKRCKHV 75 (137)
Q Consensus 49 ~~CP~C~~~i~~~~-~~~~~~C~~C~~~ 75 (137)
++||.|+..+.... ....+.|..|++.
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGYE 29 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-E
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCCc
Confidence 68999999987753 2332377777764
No 29
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=93.38 E-value=0.089 Score=29.30 Aligned_cols=28 Identities=25% Similarity=0.446 Sum_probs=16.8
Q ss_pred CCCCCCcceeecCCCCeEEeccCcceee
Q psy12853 98 CCPMCSVPIEKDEGCAQMLCKRCKHVFC 125 (137)
Q Consensus 98 ~CP~C~~~iek~~gC~hm~C~~C~~~fC 125 (137)
+||+|+..++....=..++|..||..+=
T Consensus 5 ~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 5 KCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred ECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 5677776666554433566666666543
No 30
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=93.29 E-value=0.045 Score=31.06 Aligned_cols=47 Identities=23% Similarity=0.644 Sum_probs=21.0
Q ss_pred CCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcce
Q psy12853 51 CPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPI 106 (137)
Q Consensus 51 CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~i 106 (137)
||.|...+ -..+.....| .|++.+|.-|... -. ....-+||.|+.+.
T Consensus 1 cp~C~e~~-d~~d~~~~PC-~Cgf~IC~~C~~~---i~----~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEEL-DETDKDFYPC-ECGFQICRFCYHD---IL----ENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B---CCCTT--SS-TTS----HHHHHH---HT----TSS-SB-TTT--B-
T ss_pred CCCccccc-ccCCCccccC-cCCCcHHHHHHHH---HH----hccCCCCCCCCCCC
Confidence 57777777 2245677889 7999999999532 11 12355899999865
No 31
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=93.15 E-value=0.06 Score=30.80 Aligned_cols=30 Identities=23% Similarity=0.441 Sum_probs=20.9
Q ss_pred CCcccCCCCCCceeecCCCCeeecccccccc
Q psy12853 46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVF 76 (137)
Q Consensus 46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~f 76 (137)
...++||.|+..+.. .....+.|.+|+..+
T Consensus 18 ~~~~fCP~Cg~~~m~-~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 18 RKNKFCPRCGSGFMA-EHLDRWHCGKCGYTE 47 (50)
T ss_pred EccCcCcCCCcchhe-ccCCcEECCCcCCEE
Confidence 457799999984222 233678899998764
No 32
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=92.96 E-value=0.045 Score=29.17 Aligned_cols=32 Identities=34% Similarity=0.807 Sum_probs=22.6
Q ss_pred ecccccccccccccccccCCCCcccccccCCCCCCCcce
Q psy12853 68 LCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPI 106 (137)
Q Consensus 68 ~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~i 106 (137)
.-+.|++.||..|...|-.. ...+||.|+..+
T Consensus 14 ~~~~C~H~~c~~C~~~~~~~-------~~~~Cp~C~~~~ 45 (45)
T cd00162 14 VLLPCGHVFCRSCIDKWLKS-------GKNTCPLCRTPI 45 (45)
T ss_pred EecCCCChhcHHHHHHHHHh-------CcCCCCCCCCcC
Confidence 33458999999998765432 345799988653
No 33
>PRK04023 DNA polymerase II large subunit; Validated
Probab=92.96 E-value=0.094 Score=46.75 Aligned_cols=48 Identities=19% Similarity=0.301 Sum_probs=32.4
Q ss_pred CCCCcccCCCCCCceeecCCCCeeecccccc-----cccccccccccCCCCcccccccCCCCCCCccee
Q psy12853 44 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKH-----VFCWYCLASRDYGGATFDSELIKCCPMCSVPIE 107 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~-----~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie 107 (137)
.....++||.|+... ..+.||.||. .||-.|+..-. ...||+|+..+.
T Consensus 622 VEVg~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~~~----------~y~CPKCG~El~ 674 (1121)
T PRK04023 622 VEIGRRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIEVE----------EDECEKCGREPT 674 (1121)
T ss_pred ecccCccCCCCCCcC------CcccCCCCCCCCCcceeCccccCcCC----------CCcCCCCCCCCC
Confidence 345578999999874 4578888885 47888864311 235888877654
No 34
>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=92.93 E-value=0.12 Score=31.64 Aligned_cols=21 Identities=29% Similarity=0.874 Sum_probs=7.9
Q ss_pred CCCCCcceeecCCCCeEEeccCc
Q psy12853 99 CPMCSVPIEKDEGCAQMLCKRCK 121 (137)
Q Consensus 99 CP~C~~~iek~~gC~hm~C~~C~ 121 (137)
||.|+..++..+ .+..|..|+
T Consensus 4 CP~C~~~L~~~~--~~~~C~~C~ 24 (70)
T PF07191_consen 4 CPKCQQELEWQG--GHYHCEACQ 24 (70)
T ss_dssp -SSS-SBEEEET--TEEEETTT-
T ss_pred CCCCCCccEEeC--CEEECcccc
Confidence 444444444444 244444443
No 35
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.84 E-value=0.13 Score=34.36 Aligned_cols=48 Identities=31% Similarity=0.761 Sum_probs=36.7
Q ss_pred cccCCCCCCceeec--------CCCCeeecccccccccccccccccCCCCcccccccCCCCCCC
Q psy12853 48 IKCCPMCSVPIEKD--------EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCS 103 (137)
Q Consensus 48 ~~~CP~C~~~i~~~--------~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~ 103 (137)
.+.|-+|...+... ......+|++|+..||..|..-+|+. ...||.|.
T Consensus 55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~--------Lh~CPGC~ 110 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHES--------LHCCPGCI 110 (112)
T ss_pred CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhh--------ccCCcCCC
Confidence 45699999987642 12456889999999999998766654 66799986
No 36
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=92.80 E-value=0.1 Score=47.50 Aligned_cols=49 Identities=24% Similarity=0.462 Sum_probs=29.9
Q ss_pred cccCCCCCCceeecCCCCeeecccccccc-----cccccccccCCCCcccccccCCCCCCCccee
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF-----CWYCLASRDYGGATFDSELIKCCPMCSVPIE 107 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~f-----C~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie 107 (137)
.+.||+|+..... ..||.||... |-.|+.+...+. .....||.|+..+.
T Consensus 667 ~rkCPkCG~~t~~------~fCP~CGs~te~vy~CPsCGaev~~de-----s~a~~CP~CGtplv 720 (1337)
T PRK14714 667 RRRCPSCGTETYE------NRCPDCGTHTEPVYVCPDCGAEVPPDE-----SGRVECPRCDVELT 720 (1337)
T ss_pred EEECCCCCCcccc------ccCcccCCcCCCceeCccCCCccCCCc-----cccccCCCCCCccc
Confidence 5788888886432 2788887664 777766433221 11446777776553
No 37
>PHA00626 hypothetical protein
Probab=92.66 E-value=0.11 Score=30.35 Aligned_cols=27 Identities=26% Similarity=0.602 Sum_probs=18.3
Q ss_pred CCCCCCc-ceeecCCCC----eEEeccCccee
Q psy12853 98 CCPMCSV-PIEKDEGCA----QMLCKRCKHVF 124 (137)
Q Consensus 98 ~CP~C~~-~iek~~gC~----hm~C~~C~~~f 124 (137)
.||+|+. .|-|.+-|+ ...|..||+.|
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence 5888888 466765543 37777777766
No 38
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=92.64 E-value=0.071 Score=26.15 Aligned_cols=11 Identities=36% Similarity=0.996 Sum_probs=7.3
Q ss_pred CCCCCCCccee
Q psy12853 97 KCCPMCSVPIE 107 (137)
Q Consensus 97 ~~CP~C~~~ie 107 (137)
+.||+|+..|+
T Consensus 3 ~~Cp~Cg~~~~ 13 (26)
T PF13248_consen 3 MFCPNCGAEID 13 (26)
T ss_pred CCCcccCCcCC
Confidence 56777777653
No 39
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=92.23 E-value=0.15 Score=29.17 Aligned_cols=28 Identities=21% Similarity=0.465 Sum_probs=20.8
Q ss_pred ccCCCCCCCc-ceeecCCCCeEEeccCccee
Q psy12853 95 LIKCCPMCSV-PIEKDEGCAQMLCKRCKHVF 124 (137)
Q Consensus 95 ~~~~CP~C~~-~iek~~gC~hm~C~~C~~~f 124 (137)
..+-||+|+. ...... +.+.|..||+.+
T Consensus 19 ~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~ 47 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHL--DRWHCGKCGYTE 47 (50)
T ss_pred ccCcCcCCCcchheccC--CcEECCCcCCEE
Confidence 4568999988 444434 689999999875
No 40
>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=91.65 E-value=0.17 Score=31.03 Aligned_cols=57 Identities=26% Similarity=0.718 Sum_probs=28.9
Q ss_pred cCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCeEEeccCc--ceeecc
Q psy12853 50 CCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCK--HVFCWY 127 (137)
Q Consensus 50 ~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~hm~C~~C~--~~fC~~ 127 (137)
.||.|...+...+ ....|..|...| ...-.||.|+.++|+-.. || -.||=.
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~-----------------~~~a~CPdC~~~Le~LkA--------CGAvdYFC~~ 55 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDY-----------------KKEAFCPDCGQPLEVLKA--------CGAVDYFCNH 55 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EE-----------------EEEEE-TTT-SB-EEEEE--------TTEEEEE-TT
T ss_pred cCCCCCCccEEeC--CEEECccccccc-----------------eecccCCCcccHHHHHHH--------hcccceeecc
Confidence 6999999987755 455665554432 123369999999987543 44 345555
Q ss_pred cccccc
Q psy12853 128 CLASLD 133 (137)
Q Consensus 128 C~~~~~ 133 (137)
|.+-.+
T Consensus 56 c~gLiS 61 (70)
T PF07191_consen 56 CHGLIS 61 (70)
T ss_dssp TT-EE-
T ss_pred CCceee
Confidence 554433
No 41
>KOG0317|consensus
Probab=91.36 E-value=0.056 Score=41.65 Aligned_cols=33 Identities=30% Similarity=0.882 Sum_probs=26.6
Q ss_pred cccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853 69 CKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD 109 (137)
Q Consensus 69 C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~ 109 (137)
|.-||+.|||.|-.+|-.... .||-|+.....+
T Consensus 254 aTpCGHiFCWsCI~~w~~ek~--------eCPlCR~~~~ps 286 (293)
T KOG0317|consen 254 ATPCGHIFCWSCILEWCSEKA--------ECPLCREKFQPS 286 (293)
T ss_pred cCcCcchHHHHHHHHHHcccc--------CCCcccccCCCc
Confidence 345999999999999987754 399999887654
No 42
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=91.36 E-value=0.12 Score=24.64 Aligned_cols=11 Identities=45% Similarity=1.090 Sum_probs=7.3
Q ss_pred CCCCCCcceee
Q psy12853 98 CCPMCSVPIEK 108 (137)
Q Consensus 98 ~CP~C~~~iek 108 (137)
.||+|+..|+.
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 37777777754
No 43
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=91.25 E-value=0.038 Score=31.23 Aligned_cols=30 Identities=40% Similarity=0.815 Sum_probs=23.6
Q ss_pred ccccc-ccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853 71 RCKHV-FCWYCLASRDYGGATFDSELIKCCPMCSVPIEK 108 (137)
Q Consensus 71 ~C~~~-fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek 108 (137)
.|++. ||..|...|.. ..++||-|+..|++
T Consensus 19 pCgH~~~C~~C~~~~~~--------~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 19 PCGHLCFCEECAERLLK--------RKKKCPICRQPIES 49 (50)
T ss_dssp TTCEEEEEHHHHHHHHH--------TTSBBTTTTBB-SE
T ss_pred CCCChHHHHHHhHHhcc--------cCCCCCcCChhhcC
Confidence 58999 99999876544 45789999999975
No 44
>PHA02926 zinc finger-like protein; Provisional
Probab=90.75 E-value=0.082 Score=39.50 Aligned_cols=59 Identities=20% Similarity=0.481 Sum_probs=37.9
Q ss_pred cccCCCCCCceeecC--CC-CeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853 48 IKCCPMCSVPIEKDE--GC-AQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK 108 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~--~~-~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek 108 (137)
-.-|+=|-..+.... +. ..-.=+.|++.||+.|-..|..... .....+.||-|++....
T Consensus 170 E~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~--~~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 170 EKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRR--ETGASDNCPICRTRFRN 231 (242)
T ss_pred CCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhcc--ccCcCCcCCCCcceeee
Confidence 456777776553221 11 1111236999999999999987532 23446789999988753
No 45
>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=90.54 E-value=0.26 Score=23.81 Aligned_cols=21 Identities=29% Similarity=0.684 Sum_probs=12.1
Q ss_pred CCCCceeecCCCCeeeccccc
Q psy12853 53 MCSVPIEKDEGCAQMLCKRCK 73 (137)
Q Consensus 53 ~C~~~i~~~~~~~~~~C~~C~ 73 (137)
.|+..|..-.....+.||+||
T Consensus 3 sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 3 SCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred cCCCcccCcccCceEeCCCCC
Confidence 455555543445666777765
No 46
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=90.44 E-value=0.34 Score=42.22 Aligned_cols=47 Identities=26% Similarity=0.665 Sum_probs=34.5
Q ss_pred CCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCeEEeccCcce-----eecccccc
Q psy12853 64 CAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHV-----FCWYCLAS 131 (137)
Q Consensus 64 ~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~hm~C~~C~~~-----fC~~C~~~ 131 (137)
...+.|..||+.+. ||+|.....-...=+.|.|..||++ .|-.||..
T Consensus 433 s~~l~C~~Cg~v~~---------------------Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 433 APLLLCRDCGYIAE---------------------CPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred cceeecccCCCccc---------------------CCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 44667777766553 8888888776655588888888887 68888876
No 47
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=90.44 E-value=0.3 Score=32.69 Aligned_cols=30 Identities=17% Similarity=0.595 Sum_probs=23.2
Q ss_pred cccCCCCCCceeec--CCCCeeeccccccccc
Q psy12853 48 IKCCPMCSVPIEKD--EGCAQMLCKRCKHVFC 77 (137)
Q Consensus 48 ~~~CP~C~~~i~~~--~~~~~~~C~~C~~~fC 77 (137)
.++||.|+..+... ++...+.|++|++..=
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~ 33 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEEE 33 (113)
T ss_pred ccccCCccCeeEEeEcCCCcEEECCCCCcchh
Confidence 57999999998874 3456888988877653
No 48
>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=90.31 E-value=0.25 Score=25.18 Aligned_cols=26 Identities=27% Similarity=0.871 Sum_probs=13.7
Q ss_pred CCCCCCcceeecCCCCeEEeccCccee
Q psy12853 98 CCPMCSVPIEKDEGCAQMLCKRCKHVF 124 (137)
Q Consensus 98 ~CP~C~~~iek~~gC~hm~C~~C~~~f 124 (137)
+||.|+....-.+|. .|.|..|+++|
T Consensus 4 ~Cp~C~se~~y~D~~-~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGE-LLVCPECGHEW 29 (30)
T ss_dssp --TTT-----EE-SS-SEEETTTTEEE
T ss_pred CCCCCCCcceeccCC-EEeCCcccccC
Confidence 689998888776664 46788888876
No 49
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=90.12 E-value=0.19 Score=33.47 Aligned_cols=31 Identities=19% Similarity=0.506 Sum_probs=21.9
Q ss_pred CcccCCCCCCceeecCCCCeeecccccccccc
Q psy12853 47 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCW 78 (137)
Q Consensus 47 ~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~ 78 (137)
.-+-||.|+.-|.--.. ..++||+||+.|=.
T Consensus 8 tKR~Cp~CG~kFYDLnk-~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNK-DPIVCPKCGTEFPP 38 (108)
T ss_pred CcccCCCCcchhccCCC-CCccCCCCCCccCc
Confidence 35678999988754333 67889988877643
No 50
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=90.01 E-value=0.43 Score=24.50 Aligned_cols=27 Identities=22% Similarity=0.555 Sum_probs=23.4
Q ss_pred ccCCCCCCceeecCCCCeeeccccccc
Q psy12853 49 KCCPMCSVPIEKDEGCAQMLCKRCKHV 75 (137)
Q Consensus 49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~ 75 (137)
..|.+|+..+.+..|+..+.|..|+..
T Consensus 2 ~~C~~C~t~L~yP~gA~~vrCs~C~~v 28 (31)
T TIGR01053 2 VVCGGCRTLLMYPRGASSVRCALCQTV 28 (31)
T ss_pred cCcCCCCcEeecCCCCCeEECCCCCeE
Confidence 368999999999999999999988753
No 51
>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=90.00 E-value=0.5 Score=24.15 Aligned_cols=28 Identities=25% Similarity=0.582 Sum_probs=15.7
Q ss_pred cCCCCCCCcceeecCCCCeEEeccCcce
Q psy12853 96 IKCCPMCSVPIEKDEGCAQMLCKRCKHV 123 (137)
Q Consensus 96 ~~~CP~C~~~iek~~gC~hm~C~~C~~~ 123 (137)
.+-||.|+.+.+...+=.-|.|..||.+
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred CcccCcCCccccCCCCcCEeECCCCcCE
Confidence 4568888888887766455788877765
No 52
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=89.77 E-value=0.094 Score=38.33 Aligned_cols=58 Identities=22% Similarity=0.608 Sum_probs=37.6
Q ss_pred CCCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCc-------c-cccccCCCCCCCcceee
Q psy12853 45 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGAT-------F-DSELIKCCPMCSVPIEK 108 (137)
Q Consensus 45 ~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~-------~-~~~~~~~CP~C~~~iek 108 (137)
......||-|...+. ...+ ..|++.||+.|...|...... + ...+..+||.|+..|..
T Consensus 15 ~~~~~~CpICld~~~----dPVv--T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 15 SGGDFDCNICLDQVR----DPVV--TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CCCccCCccCCCcCC----CcEE--cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 334567888876542 1222 369999999999988543211 1 12345689999998854
No 53
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=89.52 E-value=0.14 Score=31.98 Aligned_cols=61 Identities=20% Similarity=0.502 Sum_probs=24.9
Q ss_pred CcccCCCCCCceeec-CCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCe
Q psy12853 47 LIKCCPMCSVPIEKD-EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQ 114 (137)
Q Consensus 47 ~~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~h 114 (137)
+...|--|+--+-.. +|...+.|..|++-.|..|.. -..++..+-||.|++...+..|+..
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyE-------YErkeg~q~CpqCkt~ykr~kgsp~ 69 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYE-------YERKEGNQVCPQCKTRYKRHKGSPR 69 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHH-------HHHHTS-SB-TTT--B----TT---
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHH-------HHhhcCcccccccCCCcccccCCCC
Confidence 345666788777654 477889999999999999964 1124567899999999988777644
No 54
>KOG2932|consensus
Probab=89.47 E-value=0.093 Score=41.01 Aligned_cols=56 Identities=30% Similarity=0.639 Sum_probs=42.5
Q ss_pred CCCCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCe
Q psy12853 44 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQ 114 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~h 114 (137)
..+.+.+|-.|+.+|..-+ +.+ -|++.||+.|... ...|.||.|.-.|+|.+.|.-
T Consensus 86 l~p~VHfCd~Cd~PI~IYG--RmI---PCkHvFCl~CAr~----------~~dK~Cp~C~d~VqrIeq~~~ 141 (389)
T KOG2932|consen 86 LGPRVHFCDRCDFPIAIYG--RMI---PCKHVFCLECARS----------DSDKICPLCDDRVQRIEQIMM 141 (389)
T ss_pred cCcceEeecccCCcceeee--ccc---ccchhhhhhhhhc----------CccccCcCcccHHHHHHHhcc
Confidence 4566888899999986643 233 3689999999753 347889999999999887643
No 55
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.12 E-value=0.21 Score=39.07 Aligned_cols=54 Identities=24% Similarity=0.579 Sum_probs=36.2
Q ss_pred ccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecC
Q psy12853 49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDE 110 (137)
Q Consensus 49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~ 110 (137)
.-||.|..-....+.-..+.= .||+.||-.|....- ..+..+||.|+..+.+..
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~-------~~~~~~CP~C~~~lrk~~ 57 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLF-------VRGSGSCPECDTPLRKNN 57 (309)
T ss_pred CCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHh-------cCCCCCCCCCCCccchhh
Confidence 369999886555444332322 689999999986421 122348999999987753
No 56
>PRK00420 hypothetical protein; Validated
Probab=89.11 E-value=0.47 Score=31.75 Aligned_cols=40 Identities=23% Similarity=0.414 Sum_probs=25.8
Q ss_pred HHHHhhccccccCCCCcccCCCCCCceeecCCCCeeeccccccc
Q psy12853 32 IWHRTQVSGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHV 75 (137)
Q Consensus 32 ~~~r~~~~~a~~~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~ 75 (137)
+--++++..+.+. ...||.|+.++... ....+.||.|+..
T Consensus 10 ~~a~~Ll~Ga~ml---~~~CP~Cg~pLf~l-k~g~~~Cp~Cg~~ 49 (112)
T PRK00420 10 KAAELLLKGAKML---SKHCPVCGLPLFEL-KDGEVVCPVHGKV 49 (112)
T ss_pred HHHHHHHhHHHHc---cCCCCCCCCcceec-CCCceECCCCCCe
Confidence 3334445555442 36899999998874 3446778877764
No 57
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=89.04 E-value=0.34 Score=41.67 Aligned_cols=11 Identities=27% Similarity=0.709 Sum_probs=5.2
Q ss_pred cCCCCCCCcce
Q psy12853 96 IKCCPMCSVPI 106 (137)
Q Consensus 96 ~~~CP~C~~~i 106 (137)
.+-||+|+..+
T Consensus 41 ~~fC~~CG~~~ 51 (645)
T PRK14559 41 EAHCPNCGAET 51 (645)
T ss_pred cccccccCCcc
Confidence 44455554443
No 58
>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=88.96 E-value=0.53 Score=25.74 Aligned_cols=26 Identities=27% Similarity=0.611 Sum_probs=16.6
Q ss_pred cCCCCCCce-eecCCCCeeeccccccc
Q psy12853 50 CCPMCSVPI-EKDEGCAQMLCKRCKHV 75 (137)
Q Consensus 50 ~CP~C~~~i-~~~~~~~~~~C~~C~~~ 75 (137)
.||.|+... ..+.....+.|+.||..
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-BB
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCCE
Confidence 588888864 44455666777777654
No 59
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=88.84 E-value=0.18 Score=26.85 Aligned_cols=31 Identities=26% Similarity=0.752 Sum_probs=19.8
Q ss_pred CCCCCcceeecCCCCeEEeccCcceeeccccccccc
Q psy12853 99 CPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDV 134 (137)
Q Consensus 99 CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~~ 134 (137)
||-|...+.. -+.-..||+.||+.|...+..
T Consensus 1 C~iC~~~~~~-----~~~~~~CGH~fC~~C~~~~~~ 31 (39)
T PF13923_consen 1 CPICLDELRD-----PVVVTPCGHSFCKECIEKYLE 31 (39)
T ss_dssp ETTTTSB-SS-----EEEECTTSEEEEHHHHHHHHH
T ss_pred CCCCCCcccC-----cCEECCCCCchhHHHHHHHHH
Confidence 4555444432 335557999999999877643
No 60
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=88.72 E-value=0.31 Score=27.75 Aligned_cols=30 Identities=17% Similarity=0.441 Sum_probs=21.0
Q ss_pred CCcccCCCCCCceeecCCCCeeeccccccc
Q psy12853 46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHV 75 (137)
Q Consensus 46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~ 75 (137)
...+.||+|+.......-..+..|.+|+..
T Consensus 17 rk~~~CPrCG~gvfmA~H~dR~~CGkCgyT 46 (51)
T COG1998 17 RKNRFCPRCGPGVFMADHKDRWACGKCGYT 46 (51)
T ss_pred EccccCCCCCCcchhhhcCceeEeccccce
Confidence 346799999975554444458888888764
No 61
>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=88.13 E-value=0.54 Score=28.15 Aligned_cols=30 Identities=20% Similarity=0.488 Sum_probs=22.8
Q ss_pred ccCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853 95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF 124 (137)
Q Consensus 95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~f 124 (137)
+.+.||.|+...++...=..++|..||..+
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCEE
Confidence 578899999999885555568888777653
No 62
>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=87.82 E-value=0.57 Score=25.61 Aligned_cols=24 Identities=29% Similarity=0.919 Sum_probs=17.6
Q ss_pred ccCCCCCCceeecCCCCeeeccccc
Q psy12853 49 KCCPMCSVPIEKDEGCAQMLCKRCK 73 (137)
Q Consensus 49 ~~CP~C~~~i~~~~~~~~~~C~~C~ 73 (137)
..||.|+.++..+. ...+.|+.|+
T Consensus 18 ~~Cp~C~~PL~~~k-~g~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMRDK-DGKIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEEec-CCCEECCCCC
Confidence 48999999988743 3457787764
No 63
>PF14369 zf-RING_3: zinc-finger
Probab=87.71 E-value=0.54 Score=24.76 Aligned_cols=29 Identities=21% Similarity=0.446 Sum_probs=17.3
Q ss_pred cccCCCCCCceeecC-CCCeeecccccccc
Q psy12853 48 IKCCPMCSVPIEKDE-GCAQMLCKRCKHVF 76 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~-~~~~~~C~~C~~~f 76 (137)
..||=.|+..+.... +...+.||.|+..|
T Consensus 2 ~ywCh~C~~~V~~~~~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 2 RYWCHQCNRFVRIAPSPDSDVACPRCHGGF 31 (35)
T ss_pred CEeCccCCCEeEeCcCCCCCcCCcCCCCcE
Confidence 347777777776643 23334577776554
No 64
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=87.45 E-value=0.64 Score=31.92 Aligned_cols=35 Identities=26% Similarity=0.632 Sum_probs=23.7
Q ss_pred HhhccccccCCCCcccCCCCCCceeecCCCCeeecccccc
Q psy12853 35 RTQVSGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKH 74 (137)
Q Consensus 35 r~~~~~a~~~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~ 74 (137)
++++..|.+. ...||.|+.++... ...+.||.|++
T Consensus 18 ~lLl~GAkML---~~hCp~Cg~PLF~K--dG~v~CPvC~~ 52 (131)
T COG1645 18 ELLLQGAKML---AKHCPKCGTPLFRK--DGEVFCPVCGY 52 (131)
T ss_pred HHHHhhhHHH---HhhCcccCCcceee--CCeEECCCCCc
Confidence 4445555443 45899999998773 34577887775
No 65
>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=87.27 E-value=0.5 Score=28.31 Aligned_cols=33 Identities=18% Similarity=0.455 Sum_probs=26.2
Q ss_pred CCCCcccCCCCCCceeecCCCCeeecccccccc
Q psy12853 44 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVF 76 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~f 76 (137)
.....+.||.|+...........+.|+.||..+
T Consensus 24 ~~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 24 EAYTSQTCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred CCCCccCccCcccccccccccceEEcCCCCCEE
Confidence 344688999999998886677889999887653
No 66
>KOG2906|consensus
Probab=87.10 E-value=0.55 Score=30.60 Aligned_cols=27 Identities=33% Similarity=0.920 Sum_probs=21.4
Q ss_pred CCCCCCccee--ecCCCCeEEeccCccee
Q psy12853 98 CCPMCSVPIE--KDEGCAQMLCKRCKHVF 124 (137)
Q Consensus 98 ~CP~C~~~ie--k~~gC~hm~C~~C~~~f 124 (137)
-||.|+.++. ..+.||...|+.|.+.|
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~ 31 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVF 31 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCcee
Confidence 4899987654 44559999999999876
No 67
>KOG0823|consensus
Probab=87.02 E-value=0.27 Score=36.76 Aligned_cols=48 Identities=25% Similarity=0.603 Sum_probs=33.7
Q ss_pred CCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853 53 MCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK 108 (137)
Q Consensus 53 ~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek 108 (137)
+|+.-+.. ..++.+++ ||+-|||-|...|-.. ..+.+-||-|+..|..
