Query psy1749
Match_columns 87
No_of_seqs 119 out of 1010
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 23:50:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1749.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1749hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1814|consensus 99.6 1.1E-16 2.4E-21 126.6 2.4 62 12-73 363-426 (445)
2 KOG1812|consensus 99.2 1.7E-12 3.7E-17 101.7 1.1 42 14-56 303-344 (384)
3 KOG0006|consensus 99.2 8.6E-12 1.9E-16 97.5 2.6 52 12-63 392-445 (446)
4 KOG1815|consensus 99.0 9.3E-11 2E-15 92.8 0.8 54 3-56 207-267 (444)
5 smart00647 IBR In Between Ring 98.6 6.1E-08 1.3E-12 56.9 3.3 41 15-55 16-60 (64)
6 PF01485 IBR: IBR domain; Int 98.6 2.4E-08 5.3E-13 58.5 1.6 42 14-55 15-60 (64)
7 PF10571 UPF0547: Uncharacteri 95.4 0.0063 1.4E-07 31.2 0.7 24 18-45 1-24 (26)
8 smart00661 RPOL9 RNA polymeras 95.3 0.016 3.6E-07 32.7 2.3 28 18-45 1-30 (52)
9 PRK00398 rpoP DNA-directed RNA 95.3 0.025 5.3E-07 31.9 3.0 30 18-47 4-33 (46)
10 PF13719 zinc_ribbon_5: zinc-r 93.2 0.13 2.9E-06 27.9 2.9 28 18-45 3-35 (37)
11 PF09297 zf-NADH-PPase: NADH p 93.1 0.15 3.2E-06 26.7 2.9 29 16-44 2-30 (32)
12 PF14803 Nudix_N_2: Nudix N-te 93.0 0.11 2.5E-06 28.1 2.4 27 18-44 1-31 (34)
13 PF13248 zf-ribbon_3: zinc-rib 92.5 0.049 1.1E-06 27.5 0.5 12 18-29 3-14 (26)
14 PHA00626 hypothetical protein 92.5 0.12 2.6E-06 31.4 2.2 28 19-46 2-34 (59)
15 TIGR02098 MJ0042_CXXC MJ0042 f 92.3 0.23 5E-06 26.5 3.1 28 18-45 3-35 (38)
16 PF13240 zinc_ribbon_2: zinc-r 91.8 0.071 1.5E-06 26.4 0.6 11 19-29 1-11 (23)
17 KOG1815|consensus 91.7 0.12 2.7E-06 41.1 2.2 45 17-62 158-205 (444)
18 PRK14559 putative protein seri 91.5 0.095 2.1E-06 44.2 1.4 36 14-55 12-53 (645)
19 PF13717 zinc_ribbon_4: zinc-r 91.4 0.28 6.1E-06 26.5 2.8 28 18-45 3-35 (36)
20 PF01363 FYVE: FYVE zinc finge 91.4 0.24 5.2E-06 29.4 2.8 44 3-55 2-45 (69)
21 PF09538 FYDLN_acid: Protein o 91.1 0.12 2.6E-06 34.6 1.3 28 18-46 10-37 (108)
22 PRK00432 30S ribosomal protein 90.7 0.22 4.8E-06 28.9 2.0 30 14-45 17-47 (50)
23 CHL00174 accD acetyl-CoA carbo 90.5 0.073 1.6E-06 41.2 -0.1 32 15-46 36-68 (296)
24 KOG1814|consensus 90.2 0.068 1.5E-06 43.3 -0.5 41 15-55 271-313 (445)
25 PF12773 DZR: Double zinc ribb 89.7 0.16 3.4E-06 28.5 0.8 15 14-28 9-23 (50)
26 PF07282 OrfB_Zn_ribbon: Putat 89.6 0.32 6.9E-06 28.9 2.2 30 15-44 26-55 (69)
27 PF08274 PhnA_Zn_Ribbon: PhnA 88.8 0.4 8.8E-06 25.3 2.0 27 18-45 3-29 (30)
28 TIGR00515 accD acetyl-CoA carb 88.6 0.1 2.2E-06 40.0 -0.6 32 15-46 24-56 (285)
29 PRK05654 acetyl-CoA carboxylas 88.6 0.11 2.3E-06 39.9 -0.5 32 14-45 24-56 (292)
30 PRK08665 ribonucleotide-diphos 88.5 0.27 5.8E-06 42.1 1.7 27 18-46 725-751 (752)
31 PF07191 zinc-ribbons_6: zinc- 87.7 0.58 1.3E-05 29.3 2.5 35 19-55 3-42 (70)
32 TIGR01384 TFS_arch transcripti 86.9 0.41 8.9E-06 30.7 1.6 26 18-45 1-26 (104)
33 PRK14892 putative transcriptio 86.3 0.46 1E-05 31.3 1.6 48 15-62 19-69 (99)
34 PF08271 TF_Zn_Ribbon: TFIIB z 86.3 0.88 1.9E-05 25.1 2.5 25 19-43 2-27 (43)
35 smart00064 FYVE Protein presen 86.2 0.42 9E-06 28.3 1.2 45 2-55 2-46 (68)
36 TIGR01206 lysW lysine biosynth 85.9 0.94 2E-05 26.8 2.6 34 18-51 3-38 (54)
37 TIGR00686 phnA alkylphosphonat 85.3 0.65 1.4E-05 31.4 1.9 29 18-47 3-31 (109)
38 PF03119 DNA_ligase_ZBD: NAD-d 85.1 0.91 2E-05 23.3 2.0 21 19-39 1-21 (28)
39 KOG0317|consensus 84.9 0.12 2.6E-06 40.0 -2.0 38 12-55 234-271 (293)
40 smart00659 RPOLCX RNA polymera 84.8 1.1 2.5E-05 25.3 2.5 28 19-47 4-31 (44)
41 PF08792 A2L_zn_ribbon: A2L zi 84.7 1.5 3.3E-05 23.4 2.9 30 16-45 2-31 (33)
42 COG0266 Nei Formamidopyrimidin 84.1 0.73 1.6E-05 35.4 2.0 27 16-42 244-272 (273)
43 PF02150 RNA_POL_M_15KD: RNA p 83.8 0.72 1.6E-05 24.8 1.4 28 18-45 2-30 (35)
44 PF06827 zf-FPG_IleRS: Zinc fi 83.5 0.85 1.9E-05 23.3 1.5 25 18-42 2-28 (30)
45 PRK14811 formamidopyrimidine-D 83.4 0.8 1.7E-05 34.4 1.9 27 17-43 235-263 (269)
46 PF13923 zf-C3HC4_2: Zinc fing 83.4 0.45 9.7E-06 25.4 0.4 21 35-55 11-31 (39)
47 PRK01103 formamidopyrimidine/5 83.3 0.9 1.9E-05 34.1 2.1 27 17-43 245-273 (274)
48 COG0777 AccD Acetyl-CoA carbox 83.0 0.51 1.1E-05 36.6 0.7 34 14-47 25-59 (294)
49 PRK14810 formamidopyrimidine-D 82.9 0.94 2E-05 34.1 2.1 26 17-42 244-271 (272)
50 PRK10445 endonuclease VIII; Pr 82.8 0.96 2.1E-05 33.8 2.1 26 17-42 235-262 (263)
51 PF10122 Mu-like_Com: Mu-like 82.5 0.55 1.2E-05 27.8 0.6 29 17-45 4-34 (51)
52 PRK13945 formamidopyrimidine-D 82.4 0.99 2.2E-05 34.1 2.1 26 17-42 254-281 (282)
53 KOG2906|consensus 82.4 1.3 2.8E-05 29.7 2.3 30 18-47 2-33 (105)
54 PF06677 Auto_anti-p27: Sjogre 82.3 1.5 3.2E-05 24.6 2.3 24 17-42 17-41 (41)
55 TIGR00577 fpg formamidopyrimid 82.1 1.1 2.3E-05 33.7 2.1 26 17-42 245-272 (272)
56 PF14354 Lar_restr_allev: Rest 81.9 1.3 2.7E-05 25.7 2.0 28 16-43 2-37 (61)
57 TIGR03655 anti_R_Lar restricti 81.7 1.3 2.8E-05 25.5 2.0 28 18-45 2-36 (53)
58 COG1594 RPB9 DNA-directed RNA 81.4 1.5 3.2E-05 29.3 2.4 29 17-45 2-32 (113)
59 PRK10220 hypothetical protein; 81.0 1.3 2.8E-05 30.0 2.0 28 18-46 4-31 (111)
60 PRK00420 hypothetical protein; 80.8 1.5 3.2E-05 29.6 2.3 26 16-43 22-48 (112)
61 PF07975 C1_4: TFIIH C1-like d 80.7 0.39 8.5E-06 28.2 -0.5 31 20-50 2-36 (51)
62 PF00097 zf-C3HC4: Zinc finger 80.3 0.41 8.9E-06 25.5 -0.5 31 20-55 1-31 (41)
63 COG1645 Uncharacterized Zn-fin 80.2 1.7 3.6E-05 30.2 2.4 24 17-50 28-51 (131)
64 TIGR02300 FYDLN_acid conserved 79.5 1.2 2.5E-05 31.0 1.4 27 18-45 10-36 (129)
65 PF03604 DNA_RNApol_7kD: DNA d 79.1 1.4 3.1E-05 23.4 1.5 26 19-45 2-27 (32)
66 PF05129 Elf1: Transcription e 79.1 1.4 2.9E-05 27.9 1.6 37 16-52 21-63 (81)
67 PRK11827 hypothetical protein; 78.9 2.4 5.2E-05 25.7 2.5 30 16-45 7-36 (60)
68 smart00834 CxxC_CXXC_SSSS Puta 78.5 1.5 3.3E-05 23.2 1.5 25 19-43 7-34 (41)
69 PF14353 CpXC: CpXC protein 78.3 2.1 4.5E-05 28.3 2.4 27 19-45 3-48 (128)
70 PRK14714 DNA polymerase II lar 77.9 2.4 5.2E-05 38.8 3.2 35 15-55 665-704 (1337)
71 COG1998 RPS31 Ribosomal protei 77.7 1.5 3.3E-05 25.9 1.4 29 15-43 17-45 (51)
72 COG1198 PriA Primosomal protei 77.3 1.9 4.2E-05 37.1 2.4 36 17-52 444-484 (730)
73 PF13453 zf-TFIIB: Transcripti 76.9 2.4 5.3E-05 23.0 2.0 14 19-32 1-14 (41)
74 PRK09710 lar restriction allev 76.8 2.4 5.2E-05 26.1 2.1 30 15-44 4-36 (64)
75 PF09526 DUF2387: Probable met 75.1 3.4 7.3E-05 25.7 2.5 27 19-45 10-40 (71)
76 KOG0006|consensus 74.4 0.92 2E-05 36.3 -0.2 70 13-82 311-387 (446)
77 COG1997 RPL43A Ribosomal prote 74.0 3.2 6.8E-05 27.2 2.3 29 17-45 35-63 (89)
78 PF14952 zf-tcix: Putative tre 73.7 1.7 3.7E-05 25.0 0.8 22 14-39 8-29 (44)
79 PRK09521 exosome complex RNA-b 73.2 4.3 9.4E-05 28.7 3.0 26 19-45 151-176 (189)
80 PF15227 zf-C3HC4_4: zinc fing 73.0 1.5 3.1E-05 24.2 0.4 20 36-56 12-31 (42)
81 PF14369 zf-RING_3: zinc-finge 72.1 3.9 8.4E-05 22.0 2.0 26 20-45 5-31 (35)
82 COG1996 RPC10 DNA-directed RNA 71.8 2.6 5.7E-05 24.6 1.4 28 18-45 7-34 (49)
83 PRK00241 nudC NADH pyrophospha 71.5 3.7 8.1E-05 30.7 2.5 30 16-45 98-127 (256)
84 TIGR02443 conserved hypothetic 71.4 4.3 9.4E-05 24.6 2.3 27 19-45 11-41 (59)
85 TIGR00595 priA primosomal prot 70.4 3.7 8.1E-05 33.4 2.4 35 18-52 223-262 (505)
86 PRK12286 rpmF 50S ribosomal pr 69.6 4.3 9.3E-05 24.1 2.0 26 13-43 23-48 (57)
87 cd00162 RING RING-finger (Real 69.4 1.3 2.7E-05 22.8 -0.3 31 20-55 2-32 (45)
88 PRK04023 DNA polymerase II lar 69.2 3.4 7.4E-05 37.2 2.1 39 11-55 620-663 (1121)
89 PF14835 zf-RING_6: zf-RING of 68.5 2.3 5E-05 26.3 0.7 24 18-41 8-34 (65)
90 TIGR01053 LSD1 zinc finger dom 67.9 7.7 0.00017 20.4 2.5 25 19-43 3-27 (31)
91 PRK14890 putative Zn-ribbon RN 66.5 7.2 0.00016 23.6 2.5 35 17-51 7-41 (59)
92 COG2888 Predicted Zn-ribbon RN 66.1 5.4 0.00012 24.4 1.9 40 17-56 9-48 (61)
93 PF13639 zf-RING_2: Ring finge 65.6 2 4.3E-05 23.3 -0.0 34 19-55 2-35 (44)
94 PF12760 Zn_Tnp_IS1595: Transp 65.2 8.3 0.00018 21.4 2.5 26 18-43 19-45 (46)
95 PF01599 Ribosomal_S27: Riboso 65.0 6.3 0.00014 22.8 2.0 31 13-43 14-46 (47)
96 PRK05580 primosome assembly pr 64.8 5.4 0.00012 33.6 2.4 35 18-52 391-430 (679)
97 PRK14873 primosome assembly pr 64.0 6 0.00013 33.6 2.5 36 17-52 392-431 (665)
98 TIGR01031 rpmF_bact ribosomal 63.4 8.5 0.00018 22.6 2.4 25 14-43 23-47 (55)
99 PF02318 FYVE_2: FYVE-type zin 62.4 7.1 0.00015 25.8 2.2 36 16-52 53-88 (118)
100 COG1096 Predicted RNA-binding 62.0 7.4 0.00016 28.6 2.4 25 18-44 150-174 (188)
101 TIGR00622 ssl1 transcription f 61.7 6.1 0.00013 26.7 1.8 35 17-51 55-97 (112)
102 COG2824 PhnA Uncharacterized Z 61.0 7.1 0.00015 26.5 2.0 28 18-46 4-31 (112)
103 PRK13130 H/ACA RNA-protein com 60.4 7 0.00015 23.3 1.7 14 15-28 3-16 (56)
104 cd00065 FYVE FYVE domain; Zinc 60.0 4.9 0.00011 22.6 1.0 37 17-55 2-38 (57)
105 PF05715 zf-piccolo: Piccolo Z 60.0 2.8 6.1E-05 25.6 -0.1 35 18-52 3-39 (61)
106 COG2816 NPY1 NTP pyrophosphohy 59.3 6.3 0.00014 30.5 1.7 31 15-45 109-139 (279)
107 PF06943 zf-LSD1: LSD1 zinc fi 58.7 13 0.00028 18.8 2.2 24 20-43 1-24 (25)
108 PF10083 DUF2321: Uncharacteri 58.4 2.6 5.7E-05 30.1 -0.5 40 15-54 37-79 (158)
109 PLN03208 E3 ubiquitin-protein 58.4 4 8.6E-05 30.0 0.4 33 16-54 17-49 (193)
110 PRK00423 tfb transcription ini 57.6 9.5 0.0002 29.1 2.4 30 14-43 8-38 (310)
111 PRK08332 ribonucleotide-diphos 57.1 7.6 0.00016 36.7 2.1 27 19-47 1706-1738(1740)
112 smart00184 RING Ring finger. E 56.8 2.3 5E-05 20.9 -0.8 16 40-55 15-30 (39)
113 PF14205 Cys_rich_KTR: Cystein 56.1 11 0.00024 22.5 2.1 31 15-45 2-38 (55)
114 PRK14714 DNA polymerase II lar 56.1 6.2 0.00014 36.3 1.3 34 17-55 679-721 (1337)
115 PF01873 eIF-5_eIF-2B: Domain 56.0 14 0.0003 25.1 2.8 27 18-44 94-123 (125)
116 KOG0823|consensus 55.9 3.2 7E-05 31.3 -0.4 15 41-55 65-79 (230)
117 PRK14559 putative protein seri 54.9 7.3 0.00016 33.1 1.5 34 18-55 2-39 (645)
118 smart00154 ZnF_AN1 AN1-like Zi 53.9 8.4 0.00018 21.0 1.2 25 20-48 1-25 (39)
119 TIGR00570 cdk7 CDK-activating 53.4 6.2 0.00013 30.9 0.8 35 18-53 4-38 (309)
120 PF03966 Trm112p: Trm112p-like 53.2 21 0.00044 21.3 3.0 12 16-27 6-17 (68)
121 PF01783 Ribosomal_L32p: Ribos 53.1 9.3 0.0002 22.3 1.4 23 15-42 24-46 (56)
122 PRK08115 ribonucleotide-diphos 52.7 7.3 0.00016 34.3 1.2 26 18-45 828-854 (858)
123 COG5574 PEX10 RING-finger-cont 52.6 3.9 8.5E-05 31.5 -0.4 38 12-55 210-248 (271)
124 PF14634 zf-RING_5: zinc-RING 51.8 4.5 9.8E-05 22.0 -0.1 33 19-54 1-33 (44)
125 PRK12380 hydrogenase nickel in 51.5 10 0.00022 25.1 1.5 24 18-43 71-94 (113)
126 COG0675 Transposase and inacti 51.0 13 0.00027 26.9 2.1 28 15-55 307-334 (364)
127 COG1656 Uncharacterized conser 50.2 9.4 0.0002 27.5 1.3 17 15-31 95-111 (165)
128 KOG1819|consensus 49.9 4.2 9E-05 34.7 -0.7 41 4-53 895-935 (990)
129 PLN03086 PRLI-interacting fact 49.5 12 0.00026 31.6 1.9 22 23-44 441-462 (567)
130 PF04216 FdhE: Protein involve 48.2 12 0.00026 28.1 1.6 38 18-55 173-223 (290)
131 smart00531 TFIIE Transcription 47.7 8.3 0.00018 26.3 0.7 13 17-29 99-111 (147)
132 PF14447 Prok-RING_4: Prokaryo 47.3 12 0.00026 22.4 1.2 40 18-57 8-53 (55)
133 COG4888 Uncharacterized Zn rib 47.2 15 0.00033 24.6 1.8 48 16-63 21-74 (104)
134 KOG0320|consensus 47.1 4 8.6E-05 29.9 -1.0 38 13-54 127-164 (187)
135 PRK07218 replication factor A; 47.0 9.3 0.0002 30.9 0.9 15 15-29 295-309 (423)
136 PF08646 Rep_fac-A_C: Replicat 46.8 21 0.00045 23.9 2.5 27 17-44 18-46 (146)
137 smart00653 eIF2B_5 domain pres 46.6 18 0.00039 24.1 2.1 27 18-44 81-110 (110)
138 cd04476 RPA1_DBD_C RPA1_DBD_C: 46.3 16 0.00034 25.0 1.9 27 17-44 34-60 (166)
139 PRK12495 hypothetical protein; 46.1 6.7 0.00015 29.5 0.0 31 15-55 40-70 (226)
140 PF13920 zf-C3HC4_3: Zinc fing 45.9 9.8 0.00021 21.0 0.7 14 16-29 36-49 (50)
141 PF15616 TerY-C: TerY-C metal 45.7 17 0.00037 25.1 2.0 23 18-47 78-100 (131)
142 TIGR00100 hypA hydrogenase nic 45.3 15 0.00032 24.3 1.6 25 17-43 70-94 (115)
143 KOG1812|consensus 44.9 8.1 0.00018 30.7 0.3 40 20-59 241-282 (384)
144 PF06044 DRP: Dam-replacing fa 44.5 10 0.00022 29.1 0.7 27 19-45 33-63 (254)
145 TIGR00311 aIF-2beta translatio 44.2 20 0.00044 24.6 2.2 28 17-44 97-127 (133)
146 COG3024 Uncharacterized protei 43.8 12 0.00026 23.1 0.9 21 15-35 5-25 (65)
147 PRK06386 replication factor A; 43.6 12 0.00026 29.7 1.1 14 16-29 235-248 (358)
148 PF14570 zf-RING_4: RING/Ubox 43.2 13 0.00027 21.6 0.9 34 20-55 1-34 (48)
149 PRK03988 translation initiatio 42.9 22 0.00048 24.5 2.2 28 17-44 102-132 (138)
150 PF03884 DUF329: Domain of unk 42.6 18 0.0004 21.6 1.5 16 17-32 2-17 (57)
151 PF14569 zf-UDP: Zinc-binding 42.0 12 0.00026 24.0 0.7 22 14-35 48-69 (80)
152 PF14446 Prok-RING_1: Prokaryo 41.9 16 0.00035 21.7 1.2 14 16-29 20-33 (54)
153 TIGR02605 CxxC_CxxC_SSSS putat 41.7 18 0.00038 20.1 1.3 11 19-29 7-17 (52)
154 PHA02942 putative transposase; 40.9 24 0.00053 27.9 2.4 29 16-45 324-352 (383)
155 PRK00418 DNA gyrase inhibitor; 40.8 15 0.00033 22.4 1.0 15 16-30 5-19 (62)
156 PRK03681 hypA hydrogenase nick 40.2 20 0.00043 23.7 1.5 25 18-43 71-95 (114)
157 PF01428 zf-AN1: AN1-like Zinc 40.1 16 0.00035 20.0 1.0 18 34-51 12-29 (43)
158 PF01927 Mut7-C: Mut7-C RNAse 40.0 27 0.00059 23.7 2.3 16 16-31 90-105 (147)
159 PF04981 NMD3: NMD3 family ; 39.5 23 0.0005 25.9 1.9 10 20-29 1-10 (236)
160 PTZ00303 phosphatidylinositol 39.4 18 0.00039 32.6 1.6 37 17-53 460-499 (1374)
161 PF14149 YhfH: YhfH-like prote 37.6 1.7 3.6E-05 24.1 -3.3 29 13-41 9-37 (37)
162 PRK11088 rrmA 23S rRNA methylt 36.9 22 0.00048 26.0 1.5 24 19-45 4-27 (272)
163 PRK12336 translation initiatio 36.7 30 0.00064 25.1 2.1 32 17-48 98-132 (201)
164 PHA02929 N1R/p28-like protein; 35.8 18 0.00039 27.2 0.9 39 16-55 173-214 (238)
165 PRK00464 nrdR transcriptional 35.6 21 0.00047 25.1 1.2 9 19-27 2-10 (154)
166 PF01396 zf-C4_Topoisom: Topoi 35.2 21 0.00046 19.3 0.9 21 18-39 2-25 (39)
167 PF01780 Ribosomal_L37ae: Ribo 34.6 36 0.00078 22.2 2.1 29 17-45 35-63 (90)
168 TIGR00155 pqiA_fam integral me 34.5 39 0.00085 27.0 2.7 30 15-44 11-42 (403)
169 COG4416 Com Mu-like prophage p 33.5 8.2 0.00018 23.3 -1.0 27 17-43 4-32 (60)
170 PF09723 Zn-ribbon_8: Zinc rib 33.2 34 0.00074 18.6 1.6 14 16-29 25-39 (42)
171 PF14319 Zn_Tnp_IS91: Transpos 33.0 35 0.00075 22.5 1.8 30 17-54 42-71 (111)
172 KOG1729|consensus 32.8 8.7 0.00019 29.7 -1.2 33 17-52 168-202 (288)
173 PF13451 zf-trcl: Probable zin 32.6 31 0.00067 20.0 1.4 16 35-50 4-19 (49)
174 PF03833 PolC_DP2: DNA polymer 31.2 16 0.00035 32.5 0.0 36 14-55 652-692 (900)
175 PF12861 zf-Apc11: Anaphase-pr 30.8 16 0.00034 23.6 -0.1 33 20-56 35-67 (85)
176 PF11023 DUF2614: Protein of u 30.0 26 0.00057 23.8 0.9 16 12-27 64-79 (114)
177 PF09889 DUF2116: Uncharacteri 30.0 21 0.00046 21.4 0.4 13 18-30 4-16 (59)
