Query psy3498
Match_columns 81
No_of_seqs 100 out of 191
Neff 5.0
Searched_HMMs 46136
Date Fri Aug 16 18:14:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3498.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3498hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05129 Elf1: Transcription e 100.0 1.2E-43 2.6E-48 225.9 5.1 79 2-81 1-80 (81)
2 KOG3214|consensus 100.0 1.4E-42 3E-47 230.2 2.2 80 1-80 1-80 (109)
3 COG4888 Uncharacterized Zn rib 100.0 6.8E-39 1.5E-43 212.1 6.5 79 1-80 1-79 (104)
4 PRK14892 putative transcriptio 100.0 9.9E-35 2.1E-39 191.3 5.3 75 1-80 1-75 (99)
5 TIGR03655 anti_R_Lar restricti 97.4 0.00026 5.7E-09 41.2 3.3 46 25-72 3-50 (53)
6 PF14354 Lar_restr_allev: Rest 97.0 0.0013 2.9E-08 38.4 4.0 32 23-55 3-37 (61)
7 TIGR01206 lysW lysine biosynth 97.0 0.0011 2.4E-08 39.5 3.2 33 23-59 2-34 (54)
8 PRK09710 lar restriction allev 96.5 0.0046 1E-07 38.2 3.8 50 20-73 3-52 (64)
9 PF08271 TF_Zn_Ribbon: TFIIB z 96.4 0.0036 7.7E-08 34.9 2.6 31 24-59 1-31 (43)
10 PF01096 TFIIS_C: Transcriptio 96.4 0.0075 1.6E-07 33.3 3.7 35 24-58 1-39 (39)
11 TIGR02098 MJ0042_CXXC MJ0042 f 96.3 0.0016 3.6E-08 35.0 1.0 32 23-58 2-36 (38)
12 TIGR00244 transcriptional regu 96.1 0.0052 1.1E-07 43.3 2.9 36 25-60 2-41 (147)
13 PRK00398 rpoP DNA-directed RNA 96.0 0.017 3.6E-07 32.5 4.2 34 22-61 2-35 (46)
14 COG1327 Predicted transcriptio 96.0 0.0039 8.4E-08 44.3 1.9 34 25-59 2-40 (156)
15 PF13719 zinc_ribbon_5: zinc-r 95.9 0.009 1.9E-07 32.6 2.7 32 23-58 2-36 (37)
16 smart00440 ZnF_C2C2 C2C2 Zinc 95.4 0.039 8.4E-07 30.6 4.0 34 24-57 1-38 (40)
17 PF13717 zinc_ribbon_4: zinc-r 95.2 0.0093 2E-07 32.5 1.0 34 23-57 2-35 (36)
18 TIGR00280 L37a ribosomal prote 95.1 0.031 6.7E-07 36.6 3.5 33 22-60 34-66 (91)
19 PRK03976 rpl37ae 50S ribosomal 95.1 0.031 6.8E-07 36.5 3.4 40 22-67 35-74 (90)
20 PF14255 Cys_rich_CPXG: Cystei 95.1 0.028 6E-07 33.2 2.9 46 25-70 2-49 (52)
21 PTZ00255 60S ribosomal protein 95.0 0.035 7.7E-07 36.2 3.4 33 22-60 35-67 (90)
22 PRK00464 nrdR transcriptional 94.7 0.049 1.1E-06 38.3 3.8 35 25-59 2-40 (154)
23 PF01780 Ribosomal_L37ae: Ribo 94.7 0.03 6.4E-07 36.6 2.5 41 22-68 34-74 (90)
24 PF14353 CpXC: CpXC protein 94.3 0.049 1.1E-06 36.0 3.0 40 24-63 2-54 (128)
25 PF09855 DUF2082: Nucleic-acid 94.3 0.087 1.9E-06 32.3 3.8 48 24-71 1-62 (64)
26 PF08792 A2L_zn_ribbon: A2L zi 93.8 0.072 1.6E-06 28.7 2.4 30 24-59 4-33 (33)
27 PHA00626 hypothetical protein 93.7 0.073 1.6E-06 32.4 2.6 34 25-59 2-35 (59)
28 smart00778 Prim_Zn_Ribbon Zinc 93.6 0.054 1.2E-06 30.0 1.7 29 25-55 5-33 (37)
29 PF12760 Zn_Tnp_IS1595: Transp 93.3 0.07 1.5E-06 30.0 1.9 31 20-55 15-45 (46)
30 PRK09678 DNA-binding transcrip 93.3 0.11 2.3E-06 32.6 2.9 43 24-67 2-52 (72)
31 PF02150 RNA_POL_M_15KD: RNA p 92.8 0.24 5.1E-06 26.8 3.5 28 26-58 4-31 (35)
32 COG1997 RPL43A Ribosomal prote 92.6 0.11 2.5E-06 33.9 2.4 31 22-58 34-64 (89)