T Consensus 49 dCNICLd~-akdPVvTl--CGHLFCWpClyqWl~~-----~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 49 DCNICLDL-AKDPVVTL--CGHLFCWPCLYQWLQT-----RPNSKECPVCKAEVSI 96 (230)
T ss_pred eeeeeccc-cCCCEEee--cccceehHHHHHHHhh-----cCCCeeCCcccccccc
Confidence 56665544 23566666 9999999999887443 2456778999887754
No 68
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=86.98 E-value=0.84 Score=22.25 Aligned_cols=24 Identities=21% Similarity=0.577 Sum_probs=20.3
Q ss_pred CCCCCCceeecCCCCeeecccccc
Q psy12853 51 CPMCSVPIEKDEGCAQMLCKRCKH 74 (137)
Q Consensus 51 CP~C~~~i~~~~~~~~~~C~~C~~ 74 (137)
|-+|...+.+..|+..+.|..|++
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCc
Confidence 457889999989999999988865
No 69
>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=86.96 E-value=0.41 Score=31.83 Aligned_cols=27 Identities=22% Similarity=0.722 Sum_probs=12.7
Q ss_pred CCCCCCCcceeecCCCCeEEeccCccee
Q psy12853 97 KCCPMCSVPIEKDEGCAQMLCKRCKHVF 124 (137)
Q Consensus 97 ~~CP~C~~~iek~~gC~hm~C~~C~~~f 124 (137)
+.||.|+...---.. +-++|..||+.|
T Consensus 10 R~Cp~CG~kFYDLnk-~PivCP~CG~~~ 36 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK-DPIVCPKCGTEF 36 (108)
T ss_pred ccCCCCcchhccCCC-CCccCCCCCCcc
Confidence 445555554433222 445555555544
No 70
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=86.52 E-value=0.13 Score=39.94 Aligned_cols=30 Identities=27% Similarity=0.664 Sum_probs=23.6
Q ss_pred ccCCCCCCCcceeecC-CCCeEEeccCccee
Q psy12853 95 LIKCCPMCSVPIEKDE-GCAQMLCKRCKHVF 124 (137)
Q Consensus 95 ~~~~CP~C~~~iek~~-gC~hm~C~~C~~~f 124 (137)
.|.+||+|+..+.+.+ .=|.+.|..||++|
T Consensus 26 ~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 26 LWTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred CeeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 4889999998887643 44678898899887
No 71
>PLN02189 cellulose synthase
Probab=86.46 E-value=0.64 Score=41.82 Aligned_cols=63 Identities=21% Similarity=0.496 Sum_probs=48.7
Q ss_pred CCcccCCCCCCceeec-CCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCeE
Q psy12853 46 ELIKCCPMCSVPIEKD-EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQM 115 (137)
Q Consensus 46 ~~~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~hm 115 (137)
-+..-|.-|+.-+-.+ +|...+.|..|+.-.|.-|.. +. .+++.+.||.|++...+-.|++.+
T Consensus 32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cye-ye------r~eg~q~CpqCkt~Y~r~kgs~~v 95 (1040)
T PLN02189 32 LDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYE-YE------RREGTQNCPQCKTRYKRLKGSPRV 95 (1040)
T ss_pred ccCccccccccccCcCCCCCEEEeeccCCCccccchhh-hh------hhcCCccCcccCCchhhccCCCCc
Confidence 3456788899887664 467889999999999999972 22 235678999999999877777654
No 72
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=86.36 E-value=0.65 Score=31.90 Aligned_cols=25 Identities=32% Similarity=0.960 Sum_probs=19.3
Q ss_pred cCCCCCCCcceeecCCCCeEEeccCcc
Q psy12853 96 IKCCPMCSVPIEKDEGCAQMLCKRCKH 122 (137)
Q Consensus 96 ~~~CP~C~~~iek~~gC~hm~C~~C~~ 122 (137)
.+.||.|++++.+..| -+.|..||+
T Consensus 28 ~~hCp~Cg~PLF~KdG--~v~CPvC~~ 52 (131)
T COG1645 28 AKHCPKCGTPLFRKDG--EVFCPVCGY 52 (131)
T ss_pred HhhCcccCCcceeeCC--eEECCCCCc
Confidence 5689999999999666 566666664
No 73
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=86.12 E-value=0.78 Score=29.17 Aligned_cols=50 Identities=30% Similarity=0.750 Sum_probs=34.3
Q ss_pred cCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853 50 CCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK 108 (137)
Q Consensus 50 ~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek 108 (137)
-||+|..+ .++.+.+.. .|++.|=..|...|.... .....||-|+...+.
T Consensus 34 ~Cp~Ck~P---gd~Cplv~g-~C~H~FH~hCI~kWl~~~-----~~~~~CPmCR~~w~~ 83 (85)
T PF12861_consen 34 CCPDCKFP---GDDCPLVWG-KCSHNFHMHCILKWLSTQ-----SSKGQCPMCRQPWKF 83 (85)
T ss_pred CCCCccCC---CCCCceeec-cCccHHHHHHHHHHHccc-----cCCCCCCCcCCeeee
Confidence 35666554 123444444 699999999999888764 224689999988764
No 74
>PF14353 CpXC: CpXC protein
Probab=85.90 E-value=0.72 Score=31.15 Aligned_cols=39 Identities=21% Similarity=0.353 Sum_probs=25.3
Q ss_pred cCCCCCCceeec-------------------CCCCeeecccccccccccccccccCCC
Q psy12853 50 CCPMCSVPIEKD-------------------EGCAQMLCKRCKHVFCWYCLASRDYGG 88 (137)
Q Consensus 50 ~CP~C~~~i~~~-------------------~~~~~~~C~~C~~~fC~~C~~~~h~~~ 88 (137)
.||.|+..+... +.-..++||.||+.+=..=...+|.+.
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYHDPE 60 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEEcCC
Confidence 588888876642 123467888888777655555666664
No 75
>KOG0317|consensus
Probab=85.48 E-value=0.15 Score=39.33 Aligned_cols=36 Identities=25% Similarity=0.708 Sum_probs=26.5
Q ss_pred cccCCCCCCCcceeecCCCCeEEeccCcceeecccccccccC
Q psy12853 94 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDVS 135 (137)
Q Consensus 94 ~~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~~~ 135 (137)
+.+.+|--|.... .|-+|+-||+-|||.|...|-..
T Consensus 237 ~a~~kC~LCLe~~------~~pSaTpCGHiFCWsCI~~w~~e 272 (293)
T KOG0317|consen 237 EATRKCSLCLENR------SNPSATPCGHIFCWSCILEWCSE 272 (293)
T ss_pred CCCCceEEEecCC------CCCCcCcCcchHHHHHHHHHHcc
Confidence 3456777776655 35778899999999998777543
No 76
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=85.31 E-value=0.99 Score=25.83 Aligned_cols=30 Identities=20% Similarity=0.343 Sum_probs=19.0
Q ss_pred cCCCCCCCcceee------cCCCCeE-EeccCcceee
Q psy12853 96 IKCCPMCSVPIEK------DEGCAQM-LCKRCKHVFC 125 (137)
Q Consensus 96 ~~~CP~C~~~iek------~~gC~hm-~C~~C~~~fC 125 (137)
.++||.|+..-+. +.+..++ .|..||+..-
T Consensus 1 LkPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~ 37 (53)
T TIGR03655 1 LKPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGP 37 (53)
T ss_pred CCCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCcc
Confidence 4799999876662 2234444 5777777654
No 77
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=85.16 E-value=0.29 Score=26.76 Aligned_cols=28 Identities=32% Similarity=0.620 Sum_probs=16.8
Q ss_pred cccccccccccccccCCCCcccccccCCCCCC
Q psy12853 71 RCKHVFCWYCLASRDYGGATFDSELIKCCPMC 102 (137)
Q Consensus 71 ~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C 102 (137)
.||+.||..|...+-.... .....||.|
T Consensus 15 ~CGH~FC~~Cl~~~~~~~~----~~~~~CP~C 42 (42)
T PF15227_consen 15 PCGHSFCRSCLERLWKEPS----GSGFSCPEC 42 (42)
T ss_dssp SSSSEEEHHHHHHHHCCSS----SST---SSS
T ss_pred CCcCHHHHHHHHHHHHccC----CcCCCCcCC
Confidence 6999999999886544422 111578876
No 78
>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=85.12 E-value=0.5 Score=25.16 Aligned_cols=13 Identities=23% Similarity=0.848 Sum_probs=7.9
Q ss_pred cCCCCCCCcceee
Q psy12853 96 IKCCPMCSVPIEK 108 (137)
Q Consensus 96 ~~~CP~C~~~iek 108 (137)
...||.|+..++|
T Consensus 26 ~~~CP~Cg~~~~r 38 (41)
T smart00834 26 LATCPECGGDVRR 38 (41)
T ss_pred CCCCCCCCCccee
Confidence 4457777665554
No 79
>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=85.10 E-value=0.69 Score=30.09 Aligned_cols=27 Identities=22% Similarity=0.534 Sum_probs=20.1
Q ss_pred ccCCCCCCceeecCCCCeeeccccccccc
Q psy12853 49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFC 77 (137)
Q Consensus 49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC 77 (137)
.+||+|+..+.... ..+.|+.|++.+=
T Consensus 1 ~fC~~Cg~~l~~~~--~~~~C~~C~~~~~ 27 (104)
T TIGR01384 1 KFCPKCGSLMTPKN--GVYVCPSCGYEKE 27 (104)
T ss_pred CCCcccCcccccCC--CeEECcCCCCccc
Confidence 37999999986543 4688988887654
No 80
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=85.09 E-value=1.2 Score=23.17 Aligned_cols=29 Identities=21% Similarity=0.370 Sum_probs=20.4
Q ss_pred cccCCCCCCceeecCCCCeeecccccccc
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF 76 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~f 76 (137)
.+.|+.|+...+.........|+.|+..|
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 45688898887775556667777777653
No 81
>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=84.89 E-value=0.78 Score=30.40 Aligned_cols=28 Identities=25% Similarity=0.682 Sum_probs=21.4
Q ss_pred ccCCCCCCceeecCCCCeeeccccccccc
Q psy12853 49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFC 77 (137)
Q Consensus 49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC 77 (137)
-.||.|+.-+.+.++. .+.||.|++.+=
T Consensus 3 p~CP~C~seytY~dg~-~~iCpeC~~EW~ 30 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGT-QLICPSCLYEWN 30 (109)
T ss_pred CcCCcCCCcceEecCC-eeECcccccccc
Confidence 4699999999887765 588888776553
No 82
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=84.83 E-value=0.72 Score=35.12 Aligned_cols=31 Identities=23% Similarity=0.558 Sum_probs=24.9
Q ss_pred CCCcccCCCCCCceeecCCCCeeeccccccc
Q psy12853 45 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHV 75 (137)
Q Consensus 45 ~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~ 75 (137)
....+|||.|+..+....+.....|+.|+..
T Consensus 96 ~~~~~fC~~CG~~~~~~~~~~~~~C~~c~~~ 126 (256)
T PRK00241 96 YRSHRFCGYCGHPMHPSKTEWAMLCPHCRER 126 (256)
T ss_pred hhcCccccccCCCCeecCCceeEECCCCCCE
Confidence 3558899999999887777777889988743
No 83
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=84.80 E-value=0.58 Score=40.97 Aligned_cols=27 Identities=37% Similarity=1.053 Sum_probs=24.1
Q ss_pred CCCCCCCcceeecCCCCeEEeccCcceee
Q psy12853 97 KCCPMCSVPIEKDEGCAQMLCKRCKHVFC 125 (137)
Q Consensus 97 ~~CP~C~~~iek~~gC~hm~C~~C~~~fC 125 (137)
..||.|+..+...+||. +|..||+.=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCHSCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCCC--cCCCCCCCCC
Confidence 36999999999999998 8999998766
No 84
>KOG0320|consensus
Probab=84.76 E-value=0.26 Score=35.57 Aligned_cols=49 Identities=27% Similarity=0.693 Sum_probs=30.7
Q ss_pred cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK 108 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek 108 (137)
..-||.|-..+..... .=.+||+.||..|.+.. ..++.+||-|+..|.+
T Consensus 131 ~~~CPiCl~~~sek~~----vsTkCGHvFC~~Cik~a--------lk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 131 TYKCPICLDSVSEKVP----VSTKCGHVFCSQCIKDA--------LKNTNKCPTCRKKITH 179 (187)
T ss_pred ccCCCceecchhhccc----cccccchhHHHHHHHHH--------HHhCCCCCCcccccch
Confidence 3556665554433221 12379999999997531 2356789999976643
No 85
>KOG2906|consensus
Probab=84.71 E-value=0.84 Score=29.77 Aligned_cols=31 Identities=29% Similarity=0.745 Sum_probs=23.4
Q ss_pred ccCCCCCCceeecCC--CCeeeccccccccccc
Q psy12853 49 KCCPMCSVPIEKDEG--CAQMLCKRCKHVFCWY 79 (137)
Q Consensus 49 ~~CP~C~~~i~~~~~--~~~~~C~~C~~~fC~~ 79 (137)
.+||.|+..++...+ .+.+.|..|.+.+=..
T Consensus 2 ~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESGESCNRFSCRTCPYVFPIS 34 (105)
T ss_pred cccCCCCCEEEEecCCeEeeEEcCCCCceeeEe
Confidence 589999999887654 4677888777766554
No 86
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=84.40 E-value=0.52 Score=28.40 Aligned_cols=37 Identities=22% Similarity=0.671 Sum_probs=15.1
Q ss_pred ccCCCCCCCcceeec---CCCCeEEeccCccee----ecccccc
Q psy12853 95 LIKCCPMCSVPIEKD---EGCAQMLCKRCKHVF----CWYCLAS 131 (137)
Q Consensus 95 ~~~~CP~C~~~iek~---~gC~hm~C~~C~~~f----C~~C~~~ 131 (137)
..-+|++|....... +||.|+.|+.|=..+ |-+|..|
T Consensus 6 ~lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~P 49 (65)
T PF14835_consen 6 ELLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTP 49 (65)
T ss_dssp HTTS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B
T ss_pred HhcCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCCh
Confidence 345788888777653 778887777663222 5555443
No 87
>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=84.37 E-value=1.1 Score=25.94 Aligned_cols=27 Identities=26% Similarity=0.645 Sum_probs=15.8
Q ss_pred cCCCCCCceeecC--CCCeeecccccccc
Q psy12853 50 CCPMCSVPIEKDE--GCAQMLCKRCKHVF 76 (137)
Q Consensus 50 ~CP~C~~~i~~~~--~~~~~~C~~C~~~f 76 (137)
.||.|+..|...+ ....+.|+.||..+
T Consensus 4 ~CP~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 4 ECPDCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred CCCCCCCEEecCCCccCCEEeCCCCCCEE
Confidence 5777777776543 13455666666543
No 88
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=84.33 E-value=0.85 Score=24.90 Aligned_cols=26 Identities=35% Similarity=0.857 Sum_probs=19.5
Q ss_pred cccccccccccccccCCCCcccccccCCCCCCCc
Q psy12853 71 RCKHVFCWYCLASRDYGGATFDSELIKCCPMCSV 104 (137)
Q Consensus 71 ~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~ 104 (137)
.|++.||..|..... .....||-|+.
T Consensus 19 ~CgH~~C~~C~~~~~--------~~~~~CP~C~k 44 (44)
T PF14634_consen 19 SCGHIFCEKCLKKLK--------GKSVKCPICRK 44 (44)
T ss_pred ccCCHHHHHHHHhhc--------CCCCCCcCCCC
Confidence 689999999986543 33568998863
No 89
>KOG0823|consensus
Probab=84.31 E-value=0.33 Score=36.35 Aligned_cols=20 Identities=40% Similarity=1.001 Sum_probs=16.3
Q ss_pred EEeccCcceeecccccccccCC
Q psy12853 115 MLCKRCKHVFCWYCLASLDVSR 136 (137)
Q Consensus 115 m~C~~C~~~fC~~C~~~~~~~~ 136 (137)
+|+ ||+-|||-|.-.|...+
T Consensus 62 vTl--CGHLFCWpClyqWl~~~ 81 (230)
T KOG0823|consen 62 VTL--CGHLFCWPCLYQWLQTR 81 (230)
T ss_pred Eee--cccceehHHHHHHHhhc
Confidence 555 99999999998887643
No 90
>PHA02929 N1R/p28-like protein; Provisional
Probab=84.28 E-value=0.95 Score=34.22 Aligned_cols=53 Identities=26% Similarity=0.550 Sum_probs=36.5
Q ss_pred CcccCCCCCCceeecCCC--CeeecccccccccccccccccCCCCcccccccCCCCCCCccee
Q psy12853 47 LIKCCPMCSVPIEKDEGC--AQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE 107 (137)
Q Consensus 47 ~~~~CP~C~~~i~~~~~~--~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie 107 (137)
....||=|...+...... ....=+.|++.||..|..+|... ...||-|+..+.
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~--------~~tCPlCR~~~~ 227 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE--------KNTCPVCRTPFI 227 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc--------CCCCCCCCCEee
Confidence 356889888876543211 11222379999999999998754 247999998875
No 91
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=84.26 E-value=0.62 Score=35.98 Aligned_cols=32 Identities=22% Similarity=0.405 Sum_probs=26.9
Q ss_pred CCCCcccCCCCCCceeecCCCCeeeccccccc
Q psy12853 44 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHV 75 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~ 75 (137)
-..+.++||+|+.......+....+|++|++.
T Consensus 107 w~~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~ 138 (279)
T COG2816 107 WYRSHRFCGRCGTKTYPREGGWARVCPKCGHE 138 (279)
T ss_pred HHhhCcCCCCCCCcCccccCceeeeCCCCCCc
Confidence 34668999999999998888899999998654
No 92
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=84.23 E-value=0.59 Score=25.86 Aligned_cols=22 Identities=32% Similarity=0.628 Sum_probs=16.2
Q ss_pred ccccCCCCCCCcceeecCCCCeEEec
Q psy12853 93 SELIKCCPMCSVPIEKDEGCAQMLCK 118 (137)
Q Consensus 93 ~~~~~~CP~C~~~iek~~gC~hm~C~ 118 (137)
...+++||+|++.- |..-+.|.
T Consensus 8 lRGirkCp~CGt~N----G~R~~~CK 29 (44)
T PF14952_consen 8 LRGIRKCPKCGTYN----GTRGLSCK 29 (44)
T ss_pred HhccccCCcCcCcc----Cccccccc
Confidence 45689999999887 55555555
No 93
>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=84.19 E-value=0.19 Score=38.98 Aligned_cols=30 Identities=23% Similarity=0.600 Sum_probs=22.9
Q ss_pred ccCCCCCCCcceeecC-CCCeEEeccCccee
Q psy12853 95 LIKCCPMCSVPIEKDE-GCAQMLCKRCKHVF 124 (137)
Q Consensus 95 ~~~~CP~C~~~iek~~-gC~hm~C~~C~~~f 124 (137)
.|.+||+|+..+.+.+ .=|...|..||++|
T Consensus 25 ~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 25 VWTKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred CeeECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 4888999988887743 45667888888875
No 94
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=84.04 E-value=0.18 Score=39.25 Aligned_cols=30 Identities=20% Similarity=0.288 Sum_probs=20.0
Q ss_pred ccCCCCCCCcceeecC-CCCeEEeccCccee
Q psy12853 95 LIKCCPMCSVPIEKDE-GCAQMLCKRCKHVF 124 (137)
Q Consensus 95 ~~~~CP~C~~~iek~~-gC~hm~C~~C~~~f 124 (137)
.|.+||+|+..+.+.. .=|...|..||++|
T Consensus 37 lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 37 LWVQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred CeeECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 3677777777776643 35566777777765
No 95
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=83.82 E-value=0.3 Score=26.05 Aligned_cols=31 Identities=35% Similarity=0.811 Sum_probs=19.2
Q ss_pred CCCCCcceeecCCCCeEEeccCcceeeccccccccc
Q psy12853 99 CPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDV 134 (137)
Q Consensus 99 CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~~ 134 (137)
||-|....+... +=..||+.||..|...+-.
T Consensus 1 C~iC~~~~~~~~-----~~~~C~H~fC~~C~~~~~~ 31 (41)
T PF00097_consen 1 CPICLEPFEDPV-----ILLPCGHSFCRDCLRKWLE 31 (41)
T ss_dssp ETTTSSBCSSEE-----EETTTSEEEEHHHHHHHHH
T ss_pred CCcCCccccCCC-----EEecCCCcchHHHHHHHHH
Confidence 455555544332 3346889999988876643
No 96
>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=83.66 E-value=0.91 Score=29.51 Aligned_cols=25 Identities=20% Similarity=0.574 Sum_probs=16.4
Q ss_pred CCCCCCcceeecCCCCeEEeccCccee
Q psy12853 98 CCPMCSVPIEKDEGCAQMLCKRCKHVF 124 (137)
Q Consensus 98 ~CP~C~~~iek~~gC~hm~C~~C~~~f 124 (137)
-||+|+.++...+ +.+.|..||+.+
T Consensus 2 fC~~Cg~~l~~~~--~~~~C~~C~~~~ 26 (104)
T TIGR01384 2 FCPKCGSLMTPKN--GVYVCPSCGYEK 26 (104)
T ss_pred CCcccCcccccCC--CeEECcCCCCcc
Confidence 4777777775544 367777777654
No 97
>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=83.61 E-value=0.53 Score=26.94 Aligned_cols=25 Identities=28% Similarity=0.669 Sum_probs=11.0
Q ss_pred CCCCCCcceeecCCCC--eEEeccCcc
Q psy12853 98 CCPMCSVPIEKDEGCA--QMLCKRCKH 122 (137)
Q Consensus 98 ~CP~C~~~iek~~gC~--hm~C~~C~~ 122 (137)
+|++|+.++-+.++=. .|.|.+||+
T Consensus 6 RC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 6 RCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred eccchhHHHhhhcCccEEEEECCCCCc
Confidence 4555555554433222 244544443
No 98
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=83.47 E-value=1.1 Score=26.10 Aligned_cols=28 Identities=29% Similarity=0.544 Sum_probs=18.3
Q ss_pred ccCCCCCCCcceeec---CCC-----CeEEeccCcc
Q psy12853 95 LIKCCPMCSVPIEKD---EGC-----AQMLCKRCKH 122 (137)
Q Consensus 95 ~~~~CP~C~~~iek~---~gC-----~hm~C~~C~~ 122 (137)
..++||.|+...... .+= .+|.|..||.
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 478999998554432 121 4588887776
No 99
>KOG0978|consensus
Probab=83.40 E-value=0.26 Score=42.49 Aligned_cols=49 Identities=22% Similarity=0.610 Sum_probs=32.8
Q ss_pred CCCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcce
Q psy12853 45 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPI 106 (137)
Q Consensus 45 ~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~i 106 (137)
......||-|+.-. .+ .-. ++|++.||..|-.. ......++||+|+...
T Consensus 640 yK~~LkCs~Cn~R~--Kd-~vI---~kC~H~FC~~Cvq~-------r~etRqRKCP~Cn~aF 688 (698)
T KOG0978|consen 640 YKELLKCSVCNTRW--KD-AVI---TKCGHVFCEECVQT-------RYETRQRKCPKCNAAF 688 (698)
T ss_pred HHhceeCCCccCch--hh-HHH---HhcchHHHHHHHHH-------HHHHhcCCCCCCCCCC
Confidence 35578899888321 11 101 27999999999753 2334578999999876
No 100
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=83.29 E-value=1.1 Score=29.29 Aligned_cols=14 Identities=21% Similarity=0.404 Sum_probs=8.3
Q ss_pred CCCeEEeccCccee
Q psy12853 111 GCAQMLCKRCKHVF 124 (137)
Q Consensus 111 gC~hm~C~~C~~~f 124 (137)
|=-|+.|..||+.+
T Consensus 39 ~~~h~~C~~CG~y~ 52 (99)
T PRK14892 39 NIAIITCGNCGLYT 52 (99)
T ss_pred CcceEECCCCCCcc
Confidence 34466666666654
No 101
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=82.81 E-value=1.3 Score=24.47 Aligned_cols=8 Identities=25% Similarity=0.605 Sum_probs=3.1
Q ss_pred CCCCCCce
Q psy12853 51 CPMCSVPI 58 (137)
Q Consensus 51 CP~C~~~i 58 (137)
|.+|+..+
T Consensus 5 C~~Cg~~~ 12 (44)
T smart00659 5 CGECGREN 12 (44)
T ss_pred CCCCCCEe
Confidence 33444433
No 102
>PRK10220 hypothetical protein; Provisional
Probab=82.76 E-value=1.2 Score=29.61 Aligned_cols=27 Identities=22% Similarity=0.732 Sum_probs=20.2
Q ss_pred ccCCCCCCceeecCCCCeeecccccccc
Q psy12853 49 KCCPMCSVPIEKDEGCAQMLCKRCKHVF 76 (137)
Q Consensus 49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~f 76 (137)
--||.|+.-+.+.++. .+.||.|++++
T Consensus 4 P~CP~C~seytY~d~~-~~vCpeC~hEW 30 (111)
T PRK10220 4 PHCPKCNSEYTYEDNG-MYICPECAHEW 30 (111)
T ss_pred CcCCCCCCcceEcCCC-eEECCcccCcC
Confidence 4699999999887764 47788766554
No 103
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=82.69 E-value=1 Score=40.71 Aligned_cols=63 Identities=19% Similarity=0.533 Sum_probs=48.2
Q ss_pred CCcccCCCCCCceeec-CCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCeE
Q psy12853 46 ELIKCCPMCSVPIEKD-EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQM 115 (137)
Q Consensus 46 ~~~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~hm 115 (137)
.+..-|--|+--+-.+ +|...+.|..|+.-.|.-|.. +.. +++.+-||.|++...+-.|+..+
T Consensus 15 ~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYE-YEr------~eG~q~CPqCktrYkr~kgsprv 78 (1079)
T PLN02638 15 GGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYE-YER------KDGNQSCPQCKTKYKRHKGSPAI 78 (1079)
T ss_pred cCCceeeecccccCcCCCCCEEEEeccCCCccccchhh-hhh------hcCCccCCccCCchhhhcCCCCc
Confidence 3455677788877665 578889999999999999972 222 35688999999999887777653
No 104
>PRK12495 hypothetical protein; Provisional
Probab=82.64 E-value=0.52 Score=35.12 Aligned_cols=27 Identities=30% Similarity=0.716 Sum_probs=17.9
Q ss_pred CCCcccCCCCCCceeecCCCCeeeccccc
Q psy12853 45 SELIKCCPMCSVPIEKDEGCAQMLCKRCK 73 (137)
Q Consensus 45 ~~~~~~CP~C~~~i~~~~~~~~~~C~~C~ 73 (137)
.....+|+.|+.+|....| .+.|+.|+
T Consensus 39 tmsa~hC~~CG~PIpa~pG--~~~Cp~CQ 65 (226)
T PRK12495 39 TMTNAHCDECGDPIFRHDG--QEFCPTCQ 65 (226)
T ss_pred ccchhhcccccCcccCCCC--eeECCCCC
Confidence 3457899999999985433 34455444
No 105
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=81.30 E-value=1.6 Score=21.73 Aligned_cols=21 Identities=29% Similarity=0.892 Sum_probs=12.9
Q ss_pred cCCCCCCceeecCCCCeeecc
Q psy12853 50 CCPMCSVPIEKDEGCAQMLCK 70 (137)
Q Consensus 50 ~CP~C~~~i~~~~~~~~~~C~ 70 (137)
.||.|+..+.+.++.....|+
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCP 21 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE-
T ss_pred CcCCCCCEeEcCCCCEeEECC
Confidence 489999999988777677775
No 106
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=81.23 E-value=1.7 Score=33.07 Aligned_cols=62 Identities=26% Similarity=0.582 Sum_probs=41.4
Q ss_pred CCeeecccccccccccccccccCCCCcccccccCCCCCCCccee-----ecCCCCeEEeccCccee-----------ecc
Q psy12853 64 CAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE-----KDEGCAQMLCKRCKHVF-----------CWY 127 (137)
Q Consensus 64 ~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie-----k~~gC~hm~C~~C~~~f-----------C~~ 127 (137)
...+.|..|.......+.. ...+-+|-+|+..++ |.-|=-...|.+|++.| ||.
T Consensus 110 drqFaC~~Cd~~WwRrvp~----------rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~~qm~v~sPCy~ 179 (278)
T PF15135_consen 110 DRQFACSSCDHMWWRRVPQ----------RKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGFAQMGVPSPCYG 179 (278)
T ss_pred ceeeeccccchHHHhccCc----------ccccccccccccccCCCccccccceeeeecccccccchhhhhcCCCCCccC
Confidence 4677888887776654432 244567777777654 44566667787888777 888
Q ss_pred cccccccC
Q psy12853 128 CLASLDVS 135 (137)
Q Consensus 128 C~~~~~~~ 135 (137)
|+.+..++
T Consensus 180 C~~~v~P~ 187 (278)
T PF15135_consen 180 CGNPVYPS 187 (278)
T ss_pred CCCccCcc
Confidence 88776553
No 107
>PRK00420 hypothetical protein; Validated
Probab=81.22 E-value=1.6 Score=29.19 Aligned_cols=25 Identities=28% Similarity=0.856 Sum_probs=18.1
Q ss_pred cCCCCCCCcceee-cCCCCeEEeccCcc
Q psy12853 96 IKCCPMCSVPIEK-DEGCAQMLCKRCKH 122 (137)
Q Consensus 96 ~~~CP~C~~~iek-~~gC~hm~C~~C~~ 122 (137)
...||.|+.++.+ ..| ...|..||.