178 PRK09678 DNA-binding transcrip 29.5 32 0.0007 21.4 1.2 10 18-27 2-11 (72)
179 COG3529 Predicted nucleic-acid 29.4 16 0.00034 22.6 -0.3 27 19-45 12-42 (66)
180 PF15135 UPF0515: Uncharacteri 29.1 54 0.0012 25.4 2.5 31 15-45 130-165 (278)
181 PRK03564 formate dehydrogenase 27.4 44 0.00095 26.1 1.8 37 16-52 186-235 (309)
182 COG1885 Uncharacterized protei 27.4 31 0.00067 23.4 0.9 16 14-29 46-61 (115)
183 PRK12496 hypothetical protein; 27.3 30 0.00065 24.3 0.8 12 18-29 128-139 (164)
184 PHA02325 hypothetical protein 27.3 30 0.00064 21.6 0.7 12 16-27 2-13 (72)
185 COG4640 Predicted membrane pro 26.9 28 0.00061 28.7 0.7 7 18-24 2-8 (465)
186 PF11781 RRN7: RNA polymerase 26.8 66 0.0014 17.2 2.0 26 18-44 9-34 (36)
187 KOG2932|consensus 26.5 35 0.00076 27.4 1.1 38 14-51 87-131 (389)
188 PF08209 Sgf11: Sgf11 (transcr 26.2 47 0.001 17.7 1.3 14 17-30 4-17 (33)
189 COG1571 Predicted DNA-binding 25.9 34 0.00073 28.0 1.0 27 19-46 352-378 (421)
190 PF10164 DUF2367: Uncharacteri 25.8 43 0.00094 22.2 1.3 13 18-30 50-62 (98)
191 TIGR00373 conserved hypothetic 25.7 23 0.0005 24.6 0.0 26 18-43 110-136 (158)
192 PF05876 Terminase_GpA: Phage 24.8 47 0.001 27.5 1.7 13 18-30 201-213 (557)
193 PRK03976 rpl37ae 50S ribosomal 24.8 58 0.0013 21.2 1.7 30 16-45 35-64 (90)
194 TIGR00280 L37a ribosomal prote 24.7 58 0.0013 21.3 1.7 31 15-45 33-63 (91)
195 PRK03824 hypA hydrogenase nick 24.6 43 0.00093 22.7 1.2 16 17-32 107-123 (135)
196 KOG3084|consensus 24.4 47 0.001 26.5 1.5 24 16-39 149-172 (345)
197 PF08882 Acetone_carb_G: Aceto 23.9 47 0.001 22.5 1.2 12 19-30 76-87 (112)
198 TIGR01562 FdhE formate dehydro 23.7 56 0.0012 25.4 1.8 36 17-52 184-233 (305)
199 PRK00564 hypA hydrogenase nick 23.1 51 0.0011 21.8 1.3 15 18-32 89-104 (117)
200 cd02249 ZZ Zinc finger, ZZ typ 22.9 85 0.0018 17.1 2.0 31 19-53 2-33 (46)
201 PF08996 zf-DNA_Pol: DNA Polym 22.9 79 0.0017 22.4 2.3 31 16-46 17-56 (188)
202 COG5082 AIR1 Arginine methyltr 22.9 36 0.00078 25.0 0.6 39 13-51 56-105 (190)
203 PF01639 v110: Viral family 11 22.7 38 0.00082 22.9 0.6 16 31-50 34-49 (110)
204 COG2835 Uncharacterized conser 22.3 1.1E+02 0.0023 18.6 2.5 27 17-43 8-34 (60)
205 PRK08402 replication factor A; 22.1 78 0.0017 25.0 2.3 27 16-42 211-237 (355)
206 COG2260 Predicted Zn-ribbon RN 22.0 60 0.0013 19.7 1.3 15 15-29 3-17 (59)
207 PRK01343 zinc-binding protein; 21.8 41 0.00089 20.1 0.6 14 15-28 7-20 (57)
208 COG5595 Zn-ribbon-containing, 21.8 40 0.00087 25.5 0.6 24 7-30 208-231 (256)
209 PTZ00255 60S ribosomal protein 21.6 79 0.0017 20.6 1.9 31 15-45 34-64 (90)
210 KOG2893|consensus 21.6 50 0.0011 25.7 1.1 34 42-75 9-48 (341)
211 PF14690 zf-ISL3: zinc-finger 21.5 65 0.0014 17.2 1.3 13 18-30 3-15 (47)
212 PF14169 YdjO: Cold-inducible 21.4 64 0.0014 19.4 1.4 24 4-30 29-52 (59)
213 KOG2907|consensus 20.9 37 0.00079 23.2 0.2 27 17-43 7-33 (116)
214 cd07153 Fur_like Ferric uptake 20.7 64 0.0014 20.2 1.4 17 34-50 72-88 (116)
215 PF07295 DUF1451: Protein of u 20.7 94 0.002 21.6 2.3 16 15-30 110-125 (146)
216 PF02591 DUF164: Putative zinc 20.6 61 0.0013 18.4 1.2 12 15-26 44-55 (56)
217 COG2023 RPR2 RNase P subunit R 20.6 90 0.002 20.9 2.1 27 19-45 58-92 (105)
218 PF14255 Cys_rich_CPXG: Cystei 20.4 60 0.0013 18.9 1.1 12 19-30 2-13 (52)
219 KOG0824|consensus 20.4 32 0.0007 27.2 -0.1 16 39-54 23-38 (324)
220 PF04236 Transp_Tc5_C: Tc5 tra 20.1 60 0.0013 19.6 1.1 20 31-50 33-55 (63)
221 KOG3799|consensus 20.1 29 0.00063 24.7 -0.4 25 30-55 77-101 (169)
No 1
>KOG1814|consensus
Probab=99.62 E-value=1.1e-16 Score=126.59 Aligned_cols=62 Identities=32% Similarity=0.788 Sum_probs=56.4
Q ss_pred cccCCceeCCCCCCceEeCCCcCeeeccccceeeeecccccccCCccCCCCCC--CCCCCCCCC
Q psy1749 12 FDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDK--GPCKNKLGH 73 (87)
Q Consensus 12 ~~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~~~~~~Hf~~--~~C~~~~~~ 73 (87)
|...+.|+||+|+++|||++|||+|+|..|++.|||+|+.....++||.||++ +.|+++.+.
T Consensus 363 wl~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~~nPYkHF~e~~s~c~~~~~~ 426 (445)
T KOG1814|consen 363 WLESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLYPENPYKHFSEPGSECYGQFFG 426 (445)
T ss_pred HHHhcCCCCCcccceeecCCCccceeeccccccceeehhhhcCCCChhhhhcCCcCccccchhh
Confidence 55667799999999999999999999999999999999999999999999998 667888554
No 2
>KOG1812|consensus
Probab=99.24 E-value=1.7e-12 Score=101.72 Aligned_cols=42 Identities=36% Similarity=0.928 Sum_probs=39.8
Q ss_pred cCCceeCCCCCCceEeCCCcCeeeccccceeeeecccccccCC
Q psy1749 14 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDD 56 (87)
Q Consensus 14 ~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~~ 56 (87)
.+.|+.||+|+..||+++|||||+|+ ||++|||.|+.+|..+
T Consensus 303 a~~wr~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~~~ 344 (384)
T KOG1812|consen 303 AKRWRQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDWKTH 344 (384)
T ss_pred HHhcCcCcccceeeeecCCcceEEee-ccccchhhcCcchhhC
Confidence 38899999999999999999999999 9999999999999775
No 3
>KOG0006|consensus
Probab=99.19 E-value=8.6e-12 Score=97.49 Aligned_cols=52 Identities=31% Similarity=0.757 Sum_probs=48.1
Q ss_pred cccCCceeCCCCCCceEeCCCcCeeeccc--cceeeeecccccccCCccCCCCC
Q psy1749 12 FDSELIKCCPMCSVPIEKDEGCAQMLCKR--CKHVFCWYCLASLDDDFLLRHYD 63 (87)
Q Consensus 12 ~~~~~~k~CP~C~~~Iek~~GCnhm~C~~--C~~~FC~~C~~~~~~~~~~~Hf~ 63 (87)
-|+..+|+||+|++++|+++||.||.|++ ||.+|||.|+-+|.......||-
T Consensus 392 TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r~CmgdHWF 445 (446)
T KOG0006|consen 392 TIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNRVCMGDHWF 445 (446)
T ss_pred hhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhhhhcccccc
Confidence 57788999999999999999999999996 99999999999999987788874
No 4
>KOG1815|consensus
Probab=98.99 E-value=9.3e-11 Score=92.78 Aligned_cols=54 Identities=52% Similarity=1.099 Sum_probs=47.2
Q ss_pred ccccccCcc-----cccCCceeCCCCCCceEeCCCcCeeeccc--cceeeeecccccccCC
Q psy1749 3 PWFQMGGAT-----FDSELIKCCPMCSVPIEKDEGCAQMLCKR--CKHVFCWYCLASLDDD 56 (87)
Q Consensus 3 ~w~~~~~~~-----~~~~~~k~CP~C~~~Iek~~GCnhm~C~~--C~~~FC~~C~~~~~~~ 56 (87)
.|.+..++. |+..+++.||+|..+|||++|||||+|.. |+.+|||+|++.|..+
T Consensus 207 ~wl~k~~~~se~~~wi~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h 267 (444)
T KOG1815|consen 207 KWLKKCRDDSETINWILANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDH 267 (444)
T ss_pred HHHHhhhhhhhhhhhhhccCccCCCcccchhccCCccccccccCCcCCeeceeeecccccc
Confidence 455544444 78899999999999999999999999997 9999999999999985
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.57 E-value=6.1e-08 Score=56.87 Aligned_cols=41 Identities=34% Similarity=0.868 Sum_probs=36.5
Q ss_pred CCceeCC--CCCCceEeCC--CcCeeeccccceeeeecccccccC
Q psy1749 15 ELIKCCP--MCSVPIEKDE--GCAQMLCKRCKHVFCWYCLASLDD 55 (87)
Q Consensus 15 ~~~k~CP--~C~~~Iek~~--GCnhm~C~~C~~~FC~~C~~~~~~ 55 (87)
.+++.|| +|...|+..+ +..+++|..|+..|||.|+.+|-.
T Consensus 16 ~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~ 60 (64)
T smart00647 16 PDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHS 60 (64)
T ss_pred CCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCC
Confidence 4788999 9999999975 899999977999999999988743
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=98.57 E-value=2.4e-08 Score=58.49 Aligned_cols=42 Identities=36% Similarity=0.895 Sum_probs=30.3
Q ss_pred cCCceeCCC--CCCceEeCCCcCe--eeccccceeeeecccccccC
Q psy1749 14 SELIKCCPM--CSVPIEKDEGCAQ--MLCKRCKHVFCWYCLASLDD 55 (87)
Q Consensus 14 ~~~~k~CP~--C~~~Iek~~GCnh--m~C~~C~~~FC~~C~~~~~~ 55 (87)
+.+.+.||+ |...|++.++.++ |+|..|+..|||.|+.+|-.
T Consensus 15 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~ 60 (64)
T PF01485_consen 15 DPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHE 60 (64)
T ss_dssp ---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCT
T ss_pred CCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCC
Confidence 345689988 9999999999999 99999999999999998843
No 7
>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=95.40 E-value=0.0063 Score=31.23 Aligned_cols=24 Identities=29% Similarity=0.833 Sum_probs=16.1
Q ss_pred eeCCCCCCceEeCCCcCeeeccccceee
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~~F 45 (87)
|.||.|+..|..+. ..|..||+.|
T Consensus 1 K~CP~C~~~V~~~~----~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPESA----KFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhhc----CcCCCCCCCC
Confidence 57999999886432 3444577665
No 8
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=95.31 E-value=0.016 Score=32.73 Aligned_cols=28 Identities=29% Similarity=0.695 Sum_probs=22.2
Q ss_pred eeCCCCCCceEeCCC--cCeeeccccceee
Q psy1749 18 KCCPMCSVPIEKDEG--CAQMLCKRCKHVF 45 (87)
Q Consensus 18 k~CP~C~~~Iek~~G--Cnhm~C~~C~~~F 45 (87)
+.||.|+.++...++ -++..|+.||+++
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 469999999988754 4689999898764
No 9
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=95.27 E-value=0.025 Score=31.85 Aligned_cols=30 Identities=23% Similarity=0.433 Sum_probs=25.3
Q ss_pred eeCCCCCCceEeCCCcCeeeccccceeeee
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCW 47 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~ 47 (87)
-+||+|+..++.++.=..++|+.||..+-+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 579999999998877668999999987765
No 10
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.22 E-value=0.13 Score=27.88 Aligned_cols=28 Identities=32% Similarity=0.858 Sum_probs=22.5
Q ss_pred eeCCCCCCceEeCC-----CcCeeeccccceee
Q psy1749 18 KCCPMCSVPIEKDE-----GCAQMLCKRCKHVF 45 (87)
Q Consensus 18 k~CP~C~~~Iek~~-----GCnhm~C~~C~~~F 45 (87)
..||+|++..+..+ +=..+.|.+|++.|
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 57999999988764 34479999999887
No 11
>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=93.10 E-value=0.15 Score=26.68 Aligned_cols=29 Identities=24% Similarity=0.527 Sum_probs=19.1
Q ss_pred CceeCCCCCCceEeCCCcCeeecccccee
Q psy1749 16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHV 44 (87)
Q Consensus 16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~ 44 (87)
+.+.||+|+.+.+...+=-.+.|..|+.+
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 35789999999999988666889988875
No 12
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=93.01 E-value=0.11 Score=28.07 Aligned_cols=27 Identities=30% Similarity=0.936 Sum_probs=16.6
Q ss_pred eeCCCCCCceEeC----CCcCeeecccccee
Q psy1749 18 KCCPMCSVPIEKD----EGCAQMLCKRCKHV 44 (87)
Q Consensus 18 k~CP~C~~~Iek~----~GCnhm~C~~C~~~ 44 (87)
|.||.|+.+++.. ++-..+.|..||..
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 5799999999985 56788999988864
No 13
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=92.52 E-value=0.049 Score=27.48 Aligned_cols=12 Identities=33% Similarity=0.897 Sum_probs=9.2
Q ss_pred eeCCCCCCceEe
Q psy1749 18 KCCPMCSVPIEK 29 (87)
Q Consensus 18 k~CP~C~~~Iek 29 (87)
+.||+|+..|+.
T Consensus 3 ~~Cp~Cg~~~~~ 14 (26)
T PF13248_consen 3 MFCPNCGAEIDP 14 (26)
T ss_pred CCCcccCCcCCc
Confidence 678999987653
No 14
>PHA00626 hypothetical protein
Probab=92.45 E-value=0.12 Score=31.37 Aligned_cols=28 Identities=25% Similarity=0.559 Sum_probs=21.4
Q ss_pred eCCCCCC-ceEeCCCcCe----eeccccceeee
Q psy1749 19 CCPMCSV-PIEKDEGCAQ----MLCKRCKHVFC 46 (87)
Q Consensus 19 ~CP~C~~-~Iek~~GCnh----m~C~~C~~~FC 46 (87)
.||+|++ -|.|.+-|+. ..|..||+.|=
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeec
Confidence 5999999 4888876554 67887887763
No 15
>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=92.28 E-value=0.23 Score=26.48 Aligned_cols=28 Identities=25% Similarity=0.717 Sum_probs=20.8
Q ss_pred eeCCCCCCceEeCCC-----cCeeeccccceee
Q psy1749 18 KCCPMCSVPIEKDEG-----CAQMLCKRCKHVF 45 (87)
Q Consensus 18 k~CP~C~~~Iek~~G-----Cnhm~C~~C~~~F 45 (87)
..||+|++.++..+. =..+.|.+|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 479999998777631 1378899898876
No 16
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=91.78 E-value=0.071 Score=26.42 Aligned_cols=11 Identities=45% Similarity=1.090 Sum_probs=8.1
Q ss_pred eCCCCCCceEe
Q psy1749 19 CCPMCSVPIEK 29 (87)
Q Consensus 19 ~CP~C~~~Iek 29 (87)
.||+|+..|+.
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 47888888763
No 17
>KOG1815|consensus
Probab=91.72 E-value=0.12 Score=41.14 Aligned_cols=45 Identities=22% Similarity=0.550 Sum_probs=35.7
Q ss_pred ceeCC--CCCCceEe-CCCcCeeeccccceeeeecccccccCCccCCCC
Q psy1749 17 IKCCP--MCSVPIEK-DEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHY 62 (87)
Q Consensus 17 ~k~CP--~C~~~Iek-~~GCnhm~C~~C~~~FC~~C~~~~~~~~~~~Hf 62 (87)
.|-|| .|+..|.. ...+..+.|. |++.|||.|+.++-....+.++
T Consensus 158 lkwCP~~~C~~av~~~~~~~~~v~C~-~g~~FC~~C~~~~H~p~~C~~~ 205 (444)
T KOG1815|consen 158 LKWCPAPGCGLAVKFGSLESVEVDCG-CGHEFCFACGEESHSPVSCPGA 205 (444)
T ss_pred cccCCCCCCCceeeccCCCccceeCC-CCchhHhhccccccCCCcccch
Confidence 55666 69999998 7889999999 9999999999888765443333
No 18
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=91.50 E-value=0.095 Score=44.20 Aligned_cols=36 Identities=19% Similarity=0.500 Sum_probs=28.7
Q ss_pred cCCceeCCCCCCceEeCCCcCeeecccccee------eeecccccccC
Q psy1749 14 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHV------FCWYCLASLDD 55 (87)
Q Consensus 14 ~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~------FC~~C~~~~~~ 55 (87)
..+.|.||+|+..+. +..|..||+. ||-.||.....
T Consensus 12 ~~~akFC~~CG~~l~------~~~Cp~CG~~~~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 12 PNNNRFCQKCGTSLT------HKPCPQCGTEVPVDEAHCPNCGAETGT 53 (645)
T ss_pred CCCCccccccCCCCC------CCcCCCCCCCCCcccccccccCCcccc
Confidence 456789999999884 3578889877 99999987665
No 19
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=91.42 E-value=0.28 Score=26.54 Aligned_cols=28 Identities=36% Similarity=0.857 Sum_probs=21.9
Q ss_pred eeCCCCCCceEeCC-----CcCeeeccccceee
Q psy1749 18 KCCPMCSVPIEKDE-----GCAQMLCKRCKHVF 45 (87)
Q Consensus 18 k~CP~C~~~Iek~~-----GCnhm~C~~C~~~F 45 (87)
..||+|++..+..+ .=..+.|..|++.|
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 47999999988864 23468899999876
No 20
>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=91.39 E-value=0.24 Score=29.39 Aligned_cols=44 Identities=18% Similarity=0.433 Sum_probs=24.5
Q ss_pred ccccccCcccccCCceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749 3 PWFQMGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD 55 (87)
Q Consensus 3 ~w~~~~~~~~~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~ 55 (87)
+|..+.. ...|+.|++.+.. .-..-.|+.||..||-.|......