33 PF13240 zinc_ribbon_2: zinc-r 92.1 0.053 1.1E-06 26.9 0.4 21 26-56 2-22 (23)
34 smart00834 CxxC_CXXC_SSSS Puta 91.8 0.11 2.4E-06 27.7 1.4 31 23-56 5-35 (41)
35 PRK12286 rpmF 50S ribosomal pr 91.7 0.21 4.5E-06 29.8 2.7 26 19-55 23-48 (57)
36 PRK00432 30S ribosomal protein 91.5 0.12 2.7E-06 30.0 1.5 26 25-57 22-47 (50)
37 PF04606 Ogr_Delta: Ogr/Delta- 91.5 0.31 6.7E-06 27.6 3.1 36 25-60 1-40 (47)
38 PF13453 zf-TFIIB: Transcripti 91.2 0.38 8.3E-06 26.3 3.2 27 25-55 1-27 (41)
39 PF06044 DRP: Dam-replacing fa 90.8 0.24 5.2E-06 37.7 2.8 36 23-60 31-66 (254)
40 PF09723 Zn-ribbon_8: Zinc rib 90.6 0.14 3E-06 28.4 1.1 30 23-55 5-34 (42)
41 PF04216 FdhE: Protein involve 90.6 0.29 6.3E-06 36.6 3.1 35 24-58 173-208 (290)
42 PRK14890 putative Zn-ribbon RN 90.3 0.16 3.4E-06 30.9 1.2 34 21-55 23-56 (59)
43 TIGR03829 YokU_near_AblA uncha 90.1 0.36 7.8E-06 31.4 2.8 35 25-59 1-47 (89)
44 COG3677 Transposase and inacti 89.6 0.32 6.9E-06 33.1 2.4 36 24-60 31-66 (129)
45 PF04216 FdhE: Protein involve 89.5 0.51 1.1E-05 35.2 3.7 49 23-71 211-262 (290)
46 PRK03988 translation initiatio 89.3 0.59 1.3E-05 32.3 3.6 34 22-58 101-134 (138)
47 TIGR00311 aIF-2beta translatio 89.3 0.54 1.2E-05 32.3 3.4 35 21-58 95-129 (133)
48 COG3478 Predicted nucleic-acid 89.2 0.52 1.1E-05 29.4 3.0 43 21-63 2-58 (68)
49 TIGR01384 TFS_arch transcripti 89.1 1.1 2.4E-05 28.5 4.6 40 19-58 57-101 (104)
50 PRK13130 H/ACA RNA-protein com 88.8 0.36 7.8E-06 28.9 2.0 40 23-74 5-44 (56)
51 PF14205 Cys_rich_KTR: Cystein 88.8 0.48 1E-05 28.5 2.5 36 24-59 5-40 (55)
52 COG2051 RPS27A Ribosomal prote 88.7 0.7 1.5E-05 28.8 3.3 29 25-58 21-49 (67)
53 PF09986 DUF2225: Uncharacteri 88.5 0.79 1.7E-05 33.2 4.0 46 21-66 3-68 (214)
54 PF14803 Nudix_N_2: Nudix N-te 88.2 0.67 1.4E-05 25.1 2.6 28 26-55 3-30 (34)
55 smart00659 RPOLCX RNA polymera 87.9 0.57 1.2E-05 26.5 2.3 28 23-57 2-29 (44)
56 smart00531 TFIIE Transcription 87.8 0.18 3.8E-06 34.5 0.2 42 21-62 97-138 (147)
57 smart00661 RPOL9 RNA polymeras 87.5 0.61 1.3E-05 26.0 2.3 29 26-58 3-31 (52)
58 PF07754 DUF1610: Domain of un 87.4 0.37 7.9E-06 24.5 1.2 11 20-30 13-23 (24)
59 PF01873 eIF-5_eIF-2B: Domain 87.4 0.76 1.6E-05 31.2 3.1 32 22-56 92-123 (125)
60 TIGR02605 CxxC_CxxC_SSSS putat 87.0 0.35 7.6E-06 27.2 1.1 30 23-55 5-34 (52)
61 PF10571 UPF0547: Uncharacteri 86.9 0.29 6.2E-06 25.0 0.7 24 25-58 2-25 (26)
62 PF08273 Prim_Zn_Ribbon: Zinc- 86.7 0.46 9.9E-06 26.6 1.4 29 25-54 5-33 (40)
63 PF07282 OrfB_Zn_ribbon: Putat 86.6 0.36 7.9E-06 28.5 1.1 35 22-62 27-61 (69)
64 PF05605 zf-Di19: Drought indu 86.5 0.29 6.3E-06 28.1 0.6 34 23-57 2-41 (54)
65 TIGR03831 YgiT_finger YgiT-typ 86.5 1.2 2.6E-05 23.8 3.1 12 47-58 32-43 (46)
66 smart00653 eIF2B_5 domain pres 86.3 1.2 2.7E-05 29.6 3.6 32 22-56 79-110 (110)
67 COG2888 Predicted Zn-ribbon RN 86.1 0.32 7E-06 29.8 0.7 34 21-55 25-58 (61)
68 PF05180 zf-DNL: DNL zinc fing 86.1 0.95 2.1E-05 28.0 2.8 35 23-59 4-41 (66)