T Consensus 23 ~~~CP~Cg~pLf~lk~g--~~~Cp~Cg~ 48 (112)
T PRK00420 23 SKHCPVCGLPLFELKDG--EVVCPVHGK 48 (112)
T ss_pred cCCCCCCCCcceecCCC--ceECCCCCC
Confidence 4689999999987 555 566666655
No 108
>PLN02436 cellulose synthase A
Probab=81.21 E-value=1.5 Score=39.71 Aligned_cols=63 Identities=22% Similarity=0.542 Sum_probs=47.9
Q ss_pred CCcccCCCCCCceeec-CCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCeE
Q psy12853 46 ELIKCCPMCSVPIEKD-EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQM 115 (137)
Q Consensus 46 ~~~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~hm 115 (137)
-+..-|--|+--+-.+ +|...+.|..|+...|.-|.. +. .+++.+.||.|++...+-.|++.+
T Consensus 34 ~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cye-ye------r~eg~~~Cpqckt~Y~r~kgs~~~ 97 (1094)
T PLN02436 34 LSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYE-YE------RREGNQACPQCKTRYKRIKGSPRV 97 (1094)
T ss_pred cCCccccccccccCcCCCCCEEEeeccCCCccccchhh-hh------hhcCCccCcccCCchhhccCCCCc
Confidence 3455777888877654 577889999999999999972 22 235678999999999877676653
No 109
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=80.98 E-value=1.8 Score=26.01 Aligned_cols=31 Identities=26% Similarity=0.625 Sum_probs=21.4
Q ss_pred cccCCCCCCCcceee---cCCCCeEEeccCccee
Q psy12853 94 ELIKCCPMCSVPIEK---DEGCAQMLCKRCKHVF 124 (137)
Q Consensus 94 ~~~~~CP~C~~~iek---~~gC~hm~C~~C~~~f 124 (137)
.++|+||.|+..+.+ .+|=-...|..|+..-
T Consensus 4 d~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~~ 37 (64)
T PRK09710 4 DNVKPCPFCGCPSVTVKAISGYYRAKCNGCESRT 37 (64)
T ss_pred ccccCCCCCCCceeEEEecCceEEEEcCCCCcCc
Confidence 358999999877665 3443347777787753
No 110
>PRK11827 hypothetical protein; Provisional
Probab=80.78 E-value=2 Score=25.51 Aligned_cols=28 Identities=21% Similarity=0.521 Sum_probs=19.9
Q ss_pred cccCCCCCCceeecCCCCeeeccccccc
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCKHV 75 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~ 75 (137)
..-||.|...+..+.+.+...|..|+..
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~la 35 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLA 35 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCee
Confidence 4468989888888766667777665543
No 111
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=80.35 E-value=0.81 Score=33.51 Aligned_cols=35 Identities=26% Similarity=0.680 Sum_probs=24.7
Q ss_pred ccccCCCCCCCcceeecCCCCeEEeccCcceeecccccccc
Q psy12853 93 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133 (137)
Q Consensus 93 ~~~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~ 133 (137)
..+.-.||-|...++.. +. +.||+.|||.|...|.
T Consensus 15 ~~~~~~CpICld~~~dP-----Vv-T~CGH~FC~~CI~~wl 49 (193)
T PLN03208 15 SGGDFDCNICLDQVRDP-----VV-TLCGHLFCWPCIHKWT 49 (193)
T ss_pred CCCccCCccCCCcCCCc-----EE-cCCCchhHHHHHHHHH
Confidence 34556899998766321 22 4699999999998773
No 112
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=80.19 E-value=0.54 Score=36.26 Aligned_cols=31 Identities=26% Similarity=0.627 Sum_probs=24.9
Q ss_pred cccCCCCCCCcceeecC-CCCeEEeccCccee
Q psy12853 94 ELIKCCPMCSVPIEKDE-GCAQMLCKRCKHVF 124 (137)
Q Consensus 94 ~~~~~CP~C~~~iek~~-gC~hm~C~~C~~~f 124 (137)
..|.+||+|+..+-+.+ +=|...|.+|+++|
T Consensus 26 ~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 26 GLWTKCPSCGEMLYRKELESNLKVCPKCGHHM 57 (294)
T ss_pred CceeECCCccceeeHHHHHhhhhcccccCccc
Confidence 45888999999888754 67788888898876
No 113
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=79.98 E-value=1.4 Score=23.75 Aligned_cols=24 Identities=25% Similarity=0.642 Sum_probs=13.9
Q ss_pred cCCCCCCceeec--CCCCeeeccccc
Q psy12853 50 CCPMCSVPIEKD--EGCAQMLCKRCK 73 (137)
Q Consensus 50 ~CP~C~~~i~~~--~~~~~~~C~~C~ 73 (137)
.||.|+..+... .+...-.|++|+
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~ 26 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCG 26 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCC
Confidence 488888866543 233444566654
No 114
>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=79.69 E-value=2.5 Score=25.11 Aligned_cols=38 Identities=18% Similarity=0.400 Sum_probs=20.6
Q ss_pred cccCCCCCCCcceeecCCCCeEEeccCcceeecccccccc
Q psy12853 94 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133 (137)
Q Consensus 94 ~~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~ 133 (137)
.....|+.|+...-. .-..-.|+.||..||-.|.....
T Consensus 7 ~~~~~C~~C~~~F~~--~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 7 SEASNCMICGKKFSL--FRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp GG-SB-TTT--B-BS--SS-EEE-TTT--EEECCCS-EEE
T ss_pred CCCCcCcCcCCcCCC--ceeeEccCCCCCEECCchhCCEE
Confidence 456789999888833 34567899999999999986543
No 115
>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=79.47 E-value=1.6 Score=28.89 Aligned_cols=27 Identities=26% Similarity=0.730 Sum_probs=21.3
Q ss_pred CCCCCCCcceeecCCCCeEEeccCccee
Q psy12853 97 KCCPMCSVPIEKDEGCAQMLCKRCKHVF 124 (137)
Q Consensus 97 ~~CP~C~~~iek~~gC~hm~C~~C~~~f 124 (137)
-+||+|.....-..|= .+.|..|+++|
T Consensus 3 p~CP~C~seytY~dg~-~~iCpeC~~EW 29 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGT-QLICPSCLYEW 29 (109)
T ss_pred CcCCcCCCcceEecCC-eeECccccccc
Confidence 4799998888776664 47888899887
No 116
>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=79.36 E-value=0.91 Score=35.04 Aligned_cols=65 Identities=20% Similarity=0.510 Sum_probs=25.4
Q ss_pred cccCCCCCCceeec---CCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcc---------eeecCCCCeE
Q psy12853 48 IKCCPMCSVPIEKD---EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVP---------IEKDEGCAQM 115 (137)
Q Consensus 48 ~~~CP~C~~~i~~~---~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~---------iek~~gC~hm 115 (137)
..+||-|+..=... .+... .=++-+|..|+.+||..- ..||.|+.. ++-.++-.-.
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~----G~R~L~Cs~C~t~W~~~R--------~~Cp~Cg~~~~~~l~~~~~e~~~~~rve 239 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGERE----GKRYLHCSLCGTEWRFVR--------IKCPYCGNTDHEKLEYFTVEGEPAYRVE 239 (290)
T ss_dssp -SS-TTT---EEEEEEE----------EEEEEETTT--EEE--T--------TS-TTT---SS-EEE--------SEEEE
T ss_pred CCcCCCCCCcCceEEEecCCCC----ccEEEEcCCCCCeeeecC--------CCCcCCCCCCCcceeeEecCCCCcEEEE
Confidence 47999999852221 11100 114556667777887662 368888543 2223444446
Q ss_pred EeccCccee
Q psy12853 116 LCKRCKHVF 124 (137)
Q Consensus 116 ~C~~C~~~f 124 (137)
+|..||.++
T Consensus 240 ~C~~C~~Yl 248 (290)
T PF04216_consen 240 VCESCGSYL 248 (290)
T ss_dssp EETTTTEEE
T ss_pred ECCcccchH
Confidence 777777654
No 117
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=79.23 E-value=2.1 Score=27.33 Aligned_cols=29 Identities=24% Similarity=0.623 Sum_probs=24.2
Q ss_pred cCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853 96 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF 124 (137)
Q Consensus 96 ~~~CP~C~~~iek~~gC~hm~C~~C~~~f 124 (137)
...||.|+...-|..+=-.-.|..||+.|
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 45899999998887777778888899887
No 118
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=78.84 E-value=0.86 Score=24.72 Aligned_cols=34 Identities=29% Similarity=0.584 Sum_probs=22.9
Q ss_pred CCCCCCcceeecCCCCeEEeccCcceeeccccccccc
Q psy12853 98 CCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDV 134 (137)
Q Consensus 98 ~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~~ 134 (137)
.||-|...++. +=.-+.-. ||+.|++.|...|-.
T Consensus 2 ~C~IC~~~~~~--~~~~~~l~-C~H~fh~~Ci~~~~~ 35 (44)
T PF13639_consen 2 ECPICLEEFED--GEKVVKLP-CGHVFHRSCIKEWLK 35 (44)
T ss_dssp CETTTTCBHHT--TSCEEEET-TSEEEEHHHHHHHHH
T ss_pred CCcCCChhhcC--CCeEEEcc-CCCeeCHHHHHHHHH
Confidence 36667666654 22334554 999999999888754
No 119
>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=78.66 E-value=1.2 Score=23.02 Aligned_cols=6 Identities=33% Similarity=1.082 Sum_probs=2.4
Q ss_pred eccccc
Q psy12853 68 LCKRCK 73 (137)
Q Consensus 68 ~C~~C~ 73 (137)
.|+.||
T Consensus 19 rC~~CG 24 (32)
T PF03604_consen 19 RCPECG 24 (32)
T ss_dssp SBSSSS
T ss_pred ECCcCC
Confidence 343333
No 120
>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=78.27 E-value=1.4 Score=30.06 Aligned_cols=29 Identities=10% Similarity=0.116 Sum_probs=20.8
Q ss_pred CcccCCCCCCceeecCCCCeeecccccccc
Q psy12853 47 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF 76 (137)
Q Consensus 47 ~~~~CP~C~~~i~~~~~~~~~~C~~C~~~f 76 (137)
.-+-||.|+.-+.- .+-..+.||+||..|
T Consensus 8 tKr~Cp~cg~kFYD-Lnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 8 TKRICPNTGSKFYD-LNRRPAVSPYTGEQF 36 (129)
T ss_pred ccccCCCcCccccc-cCCCCccCCCcCCcc
Confidence 35678999887743 344778888888765
No 121
>PRK11827 hypothetical protein; Provisional
Probab=78.21 E-value=2.2 Score=25.29 Aligned_cols=30 Identities=23% Similarity=0.533 Sum_probs=22.4
Q ss_pred ccCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853 95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF 124 (137)
Q Consensus 95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~f 124 (137)
.+..||.|+..++-..+=+...|..||..|
T Consensus 7 eILaCP~ckg~L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 7 EIIACPVCNGKLWYNQEKQELICKLDNLAF 36 (60)
T ss_pred hheECCCCCCcCeEcCCCCeEECCccCeec
Confidence 356799999888876665678888877554
No 122
>PLN03086 PRLI-interacting factor K; Provisional
Probab=78.16 E-value=1.2 Score=37.80 Aligned_cols=22 Identities=18% Similarity=0.703 Sum_probs=10.8
Q ss_pred CCcceeecCCCCeEEeccCcce
Q psy12853 102 CSVPIEKDEGCAQMLCKRCKHV 123 (137)
Q Consensus 102 C~~~iek~~gC~hm~C~~C~~~ 123 (137)
|+..+.+...=+|..|..||..
T Consensus 441 Cg~v~~r~el~~H~~C~~Cgk~ 462 (567)
T PLN03086 441 CGIVLRVEEAKNHVHCEKCGQA 462 (567)
T ss_pred ccceeeccccccCccCCCCCCc
Confidence 5555555444455555544443
No 123
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=77.39 E-value=2.3 Score=25.68 Aligned_cols=30 Identities=17% Similarity=0.317 Sum_probs=22.9
Q ss_pred cccCCCCCCceeec-CCCCeeeccccccccc
Q psy12853 48 IKCCPMCSVPIEKD-EGCAQMLCKRCKHVFC 77 (137)
Q Consensus 48 ~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC 77 (137)
.+.||+|+..-... ..+..++|..|+...+
T Consensus 19 ~VkCpdC~N~q~vFshast~V~C~~CG~~l~ 49 (67)
T COG2051 19 RVKCPDCGNEQVVFSHASTVVTCLICGTTLA 49 (67)
T ss_pred EEECCCCCCEEEEeccCceEEEecccccEEE
Confidence 56899999865544 4577889999888776
No 124
>PLN02400 cellulose synthase
Probab=77.09 E-value=2.6 Score=38.26 Aligned_cols=62 Identities=19% Similarity=0.599 Sum_probs=47.5
Q ss_pred CcccCCCCCCceeec-CCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCeE
Q psy12853 47 LIKCCPMCSVPIEKD-EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQM 115 (137)
Q Consensus 47 ~~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~hm 115 (137)
+..-|--|+--+-.+ +|...+.|..|+.-.|.-|.. +. .+++.+-||.|++...+-.|+..+
T Consensus 35 ~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYE-YE------RkeGnq~CPQCkTrYkR~KgsprV 97 (1085)
T PLN02400 35 NGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYE-YE------RKDGTQCCPQCKTRYRRHKGSPRV 97 (1085)
T ss_pred CCceeeecccccCcCCCCCEEEEEccCCCccccchhh-ee------cccCCccCcccCCccccccCCCCC
Confidence 455677788877654 577889999999999999972 22 235688999999999987777653
No 125
>KOG2164|consensus
Probab=76.45 E-value=0.88 Score=37.82 Aligned_cols=52 Identities=25% Similarity=0.505 Sum_probs=33.1
Q ss_pred cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK 108 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek 108 (137)
-..||-|-..-.. ...+ .||+.||+.|...+-.-. ....++.||-|...|-.
T Consensus 186 ~~~CPICL~~~~~---p~~t---~CGHiFC~~CiLqy~~~s---~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 186 DMQCPICLEPPSV---PVRT---NCGHIFCGPCILQYWNYS---AIKGPCSCPICRSTITL 237 (513)
T ss_pred CCcCCcccCCCCc---cccc---ccCceeeHHHHHHHHhhh---cccCCccCCchhhhccc
Confidence 4456666554322 1111 589999999987543332 23568899999988854
No 126
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 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 family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=76.31 E-value=1.8 Score=24.41 Aligned_cols=28 Identities=29% Similarity=0.568 Sum_probs=21.1
Q ss_pred ccCCCC--CCCcceeecCCCCeEEeccCcc
Q psy12853 95 LIKCCP--MCSVPIEKDEGCAQMLCKRCKH 122 (137)
Q Consensus 95 ~~~~CP--~C~~~iek~~gC~hm~C~~C~~ 122 (137)
..+.|| .|+.-|.-..--+...|.+||+
T Consensus 17 ~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 357899 9999887777778899998875
No 127
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=75.89 E-value=2.8 Score=29.96 Aligned_cols=33 Identities=21% Similarity=0.488 Sum_probs=22.3
Q ss_pred CCCcccCCCCCCceeecCC---------------CCeeeccccccccc
Q psy12853 45 SELIKCCPMCSVPIEKDEG---------------CAQMLCKRCKHVFC 77 (137)
Q Consensus 45 ~~~~~~CP~C~~~i~~~~~---------------~~~~~C~~C~~~fC 77 (137)
.+....||.|+..+.+... .....|++|+..+.
T Consensus 94 ~~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW 141 (165)
T COG1656 94 FPEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYW 141 (165)
T ss_pred ccccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccccc
Confidence 4668899999999887431 11344777776664
No 128
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=75.63 E-value=0.64 Score=36.98 Aligned_cols=51 Identities=24% Similarity=0.629 Sum_probs=35.7
Q ss_pred cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCccee
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE 107 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie 107 (137)
--+||-|-.+|-.. +-+.+.|+ ||+.+|.-| ||.-... ..-+||.|+....
T Consensus 14 ed~cplcie~mdit-dknf~pc~-cgy~ic~fc---~~~irq~----lngrcpacrr~y~ 64 (480)
T COG5175 14 EDYCPLCIEPMDIT-DKNFFPCP-CGYQICQFC---YNNIRQN----LNGRCPACRRKYD 64 (480)
T ss_pred cccCcccccccccc-cCCcccCC-cccHHHHHH---HHHHHhh----ccCCChHhhhhcc
Confidence 34699998888654 45778895 999999888 4443322 3457999987653
No 129
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=75.45 E-value=2.7 Score=36.81 Aligned_cols=36 Identities=28% Similarity=0.635 Sum_probs=26.1
Q ss_pred cccCCCCCCceeecCCCCeeeccccccc-----cccccccc
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCKHV-----FCWYCLAS 83 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~-----fC~~C~~~ 83 (137)
...||+|+.++......+.+.|..|++. .|-.|+.+
T Consensus 444 v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 444 IAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred cccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 4567888888888877788888887765 45555543
No 130
>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=75.45 E-value=1.9 Score=27.08 Aligned_cols=17 Identities=35% Similarity=0.806 Sum_probs=10.2
Q ss_pred ecCCCCeEEeccCccee
Q psy12853 108 KDEGCAQMLCKRCKHVF 124 (137)
Q Consensus 108 k~~gC~hm~C~~C~~~f 124 (137)
+..|=-++.|+.||..|
T Consensus 40 kk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 40 KKEGIGILSCRVCGESF 56 (81)
T ss_dssp TTTTEEEEEESSS--EE
T ss_pred ccCCEEEEEecCCCCeE
Confidence 34555578888888776
No 131
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=75.10 E-value=5.7 Score=27.01 Aligned_cols=46 Identities=17% Similarity=0.459 Sum_probs=30.2
Q ss_pred cccccchhhhHHHHhhccccccCCCCcccCCCCCCc---eeecCCCCeeeccccccc
Q psy12853 22 NKLGHSRASVIWHRTQVSGATFDSELIKCCPMCSVP---IEKDEGCAQMLCKRCKHV 75 (137)
Q Consensus 22 ~~l~~~~~~~~~~r~~~~~a~~~~~~~~~CP~C~~~---i~~~~~~~~~~C~~C~~~ 75 (137)
..+..+.+.....++ +.. ++.||.|+.+ +.++.....+.|..||..
T Consensus 75 G~~~~~~i~~~L~~f-I~~-------yVlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 75 GRFSSKQIQDLLDKF-IKE-------YVLCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp SSSSCCHHHHHHHHH-HCH-------HSSCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred EecCHHHHHHHHHHH-HHH-------EEEcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 344555555455554 332 7889999987 445567778899988864
No 132
>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=75.02 E-value=3.1 Score=34.74 Aligned_cols=35 Identities=26% Similarity=0.674 Sum_probs=23.0
Q ss_pred CCCCCCCcceeecCCCCeEEeccCcce-----eecccccc
Q psy12853 97 KCCPMCSVPIEKDEGCAQMLCKRCKHV-----FCWYCLAS 131 (137)
Q Consensus 97 ~~CP~C~~~iek~~gC~hm~C~~C~~~-----fC~~C~~~ 131 (137)
.+||+|.....-...=+.+.|..||+. .|-.|+..
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 367777777665444457777777766 47777653
No 133
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=74.00 E-value=2.6 Score=38.21 Aligned_cols=61 Identities=26% Similarity=0.722 Sum_probs=45.4
Q ss_pred cccCCCCCCceeec-CCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCeE
Q psy12853 48 IKCCPMCSVPIEKD-EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQM 115 (137)
Q Consensus 48 ~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~hm 115 (137)
..-|--|+.-+-.+ +|...+.|..|+.-.|..|. ++. .+++.+.||.|++...+-.|.+.+
T Consensus 15 ~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cy-eye------~~~g~~~cp~c~t~y~~~~~~~~~ 76 (1044)
T PLN02915 15 AKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCY-EYE------RSEGNQCCPQCNTRYKRHKGCPRV 76 (1044)
T ss_pred cchhhccccccCcCCCCCEEEEeccCCCccccchh-hhh------hhcCCccCCccCCchhhhcCCCCc
Confidence 44555688777654 47788999999999999997 222 235678999999999876666543
No 134
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=73.87 E-value=2.1 Score=24.37 Aligned_cols=7 Identities=43% Similarity=1.312 Sum_probs=2.9
Q ss_pred CCCCCCc
Q psy12853 98 CCPMCSV 104 (137)
Q Consensus 98 ~CP~C~~ 104 (137)
+||.|+.
T Consensus 26 rCp~Cg~ 32 (49)
T COG1996 26 RCPYCGS 32 (49)
T ss_pred eCCCCCc
Confidence 3444433
No 135
>PRK10220 hypothetical protein; Provisional
Probab=73.70 E-value=3.1 Score=27.68 Aligned_cols=27 Identities=22% Similarity=0.732 Sum_probs=21.2
Q ss_pred CCCCCCCcceeecCCCCeEEeccCccee
Q psy12853 97 KCCPMCSVPIEKDEGCAQMLCKRCKHVF 124 (137)
Q Consensus 97 ~~CP~C~~~iek~~gC~hm~C~~C~~~f 124 (137)
-+||+|.....-..|= .+.|..|+++|
T Consensus 4 P~CP~C~seytY~d~~-~~vCpeC~hEW 30 (111)
T PRK10220 4 PHCPKCNSEYTYEDNG-MYICPECAHEW 30 (111)
T ss_pred CcCCCCCCcceEcCCC-eEECCcccCcC
Confidence 4799998888766663 58888999887
No 136
>PF15616 TerY-C: TerY-C metal binding domain
Probab=73.50 E-value=3 Score=28.67 Aligned_cols=25 Identities=32% Similarity=0.794 Sum_probs=17.2
Q ss_pred ccCCCCCCCcceeecCCCCeEEeccCcceeec
Q psy12853 95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCW 126 (137)
Q Consensus 95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~ 126 (137)
..--||.|+... ....|. ||+-|||
T Consensus 76 g~PgCP~CGn~~------~fa~C~-CGkl~Ci 100 (131)
T PF15616_consen 76 GAPGCPHCGNQY------AFAVCG-CGKLFCI 100 (131)
T ss_pred CCCCCCCCcChh------cEEEec-CCCEEEe
Confidence 356899999886 345663 6666665
No 137
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=72.13 E-value=3.9 Score=27.32 Aligned_cols=29 Identities=21% Similarity=0.698 Sum_probs=20.4
Q ss_pred cCCCCCCCcceee--cCCCCeEEeccCccee
Q psy12853 96 IKCCPMCSVPIEK--DEGCAQMLCKRCKHVF 124 (137)
Q Consensus 96 ~~~CP~C~~~iek--~~gC~hm~C~~C~~~f 124 (137)
.+-||+|+.++.- .++=+-+.|+.||+++
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred ccccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 3568999887765 2233488899898864
No 138
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=71.62 E-value=5.1 Score=23.98 Aligned_cols=11 Identities=18% Similarity=0.993 Sum_probs=7.1
Q ss_pred eEEeccCccee
Q psy12853 114 QMLCKRCKHVF 124 (137)
Q Consensus 114 hm~C~~C~~~f 124 (137)
.++|..||..|
T Consensus 53 ~L~Cp~c~r~Y 63 (68)
T PF03966_consen 53 ELICPECGREY 63 (68)
T ss_dssp EEEETTTTEEE
T ss_pred EEEcCCCCCEE
Confidence 66676666654
No 139
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=71.62 E-value=4.7 Score=23.83 Aligned_cols=30 Identities=17% Similarity=0.325 Sum_probs=22.2
Q ss_pred cccCCCCCCceeec-CCCCeeeccccccccc
Q psy12853 48 IKCCPMCSVPIEKD-EGCAQMLCKRCKHVFC 77 (137)
Q Consensus 48 ~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC 77 (137)
.+.||+|....... .....+.|..|+...+
T Consensus 11 ~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHASTVVRCLVCGKTLA 41 (59)
T ss_pred EEECCCCCCeEEEEecCCcEEECcccCCCcc
Confidence 46799999865443 4567888988888776
No 140
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=71.15 E-value=4 Score=26.05 Aligned_cols=32 Identities=22% Similarity=0.562 Sum_probs=23.6
Q ss_pred CCcccCCCCCCceeecCCCCeeeccccccccc
Q psy12853 46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFC 77 (137)
Q Consensus 46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC 77 (137)
....-||.|+....+-.......|.+|+..|=
T Consensus 33 ~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 33 RAKHVCPFCGRTTVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred hcCCcCCCCCCcceeeeccCeEEcCCCCCeec
Confidence 34568999999865555667788888877764
No 141
>KOG1039|consensus
Probab=71.09 E-value=1.8 Score=34.51 Aligned_cols=38 Identities=32% Similarity=0.746 Sum_probs=30.7
Q ss_pred ccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853 70 KRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK 108 (137)
Q Consensus 70 ~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek 108 (137)
|.|.+.||..|...|...... .....+-||.|++....
T Consensus 185 pnC~H~~Cl~Cir~wr~~~q~-~~~~sksCP~CRv~s~~ 222 (344)
T KOG1039|consen 185 PNCNHSFCLNCIRKWRQATQF-ESKTSKSCPFCRVPSSF 222 (344)
T ss_pred CCcchhhhhcHhHhhhhhhcc-ccccccCCCcccCcccc
Confidence 579999999999999866433 55668999999988765
No 142
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=70.51 E-value=4.1 Score=24.96 Aligned_cols=27 Identities=22% Similarity=0.581 Sum_probs=20.4
Q ss_pred CCCCCCCcce----eecCCCCeEEeccCcce
Q psy12853 97 KCCPMCSVPI----EKDEGCAQMLCKRCKHV 123 (137)
Q Consensus 97 ~~CP~C~~~i----ek~~gC~hm~C~~C~~~ 123 (137)
-.||+|+.+= -+..+=.++.|..||+.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~ 39 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYT 39 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCe
Confidence 3699997653 34577889999999985
No 143
>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=70.45 E-value=4.4 Score=33.89 Aligned_cols=34 Identities=26% Similarity=0.692 Sum_probs=26.0
Q ss_pred ccCCCCCCceeecCCCCeeeccccccc-----ccccccc
Q psy12853 49 KCCPMCSVPIEKDEGCAQMLCKRCKHV-----FCWYCLA 82 (137)
Q Consensus 49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~-----fC~~C~~ 82 (137)
..||+|+.++......+...|..||+. .|-.|+.
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s 261 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGS 261 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCC
Confidence 348889998888777788899888765 4666654
No 144
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=70.17 E-value=2.6 Score=29.26 Aligned_cols=31 Identities=23% Similarity=0.389 Sum_probs=18.6
Q ss_pred CCCcccCCCCCCceeecC------CCCeeeccccccc
Q psy12853 45 SELIKCCPMCSVPIEKDE------GCAQMLCKRCKHV 75 (137)
Q Consensus 45 ~~~~~~CP~C~~~i~~~~------~~~~~~C~~C~~~ 75 (137)
......||+|+.-+...+ ....+.||.||..
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~ 132 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEE 132 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence 345677888887766532 1223777766654
No 145
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=70.15 E-value=1.4 Score=38.89 Aligned_cols=10 Identities=30% Similarity=0.849 Sum_probs=0.0
Q ss_pred cccCCCCCCc
Q psy12853 48 IKCCPMCSVP 57 (137)
Q Consensus 48 ~~~CP~C~~~ 57 (137)
.+.||+|+..
T Consensus 655 ~r~Cp~Cg~~ 664 (900)
T PF03833_consen 655 RRRCPKCGKE 664 (900)
T ss_dssp ----------
T ss_pred cccCcccCCc
Confidence 4556666554
No 146
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=70.00 E-value=4.3 Score=26.99 Aligned_cols=16 Identities=25% Similarity=0.285 Sum_probs=8.8
Q ss_pred CCCcccCCCCCCceee
Q psy12853 45 SELIKCCPMCSVPIEK 60 (137)
Q Consensus 45 ~~~~~~CP~C~~~i~~ 60 (137)
-+...+|++|+..+..
T Consensus 67 vp~~~~C~~Cg~~~~~ 82 (113)
T PRK12380 67 KPAQAWCWDCSQVVEI 82 (113)
T ss_pred eCcEEEcccCCCEEec
Confidence 3445666666654443
No 147
>PLN03086 PRLI-interacting factor K; Provisional
Probab=69.77 E-value=1.7 Score=36.88 Aligned_cols=17 Identities=18% Similarity=0.149 Sum_probs=11.7
Q ss_pred CCCcccCCCCCCceeec
Q psy12853 45 SELIKCCPMCSVPIEKD 61 (137)
Q Consensus 45 ~~~~~~CP~C~~~i~~~ 61 (137)
..+.+.||+|...+...
T Consensus 404 ~~~~V~C~NC~~~i~l~ 420 (567)
T PLN03086 404 DVDTVECRNCKHYIPSR 420 (567)
T ss_pred CCCeEECCCCCCccchh
Confidence 45567788888777653
No 148
>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=69.64 E-value=2.9 Score=31.37 Aligned_cols=34 Identities=21% Similarity=0.161 Sum_probs=19.8
Q ss_pred cccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853 75 VFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK 108 (137)
Q Consensus 75 ~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek 108 (137)
..|..|..+-+.-....+..++..||.|+....+
T Consensus 14 ~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~ 47 (236)
T PF04981_consen 14 GLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIG 47 (236)
T ss_pred ccChHHhcccCCeeecCCccCceECCCCCCEECC
Confidence 4566666655544443334466777777776654
No 149
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=69.42 E-value=4.6 Score=23.86 Aligned_cols=27 Identities=26% Similarity=0.618 Sum_probs=20.0
Q ss_pred CCCCCCCcc----eeecCCCCeEEeccCcce
Q psy12853 97 KCCPMCSVP----IEKDEGCAQMLCKRCKHV 123 (137)
Q Consensus 97 ~~CP~C~~~----iek~~gC~hm~C~~C~~~ 123 (137)
-.||+|+.+ .-+..+=.++.|..||+.