T Consensus 2 ~W~~d~~-------~~~C~~C~~~F~~--~~rrhhCr~CG~~vC~~Cs~~~~~ 45 (69)
T PF01363_consen 2 HWVPDSE-------ASNCMICGKKFSL--FRRRHHCRNCGRVVCSSCSSQRIP 45 (69)
T ss_dssp -SSSGGG--------SB-TTT--B-BS--SS-EEE-TTT--EEECCCS-EEEE
T ss_pred CcCCCCC-------CCcCcCcCCcCCC--ceeeEccCCCCCEECCchhCCEEc
Confidence 4666555 4899999999843 355678999999999999865543
No 21
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=91.05 E-value=0.12 Score=34.55 Aligned_cols=28 Identities=21% Similarity=0.660 Sum_probs=21.1
Q ss_pred eeCCCCCCceEeCCCcCeeeccccceeee
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKHVFC 46 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~~FC 46 (87)
+.||+|++.+.=-.- +.++|++||+.|=
T Consensus 10 R~Cp~CG~kFYDLnk-~PivCP~CG~~~~ 37 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK-DPIVCPKCGTEFP 37 (108)
T ss_pred ccCCCCcchhccCCC-CCccCCCCCCccC
Confidence 559999987764444 7899998887763
No 22
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=90.65 E-value=0.22 Score=28.95 Aligned_cols=30 Identities=20% Similarity=0.440 Sum_probs=21.6
Q ss_pred cCCceeCCCCCC-ceEeCCCcCeeeccccceee
Q psy1749 14 SELIKCCPMCSV-PIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 14 ~~~~k~CP~C~~-~Iek~~GCnhm~C~~C~~~F 45 (87)
....+.||+|+. .+.... +.+.|..||..+
T Consensus 17 ~~~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~ 47 (50)
T PRK00432 17 KRKNKFCPRCGSGFMAEHL--DRWHCGKCGYTE 47 (50)
T ss_pred EEccCcCcCCCcchheccC--CcEECCCcCCEE
Confidence 345678999998 444434 688999998764
No 23
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=90.53 E-value=0.073 Score=41.18 Aligned_cols=32 Identities=19% Similarity=0.211 Sum_probs=26.9
Q ss_pred CCceeCCCCCCceEeCCC-cCeeeccccceeee
Q psy1749 15 ELIKCCPMCSVPIEKDEG-CAQMLCKRCKHVFC 46 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek~~G-Cnhm~C~~C~~~FC 46 (87)
..|.+||+|+..|.+.+= =|...|++|+++|=
T Consensus 36 ~lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 36 HLWVQCENCYGLNYKKFLKSKMNICEQCGYHLK 68 (296)
T ss_pred CCeeECCCccchhhHHHHHHcCCCCCCCCCCcC
Confidence 469999999999988754 67789999999874
No 24
>KOG1814|consensus
Probab=90.24 E-value=0.068 Score=43.33 Aligned_cols=41 Identities=29% Similarity=0.845 Sum_probs=37.2
Q ss_pred CCceeCCC--CCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749 15 ELIKCCPM--CSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD 55 (87)
Q Consensus 15 ~~~k~CP~--C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~ 55 (87)
.+++.||+ |..++-.+.|++-..|..|...||..|...|-+
T Consensus 271 sdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG 313 (445)
T KOG1814|consen 271 SDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG 313 (445)
T ss_pred cccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcC
Confidence 46789998 999997789999999999999999999988765
No 25
>PF12773 DZR: Double zinc ribbon
Probab=89.67 E-value=0.16 Score=28.53 Aligned_cols=15 Identities=33% Similarity=0.895 Sum_probs=10.5
Q ss_pred cCCceeCCCCCCceE
Q psy1749 14 SELIKCCPMCSVPIE 28 (87)
Q Consensus 14 ~~~~k~CP~C~~~Ie 28 (87)
..+.+.||+|++.+.
T Consensus 9 ~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLP 23 (50)
T ss_pred CccccCChhhcCChh
Confidence 345677777777777
No 26
>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=89.59 E-value=0.32 Score=28.93 Aligned_cols=30 Identities=20% Similarity=0.440 Sum_probs=22.9
Q ss_pred CCceeCCCCCCceEeCCCcCeeecccccee
Q psy1749 15 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHV 44 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~ 44 (87)
..++.||.|+...++...=...+|..||..
T Consensus 26 ~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 26 YTSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CCccCccCcccccccccccceEEcCCCCCE
Confidence 368999999999999444445778877765
No 27
>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=88.82 E-value=0.4 Score=25.31 Aligned_cols=27 Identities=26% Similarity=0.837 Sum_probs=14.4
Q ss_pred eeCCCCCCceEeCCCcCeeeccccceee
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~~F 45 (87)
-.||.|+......+|.. |.|..|+++|
T Consensus 3 p~Cp~C~se~~y~D~~~-~vCp~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGEL-LVCPECGHEW 29 (30)
T ss_dssp ---TTT-----EE-SSS-EEETTTTEEE
T ss_pred CCCCCCCCcceeccCCE-EeCCcccccC
Confidence 36999999999887765 5788898876
No 28
>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=88.64 E-value=0.1 Score=40.00 Aligned_cols=32 Identities=22% Similarity=0.532 Sum_probs=26.3
Q ss_pred CCceeCCCCCCceEeCC-CcCeeeccccceeee
Q psy1749 15 ELIKCCPMCSVPIEKDE-GCAQMLCKRCKHVFC 46 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek~~-GCnhm~C~~C~~~FC 46 (87)
..|.+||+|+..|.+.+ .=|...|++|+++|=
T Consensus 24 ~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 24 GVWTKCPKCGQVLYTKELERNLEVCPKCDHHMR 56 (285)
T ss_pred CCeeECCCCcchhhHHHHHhhCCCCCCCCCcCc
Confidence 35999999999998874 356789999999863
No 29
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=88.62 E-value=0.11 Score=39.94 Aligned_cols=32 Identities=25% Similarity=0.616 Sum_probs=26.5
Q ss_pred cCCceeCCCCCCceEeCC-CcCeeeccccceee
Q psy1749 14 SELIKCCPMCSVPIEKDE-GCAQMLCKRCKHVF 45 (87)
Q Consensus 14 ~~~~k~CP~C~~~Iek~~-GCnhm~C~~C~~~F 45 (87)
...|.+||+|+..|.+.+ .-|...|+.|+++|
T Consensus 24 ~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 24 EGLWTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred CCCeeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 345999999999998864 35678999999998
No 30
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=88.46 E-value=0.27 Score=42.10 Aligned_cols=27 Identities=37% Similarity=1.053 Sum_probs=24.1
Q ss_pred eeCCCCCCceEeCCCcCeeeccccceeee
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKHVFC 46 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~~FC 46 (87)
..||.|+..+...+||. +|..||..-|
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 31
>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=87.65 E-value=0.58 Score=29.28 Aligned_cols=35 Identities=29% Similarity=0.706 Sum_probs=23.3
Q ss_pred eCCCCCCceEeCCCcCeeecccccee-----eeecccccccC
Q psy1749 19 CCPMCSVPIEKDEGCAQMLCKRCKHV-----FCWYCLASLDD 55 (87)
Q Consensus 19 ~CP~C~~~Iek~~GCnhm~C~~C~~~-----FC~~C~~~~~~ 55 (87)
.||.|+..++..+ .+..|..|+.+ +|-.|++++..
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~~~~a~CPdC~~~Le~ 42 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDYKKEAFCPDCGQPLEV 42 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EEEEEEE-TTT-SB-EE
T ss_pred cCCCCCCccEEeC--CEEECccccccceecccCCCcccHHHH
Confidence 5999999999988 78888888765 57788887765
No 32
>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=86.93 E-value=0.41 Score=30.68 Aligned_cols=26 Identities=23% Similarity=0.593 Sum_probs=20.3
Q ss_pred eeCCCCCCceEeCCCcCeeeccccceee
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~~F 45 (87)
+.||.|+.++...+ +.+.|..|+..+
T Consensus 1 ~fC~~Cg~~l~~~~--~~~~C~~C~~~~ 26 (104)
T TIGR01384 1 KFCPKCGSLMTPKN--GVYVCPSCGYEK 26 (104)
T ss_pred CCCcccCcccccCC--CeEECcCCCCcc
Confidence 36999999997765 478898888764
No 33
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=86.34 E-value=0.46 Score=31.35 Aligned_cols=48 Identities=17% Similarity=0.315 Sum_probs=32.8
Q ss_pred CCceeCCCCCCc---eEeCCCcCeeeccccceeeeecccccccCCccCCCC
Q psy1749 15 ELIKCCPMCSVP---IEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHY 62 (87)
Q Consensus 15 ~~~k~CP~C~~~---Iek~~GCnhm~C~~C~~~FC~~C~~~~~~~~~~~Hf 62 (87)
...-.||+|+.. |.+..|=.|+.|..||..+=..-......-+.|+-|
T Consensus 19 pt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~~V~~l~epIDVY~~w 69 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEFEVPSVYDEVDVYNKF 69 (99)
T ss_pred CcEeECCCCCCeEeeeecCCCcceEECCCCCCccCEECCccccchhhHHHH
Confidence 355679999943 233457889999999998876655555554566555
No 34
>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=86.28 E-value=0.88 Score=25.05 Aligned_cols=25 Identities=24% Similarity=0.590 Sum_probs=15.4
Q ss_pred eCCCCCCce-EeCCCcCeeeccccce
Q psy1749 19 CCPMCSVPI-EKDEGCAQMLCKRCKH 43 (87)
Q Consensus 19 ~CP~C~~~I-ek~~GCnhm~C~~C~~ 43 (87)
.||.|+..- .-+..=..+.|..||.
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCC
Confidence 588888863 4445555567775554
No 35
>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 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=85.94 E-value=0.94 Score=26.84 Aligned_cols=34 Identities=24% Similarity=0.469 Sum_probs=24.3
Q ss_pred eeCCCCCCceEeCCCc--Ceeeccccceeeeecccc
Q psy1749 18 KCCPMCSVPIEKDEGC--AQMLCKRCKHVFCWYCLA 51 (87)
Q Consensus 18 k~CP~C~~~Iek~~GC--nhm~C~~C~~~FC~~C~~ 51 (87)
-.||.|+..|+..+.- .-+.|..||+.+=-+-..
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGaeleVv~~~ 38 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAELEVVSLD 38 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCEEEEEeCC
Confidence 4799999999997643 247788888877544433
No 37
>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=85.32 E-value=0.65 Score=31.36 Aligned_cols=29 Identities=21% Similarity=0.576 Sum_probs=23.4
Q ss_pred eeCCCCCCceEeCCCcCeeeccccceeeee
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCW 47 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~ 47 (87)
-.||+|..-..-.+|=+ +.|+.|+++|=-
T Consensus 3 p~CP~C~seytY~dg~~-~iCpeC~~EW~~ 31 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQ-LICPSCLYEWNE 31 (109)
T ss_pred CcCCcCCCcceEecCCe-eECccccccccc
Confidence 47999999998888865 789988887643
No 38
>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=85.09 E-value=0.91 Score=23.34 Aligned_cols=21 Identities=29% Similarity=0.892 Sum_probs=13.2
Q ss_pred eCCCCCCceEeCCCcCeeecc
Q psy1749 19 CCPMCSVPIEKDEGCAQMLCK 39 (87)
Q Consensus 19 ~CP~C~~~Iek~~GCnhm~C~ 39 (87)
.||.|++.+.+.++=..+.|.
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 499999999999886677765
No 39
>KOG0317|consensus
Probab=84.88 E-value=0.12 Score=40.04 Aligned_cols=38 Identities=24% Similarity=0.621 Sum_probs=28.3
Q ss_pred cccCCceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749 12 FDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD 55 (87)
Q Consensus 12 ~~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~ 55 (87)
.+..++..|--|....+ +-+|+.||+.|||.|...|-.
T Consensus 234 ~i~~a~~kC~LCLe~~~------~pSaTpCGHiFCWsCI~~w~~ 271 (293)
T KOG0317|consen 234 SIPEATRKCSLCLENRS------NPSATPCGHIFCWSCILEWCS 271 (293)
T ss_pred cCCCCCCceEEEecCCC------CCCcCcCcchHHHHHHHHHHc
Confidence 34455666766665543 567788999999999999986
No 40
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=84.77 E-value=1.1 Score=25.29 Aligned_cols=28 Identities=18% Similarity=0.436 Sum_probs=20.7
Q ss_pred eCCCCCCceEeCCCcCeeeccccceeeee
Q psy1749 19 CCPMCSVPIEKDEGCAQMLCKRCKHVFCW 47 (87)
Q Consensus 19 ~CP~C~~~Iek~~GCnhm~C~~C~~~FC~ 47 (87)
.|..|+..++...+ .-+.|++||+..=|
T Consensus 4 ~C~~Cg~~~~~~~~-~~irC~~CG~rIly 31 (44)
T smart00659 4 ICGECGRENEIKSK-DVVRCRECGYRILY 31 (44)
T ss_pred ECCCCCCEeecCCC-CceECCCCCceEEE
Confidence 58888888887743 66888888876543
No 41
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=84.71 E-value=1.5 Score=23.38 Aligned_cols=30 Identities=20% Similarity=0.325 Sum_probs=22.2
Q ss_pred CceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749 16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~F 45 (87)
+.+.|+.|+.......-=..+.|..|+..|
T Consensus 2 ~~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 2 NLKKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred CceEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 347899999888776666677787777654
No 42
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=84.07 E-value=0.73 Score=35.35 Aligned_cols=27 Identities=33% Similarity=0.691 Sum_probs=23.5
Q ss_pred CceeCCCCCCceEeC--CCcCeeeccccc
Q psy1749 16 LIKCCPMCSVPIEKD--EGCAQMLCKRCK 42 (87)
Q Consensus 16 ~~k~CP~C~~~Iek~--~GCnhm~C~~C~ 42 (87)
.-++|+.|+++|+|. +|-+.-.|+.|+
T Consensus 244 ~GepC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 244 AGEPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 457899999999997 889888898886
No 43
>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=83.85 E-value=0.72 Score=24.82 Aligned_cols=28 Identities=21% Similarity=0.539 Sum_probs=17.6
Q ss_pred eeCCCCCCceEeCCCc-Ceeeccccceee
Q psy1749 18 KCCPMCSVPIEKDEGC-AQMLCKRCKHVF 45 (87)
Q Consensus 18 k~CP~C~~~Iek~~GC-nhm~C~~C~~~F 45 (87)
+.||.|+.+..-..+= ....|+.|++++
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y~~ 30 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGYEE 30 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-EE
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCCcc
Confidence 5799999887665332 223788887764
No 44
>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=83.50 E-value=0.85 Score=23.25 Aligned_cols=25 Identities=40% Similarity=0.824 Sum_probs=15.2
Q ss_pred eeCCCCCCceEeC--CCcCeeeccccc
Q psy1749 18 KCCPMCSVPIEKD--EGCAQMLCKRCK 42 (87)
Q Consensus 18 k~CP~C~~~Iek~--~GCnhm~C~~C~ 42 (87)
+.||+|...|+.. .+-+...|..|.
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 5799999999775 456666677664
No 45
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=83.41 E-value=0.8 Score=34.43 Aligned_cols=27 Identities=37% Similarity=0.826 Sum_probs=21.9
Q ss_pred ceeCCCCCCceEeC--CCcCeeeccccce
Q psy1749 17 IKCCPMCSVPIEKD--EGCAQMLCKRCKH 43 (87)
Q Consensus 17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~~ 43 (87)
-++||.|+..|++. +|-.-..|+.|+.
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~ 263 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQP 263 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCcC
Confidence 47899999999986 7777777877764
No 46
>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=83.35 E-value=0.45 Score=25.43 Aligned_cols=21 Identities=24% Similarity=0.686 Sum_probs=16.2
Q ss_pred eeeccccceeeeecccccccC
Q psy1749 35 QMLCKRCKHVFCWYCLASLDD 55 (87)
Q Consensus 35 hm~C~~C~~~FC~~C~~~~~~ 55 (87)
.++...||+.||+.|...+..
T Consensus 11 ~~~~~~CGH~fC~~C~~~~~~ 31 (39)
T PF13923_consen 11 PVVVTPCGHSFCKECIEKYLE 31 (39)
T ss_dssp EEEECTTSEEEEHHHHHHHHH
T ss_pred cCEECCCCCchhHHHHHHHHH
Confidence 445556999999999887755
No 47
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=83.27 E-value=0.9 Score=34.06 Aligned_cols=27 Identities=37% Similarity=0.821 Sum_probs=22.0
Q ss_pred ceeCCCCCCceEeC--CCcCeeeccccce
Q psy1749 17 IKCCPMCSVPIEKD--EGCAQMLCKRCKH 43 (87)
Q Consensus 17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~~ 43 (87)
-++||.|++.|++. +|-.-..|+.|+.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCCC
Confidence 46899999999986 6777778887764
No 48
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=82.96 E-value=0.51 Score=36.63 Aligned_cols=34 Identities=24% Similarity=0.535 Sum_probs=28.2
Q ss_pred cCCceeCCCCCCceEeCC-CcCeeeccccceeeee
Q psy1749 14 SELIKCCPMCSVPIEKDE-GCAQMLCKRCKHVFCW 47 (87)
Q Consensus 14 ~~~~k~CP~C~~~Iek~~-GCnhm~C~~C~~~FC~ 47 (87)
...|..||+|+..+.+.+ +=|...|++|+++|=-
T Consensus 25 e~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri 59 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKELESNLKVCPKCGHHMRI 59 (294)
T ss_pred CCceeECCCccceeeHHHHHhhhhcccccCccccc
Confidence 467899999999998875 6778999999988743
No 49
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=82.88 E-value=0.94 Score=34.06 Aligned_cols=26 Identities=27% Similarity=0.678 Sum_probs=21.6
Q ss_pred ceeCCCCCCceEeC--CCcCeeeccccc
Q psy1749 17 IKCCPMCSVPIEKD--EGCAQMLCKRCK 42 (87)
Q Consensus 17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~ 42 (87)
.++||.|+..|++. +|-.-..|+.|+
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 57899999999986 777777788775
No 50
>PRK10445 endonuclease VIII; Provisional
Probab=82.79 E-value=0.96 Score=33.85 Aligned_cols=26 Identities=27% Similarity=0.532 Sum_probs=22.0
Q ss_pred ceeCCCCCCceEeC--CCcCeeeccccc
Q psy1749 17 IKCCPMCSVPIEKD--EGCAQMLCKRCK 42 (87)
Q Consensus 17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~ 42 (87)
-+.||.|+..|++. +|-.-..|+.|+
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 47899999999986 788778888775
No 51
>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=82.52 E-value=0.55 Score=27.79 Aligned_cols=29 Identities=24% Similarity=0.522 Sum_probs=22.3
Q ss_pred ceeCCCCCCceEeCCCcC--eeeccccceee
Q psy1749 17 IKCCPMCSVPIEKDEGCA--QMLCKRCKHVF 45 (87)
Q Consensus 17 ~k~CP~C~~~Iek~~GCn--hm~C~~C~~~F 45 (87)
-.+|++|+.++-+.++-. .|.|++|++..
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 368999999999975554 48899887643
No 52
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=82.43 E-value=0.99 Score=34.06 Aligned_cols=26 Identities=35% Similarity=0.750 Sum_probs=22.1
Q ss_pred ceeCCCCCCceEeC--CCcCeeeccccc
Q psy1749 17 IKCCPMCSVPIEKD--EGCAQMLCKRCK 42 (87)
Q Consensus 17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~ 42 (87)
-++||.|+..|++. +|-+-..|+.|+
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCCc
Confidence 47899999999986 788888888776
No 53
>KOG2906|consensus
Probab=82.41 E-value=1.3 Score=29.71 Aligned_cols=30 Identities=30% Similarity=0.791 Sum_probs=23.3
Q ss_pred eeCCCCCCceEeCCC--cCeeeccccceeeee
Q psy1749 18 KCCPMCSVPIEKDEG--CAQMLCKRCKHVFCW 47 (87)
Q Consensus 18 k~CP~C~~~Iek~~G--Cnhm~C~~C~~~FC~ 47 (87)
..||.|+.++...+| |+...|..|.+.|=-
T Consensus 2 ~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I 33 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESGESCNRFSCRTCPYVFPI 33 (105)
T ss_pred cccCCCCCEEEEecCCeEeeEEcCCCCceeeE
Confidence 369999987666544 899999999887754
No 54
>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=82.30 E-value=1.5 Score=24.60 Aligned_cols=24 Identities=29% Similarity=0.958 Sum_probs=17.9
Q ss_pred ceeCCCCCCceEe-CCCcCeeeccccc
Q psy1749 17 IKCCPMCSVPIEK-DEGCAQMLCKRCK 42 (87)
Q Consensus 17 ~k~CP~C~~~Iek-~~GCnhm~C~~C~ 42 (87)
...||.|++++-+ .+| .+.|+.|+
T Consensus 17 ~~~Cp~C~~PL~~~k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGTPLMRDKDG--KIYCVSCG 41 (41)
T ss_pred cCccCCCCCeeEEecCC--CEECCCCC
Confidence 4679999999998 454 46777663
No 55
>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=82.14 E-value=1.1 Score=33.73 Aligned_cols=26 Identities=35% Similarity=0.759 Sum_probs=21.3
Q ss_pred ceeCCCCCCceEeC--CCcCeeeccccc
Q psy1749 17 IKCCPMCSVPIEKD--EGCAQMLCKRCK 42 (87)
Q Consensus 17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~ 42 (87)
-++||.|+..|++. +|-+-..|+.|+
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCCC
Confidence 46899999999986 777777787774
No 56
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=81.90 E-value=1.3 Score=25.71 Aligned_cols=28 Identities=25% Similarity=0.506 Sum_probs=17.7
Q ss_pred CceeCCCCCCceEeCC---Cc-----Ceeeccccce
Q psy1749 16 LIKCCPMCSVPIEKDE---GC-----AQMLCKRCKH 43 (87)
Q Consensus 16 ~~k~CP~C~~~Iek~~---GC-----nhm~C~~C~~ 43 (87)
..|+||.|+....... += ..+.|..||.
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 4589999986555432 21 3466776665
No 57
>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=81.71 E-value=1.3 Score=25.51 Aligned_cols=28 Identities=21% Similarity=0.376 Sum_probs=16.8
Q ss_pred eeCCCCCCceEe-C-----CCcCee-eccccceee
Q psy1749 18 KCCPMCSVPIEK-D-----EGCAQM-LCKRCKHVF 45 (87)
Q Consensus 18 k~CP~C~~~Iek-~-----~GCnhm-~C~~C~~~F 45 (87)
|+||.|+..-+. . .+..++ .|..|+++.