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~ 40 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQ 40 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence 369999754 334567788999999975
No 150
>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=68.96 E-value=4 Score=27.24 Aligned_cols=36 Identities=25% Similarity=0.440 Sum_probs=26.9
Q ss_pred CcccCCCCCCceeecCCCCeeeccccccccccccccc
Q psy12853 47 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS 83 (137)
Q Consensus 47 ~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~ 83 (137)
+...|..|..++.... .....|..|+..+|..|+..
T Consensus 53 ~~~~C~~C~~~fg~l~-~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLF-NRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTS-TTCEEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccC-CCCCcCCcCCccccCccCCc
Confidence 5678999998865433 34489999999999999975
No 151
>PRK05580 primosome assembly protein PriA; Validated
Probab=68.85 E-value=4.9 Score=34.85 Aligned_cols=35 Identities=20% Similarity=0.504 Sum_probs=20.5
Q ss_pred CCCCCCCcceeecCCCCeEEeccCcce-----eecccccc
Q psy12853 97 KCCPMCSVPIEKDEGCAQMLCKRCKHV-----FCWYCLAS 131 (137)
Q Consensus 97 ~~CP~C~~~iek~~gC~hm~C~~C~~~-----fC~~C~~~ 131 (137)
.+||+|.....-...=+.+.|..||+. .|-.||..
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 357777666654333456677777665 36666553
No 152
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=68.81 E-value=6.2 Score=27.35 Aligned_cols=34 Identities=18% Similarity=0.491 Sum_probs=22.9
Q ss_pred CCCCcccCCCCCCceeecCC---------------CCeeeccccccccc
Q psy12853 44 DSELIKCCPMCSVPIEKDEG---------------CAQMLCKRCKHVFC 77 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~~~~---------------~~~~~C~~C~~~fC 77 (137)
..+.+..||.|+..+...+. .....|+.|+..|.
T Consensus 87 ~~~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW 135 (147)
T PF01927_consen 87 LDPIFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYW 135 (147)
T ss_pred cCCCCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEec
Confidence 44558899999998865321 22566777777664
No 153
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=68.54 E-value=6.3 Score=26.20 Aligned_cols=27 Identities=26% Similarity=0.662 Sum_probs=20.3
Q ss_pred cccCCCCCCc---eeecCCCCeeecccccc
Q psy12853 48 IKCCPMCSVP---IEKDEGCAQMLCKRCKH 74 (137)
Q Consensus 48 ~~~CP~C~~~---i~~~~~~~~~~C~~C~~ 74 (137)
++-||.|+.+ +++++....+.|..||+
T Consensus 80 yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 80 YVLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred cEECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 7889999987 44455566788988875
No 154
>PRK14873 primosome assembly protein PriA; Provisional
Probab=68.46 E-value=6.5 Score=34.12 Aligned_cols=27 Identities=19% Similarity=0.480 Sum_probs=16.8
Q ss_pred cccCCCCCCceeecCCCCeeecccccc
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCKH 74 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~ 74 (137)
...||+|+.++......+...|..||+
T Consensus 392 ~~~C~~C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 392 PARCRHCTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred eeECCCCCCceeEecCCCeeECCCCcC
Confidence 345667777776655555666766654
No 155
>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=68.45 E-value=1.5 Score=34.03 Aligned_cols=33 Identities=21% Similarity=0.533 Sum_probs=24.7
Q ss_pred CCCCcccCCCCCCceeecC-CCCeeecccccccc
Q psy12853 44 DSELIKCCPMCSVPIEKDE-GCAQMLCKRCKHVF 76 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~~~-~~~~~~C~~C~~~f 76 (137)
....+..||.|+..+...+ ..+...||+|+++|
T Consensus 22 ~~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 22 PEGVWTKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred CCCCeeECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 4445889999999887754 45667899888754
No 156
>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=68.36 E-value=4.4 Score=22.99 Aligned_cols=33 Identities=24% Similarity=0.706 Sum_probs=24.4
Q ss_pred ccCCCCCCceeecCCCCeeeccccccccccccccc
Q psy12853 49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS 83 (137)
Q Consensus 49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~ 83 (137)
..|+.|+..+.. ......|..||..||..|...
T Consensus 3 ~~C~~C~~~F~~--~~rk~~Cr~Cg~~~C~~C~~~ 35 (57)
T cd00065 3 SSCMGCGKPFTL--TRRRHHCRNCGRIFCSKCSSN 35 (57)
T ss_pred CcCcccCccccC--CccccccCcCcCCcChHHcCC
Confidence 457777776654 345678999999999999763
No 157
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=68.33 E-value=1.9 Score=33.32 Aligned_cols=33 Identities=24% Similarity=0.569 Sum_probs=26.0
Q ss_pred CCCcccCCCCCCceeecC-CCCeeeccccccccc
Q psy12853 45 SELIKCCPMCSVPIEKDE-GCAQMLCKRCKHVFC 77 (137)
Q Consensus 45 ~~~~~~CP~C~~~i~~~~-~~~~~~C~~C~~~fC 77 (137)
...+..||.|+..+...+ +.+...||+|++++=
T Consensus 25 e~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~r 58 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKELESNLKVCPKCGHHMR 58 (294)
T ss_pred CCceeECCCccceeeHHHHHhhhhcccccCcccc
Confidence 455789999999887755 678889999887653
No 158
>KOG2807|consensus
Probab=68.21 E-value=2.7 Score=33.31 Aligned_cols=49 Identities=24% Similarity=0.586 Sum_probs=35.3
Q ss_pred CCCCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCC
Q psy12853 44 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCS 103 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~ 103 (137)
...+..+|-.|+... .+....+|+.|+..||..|..-.|+ ....||.|.
T Consensus 326 ~~~~~~~Cf~C~~~~---~~~~~y~C~~Ck~~FCldCDv~iHe--------sLh~CpgCe 374 (378)
T KOG2807|consen 326 EYNGSRFCFACQGEL---LSSGRYRCESCKNVFCLDCDVFIHE--------SLHNCPGCE 374 (378)
T ss_pred ccCCCcceeeecccc---CCCCcEEchhccceeeccchHHHHh--------hhhcCCCcC
Confidence 445566788883322 3466789999999999999875554 466899886
No 159
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=68.07 E-value=3.2 Score=38.34 Aligned_cols=16 Identities=25% Similarity=0.478 Sum_probs=9.5
Q ss_pred eecccccc----cccccccc
Q psy12853 67 MLCKRCKH----VFCWYCLA 82 (137)
Q Consensus 67 ~~C~~C~~----~fC~~C~~ 82 (137)
..||+||. .||..|+.
T Consensus 668 rkCPkCG~~t~~~fCP~CGs 687 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGT 687 (1337)
T ss_pred EECCCCCCccccccCcccCC
Confidence 56777764 35655654
No 160
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=67.93 E-value=1.7 Score=33.83 Aligned_cols=33 Identities=24% Similarity=0.590 Sum_probs=25.0
Q ss_pred CCCCcccCCCCCCceeecC-CCCeeecccccccc
Q psy12853 44 DSELIKCCPMCSVPIEKDE-GCAQMLCKRCKHVF 76 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~~~-~~~~~~C~~C~~~f 76 (137)
....+..||.|+..+...+ ..+...||+|+++|
T Consensus 23 ~~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 23 PEGLWTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred CCCCeeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 4455889999999887654 45567899988766
No 161
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=67.86 E-value=6.5 Score=27.06 Aligned_cols=29 Identities=24% Similarity=0.534 Sum_probs=20.8
Q ss_pred cccCCCCCCc---eeecCCCCeeecccccccc
Q psy12853 48 IKCCPMCSVP---IEKDEGCAQMLCKRCKHVF 76 (137)
Q Consensus 48 ~~~CP~C~~~---i~~~~~~~~~~C~~C~~~f 76 (137)
++-||.|+.+ +++++......|..||+.-
T Consensus 97 yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~~ 128 (133)
T TIGR00311 97 YVICRECNRPDTRIIKEGRVSLLKCEACGAKA 128 (133)
T ss_pred eEECCCCCCCCcEEEEeCCeEEEecccCCCCC
Confidence 7899999986 4444445567898888753
No 162
>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=67.85 E-value=3.1 Score=22.61 Aligned_cols=13 Identities=23% Similarity=0.675 Sum_probs=7.9
Q ss_pred cCCCCCCCc-ceee
Q psy12853 96 IKCCPMCSV-PIEK 108 (137)
Q Consensus 96 ~~~CP~C~~-~iek 108 (137)
...||.|+. .++|
T Consensus 26 ~~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 26 PVPCPECGSTEVRR 39 (42)
T ss_pred CCcCCCCCCCceEE
Confidence 456777776 5544
No 163
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=67.82 E-value=1.5 Score=34.25 Aligned_cols=33 Identities=18% Similarity=0.239 Sum_probs=24.1
Q ss_pred CCCCcccCCCCCCceeecC-CCCeeecccccccc
Q psy12853 44 DSELIKCCPMCSVPIEKDE-GCAQMLCKRCKHVF 76 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~~~-~~~~~~C~~C~~~f 76 (137)
....+..||.|+..+...+ ..+...||+|+++|
T Consensus 34 p~~lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 34 YKHLWVQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred CCCCeeECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 3345888999999887654 46667888888743
No 164
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=67.63 E-value=1.2 Score=22.38 Aligned_cols=16 Identities=31% Similarity=0.763 Sum_probs=13.0
Q ss_pred cccccccccccccccC
Q psy12853 71 RCKHVFCWYCLASRDY 86 (137)
Q Consensus 71 ~C~~~fC~~C~~~~h~ 86 (137)
.|++.||..|...|-.
T Consensus 15 ~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 15 PCGHTFCRSCIRKWLK 30 (39)
T ss_pred cCCChHHHHHHHHHHH
Confidence 5899999999876644
No 165
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=67.59 E-value=6.7 Score=27.17 Aligned_cols=29 Identities=24% Similarity=0.557 Sum_probs=21.4
Q ss_pred cccCCCCCCc---eeecCCCCeeecccccccc
Q psy12853 48 IKCCPMCSVP---IEKDEGCAQMLCKRCKHVF 76 (137)
Q Consensus 48 ~~~CP~C~~~---i~~~~~~~~~~C~~C~~~f 76 (137)
++-||.|+.+ +++++......|..||+.-
T Consensus 102 yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~~ 133 (138)
T PRK03988 102 YVICPECGSPDTKLIKEGRIWVLKCEACGAET 133 (138)
T ss_pred cEECCCCCCCCcEEEEcCCeEEEEcccCCCCC
Confidence 7899999986 4444555678898888753
No 166
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=67.55 E-value=5 Score=29.25 Aligned_cols=27 Identities=22% Similarity=0.559 Sum_probs=19.9
Q ss_pred cccCCCCCCceeecCCCCeeecccccccc
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF 76 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~f 76 (137)
+..|++|+..+.+ ..+.+.||+|+..=
T Consensus 149 ~A~CsrC~~~L~~--~~~~l~Cp~Cg~tE 175 (188)
T COG1096 149 YARCSRCRAPLVK--KGNMLKCPNCGNTE 175 (188)
T ss_pred EEEccCCCcceEE--cCcEEECCCCCCEE
Confidence 4578888888887 55778888887643
No 167
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=67.02 E-value=1.8 Score=25.63 Aligned_cols=35 Identities=23% Similarity=0.624 Sum_probs=26.4
Q ss_pred CCCCCCCcceeec--CCCCeEEeccCcceeecccccc
Q psy12853 97 KCCPMCSVPIEKD--EGCAQMLCKRCKHVFCWYCLAS 131 (137)
Q Consensus 97 ~~CP~C~~~iek~--~gC~hm~C~~C~~~fC~~C~~~ 131 (137)
..||-|++..-.. +-=||-+|+.|+...|-.||=.
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFN 39 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFN 39 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHhhhhhcccCCC
Confidence 4688888776332 3358899999999999999843
No 168
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=66.90 E-value=1.5 Score=33.58 Aligned_cols=29 Identities=34% Similarity=0.744 Sum_probs=19.9
Q ss_pred CCCCCCCcceeecCCCCeEEeccCcceeecccccc
Q psy12853 97 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS 131 (137)
Q Consensus 97 ~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~ 131 (137)
.+|+-|....+. -.|+.||+-|||.|.-.
T Consensus 216 ~kC~lC~e~~~~------ps~t~CgHlFC~~Cl~~ 244 (271)
T COG5574 216 YKCFLCLEEPEV------PSCTPCGHLFCLSCLLI 244 (271)
T ss_pred cceeeeecccCC------cccccccchhhHHHHHH
Confidence 458888877754 34556777777777655
No 169
>PRK14873 primosome assembly protein PriA; Provisional
Probab=66.49 E-value=5 Score=34.78 Aligned_cols=34 Identities=21% Similarity=0.512 Sum_probs=20.0
Q ss_pred CCCCCCcceeecCCCCeEEeccCcce----eecccccc
Q psy12853 98 CCPMCSVPIEKDEGCAQMLCKRCKHV----FCWYCLAS 131 (137)
Q Consensus 98 ~CP~C~~~iek~~gC~hm~C~~C~~~----fC~~C~~~ 131 (137)
+||+|.....-..+=+.+.|..||+. .|-.||..
T Consensus 394 ~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 394 RCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred ECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 57777666655444456677767653 25566553
No 170
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=65.31 E-value=3.5 Score=24.98 Aligned_cols=59 Identities=24% Similarity=0.445 Sum_probs=22.7
Q ss_pred cCCCCCCceeecCCCCeeecc--cccccccccccccccCCCCcc---cccccCCCCCCCcceee
Q psy12853 50 CCPMCSVPIEKDEGCAQMLCK--RCKHVFCWYCLASRDYGGATF---DSELIKCCPMCSVPIEK 108 (137)
Q Consensus 50 ~CP~C~~~i~~~~~~~~~~C~--~C~~~fC~~C~~~~h~~~~~~---~~~~~~~CP~C~~~iek 108 (137)
.|+=|-..+..++....+.|+ .|+..|=..|..+|-...+.. ..-..-+||.|+..|.-
T Consensus 4 ~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 4 ECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW 67 (70)
T ss_dssp S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred CCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence 355555554433445678886 788888888888774432111 11123369999999864
No 171
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=65.29 E-value=6.1 Score=26.18 Aligned_cols=26 Identities=31% Similarity=0.916 Sum_probs=19.3
Q ss_pred cccCCCCCCceeecCCCCeeecccccc
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCKH 74 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~ 74 (137)
+-.||.|+.-+.+.++. .+.||.|.+
T Consensus 3 lp~cp~c~sEytYed~~-~~~cpec~~ 28 (112)
T COG2824 3 LPPCPKCNSEYTYEDGG-QLICPECAH 28 (112)
T ss_pred CCCCCccCCceEEecCc-eEeCchhcc
Confidence 44689999988887765 788877443
No 172
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=65.02 E-value=7 Score=22.75 Aligned_cols=30 Identities=20% Similarity=0.332 Sum_probs=18.2
Q ss_pred cccCCCCCCceee-cCCCCeeeccccccccc
Q psy12853 48 IKCCPMCSVPIEK-DEGCAQMLCKRCKHVFC 77 (137)
Q Consensus 48 ~~~CP~C~~~i~~-~~~~~~~~C~~C~~~fC 77 (137)
.+.||+|...-.. ......+.|..|+..+|
T Consensus 7 ~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~ 37 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHAQTVVKCVVCGTVLA 37 (55)
T ss_dssp EEE-TTT-SEEEEETT-SS-EE-SSSTSEEE
T ss_pred EEECCCCCCeeEEEecCCeEEEcccCCCEec
Confidence 4578999886544 44677888988888877
No 173
>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=64.44 E-value=4.4 Score=30.77 Aligned_cols=35 Identities=23% Similarity=0.477 Sum_probs=14.6
Q ss_pred cccCCCCCCc-eeecC---CCCeeecccccccccccccc
Q psy12853 48 IKCCPMCSVP-IEKDE---GCAQMLCKRCKHVFCWYCLA 82 (137)
Q Consensus 48 ~~~CP~C~~~-i~~~~---~~~~~~C~~C~~~fC~~C~~ 82 (137)
-.+||+|+.. +..-. -+..+.|+.|+..|=.+-+.
T Consensus 31 n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyELKSk~ 69 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKFENNRPVADFYCPNCNEEYELKSKK 69 (254)
T ss_dssp H---TTT--SS-EE--------EEE-TTT--EEEEEEEE
T ss_pred CCcCCCCCChhHhhccCCCccceeECCCCchHHhhhhhc
Confidence 4599999997 55533 36678899988776544443
No 174
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=64.39 E-value=4.6 Score=26.93 Aligned_cols=13 Identities=23% Similarity=0.424 Sum_probs=6.9
Q ss_pred CCcccCCCCCCce
Q psy12853 46 ELIKCCPMCSVPI 58 (137)
Q Consensus 46 ~~~~~CP~C~~~i 58 (137)
+...+|++|+..+
T Consensus 68 p~~~~C~~Cg~~~ 80 (114)
T PRK03681 68 EAECWCETCQQYV 80 (114)
T ss_pred CcEEEcccCCCee
Confidence 4455566665443
No 175
>PLN02195 cellulose synthase A
Probab=64.12 E-value=6.4 Score=35.52 Aligned_cols=53 Identities=28% Similarity=0.616 Sum_probs=40.7
Q ss_pred cccCCCCCCceeec-CCCCeeecccccccccccccccccCCCCcccccccCCCCCCCccee
Q psy12853 48 IKCCPMCSVPIEKD-EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE 107 (137)
Q Consensus 48 ~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie 107 (137)
..-|--|+.-+-.+ +|...+.|..|+.-.|.-|. ++.. +++.+-||.|++...
T Consensus 6 ~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCy-eyer------~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 6 APICATCGEEVGVDSNGEAFVACHECSYPLCKACL-EYEI------KEGRKVCLRCGGPYD 59 (977)
T ss_pred CccceecccccCcCCCCCeEEEeccCCCccccchh-hhhh------hcCCccCCccCCccc
Confidence 44566788877655 47788999999999999996 2222 356889999999886
No 176
>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=62.59 E-value=5.1 Score=26.71 Aligned_cols=14 Identities=21% Similarity=0.368 Sum_probs=7.1
Q ss_pred CCcccCCCCCCcee
Q psy12853 46 ELIKCCPMCSVPIE 59 (137)
Q Consensus 46 ~~~~~CP~C~~~i~ 59 (137)
+...+|++|+..+.
T Consensus 68 p~~~~C~~Cg~~~~ 81 (115)
T TIGR00100 68 PVECECEDCSEEVS 81 (115)
T ss_pred CcEEEcccCCCEEe
Confidence 44555555554443
No 177
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=62.56 E-value=6.7 Score=30.30 Aligned_cols=27 Identities=33% Similarity=0.691 Sum_probs=21.7
Q ss_pred ccCCCCCCCcceeec--CCCCeEEeccCc
Q psy12853 95 LIKCCPMCSVPIEKD--EGCAQMLCKRCK 121 (137)
Q Consensus 95 ~~~~CP~C~~~iek~--~gC~hm~C~~C~ 121 (137)
..++|+.|+.+|+|. +|=+-..|..|+
T Consensus 244 ~GepC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 244 AGEPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 467999999999984 777777777665
No 178
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the 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=62.37 E-value=5.9 Score=19.64 Aligned_cols=25 Identities=40% Similarity=0.824 Sum_probs=12.9
Q ss_pred CCCCCCCcceeec--CCCCeEEeccCc
Q psy12853 97 KCCPMCSVPIEKD--EGCAQMLCKRCK 121 (137)
Q Consensus 97 ~~CP~C~~~iek~--~gC~hm~C~~C~ 121 (137)
++||.|...|++. ++=+...|..|.
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCc
Confidence 5799999998774 344445555553
No 180
>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=62.29 E-value=1.4 Score=31.08 Aligned_cols=26 Identities=46% Similarity=0.952 Sum_probs=19.8
Q ss_pred cccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853 73 KHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD 109 (137)
Q Consensus 73 ~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~ 109 (137)
...||-+|+. +.+..||+|+.+|.-.
T Consensus 27 ~~~fC~kCG~-----------~tI~~Cp~C~~~IrG~ 52 (158)
T PF10083_consen 27 REKFCSKCGA-----------KTITSCPNCSTPIRGD 52 (158)
T ss_pred HHHHHHHhhH-----------HHHHHCcCCCCCCCCc
Confidence 4678888874 5677899999999743
No 181
>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=61.81 E-value=13 Score=20.43 Aligned_cols=29 Identities=21% Similarity=0.404 Sum_probs=18.9
Q ss_pred CCcccCCCCCCceee-cCCCCeeecccccc
Q psy12853 46 ELIKCCPMCSVPIEK-DEGCAQMLCKRCKH 74 (137)
Q Consensus 46 ~~~~~CP~C~~~i~~-~~~~~~~~C~~C~~ 74 (137)
++...||.|+..-.. ..+.....|..|++
T Consensus 16 ~~g~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 16 PDGFVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 344669999986222 23457788888765
No 182
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=61.77 E-value=6.2 Score=23.07 Aligned_cols=24 Identities=25% Similarity=0.589 Sum_probs=16.5
Q ss_pred cccCCCCCCCcceeecCCCCeEEeccCcc
Q psy12853 94 ELIKCCPMCSVPIEKDEGCAQMLCKRCKH 122 (137)
Q Consensus 94 ~~~~~CP~C~~~iek~~gC~hm~C~~C~~ 122 (137)
.++..||+|+.+... |-.|..||+
T Consensus 25 ~~l~~C~~CG~~~~~-----H~vC~~CG~ 48 (57)
T PRK12286 25 PGLVECPNCGEPKLP-----HRVCPSCGY 48 (57)
T ss_pred CcceECCCCCCccCC-----eEECCCCCc
Confidence 345678888887743 677766774
No 183
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=61.48 E-value=9.2 Score=22.67 Aligned_cols=27 Identities=41% Similarity=0.962 Sum_probs=15.6
Q ss_pred cccCCCCCCceeecCCCCeeecccccc
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCKH 74 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~ 74 (137)
..-||-|..++..+.......|+.|+.
T Consensus 8 iLaCP~~kg~L~~~~~~~~L~c~~~~~ 34 (60)
T COG2835 8 ILACPVCKGPLVYDEEKQELICPRCKL 34 (60)
T ss_pred eeeccCcCCcceEeccCCEEEecccCc
Confidence 345666666666665555555555443
No 184
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=61.18 E-value=7.6 Score=29.78 Aligned_cols=26 Identities=27% Similarity=0.678 Sum_probs=18.0
Q ss_pred cCCCCCCCcceeec--CCCCeEEeccCc
Q psy12853 96 IKCCPMCSVPIEKD--EGCAQMLCKRCK 121 (137)
Q Consensus 96 ~~~CP~C~~~iek~--~gC~hm~C~~C~ 121 (137)
.++||.|+..|++. +|=.-..|..|+
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 57999999999983 564444444443
No 185
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=61.11 E-value=7.9 Score=29.66 Aligned_cols=26 Identities=38% Similarity=0.844 Sum_probs=18.0
Q ss_pred cCCCCCCCcceeec--CCCCeEEeccCc
Q psy12853 96 IKCCPMCSVPIEKD--EGCAQMLCKRCK 121 (137)
Q Consensus 96 ~~~CP~C~~~iek~--~gC~hm~C~~C~ 121 (137)
.++||.|+..|++. +|=.-..|..|+
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 57899999999983 564444454443
No 186
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=61.08 E-value=7.5 Score=29.80 Aligned_cols=26 Identities=38% Similarity=0.871 Sum_probs=17.7
Q ss_pred cCCCCCCCcceeec--CCCCeEEeccCc
Q psy12853 96 IKCCPMCSVPIEKD--EGCAQMLCKRCK 121 (137)
Q Consensus 96 ~~~CP~C~~~iek~--~gC~hm~C~~C~ 121 (137)
.++||.|+..|++. +|=.-..|..|+
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ 262 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQ 262 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCc
Confidence 57999999999983 564444444443
No 187
>KOG2907|consensus
Probab=61.01 E-value=3.5 Score=27.55 Aligned_cols=27 Identities=30% Similarity=0.700 Sum_probs=18.7
Q ss_pred CcccCCCCCCceeecCCCCeeeccccc
Q psy12853 47 LIKCCPMCSVPIEKDEGCAQMLCKRCK 73 (137)
Q Consensus 47 ~~~~CP~C~~~i~~~~~~~~~~C~~C~ 73 (137)
...+|++|+..++.......+.|..|+
T Consensus 6 ~~~FC~~CG~ll~~~~~~~~~~C~~Ck 32 (116)
T KOG2907|consen 6 DLDFCSDCGSLLEEPSAQSTVLCIRCK 32 (116)
T ss_pred CcchhhhhhhhcccccccCceEecccc
Confidence 567899999998876655555554433
No 188
>KOG2177|consensus
Probab=61.00 E-value=7.3 Score=28.75 Aligned_cols=68 Identities=24% Similarity=0.586 Sum_probs=43.1
Q ss_pred cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCc----------------------c
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSV----------------------P 105 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~----------------------~ 105 (137)
...||-|-..+... .-..|++.||..|...+-. ....||.|+. .
T Consensus 13 ~~~C~iC~~~~~~p------~~l~C~H~~c~~C~~~~~~--------~~~~Cp~cr~~~~~~~~n~~l~~~~~~~~~~~~ 78 (386)
T KOG2177|consen 13 ELTCPICLEYFREP------VLLPCGHNFCRACLTRSWE--------GPLSCPVCRPPSRNLRPNVLLANLVERLRQLRL 78 (386)
T ss_pred cccChhhHHHhhcC------ccccccchHhHHHHHHhcC--------CCcCCcccCCchhccCccHHHHHHHHHHHhcCC
Confidence 45667666655433 2225899999999875433 2367888881 1
Q ss_pred eeecCC----C------CeEEeccCcceeecccc
Q psy12853 106 IEKDEG----C------AQMLCKRCKHVFCWYCL 129 (137)
Q Consensus 106 iek~~g----C------~hm~C~~C~~~fC~~C~ 129 (137)
....+. | .++.|..|+...|+.|.
T Consensus 79 ~~~~~~~~~~c~~~~~~~~~~c~~~~~~~c~~c~ 112 (386)
T KOG2177|consen 79 SRPLGSKEELCEKHGEELKLFCEEDEKLLCVLCR 112 (386)
T ss_pred cccccccchhhhhcCCcceEEecccccccCCCCC
Confidence 111000 0 46889999999999997
No 189
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=60.98 E-value=8.6 Score=27.73 Aligned_cols=26 Identities=23% Similarity=0.709 Sum_probs=21.8
Q ss_pred CCCCCCcceeecCCCCeEEeccCccee
Q psy12853 98 CCPMCSVPIEKDEGCAQMLCKRCKHVF 124 (137)
Q Consensus 98 ~CP~C~~~iek~~gC~hm~C~~C~~~f 124 (137)
.|+.|+.+..+.+. |.|.|..||+..
T Consensus 151 ~~~~~g~~~~~~~~-~~~~c~~~~~~e 176 (189)
T PRK09521 151 MCSRCRTPLVKKGE-NELKCPNCGNIE 176 (189)
T ss_pred EccccCCceEECCC-CEEECCCCCCEE
Confidence 69999999988655 999999998753
No 190
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=60.68 E-value=6.1 Score=27.15 Aligned_cols=16 Identities=31% Similarity=0.650 Sum_probs=9.2
Q ss_pred cCCCCCCCcc-eeecCC
Q psy12853 96 IKCCPMCSVP-IEKDEG 111 (137)
Q Consensus 96 ~~~CP~C~~~-iek~~g 111 (137)
..+||.|+.. ++..+|
T Consensus 107 ~~~CP~Cgs~~~~i~~G 123 (135)
T PRK03824 107 FLKCPKCGSRDFEIVKG 123 (135)
T ss_pred CcCCcCCCCCCcEEecC
Confidence 3568888765 443444
No 191
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=60.57 E-value=8.8 Score=29.98 Aligned_cols=31 Identities=26% Similarity=0.551 Sum_probs=22.0
Q ss_pred CCcccCCCCCC-ceeecCCCCeeecccccccc
Q psy12853 46 ELIKCCPMCSV-PIEKDEGCAQMLCKRCKHVF 76 (137)
Q Consensus 46 ~~~~~CP~C~~-~i~~~~~~~~~~C~~C~~~f 76 (137)
.....||.|+. .+..+.....+.|..||..+
T Consensus 9 ~~~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 9 EEKLVCPECGSDKLIYDYERGEIVCADCGLVI 40 (310)
T ss_pred ccCCcCcCCCCCCeeEECCCCeEeecccCCcc
Confidence 34568999998 45555566778888887654
No 192
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=60.37 E-value=5.7 Score=32.33 Aligned_cols=49 Identities=20% Similarity=0.550 Sum_probs=33.8
Q ss_pred CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853 46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK 108 (137)
Q Consensus 46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek 108 (137)
.....||-|...+... .+ ..|++.||..|...|-.. ...||.|+..+..
T Consensus 24 e~~l~C~IC~d~~~~P----vi--tpCgH~FCs~CI~~~l~~--------~~~CP~Cr~~~~~ 72 (397)
T TIGR00599 24 DTSLRCHICKDFFDVP----VL--TSCSHTFCSLCIRRCLSN--------QPKCPLCRAEDQE 72 (397)
T ss_pred ccccCCCcCchhhhCc----cC--CCCCCchhHHHHHHHHhC--------CCCCCCCCCcccc
Confidence 3456899888766321 11 269999999998765322 2379999998764
No 193
>PRK10445 endonuclease VIII; Provisional
Probab=60.09 E-value=8.4 Score=29.40 Aligned_cols=26 Identities=27% Similarity=0.480 Sum_probs=18.8
Q ss_pred cCCCCCCCcceee--cCCCCeEEeccCc
Q psy12853 96 IKCCPMCSVPIEK--DEGCAQMLCKRCK 121 (137)
Q Consensus 96 ~~~CP~C~~~iek--~~gC~hm~C~~C~ 121 (137)
.++||.|+..|++ .+|=.-..|.+|+
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 5799999999998 4665555555554
No 194
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=59.71 E-value=7.2 Score=22.65 Aligned_cols=28 Identities=25% Similarity=0.666 Sum_probs=14.3
Q ss_pred cccCCCCCCcee----ecC--CCCeeeccccccc
Q psy12853 48 IKCCPMCSVPIE----KDE--GCAQMLCKRCKHV 75 (137)
Q Consensus 48 ~~~CP~C~~~i~----~~~--~~~~~~C~~C~~~ 75 (137)
...||-|+.--. .+. ....+.||+|.++
T Consensus 4 Wi~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~E 37 (55)
T PF14205_consen 4 WILCPICGNKTRLKIREDTVLKNFPLYCPKCKQE 37 (55)
T ss_pred EEECCCCCCccceeeecCceeccccccCCCCCce
Confidence 556777775321 111 2445556665543
No 195
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=59.68 E-value=6.4 Score=28.35 Aligned_cols=31 Identities=23% Similarity=0.563 Sum_probs=21.8
Q ss_pred CCCcccCCCCCCceeecC-CCCeeeccccccc
Q psy12853 45 SELIKCCPMCSVPIEKDE-GCAQMLCKRCKHV 75 (137)
Q Consensus 45 ~~~~~~CP~C~~~i~~~~-~~~~~~C~~C~~~ 75 (137)
...+-.||+|+.-+...+ -...+.||.||..
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~ 145 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAMEYGFRCPQCGEM 145 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhhcCCcCCCCCCC
Confidence 455778999998776653 3456888887754
No 196
>KOG0320|consensus
Probab=59.63 E-value=2.3 Score=30.76 Aligned_cols=28 Identities=25% Similarity=0.782 Sum_probs=18.7
Q ss_pred ccccCCCCCCCcceeecC----CCCeEEeccC
Q psy12853 93 SELIKCCPMCSVPIEKDE----GCAQMLCKRC 120 (137)
Q Consensus 93 ~~~~~~CP~C~~~iek~~----gC~hm~C~~C 120 (137)
.+..-.||.|...+++.. .|-|+.|.+|
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~C 159 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQC 159 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHH
Confidence 345678999999888754 3555555544
No 197
>KOG2879|consensus
Probab=59.63 E-value=5.9 Score=30.64 Aligned_cols=51 Identities=27% Similarity=0.729 Sum_probs=31.3
Q ss_pred CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCccee
Q psy12853 46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE 107 (137)
Q Consensus 46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie 107 (137)
...+-||-|+.+=... -.+. .|++.+|+-|-... ....-.-.||+|+..++
T Consensus 237 t~~~~C~~Cg~~PtiP---~~~~--~C~HiyCY~Ci~ts------~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTIP---HVIG--KCGHIYCYYCIATS------RLWDASFTCPLCGENVE 287 (298)
T ss_pred cCCceeeccCCCCCCC---eeec--cccceeehhhhhhh------hcchhhcccCccCCCCc
Confidence 4457888888742110 0111 48999999997531 11112348999999887
No 198
>PLN00209 ribosomal protein S27; Provisional
Probab=59.33 E-value=9.5 Score=24.25 Aligned_cols=30 Identities=20% Similarity=0.414 Sum_probs=23.2
Q ss_pred cccCCCCCCceeec-CCCCeeeccccccccc
Q psy12853 48 IKCCPMCSVPIEKD-EGCAQMLCKRCKHVFC 77 (137)
Q Consensus 48 ~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC 77 (137)
.+.||+|...-... -....+.|..|+..++
T Consensus 36 ~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~ 66 (86)
T PLN00209 36 DVKCQGCFNITTVFSHSQTVVVCGSCQTVLC 66 (86)
T ss_pred EEECCCCCCeeEEEecCceEEEccccCCEee
Confidence 46799999865543 4677889999998887
No 199
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=59.24 E-value=8.7 Score=29.61 Aligned_cols=26 Identities=35% Similarity=0.747 Sum_probs=19.1
Q ss_pred cCCCCCCCcceee--cCCCCeEEeccCc
Q psy12853 96 IKCCPMCSVPIEK--DEGCAQMLCKRCK 121 (137)
Q Consensus 96 ~~~CP~C~~~iek--~~gC~hm~C~~C~ 121 (137)
.++||.|+..|++ .+|=.-..|..|+
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCCc
Confidence 5799999999998 4675555555554
No 200
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=59.01 E-value=9.8 Score=24.14 Aligned_cols=30 Identities=27% Similarity=0.512 Sum_probs=23.3
Q ss_pred cccCCCCCCceeec-CCCCeeeccccccccc
Q psy12853 48 IKCCPMCSVPIEKD-EGCAQMLCKRCKHVFC 77 (137)
Q Consensus 48 ~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC 77 (137)
.+.||+|...-... -....+.|..|+..+|
T Consensus 35 ~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~ 65 (85)
T PTZ00083 35 DVKCPGCSQITTVFSHAQTVVLCGGCSSQLC 65 (85)
T ss_pred EEECCCCCCeeEEEecCceEEEccccCCEee
Confidence 46799999865543 4677899999998887
No 201
>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=59.00 E-value=3.6 Score=29.04 Aligned_cols=32 Identities=22% Similarity=0.452 Sum_probs=21.7
Q ss_pred CCCCcccCCCCCCceeecC-CCCeeeccccccc
Q psy12853 44 DSELIKCCPMCSVPIEKDE-GCAQMLCKRCKHV 75 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~~~-~~~~~~C~~C~~~ 75 (137)
.+...-.||+|+.-+..++ -...+.||.||..
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHHcCCcCCCCCCE
Confidence 3455778999987766543 2356888888764
No 202
>PRK04023 DNA polymerase II large subunit; Validated
Probab=58.82 E-value=7 Score=35.47 Aligned_cols=7 Identities=43% Similarity=1.194 Sum_probs=2.6
Q ss_pred CCCCCCc
Q psy12853 98 CCPMCSV 104 (137)
Q Consensus 98 ~CP~C~~ 104 (137)
.||.|+.
T Consensus 628 fCpsCG~ 634 (1121)
T PRK04023 628 KCPSCGK 634 (1121)
T ss_pred cCCCCCC
Confidence 3333333
No 203
>PRK05580 primosome assembly protein PriA; Validated
Probab=58.79 E-value=9.6 Score=33.07 Aligned_cols=34 Identities=21% Similarity=0.504 Sum_probs=24.1
Q ss_pred ccCCCCCCceeecCCCCeeeccccccc-----ccccccc
Q psy12853 49 KCCPMCSVPIEKDEGCAQMLCKRCKHV-----FCWYCLA 82 (137)
Q Consensus 49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~-----fC~~C~~ 82 (137)
..||+|+.++......+.+.|..||+. .|..|+.
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~ 429 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGS 429 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcC
Confidence 467888888877666777888888764 4666644
No 204
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=58.57 E-value=9 Score=29.35 Aligned_cols=25 Identities=36% Similarity=0.769 Sum_probs=18.0
Q ss_pred cCCCCCCCcceeec--CCCCeEEeccC
Q psy12853 96 IKCCPMCSVPIEKD--EGCAQMLCKRC 120 (137)
Q Consensus 96 ~~~CP~C~~~iek~--~gC~hm~C~~C 120 (137)
.++||.|+..|++. +|=.-..|..|
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCC
Confidence 56999999999984 66444555544
No 205
>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=57.95 E-value=7 Score=19.97 Aligned_cols=8 Identities=38% Similarity=1.173 Sum_probs=3.8
Q ss_pred CCCCCCce
Q psy12853 51 CPMCSVPI 58 (137)
Q Consensus 51 CP~C~~~i 58 (137)
|+.|++.+
T Consensus 4 C~~CGy~y 11 (33)
T cd00350 4 CPVCGYIY 11 (33)
T ss_pred CCCCCCEE
Confidence 44555443
No 206
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=57.64 E-value=8 Score=34.07 Aligned_cols=27 Identities=37% Similarity=1.072 Sum_probs=22.6
Q ss_pred ccCCCCCCceeecCCCCeeeccccccccc
Q psy12853 49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFC 77 (137)
Q Consensus 49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC 77 (137)
..||.|+..+...+|+ .+|..||+.-|
T Consensus 725 ~~Cp~Cg~~l~~~~GC--~~C~~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGC--VVCHSCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCC--CcCCCCCCCCC
Confidence 4799999988888877 48999998776
No 207
>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=57.62 E-value=8.5 Score=21.49 Aligned_cols=8 Identities=38% Similarity=1.032 Sum_probs=4.4
Q ss_pred CCCCCCCc
Q psy12853 97 KCCPMCSV 104 (137)
Q Consensus 97 ~~CP~C~~ 104 (137)
..||.|+.
T Consensus 27 ~~CP~Cg~ 34 (52)
T TIGR02605 27 ATCPECGG 34 (52)
T ss_pred CCCCCCCC
Confidence 34666655
No 208
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=56.71 E-value=14 Score=21.47 Aligned_cols=23 Identities=26% Similarity=0.810 Sum_probs=10.9
Q ss_pred ccCCCCCCceeecCCCCeeeccccc
Q psy12853 49 KCCPMCSVPIEKDEGCAQMLCKRCK 73 (137)
Q Consensus 49 ~~CP~C~~~i~~~~~~~~~~C~~C~ 73 (137)
..|+-|+..|. ++...++||.|+
T Consensus 6 ~~C~~Cg~~~~--~~dDiVvCp~Cg 28 (54)
T PF14446_consen 6 CKCPVCGKKFK--DGDDIVVCPECG 28 (54)
T ss_pred ccChhhCCccc--CCCCEEECCCCC
Confidence 34555665553 223345555443
No 209
>KOG2691|consensus
Probab=55.99 E-value=12 Score=24.92 Aligned_cols=31 Identities=23% Similarity=0.410 Sum_probs=18.8
Q ss_pred CcccCCCCCCceeecCC--C--Ceeeccccccccc
Q psy12853 47 LIKCCPMCSVPIEKDEG--C--AQMLCKRCKHVFC 77 (137)
Q Consensus 47 ~~~~CP~C~~~i~~~~~--~--~~~~C~~C~~~fC 77 (137)
+.++|+.|+..+....+ + -...|..|.+.+=
T Consensus 3 ~~rfC~eCNNmLYPkEDked~~L~laCrnCd~ve~ 37 (113)
T KOG2691|consen 3 GIRFCRECNNMLYPKEDKEDRILLLACRNCDYVEE 37 (113)
T ss_pred ccchhhhhhccccccccccccEEEEEecCCcceEe
Confidence 46788888887765322 2 2355777665543
No 210
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=55.32 E-value=9.4 Score=31.08 Aligned_cols=34 Identities=21% Similarity=0.579 Sum_probs=25.9
Q ss_pred CCCCcccCCCCCCceeec--CCCCeeeccccccccc
Q psy12853 44 DSELIKCCPMCSVPIEKD--EGCAQMLCKRCKHVFC 77 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~~--~~~~~~~C~~C~~~fC 77 (137)
.......||.|+..+... +......||+|++..=
T Consensus 14 ~~~~~~~C~eCd~~~~~P~l~~~q~A~CPRC~~~l~ 49 (418)
T COG2995 14 PPGHLILCPECDMLVSLPRLDSGQSAYCPRCGHTLT 49 (418)
T ss_pred CccceecCCCCCceeccccCCCCCcccCCCCCCccc
Confidence 456688999999887654 4677889999987653
No 211
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.00 E-value=10 Score=23.74 Aligned_cols=32 Identities=28% Similarity=0.565 Sum_probs=18.3
Q ss_pred ccCCCCCCceeecC--CCCeeecccccccccccccccccCCC
Q psy12853 49 KCCPMCSVPIEKDE--GCAQMLCKRCKHVFCWYCLASRDYGG 88 (137)
Q Consensus 49 ~~CP~C~~~i~~~~--~~~~~~C~~C~~~fC~~C~~~~h~~~ 88 (137)
.-||.|+..+.... +.-.-.||+ |+..|-..+
T Consensus 2 llCP~C~v~l~~~~rs~vEiD~CPr--------CrGVWLDrG 35 (88)
T COG3809 2 LLCPICGVELVMSVRSGVEIDYCPR--------CRGVWLDRG 35 (88)
T ss_pred cccCcCCceeeeeeecCceeeeCCc--------cccEeecch
Confidence 35888888776543 333344554 555565543
No 212
>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=53.87 E-value=3.6 Score=27.35 Aligned_cols=15 Identities=20% Similarity=0.319 Sum_probs=6.6
Q ss_pred CCcccCCCCCCceee
Q psy12853 46 ELIKCCPMCSVPIEK 60 (137)
Q Consensus 46 ~~~~~CP~C~~~i~~ 60 (137)
+...+|++|+..+..
T Consensus 68 p~~~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 68 PARARCRDCGHEFEP 82 (113)
T ss_dssp --EEEETTTS-EEEC
T ss_pred CCcEECCCCCCEEec
Confidence 445555556555544
No 213
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=52.78 E-value=17 Score=29.64 Aligned_cols=43 Identities=16% Similarity=0.425 Sum_probs=23.5
Q ss_pred hHHHHhhccc-cccCCCCcccCCCCCCceeecCCCCeeecccccccc
Q psy12853 31 VIWHRTQVSG-ATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVF 76 (137)
Q Consensus 31 ~~~~r~~~~~-a~~~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~f 76 (137)
..|++...+- ..-..++..-||.|+..+.. .....||+|++..
T Consensus 197 ~lW~~~~~~~~~~~~~~~~~~C~~Cd~~~~~---~~~a~CpRC~~~L 240 (403)
T TIGR00155 197 WLWDDFYPEMPELRQPLKLRSCSACHTTILP---AQEPVCPRCSTPL 240 (403)
T ss_pred HHHHhcccccCCCCCccCCCcCCCCCCccCC---CCCcCCcCCCCcc
Confidence 6777764221 11123345668888886532 3345677776665
No 214
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=52.71 E-value=26 Score=23.17 Aligned_cols=30 Identities=23% Similarity=0.305 Sum_probs=18.3
Q ss_pred CCCcccCCCCCCceeecCCCCeeecccccccccccccc
Q psy12853 45 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLA 82 (137)
Q Consensus 45 ~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~ 82 (137)
......|++|+..-... ..|+..+|..|+.
T Consensus 39 G~~~~~C~~Cg~~~~~~--------~SCk~R~CP~C~~ 68 (111)
T PF14319_consen 39 GFHRYRCEDCGHEKIVY--------NSCKNRHCPSCQA 68 (111)
T ss_pred CcceeecCCCCceEEec--------CcccCcCCCCCCC
Confidence 34456777777654332 2567777777764
No 215
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=52.66 E-value=16 Score=26.81 Aligned_cols=35 Identities=17% Similarity=0.356 Sum_probs=24.9
Q ss_pred cccCCCCCCc---eeecCCCCeeecccccccccccccc
Q psy12853 48 IKCCPMCSVP---IEKDEGCAQMLCKRCKHVFCWYCLA 82 (137)
Q Consensus 48 ~~~CP~C~~~---i~~~~~~~~~~C~~C~~~fC~~C~~ 82 (137)
++.||.|+.+ +.+++......|..||..--..=..
T Consensus 98 yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~v~~~~ 135 (201)
T PRK12336 98 YVICSECGLPDTRLVKEDRVLMLRCDACGAHRPVKKRK 135 (201)
T ss_pred eEECCCCCCCCcEEEEcCCeEEEEcccCCCCccccccc
Confidence 7899999986 4444555567898888876655443
No 216
>PRK02935 hypothetical protein; Provisional
Probab=52.59 E-value=10 Score=25.08 Aligned_cols=11 Identities=27% Similarity=0.830 Sum_probs=5.1
Q ss_pred CCCCCCcceee
Q psy12853 98 CCPMCSVPIEK 108 (137)
Q Consensus 98 ~CP~C~~~iek 108 (137)
.|..|+.++..
T Consensus 88 ~CM~C~~PLTL 98 (110)
T PRK02935 88 ACMHCNQPLTL 98 (110)
T ss_pred ecCcCCCcCCc
Confidence 34444444443
No 217
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=52.57 E-value=6.5 Score=26.28 Aligned_cols=11 Identities=27% Similarity=0.793 Sum_probs=6.5
Q ss_pred CCCCCCcceee
Q psy12853 98 CCPMCSVPIEK 108 (137)
Q Consensus 98 ~CP~C~~~iek 108 (137)
.|+.|+.++..
T Consensus 87 ~CM~C~~pLTL 97 (114)
T PF11023_consen 87 ACMHCKEPLTL 97 (114)
T ss_pred ccCcCCCcCcc
Confidence 56666666544
No 218
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=52.25 E-value=15 Score=28.02 Aligned_cols=12 Identities=33% Similarity=0.642 Sum_probs=10.0
Q ss_pred CCCcccCCCCCC
Q psy12853 45 SELIKCCPMCSV 56 (137)
Q Consensus 45 ~~~~~~CP~C~~ 56 (137)
..+.+.||.|+.
T Consensus 306 ~~tS~~C~~cg~ 317 (364)
T COG0675 306 YYTSKTCPCCGH 317 (364)
T ss_pred CCCcccccccCC
Confidence 566789999999
No 219
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=51.88 E-value=12 Score=27.33 Aligned_cols=25 Identities=28% Similarity=0.809 Sum_probs=20.3
Q ss_pred CCCCCCCcceeecCCCCeEEeccCcce
Q psy12853 97 KCCPMCSVPIEKDEGCAQMLCKRCKHV 123 (137)
Q Consensus 97 ~~CP~C~~~iek~~gC~hm~C~~C~~~ 123 (137)
-+|++|+...++ .| +.|+|.+||+.
T Consensus 150 A~CsrC~~~L~~-~~-~~l~Cp~Cg~t 174 (188)
T COG1096 150 ARCSRCRAPLVK-KG-NMLKCPNCGNT 174 (188)
T ss_pred EEccCCCcceEE-cC-cEEECCCCCCE
Confidence 489999999999 33 67899988864
No 220
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=51.43 E-value=8.1 Score=25.96 Aligned_cols=15 Identities=20% Similarity=0.279 Sum_probs=7.2
Q ss_pred CCcccCCCCCCceee
Q psy12853 46 ELIKCCPMCSVPIEK 60 (137)
Q Consensus 46 ~~~~~CP~C~~~i~~ 60 (137)
+..-||.+|+..+..
T Consensus 68 p~~~~C~~C~~~~~~ 82 (115)
T COG0375 68 PAECWCLDCGQEVEL 82 (115)
T ss_pred ccEEEeccCCCeecc
Confidence 334455555444443
No 221
>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=50.48 E-value=8.9 Score=29.57 Aligned_cols=36 Identities=31% Similarity=0.792 Sum_probs=17.6
Q ss_pred CCCCCCCcc-----eeecC--CCCeEEeccCccee------eccccccc
Q psy12853 97 KCCPMCSVP-----IEKDE--GCAQMLCKRCKHVF------CWYCLASL 132 (137)
Q Consensus 97 ~~CP~C~~~-----iek~~--gC~hm~C~~C~~~f------C~~C~~~~ 132 (137)
..||-|+.. |...+ |=.|+.|+.|+++| |-.||..-
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~ 221 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTD 221 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---S
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCC
Confidence 589999765 33333 77899999999988 77787653
No 222
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=50.23 E-value=14 Score=24.80 Aligned_cols=22 Identities=23% Similarity=0.768 Sum_probs=13.2
Q ss_pred CCCCCCceeecCCCCeeecccccccc
Q psy12853 51 CPMCSVPIEKDEGCAQMLCKRCKHVF 76 (137)
Q Consensus 51 CP~C~~~i~~~~~~~~~~C~~C~~~f 76 (137)
||-|+..+.. ..+.|+.|++.+
T Consensus 1 CPvCg~~l~v----t~l~C~~C~t~i 22 (113)
T PF09862_consen 1 CPVCGGELVV----TRLKCPSCGTEI 22 (113)
T ss_pred CCCCCCceEE----EEEEcCCCCCEE
Confidence 6777776654 446666665443
No 223
>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=50.12 E-value=20 Score=23.82 Aligned_cols=34 Identities=26% Similarity=0.556 Sum_probs=15.9
Q ss_pred CCCCCCCcceeecCCCCeEEeccCcceeecccccc
Q psy12853 97 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS 131 (137)
Q Consensus 97 ~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~ 131 (137)
+.|..|..+.-...+.. ..|..|++.+|-.|+..
T Consensus 55 ~~C~~C~~~fg~l~~~~-~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 55 RHCARCGKPFGFLFNRG-RVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp SB-TTTS-BCSCTSTTC-EEETTTTEEEETTSEEE
T ss_pred cchhhhCCcccccCCCC-CcCCcCCccccCccCCc
Confidence 34555554433322222 55556666666666544
No 224
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=49.70 E-value=5.5 Score=35.43 Aligned_cols=31 Identities=23% Similarity=0.518 Sum_probs=0.0
Q ss_pred cCCCCCCCcceeecCCCCeEEeccCcce-----eeccccccc
Q psy12853 96 IKCCPMCSVPIEKDEGCAQMLCKRCKHV-----FCWYCLASL 132 (137)
Q Consensus 96 ~~~CP~C~~~iek~~gC~hm~C~~C~~~-----fC~~C~~~~ 132 (137)
.++||+|+... ...+|..||.. +|..|+...
T Consensus 655 ~r~Cp~Cg~~t------~~~~Cp~CG~~T~~~~~Cp~C~~~~ 690 (900)
T PF03833_consen 655 RRRCPKCGKET------FYNRCPECGSHTEPVYVCPDCGIEV 690 (900)
T ss_dssp ------------------------------------------
T ss_pred cccCcccCCcc------hhhcCcccCCccccceecccccccc
Confidence 45666666654 23445445544 455555444
No 225
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=49.25 E-value=7.9 Score=20.48 Aligned_cols=23 Identities=26% Similarity=0.739 Sum_probs=19.5
Q ss_pred CeeecccccccccccccccccCC
Q psy12853 65 AQMLCKRCKHVFCWYCLASRDYG 87 (137)
Q Consensus 65 ~~~~C~~C~~~fC~~C~~~~h~~ 87 (137)
..+.|..|+..+|..|...-|.+
T Consensus 14 ~~~~C~~C~~~~C~~C~~~~H~~ 36 (42)
T PF00643_consen 14 LSLFCEDCNEPLCSECTVSGHKG 36 (42)
T ss_dssp EEEEETTTTEEEEHHHHHTSTTT
T ss_pred eEEEecCCCCccCccCCCCCCCC
Confidence 56889999999999999877765
No 226
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=48.93 E-value=9.6 Score=34.09 Aligned_cols=27 Identities=30% Similarity=0.837 Sum_probs=21.3
Q ss_pred cCCCCCCCc-ceeecCCCCeEEeccCccee
Q psy12853 96 IKCCPMCSV-PIEKDEGCAQMLCKRCKHVF 124 (137)
Q Consensus 96 ~~~CP~C~~-~iek~~gC~hm~C~~C~~~f 124 (137)
.-.||-|+. .||..|||| ||+.||.+.
T Consensus 827 ~~~cp~c~~~~~~~~~~c~--~c~~c~~~~ 854 (858)
T PRK08115 827 GNTCPVCREGTVEEIGGCN--TCTNCGAQL 854 (858)
T ss_pred CCCCCccCCCceeecCCCc--cccchhhhh
Confidence 358999976 567799999 688888764
No 227
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=48.59 E-value=13 Score=20.53 Aligned_cols=11 Identities=27% Similarity=0.709 Sum_probs=8.1
Q ss_pred cCCCCCCceee
Q psy12853 50 CCPMCSVPIEK 60 (137)
Q Consensus 50 ~CP~C~~~i~~ 60 (137)
+||.|+.....
T Consensus 1 ~CP~Cg~~a~i 11 (47)
T PF04606_consen 1 RCPHCGSKARI 11 (47)
T ss_pred CcCCCCCeeEE
Confidence 58999986554
No 228
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=48.50 E-value=14 Score=19.75 Aligned_cols=13 Identities=31% Similarity=1.055 Sum_probs=10.2
Q ss_pred eEEeccCcceeec
Q psy12853 114 QMLCKRCKHVFCW 126 (137)
Q Consensus 114 hm~C~~C~~~fC~ 126 (137)
-++|..|+..||-
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 4678779999986
No 229
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=48.02 E-value=18 Score=27.50 Aligned_cols=30 Identities=23% Similarity=0.649 Sum_probs=22.3
Q ss_pred ccCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853 95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF 124 (137)
Q Consensus 95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~f 124 (137)
..+-||.|+..++...+=..+.|..||..+
T Consensus 98 ~~~fC~~CG~~~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 98 SHRFCGYCGHPMHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred cCccccccCCCCeecCCceeEECCCCCCEE
Confidence 478899999988776554668888887543
No 230
>KOG3002|consensus
Probab=47.93 E-value=13 Score=29.17 Aligned_cols=49 Identities=27% Similarity=0.668 Sum_probs=30.8
Q ss_pred cCCCCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCccee
Q psy12853 43 FDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE 107 (137)
Q Consensus 43 ~~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie 107 (137)
....++.-||-|-.+|.+ +.++|+. |+..|..|..+ ...+||-|+.+|-
T Consensus 43 ~~~~~lleCPvC~~~l~~----Pi~QC~n-GHlaCssC~~~-----------~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 43 LLDLDLLDCPVCFNPLSP----PIFQCDN-GHLACSSCRTK-----------VSNKCPTCRLPIG 91 (299)
T ss_pred ccchhhccCchhhccCcc----cceecCC-CcEehhhhhhh-----------hcccCCccccccc
Confidence 345668899999998875 4456644 66677777631 2335666655553
No 231
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=47.73 E-value=15 Score=25.11 Aligned_cols=37 Identities=24% Similarity=0.354 Sum_probs=25.4
Q ss_pred CCcccCCCCCCce-eecC----CCCeeecccccccccccccc
Q psy12853 46 ELIKCCPMCSVPI-EKDE----GCAQMLCKRCKHVFCWYCLA 82 (137)
Q Consensus 46 ~~~~~CP~C~~~i-~~~~----~~~~~~C~~C~~~fC~~C~~ 82 (137)
.....||.|.... .+.+ +.....|+.|+..|=..=+.
T Consensus 28 ~~~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~~~~~ 69 (129)
T COG3677 28 ITKVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFTVETGS 69 (129)
T ss_pred cccCcCCCCCccceeeECCccccccccccCCcCcceeeeccC
Confidence 3357999999877 3322 46778899998887654443
No 232
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=47.61 E-value=14 Score=21.50 Aligned_cols=28 Identities=43% Similarity=1.047 Sum_probs=19.5
Q ss_pred ccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853 72 CKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD 109 (137)
Q Consensus 72 C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~ 109 (137)
|++.+|..| ++.+..--||-|+++++..
T Consensus 25 CgH~I~~~~----------f~~~rYngCPfC~~~~~~~ 52 (55)
T PF14447_consen 25 CGHLICDNC----------FPGERYNGCPFCGTPFEFD 52 (55)
T ss_pred ccceeeccc----------cChhhccCCCCCCCcccCC
Confidence 666666555 4455566799999988764
No 233
>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=47.27 E-value=15 Score=18.97 Aligned_cols=8 Identities=38% Similarity=1.111 Sum_probs=4.1
Q ss_pred CCCCCCce
Q psy12853 51 CPMCSVPI 58 (137)
Q Consensus 51 CP~C~~~i 58 (137)
|+.|++.+
T Consensus 5 C~~CG~i~ 12 (34)
T cd00729 5 CPVCGYIH 12 (34)
T ss_pred CCCCCCEe
Confidence 55555443
No 234
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.82 E-value=10 Score=25.31 Aligned_cols=8 Identities=25% Similarity=0.804 Sum_probs=4.8
Q ss_pred CCCCCCcc
Q psy12853 98 CCPMCSVP 105 (137)
Q Consensus 98 ~CP~C~~~ 105 (137)
+||+|+..