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~ 36 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASG 36 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCc
Confidence 789999987772 1 233333 366555553
No 58
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=81.40 E-value=1.5 Score=29.30 Aligned_cols=29 Identities=17% Similarity=0.650 Sum_probs=21.8
Q ss_pred ceeCCCCCCceEeC--CCcCeeeccccceee
Q psy1749 17 IKCCPMCSVPIEKD--EGCAQMLCKRCKHVF 45 (87)
Q Consensus 17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~~~F 45 (87)
.+.||+|+.++.-. ++=+-+.|..||+++
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred ccccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 47899999998773 233388899888765
No 59
>PRK10220 hypothetical protein; Provisional
Probab=80.98 E-value=1.3 Score=30.05 Aligned_cols=28 Identities=21% Similarity=0.688 Sum_probs=22.7
Q ss_pred eeCCCCCCceEeCCCcCeeeccccceeee
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKHVFC 46 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~~FC 46 (87)
-.||+|..-..-.+|=. +.|+.|+++|=
T Consensus 4 P~CP~C~seytY~d~~~-~vCpeC~hEW~ 31 (111)
T PRK10220 4 PHCPKCNSEYTYEDNGM-YICPECAHEWN 31 (111)
T ss_pred CcCCCCCCcceEcCCCe-EECCcccCcCC
Confidence 57999999988888754 78888888764
No 60
>PRK00420 hypothetical protein; Validated
Probab=80.80 E-value=1.5 Score=29.59 Aligned_cols=26 Identities=31% Similarity=0.874 Sum_probs=18.1
Q ss_pred CceeCCCCCCceEe-CCCcCeeeccccce
Q psy1749 16 LIKCCPMCSVPIEK-DEGCAQMLCKRCKH 43 (87)
Q Consensus 16 ~~k~CP~C~~~Iek-~~GCnhm~C~~C~~ 43 (87)
....||.|+.++.+ .+| ...|+.||.
T Consensus 22 l~~~CP~Cg~pLf~lk~g--~~~Cp~Cg~ 48 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDG--EVVCPVHGK 48 (112)
T ss_pred ccCCCCCCCCcceecCCC--ceECCCCCC
Confidence 34889999999997 444 455555544
No 61
>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=80.67 E-value=0.39 Score=28.24 Aligned_cols=31 Identities=29% Similarity=0.771 Sum_probs=16.7
Q ss_pred CCCCCCceEeCC----CcCeeeccccceeeeeccc
Q psy1749 20 CPMCSVPIEKDE----GCAQMLCKRCKHVFCWYCL 50 (87)
Q Consensus 20 CP~C~~~Iek~~----GCnhm~C~~C~~~FC~~C~ 50 (87)
|..|..++.... +-....|.+|+..||..|-
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD 36 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCD 36 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHH
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcC
Confidence 666777666542 3466889999999999985
No 62
>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=80.30 E-value=0.41 Score=25.46 Aligned_cols=31 Identities=35% Similarity=0.860 Sum_probs=20.2
Q ss_pred CCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749 20 CPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD 55 (87)
Q Consensus 20 CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~ 55 (87)
||-|...++... +=..||+.||..|...+-.
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 445555444333 3345999999999987765
No 63
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=80.19 E-value=1.7 Score=30.22 Aligned_cols=24 Identities=42% Similarity=1.013 Sum_probs=17.8
Q ss_pred ceeCCCCCCceEeCCCcCeeeccccceeeeeccc
Q psy1749 17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCL 50 (87)
Q Consensus 17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~ 50 (87)
-+.||.|+++..+.+| .-||-+|+
T Consensus 28 ~~hCp~Cg~PLF~KdG----------~v~CPvC~ 51 (131)
T COG1645 28 AKHCPKCGTPLFRKDG----------EVFCPVCG 51 (131)
T ss_pred HhhCcccCCcceeeCC----------eEECCCCC
Confidence 4679999999998654 45555666
No 64
>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=79.45 E-value=1.2 Score=30.98 Aligned_cols=27 Identities=11% Similarity=0.172 Sum_probs=20.4
Q ss_pred eeCCCCCCceEeCCCcCeeeccccceee
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~~F 45 (87)
+.||+|++.+.--.. +.++|++||..|
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP~cg~~~ 36 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSPYTGEQF 36 (129)
T ss_pred ccCCCcCccccccCC-CCccCCCcCCcc
Confidence 569999987764333 779999888775
No 65
>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=79.14 E-value=1.4 Score=23.41 Aligned_cols=26 Identities=27% Similarity=0.718 Sum_probs=16.2
Q ss_pred eCCCCCCceEeCCCcCeeeccccceee
Q psy1749 19 CCPMCSVPIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 19 ~CP~C~~~Iek~~GCnhm~C~~C~~~F 45 (87)
.|..|+..++...+ ..+.|+.||+..
T Consensus 2 ~C~~Cg~~~~~~~~-~~irC~~CG~RI 27 (32)
T PF03604_consen 2 ICGECGAEVELKPG-DPIRCPECGHRI 27 (32)
T ss_dssp BESSSSSSE-BSTS-STSSBSSSS-SE
T ss_pred CCCcCCCeeEcCCC-CcEECCcCCCeE
Confidence 37778888885543 557787777653
No 66
>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=79.09 E-value=1.4 Score=27.92 Aligned_cols=37 Identities=27% Similarity=0.531 Sum_probs=19.8
Q ss_pred CceeCCCCCC------ceEeCCCcCeeeccccceeeeeccccc
Q psy1749 16 LIKCCPMCSV------PIEKDEGCAQMLCKRCKHVFCWYCLAS 52 (87)
Q Consensus 16 ~~k~CP~C~~------~Iek~~GCnhm~C~~C~~~FC~~C~~~ 52 (87)
..-.||.|+. -|.+..|=..++|..||..|=+.-...
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~~L 63 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKINPL 63 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE--SS
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccCcc
Confidence 4456999992 345567888899999988886654433
No 67
>PRK11827 hypothetical protein; Provisional
Probab=78.89 E-value=2.4 Score=25.67 Aligned_cols=30 Identities=23% Similarity=0.533 Sum_probs=23.3
Q ss_pred CceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749 16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~F 45 (87)
.+-.||.|+..++....=+.++|..|+-.|
T Consensus 7 eILaCP~ckg~L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 7 EIIACPVCNGKLWYNQEKQELICKLDNLAF 36 (60)
T ss_pred hheECCCCCCcCeEcCCCCeEECCccCeec
Confidence 356799999999987776778888766543
No 68
>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=78.54 E-value=1.5 Score=23.24 Aligned_cols=25 Identities=20% Similarity=0.389 Sum_probs=13.7
Q ss_pred eCCCCCCceEeCCC---cCeeeccccce
Q psy1749 19 CCPMCSVPIEKDEG---CAQMLCKRCKH 43 (87)
Q Consensus 19 ~CP~C~~~Iek~~G---Cnhm~C~~C~~ 43 (87)
+|+.|+..+|...+ -....|..||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 57777776654432 23455665554
No 69
>PF14353 CpXC: CpXC protein
Probab=78.34 E-value=2.1 Score=28.29 Aligned_cols=27 Identities=30% Similarity=0.720 Sum_probs=18.7
Q ss_pred eCCCCCCceEeCC-------------------CcCeeeccccceee
Q psy1749 19 CCPMCSVPIEKDE-------------------GCAQMLCKRCKHVF 45 (87)
Q Consensus 19 ~CP~C~~~Iek~~-------------------GCnhm~C~~C~~~F 45 (87)
.||+|+...+... -=+..+|+.||+.|
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKF 48 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCce
Confidence 6888888776541 24457788888776
No 70
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=77.87 E-value=2.4 Score=38.82 Aligned_cols=35 Identities=23% Similarity=0.468 Sum_probs=26.0
Q ss_pred CCceeCCCCCCceEeCCCcCeeeccccceee-----eecccccccC
Q psy1749 15 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVF-----CWYCLASLDD 55 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~F-----C~~C~~~~~~ 55 (87)
....+||+|+..+... .|..||... |-.|+.....
T Consensus 665 V~~rkCPkCG~~t~~~------fCP~CGs~te~vy~CPsCGaev~~ 704 (1337)
T PRK14714 665 VGRRRCPSCGTETYEN------RCPDCGTHTEPVYVCPDCGAEVPP 704 (1337)
T ss_pred EEEEECCCCCCccccc------cCcccCCcCCCceeCccCCCccCC
Confidence 3458999999987532 788888664 8888887665
No 71
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=77.69 E-value=1.5 Score=25.91 Aligned_cols=29 Identities=17% Similarity=0.456 Sum_probs=20.7
Q ss_pred CCceeCCCCCCceEeCCCcCeeeccccce
Q psy1749 15 ELIKCCPMCSVPIEKDEGCAQMLCKRCKH 43 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek~~GCnhm~C~~C~~ 43 (87)
..-+.||+|+--+.....=+...|.+||.
T Consensus 17 rk~~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 17 RKNRFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred EccccCCCCCCcchhhhcCceeEeccccc
Confidence 34577999997666666556777877764
No 72
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=77.32 E-value=1.9 Score=37.11 Aligned_cols=36 Identities=28% Similarity=0.635 Sum_probs=30.9
Q ss_pred ceeCCCCCCceEeCCCcCeeecccccee-----eeeccccc
Q psy1749 17 IKCCPMCSVPIEKDEGCAQMLCKRCKHV-----FCWYCLAS 52 (87)
Q Consensus 17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~-----FC~~C~~~ 52 (87)
+-.||+|..+...-..=+.|.|..||++ .|-.||..
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 3469999999888877799999999987 89999876
No 73
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=76.88 E-value=2.4 Score=23.04 Aligned_cols=14 Identities=29% Similarity=0.593 Sum_probs=10.7
Q ss_pred eCCCCCCceEeCCC
Q psy1749 19 CCPMCSVPIEKDEG 32 (87)
Q Consensus 19 ~CP~C~~~Iek~~G 32 (87)
.||+|+..++...-
T Consensus 1 ~CP~C~~~l~~~~~ 14 (41)
T PF13453_consen 1 KCPRCGTELEPVRL 14 (41)
T ss_pred CcCCCCcccceEEE
Confidence 49999998776544
No 74
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=76.77 E-value=2.4 Score=26.14 Aligned_cols=30 Identities=27% Similarity=0.680 Sum_probs=20.7
Q ss_pred CCceeCCCCCCceEeC---CCcCeeecccccee
Q psy1749 15 ELIKCCPMCSVPIEKD---EGCAQMLCKRCKHV 44 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek~---~GCnhm~C~~C~~~ 44 (87)
.+.|+||.|+..+.+. +|=-...|..|++.
T Consensus 4 d~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 4 DNVKPCPFCGCPSVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred ccccCCCCCCCceeEEEecCceEEEEcCCCCcC
Confidence 4679999999876664 44444666667664
No 75
>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=75.05 E-value=3.4 Score=25.67 Aligned_cols=27 Identities=22% Similarity=0.538 Sum_probs=21.1
Q ss_pred eCCCCCCce----EeCCCcCeeeccccceee
Q psy1749 19 CCPMCSVPI----EKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 19 ~CP~C~~~I----ek~~GCnhm~C~~C~~~F 45 (87)
.||+|+.+= -+..+=.++.|..||+..
T Consensus 10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e 40 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWRENGVEYVECVECGYTE 40 (71)
T ss_pred cCCCCcCccEEEEEEeCCceEEEecCCCCee
Confidence 699999763 345788999999998753
No 76
>KOG0006|consensus
Probab=74.36 E-value=0.92 Score=36.34 Aligned_cols=70 Identities=16% Similarity=0.397 Sum_probs=49.9
Q ss_pred ccCCceeCC--CCCCceEeCCCcCeeeccc-cceeeeecccccccCCccCCCCCC---CCCCCCCCCCCcc-cceee
Q psy1749 13 DSELIKCCP--MCSVPIEKDEGCAQMLCKR-CKHVFCWYCLASLDDDFLLRHYDK---GPCKNKLGHSRAS-VIWHR 82 (87)
Q Consensus 13 ~~~~~k~CP--~C~~~Iek~~GCnhm~C~~-C~~~FC~~C~~~~~~~~~~~Hf~~---~~C~~~~~~~~~~-~~~~~ 82 (87)
.+.+...|| .|+.-+--+..+.+++|.. ||..||-.|.+.+-.+....-|.. ..|.-++-++++- .+|+.
T Consensus 311 lq~gGVlCP~pgCG~gll~EPD~rkvtC~~gCgf~FCR~C~e~yh~geC~~~~~as~t~tc~y~vde~~a~~arwd~ 387 (446)
T KOG0006|consen 311 LQMGGVLCPRPGCGAGLLPEPDQRKVTCEGGCGFAFCRECKEAYHEGECSAVFEASGTTTCAYRVDERAAEQARWDA 387 (446)
T ss_pred eecCCEecCCCCCCcccccCCCCCcccCCCCchhHhHHHHHhhhccccceeeeccccccceeeecChhhhhhhhhhh
Confidence 344557888 6999999999999999996 999999999987776544444433 3355455554443 66764
No 77
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=74.02 E-value=3.2 Score=27.15 Aligned_cols=29 Identities=24% Similarity=0.623 Sum_probs=21.0
Q ss_pred ceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749 17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~F 45 (87)
--.||.|+...-+..+-.=-.|..||..|
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 35699999998887766556666566654
No 78
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=73.73 E-value=1.7 Score=24.99 Aligned_cols=22 Identities=32% Similarity=0.628 Sum_probs=15.7
Q ss_pred cCCceeCCCCCCceEeCCCcCeeecc
Q psy1749 14 SELIKCCPMCSVPIEKDEGCAQMLCK 39 (87)
Q Consensus 14 ~~~~k~CP~C~~~Iek~~GCnhm~C~ 39 (87)
.-+++.||+|++.= |+--+.|.
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 34679999999864 55556665
No 79
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=73.19 E-value=4.3 Score=28.70 Aligned_cols=26 Identities=23% Similarity=0.709 Sum_probs=21.7
Q ss_pred eCCCCCCceEeCCCcCeeeccccceee
Q psy1749 19 CCPMCSVPIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 19 ~CP~C~~~Iek~~GCnhm~C~~C~~~F 45 (87)
+|+.|+.+..+.+. +.|.|+.|+...
T Consensus 151 ~~~~~g~~~~~~~~-~~~~c~~~~~~e 176 (189)
T PRK09521 151 MCSRCRTPLVKKGE-NELKCPNCGNIE 176 (189)
T ss_pred EccccCCceEECCC-CEEECCCCCCEE
Confidence 69999999988555 999999888653
No 80
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=72.96 E-value=1.5 Score=24.23 Aligned_cols=20 Identities=35% Similarity=0.752 Sum_probs=15.1
Q ss_pred eeccccceeeeecccccccCC
Q psy1749 36 MLCKRCKHVFCWYCLASLDDD 56 (87)
Q Consensus 36 m~C~~C~~~FC~~C~~~~~~~ 56 (87)
++=. ||+.||..|...+...
T Consensus 12 v~l~-CGH~FC~~Cl~~~~~~ 31 (42)
T PF15227_consen 12 VSLP-CGHSFCRSCLERLWKE 31 (42)
T ss_dssp EE-S-SSSEEEHHHHHHHHCC
T ss_pred cccC-CcCHHHHHHHHHHHHc
Confidence 4434 9999999999887763
No 81
>PF14369 zf-RING_3: zinc-finger
Probab=72.08 E-value=3.9 Score=21.97 Aligned_cols=26 Identities=23% Similarity=0.593 Sum_probs=12.5
Q ss_pred CCCCCCceEeCCC-cCeeeccccceee
Q psy1749 20 CPMCSVPIEKDEG-CAQMLCKRCKHVF 45 (87)
Q Consensus 20 CP~C~~~Iek~~G-Cnhm~C~~C~~~F 45 (87)
|..|...|..... =.-.+|+.|+..|
T Consensus 5 Ch~C~~~V~~~~~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 5 CHQCNRFVRIAPSPDSDVACPRCHGGF 31 (35)
T ss_pred CccCCCEeEeCcCCCCCcCCcCCCCcE
Confidence 5666666665322 1222355555444
No 82
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=71.80 E-value=2.6 Score=24.63 Aligned_cols=28 Identities=21% Similarity=0.493 Sum_probs=19.8
Q ss_pred eeCCCCCCceEeCCCcCeeeccccceee
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~~F 45 (87)
=.|-+|+..++....=.-+.|+.||+..
T Consensus 7 Y~C~~Cg~~~~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 7 YKCARCGREVELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EEhhhcCCeeehhhccCceeCCCCCcEE
Confidence 3577788888777666777777777653
No 83
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=71.52 E-value=3.7 Score=30.66 Aligned_cols=30 Identities=23% Similarity=0.649 Sum_probs=23.4
Q ss_pred CceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749 16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~F 45 (87)
..+.||.|+.+++...+=..+.|..|+...
T Consensus 98 ~~~fC~~CG~~~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 98 SHRFCGYCGHPMHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred cCccccccCCCCeecCCceeEECCCCCCEE
Confidence 467899999999887665678898887543
No 84
>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=71.37 E-value=4.3 Score=24.62 Aligned_cols=27 Identities=26% Similarity=0.575 Sum_probs=20.7
Q ss_pred eCCCCCCc----eEeCCCcCeeeccccceee
Q psy1749 19 CCPMCSVP----IEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 19 ~CP~C~~~----Iek~~GCnhm~C~~C~~~F 45 (87)
.||+|+.+ +-+..+=.++.|..||+..
T Consensus 11 ~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 11 VCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred cCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 69999875 3346778899999888753
No 85
>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=70.40 E-value=3.7 Score=33.41 Aligned_cols=35 Identities=26% Similarity=0.674 Sum_probs=27.4
Q ss_pred eeCCCCCCceEeCCCcCeeecccccee-----eeeccccc
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKHV-----FCWYCLAS 52 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~~-----FC~~C~~~ 52 (87)
-.||+|..+..--..=+.+.|..||.. .|-.|+..
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 359999988876666678999999876 58888764
No 86
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=69.62 E-value=4.3 Score=24.14 Aligned_cols=26 Identities=23% Similarity=0.576 Sum_probs=19.1
Q ss_pred ccCCceeCCCCCCceEeCCCcCeeeccccce
Q psy1749 13 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKH 43 (87)
Q Consensus 13 ~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~ 43 (87)
...+...||.|+.++. .|-.|..||.
T Consensus 23 ~~~~l~~C~~CG~~~~-----~H~vC~~CG~ 48 (57)
T PRK12286 23 KAPGLVECPNCGEPKL-----PHRVCPSCGY 48 (57)
T ss_pred cCCcceECCCCCCccC-----CeEECCCCCc
Confidence 3456778999999887 3777776764
No 87
>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=69.42 E-value=1.3 Score=22.78 Aligned_cols=31 Identities=29% Similarity=0.761 Sum_probs=20.1
Q ss_pred CCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749 20 CPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD 55 (87)
Q Consensus 20 CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~ 55 (87)
|+-|...+ -+-+.-..|++.||..|...|..
T Consensus 2 C~iC~~~~-----~~~~~~~~C~H~~c~~C~~~~~~ 32 (45)
T cd00162 2 CPICLEEF-----REPVVLLPCGHVFCRSCIDKWLK 32 (45)
T ss_pred CCcCchhh-----hCceEecCCCChhcHHHHHHHHH
Confidence 66666655 12223334899999999987765
No 88
>PRK04023 DNA polymerase II large subunit; Validated
Probab=69.21 E-value=3.4 Score=37.18 Aligned_cols=39 Identities=18% Similarity=0.292 Sum_probs=29.2
Q ss_pred ccccCCceeCCCCCCceEeCCCcCeeeccccce-----eeeecccccccC
Q psy1749 11 TFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKH-----VFCWYCLASLDD 55 (87)
Q Consensus 11 ~~~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~-----~FC~~C~~~~~~ 55 (87)
.-.....+.||+|+... ..-.|..||. .||-.|+.....
T Consensus 620 ~eVEVg~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~~~~ 663 (1121)
T PRK04023 620 IEVEIGRRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIEVEE 663 (1121)
T ss_pred eeecccCccCCCCCCcC------CcccCCCCCCCCCcceeCccccCcCCC
Confidence 34566778999999985 4567888985 489999766543
No 89
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=68.53 E-value=2.3 Score=26.28 Aligned_cols=24 Identities=25% Similarity=0.884 Sum_probs=10.2
Q ss_pred eeCCCCCCceEeC---CCcCeeecccc
Q psy1749 18 KCCPMCSVPIEKD---EGCAQMLCKRC 41 (87)
Q Consensus 18 k~CP~C~~~Iek~---~GCnhm~C~~C 41 (87)
-+|++|....... ++|.|+.|..|
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~C 34 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSC 34 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTT
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHH
Confidence 4789998876554 56777666644
No 90
>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=67.91 E-value=7.7 Score=20.42 Aligned_cols=25 Identities=20% Similarity=0.576 Sum_probs=22.0
Q ss_pred eCCCCCCceEeCCCcCeeeccccce
Q psy1749 19 CCPMCSVPIEKDEGCAQMLCKRCKH 43 (87)
Q Consensus 19 ~CP~C~~~Iek~~GCnhm~C~~C~~ 43 (87)
.|..|++++..-.|=.++.|..|+.
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCALCQT 27 (31)
T ss_pred CcCCCCcEeecCCCCCeEECCCCCe
Confidence 6999999999999999999987764
No 91
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=66.52 E-value=7.2 Score=23.65 Aligned_cols=35 Identities=26% Similarity=0.647 Sum_probs=26.3
Q ss_pred ceeCCCCCCceEeCCCcCeeeccccceeeeecccc
Q psy1749 17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLA 51 (87)
Q Consensus 17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~ 51 (87)
...|-+|+..|.-.+...+..|++||...=|.|.+
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~ 41 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEK 41 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCeeEeechh
Confidence 45688888888877767888888888875555543
No 92
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=66.08 E-value=5.4 Score=24.37 Aligned_cols=40 Identities=20% Similarity=0.425 Sum_probs=31.2
Q ss_pred ceeCCCCCCceEeCCCcCeeeccccceeeeecccccccCC
Q psy1749 17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDD 56 (87)
Q Consensus 17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~~ 56 (87)
.-.|-+|+..|.-.++-.+..|++||...-|.|-+--..+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~CRk~g 48 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKCRKLG 48 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceeeehhhhHHHcC
Confidence 4578899999988888888889999988878776544443
No 93
>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=65.57 E-value=2 Score=23.26 Aligned_cols=34 Identities=29% Similarity=0.606 Sum_probs=22.7
Q ss_pred eCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749 19 CCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD 55 (87)
Q Consensus 19 ~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~ 55 (87)
.||=|...++..+ .-+.-. |++.|+..|...|-.