T Consensus 90 ~CP~Cgs~ 97 (117)
T PRK00564 90 VCEKCHSK 97 (117)
T ss_pred cCcCCCCC
Confidence 46666654
No 235
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=46.56 E-value=17 Score=29.57 Aligned_cols=30 Identities=17% Similarity=0.451 Sum_probs=23.0
Q ss_pred CcccCCCCCCceeecC--CCCeeecccccccc
Q psy12853 47 LIKCCPMCSVPIEKDE--GCAQMLCKRCKHVF 76 (137)
Q Consensus 47 ~~~~CP~C~~~i~~~~--~~~~~~C~~C~~~f 76 (137)
+..-||.|+..+...+ ......||+|++..
T Consensus 12 ~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 12 KHILCSQCDMLVALPRIESGQKAACPRCGTTL 43 (403)
T ss_pred CeeeCCCCCCcccccCCCCCCeeECCCCCCCC
Confidence 3567999999887653 45678899988877
No 236
>KOG4537|consensus
Probab=46.54 E-value=4.4 Score=28.68 Aligned_cols=44 Identities=25% Similarity=0.472 Sum_probs=26.9
Q ss_pred ccchhhhHHHHhhccccccCCCCcccCCCCCCceeecCCCCeeecccc
Q psy12853 25 GHSRASVIWHRTQVSGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRC 72 (137)
Q Consensus 25 ~~~~~~~~~~r~~~~~a~~~~~~~~~CP~C~~~i~~~~~~~~~~C~~C 72 (137)
.+++.++....+++..+.+.+. +||+|+..+..+ .++.+.|-.|
T Consensus 20 ~qDeVS~~mG~ylLrGytmLde---~Cp~C~~Ilm~d-r~~~~~CVsC 63 (178)
T KOG4537|consen 20 TQDEVSAQMGQYLLRGYTMLDE---ICPKCEKILMRD-RDNPMFCVSC 63 (178)
T ss_pred HHHHHHHHHHHHHHhhhHHhhh---hcchHHHHHHhh-ccCceEEEee
Confidence 4445555666666666655444 899999986654 3444544433
No 237
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=46.53 E-value=7.9 Score=30.63 Aligned_cols=53 Identities=23% Similarity=0.515 Sum_probs=38.6
Q ss_pred CCCCcccCCCCCCceeecC--------CCCeeecccccccccccccccccCCCCcccccccCCCCCCCc
Q psy12853 44 DSELIKCCPMCSVPIEKDE--------GCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSV 104 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~~~--------~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~ 104 (137)
.++....|-.|..++.+.. .....+|+.|+..||..|.+-.|+. ...||.|..
T Consensus 358 ~~~ks~~Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~--------Lh~C~gCe~ 418 (421)
T COG5151 358 TNPKSTHCFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHET--------LHFCIGCEL 418 (421)
T ss_pred CCCCCccceeccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHHH--------HhhCCCCcC
Confidence 4556677888988776542 2557889999999999998755543 456777754
No 238
>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=46.37 E-value=12 Score=20.26 Aligned_cols=18 Identities=28% Similarity=0.637 Sum_probs=12.8
Q ss_pred Ceeecccccccccccccc
Q psy12853 65 AQMLCKRCKHVFCWYCLA 82 (137)
Q Consensus 65 ~~~~C~~C~~~fC~~C~~ 82 (137)
..+.|+.|+..||...+.
T Consensus 12 ~~~~C~~C~~~FC~~Hr~ 29 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHRL 29 (43)
T ss_dssp SHEE-TTTS-EE-TTTHS
T ss_pred CCeECCCCCcccCccccC
Confidence 578999999999988876
No 239
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=45.79 E-value=14 Score=26.12 Aligned_cols=28 Identities=32% Similarity=0.768 Sum_probs=15.3
Q ss_pred cCCCCCCce-ee-c-----CC--C-Ceeeccccccccc
Q psy12853 50 CCPMCSVPI-EK-D-----EG--C-AQMLCKRCKHVFC 77 (137)
Q Consensus 50 ~CP~C~~~i-~~-~-----~~--~-~~~~C~~C~~~fC 77 (137)
.||.|+.+- .. + +| . ..-+|+.||..|=
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~ 39 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFT 39 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcce
Confidence 488888644 11 1 11 1 2356777776664
No 240
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=45.67 E-value=18 Score=24.42 Aligned_cols=6 Identities=50% Similarity=1.641 Sum_probs=3.7
Q ss_pred CCCCCC
Q psy12853 98 CCPMCS 103 (137)
Q Consensus 98 ~CP~C~ 103 (137)
.||.|+
T Consensus 94 ~CP~Cg 99 (124)
T PRK00762 94 ECPVCG 99 (124)
T ss_pred cCcCCC
Confidence 466665
No 241
>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=44.82 E-value=22 Score=20.54 Aligned_cols=24 Identities=21% Similarity=0.528 Sum_probs=15.5
Q ss_pred cccCCCCCCCcceeecCCCCeEEeccCcc
Q psy12853 94 ELIKCCPMCSVPIEKDEGCAQMLCKRCKH 122 (137)
Q Consensus 94 ~~~~~CP~C~~~iek~~gC~hm~C~~C~~ 122 (137)
.+...||+|+.+.. .|-.|..||+
T Consensus 24 p~l~~C~~cG~~~~-----~H~vc~~cG~ 47 (55)
T TIGR01031 24 PTLVVCPNCGEFKL-----PHRVCPSCGY 47 (55)
T ss_pred CcceECCCCCCccc-----CeeECCccCe
Confidence 34556888887663 4666666664
No 242
>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=44.48 E-value=13 Score=17.73 Aligned_cols=14 Identities=29% Similarity=0.638 Sum_probs=9.4
Q ss_pred CCCeeecccccccc
Q psy12853 63 GCAQMLCKRCKHVF 76 (137)
Q Consensus 63 ~~~~~~C~~C~~~f 76 (137)
+.....|+.|+..|
T Consensus 11 ~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 11 GEKPYKCPYCGKSF 24 (26)
T ss_dssp SSSSEEESSSSEEE
T ss_pred CCCCCCCCCCcCee
Confidence 45667777777655
No 243
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=44.36 E-value=9.4 Score=18.24 Aligned_cols=9 Identities=33% Similarity=0.833 Sum_probs=3.9
Q ss_pred ecccccccc
Q psy12853 68 LCKRCKHVF 76 (137)
Q Consensus 68 ~C~~C~~~f 76 (137)
.|+.|+..|
T Consensus 4 ~C~~CgR~F 12 (25)
T PF13913_consen 4 PCPICGRKF 12 (25)
T ss_pred cCCCCCCEE
Confidence 344444443
No 244
>KOG3183|consensus
Probab=44.00 E-value=20 Score=27.25 Aligned_cols=46 Identities=20% Similarity=0.442 Sum_probs=30.2
Q ss_pred CCCCeeecccccccccccccc-cccCCC-CcccccccCCCCCCCccee
Q psy12853 62 EGCAQMLCKRCKHVFCWYCLA-SRDYGG-ATFDSELIKCCPMCSVPIE 107 (137)
Q Consensus 62 ~~~~~~~C~~C~~~fC~~C~~-~~h~~~-~~~~~~~~~~CP~C~~~ie 107 (137)
.+--.+.|..|+..||...+. +.|.-- ..-....++.||.|..+|.
T Consensus 19 lDFLPf~Cd~C~~~FC~eHrsye~H~Cp~~~~~~~~v~icp~cs~pv~ 66 (250)
T KOG3183|consen 19 LDFLPFKCDGCSGIFCLEHRSYESHHCPKGLRIDVQVPICPLCSKPVP 66 (250)
T ss_pred ccccceeeCCccchhhhccchHhhcCCCcccccceeecccCCCCCCCC
Confidence 344578899999999988765 333332 2233455777887776665
No 245
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=43.64 E-value=19 Score=27.94 Aligned_cols=30 Identities=23% Similarity=0.505 Sum_probs=21.3
Q ss_pred ccCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853 95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF 124 (137)
Q Consensus 95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~f 124 (137)
..+-||+|+...+-..|=-.+.|..||+.+
T Consensus 110 ~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 110 SHRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred hCcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 467788888877777666667777776653
No 246
>PF14149 YhfH: YhfH-like protein
Probab=43.61 E-value=1.2 Score=23.82 Aligned_cols=27 Identities=33% Similarity=0.647 Sum_probs=18.4
Q ss_pred cccCCCCCCCcceeecCCCCeEEeccC
Q psy12853 94 ELIKCCPMCSVPIEKDEGCAQMLCKRC 120 (137)
Q Consensus 94 ~~~~~CP~C~~~iek~~gC~hm~C~~C 120 (137)
...|.|+.|+..|+-..-|..++|..|
T Consensus 11 Lp~K~C~~CG~~i~EQ~E~Y~n~C~~C 37 (37)
T PF14149_consen 11 LPPKKCTECGKEIEEQAECYGNECDRC 37 (37)
T ss_pred CCCcccHHHHHHHHHHHHHHhCcCCCC
Confidence 346788888888876666665665543
No 247
>PRK10445 endonuclease VIII; Provisional
Probab=43.41 E-value=21 Score=27.22 Aligned_cols=26 Identities=27% Similarity=0.532 Sum_probs=18.3
Q ss_pred cccCCCCCCceeec--CCCCeeeccccc
Q psy12853 48 IKCCPMCSVPIEKD--EGCAQMLCKRCK 73 (137)
Q Consensus 48 ~~~CP~C~~~i~~~--~~~~~~~C~~C~ 73 (137)
-..||.|+..|... .+-....||.|+
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 46788999888765 355566677765
No 248
>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=42.82 E-value=11 Score=19.71 Aligned_cols=30 Identities=17% Similarity=0.143 Sum_probs=14.9
Q ss_pred cccccccccCCCCcccccccCCCCCCCcce
Q psy12853 77 CWYCLASRDYGGATFDSELIKCCPMCSVPI 106 (137)
Q Consensus 77 C~~C~~~~h~~~~~~~~~~~~~CP~C~~~i 106 (137)
|-.|..++..+....-.....-|++|+-.+
T Consensus 2 C~~C~~Ey~~p~~RR~~~~~isC~~CGPr~ 31 (35)
T PF07503_consen 2 CDDCLKEYFDPSNRRFHYQFISCTNCGPRY 31 (35)
T ss_dssp -HHHHHHHCSTTSTTTT-TT--BTTCC-SC
T ss_pred CHHHHHHHcCCCCCcccCcCccCCCCCCCE
Confidence 556777666655443344456677776544
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 PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=42.36 E-value=22 Score=27.26 Aligned_cols=26 Identities=27% Similarity=0.678 Sum_probs=18.5
Q ss_pred cccCCCCCCceeec--CCCCeeeccccc
Q psy12853 48 IKCCPMCSVPIEKD--EGCAQMLCKRCK 73 (137)
Q Consensus 48 ~~~CP~C~~~i~~~--~~~~~~~C~~C~ 73 (137)
-..||.|+..|... .+-....||.|+
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 46799999988765 345566777775
No 251
>KOG2324|consensus
Probab=42.27 E-value=25 Score=28.57 Aligned_cols=37 Identities=24% Similarity=0.499 Sum_probs=21.1
Q ss_pred CCCeeecccccccccccccccccCCCCcccccccCCCCCCCc-ceeec
Q psy12853 63 GCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSV-PIEKD 109 (137)
Q Consensus 63 ~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~-~iek~ 109 (137)
++..++|+.|+ +....+..+...+..||+|.. .+++.
T Consensus 224 ED~l~~C~~C~----------~s~n~e~~~~sk~~~Cp~C~~~~L~~~ 261 (457)
T KOG2324|consen 224 EDTLMSCPSCG----------YSKNSEDLDLSKIASCPKCNEGRLTKT 261 (457)
T ss_pred ccceeecCcCC----------ccCchhhhcCCccccCCcccCCCcccc
Confidence 46677777776 223333444444567888876 44443
No 252
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=41.43 E-value=14 Score=30.27 Aligned_cols=26 Identities=23% Similarity=0.598 Sum_probs=19.6
Q ss_pred cCCCCCCceeecCCCCeeecccccccc
Q psy12853 50 CCPMCSVPIEKDEGCAQMLCKRCKHVF 76 (137)
Q Consensus 50 ~CP~C~~~i~~~~~~~~~~C~~C~~~f 76 (137)
-||.|+.-+.-.+.. -+.|++|++.+
T Consensus 352 ~Cp~Cg~~m~S~G~~-g~rC~kCg~~~ 377 (421)
T COG1571 352 VCPRCGGRMKSAGRN-GFRCKKCGTRA 377 (421)
T ss_pred CCCccCCchhhcCCC-CcccccccccC
Confidence 689999888665544 78888887765
No 253
>PHA02942 putative transposase; Provisional
Probab=41.22 E-value=28 Score=28.11 Aligned_cols=31 Identities=19% Similarity=0.346 Sum_probs=21.6
Q ss_pred CCCcccCCCCCCceeecCCCCeeecccccccc
Q psy12853 45 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHVF 76 (137)
Q Consensus 45 ~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~f 76 (137)
..+.+.||.|+.... ..+...+.|+.||+..
T Consensus 322 ~yTSq~Cs~CG~~~~-~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 322 SYSSVSCPKCGHKMV-EIAHRYFHCPSCGYEN 352 (383)
T ss_pred CCCCccCCCCCCccC-cCCCCEEECCCCCCEe
Confidence 346788999998653 3345678888877653
No 254
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=41.06 E-value=25 Score=28.81 Aligned_cols=30 Identities=20% Similarity=0.511 Sum_probs=22.6
Q ss_pred CcccCCCCCCceeecC--CCCeeecccccccc
Q psy12853 47 LIKCCPMCSVPIEKDE--GCAQMLCKRCKHVF 76 (137)
Q Consensus 47 ~~~~CP~C~~~i~~~~--~~~~~~C~~C~~~f 76 (137)
+..-||.|+..+...+ ......||+|++..
T Consensus 9 ~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 40 (419)
T PRK15103 9 KHILCPQCDMLVALPRLEHGQKAACPRCGTTL 40 (419)
T ss_pred CcccCCCCCceeecCCCCCCCeeECCCCCCCC
Confidence 3456999999887653 34578899988877
No 255
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=40.04 E-value=24 Score=27.35 Aligned_cols=27 Identities=33% Similarity=0.691 Sum_probs=20.6
Q ss_pred CcccCCCCCCceeec--CCCCeeeccccc
Q psy12853 47 LIKCCPMCSVPIEKD--EGCAQMLCKRCK 73 (137)
Q Consensus 47 ~~~~CP~C~~~i~~~--~~~~~~~C~~C~ 73 (137)
.-..|+.|+.+|++. .+-..+.||.|.
T Consensus 244 ~GepC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 244 AGEPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 456799999999876 456677788875
No 256
>PRK12496 hypothetical protein; Provisional
Probab=39.87 E-value=15 Score=26.00 Aligned_cols=12 Identities=25% Similarity=0.553 Sum_probs=8.3
Q ss_pred CCCCCCCcceee
Q psy12853 97 KCCPMCSVPIEK 108 (137)
Q Consensus 97 ~~CP~C~~~iek 108 (137)
++|+.|+..+..
T Consensus 128 ~~C~gC~~~~~~ 139 (164)
T PRK12496 128 KVCKGCKKKYPE 139 (164)
T ss_pred EECCCCCccccC
Confidence 458888877643
No 257
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=39.85 E-value=17 Score=21.20 Aligned_cols=11 Identities=45% Similarity=1.005 Sum_probs=6.1
Q ss_pred cCCCCCCCcce
Q psy12853 96 IKCCPMCSVPI 106 (137)
Q Consensus 96 ~~~CP~C~~~i 106 (137)
.+.||+|++..
T Consensus 5 mr~C~~CgvYT 15 (56)
T PRK13130 5 IRKCPKCGVYT 15 (56)
T ss_pred ceECCCCCCEE
Confidence 44566665555
No 258
>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=39.44 E-value=31 Score=23.52 Aligned_cols=27 Identities=22% Similarity=0.782 Sum_probs=15.9
Q ss_pred cCCCC--CCCcceeecCCCCeEEeccCcce
Q psy12853 96 IKCCP--MCSVPIEKDEGCAQMLCKRCKHV 123 (137)
Q Consensus 96 ~~~CP--~C~~~iek~~gC~hm~C~~C~~~ 123 (137)
...|| .|+..+... +=+...|..|+..
T Consensus 18 Y~aC~~~~C~kKv~~~-~~~~y~C~~C~~~ 46 (146)
T PF08646_consen 18 YPACPNEKCNKKVTEN-GDGSYRCEKCNKT 46 (146)
T ss_dssp EEE-TSTTTS-B-EEE-TTTEEEETTTTEE
T ss_pred ECCCCCccCCCEeecC-CCcEEECCCCCCc
Confidence 45688 888877776 3356777767654
No 259
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=39.00 E-value=28 Score=26.66 Aligned_cols=27 Identities=37% Similarity=0.821 Sum_probs=18.9
Q ss_pred cccCCCCCCceeec--CCCCeeecccccc
Q psy12853 48 IKCCPMCSVPIEKD--EGCAQMLCKRCKH 74 (137)
Q Consensus 48 ~~~CP~C~~~i~~~--~~~~~~~C~~C~~ 74 (137)
-..||.|+..|.+. .+-....||.|..
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCCC
Confidence 35699999988775 3455677877764
No 260
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=38.24 E-value=22 Score=34.35 Aligned_cols=27 Identities=33% Similarity=0.917 Sum_probs=23.5
Q ss_pred CCCCCCcc------eeecCCCCeEEeccCcceeec
Q psy12853 98 CCPMCSVP------IEKDEGCAQMLCKRCKHVFCW 126 (137)
Q Consensus 98 ~CP~C~~~------iek~~gC~hm~C~~C~~~fC~ 126 (137)
.||-|+.. +...+||. +|..||..-|-
T Consensus 1706 ~cp~c~~~~~~~~~~~~~~gc~--~c~~cg~s~c~ 1738 (1740)
T PRK08332 1706 YCPVCYEKEGKLVELRMESGCA--TCPVCGWSKCV 1738 (1740)
T ss_pred CCCCCCCCCCcceeeEecCCce--eCCCCCCcccc
Confidence 49999998 77889997 89999998774
No 261
>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=38.24 E-value=32 Score=18.00 Aligned_cols=25 Identities=28% Similarity=0.582 Sum_probs=15.2
Q ss_pred cCCCCCCceeecCCCCeeeccccccc
Q psy12853 50 CCPMCSVPIEKDEGCAQMLCKRCKHV 75 (137)
Q Consensus 50 ~CP~C~~~i~~~~~~~~~~C~~C~~~ 75 (137)
.|+.|+.. .....+....|..|++.
T Consensus 10 ~C~~C~~~-~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 10 PCPVCGSR-WFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred cCCCCCCe-EeEccCCEEEhhhCceE
Confidence 47888887 33344556666666653
No 262
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=38.00 E-value=35 Score=26.10 Aligned_cols=26 Identities=38% Similarity=0.915 Sum_probs=17.9
Q ss_pred ccCCCCCCceeec--CCCCeeecccccc
Q psy12853 49 KCCPMCSVPIEKD--EGCAQMLCKRCKH 74 (137)
Q Consensus 49 ~~CP~C~~~i~~~--~~~~~~~C~~C~~ 74 (137)
..||.|+..|.+. .+-....||.|+.
T Consensus 236 ~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~ 263 (269)
T PRK14811 236 QPCPRCGTPIEKIVVGGRGTHFCPQCQP 263 (269)
T ss_pred CCCCcCCCeeEEEEECCCCcEECCCCcC
Confidence 4688999888765 3455666777654
No 263
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=37.02 E-value=20 Score=19.57 Aligned_cols=33 Identities=39% Similarity=0.833 Sum_probs=16.2
Q ss_pred CCCCCcceeecCCCCeEEeccCcceeeccccccccc
Q psy12853 99 CPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDV 134 (137)
Q Consensus 99 CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~~ 134 (137)
||-|+. +.+..-.-|.= .||+.||..|.+.+..
T Consensus 1 CpIc~e--~~~~~n~P~~L-~CGH~~c~~cl~~l~~ 33 (43)
T PF13445_consen 1 CPICKE--FSTEENPPMVL-PCGHVFCKDCLQKLSK 33 (43)
T ss_dssp -TTT------TTSS-EEE--SSS-EEEHHHHHHHHH
T ss_pred CCcccc--ccCCCCCCEEE-eCccHHHHHHHHHHHh
Confidence 566665 22222223443 4999999999887654
No 264
>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=36.89 E-value=38 Score=17.78 Aligned_cols=26 Identities=31% Similarity=0.735 Sum_probs=17.2
Q ss_pred cccCCCCCCce--eecC----CCCeeeccccc
Q psy12853 48 IKCCPMCSVPI--EKDE----GCAQMLCKRCK 73 (137)
Q Consensus 48 ~~~CP~C~~~i--~~~~----~~~~~~C~~C~ 73 (137)
.+.||.|+..- .+.+ |.....|..|.
T Consensus 5 ~v~CP~C~s~~~v~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 5 DVHCPRCQSTEGVKKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeeCCCCCCCCcceeCCCCCCCCEeEecCcCC
Confidence 56899999865 3332 45677787663
No 265
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=36.80 E-value=34 Score=22.48 Aligned_cols=18 Identities=28% Similarity=0.530 Sum_probs=11.7
Q ss_pred CCeeeccccccccccccc
Q psy12853 64 CAQMLCKRCKHVFCWYCL 81 (137)
Q Consensus 64 ~~~~~C~~C~~~fC~~C~ 81 (137)
...++||.|++..=.+|.
T Consensus 20 ~k~FtCp~Cghe~vs~ct 37 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCT 37 (104)
T ss_pred CceEecCccCCeeeeEEE
Confidence 456777777766655554
No 266
>KOG4739|consensus
Probab=36.68 E-value=17 Score=27.47 Aligned_cols=27 Identities=41% Similarity=1.038 Sum_probs=21.5
Q ss_pred cccccccccccccccCCCCcccccccCCCCCCCccee
Q psy12853 71 RCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE 107 (137)
Q Consensus 71 ~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie 107 (137)
.|++.||-.|....|.+ .||-|+..|-
T Consensus 22 aC~HvfC~~C~k~~~~~----------~C~lCkk~ir 48 (233)
T KOG4739|consen 22 ACRHVFCEPCLKASSPD----------VCPLCKKSIR 48 (233)
T ss_pred echhhhhhhhcccCCcc----------ccccccceee
Confidence 68999999998766654 6999988753
No 267
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=36.49 E-value=24 Score=19.98 Aligned_cols=15 Identities=27% Similarity=0.729 Sum_probs=11.9
Q ss_pred eEEeccCcceeeccc
Q psy12853 114 QMLCKRCKHVFCWYC 128 (137)
Q Consensus 114 hm~C~~C~~~fC~~C 128 (137)
+++|..||.+|-|.=
T Consensus 4 ~l~C~dCg~~FvfTa 18 (49)
T PF13451_consen 4 TLTCKDCGAEFVFTA 18 (49)
T ss_pred eEEcccCCCeEEEeh
Confidence 578999999987743
No 268
>PF10238 Eapp_C: E2F-associated phosphoprotein; InterPro: IPR019370 This entry represents E2F binding proteins. E2F transcription factors play an essential role in cell proliferation and apoptosis and their activity is frequently deregulated in human cancers. E2F activity is regulated by a variety of mechanisms, frequently mediated by proteins binding to individual members or a subgroup of the family. E2F-associated phosphoprotein (EAPP)interacts with a subset of E2F factors and influences E2F-dependent promoter activity. EAPP is present throughout the cell cycle but disappears during mitosis [].
Probab=36.29 E-value=40 Score=23.32 Aligned_cols=20 Identities=25% Similarity=0.605 Sum_probs=16.3
Q ss_pred CCCeeecccccccccccccc
Q psy12853 63 GCAQMLCKRCKHVFCWYCLA 82 (137)
Q Consensus 63 ~~~~~~C~~C~~~fC~~C~~ 82 (137)
.+....||.|.+..|..|.+
T Consensus 26 sDavLsCp~Cft~lc~dcQr 45 (136)
T PF10238_consen 26 SDAVLSCPACFTTLCLDCQR 45 (136)
T ss_pred CCceEeCccccceeeecccc
Confidence 45667889999999999986
No 269
>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=35.79 E-value=41 Score=18.29 Aligned_cols=23 Identities=26% Similarity=0.920 Sum_probs=13.1
Q ss_pred CCCCCCceeecCCCCeeecccccccc
Q psy12853 51 CPMCSVPIEKDEGCAQMLCKRCKHVF 76 (137)
Q Consensus 51 CP~C~~~i~~~~~~~~~~C~~C~~~f 76 (137)
|+-|+. ..++...+.|..|+..|
T Consensus 2 C~vC~~---~~~~~~~i~C~~C~~~~ 24 (51)
T PF00628_consen 2 CPVCGQ---SDDDGDMIQCDSCNRWY 24 (51)
T ss_dssp BTTTTS---SCTTSSEEEBSTTSCEE
T ss_pred CcCCCC---cCCCCCeEEcCCCChhh
Confidence 555666 33456677776655443
No 270
>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=35.57 E-value=27 Score=20.42 Aligned_cols=12 Identities=33% Similarity=1.076 Sum_probs=8.0
Q ss_pred cCCCCCCCccee
Q psy12853 96 IKCCPMCSVPIE 107 (137)
Q Consensus 96 ~~~CP~C~~~ie 107 (137)
..+||.|+.++-
T Consensus 35 ~~pC~fCg~~l~ 46 (57)
T PF06221_consen 35 LGPCPFCGTPLL 46 (57)
T ss_pred cCcCCCCCCccc
Confidence 457888776653
No 271
>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=35.46 E-value=25 Score=22.57 Aligned_cols=29 Identities=28% Similarity=0.607 Sum_probs=21.7
Q ss_pred cCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853 96 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF 124 (137)
Q Consensus 96 ~~~CP~C~~~iek~~gC~hm~C~~C~~~f 124 (137)
-..||.|+..--+..+--.-.|..|+..|
T Consensus 35 ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRVATGIWKCKKCGKKF 63 (90)
T ss_dssp -BEESSSSSSEEEEEETTEEEETTTTEEE
T ss_pred CCcCCCCCCceeEEeeeEEeecCCCCCEE
Confidence 45799998887776666677888888776
No 272
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=35.05 E-value=21 Score=22.97 Aligned_cols=34 Identities=24% Similarity=0.512 Sum_probs=21.6
Q ss_pred CCCCcccCCCCCCceeecCCCCeeeccccccccc
Q psy12853 44 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFC 77 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC 77 (137)
.......||.|+..-.+-.......|..|+..|-
T Consensus 32 ~q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 32 SQHAKYFCPFCGKHAVKRQAVGIWRCKGCKKTVA 65 (90)
T ss_pred HHhCCccCCCCCCCceeeeeeEEEEcCCCCCEEe
Confidence 3344678999986544434455677777776654
No 273
>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=34.80 E-value=19 Score=16.12 Aligned_cols=9 Identities=33% Similarity=0.866 Sum_probs=4.1
Q ss_pred ecccccccc
Q psy12853 68 LCKRCKHVF 76 (137)
Q Consensus 68 ~C~~C~~~f 76 (137)
.|+.|+..|
T Consensus 2 ~C~~C~~~f 10 (23)
T PF00096_consen 2 KCPICGKSF 10 (23)
T ss_dssp EETTTTEEE
T ss_pred CCCCCCCcc
Confidence 344444443
No 274
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=34.50 E-value=21 Score=26.27 Aligned_cols=29 Identities=24% Similarity=0.557 Sum_probs=16.7
Q ss_pred cccCCCCCCc-e----eec-CCCCeeecccccccc
Q psy12853 48 IKCCPMCSVP-I----EKD-EGCAQMLCKRCKHVF 76 (137)
Q Consensus 48 ~~~CP~C~~~-i----~~~-~~~~~~~C~~C~~~f 76 (137)
...||.|+.- . ++. .....+.|..||+.+
T Consensus 6 y~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~ 40 (201)
T COG1326 6 YIECPSCGSEEVSHEVIKERGREPLVRCEECGTVH 40 (201)
T ss_pred EEECCCCCcchhhHHHHHhcCCceEEEccCCCcEe
Confidence 4578888821 1 112 334577788877654
No 275
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.22 E-value=24 Score=21.20 Aligned_cols=21 Identities=24% Similarity=0.517 Sum_probs=15.6
Q ss_pred cccCCCCCCCcceeecCCCCe
Q psy12853 94 ELIKCCPMCSVPIEKDEGCAQ 114 (137)
Q Consensus 94 ~~~~~CP~C~~~iek~~gC~h 114 (137)
..+.+||.|+.+++....-.+
T Consensus 5 ~~~v~CP~Cgkpv~w~~~s~f 25 (65)
T COG3024 5 RITVPCPTCGKPVVWGEESPF 25 (65)
T ss_pred cccccCCCCCCcccccccCCc
Confidence 346789999999998655433
No 276
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=33.48 E-value=34 Score=23.87 Aligned_cols=26 Identities=19% Similarity=0.718 Sum_probs=13.4
Q ss_pred cCCCCCCCcceeecCCCCeEEeccCcc
Q psy12853 96 IKCCPMCSVPIEKDEGCAQMLCKRCKH 122 (137)
Q Consensus 96 ~~~CP~C~~~iek~~gC~hm~C~~C~~ 122 (137)
...||.|+..+...+. ....|..|+.
T Consensus 34 Y~aC~~C~kkv~~~~~-~~~~C~~C~~ 59 (166)
T cd04476 34 YPACPGCNKKVVEEGN-GTYRCEKCNK 59 (166)
T ss_pred EccccccCcccEeCCC-CcEECCCCCC
Confidence 4456666666655442 3344444443
No 277
>KOG3084|consensus
Probab=33.19 E-value=30 Score=27.51 Aligned_cols=35 Identities=26% Similarity=0.584 Sum_probs=23.8
Q ss_pred CCcccCCCCCCceeecCCCCeeeccccccccccccccc
Q psy12853 46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS 83 (137)
Q Consensus 46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~ 83 (137)
...++||.|+.+.....+....+|. ...|..++..
T Consensus 148 skykFCp~CG~~tkp~e~g~k~~Cs---~~~C~~~n~~ 182 (345)
T KOG3084|consen 148 SKYKFCPGCGSPTKPEEAGTKLQCS---DETCPSCNVI 182 (345)
T ss_pred HHhccCcccCCCcccccCCccceee---cccCCcCCee
Confidence 4478999999998887666666664 4445444443
No 278
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=32.47 E-value=17 Score=21.56 Aligned_cols=26 Identities=23% Similarity=0.726 Sum_probs=18.2
Q ss_pred CCCCCCccee----ecCCCCeEEeccCcce
Q psy12853 98 CCPMCSVPIE----KDEGCAQMLCKRCKHV 123 (137)
Q Consensus 98 ~CP~C~~~ie----k~~gC~hm~C~~C~~~ 123 (137)
.||.|+..=. +..+-.++.|..||++
T Consensus 12 ~CP~C~~~Dtl~mW~En~ve~vECV~CG~~ 41 (66)
T COG3529 12 VCPACQAQDTLAMWRENNVEIVECVKCGHH 41 (66)
T ss_pred CCcccchhhHHHHHHhcCCceEehhhcchH
Confidence 5888866433 2466778888888875
No 279
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=32.13 E-value=36 Score=26.84 Aligned_cols=35 Identities=23% Similarity=0.737 Sum_probs=25.6
Q ss_pred cCCCCCCCcc-----ee--ecCCCCeEEeccCccee------eccccc
Q psy12853 96 IKCCPMCSVP-----IE--KDEGCAQMLCKRCKHVF------CWYCLA 130 (137)
Q Consensus 96 ~~~CP~C~~~-----ie--k~~gC~hm~C~~C~~~f------C~~C~~ 130 (137)
-..||-|+.. |. -.+|=.|+.|..|+++| |-.||.
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 4679999765 21 13677889999998887 667775
No 280
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=32.03 E-value=53 Score=17.47 Aligned_cols=8 Identities=38% Similarity=0.974 Sum_probs=5.2
Q ss_pred cCCCCCCc
Q psy12853 50 CCPMCSVP 57 (137)
Q Consensus 50 ~CP~C~~~ 57 (137)
.||+|+..
T Consensus 2 ~Cp~C~~~ 9 (40)
T smart00440 2 PCPKCGNR 9 (40)
T ss_pred cCCCCCCC
Confidence 47777763
No 281
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=32.02 E-value=28 Score=17.63 Aligned_cols=24 Identities=21% Similarity=0.465 Sum_probs=18.2
Q ss_pred CCeeecccccccccccccccccCC
Q psy12853 64 CAQMLCKRCKHVFCWYCLASRDYG 87 (137)
Q Consensus 64 ~~~~~C~~C~~~fC~~C~~~~h~~ 87 (137)
...+.|..|+..+|..|....|.+
T Consensus 10 ~~~~fC~~~~~~iC~~C~~~~H~~ 33 (39)
T cd00021 10 PLSLFCETDRALLCVDCDLSVHSG 33 (39)
T ss_pred ceEEEeCccChhhhhhcChhhcCC
Confidence 346788889999999998755654
No 282
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=31.86 E-value=25 Score=23.49 Aligned_cols=12 Identities=42% Similarity=1.049 Sum_probs=10.1
Q ss_pred eEEeccCcceeec
Q psy12853 114 QMLCKRCKHVFCW 126 (137)
Q Consensus 114 hm~C~~C~~~fC~ 126 (137)
-++|. ||++||-
T Consensus 24 ~vkc~-CGh~f~d 35 (112)
T PF08882_consen 24 VVKCD-CGHEFCD 35 (112)
T ss_pred eeecc-CCCeecC
Confidence 78895 9999984
No 283
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=31.28 E-value=32 Score=18.25 Aligned_cols=21 Identities=29% Similarity=0.724 Sum_probs=14.1
Q ss_pred CCCCCCCcceee-c--CCCCeEEec
Q psy12853 97 KCCPMCSVPIEK-D--EGCAQMLCK 118 (137)
Q Consensus 97 ~~CP~C~~~iek-~--~gC~hm~C~ 118 (137)
+.||.|+..+.. . .| ..+.|+
T Consensus 2 ~~CP~Cg~~lv~r~~k~g-~F~~Cs 25 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG-KFLGCS 25 (39)
T ss_pred cCCCCCCceeEEEECCCC-CEEECC
Confidence 579999765543 2 35 667777
No 284
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=31.25 E-value=21 Score=20.90 Aligned_cols=19 Identities=26% Similarity=0.573 Sum_probs=9.4
Q ss_pred cCCCCCCCcceeecCCCCe
Q psy12853 96 IKCCPMCSVPIEKDEGCAQ 114 (137)
Q Consensus 96 ~~~CP~C~~~iek~~gC~h 114 (137)
+.+||.|+..++-..+-.+
T Consensus 2 ~v~CP~C~k~~~~~~~n~~ 20 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPENPF 20 (57)
T ss_dssp EEE-TTT--EEE-SSSSS-
T ss_pred cccCCCCCCeecccCCCCc
Confidence 4578999988887554333
No 285
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=31.21 E-value=22 Score=22.84 Aligned_cols=33 Identities=27% Similarity=0.654 Sum_probs=21.4
Q ss_pred CCCcccCCCCCCceeecCCCCeeeccccccccc
Q psy12853 45 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFC 77 (137)
Q Consensus 45 ~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC 77 (137)
......||.|+..-.+-.......|..|+..|-
T Consensus 33 q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 33 MRAKHVCPVCGRPKVKRVGTGIWECRKCGAKFA 65 (90)
T ss_pred HhcCccCCCCCCCceEEEEEEEEEcCCCCCEEe
Confidence 344668999976654444555677777776654
No 286
>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=31.02 E-value=25 Score=20.23 Aligned_cols=9 Identities=33% Similarity=0.914 Sum_probs=4.8
Q ss_pred cCCCCCCCc
Q psy12853 96 IKCCPMCSV 104 (137)
Q Consensus 96 ~~~CP~C~~ 104 (137)
.-+||.|+.
T Consensus 44 ~y~C~~Cg~ 52 (54)
T PF10058_consen 44 QYRCPYCGA 52 (54)
T ss_pred EEEcCCCCC
Confidence 335666654
No 287
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=30.96 E-value=21 Score=28.14 Aligned_cols=44 Identities=27% Similarity=0.576 Sum_probs=28.2
Q ss_pred ccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCc
Q psy12853 49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSV 104 (137)
Q Consensus 49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~ 104 (137)
.-||-|+..+...- -+ +-|++.||-.|... .....-..||+|..
T Consensus 275 LkCplc~~Llrnp~----kT-~cC~~~fc~eci~~-------al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLRNPM----KT-PCCGHTFCDECIGT-------ALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhhCcc----cC-ccccchHHHHHHhh-------hhhhccccCCCccc
Confidence 67888877664311 11 34999999888642 22234567999976
No 288
>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=30.85 E-value=22 Score=22.89 Aligned_cols=33 Identities=21% Similarity=0.550 Sum_probs=21.1
Q ss_pred CCCcccCCCCCCceeecCCCCeeeccccccccc
Q psy12853 45 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFC 77 (137)
Q Consensus 45 ~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC 77 (137)
......||.|+..-.+-.......|..|+..|-
T Consensus 32 q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 32 QKAKYVCPFCGKKTVKRGSTGIWTCRKCGAKFA 64 (91)
T ss_pred HhcCccCCCCCCCceEEEeeEEEEcCCCCCEEe
Confidence 344668999986544434455677777776654
No 289
>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=30.84 E-value=38 Score=19.48 Aligned_cols=25 Identities=24% Similarity=0.638 Sum_probs=15.2
Q ss_pred CCCCcccCCCCCCceeecCCCCeeeccccc
Q psy12853 44 DSELIKCCPMCSVPIEKDEGCAQMLCKRCK 73 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~ 73 (137)
..++...||.|+.+... ...|+.||
T Consensus 22 ~~~~l~~c~~cg~~~~~-----H~vc~~cG 46 (56)
T PF01783_consen 22 KAPNLVKCPNCGEPKLP-----HRVCPSCG 46 (56)
T ss_dssp -TTSEEESSSSSSEEST-----TSBCTTTB
T ss_pred cccceeeeccCCCEecc-----cEeeCCCC
Confidence 33478889999876543 34455554
No 290
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=30.73 E-value=42 Score=23.13 Aligned_cols=24 Identities=17% Similarity=0.393 Sum_probs=15.4
Q ss_pred cccCCCCCCceeecCCCCeeeccccccc
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCKHV 75 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~ 75 (137)
...|++|+..+.. +...|+.|+..
T Consensus 29 g~kC~~CG~v~~P----Pr~~Cp~C~~~ 52 (140)
T COG1545 29 GTKCKKCGRVYFP----PRAYCPKCGSE 52 (140)
T ss_pred EEEcCCCCeEEcC----CcccCCCCCCC
Confidence 5678888887664 34556665554
No 291
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=30.59 E-value=45 Score=20.45 Aligned_cols=10 Identities=30% Similarity=0.883 Sum_probs=7.1
Q ss_pred ccCCCCCCce
Q psy12853 49 KCCPMCSVPI 58 (137)
Q Consensus 49 ~~CP~C~~~i 58 (137)
..||.|+...
T Consensus 2 m~CP~Cg~~a 11 (72)
T PRK09678 2 FHCPLCQHAA 11 (72)
T ss_pred ccCCCCCCcc
Confidence 3688888765
No 292
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=30.56 E-value=12 Score=29.43 Aligned_cols=30 Identities=30% Similarity=0.916 Sum_probs=14.8
Q ss_pred cCCCCCCCcceeecCCCCeEEec-cCcceeeccccccc
Q psy12853 96 IKCCPMCSVPIEKDEGCAQMLCK-RCKHVFCWYCLASL 132 (137)
Q Consensus 96 ~~~CP~C~~~iek~~gC~hm~C~-~C~~~fC~~C~~~~ 132 (137)
.-+|--|.-.|. +-|- -||+.||+.|-+.+
T Consensus 25 ~lrC~IC~~~i~-------ip~~TtCgHtFCslCIR~h 55 (391)
T COG5432 25 MLRCRICDCRIS-------IPCETTCGHTFCSLCIRRH 55 (391)
T ss_pred HHHhhhhhheee-------cceecccccchhHHHHHHH
Confidence 346666665552 2222 35555555554443
No 293
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=29.82 E-value=48 Score=24.28 Aligned_cols=55 Identities=20% Similarity=0.366 Sum_probs=29.2
Q ss_pred cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCC
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCA 113 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~ 113 (137)
...|++|+.. |....-|| +.+|+.|...-|.-..-. ..+.|++|+..--..+.|+
T Consensus 60 ~~~C~nCg~~-----GH~~~DCP---~~iC~~C~~~~H~s~~C~---~~~~C~~Cg~~GH~~~dC~ 114 (190)
T COG5082 60 NPVCFNCGQN-----GHLRRDCP---HSICYNCSWDGHRSNHCP---KPKKCYNCGETGHLSRDCN 114 (190)
T ss_pred ccccchhccc-----CcccccCC---hhHhhhcCCCCcccccCC---cccccccccccCccccccC
Confidence 4456666542 33334444 477777743434432111 1267777777766666664
No 294
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=29.69 E-value=9.3 Score=22.18 Aligned_cols=13 Identities=38% Similarity=0.526 Sum_probs=9.2
Q ss_pred cCCCCCCCcceee
Q psy12853 96 IKCCPMCSVPIEK 108 (137)
Q Consensus 96 ~~~CP~C~~~iek 108 (137)
-++||+|+..-+-
T Consensus 24 e~KCPrCK~vN~~ 36 (60)
T COG4416 24 EKKCPRCKEVNEF 36 (60)
T ss_pred eecCCccceeeee
Confidence 4678888876653
No 295
>PRK07218 replication factor A; Provisional
Probab=29.05 E-value=26 Score=28.82 Aligned_cols=13 Identities=46% Similarity=0.951 Sum_probs=11.7
Q ss_pred cCCCCCCCcceee
Q psy12853 96 IKCCPMCSVPIEK 108 (137)
Q Consensus 96 ~~~CP~C~~~iek 108 (137)
+++||.|+..+++
T Consensus 297 i~rCP~C~r~v~~ 309 (423)
T PRK07218 297 IERCPECGRVIQK 309 (423)
T ss_pred eecCcCccccccC
Confidence 6899999999976
No 296
>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=28.72 E-value=46 Score=23.24 Aligned_cols=32 Identities=25% Similarity=0.575 Sum_probs=17.4
Q ss_pred CCCeeecccccccccccccccccCCCCcccccccCCCCCCCcce
Q psy12853 63 GCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPI 106 (137)
Q Consensus 63 ~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~i 106 (137)
|...+.|.+||+..-+.= ...+-+||+|+...
T Consensus 109 g~G~l~C~~Cg~~~~~~~------------~~~l~~Cp~C~~~~ 140 (146)
T PF07295_consen 109 GPGTLVCENCGHEVELTH------------PERLPPCPKCGHTE 140 (146)
T ss_pred cCceEecccCCCEEEecC------------CCcCCCCCCCCCCe
Confidence 344566666666555321 12356788886543
No 297
>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=28.54 E-value=44 Score=26.26 Aligned_cols=35 Identities=29% Similarity=0.813 Sum_probs=25.9
Q ss_pred CCCCCCCcc-----eee---cCCCCeEEeccCccee------ecccccc
Q psy12853 97 KCCPMCSVP-----IEK---DEGCAQMLCKRCKHVF------CWYCLAS 131 (137)
Q Consensus 97 ~~CP~C~~~-----iek---~~gC~hm~C~~C~~~f------C~~C~~~ 131 (137)
..||-|+.. |.. .+|=.|+.|..|+++| |-.||..
T Consensus 185 ~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 185 TLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred CcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence 389999865 222 4677889999998887 7777764
No 298
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=28.44 E-value=32 Score=28.33 Aligned_cols=27 Identities=22% Similarity=0.587 Sum_probs=20.6
Q ss_pred CCCCCCCcceeecCCCCeEEeccCccee
Q psy12853 97 KCCPMCSVPIEKDEGCAQMLCKRCKHVF 124 (137)
Q Consensus 97 ~~CP~C~~~iek~~gC~hm~C~~C~~~f 124 (137)
-.||.|+...+-.|. |-..|.+||+.+
T Consensus 351 p~Cp~Cg~~m~S~G~-~g~rC~kCg~~~ 377 (421)
T COG1571 351 PVCPRCGGRMKSAGR-NGFRCKKCGTRA 377 (421)
T ss_pred CCCCccCCchhhcCC-CCcccccccccC
Confidence 389999998855443 488999998754
No 299
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=28.32 E-value=32 Score=24.59 Aligned_cols=24 Identities=29% Similarity=0.675 Sum_probs=14.4
Q ss_pred cccCCCCCCceeecCCCCeeecccccc
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCKH 74 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~ 74 (137)
..-||-|++.... .+.-.||.|++
T Consensus 134 ~~vC~vCGy~~~g---e~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTHEG---EAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcccC---CCCCcCCCCCC
Confidence 5567777776543 44455666653
No 300
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=28.31 E-value=42 Score=27.82 Aligned_cols=55 Identities=29% Similarity=0.777 Sum_probs=29.7
Q ss_pred ccCC--CCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCeEEeccCcc
Q psy12853 49 KCCP--MCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKH 122 (137)
Q Consensus 49 ~~CP--~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~hm~C~~C~~ 122 (137)
+.|- .|...+..++ ..--.| .-...||..|. |+-|...-.-.++|.++.|-.||+
T Consensus 98 ~rCrN~aC~s~LP~dd-c~C~iC-~~~~gFC~~C~-----------------C~iC~kfD~~~n~~~Wi~Cd~CgH 154 (446)
T PF07227_consen 98 KRCRNLACRSQLPVDD-CDCKIC-CSEPGFCRRCM-----------------CCICSKFDDNKNTCSWIGCDVCGH 154 (446)
T ss_pred HhcCCHHhhccCCccc-cCcchh-cCCCCccccCC-----------------ccccCCcccCCCCeeEEeccCCCc
Confidence 4564 5777664433 211122 12467888884 666655444456666666665554
No 301
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=28.14 E-value=40 Score=27.10 Aligned_cols=47 Identities=15% Similarity=0.254 Sum_probs=27.7
Q ss_pred CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCC
Q psy12853 46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCS 103 (137)
Q Consensus 46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~ 103 (137)
.....||.|+..+... ....|..|..+-|.-....+..++..|++|+
T Consensus 4 ~~~~~C~~CGr~~~~~-----------~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cg 50 (355)
T COG1499 4 ASTILCVRCGRSVDPL-----------IDGLCGDCYVETTPLIEIPDEVNVEVCRHCG 50 (355)
T ss_pred CcccEeccCCCcCchh-----------hccccHHHHhccCccccCCCceEEEECCcCC
Confidence 4566777777776411 1334566666645444444555677777777
No 302
>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=27.98 E-value=31 Score=15.02 Aligned_cols=7 Identities=29% Similarity=0.880 Sum_probs=2.1
Q ss_pred ccccccc
Q psy12853 69 CKRCKHV 75 (137)
Q Consensus 69 C~~C~~~ 75 (137)
|+.|+..
T Consensus 3 C~~C~~~ 9 (24)
T PF13894_consen 3 CPICGKS 9 (24)
T ss_dssp -SSTS-E
T ss_pred CcCCCCc
Confidence 4444433
No 303
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.94 E-value=19 Score=24.76 Aligned_cols=15 Identities=40% Similarity=0.877 Sum_probs=11.4
Q ss_pred cccCCCCCCCcceee
Q psy12853 94 ELIKCCPMCSVPIEK 108 (137)
Q Consensus 94 ~~~~~CP~C~~~iek 108 (137)
+.+.+||.|...|.-
T Consensus 37 ati~qcp~csasirg 51 (160)
T COG4306 37 ATITQCPICSASIRG 51 (160)
T ss_pred HHHhcCCccCCcccc
Confidence 457789999888853
No 304
>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=27.48 E-value=78 Score=16.73 Aligned_cols=7 Identities=43% Similarity=1.170 Sum_probs=4.9
Q ss_pred CCCCCCC
Q psy12853 97 KCCPMCS 103 (137)
Q Consensus 97 ~~CP~C~ 103 (137)
.+||.|+
T Consensus 4 ~pCP~CG 10 (37)
T smart00778 4 GPCPNCG 10 (37)
T ss_pred cCCCCCC
Confidence 4788874
No 305
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=27.45 E-value=31 Score=20.30 Aligned_cols=13 Identities=46% Similarity=1.053 Sum_probs=10.7
Q ss_pred cCCCCCCCcceee
Q psy12853 96 IKCCPMCSVPIEK 108 (137)
Q Consensus 96 ~~~CP~C~~~iek 108 (137)
-+-||.|+.+|.-
T Consensus 3 HkHC~~CG~~Ip~ 15 (59)
T PF09889_consen 3 HKHCPVCGKPIPP 15 (59)
T ss_pred CCcCCcCCCcCCc
Confidence 3679999999975
No 306
>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=27.06 E-value=49 Score=20.10 Aligned_cols=26 Identities=23% Similarity=0.511 Sum_probs=17.1
Q ss_pred cCCCCCCceeecCCCCeeeccccccccc
Q psy12853 50 CCPMCSVPIEKDEGCAQMLCKRCKHVFC 77 (137)
Q Consensus 50 ~CP~C~~~i~~~~~~~~~~C~~C~~~fC 77 (137)
.| +|+..+..+++...-.| .||...=
T Consensus 5 rC-~Cgr~lya~e~~kTkkC-~CG~~l~ 30 (68)
T PF09082_consen 5 RC-DCGRYLYAKEGAKTKKC-VCGKTLK 30 (68)
T ss_dssp EE-TTS--EEEETT-SEEEE-TTTEEEE
T ss_pred Ee-cCCCEEEecCCcceeEe-cCCCeee
Confidence 45 78888888888888888 6776554
No 307
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=27.04 E-value=26 Score=25.74 Aligned_cols=18 Identities=22% Similarity=0.434 Sum_probs=12.5
Q ss_pred cCCCCCCCcceeecCCCC
Q psy12853 96 IKCCPMCSVPIEKDEGCA 113 (137)
Q Consensus 96 ~~~CP~C~~~iek~~gC~ 113 (137)
.-+||+|+..+.|.-.++
T Consensus 24 Lt~C~~C~~vaDkYiE~d 41 (208)
T PF04161_consen 24 LTKCPNCGKVADKYIEYD 41 (208)
T ss_pred EeeccccCCcccceeccc
Confidence 457888888887754444
No 308
>PF12675 DUF3795: Protein of unknown function (DUF3795); InterPro: IPR024227 This family of proteins is functionally uncharacterised and is found in bacteria and archaea. Proteins in this family are typically between 99 and 171 amino acids in length. These proteins are likely to be zinc binding given the conserved cysteines.
Probab=26.95 E-value=50 Score=20.21 Aligned_cols=35 Identities=23% Similarity=0.361 Sum_probs=22.6
Q ss_pred cCCCCCCCccee--ecCCCCeEEec-cCcceeeccccc
Q psy12853 96 IKCCPMCSVPIE--KDEGCAQMLCK-RCKHVFCWYCLA 130 (137)
Q Consensus 96 ~~~CP~C~~~ie--k~~gC~hm~C~-~C~~~fC~~C~~ 130 (137)
-..||.|+..-. ....|..-.|. .=|.+||+.|.+
T Consensus 34 ~~~C~GCr~~~~~~~~~~C~i~~C~~ekgv~~C~eC~e 71 (78)
T PF12675_consen 34 KIRCPGCRSGGGKCCCKSCKIRQCAKEKGVDFCGECPE 71 (78)
T ss_pred CCcCcCCcCCCCCcCCCCCCcCcHHhhCCCCeeecCCC
Confidence 446888877663 44556666664 127788888864
No 309
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=26.91 E-value=35 Score=23.35 Aligned_cols=28 Identities=29% Similarity=0.439 Sum_probs=17.9
Q ss_pred ccccccccccccCCCCcccccccCCCCCCCcceeecC
Q psy12853 74 HVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDE 110 (137)
Q Consensus 74 ~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~ 110 (137)
..+|..|+..||+ .|.||+|+.-|--.+
T Consensus 97 ~W~Cv~C~~~Y~G---------eK~C~~C~tGiYS~e 124 (128)
T PF11682_consen 97 DWHCVMCGNHYHG---------EKYCPKCGTGIYSIE 124 (128)
T ss_pred eEEEecCCCccCc---------CEecCCCCCccccee
Confidence 4455566555444 368999998875443
No 310
>PRK05978 hypothetical protein; Provisional
Probab=26.91 E-value=39 Score=23.71 Aligned_cols=12 Identities=25% Similarity=0.451 Sum_probs=8.3
Q ss_pred cccCCCCCCcee
Q psy12853 48 IKCCPMCSVPIE 59 (137)
Q Consensus 48 ~~~CP~C~~~i~ 59 (137)
.-.||+|+..=.
T Consensus 33 ~grCP~CG~G~L 44 (148)
T PRK05978 33 RGRCPACGEGKL 44 (148)
T ss_pred cCcCCCCCCCcc
Confidence 557888887543
No 311
>PRK06386 replication factor A; Reviewed
Probab=26.88 E-value=30 Score=27.84 Aligned_cols=13 Identities=31% Similarity=0.718 Sum_probs=11.7
Q ss_pred cCCCCCCCcceee
Q psy12853 96 IKCCPMCSVPIEK 108 (137)
Q Consensus 96 ~~~CP~C~~~iek 108 (137)
.++||.|+..+++
T Consensus 236 i~rCP~C~R~l~~ 248 (358)
T PRK06386 236 FTKCSVCNKIIED 248 (358)
T ss_pred EecCcCCCeEccC
Confidence 6899999999985
No 312
>TIGR01623 put_zinc_LRP1 putative zinc finger domain, LRP1 type. This model represents a putative zinc finger domain found in plants. Arabidopsis thaliana has at least 10 distinct members. Proteins containing this domain, including LRP1, generally share the same size, about 300 amino acids, and architecture. This 43-residue domain, and a more C-terminal companion domain of similar size, appear as tightly conserved islands of sequence similarity. The remainder consists largely of low-complexity sequence. Several animal proteins have regions with matching patterns of Cys, Gly, and His residues. These are not included in the model but score between trusted and noise cutoffs.
Probab=26.82 E-value=16 Score=20.11 Aligned_cols=24 Identities=17% Similarity=0.504 Sum_probs=19.5
Q ss_pred ecCCCCeEEeccCcceeecccccc
Q psy12853 108 KDEGCAQMLCKRCKHVFCWYCLAS 131 (137)
Q Consensus 108 k~~gC~hm~C~~C~~~fC~~C~~~ 131 (137)
...+|.|+.|+.|-..-+|.|-.-
T Consensus 9 a~k~C~~~~CRtCCK~r~~DC~tH 32 (43)
T TIGR01623 9 AKKECLFERCRTCCKSRGFHCVTH 32 (43)
T ss_pred hhCCCchhhhhHHhcccCcCCcch
Confidence 356899999999999988887543
No 313
>KOG1842|consensus
Probab=26.76 E-value=15 Score=30.43 Aligned_cols=40 Identities=23% Similarity=0.589 Sum_probs=31.1
Q ss_pred CCCCcccCCCCCCceeecCCCCeeeccccccccccccccccc
Q psy12853 44 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRD 85 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h 85 (137)
++..+.+||.|+..+.... +.-.|.-||...|..|.....
T Consensus 176 DDs~V~~CP~Ca~~F~l~r--RrHHCRLCG~VmC~~C~k~iS 215 (505)
T KOG1842|consen 176 DDSSVQFCPECANSFGLTR--RRHHCRLCGRVMCRDCSKFIS 215 (505)
T ss_pred CCCcccccccccchhhhHH--HhhhhhhcchHHHHHHHHhcC
Confidence 6788999999999876532 344577899999999987544
No 314
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=26.73 E-value=57 Score=17.63 Aligned_cols=29 Identities=31% Similarity=0.625 Sum_probs=20.6
Q ss_pred cCCCCCCceeecCCCCeeecccc-cccccccccc
Q psy12853 50 CCPMCSVPIEKDEGCAQMLCKRC-KHVFCWYCLA 82 (137)
Q Consensus 50 ~CP~C~~~i~~~~~~~~~~C~~C-~~~fC~~C~~ 82 (137)
.|-+|+.+|. .....|..| ...+|..|-.
T Consensus 2 ~Cd~C~~~i~----G~ry~C~~C~d~dLC~~C~~ 31 (43)
T cd02340 2 ICDGCQGPIV----GVRYKCLVCPDYDLCESCEA 31 (43)
T ss_pred CCCCCCCcCc----CCeEECCCCCCccchHHhhC
Confidence 4667877442 357788888 6889988854
No 315
>COG4640 Predicted membrane protein [Function unknown]
Probab=26.66 E-value=37 Score=27.83 Aligned_cols=7 Identities=57% Similarity=1.521 Sum_probs=4.5
Q ss_pred ccCCCCC
Q psy12853 49 KCCPMCS 55 (137)
Q Consensus 49 ~~CP~C~ 55 (137)
++||.|+
T Consensus 2 ~fC~kcG 8 (465)
T COG4640 2 KFCPKCG 8 (465)
T ss_pred Ccccccc
Confidence 4667666
No 316
>PLN02248 cellulose synthase-like protein
Probab=26.52 E-value=41 Score=31.10 Aligned_cols=50 Identities=26% Similarity=0.598 Sum_probs=37.0
Q ss_pred ccCC--CCCCceeecC-CCCeeecccccccccccccccccCCCCcccccccCCCCCCCccee
Q psy12853 49 KCCP--MCSVPIEKDE-GCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE 107 (137)
Q Consensus 49 ~~CP--~C~~~i~~~~-~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie 107 (137)
..|. +|......+. |.....| .|+..+|..|-.+.-. +.-.||.|+.+..