T Consensus 2 ~C~IC~~~~~~~~--~~~~l~-C~H~fh~~Ci~~~~~ 35 (44)
T PF13639_consen 2 ECPICLEEFEDGE--KVVKLP-CGHVFHRSCIKEWLK 35 (44)
T ss_dssp CETTTTCBHHTTS--CEEEET-TSEEEEHHHHHHHHH
T ss_pred CCcCCChhhcCCC--eEEEcc-CCCeeCHHHHHHHHH
Confidence 3666666665422 223344 999999999998875
No 94
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=65.21 E-value=8.3 Score=21.40 Aligned_cols=26 Identities=23% Similarity=0.586 Sum_probs=16.4
Q ss_pred eeCCCCCCc-eEeCCCcCeeeccccce
Q psy1749 18 KCCPMCSVP-IEKDEGCAQMLCKRCKH 43 (87)
Q Consensus 18 k~CP~C~~~-Iek~~GCnhm~C~~C~~ 43 (87)
-.||+|+.. +-...+=....|..|+.
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 459999984 33334455566776765
No 95
>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=65.05 E-value=6.3 Score=22.79 Aligned_cols=31 Identities=26% Similarity=0.488 Sum_probs=22.4
Q ss_pred ccCCceeCC--CCCCceEeCCCcCeeeccccce
Q psy1749 13 DSELIKCCP--MCSVPIEKDEGCAQMLCKRCKH 43 (87)
Q Consensus 13 ~~~~~k~CP--~C~~~Iek~~GCnhm~C~~C~~ 43 (87)
+...-+.|| .|+.-|.-..--+...|..|+.
T Consensus 14 v~r~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 14 VKRLRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp EEESSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred EEEhhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 344568899 9999887777778888887764
No 96
>PRK05580 primosome assembly protein PriA; Validated
Probab=64.83 E-value=5.4 Score=33.62 Aligned_cols=35 Identities=20% Similarity=0.504 Sum_probs=26.9
Q ss_pred eeCCCCCCceEeCCCcCeeecccccee-----eeeccccc
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKHV-----FCWYCLAS 52 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~~-----FC~~C~~~ 52 (87)
-+||+|..+......=+.+.|..||.. .|-.|+..
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 468999988775555678999999876 58888754
No 97
>PRK14873 primosome assembly protein PriA; Provisional
Probab=63.96 E-value=6 Score=33.59 Aligned_cols=36 Identities=19% Similarity=0.456 Sum_probs=26.5
Q ss_pred ceeCCCCCCceEeCCCcCeeecccccee----eeeccccc
Q psy1749 17 IKCCPMCSVPIEKDEGCAQMLCKRCKHV----FCWYCLAS 52 (87)
Q Consensus 17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~----FC~~C~~~ 52 (87)
.-+||+|..+...-..=+.+.|..||.. .|-.|+..
T Consensus 392 ~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 392 PARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eeECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 3579999988887656678999989864 46667654
No 98
>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=63.38 E-value=8.5 Score=22.62 Aligned_cols=25 Identities=20% Similarity=0.522 Sum_probs=17.7
Q ss_pred cCCceeCCCCCCceEeCCCcCeeeccccce
Q psy1749 14 SELIKCCPMCSVPIEKDEGCAQMLCKRCKH 43 (87)
Q Consensus 14 ~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~ 43 (87)
..+...||.|+.+.. .|-.|..||.
T Consensus 23 ~p~l~~C~~cG~~~~-----~H~vc~~cG~ 47 (55)
T TIGR01031 23 APTLVVCPNCGEFKL-----PHRVCPSCGY 47 (55)
T ss_pred CCcceECCCCCCccc-----CeeECCccCe
Confidence 345677999998765 5667766764
No 99
>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=62.43 E-value=7.1 Score=25.75 Aligned_cols=36 Identities=25% Similarity=0.459 Sum_probs=27.1
Q ss_pred CceeCCCCCCceEeCCCcCeeeccccceeeeeccccc
Q psy1749 16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS 52 (87)
Q Consensus 16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~ 52 (87)
+.+.|..|+.+.-...+.. ..|..|+..+|-.|+..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCC-CcCCcCCccccCccCCc
Confidence 5678999999876666555 78888999999988865
No 100
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=62.04 E-value=7.4 Score=28.56 Aligned_cols=25 Identities=24% Similarity=0.664 Sum_probs=20.3
Q ss_pred eeCCCCCCceEeCCCcCeeecccccee
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKHV 44 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~~ 44 (87)
-+|++|+...++ .=+.|.|++||..
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGNT 174 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCCE
Confidence 369999999999 4467889988764
No 101
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=61.66 E-value=6.1 Score=26.69 Aligned_cols=35 Identities=31% Similarity=0.725 Sum_probs=26.0
Q ss_pred ceeCCCCCCceEeC--------CCcCeeeccccceeeeecccc
Q psy1749 17 IKCCPMCSVPIEKD--------EGCAQMLCKRCKHVFCWYCLA 51 (87)
Q Consensus 17 ~k~CP~C~~~Iek~--------~GCnhm~C~~C~~~FC~~C~~ 51 (87)
.+.|..|...+... ..-....|..|+..||..|-.
T Consensus 55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~ 97 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDV 97 (112)
T ss_pred CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccch
Confidence 45699999987542 223456799999999998863
No 102
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=61.05 E-value=7.1 Score=26.45 Aligned_cols=28 Identities=29% Similarity=0.816 Sum_probs=20.6
Q ss_pred eeCCCCCCceEeCCCcCeeeccccceeee
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKHVFC 46 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~~FC 46 (87)
..||+|..-.--.+|= .+.|+.|.++|-
T Consensus 4 p~cp~c~sEytYed~~-~~~cpec~~ew~ 31 (112)
T COG2824 4 PPCPKCNSEYTYEDGG-QLICPECAHEWN 31 (112)
T ss_pred CCCCccCCceEEecCc-eEeCchhccccc
Confidence 5799998776666554 888887776653
No 103
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=60.38 E-value=7 Score=23.31 Aligned_cols=14 Identities=36% Similarity=0.679 Sum_probs=11.2
Q ss_pred CCceeCCCCCCceE
Q psy1749 15 ELIKCCPMCSVPIE 28 (87)
Q Consensus 15 ~~~k~CP~C~~~Ie 28 (87)
...+.||+|++..-
T Consensus 3 s~mr~C~~CgvYTL 16 (56)
T PRK13130 3 SKIRKCPKCGVYTL 16 (56)
T ss_pred ccceECCCCCCEEc
Confidence 46789999998776
No 104
>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=60.03 E-value=4.9 Score=22.60 Aligned_cols=37 Identities=22% Similarity=0.572 Sum_probs=26.2
Q ss_pred ceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749 17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD 55 (87)
Q Consensus 17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~ 55 (87)
.+.|+.|....... -..-.|..||..||..|......
T Consensus 2 ~~~C~~C~~~F~~~--~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 2 ASSCMGCGKPFTLT--RRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred cCcCcccCccccCC--ccccccCcCcCCcChHHcCCeee
Confidence 35688888766652 23456788999999999865544
No 105
>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=60.02 E-value=2.8 Score=25.62 Aligned_cols=35 Identities=23% Similarity=0.624 Sum_probs=28.3
Q ss_pred eeCCCCCCceEeC--CCcCeeeccccceeeeeccccc
Q psy1749 18 KCCPMCSVPIEKD--EGCAQMLCKRCKHVFCWYCLAS 52 (87)
Q Consensus 18 k~CP~C~~~Iek~--~GCnhm~C~~C~~~FC~~C~~~ 52 (87)
..||-|++..... +-=|+-+|++|+...|-.||-.
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFN 39 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFN 39 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHhhhhhcccCCC
Confidence 5699999877332 3478999999999999999943
No 106
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=59.28 E-value=6.3 Score=30.46 Aligned_cols=31 Identities=23% Similarity=0.493 Sum_probs=25.4
Q ss_pred CCceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749 15 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~F 45 (87)
.+-|.||+|++..+-..|=-.+.|..|++.+
T Consensus 109 ~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 109 RSHRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred hhCcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 4568899999999999888888888777654
No 107
>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=58.70 E-value=13 Score=18.84 Aligned_cols=24 Identities=21% Similarity=0.577 Sum_probs=19.3
Q ss_pred CCCCCCceEeCCCcCeeeccccce
Q psy1749 20 CPMCSVPIEKDEGCAQMLCKRCKH 43 (87)
Q Consensus 20 CP~C~~~Iek~~GCnhm~C~~C~~ 43 (87)
|-+|++++.--.|=.++.|..|++
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCc
Confidence 667888888888888888886653
No 108
>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=58.37 E-value=2.6 Score=30.13 Aligned_cols=40 Identities=25% Similarity=0.446 Sum_probs=22.3
Q ss_pred CCceeCCCCCCceEeCCCc---Ceeeccccceeeeeccccccc
Q psy1749 15 ELIKCCPMCSVPIEKDEGC---AQMLCKRCKHVFCWYCLASLD 54 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek~~GC---nhm~C~~C~~~FC~~C~~~~~ 54 (87)
+.+..||+|+++|.-..-. -.+.=..=-..||..||.++.
T Consensus 37 ~tI~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyP 79 (158)
T PF10083_consen 37 KTITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYP 79 (158)
T ss_pred HHHHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCc
Confidence 4567899999999865322 111000113456677776543
No 109
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=58.36 E-value=4 Score=29.99 Aligned_cols=33 Identities=24% Similarity=0.712 Sum_probs=23.7
Q ss_pred CceeCCCCCCceEeCCCcCeeeccccceeeeeccccccc
Q psy1749 16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD 54 (87)
Q Consensus 16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~ 54 (87)
..-.||-|...++. -+. ..||+.|||.|...|-
T Consensus 17 ~~~~CpICld~~~d-----PVv-T~CGH~FC~~CI~~wl 49 (193)
T PLN03208 17 GDFDCNICLDQVRD-----PVV-TLCGHLFCWPCIHKWT 49 (193)
T ss_pred CccCCccCCCcCCC-----cEE-cCCCchhHHHHHHHHH
Confidence 45679999886642 123 3599999999998774
No 110
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=57.56 E-value=9.5 Score=29.11 Aligned_cols=30 Identities=23% Similarity=0.523 Sum_probs=17.2
Q ss_pred cCCceeCCCCCC-ceEeCCCcCeeeccccce
Q psy1749 14 SELIKCCPMCSV-PIEKDEGCAQMLCKRCKH 43 (87)
Q Consensus 14 ~~~~k~CP~C~~-~Iek~~GCnhm~C~~C~~ 43 (87)
.+....||.|+. .|..+..=.-+.|..||.
T Consensus 8 ~~~~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~ 38 (310)
T PRK00423 8 EEEKLVCPECGSDKLIYDYERGEIVCADCGL 38 (310)
T ss_pred cccCCcCcCCCCCCeeEECCCCeEeecccCC
Confidence 345578999997 443343333455555543
No 111
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=57.12 E-value=7.6 Score=36.67 Aligned_cols=27 Identities=33% Similarity=0.917 Sum_probs=23.6
Q ss_pred eCCCCCCc------eEeCCCcCeeeccccceeeee
Q psy1749 19 CCPMCSVP------IEKDEGCAQMLCKRCKHVFCW 47 (87)
Q Consensus 19 ~CP~C~~~------Iek~~GCnhm~C~~C~~~FC~ 47 (87)
.||-|+.. ++..+||. +|+.||..-|-
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 39999999 88899997 89999988774
No 112
>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=56.84 E-value=2.3 Score=20.87 Aligned_cols=16 Identities=31% Similarity=0.835 Sum_probs=12.6
Q ss_pred ccceeeeecccccccC
Q psy1749 40 RCKHVFCWYCLASLDD 55 (87)
Q Consensus 40 ~C~~~FC~~C~~~~~~ 55 (87)
.|++.||+.|...|..
T Consensus 15 ~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 15 PCGHTFCRSCIRKWLK 30 (39)
T ss_pred cCCChHHHHHHHHHHH
Confidence 4899999999877643
No 113
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=56.14 E-value=11 Score=22.54 Aligned_cols=31 Identities=26% Similarity=0.561 Sum_probs=18.0
Q ss_pred CCceeCCCCCCc----eEeCCC-cCe-eeccccceee
Q psy1749 15 ELIKCCPMCSVP----IEKDEG-CAQ-MLCKRCKHVF 45 (87)
Q Consensus 15 ~~~k~CP~C~~~----Iek~~G-Cnh-m~C~~C~~~F 45 (87)
..|-.||.|+.. |..+.- =|. +.|+.|..+.
T Consensus 2 ~~Wi~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~Et 38 (55)
T PF14205_consen 2 SEWILCPICGNKTRLKIREDTVLKNFPLYCPKCKQET 38 (55)
T ss_pred CeEEECCCCCCccceeeecCceeccccccCCCCCceE
Confidence 457889999833 332222 233 6677777654
No 114
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=56.06 E-value=6.2 Score=36.27 Aligned_cols=34 Identities=26% Similarity=0.545 Sum_probs=26.0
Q ss_pred ceeCCCCCCceEeCCCcCeeecccccee---------eeecccccccC
Q psy1749 17 IKCCPMCSVPIEKDEGCAQMLCKRCKHV---------FCWYCLASLDD 55 (87)
Q Consensus 17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~---------FC~~C~~~~~~ 55 (87)
..+||+|+...+. ...|..||.. +|-.|+.+...
T Consensus 679 ~~fCP~CGs~te~-----vy~CPsCGaev~~des~a~~CP~CGtplv~ 721 (1337)
T PRK14714 679 ENRCPDCGTHTEP-----VYVCPDCGAEVPPDESGRVECPRCDVELTP 721 (1337)
T ss_pred cccCcccCCcCCC-----ceeCccCCCccCCCccccccCCCCCCcccc
Confidence 3589999998754 3477788886 89999977665
No 115
>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=56.01 E-value=14 Score=25.11 Aligned_cols=27 Identities=30% Similarity=0.680 Sum_probs=22.0
Q ss_pred eeCCCCCCc---eEeCCCcCeeecccccee
Q psy1749 18 KCCPMCSVP---IEKDEGCAQMLCKRCKHV 44 (87)
Q Consensus 18 k~CP~C~~~---Iek~~GCnhm~C~~C~~~ 44 (87)
..||.|+.+ +.++++--.+.|..||+.
T Consensus 94 VlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred EEcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 569999976 666788888999999875
No 116
>KOG0823|consensus
Probab=55.90 E-value=3.2 Score=31.29 Aligned_cols=15 Identities=47% Similarity=1.276 Sum_probs=12.7
Q ss_pred cceeeeecccccccC
Q psy1749 41 CKHVFCWYCLASLDD 55 (87)
Q Consensus 41 C~~~FC~~C~~~~~~ 55 (87)
||+-|||-|+-.|-.
T Consensus 65 CGHLFCWpClyqWl~ 79 (230)
T KOG0823|consen 65 CGHLFCWPCLYQWLQ 79 (230)
T ss_pred cccceehHHHHHHHh
Confidence 899999998888865
No 117
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=54.94 E-value=7.3 Score=33.11 Aligned_cols=34 Identities=21% Similarity=0.579 Sum_probs=22.1
Q ss_pred eeCCCCCCceEeCCCcCeeecccccee----eeecccccccC
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKHV----FCWYCLASLDD 55 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~~----FC~~C~~~~~~ 55 (87)
+.||+|+..+.... -.|.+||+. +|-.||.....
T Consensus 2 ~~Cp~Cg~~n~~~a----kFC~~CG~~l~~~~Cp~CG~~~~~ 39 (645)
T PRK14559 2 LICPQCQFENPNNN----RFCQKCGTSLTHKPCPQCGTEVPV 39 (645)
T ss_pred CcCCCCCCcCCCCC----ccccccCCCCCCCcCCCCCCCCCc
Confidence 57999998875432 245557665 47777776655
No 118
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=53.94 E-value=8.4 Score=21.01 Aligned_cols=25 Identities=24% Similarity=0.796 Sum_probs=15.7
Q ss_pred CCCCCCceEeCCCcCeeeccccceeeeec
Q psy1749 20 CPMCSVPIEKDEGCAQMLCKRCKHVFCWY 48 (87)
Q Consensus 20 CP~C~~~Iek~~GCnhm~C~~C~~~FC~~ 48 (87)
|-.|+..+... -+.|..|+..||-.
T Consensus 1 C~~C~~~~~l~----~f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLT----GFKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCccccc----CeECCccCCccccc
Confidence 34455555443 46677799998853
No 119
>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=53.38 E-value=6.2 Score=30.90 Aligned_cols=35 Identities=26% Similarity=0.629 Sum_probs=26.2
Q ss_pred eeCCCCCCceEeCCCcCeeeccccceeeeecccccc
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASL 53 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~ 53 (87)
..||.|++-.-.+..=..|+= .||+.||-.|...+
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l 38 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLL 38 (309)
T ss_pred CCCCcCCCCCccCcccccccC-CCCCcccHHHHHHH
Confidence 479999997777665444444 48999998888774
No 120
>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=53.23 E-value=21 Score=21.27 Aligned_cols=12 Identities=42% Similarity=1.077 Sum_probs=7.3
Q ss_pred CceeCCCCCCce
Q psy1749 16 LIKCCPMCSVPI 27 (87)
Q Consensus 16 ~~k~CP~C~~~I 27 (87)
+.-.||.|+.++
T Consensus 6 niL~Cp~ck~pL 17 (68)
T PF03966_consen 6 NILACPVCKGPL 17 (68)
T ss_dssp GTBB-TTTSSBE
T ss_pred hhhcCCCCCCcc
Confidence 345677777766
No 121
>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=53.07 E-value=9.3 Score=22.31 Aligned_cols=23 Identities=26% Similarity=0.683 Sum_probs=15.8
Q ss_pred CCceeCCCCCCceEeCCCcCeeeccccc
Q psy1749 15 ELIKCCPMCSVPIEKDEGCAQMLCKRCK 42 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek~~GCnhm~C~~C~ 42 (87)
.+...||.|+.+.. .|..|..||
T Consensus 24 ~~l~~c~~cg~~~~-----~H~vc~~cG 46 (56)
T PF01783_consen 24 PNLVKCPNCGEPKL-----PHRVCPSCG 46 (56)
T ss_dssp TSEEESSSSSSEES-----TTSBCTTTB
T ss_pred cceeeeccCCCEec-----ccEeeCCCC
Confidence 36688999997654 456666565
No 122
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=52.74 E-value=7.3 Score=34.34 Aligned_cols=26 Identities=31% Similarity=0.926 Sum_probs=20.8
Q ss_pred eeCCCCCC-ceEeCCCcCeeeccccceee
Q psy1749 18 KCCPMCSV-PIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 18 k~CP~C~~-~Iek~~GCnhm~C~~C~~~F 45 (87)
-.||-|+. -||..+||| +|++|+++.
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~c~~~~ 854 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTNCGAQL 854 (858)
T ss_pred CCCCccCCCceeecCCCc--cccchhhhh
Confidence 57999986 577789999 588888763
No 123
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.63 E-value=3.9 Score=31.51 Aligned_cols=38 Identities=29% Similarity=0.530 Sum_probs=27.4
Q ss_pred cccCCceeCCCCCCceEeCCCcCeeeccccceeeeeccccc-ccC
Q psy1749 12 FDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS-LDD 55 (87)
Q Consensus 12 ~~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~-~~~ 55 (87)
++...-.+|+-|.-..+. -.|+.||+-|||.|.-. |..
T Consensus 210 fip~~d~kC~lC~e~~~~------ps~t~CgHlFC~~Cl~~~~t~ 248 (271)
T COG5574 210 FIPLADYKCFLCLEEPEV------PSCTPCGHLFCLSCLLISWTK 248 (271)
T ss_pred cccccccceeeeecccCC------cccccccchhhHHHHHHHHHh
Confidence 444555678888777764 34667999999999877 665
No 124
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=51.84 E-value=4.5 Score=22.05 Aligned_cols=33 Identities=27% Similarity=0.666 Sum_probs=21.9
Q ss_pred eCCCCCCceEeCCCcCeeeccccceeeeeccccccc
Q psy1749 19 CCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD 54 (87)
Q Consensus 19 ~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~ 54 (87)
.|+.|...+..+.. ..=..||+.||..|.....
T Consensus 1 ~C~~C~~~~~~~~~---~~l~~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 1 HCNICFEKYSEERR---PRLTSCGHIFCEKCLKKLK 33 (44)
T ss_pred CCcCcCccccCCCC---eEEcccCCHHHHHHHHhhc
Confidence 37888888822222 3333588999999887766
No 125
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=51.52 E-value=10 Score=25.07 Aligned_cols=24 Identities=25% Similarity=0.545 Sum_probs=14.4
Q ss_pred eeCCCCCCceEeCCCcCeeeccccce
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKH 43 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~ 43 (87)
-+|+.|+...+... .++.|+.||.
T Consensus 71 ~~C~~Cg~~~~~~~--~~~~CP~Cgs 94 (113)
T PRK12380 71 AWCWDCSQVVEIHQ--HDAQCPHCHG 94 (113)
T ss_pred EEcccCCCEEecCC--cCccCcCCCC
Confidence 46777876666543 3445666653
No 126
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=50.97 E-value=13 Score=26.89 Aligned_cols=28 Identities=25% Similarity=0.350 Sum_probs=20.4
Q ss_pred CCceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749 15 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD 55 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~ 55 (87)
...+.||.|+. ..++..+|..||..++.
T Consensus 307 ~tS~~C~~cg~-------------~~~r~~~C~~cg~~~~r 334 (364)
T COG0675 307 YTSKTCPCCGH-------------LSGRLFKCPRCGFVHDR 334 (364)
T ss_pred CCcccccccCC-------------ccceeEECCCCCCeehh
Confidence 45699999999 23667777778766554
No 127
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=50.22 E-value=9.4 Score=27.46 Aligned_cols=17 Identities=29% Similarity=0.554 Sum_probs=13.9
Q ss_pred CCceeCCCCCCceEeCC
Q psy1749 15 ELIKCCPMCSVPIEKDE 31 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek~~ 31 (87)
..-.+||.|+..+++.+
T Consensus 95 ~e~~RCp~CN~~L~~vs 111 (165)
T COG1656 95 PEFSRCPECNGELEKVS 111 (165)
T ss_pred cccccCcccCCEeccCc
Confidence 34578999999999864
No 128
>KOG1819|consensus
Probab=49.86 E-value=4.2 Score=34.74 Aligned_cols=41 Identities=24% Similarity=0.656 Sum_probs=28.2
Q ss_pred cccccCcccccCCceeCCCCCCceEeCCCcCeeeccccceeeeecccccc
Q psy1749 4 WFQMGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASL 53 (87)
Q Consensus 4 w~~~~~~~~~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~ 53 (87)
|+.++.+ -+|-.|.+++.--.-- -.|++||-.||-.|...-
T Consensus 895 wipd~~a-------~~cmacq~pf~afrrr--hhcrncggifcg~cs~as 935 (990)
T KOG1819|consen 895 WIPDEDA-------EQCMACQMPFNAFRRR--HHCRNCGGIFCGKCSCAS 935 (990)
T ss_pred cCCCCcc-------hhhhhccCcHHHHHHh--hhhcccCceeecccccCC
Confidence 5555554 6788888887533222 348899999999997543
No 129
>PLN03086 PRLI-interacting factor K; Provisional
Probab=49.45 E-value=12 Score=31.57 Aligned_cols=22 Identities=18% Similarity=0.703 Sum_probs=10.1
Q ss_pred CCCceEeCCCcCeeecccccee
Q psy1749 23 CSVPIEKDEGCAQMLCKRCKHV 44 (87)
Q Consensus 23 C~~~Iek~~GCnhm~C~~C~~~ 44 (87)
|+..+.+.+.=+|..|..|+..
T Consensus 441 Cg~v~~r~el~~H~~C~~Cgk~ 462 (567)
T PLN03086 441 CGIVLRVEEAKNHVHCEKCGQA 462 (567)
T ss_pred ccceeeccccccCccCCCCCCc
Confidence 4444444444445555545443
No 130
>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=48.16 E-value=12 Score=28.11 Aligned_cols=38 Identities=29% Similarity=0.778 Sum_probs=18.4
Q ss_pred eeCCCCCCc-----eEeCC--CcCeeeccccceee------eecccccccC
Q psy1749 18 KCCPMCSVP-----IEKDE--GCAQMLCKRCKHVF------CWYCLASLDD 55 (87)
Q Consensus 18 k~CP~C~~~-----Iek~~--GCnhm~C~~C~~~F------C~~C~~~~~~ 55 (87)
..||-|+.. |...+ |=-++.|..|+++| |-.||..-..
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~ 223 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTDHE 223 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---SS-
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCCCc
Confidence 689999987 33334 78899999999988 5678866443
No 131
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=47.69 E-value=8.3 Score=26.33 Aligned_cols=13 Identities=23% Similarity=0.444 Sum_probs=8.6
Q ss_pred ceeCCCCCCceEe
Q psy1749 17 IKCCPMCSVPIEK 29 (87)
Q Consensus 17 ~k~CP~C~~~Iek 29 (87)
.=.||+|+..+.-
T Consensus 99 ~Y~Cp~C~~~y~~ 111 (147)
T smart00531 99 YYKCPNCQSKYTF 111 (147)
T ss_pred EEECcCCCCEeeH
Confidence 4568888766654
No 132
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=47.31 E-value=12 Score=22.38 Aligned_cols=40 Identities=23% Similarity=0.559 Sum_probs=26.1
Q ss_pred eeCCCCCCceEe--CCCcCeeecccc----ceeeeecccccccCCc
Q psy1749 18 KCCPMCSVPIEK--DEGCAQMLCKRC----KHVFCWYCLASLDDDF 57 (87)
Q Consensus 18 k~CP~C~~~Iek--~~GCnhm~C~~C----~~~FC~~C~~~~~~~~ 57 (87)
+.|-.|...-.+ ...|.|+.|..| .+.=|-+|+.+++.++
T Consensus 8 ~~~~~~~~~~~~~~~~pCgH~I~~~~f~~~rYngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 8 QPCVFCGFVGTKGTVLPCGHLICDNCFPGERYNGCPFCGTPFEFDD 53 (55)
T ss_pred eeEEEccccccccccccccceeeccccChhhccCCCCCCCcccCCC
Confidence 555566554333 356999999876 5566777777777643
No 133
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=47.25 E-value=15 Score=24.60 Aligned_cols=48 Identities=15% Similarity=0.247 Sum_probs=32.8
Q ss_pred CceeCCCCCCc------eEeCCCcCeeeccccceeeeecccccccCCccCCCCC
Q psy1749 16 LIKCCPMCSVP------IEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYD 63 (87)
Q Consensus 16 ~~k~CP~C~~~------Iek~~GCnhm~C~~C~~~FC~~C~~~~~~~~~~~Hf~ 63 (87)
.+-.||.|+.. |.|..+=..++|..||..|=..=-..+.+-+.|+-|-
T Consensus 21 k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l~~~vDvYs~wv 74 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPELSEPVDVYSAWV 74 (104)
T ss_pred ceEecCccCCeeeeEEEEEecCceeEEEcccCcceEEEeccccccchhHHHHHH
Confidence 34569999875 4556667778888888887665555666656665553
No 134
>KOG0320|consensus
Probab=47.09 E-value=4 Score=29.93 Aligned_cols=38 Identities=26% Similarity=0.620 Sum_probs=23.3
Q ss_pred ccCCceeCCCCCCceEeCCCcCeeeccccceeeeeccccccc
Q psy1749 13 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD 54 (87)
Q Consensus 13 ~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~ 54 (87)
.++..-.||-|.-.+++..- .-++||+-||-.|.+..-
T Consensus 127 ~~~~~~~CPiCl~~~sek~~----vsTkCGHvFC~~Cik~al 164 (187)
T KOG0320|consen 127 RKEGTYKCPICLDSVSEKVP----VSTKCGHVFCSQCIKDAL 164 (187)
T ss_pred ccccccCCCceecchhhccc----cccccchhHHHHHHHHHH
Confidence 34556789999988887653 223455556555554443
No 135
>PRK07218 replication factor A; Provisional
Probab=47.01 E-value=9.3 Score=30.93 Aligned_cols=15 Identities=47% Similarity=0.895 Sum_probs=12.7
Q ss_pred CCceeCCCCCCceEe
Q psy1749 15 ELIKCCPMCSVPIEK 29 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek 29 (87)
-.+++||.|+..|++
T Consensus 295 gli~rCP~C~r~v~~ 309 (423)
T PRK07218 295 GLIERCPECGRVIQK 309 (423)
T ss_pred cceecCcCccccccC
Confidence 356899999999976
No 136
>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=46.80 E-value=21 Score=23.85 Aligned_cols=27 Identities=22% Similarity=0.782 Sum_probs=16.8
Q ss_pred ceeCC--CCCCceEeCCCcCeeecccccee
Q psy1749 17 IKCCP--MCSVPIEKDEGCAQMLCKRCKHV 44 (87)
Q Consensus 17 ~k~CP--~C~~~Iek~~GCnhm~C~~C~~~ 44 (87)
-.-|| .|+..+... +=+...|..|+..
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 36799 999988877 3355777767655
No 137
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=46.62 E-value=18 Score=24.07 Aligned_cols=27 Identities=26% Similarity=0.646 Sum_probs=20.6
Q ss_pred eeCCCCCCc---eEeCCCcCeeecccccee
Q psy1749 18 KCCPMCSVP---IEKDEGCAQMLCKRCKHV 44 (87)
Q Consensus 18 k~CP~C~~~---Iek~~GCnhm~C~~C~~~ 44 (87)
..||.|+.+ ++++++=-.+.|..||+.
T Consensus 81 VlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 110 (110)
T smart00653 81 VLCPECGSPDTELIKENRLFFLKCEACGAR 110 (110)
T ss_pred EECCCCCCCCcEEEEeCCeEEEEccccCCC
Confidence 679999876 666666667889988863
No 138
>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=46.26 E-value=16 Score=24.95 Aligned_cols=27 Identities=19% Similarity=0.679 Sum_probs=18.3
Q ss_pred ceeCCCCCCceEeCCCcCeeecccccee
Q psy1749 17 IKCCPMCSVPIEKDEGCAQMLCKRCKHV 44 (87)
Q Consensus 17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~ 44 (87)
...||.|+..+...+. ....|..|+..
T Consensus 34 Y~aC~~C~kkv~~~~~-~~~~C~~C~~~ 60 (166)
T cd04476 34 YPACPGCNKKVVEEGN-GTYRCEKCNKS 60 (166)
T ss_pred EccccccCcccEeCCC-CcEECCCCCCc
Confidence 4679999999987654 44555555543
No 139
>PRK12495 hypothetical protein; Provisional
Probab=46.07 E-value=6.7 Score=29.53 Aligned_cols=31 Identities=26% Similarity=0.598 Sum_probs=21.2
Q ss_pred CCceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749 15 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD 55 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~ 55 (87)
..-+.|+.|+.+|.+..| ..||-.|......
T Consensus 40 msa~hC~~CG~PIpa~pG----------~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 40 MTNAHCDECGDPIFRHDG----------QEFCPTCQQPVTE 70 (226)
T ss_pred cchhhcccccCcccCCCC----------eeECCCCCCcccc
Confidence 455789999999995544 4455566655543
No 140
>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=45.91 E-value=9.8 Score=21.03 Aligned_cols=14 Identities=50% Similarity=1.018 Sum_probs=11.0
Q ss_pred CceeCCCCCCceEe
Q psy1749 16 LIKCCPMCSVPIEK 29 (87)
Q Consensus 16 ~~k~CP~C~~~Iek 29 (87)
..+.||-|+.+|++
T Consensus 36 ~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 36 RKKKCPICRQPIES 49 (50)
T ss_dssp TTSBBTTTTBB-SE
T ss_pred cCCCCCcCChhhcC
Confidence 55899999999975
No 141
>PF15616 TerY-C: TerY-C metal binding domain
Probab=45.69 E-value=17 Score=25.10 Aligned_cols=23 Identities=30% Similarity=0.904 Sum_probs=14.8
Q ss_pred eeCCCCCCceEeCCCcCeeeccccceeeee
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCW 47 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~ 47 (87)
--||.|+...- ...|. ||..||+
T Consensus 78 PgCP~CGn~~~------fa~C~-CGkl~Ci 100 (131)
T PF15616_consen 78 PGCPHCGNQYA------FAVCG-CGKLFCI 100 (131)
T ss_pred CCCCCCcChhc------EEEec-CCCEEEe
Confidence 56999998743 34454 6666665
No 142
>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=45.26 E-value=15 Score=24.28 Aligned_cols=25 Identities=20% Similarity=0.453 Sum_probs=15.5
Q ss_pred ceeCCCCCCceEeCCCcCeeeccccce
Q psy1749 17 IKCCPMCSVPIEKDEGCAQMLCKRCKH 43 (87)
Q Consensus 17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~ 43 (87)
.-+|+.|+...+...- +..|+.||.
T Consensus 70 ~~~C~~Cg~~~~~~~~--~~~CP~Cgs 94 (115)
T TIGR00100 70 ECECEDCSEEVSPEID--LYRCPKCHG 94 (115)
T ss_pred EEEcccCCCEEecCCc--CccCcCCcC
Confidence 3468888876666542 456766664
No 143
>KOG1812|consensus
Probab=44.90 E-value=8.1 Score=30.67 Aligned_cols=40 Identities=18% Similarity=0.453 Sum_probs=25.5
Q ss_pred CCCCCCceEeCC--CcCeeeccccceeeeecccccccCCccC
Q psy1749 20 CPMCSVPIEKDE--GCAQMLCKRCKHVFCWYCLASLDDDFLL 59 (87)
Q Consensus 20 CP~C~~~Iek~~--GCnhm~C~~C~~~FC~~C~~~~~~~~~~ 59 (87)
||.+-...|.++ -=.--.|..|+..||..|..+|...-.+
T Consensus 241 C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC 282 (384)
T KOG1812|consen 241 CSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSC 282 (384)
T ss_pred chHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCH
Confidence 444444444332 2233457789999999999999875333
No 144
>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=44.54 E-value=10 Score=29.05 Aligned_cols=27 Identities=30% Similarity=0.795 Sum_probs=8.9
Q ss_pred eCCCCCCc-eEeCCC---cCeeeccccceee
Q psy1749 19 CCPMCSVP-IEKDEG---CAQMLCKRCKHVF 45 (87)
Q Consensus 19 ~CP~C~~~-Iek~~G---Cnhm~C~~C~~~F 45 (87)
.||+|+.. +.+-.- -.-..|..|+.+|
T Consensus 33 yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 33 YCPNCGSKPLSKFENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp --TTT--SS-EE--------EEE-TTT--EE
T ss_pred cCCCCCChhHhhccCCCccceeECCCCchHH
Confidence 59999988 665421 2234455555554
No 145
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=44.18 E-value=20 Score=24.59 Aligned_cols=28 Identities=25% Similarity=0.580 Sum_probs=20.6
Q ss_pred ceeCCCCCCc---eEeCCCcCeeecccccee
Q psy1749 17 IKCCPMCSVP---IEKDEGCAQMLCKRCKHV 44 (87)
Q Consensus 17 ~k~CP~C~~~---Iek~~GCnhm~C~~C~~~ 44 (87)
-..||.|+.+ +.|++.=..+.|..||+.
T Consensus 97 yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 97 YVICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred eEECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 3679999875 566655556889988875
No 146
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.78 E-value=12 Score=23.12 Aligned_cols=21 Identities=24% Similarity=0.517 Sum_probs=15.8
Q ss_pred CCceeCCCCCCceEeCCCcCe
Q psy1749 15 ELIKCCPMCSVPIEKDEGCAQ 35 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek~~GCnh 35 (87)
..+..||.|+++|+...--.+
T Consensus 5 ~~~v~CP~Cgkpv~w~~~s~f 25 (65)
T COG3024 5 RITVPCPTCGKPVVWGEESPF 25 (65)
T ss_pred cccccCCCCCCcccccccCCc
Confidence 356889999999998654333
No 147
>PRK06386 replication factor A; Reviewed
Probab=43.57 E-value=12 Score=29.70 Aligned_cols=14 Identities=29% Similarity=0.733 Sum_probs=12.3
Q ss_pred CceeCCCCCCceEe
Q psy1749 16 LIKCCPMCSVPIEK 29 (87)
Q Consensus 16 ~~k~CP~C~~~Iek 29 (87)
..++||.|+..|++
T Consensus 235 li~rCP~C~R~l~~ 248 (358)
T PRK06386 235 IFTKCSVCNKIIED 248 (358)
T ss_pred eEecCcCCCeEccC
Confidence 46999999999995
No 148
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=43.24 E-value=13 Score=21.58 Aligned_cols=34 Identities=21% Similarity=0.779 Sum_probs=17.2
Q ss_pred CCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749 20 CPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD 55 (87)
Q Consensus 20 CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~ 55 (87)
||-|-..+ -..|=+..-|. |+.+.|..|-.....
T Consensus 1 cp~C~e~~-d~~d~~~~PC~-Cgf~IC~~C~~~i~~ 34 (48)
T PF14570_consen 1 CPLCDEEL-DETDKDFYPCE-CGFQICRFCYHDILE 34 (48)
T ss_dssp -TTTS-B---CCCTT--SST-TS----HHHHHHHTT
T ss_pred CCCccccc-ccCCCccccCc-CCCcHHHHHHHHHHh
Confidence 67777777 44566888898 999999998655543
No 149
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=42.85 E-value=22 Score=24.54 Aligned_cols=28 Identities=25% Similarity=0.603 Sum_probs=21.0
Q ss_pred ceeCCCCCCc---eEeCCCcCeeecccccee
Q psy1749 17 IKCCPMCSVP---IEKDEGCAQMLCKRCKHV 44 (87)
Q Consensus 17 ~k~CP~C~~~---Iek~~GCnhm~C~~C~~~ 44 (87)
-..||.|+.+ ++|.+.=-.+.|..||+.
T Consensus 102 yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 102 YVICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred cEECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 3679999875 666656567889988875
No 150
>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=42.55 E-value=18 Score=21.58 Aligned_cols=16 Identities=31% Similarity=0.765 Sum_probs=8.8
Q ss_pred ceeCCCCCCceEeCCC
Q psy1749 17 IKCCPMCSVPIEKDEG 32 (87)
Q Consensus 17 ~k~CP~C~~~Iek~~G 32 (87)
+.+||.|+..++-...
T Consensus 2 ~v~CP~C~k~~~~~~~ 17 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPE 17 (57)
T ss_dssp EEE-TTT--EEE-SSS
T ss_pred cccCCCCCCeecccCC
Confidence 4689999999987543
No 151
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=41.96 E-value=12 Score=23.97 Aligned_cols=22 Identities=23% Similarity=0.608 Sum_probs=8.8
Q ss_pred cCCceeCCCCCCceEeCCCcCe
Q psy1749 14 SELIKCCPMCSVPIEKDEGCAQ 35 (87)
Q Consensus 14 ~~~~k~CP~C~~~Iek~~GCnh 35 (87)
+.+.+-||.|++...+..|+..
T Consensus 48 keg~q~CpqCkt~ykr~kgsp~ 69 (80)
T PF14569_consen 48 KEGNQVCPQCKTRYKRHKGSPR 69 (80)
T ss_dssp HTS-SB-TTT--B----TT---
T ss_pred hcCcccccccCCCcccccCCCC
Confidence 4567889999999888877654
No 152
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=41.87 E-value=16 Score=21.69 Aligned_cols=14 Identities=36% Similarity=0.890 Sum_probs=6.6
Q ss_pred CceeCCCCCCceEe
Q psy1749 16 LIKCCPMCSVPIEK 29 (87)
Q Consensus 16 ~~k~CP~C~~~Iek 29 (87)
.+..||.|+++.-+
T Consensus 20 DiVvCp~CgapyHR 33 (54)
T PF14446_consen 20 DIVVCPECGAPYHR 33 (54)
T ss_pred CEEECCCCCCcccH
Confidence 34445555555433
No 153
>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=41.75 E-value=18 Score=20.12 Aligned_cols=11 Identities=27% Similarity=0.625 Sum_probs=5.4
Q ss_pred eCCCCCCceEe
Q psy1749 19 CCPMCSVPIEK 29 (87)
Q Consensus 19 ~CP~C~~~Iek 29 (87)
+|+.|+...|.
T Consensus 7 ~C~~Cg~~fe~ 17 (52)
T TIGR02605 7 RCTACGHRFEV 17 (52)
T ss_pred EeCCCCCEeEE
Confidence 45555554443
No 154
>PHA02942 putative transposase; Provisional
Probab=40.87 E-value=24 Score=27.87 Aligned_cols=29 Identities=17% Similarity=0.339 Sum_probs=18.4
Q ss_pred CceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749 16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~F 45 (87)
..+.||.|+......++ ....|..||...
T Consensus 324 TSq~Cs~CG~~~~~l~~-r~f~C~~CG~~~ 352 (383)
T PHA02942 324 SSVSCPKCGHKMVEIAH-RYFHCPSCGYEN 352 (383)
T ss_pred CCccCCCCCCccCcCCC-CEEECCCCCCEe
Confidence 67899999986542222 246676676653
No 155
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=40.77 E-value=15 Score=22.39 Aligned_cols=15 Identities=33% Similarity=0.851 Sum_probs=11.8
Q ss_pred CceeCCCCCCceEeC
Q psy1749 16 LIKCCPMCSVPIEKD 30 (87)
Q Consensus 16 ~~k~CP~C~~~Iek~ 30 (87)
.+.+||.|++.++-.
T Consensus 5 ~~v~CP~C~k~~~w~ 19 (62)
T PRK00418 5 ITVNCPTCGKPVEWG 19 (62)
T ss_pred ccccCCCCCCccccc
Confidence 467899999998743
No 156
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=40.20 E-value=20 Score=23.72 Aligned_cols=25 Identities=16% Similarity=0.356 Sum_probs=13.4
Q ss_pred eeCCCCCCceEeCCCcCeeeccccce
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKH 43 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~ 43 (87)
-+|+.|+..++.... ..+.|+.||.
T Consensus 71 ~~C~~Cg~~~~~~~~-~~~~CP~Cgs 95 (114)
T PRK03681 71 CWCETCQQYVTLLTQ-RVRRCPQCHG 95 (114)
T ss_pred EEcccCCCeeecCCc-cCCcCcCcCC
Confidence 457777766655422 2244665653
No 157
>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=40.11 E-value=16 Score=19.97 Aligned_cols=18 Identities=28% Similarity=0.637 Sum_probs=10.8
Q ss_pred Ceeeccccceeeeecccc
Q psy1749 34 AQMLCKRCKHVFCWYCLA 51 (87)
Q Consensus 34 nhm~C~~C~~~FC~~C~~ 51 (87)
.-+.|..|+..||..=..