T Consensus 125 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~ 177 (1135)
T PLN02248 125 SSCAMPGCDGKVMRDERGEDLLPC-ECGFKICRDCYIDAVK--------SGGICPGCKEPYK 177 (1135)
T ss_pred CcccccCcccccccccccccCCcc-cccchhHHhHhhhhhh--------cCCCCCCCccccc
Confidence 5664 8988877764 6778889 7999999999764221 2447999988873
No 317
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=26.50 E-value=38 Score=22.36 Aligned_cols=30 Identities=20% Similarity=0.516 Sum_probs=20.3
Q ss_pred CCcccCCCCCCceeec--------CCCCeeeccccccc
Q psy12853 46 ELIKCCPMCSVPIEKD--------EGCAQMLCKRCKHV 75 (137)
Q Consensus 46 ~~~~~CP~C~~~i~~~--------~~~~~~~C~~C~~~ 75 (137)
-...+|++|..++.+- .+.-.++|..||+.
T Consensus 54 iKR~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~ 91 (105)
T COG2023 54 IKRTICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTI 91 (105)
T ss_pred HHHHhccccCcccccCcceEEEEcCCeEEEEecCCCcE
Confidence 3468999999986542 12346778888754
No 318
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=26.13 E-value=35 Score=17.56 Aligned_cols=22 Identities=18% Similarity=0.413 Sum_probs=9.5
Q ss_pred cccCCCCCCceeecCCCCeeeccccc
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCK 73 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~ 73 (137)
...|++|+..... +...|+.|+
T Consensus 11 ~~rC~~Cg~~~~p----Pr~~Cp~C~ 32 (37)
T PF12172_consen 11 GQRCRDCGRVQFP----PRPVCPHCG 32 (37)
T ss_dssp EEE-TTT--EEES------SEETTTT
T ss_pred EEEcCCCCCEecC----CCcCCCCcC
Confidence 4567777776554 224455554
No 319
>KOG4367|consensus
Probab=25.86 E-value=25 Score=29.22 Aligned_cols=63 Identities=22% Similarity=0.558 Sum_probs=41.7
Q ss_pred CeeecccccccccccccccccCCCCcc---------cc--------cccCCCCCCCcceeecCCCCe-EEeccCcceeec
Q psy12853 65 AQMLCKRCKHVFCWYCLASRDYGGATF---------DS--------ELIKCCPMCSVPIEKDEGCAQ-MLCKRCKHVFCW 126 (137)
Q Consensus 65 ~~~~C~~C~~~fC~~C~~~~h~~~~~~---------~~--------~~~~~CP~C~~~iek~~gC~h-m~C~~C~~~fC~ 126 (137)
..+.|..|...+|.-|+..-|++...+ +. ....+|- --++=|| |.|.+|+...||
T Consensus 175 a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs~~~s~r~~~~ct-------~h~~e~~smyc~~ck~pvc~ 247 (699)
T KOG4367|consen 175 ATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVSRRLSPRKVSTCT-------DHELENHSMYCVQCKMPVCY 247 (699)
T ss_pred hhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCceeeccchhhhhhcc-------CCCCCCceEEEEecCChHHH
Confidence 346677889999999999888884211 11 0112221 1233345 999999999999
Q ss_pred cccccccc
Q psy12853 127 YCLASLDV 134 (137)
Q Consensus 127 ~C~~~~~~ 134 (137)
.|++....
T Consensus 248 ~clee~kh 255 (699)
T KOG4367|consen 248 QCLEEGKH 255 (699)
T ss_pred HHHHhhcc
Confidence 99987653
No 320
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=25.68 E-value=26 Score=30.75 Aligned_cols=64 Identities=16% Similarity=0.250 Sum_probs=38.3
Q ss_pred CCCcccCCCCCCceeecCC----CCeeeccccc--------------------ccccccccccccCCCCcccccccCCCC
Q psy12853 45 SELIKCCPMCSVPIEKDEG----CAQMLCKRCK--------------------HVFCWYCLASRDYGGATFDSELIKCCP 100 (137)
Q Consensus 45 ~~~~~~CP~C~~~i~~~~~----~~~~~C~~C~--------------------~~fC~~C~~~~h~~~~~~~~~~~~~CP 100 (137)
.++.-.|++|-.-|.-..+ -+...|.+|| ...|-.|..+++.+...--.+...-||
T Consensus 98 ~pD~a~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRfHAQp~aCp 177 (750)
T COG0068 98 PPDAATCEDCLEEIFDPNSRRYLYPFINCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRFHAQPIACP 177 (750)
T ss_pred CCchhhhHHHHHHhcCCCCcceeccccccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccccccccccccCc
Confidence 4556666666655432221 2345566665 345777777777776544455567799
Q ss_pred CCCcceee
Q psy12853 101 MCSVPIEK 108 (137)
Q Consensus 101 ~C~~~iek 108 (137)
+|+-.+..
T Consensus 178 ~CGP~~~l 185 (750)
T COG0068 178 KCGPHLFL 185 (750)
T ss_pred ccCCCeEE
Confidence 99876654
No 321
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=25.50 E-value=91 Score=22.84 Aligned_cols=44 Identities=20% Similarity=0.350 Sum_probs=26.4
Q ss_pred CCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcce
Q psy12853 54 CSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPI 106 (137)
Q Consensus 54 C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~i 106 (137)
....++..+....++|..|+..+ ... ........-+||.|+..+
T Consensus 97 ~~~v~e~HG~~~~~~C~~C~~~~--------~~~-~~~~~~~~p~C~~Cgg~l 140 (224)
T cd01412 97 SRNVIELHGSLFRVRCSSCGYVG--------ENN-EEIPEEELPRCPKCGGLL 140 (224)
T ss_pred CCceEeeCCCcCccccCCCCCCC--------Ccc-hhhhccCCCCCCCCCCcc
Confidence 46667777777778887776554 111 112233467899997654
No 322
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 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 domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=25.50 E-value=19 Score=21.79 Aligned_cols=45 Identities=24% Similarity=0.780 Sum_probs=26.2
Q ss_pred CCCCCCceeec-------CCCCeeecccccccccccccccccCCCCcccccccCCCCCCC
Q psy12853 51 CPMCSVPIEKD-------EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCS 103 (137)
Q Consensus 51 CP~C~~~i~~~-------~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~ 103 (137)
|+=|...+... +..-.+.=..|++.|-..|...|-... ..||-|+
T Consensus 22 C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~--------~~CP~CR 73 (73)
T PF12678_consen 22 CAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN--------NTCPLCR 73 (73)
T ss_dssp ETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS--------SB-TTSS
T ss_pred ccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC--------CcCCCCC
Confidence 77777766321 111222223699999999998775442 2788875
No 323
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=25.43 E-value=47 Score=21.76 Aligned_cols=36 Identities=31% Similarity=0.609 Sum_probs=20.7
Q ss_pred cccccCCCCCCCcceeecCCCCeEEe------ccC---cceeecccccc
Q psy12853 92 DSELIKCCPMCSVPIEKDEGCAQMLC------KRC---KHVFCWYCLAS 131 (137)
Q Consensus 92 ~~~~~~~CP~C~~~iek~~gC~hm~C------~~C---~~~fC~~C~~~ 131 (137)
++...+.|..|+.... + .+|.| ..| ...||..|+..
T Consensus 3 d~~~g~~CHqCrqKt~---~-~~~~C~~~~~~~~C~~~~~~fC~~CL~~ 47 (105)
T PF10497_consen 3 DSVNGKTCHQCRQKTL---D-FKTICTGHWKNSSCRGCRGKFCGGCLRN 47 (105)
T ss_pred cCCCCCCchhhcCCCC---C-CceEcCCCCCCCCCccCcceehHhHHHH
Confidence 4455566666665332 1 12444 455 88899888654
No 324
>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=25.27 E-value=41 Score=18.92 Aligned_cols=6 Identities=50% Similarity=1.614 Sum_probs=2.9
Q ss_pred CCCCCC
Q psy12853 51 CPMCSV 56 (137)
Q Consensus 51 CP~C~~ 56 (137)
||.|+.
T Consensus 5 CP~C~~ 10 (54)
T PF05605_consen 5 CPYCGK 10 (54)
T ss_pred CCCCCC
Confidence 444444
No 325
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=25.20 E-value=37 Score=19.60 Aligned_cols=14 Identities=29% Similarity=0.925 Sum_probs=9.8
Q ss_pred cceeeccccccccc
Q psy12853 121 KHVFCWYCLASLDV 134 (137)
Q Consensus 121 ~~~fC~~C~~~~~~ 134 (137)
.+.||+-||..+.+
T Consensus 26 ~~~YC~~Cg~~Y~d 39 (55)
T PF13821_consen 26 EHNYCFWCGTKYDD 39 (55)
T ss_pred hCceeeeeCCccCC
Confidence 45678888877764
No 326
>KOG1952|consensus
Probab=24.72 E-value=29 Score=31.11 Aligned_cols=69 Identities=23% Similarity=0.448 Sum_probs=43.7
Q ss_pred cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCeEEeccCcc
Q psy12853 48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKH 122 (137)
Q Consensus 48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~hm~C~~C~~ 122 (137)
..-|.-|-..| ...++.+.|..|-+.|=..|-..|-...+ ......-+||.|....++..- +-+|. ||.
T Consensus 191 ~yeCmIC~e~I--~~t~~~WSC~sCYhVFHl~CI~~WArs~e-k~~~~~WrCP~Cqsv~~~~~~--~y~C~-CGk 259 (950)
T KOG1952|consen 191 KYECMICTERI--KRTAPVWSCKSCYHVFHLNCIKKWARSSE-KTGQDGWRCPACQSVSKTVPK--TYLCF-CGK 259 (950)
T ss_pred ceEEEEeeeec--cccCCceecchhhhhhhHHHHHHHHHHhh-hccCccccCCcccchhccCCc--cccee-cCc
Confidence 34444443333 23567888999999998899998877722 223344469999966655443 55565 554
No 327
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=24.54 E-value=42 Score=19.68 Aligned_cols=12 Identities=25% Similarity=0.755 Sum_probs=6.2
Q ss_pred cccCCCCCCcee
Q psy12853 48 IKCCPMCSVPIE 59 (137)
Q Consensus 48 ~~~CP~C~~~i~ 59 (137)
+..||.|+..+.
T Consensus 17 ~lrCPRC~~~FR 28 (65)
T COG4049 17 FLRCPRCGMVFR 28 (65)
T ss_pred eeeCCchhHHHH
Confidence 445555555544
No 328
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=24.52 E-value=42 Score=19.06 Aligned_cols=13 Identities=31% Similarity=0.728 Sum_probs=10.1
Q ss_pred CCcccCCCCCCce
Q psy12853 46 ELIKCCPMCSVPI 58 (137)
Q Consensus 46 ~~~~~CP~C~~~i 58 (137)
....+||+|+..+
T Consensus 44 ~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 44 DEIVFCPNCGRIL 56 (56)
T ss_pred CCeEECcCCCccC
Confidence 5588999998753
No 329
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=24.50 E-value=41 Score=21.72 Aligned_cols=22 Identities=23% Similarity=0.643 Sum_probs=11.1
Q ss_pred CCCCCCceeecCCCCeeecccc
Q psy12853 51 CPMCSVPIEKDEGCAQMLCKRC 72 (137)
Q Consensus 51 CP~C~~~i~~~~~~~~~~C~~C 72 (137)
|-+|++.+..+.-.....||+|
T Consensus 61 CkkCGfef~~~~ik~pSRCP~C 82 (97)
T COG3357 61 CKKCGFEFRDDKIKKPSRCPKC 82 (97)
T ss_pred hcccCccccccccCCcccCCcc
Confidence 4466666544333334556553
No 330
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=24.40 E-value=53 Score=29.61 Aligned_cols=37 Identities=22% Similarity=0.679 Sum_probs=28.5
Q ss_pred cCCCCCCCccee---ecCCCCeEEeccCcceeeccccccc
Q psy12853 96 IKCCPMCSVPIE---KDEGCAQMLCKRCKHVFCWYCLASL 132 (137)
Q Consensus 96 ~~~CP~C~~~ie---k~~gC~hm~C~~C~~~fC~~C~~~~ 132 (137)
...|..|+.... |.-+...=.|+.||..||-.|-...
T Consensus 460 SdtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSnR 499 (1374)
T PTZ00303 460 SDSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKR 499 (1374)
T ss_pred CCcccCcCCcccccccccccccccccCCccccCccccCCc
Confidence 356999988774 3345666789999999999998543
No 331
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=24.39 E-value=39 Score=17.26 Aligned_cols=9 Identities=44% Similarity=1.220 Sum_probs=6.0
Q ss_pred CCCCCCcce
Q psy12853 98 CCPMCSVPI 106 (137)
Q Consensus 98 ~CP~C~~~i 106 (137)
.||+|++-+
T Consensus 3 lcpkcgvgv 11 (36)
T PF09151_consen 3 LCPKCGVGV 11 (36)
T ss_dssp B-TTTSSSB
T ss_pred cCCccCceE
Confidence 589998755
No 332
>COG3634 AhpF Alkyl hydroperoxide reductase, large subunit [Posttranslational modification, protein turnover, chaperones]
Probab=24.35 E-value=31 Score=28.23 Aligned_cols=30 Identities=27% Similarity=0.709 Sum_probs=20.9
Q ss_pred hHHHHhhccc-cccCCCCcccCCCCCCceee
Q psy12853 31 VIWHRTQVSG-ATFDSELIKCCPMCSVPIEK 60 (137)
Q Consensus 31 ~~~~r~~~~~-a~~~~~~~~~CP~C~~~i~~ 60 (137)
++|....+-. ..+.+....|||+|..++.+
T Consensus 323 ArWRn~nvPGE~e~rnKGVayCPHCDGPLF~ 353 (520)
T COG3634 323 ARWRNMNVPGEDEYRNKGVAYCPHCDGPLFK 353 (520)
T ss_pred cchhcCCCCchHHHhhCCeeeCCCCCCcccC
Confidence 3565554333 34577889999999999875
No 333
>KOG1356|consensus
Probab=23.92 E-value=52 Score=29.51 Aligned_cols=33 Identities=21% Similarity=0.500 Sum_probs=25.4
Q ss_pred CCCCCCcceeecCCCCeEEeccCcceeeccccccccc
Q psy12853 98 CCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDV 134 (137)
Q Consensus 98 ~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~~ 134 (137)
-|-.|..-. .-.|-.|+.||..+|..|.+.|.+
T Consensus 231 mC~~C~~tl----fn~hw~C~~C~~~~Cl~C~r~~~p 263 (889)
T KOG1356|consen 231 MCDRCETTL----FNIHWRCPRCGFGVCLDCYRKWYP 263 (889)
T ss_pred hhhhhcccc----cceeEEccccCCeeeecchhhccc
Confidence 455554433 455999999999999999999864
No 334
>KOG2462|consensus
Probab=23.62 E-value=43 Score=25.98 Aligned_cols=31 Identities=16% Similarity=0.295 Sum_probs=17.8
Q ss_pred CCcccCCCCCCceeecC--------CCCeeecccccccc
Q psy12853 46 ELIKCCPMCSVPIEKDE--------GCAQMLCKRCKHVF 76 (137)
Q Consensus 46 ~~~~~CP~C~~~i~~~~--------~~~~~~C~~C~~~f 76 (137)
+....|+.|+..+...+ ......|+.||+.|
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaF 197 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAF 197 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccCCCcccccccccc
Confidence 55677888887765432 12244555665555
No 335
>smart00336 BBOX B-Box-type zinc finger.
Probab=23.39 E-value=62 Score=16.54 Aligned_cols=23 Identities=26% Similarity=0.817 Sum_probs=16.7
Q ss_pred CeeecccccccccccccccccCC
Q psy12853 65 AQMLCKRCKHVFCWYCLASRDYG 87 (137)
Q Consensus 65 ~~~~C~~C~~~fC~~C~~~~h~~ 87 (137)
..+.|..|....|..|...-|.+
T Consensus 14 ~~~~C~~c~~~iC~~C~~~~H~~ 36 (42)
T smart00336 14 AEFFCEECGALLCRTCDEAEHRG 36 (42)
T ss_pred eEEECCCCCcccccccChhhcCC
Confidence 45678888888898888654543
No 336
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=23.15 E-value=47 Score=19.80 Aligned_cols=16 Identities=38% Similarity=0.873 Sum_probs=12.3
Q ss_pred ccCCCCCCCcceeecC
Q psy12853 95 LIKCCPMCSVPIEKDE 110 (137)
Q Consensus 95 ~~~~CP~C~~~iek~~ 110 (137)
...+||.|+..++-..
T Consensus 5 ~~v~CP~C~k~~~w~~ 20 (62)
T PRK00418 5 ITVNCPTCGKPVEWGE 20 (62)
T ss_pred ccccCCCCCCcccccC
Confidence 4578999999987543
No 337
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=23.02 E-value=1.7e+02 Score=19.80 Aligned_cols=26 Identities=23% Similarity=0.405 Sum_probs=17.7
Q ss_pred CCCcccCCCCCCceeecCCC--Ceeecc
Q psy12853 45 SELIKCCPMCSVPIEKDEGC--AQMLCK 70 (137)
Q Consensus 45 ~~~~~~CP~C~~~i~~~~~~--~~~~C~ 70 (137)
.....-||.|+..+....+. ..+-|.
T Consensus 14 ~~~~~~Cp~Cg~~m~~~~~~~g~f~gCs 41 (140)
T COG0551 14 LKTGQICPKCGKNMVKKFGKYGIFLGCS 41 (140)
T ss_pred cccCccCCcCCCeeEEEEccCCeEEEeC
Confidence 34577899999988764322 566674
No 338
>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=22.87 E-value=68 Score=19.32 Aligned_cols=42 Identities=12% Similarity=0.139 Sum_probs=16.4
Q ss_pred eecccccc-cccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853 67 MLCKRCKH-VFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK 108 (137)
Q Consensus 67 ~~C~~C~~-~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek 108 (137)
+.++-|+. .-|..|..+.....-.........|-.|+.....
T Consensus 11 ~~~~cC~~~y~C~~CHde~~~H~~~~~~~~~v~Cg~C~~~~~~ 53 (71)
T PF05495_consen 11 IRFPCCGKYYPCRFCHDELEDHPFDRWPVKRVICGKCRTEQPI 53 (71)
T ss_dssp EEETTTTEEESSHHHHHHCSSS---TTT--EEEETTT--EEES
T ss_pred EECCcccCeecHHHHHHHhccCccccccccCeECCCCCCccCh
Confidence 44444543 3466676543221111111224456666655544
No 339
>PHA02325 hypothetical protein
Probab=22.66 E-value=44 Score=20.11 Aligned_cols=12 Identities=33% Similarity=0.681 Sum_probs=9.0
Q ss_pred ccCCCCCCCcce
Q psy12853 95 LIKCCPMCSVPI 106 (137)
Q Consensus 95 ~~~~CP~C~~~i 106 (137)
+.+.||+|+..-
T Consensus 2 ~~k~CPkC~A~W 13 (72)
T PHA02325 2 DTKICPKCGARW 13 (72)
T ss_pred CccccCccCCEe
Confidence 367899998754
No 340
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=22.48 E-value=75 Score=31.01 Aligned_cols=29 Identities=28% Similarity=0.834 Sum_probs=22.3
Q ss_pred cccCCCCCCc------eeecCCCCeeecccccccccc
Q psy12853 48 IKCCPMCSVP------IEKDEGCAQMLCKRCKHVFCW 78 (137)
Q Consensus 48 ~~~CP~C~~~------i~~~~~~~~~~C~~C~~~fC~ 78 (137)
..+||.|+.. +....|+ .+|+.||..-|.
T Consensus 1704 ~~~cp~c~~~~~~~~~~~~~~gc--~~c~~cg~s~c~ 1738 (1740)
T PRK08332 1704 VVYCPVCYEKEGKLVELRMESGC--ATCPVCGWSKCV 1738 (1740)
T ss_pred cCCCCCCCCCCCcceeeEecCCc--eeCCCCCCcccc
Confidence 4569999998 5555565 689999998874
No 341
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=22.26 E-value=45 Score=17.21 Aligned_cols=12 Identities=33% Similarity=0.899 Sum_probs=7.1
Q ss_pred CCCCCCCcceee
Q psy12853 97 KCCPMCSVPIEK 108 (137)
Q Consensus 97 ~~CP~C~~~iek 108 (137)
-.||+|+..|..
T Consensus 5 ~~C~nC~R~v~a 16 (33)
T PF08209_consen 5 VECPNCGRPVAA 16 (33)
T ss_dssp EE-TTTSSEEEG
T ss_pred EECCCCcCCcch
Confidence 357888777643
No 342
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=22.24 E-value=49 Score=20.14 Aligned_cols=17 Identities=12% Similarity=0.176 Sum_probs=7.5
Q ss_pred CCCCcccCCCCCCceee
Q psy12853 44 DSELIKCCPMCSVPIEK 60 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~ 60 (137)
..-...+|.+|+.++++
T Consensus 42 ~~~kr~~Ck~C~~~liP 58 (85)
T PF04032_consen 42 PEIKRTICKKCGSLLIP 58 (85)
T ss_dssp TTCCCTB-TTT--B--C
T ss_pred hHHhcccccCCCCEEeC
Confidence 34456777777777665
No 343
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=22.18 E-value=42 Score=20.64 Aligned_cols=15 Identities=20% Similarity=0.521 Sum_probs=6.0
Q ss_pred CCCCcccCCCCCCce
Q psy12853 44 DSELIKCCPMCSVPI 58 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i 58 (137)
.+....+||.|+..-
T Consensus 20 ~~~~k~FCp~CGn~T 34 (73)
T PF08772_consen 20 KDMTKQFCPKCGNAT 34 (73)
T ss_dssp S-SS--S-SSS--S-
T ss_pred CCCCceeCcccCCCc
Confidence 455678999998863
No 344
>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=22.13 E-value=72 Score=16.86 Aligned_cols=25 Identities=24% Similarity=0.676 Sum_probs=9.1
Q ss_pred cCCCCCCceee----cCCCCeeecccccc
Q psy12853 50 CCPMCSVPIEK----DEGCAQMLCKRCKH 74 (137)
Q Consensus 50 ~CP~C~~~i~~----~~~~~~~~C~~C~~ 74 (137)
.|.+|+..|-. +.+....+|+-|+.
T Consensus 4 rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 4 RCRRCRAYLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp B-TTT--BS-TTSEEETTTTEEEETTT--
T ss_pred ccCCCCCEECCcceEcCCCCEEECcCCCC
Confidence 45555554432 23445555655543
No 345
>KOG3800|consensus
Probab=21.86 E-value=43 Score=26.19 Aligned_cols=52 Identities=27% Similarity=0.533 Sum_probs=35.3
Q ss_pred cCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853 50 CCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD 109 (137)
Q Consensus 50 ~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~ 109 (137)
-||.|..-....+....+.= .|++..|-.|-- ..-..+--.||.|+++.-|+
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in-~C~H~lCEsCvd-------~iF~~g~~~CpeC~~iLRk~ 53 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMIN-ECGHRLCESCVD-------RIFSLGPAQCPECMVILRKN 53 (300)
T ss_pred CCcccccceecCccceeeec-cccchHHHHHHH-------HHHhcCCCCCCcccchhhhc
Confidence 48888887766655433333 689999988842 22234566899999988765
No 346
>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=21.73 E-value=79 Score=17.01 Aligned_cols=13 Identities=15% Similarity=0.587 Sum_probs=9.2
Q ss_pred CCeeecccccccc
Q psy12853 64 CAQMLCKRCKHVF 76 (137)
Q Consensus 64 ~~~~~C~~C~~~f 76 (137)
...+.|+-|+..|
T Consensus 27 ~~~~~CpYCg~~y 39 (40)
T PF10276_consen 27 PGPVVCPYCGTRY 39 (40)
T ss_dssp TCEEEETTTTEEE
T ss_pred CCeEECCCCCCEE
Confidence 3468888887765
No 347
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=21.42 E-value=32 Score=26.08 Aligned_cols=28 Identities=14% Similarity=0.501 Sum_probs=16.9
Q ss_pred cccCCCCCCceeec------CCCCeeeccccccc
Q psy12853 48 IKCCPMCSVPIEKD------EGCAQMLCKRCKHV 75 (137)
Q Consensus 48 ~~~CP~C~~~i~~~------~~~~~~~C~~C~~~ 75 (137)
-.-|-+|++.+... .+...++||.||..
T Consensus 197 g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 197 GRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred CCcccCCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 44677777776542 14556677776643
No 348
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=21.25 E-value=1e+02 Score=19.22 Aligned_cols=26 Identities=23% Similarity=0.519 Sum_probs=15.5
Q ss_pred CCCCCCcceeecCCC-CeEEeccCcce
Q psy12853 98 CCPMCSVPIEKDEGC-AQMLCKRCKHV 123 (137)
Q Consensus 98 ~CP~C~~~iek~~gC-~hm~C~~C~~~ 123 (137)
+||-|+..+.-..+- .+-.|..|+.+
T Consensus 3 ~CPCCg~~Tl~~~~~~~ydIC~VC~WE 29 (78)
T PF14206_consen 3 PCPCCGYYTLEERGEGTYDICPVCFWE 29 (78)
T ss_pred cCCCCCcEEeccCCCcCceECCCCCcc
Confidence 577777777655443 35566656543
No 349
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=21.23 E-value=24 Score=31.02 Aligned_cols=43 Identities=14% Similarity=0.196 Sum_probs=22.2
Q ss_pred CCCCcccCCCCCCceeecC----CCCeeecccccccccccccccccC
Q psy12853 44 DSELIKCCPMCSVPIEKDE----GCAQMLCKRCKHVFCWYCLASRDY 86 (137)
Q Consensus 44 ~~~~~~~CP~C~~~i~~~~----~~~~~~C~~C~~~fC~~C~~~~h~ 86 (137)
..++.--|++|-.-+.-.. .-+...|..||-.|=..=..++..
T Consensus 64 ippD~a~C~~Cl~E~~dp~~Rry~YpF~nCt~CGPr~~i~~~lpydr 110 (711)
T TIGR00143 64 IPADVATCSDCLEEMLDKNDRRYLYPFISCTHCGPRFTIIEALPYDR 110 (711)
T ss_pred cCCchhhHHHHHHHhcCCCcccccCCcccccCCCCCeEEeecCCCCC
Confidence 3456666766666553211 234566777765554444434333
No 350
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=21.11 E-value=61 Score=27.55 Aligned_cols=41 Identities=22% Similarity=0.324 Sum_probs=21.3
Q ss_pred Ceeecccccccccccc-cccccCCCCcccccccCCCCCCCccee
Q psy12853 65 AQMLCKRCKHVFCWYC-LASRDYGGATFDSELIKCCPMCSVPIE 107 (137)
Q Consensus 65 ~~~~C~~C~~~fC~~C-~~~~h~~~~~~~~~~~~~CP~C~~~ie 107 (137)
..+.||.|++.+=..= ...|..+. ....-.-.||.|+..|+
T Consensus 199 ~~vpCPhCg~~~~l~~~~l~w~~~~--~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 199 YYVPCPHCGEEQVLEWENLKWDKGE--APETARYVCPHCGCEIE 240 (557)
T ss_pred EEccCCCCCCCccccccceeecCCC--CccceEEECCCCcCCCC
Confidence 3566777776665330 11222111 12223557888888776
No 351
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=20.95 E-value=60 Score=22.96 Aligned_cols=28 Identities=32% Similarity=0.634 Sum_probs=15.4
Q ss_pred cCCCCCCceeec-------CC---CCeeeccccccccc
Q psy12853 50 CCPMCSVPIEKD-------EG---CAQMLCKRCKHVFC 77 (137)
Q Consensus 50 ~CP~C~~~i~~~-------~~---~~~~~C~~C~~~fC 77 (137)
.||.|++.=.+. +| -..-.|+.|+..|=
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFT 39 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFT 39 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccc
Confidence 578887764431 11 12345777766664
No 352
>KOG1002|consensus
Probab=20.92 E-value=22 Score=30.35 Aligned_cols=34 Identities=24% Similarity=0.689 Sum_probs=24.8
Q ss_pred cccccccccccccccCCCCcccccccCCCCCCCccee
Q psy12853 71 RCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE 107 (137)
Q Consensus 71 ~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie 107 (137)
+|.+.||..|..++-.+-. ++. ...||-|...+.
T Consensus 553 ~ChH~FCrlCi~eyv~~f~--~~~-nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 553 SCHHKFCRLCIKEYVESFM--ENN-NVTCPVCHIGLS 586 (791)
T ss_pred hhhHHHHHHHHHHHHHhhh--ccc-CCCCcccccccc
Confidence 5899999999987765532 223 378999988764
Done!