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 457888899999975443
No 158
>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=40.02 E-value=27 Score=23.72 Aligned_cols=16 Identities=25% Similarity=0.750 Sum_probs=13.1
Q ss_pred CceeCCCCCCceEeCC
Q psy1749 16 LIKCCPMCSVPIEKDE 31 (87)
Q Consensus 16 ~~k~CP~C~~~Iek~~ 31 (87)
...+||.|+..+++.+
T Consensus 90 ~~sRC~~CN~~L~~v~ 105 (147)
T PF01927_consen 90 IFSRCPKCNGPLRPVS 105 (147)
T ss_pred CCCccCCCCcEeeech
Confidence 4679999999988764
No 159
>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=39.52 E-value=23 Score=25.92 Aligned_cols=10 Identities=50% Similarity=1.125 Sum_probs=5.7
Q ss_pred CCCCCCceEe
Q psy1749 20 CPMCSVPIEK 29 (87)
Q Consensus 20 CP~C~~~Iek 29 (87)
||.|+.+++.
T Consensus 1 C~~CG~~~~~ 10 (236)
T PF04981_consen 1 CPRCGREIEP 10 (236)
T ss_pred CCCCCCCCCC
Confidence 5666665554
No 160
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=39.44 E-value=18 Score=32.56 Aligned_cols=37 Identities=22% Similarity=0.679 Sum_probs=28.9
Q ss_pred ceeCCCCCCceE---eCCCcCeeeccccceeeeecccccc
Q psy1749 17 IKCCPMCSVPIE---KDEGCAQMLCKRCKHVFCWYCLASL 53 (87)
Q Consensus 17 ~k~CP~C~~~Ie---k~~GCnhm~C~~C~~~FC~~C~~~~ 53 (87)
...|..|+.... |.-+...=.|+.||..||-.|-...
T Consensus 460 SdtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSnR 499 (1374)
T PTZ00303 460 SDSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKR 499 (1374)
T ss_pred CCcccCcCCcccccccccccccccccCCccccCccccCCc
Confidence 467999998874 3346666789999999999998544
No 161
>PF14149 YhfH: YhfH-like protein
Probab=37.61 E-value=1.7 Score=24.13 Aligned_cols=29 Identities=31% Similarity=0.610 Sum_probs=20.6
Q ss_pred ccCCceeCCCCCCceEeCCCcCeeecccc
Q psy1749 13 DSELIKCCPMCSVPIEKDEGCAQMLCKRC 41 (87)
Q Consensus 13 ~~~~~k~CP~C~~~Iek~~GCnhm~C~~C 41 (87)
.+.-.|.|+.|+..|+-..-|-...|..|
T Consensus 9 rnLp~K~C~~CG~~i~EQ~E~Y~n~C~~C 37 (37)
T PF14149_consen 9 RNLPPKKCTECGKEIEEQAECYGNECDRC 37 (37)
T ss_pred HhCCCcccHHHHHHHHHHHHHHhCcCCCC
Confidence 34556899999999887666666666544
No 162
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=36.87 E-value=22 Score=25.99 Aligned_cols=24 Identities=33% Similarity=0.920 Sum_probs=19.0
Q ss_pred eCCCCCCceEeCCCcCeeeccccceee
Q psy1749 19 CCPMCSVPIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 19 ~CP~C~~~Iek~~GCnhm~C~~C~~~F 45 (87)
.||.|+.++...+ +...|. .++.|
T Consensus 4 ~CP~C~~~l~~~~--~~~~C~-~~h~f 27 (272)
T PRK11088 4 QCPLCHQPLTLEE--NSWICP-QNHQF 27 (272)
T ss_pred cCCCCCcchhcCC--CEEEcC-CCCCC
Confidence 6999999997655 568888 47776
No 163
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=36.69 E-value=30 Score=25.08 Aligned_cols=32 Identities=19% Similarity=0.445 Sum_probs=23.7
Q ss_pred ceeCCCCCCc---eEeCCCcCeeeccccceeeeec
Q psy1749 17 IKCCPMCSVP---IEKDEGCAQMLCKRCKHVFCWY 48 (87)
Q Consensus 17 ~k~CP~C~~~---Iek~~GCnhm~C~~C~~~FC~~ 48 (87)
-..||.|+.+ +++++.=..+.|..||+.-.-.
T Consensus 98 yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~v~ 132 (201)
T PRK12336 98 YVICSECGLPDTRLVKEDRVLMLRCDACGAHRPVK 132 (201)
T ss_pred eEECCCCCCCCcEEEEcCCeEEEEcccCCCCcccc
Confidence 3679999875 6666666678999888876543
No 164
>PHA02929 N1R/p28-like protein; Provisional
Probab=35.80 E-value=18 Score=27.18 Aligned_cols=39 Identities=28% Similarity=0.579 Sum_probs=26.9
Q ss_pred CceeCCCCCCceEeCCCcC---eeeccccceeeeecccccccC
Q psy1749 16 LIKCCPMCSVPIEKDEGCA---QMLCKRCKHVFCWYCLASLDD 55 (87)
Q Consensus 16 ~~k~CP~C~~~Iek~~GCn---hm~C~~C~~~FC~~C~~~~~~ 55 (87)
....||=|...+.....-+ -+.- .|++.||..|...|-.
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~-~C~H~FC~~CI~~Wl~ 214 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILS-NCNHVFCIECIDIWKK 214 (238)
T ss_pred CCCCCccCCcccccCccccccceecC-CCCCcccHHHHHHHHh
Confidence 3468999999876543211 1222 4889999999988875
No 165
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=35.64 E-value=21 Score=25.05 Aligned_cols=9 Identities=44% Similarity=1.191 Sum_probs=6.7
Q ss_pred eCCCCCCce
Q psy1749 19 CCPMCSVPI 27 (87)
Q Consensus 19 ~CP~C~~~I 27 (87)
.||.|+.+-
T Consensus 2 ~cp~c~~~~ 10 (154)
T PRK00464 2 RCPFCGHPD 10 (154)
T ss_pred cCCCCCCCC
Confidence 699999643
No 166
>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=35.23 E-value=21 Score=19.29 Aligned_cols=21 Identities=29% Similarity=0.724 Sum_probs=14.8
Q ss_pred eeCCCCCCceEeC---CCcCeeecc
Q psy1749 18 KCCPMCSVPIEKD---EGCAQMLCK 39 (87)
Q Consensus 18 k~CP~C~~~Iek~---~GCnhm~C~ 39 (87)
+.||.|+..+... .| .++.|.
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 5799999776654 34 567776
No 167
>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=34.60 E-value=36 Score=22.15 Aligned_cols=29 Identities=28% Similarity=0.607 Sum_probs=19.7
Q ss_pred ceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749 17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~F 45 (87)
--.||.|+..--+..+-.-=.|..|+..|
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 35699999988776665556666666554
No 168
>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=34.49 E-value=39 Score=26.96 Aligned_cols=30 Identities=17% Similarity=0.429 Sum_probs=19.8
Q ss_pred CCceeCCCCCCceEeCC--CcCeeecccccee
Q psy1749 15 ELIKCCPMCSVPIEKDE--GCAQMLCKRCKHV 44 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek~~--GCnhm~C~~C~~~ 44 (87)
.+...||.|+..+++.. .=..-.|++||+.
T Consensus 11 ~~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~ 42 (403)
T TIGR00155 11 AKHILCSQCDMLVALPRIESGQKAACPRCGTT 42 (403)
T ss_pred CCeeeCCCCCCcccccCCCCCCeeECCCCCCC
Confidence 45678999999998763 1223557666654
No 169
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=33.48 E-value=8.2 Score=23.33 Aligned_cols=27 Identities=33% Similarity=0.658 Sum_probs=19.8
Q ss_pred ceeCCCCCCceEeCCCcCe--eeccccce
Q psy1749 17 IKCCPMCSVPIEKDEGCAQ--MLCKRCKH 43 (87)
Q Consensus 17 ~k~CP~C~~~Iek~~GCnh--m~C~~C~~ 43 (87)
+.+|-+|+.++-+.+|-.| +.|++|..
T Consensus 4 tiRC~~CnKlLa~a~~~~yle~KCPrCK~ 32 (60)
T COG4416 4 TIRCAKCNKLLAEAEGQAYLEKKCPRCKE 32 (60)
T ss_pred eeehHHHhHHHHhcccceeeeecCCccce
Confidence 5678888888888877655 56777754
No 170
>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=33.17 E-value=34 Score=18.60 Aligned_cols=14 Identities=21% Similarity=0.532 Sum_probs=8.5
Q ss_pred CceeCCCCCC-ceEe
Q psy1749 16 LIKCCPMCSV-PIEK 29 (87)
Q Consensus 16 ~~k~CP~C~~-~Iek 29 (87)
....||.|+. .++|
T Consensus 25 ~~~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 25 DPVPCPECGSTEVRR 39 (42)
T ss_pred CCCcCCCCCCCceEE
Confidence 4556777776 5554
No 171
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=33.03 E-value=35 Score=22.45 Aligned_cols=30 Identities=23% Similarity=0.378 Sum_probs=16.4
Q ss_pred ceeCCCCCCceEeCCCcCeeeccccceeeeeccccccc
Q psy1749 17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD 54 (87)
Q Consensus 17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~ 54 (87)
.-.|+.|+..-.. .-.|+..||-.|+....
T Consensus 42 ~~~C~~Cg~~~~~--------~~SCk~R~CP~C~~~~~ 71 (111)
T PF14319_consen 42 RYRCEDCGHEKIV--------YNSCKNRHCPSCQAKAT 71 (111)
T ss_pred eeecCCCCceEEe--------cCcccCcCCCCCCChHH
Confidence 3456665544332 23467777777775433
No 172
>KOG1729|consensus
Probab=32.79 E-value=8.7 Score=29.68 Aligned_cols=33 Identities=24% Similarity=0.638 Sum_probs=21.5
Q ss_pred ceeCCCCCCceEeC--CCcCeeeccccceeeeeccccc
Q psy1749 17 IKCCPMCSVPIEKD--EGCAQMLCKRCKHVFCWYCLAS 52 (87)
Q Consensus 17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~~~FC~~C~~~ 52 (87)
.-.|+.|+.. +.+ .---| |+.||..||.-|...
T Consensus 168 a~~C~~C~~~-~Ftl~~RRHH--CR~CG~ivC~~Cs~n 202 (288)
T KOG1729|consen 168 ATECMVCGCT-EFTLSERRHH--CRNCGDIVCAPCSRN 202 (288)
T ss_pred ceecccCCCc-cccHHHHHHH--HHhcchHhhhhhhcC
Confidence 3679988884 322 22222 778888888877654
No 173
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=32.59 E-value=31 Score=20.03 Aligned_cols=16 Identities=25% Similarity=0.592 Sum_probs=12.6
Q ss_pred eeeccccceeeeeccc
Q psy1749 35 QMLCKRCKHVFCWYCL 50 (87)
Q Consensus 35 hm~C~~C~~~FC~~C~ 50 (87)
+++|..||.+|-|.=+
T Consensus 4 ~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 4 TLTCKDCGAEFVFTAG 19 (49)
T ss_pred eEEcccCCCeEEEehh
Confidence 4788889999988655
No 174
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=31.25 E-value=16 Score=32.46 Aligned_cols=36 Identities=19% Similarity=0.414 Sum_probs=0.0
Q ss_pred cCCceeCCCCCCceEeCCCcCeeecccccee-----eeecccccccC
Q psy1749 14 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHV-----FCWYCLASLDD 55 (87)
Q Consensus 14 ~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~-----FC~~C~~~~~~ 55 (87)
....++||+|+..... .+|..||.+ +|-.|+...+.
T Consensus 652 ei~~r~Cp~Cg~~t~~------~~Cp~CG~~T~~~~~Cp~C~~~~~~ 692 (900)
T PF03833_consen 652 EIGRRRCPKCGKETFY------NRCPECGSHTEPVYVCPDCGIEVEE 692 (900)
T ss_dssp -----------------------------------------------
T ss_pred eeecccCcccCCcchh------hcCcccCCccccceeccccccccCc
Confidence 3455789999887543 345556555 56666555443
No 175
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=30.75 E-value=16 Score=23.59 Aligned_cols=33 Identities=30% Similarity=0.783 Sum_probs=25.3
Q ss_pred CCCCCCceEeCCCcCeeeccccceeeeecccccccCC
Q psy1749 20 CPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDD 56 (87)
Q Consensus 20 CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~~ 56 (87)
||.|+.+ .+.|.-+... |++.|=..|...|-..
T Consensus 35 Cp~Ck~P---gd~Cplv~g~-C~H~FH~hCI~kWl~~ 67 (85)
T PF12861_consen 35 CPDCKFP---GDDCPLVWGK-CSHNFHMHCILKWLST 67 (85)
T ss_pred CCCccCC---CCCCceeecc-CccHHHHHHHHHHHcc
Confidence 6666665 3567777777 9999999999888874
No 176
>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=29.99 E-value=26 Score=23.82 Aligned_cols=16 Identities=19% Similarity=0.393 Sum_probs=11.7
Q ss_pred cccCCceeCCCCCCce
Q psy1749 12 FDSELIKCCPMCSVPI 27 (87)
Q Consensus 12 ~~~~~~k~CP~C~~~I 27 (87)
..++-.-.||+|+...
T Consensus 64 Stkav~V~CP~C~K~T 79 (114)
T PF11023_consen 64 STKAVQVECPNCGKQT 79 (114)
T ss_pred cccceeeECCCCCChH
Confidence 4455667799999875
No 177
>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=29.97 E-value=21 Score=21.42 Aligned_cols=13 Identities=54% Similarity=1.229 Sum_probs=10.6
Q ss_pred eeCCCCCCceEeC
Q psy1749 18 KCCPMCSVPIEKD 30 (87)
Q Consensus 18 k~CP~C~~~Iek~ 30 (87)
|-||.|+.+|.-+
T Consensus 4 kHC~~CG~~Ip~~ 16 (59)
T PF09889_consen 4 KHCPVCGKPIPPD 16 (59)
T ss_pred CcCCcCCCcCCcc
Confidence 6799999999853
No 178
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=29.54 E-value=32 Score=21.37 Aligned_cols=10 Identities=30% Similarity=0.883 Sum_probs=8.1
Q ss_pred eeCCCCCCce
Q psy1749 18 KCCPMCSVPI 27 (87)
Q Consensus 18 k~CP~C~~~I 27 (87)
..||.|+...
T Consensus 2 m~CP~Cg~~a 11 (72)
T PRK09678 2 FHCPLCQHAA 11 (72)
T ss_pred ccCCCCCCcc
Confidence 4799999876
No 179
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=29.44 E-value=16 Score=22.57 Aligned_cols=27 Identities=22% Similarity=0.660 Sum_probs=21.1
Q ss_pred eCCCCCCceEe----CCCcCeeeccccceee
Q psy1749 19 CCPMCSVPIEK----DEGCAQMLCKRCKHVF 45 (87)
Q Consensus 19 ~CP~C~~~Iek----~~GCnhm~C~~C~~~F 45 (87)
.||.|...=.. +++-.+..|..||++.
T Consensus 12 ~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~ 42 (66)
T COG3529 12 VCPACQAQDTLAMWRENNVEIVECVKCGHHM 42 (66)
T ss_pred CCcccchhhHHHHHHhcCCceEehhhcchHh
Confidence 59999875433 5788899999999875
No 180
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=29.14 E-value=54 Score=25.39 Aligned_cols=31 Identities=26% Similarity=0.639 Sum_probs=19.8
Q ss_pred CCceeCCCCCCceEeC-----CCcCeeeccccceee
Q psy1749 15 ELIKCCPMCSVPIEKD-----EGCAQMLCKRCKHVF 45 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek~-----~GCnhm~C~~C~~~F 45 (87)
...-+|-+|++..+-. -|-....|.+|++.|
T Consensus 130 KeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F 165 (278)
T PF15135_consen 130 KEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNF 165 (278)
T ss_pred cccccccccccccCCCccccccceeeeecccccccc
Confidence 3456777888765443 455556677777766
No 181
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=27.42 E-value=44 Score=26.10 Aligned_cols=37 Identities=24% Similarity=0.683 Sum_probs=28.0
Q ss_pred CceeCCCCCCc-----eEe--CCCcCeeeccccceee------eeccccc
Q psy1749 16 LIKCCPMCSVP-----IEK--DEGCAQMLCKRCKHVF------CWYCLAS 52 (87)
Q Consensus 16 ~~k~CP~C~~~-----Iek--~~GCnhm~C~~C~~~F------C~~C~~~ 52 (87)
.-..||-|+.. |.. .+|=-++.|.-|+++| |-.|+..
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~ 235 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQS 235 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence 34779999987 222 4678899999999887 6678863
No 182
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.38 E-value=31 Score=23.40 Aligned_cols=16 Identities=31% Similarity=0.673 Sum_probs=12.1
Q ss_pred cCCceeCCCCCCceEe
Q psy1749 14 SELIKCCPMCSVPIEK 29 (87)
Q Consensus 14 ~~~~k~CP~C~~~Iek 29 (87)
..+...||+|+.+++-
T Consensus 46 e~G~t~CP~Cg~~~e~ 61 (115)
T COG1885 46 EVGSTSCPKCGEPFES 61 (115)
T ss_pred ecccccCCCCCCccce
Confidence 4456789999988874
No 183
>PRK12496 hypothetical protein; Provisional
Probab=27.29 E-value=30 Score=24.26 Aligned_cols=12 Identities=25% Similarity=0.553 Sum_probs=8.1
Q ss_pred eeCCCCCCceEe
Q psy1749 18 KCCPMCSVPIEK 29 (87)
Q Consensus 18 k~CP~C~~~Iek 29 (87)
++|+.|+..+..
T Consensus 128 ~~C~gC~~~~~~ 139 (164)
T PRK12496 128 KVCKGCKKKYPE 139 (164)
T ss_pred EECCCCCccccC
Confidence 348888877653
No 184
>PHA02325 hypothetical protein
Probab=27.27 E-value=30 Score=21.61 Aligned_cols=12 Identities=33% Similarity=0.681 Sum_probs=7.9
Q ss_pred CceeCCCCCCce
Q psy1749 16 LIKCCPMCSVPI 27 (87)
Q Consensus 16 ~~k~CP~C~~~I 27 (87)
.+|.||+|+..-
T Consensus 2 ~~k~CPkC~A~W 13 (72)
T PHA02325 2 DTKICPKCGARW 13 (72)
T ss_pred CccccCccCCEe
Confidence 357788877653
No 185
>COG4640 Predicted membrane protein [Function unknown]
Probab=26.91 E-value=28 Score=28.66 Aligned_cols=7 Identities=57% Similarity=1.521 Sum_probs=5.0
Q ss_pred eeCCCCC
Q psy1749 18 KCCPMCS 24 (87)
Q Consensus 18 k~CP~C~ 24 (87)
+.||+|+
T Consensus 2 ~fC~kcG 8 (465)
T COG4640 2 KFCPKCG 8 (465)
T ss_pred Ccccccc
Confidence 5677777
No 186
>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=26.75 E-value=66 Score=17.20 Aligned_cols=26 Identities=27% Similarity=0.612 Sum_probs=14.4
Q ss_pred eeCCCCCCceEeCCCcCeeecccccee
Q psy1749 18 KCCPMCSVPIEKDEGCAQMLCKRCKHV 44 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCnhm~C~~C~~~ 44 (87)
.+|+.|+...... .=....|..||+.
T Consensus 9 ~~C~~C~~~~~~~-~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYS-DDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEc-cCCEEEhhhCceE
Confidence 4588888874433 1124455446653
No 187
>KOG2932|consensus
Probab=26.53 E-value=35 Score=27.38 Aligned_cols=38 Identities=24% Similarity=0.676 Sum_probs=25.6
Q ss_pred cCCceeCCCCCCceEeCCC---cCeeeccccce----eeeecccc
Q psy1749 14 SELIKCCPMCSVPIEKDEG---CAQMLCKRCKH----VFCWYCLA 51 (87)
Q Consensus 14 ~~~~k~CP~C~~~Iek~~G---Cnhm~C~~C~~----~FC~~C~~ 51 (87)
...+..|-+|..+|-..+- |.|+.|..|-. ..|+.|-.
T Consensus 87 ~p~VHfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d 131 (389)
T KOG2932|consen 87 GPRVHFCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDD 131 (389)
T ss_pred CcceEeecccCCcceeeecccccchhhhhhhhhcCccccCcCccc
Confidence 3456789999999987754 77777776621 25555543
No 188
>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=26.19 E-value=47 Score=17.67 Aligned_cols=14 Identities=29% Similarity=0.767 Sum_probs=9.4
Q ss_pred ceeCCCCCCceEeC
Q psy1749 17 IKCCPMCSVPIEKD 30 (87)
Q Consensus 17 ~k~CP~C~~~Iek~ 30 (87)
.-.||+|+..|.-+
T Consensus 4 ~~~C~nC~R~v~a~ 17 (33)
T PF08209_consen 4 YVECPNCGRPVAAS 17 (33)
T ss_dssp EEE-TTTSSEEEGG
T ss_pred eEECCCCcCCcchh
Confidence 45788888888654
No 189
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=25.87 E-value=34 Score=27.98 Aligned_cols=27 Identities=26% Similarity=0.644 Sum_probs=20.2
Q ss_pred eCCCCCCceEeCCCcCeeeccccceeee
Q psy1749 19 CCPMCSVPIEKDEGCAQMLCKRCKHVFC 46 (87)
Q Consensus 19 ~CP~C~~~Iek~~GCnhm~C~~C~~~FC 46 (87)
.||.|+...+-. |-+-..|.+||..+=
T Consensus 352 ~Cp~Cg~~m~S~-G~~g~rC~kCg~~~~ 378 (421)
T COG1571 352 VCPRCGGRMKSA-GRNGFRCKKCGTRAR 378 (421)
T ss_pred CCCccCCchhhc-CCCCcccccccccCC
Confidence 699999987644 444888988887653
No 190
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=25.81 E-value=43 Score=22.21 Aligned_cols=13 Identities=38% Similarity=0.887 Sum_probs=9.6
Q ss_pred eeCCCCCCceEeC
Q psy1749 18 KCCPMCSVPIEKD 30 (87)
Q Consensus 18 k~CP~C~~~Iek~ 30 (87)
-.||.|+.-+-++
T Consensus 50 ggCp~CrvG~le~ 62 (98)
T PF10164_consen 50 GGCPACRVGVLED 62 (98)
T ss_pred cCCCCCceeeecc
Confidence 3599999877654
No 191
>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=25.71 E-value=23 Score=24.59 Aligned_cols=26 Identities=27% Similarity=0.557 Sum_probs=12.1
Q ss_pred eeCCCCCCceEeCCCcC-eeeccccce
Q psy1749 18 KCCPMCSVPIEKDEGCA-QMLCKRCKH 43 (87)
Q Consensus 18 k~CP~C~~~Iek~~GCn-hm~C~~C~~ 43 (87)
=.||+|+..+.-.+.=+ .-+|+.||.
T Consensus 110 Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~ 136 (158)
T TIGR00373 110 FICPNMCVRFTFNEAMELNFTCPRCGA 136 (158)
T ss_pred EECCCCCcEeeHHHHHHcCCcCCCCCC
Confidence 34777765554432222 244444443
No 192
>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=24.78 E-value=47 Score=27.51 Aligned_cols=13 Identities=23% Similarity=0.495 Sum_probs=10.0
Q ss_pred eeCCCCCCceEeC
Q psy1749 18 KCCPMCSVPIEKD 30 (87)
Q Consensus 18 k~CP~C~~~Iek~ 30 (87)
-+||+|+...+..
T Consensus 201 vpCPhCg~~~~l~ 213 (557)
T PF05876_consen 201 VPCPHCGEEQVLE 213 (557)
T ss_pred ccCCCCCCCcccc
Confidence 4699999887765
No 193
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=24.75 E-value=58 Score=21.20 Aligned_cols=30 Identities=30% Similarity=0.724 Sum_probs=18.7
Q ss_pred CceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749 16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~F 45 (87)
..-.||.|+..-.+..+-.--.|..|+..|
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 64 (90)
T PRK03976 35 AKHVCPVCGRPKVKRVGTGIWECRKCGAKF 64 (90)
T ss_pred cCccCCCCCCCceEEEEEEEEEcCCCCCEE
Confidence 345799997776666554445555555544
No 194
>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=24.66 E-value=58 Score=21.25 Aligned_cols=31 Identities=23% Similarity=0.578 Sum_probs=18.3
Q ss_pred CCceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749 15 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~F 45 (87)
...-.||.|+..-.+..+-.--.|..|+..|
T Consensus 33 ~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 33 KAKYVCPFCGKKTVKRGSTGIWTCRKCGAKF 63 (91)
T ss_pred hcCccCCCCCCCceEEEeeEEEEcCCCCCEE
Confidence 3445799997765555554444555555544
No 195
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=24.63 E-value=43 Score=22.72 Aligned_cols=16 Identities=31% Similarity=0.650 Sum_probs=9.8
Q ss_pred ceeCCCCCCc-eEeCCC
Q psy1749 17 IKCCPMCSVP-IEKDEG 32 (87)
Q Consensus 17 ~k~CP~C~~~-Iek~~G 32 (87)
..+||.|+.. ++..+|
T Consensus 107 ~~~CP~Cgs~~~~i~~G 123 (135)
T PRK03824 107 FLKCPKCGSRDFEIVKG 123 (135)
T ss_pred CcCCcCCCCCCcEEecC
Confidence 3558888765 554544
No 196
>KOG3084|consensus
Probab=24.44 E-value=47 Score=26.53 Aligned_cols=24 Identities=29% Similarity=0.742 Sum_probs=16.9
Q ss_pred CceeCCCCCCceEeCCCcCeeecc
Q psy1749 16 LIKCCPMCSVPIEKDEGCAQMLCK 39 (87)
Q Consensus 16 ~~k~CP~C~~~Iek~~GCnhm~C~ 39 (87)
..|.||.|+.+..-..+=....|.
T Consensus 149 kykFCp~CG~~tkp~e~g~k~~Cs 172 (345)
T KOG3084|consen 149 KYKFCPGCGSPTKPEEAGTKLQCS 172 (345)
T ss_pred HhccCcccCCCcccccCCccceee
Confidence 468999999998877653333333
No 197
>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=23.89 E-value=47 Score=22.54 Aligned_cols=12 Identities=33% Similarity=0.949 Sum_probs=10.5
Q ss_pred eCCCCCCceEeC
Q psy1749 19 CCPMCSVPIEKD 30 (87)
Q Consensus 19 ~CP~C~~~Iek~ 30 (87)
-||.|++++|-+
T Consensus 76 yCP~Cgt~levE 87 (112)
T PF08882_consen 76 YCPGCGTQLEVE 87 (112)
T ss_pred ECCCCcceeEEc
Confidence 499999999965
No 198
>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=23.74 E-value=56 Score=25.41 Aligned_cols=36 Identities=28% Similarity=0.768 Sum_probs=27.5
Q ss_pred ceeCCCCCCc-----eEe---CCCcCeeeccccceee------eeccccc
Q psy1749 17 IKCCPMCSVP-----IEK---DEGCAQMLCKRCKHVF------CWYCLAS 52 (87)
Q Consensus 17 ~k~CP~C~~~-----Iek---~~GCnhm~C~~C~~~F------C~~C~~~ 52 (87)
-..||-|+.. |.. .+|=-++.|.-|+++| |-.|+..
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence 3489999986 332 4678899999999887 6678865
No 199
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.13 E-value=51 Score=21.79 Aligned_cols=15 Identities=20% Similarity=0.552 Sum_probs=8.6
Q ss_pred eeCCCCCCc-eEeCCC
Q psy1749 18 KCCPMCSVP-IEKDEG 32 (87)
Q Consensus 18 k~CP~C~~~-Iek~~G 32 (87)
.+||+|+.. ++..+|
T Consensus 89 ~~CP~Cgs~~~~i~~G 104 (117)
T PRK00564 89 GVCEKCHSKNVIITQG 104 (117)
T ss_pred CcCcCCCCCceEEecC
Confidence 358888765 443444
No 200
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=22.87 E-value=85 Score=17.13 Aligned_cols=31 Identities=32% Similarity=0.708 Sum_probs=22.8
Q ss_pred eCCCCCCceEeCCCcCeeeccccc-eeeeecccccc
Q psy1749 19 CCPMCSVPIEKDEGCAQMLCKRCK-HVFCWYCLASL 53 (87)
Q Consensus 19 ~CP~C~~~Iek~~GCnhm~C~~C~-~~FC~~C~~~~ 53 (87)
.|-.|+.+|. | ....|..|. ...|-.|-..-
T Consensus 2 ~C~~C~~~i~---g-~r~~C~~C~d~dLC~~Cf~~~ 33 (46)
T cd02249 2 SCDGCLKPIV---G-VRYHCLVCEDFDLCSSCYAKG 33 (46)
T ss_pred CCcCCCCCCc---C-CEEECCCCCCCcCHHHHHCcC
Confidence 4778888654 4 688888886 78888887544
No 201
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 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 DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=22.86 E-value=79 Score=22.38 Aligned_cols=31 Identities=23% Similarity=0.494 Sum_probs=15.3
Q ss_pred CceeCCCCCCceEeCCC---------cCeeeccccceeee
Q psy1749 16 LIKCCPMCSVPIEKDEG---------CAQMLCKRCKHVFC 46 (87)
Q Consensus 16 ~~k~CP~C~~~Iek~~G---------Cnhm~C~~C~~~FC 46 (87)
-.-.||+|+...+-.+- -+-+.|.+|+..+.
T Consensus 17 l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~~~~ 56 (188)
T PF08996_consen 17 LKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCSTPLS 56 (188)
T ss_dssp EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--B--
T ss_pred eEeECCCCCCCccccccccCCccccccCcCcCCCCCCcCC
Confidence 34679999998876543 23577887777554
No 202
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=22.86 E-value=36 Score=24.99 Aligned_cols=39 Identities=23% Similarity=0.483 Sum_probs=26.8
Q ss_pred ccCCceeCCCCCCceEeCCCcCeeecccc-----------ceeeeecccc
Q psy1749 13 DSELIKCCPMCSVPIEKDEGCAQMLCKRC-----------KHVFCWYCLA 51 (87)
Q Consensus 13 ~~~~~k~CP~C~~~Iek~~GCnhm~C~~C-----------~~~FC~~C~~ 51 (87)
+...-+.|++|+..=-+..-|.|..|.+| ....|+.||+
T Consensus 56 ~~~~~~~C~nCg~~GH~~~DCP~~iC~~C~~~~H~s~~C~~~~~C~~Cg~ 105 (190)
T COG5082 56 IREENPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPKPKKCYNCGE 105 (190)
T ss_pred ccccccccchhcccCcccccCChhHhhhcCCCCcccccCCcccccccccc
Confidence 34556788888887777777887777666 1246777774
No 203
>PF01639 v110: Viral family 110; InterPro: IPR004848 This entry represents a family of viral proteins of unknown function known as the 110 family []. They contain a central cysteine rich region with eight conserved cysteines. Some proteins in this entry contain two copies of the cysteine rich region eg P18560 from SWISSPROT.
Probab=22.73 E-value=38 Score=22.90 Aligned_cols=16 Identities=31% Similarity=0.773 Sum_probs=9.8
Q ss_pred CCcCeeeccccceeeeeccc
Q psy1749 31 EGCAQMLCKRCKHVFCWYCL 50 (87)
Q Consensus 31 ~GCnhm~C~~C~~~FC~~C~ 50 (87)
-.|.++. ...|||.|-
T Consensus 34 YWCTY~~----~CdFCWdCq 49 (110)
T PF01639_consen 34 YWCTYAK----HCDFCWDCQ 49 (110)
T ss_pred eeccccc----cCcchhhCc
Confidence 3455543 336999886
No 204
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=22.29 E-value=1.1e+02 Score=18.61 Aligned_cols=27 Identities=41% Similarity=0.962 Sum_probs=19.2
Q ss_pred ceeCCCCCCceEeCCCcCeeeccccce
Q psy1749 17 IKCCPMCSVPIEKDEGCAQMLCKRCKH 43 (87)
Q Consensus 17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~ 43 (87)
+--||-|+.+......=+-+.|..|+-
T Consensus 8 iLaCP~~kg~L~~~~~~~~L~c~~~~~ 34 (60)
T COG2835 8 ILACPVCKGPLVYDEEKQELICPRCKL 34 (60)
T ss_pred eeeccCcCCcceEeccCCEEEecccCc
Confidence 456899988887776666777775543
No 205
>PRK08402 replication factor A; Reviewed
Probab=22.10 E-value=78 Score=25.05 Aligned_cols=27 Identities=19% Similarity=0.571 Sum_probs=18.6
Q ss_pred CceeCCCCCCceEeCCCcCeeeccccc
Q psy1749 16 LIKCCPMCSVPIEKDEGCAQMLCKRCK 42 (87)
Q Consensus 16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~ 42 (87)
....||.|+..|....+=+.-.|..|+
T Consensus 211 ~y~aCp~CnKkv~~~~~~~~~~Ce~~~ 237 (355)
T PRK08402 211 VYDACPECRRKVDYDPATDTWICPEHG 237 (355)
T ss_pred eEecCCCCCeEEEEecCCCCEeCCCCC
Confidence 357899999999865544555566554
No 206
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=21.96 E-value=60 Score=19.68 Aligned_cols=15 Identities=40% Similarity=0.720 Sum_probs=11.3
Q ss_pred CCceeCCCCCCceEe
Q psy1749 15 ELIKCCPMCSVPIEK 29 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek 29 (87)
...+.||+|+...-+
T Consensus 3 ~~~rkC~~cg~YTLk 17 (59)
T COG2260 3 SLIRKCPKCGRYTLK 17 (59)
T ss_pred chhhcCcCCCceeec
Confidence 346789998888765
No 207
>PRK01343 zinc-binding protein; Provisional
Probab=21.84 E-value=41 Score=20.15 Aligned_cols=14 Identities=29% Similarity=0.717 Sum_probs=11.5
Q ss_pred CCceeCCCCCCceE
Q psy1749 15 ELIKCCPMCSVPIE 28 (87)
Q Consensus 15 ~~~k~CP~C~~~Ie 28 (87)
.-.++||.|+.++.
T Consensus 7 ~p~~~CP~C~k~~~ 20 (57)
T PRK01343 7 RPTRPCPECGKPST 20 (57)
T ss_pred CCCCcCCCCCCcCc
Confidence 35689999999876
No 208
>COG5595 Zn-ribbon-containing, possibly nucleic-acid-binding protein [General function prediction only]
Probab=21.83 E-value=40 Score=25.49 Aligned_cols=24 Identities=29% Similarity=0.811 Sum_probs=18.3
Q ss_pred ccCcccccCCceeCCCCCCceEeC
Q psy1749 7 MGGATFDSELIKCCPMCSVPIEKD 30 (87)
Q Consensus 7 ~~~~~~~~~~~k~CP~C~~~Iek~ 30 (87)
-+|.-+++++.+.||+|+.--...
T Consensus 208 VgGnSlAqek~r~CPsC~k~Wqlk 231 (256)
T COG5595 208 VGGNSLAQEKYRCCPSCGKDWQLK 231 (256)
T ss_pred ecCchhhhhccCCCCcccccceec
Confidence 456668888999999998765554
No 209
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=21.58 E-value=79 Score=20.57 Aligned_cols=31 Identities=26% Similarity=0.548 Sum_probs=17.8
Q ss_pred CCceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749 15 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~F 45 (87)
...-.||.|+..--+..+-.--.|..|+..|
T Consensus 34 ~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 34 HAKYFCPFCGKHAVKRQAVGIWRCKGCKKTV 64 (90)
T ss_pred hCCccCCCCCCCceeeeeeEEEEcCCCCCEE
Confidence 3445799997665555444444455455443
No 210
>KOG2893|consensus
Probab=21.57 E-value=50 Score=25.74 Aligned_cols=34 Identities=29% Similarity=0.770 Sum_probs=24.2
Q ss_pred ceeeeecccccccCCcc------CCCCCCCCCCCCCCCCC
Q psy1749 42 KHVFCWYCLASLDDDFL------LRHYDKGPCKNKLGHSR 75 (87)
Q Consensus 42 ~~~FC~~C~~~~~~~~~------~~Hf~~~~C~~~~~~~~ 75 (87)
..-|||.|.++|+.+.+ ..||+---|-.+||...
T Consensus 9 ~kpwcwycnrefddekiliqhqkakhfkchichkkl~sgp 48 (341)
T KOG2893|consen 9 DKPWCWYCNREFDDEKILIQHQKAKHFKCHICHKKLFSGP 48 (341)
T ss_pred CCceeeecccccchhhhhhhhhhhccceeeeehhhhccCC
Confidence 45799999999998532 46776556667776543
No 211
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=21.53 E-value=65 Score=17.19 Aligned_cols=13 Identities=31% Similarity=0.772 Sum_probs=8.3
Q ss_pred eeCCCCCCceEeC
Q psy1749 18 KCCPMCSVPIEKD 30 (87)
Q Consensus 18 k~CP~C~~~Iek~ 30 (87)
..||.|+..-.+.
T Consensus 3 ~~Cp~Cg~~~~~~ 15 (47)
T PF14690_consen 3 PRCPHCGSPSVHR 15 (47)
T ss_pred ccCCCcCCCceEC
Confidence 3588888665443
No 212
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=21.44 E-value=64 Score=19.44 Aligned_cols=24 Identities=25% Similarity=0.642 Sum_probs=16.1
Q ss_pred cccccCcccccCCceeCCCCCCceEeC
Q psy1749 4 WFQMGGATFDSELIKCCPMCSVPIEKD 30 (87)
Q Consensus 4 w~~~~~~~~~~~~~k~CP~C~~~Iek~ 30 (87)
|++++-. ......||-|++...+.
T Consensus 29 WmR~nFs---~~~~p~CPlC~s~M~~~ 52 (59)
T PF14169_consen 29 WMRDNFS---FEEEPVCPLCKSPMVSG 52 (59)
T ss_pred ccccccc---cCCCccCCCcCCccccc
Confidence 5555543 45667899999887654
No 213
>KOG2907|consensus
Probab=20.90 E-value=37 Score=23.20 Aligned_cols=27 Identities=30% Similarity=0.722 Sum_probs=16.5
Q ss_pred ceeCCCCCCceEeCCCcCeeeccccce
Q psy1749 17 IKCCPMCSVPIEKDEGCAQMLCKRCKH 43 (87)
Q Consensus 17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~ 43 (87)
--.|+-|+.+++...-=.-..|.+|+.
T Consensus 7 ~~FC~~CG~ll~~~~~~~~~~C~~Ck~ 33 (116)
T KOG2907|consen 7 LDFCSDCGSLLEEPSAQSTVLCIRCKI 33 (116)
T ss_pred cchhhhhhhhcccccccCceEeccccc
Confidence 356888888888765544444444443
No 214
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=20.75 E-value=64 Score=20.23 Aligned_cols=17 Identities=18% Similarity=0.563 Sum_probs=14.0
Q ss_pred Ceeeccccceeeeeccc
Q psy1749 34 AQMLCKRCKHVFCWYCL 50 (87)
Q Consensus 34 nhm~C~~C~~~FC~~C~ 50 (87)
.|+.|..||..++...-
T Consensus 72 ~H~~C~~Cg~i~~~~~~ 88 (116)
T cd07153 72 HHLICTKCGKVIDFEDC 88 (116)
T ss_pred CceEeCCCCCEEEecCc
Confidence 47999999999997653
No 215
>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=20.70 E-value=94 Score=21.61 Aligned_cols=16 Identities=19% Similarity=0.318 Sum_probs=7.5
Q ss_pred CCceeCCCCCCceEeC
Q psy1749 15 ELIKCCPMCSVPIEKD 30 (87)
Q Consensus 15 ~~~k~CP~C~~~Iek~ 30 (87)
.++-.|-+|+..+...
T Consensus 110 ~G~l~C~~Cg~~~~~~ 125 (146)
T PF07295_consen 110 PGTLVCENCGHEVELT 125 (146)
T ss_pred CceEecccCCCEEEec
Confidence 3444455554444443
No 216
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=20.64 E-value=61 Score=18.39 Aligned_cols=12 Identities=33% Similarity=0.711 Sum_probs=9.1
Q ss_pred CCceeCCCCCCc
Q psy1749 15 ELIKCCPMCSVP 26 (87)
Q Consensus 15 ~~~k~CP~C~~~ 26 (87)
.....||+|+..
T Consensus 44 ~~i~~Cp~CgRi 55 (56)
T PF02591_consen 44 DEIVFCPNCGRI 55 (56)
T ss_pred CCeEECcCCCcc
Confidence 467889999864
No 217
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=20.64 E-value=90 Score=20.89 Aligned_cols=27 Identities=22% Similarity=0.626 Sum_probs=18.4
Q ss_pred eCCCCCCce--------EeCCCcCeeeccccceee
Q psy1749 19 CCPMCSVPI--------EKDEGCAQMLCKRCKHVF 45 (87)
Q Consensus 19 ~CP~C~~~I--------ek~~GCnhm~C~~C~~~F 45 (87)
.|++|.+++ -..++---++|..||...
T Consensus 58 ~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~ 92 (105)
T COG2023 58 ICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIR 92 (105)
T ss_pred hccccCcccccCcceEEEEcCCeEEEEecCCCcEE
Confidence 499999863 223445678898788754
No 218
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=20.44 E-value=60 Score=18.92 Aligned_cols=12 Identities=50% Similarity=0.988 Sum_probs=9.7
Q ss_pred eCCCCCCceEeC
Q psy1749 19 CCPMCSVPIEKD 30 (87)
Q Consensus 19 ~CP~C~~~Iek~ 30 (87)
.||.|+..|+..
T Consensus 2 ~CPyCge~~~~~ 13 (52)
T PF14255_consen 2 QCPYCGEPIEIL 13 (52)
T ss_pred CCCCCCCeeEEE
Confidence 589999888764
No 219
>KOG0824|consensus
Probab=20.44 E-value=32 Score=27.18 Aligned_cols=16 Identities=31% Similarity=0.831 Sum_probs=12.4
Q ss_pred cccceeeeeccccccc
Q psy1749 39 KRCKHVFCWYCLASLD 54 (87)
Q Consensus 39 ~~C~~~FC~~C~~~~~ 54 (87)
..|++.|||+|.+.-.
T Consensus 23 l~C~HkFCyiCiKGsy 38 (324)
T KOG0824|consen 23 LYCFHKFCYICIKGSY 38 (324)
T ss_pred ccccchhhhhhhcchh
Confidence 3699999999986544
No 220
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=20.14 E-value=60 Score=19.60 Aligned_cols=20 Identities=30% Similarity=0.977 Sum_probs=14.2
Q ss_pred CCcCe---eeccccceeeeeccc
Q psy1749 31 EGCAQ---MLCKRCKHVFCWYCL 50 (87)
Q Consensus 31 ~GCnh---m~C~~C~~~FC~~C~ 50 (87)
.||+. |.|..|...+|+...
T Consensus 33 ~gC~~~s~I~C~~Ckk~~Cf~Hf 55 (63)
T PF04236_consen 33 TGCNNTSFIRCAYCKKSLCFNHF 55 (63)
T ss_pred CCCCCcCEEEccccCCcccccce
Confidence 45665 668888888887544
No 221
>KOG3799|consensus
Probab=20.10 E-value=29 Score=24.74 Aligned_cols=25 Identities=28% Similarity=0.790 Sum_probs=20.9
Q ss_pred CCCcCeeeccccceeeeecccccccC
Q psy1749 30 DEGCAQMLCKRCKHVFCWYCLASLDD 55 (87)
Q Consensus 30 ~~GCnhm~C~~C~~~FC~~C~~~~~~ 55 (87)
.+||.|. |..|...||-.||.....
T Consensus 77 ADG~GH~-C~YCq~r~CARCGGrv~l 101 (169)
T KOG3799|consen 77 ADGCGHN-CSYCQTRFCARCGGRVSL 101 (169)
T ss_pred ccccCcc-cchhhhhHHHhcCCeeee
Confidence 6899995 666999999999977665
Done!