69 TIGR01385 TFSII transcription 86.0 1.4 3.1E-05 33.8 4.3 40 20-59 255-298 (299)
70 COG1326 Uncharacterized archae 85.7 0.38 8.3E-06 35.5 1.0 36 23-58 6-41 (201)
71 PF13248 zf-ribbon_3: zinc-rib 85.6 0.37 7.9E-06 24.2 0.6 22 25-56 4-25 (26)
72 PF09526 DUF2387: Probable met 85.5 2.1 4.6E-05 26.5 4.2 36 25-62 10-45 (71)
73 TIGR02443 conserved hypothetic 85.4 1.5 3.2E-05 26.7 3.3 33 25-59 11-43 (59)
74 PF09862 DUF2089: Protein of u 85.2 1 2.2E-05 30.4 2.9 23 26-58 1-23 (113)
75 COG1594 RPB9 DNA-directed RNA 84.8 1 2.2E-05 30.0 2.6 29 26-58 5-33 (113)
76 PRK12336 translation initiatio 84.8 1.1 2.4E-05 32.3 3.1 35 21-58 96-130 (201)
77 PRK00423 tfb transcription ini 84.5 0.83 1.8E-05 34.6 2.4 31 23-58 11-41 (310)
78 TIGR01031 rpmF_bact ribosomal 83.4 1.8 3.8E-05 25.6 3.0 26 19-55 22-47 (55)
79 KOG0478|consensus 83.4 0.54 1.2E-05 40.6 1.1 36 22-59 263-298 (804)
80 COG1405 SUA7 Transcription ini 82.8 0.82 1.8E-05 34.9 1.8 40 25-75 3-42 (285)
81 PRK03564 formate dehydrogenase 82.7 1.2 2.6E-05 34.5 2.7 37 21-57 185-222 (309)
82 PHA02540 61 DNA primase; Provi 82.6 1.6 3.6E-05 34.1 3.4 41 22-64 26-77 (337)
83 PF13465 zf-H2C2_2: Zinc-finge 82.6 0.56 1.2E-05 23.3 0.5 11 21-31 12-22 (26)
84 PF03367 zf-ZPR1: ZPR1 zinc-fi 82.6 1.9 4E-05 30.2 3.4 34 25-58 3-41 (161)
85 PRK05978 hypothetical protein; 82.3 0.61 1.3E-05 32.7 0.9 31 24-59 34-64 (148)
86 PF05876 Terminase_GpA: Phage 82.3 1.3 2.9E-05 36.2 2.9 34 24-57 201-239 (557)
87 COG1645 Uncharacterized Zn-fin 81.8 1.3 2.7E-05 30.8 2.2 27 23-57 28-54 (131)
88 PF03811 Zn_Tnp_IS1: InsA N-te 81.8 2 4.4E-05 23.4 2.6 30 24-54 6-36 (36)
89 COG0675 Transposase and inacti 81.7 0.91 2E-05 32.4 1.6 34 19-63 305-338 (364)
90 TIGR01562 FdhE formate dehydro 81.1 0.98 2.1E-05 34.9 1.7 35 23-57 184-220 (305)
91 KOG0402|consensus 80.4 0.72 1.6E-05 30.2 0.6 30 22-57 35-64 (92)
92 PRK00415 rps27e 30S ribosomal 80.4 2.6 5.7E-05 25.5 3.1 28 25-57 13-40 (59)
93 PHA02998 RNA polymerase subuni 80.0 3.6 7.7E-05 30.3 4.2 37 22-58 142-182 (195)
94 PF03966 Trm112p: Trm112p-like 79.8 0.45 9.8E-06 28.5 -0.5 18 42-59 48-65 (68)
95 TIGR02159 PA_CoA_Oxy4 phenylac 79.1 0.53 1.2E-05 32.6 -0.3 36 23-58 105-141 (146)
96 PF04810 zf-Sec23_Sec24: Sec23 78.8 0.59 1.3E-05 25.6 -0.1 14 22-35 23-36 (40)
97 TIGR00340 zpr1_rel ZPR1-relate 78.7 2.5 5.4E-05 29.9 3.0 14 44-57 25-38 (163)
98 PRK03564 formate dehydrogenase 78.0 4 8.8E-05 31.7 4.2 55 23-77 226-287 (309)
99 PRK11827 hypothetical protein; 77.7 2.6 5.6E-05 25.5 2.5 34 20-59 5-38 (60)
100 PF13894 zf-C2H2_4: C2H2-type 77.4 1.1 2.4E-05 20.3 0.6 8 24-31 1-8 (24)
101 cd00730 rubredoxin Rubredoxin; 77.0 1.2 2.6E-05 25.9 0.8 18 17-34 28-45 (50)
102 TIGR00310 ZPR1_znf ZPR1 zinc f 76.9 3.9 8.5E-05 29.6 3.6 33 25-57 2-40 (192)
103 COG1779 C4-type Zn-finger prot 76.8 2.7 5.9E-05 31.0 2.8 38 20-58 11-54 (201)
104 KOG2906|consensus 76.7 5.4 0.00012 26.8 3.9 30 25-58 3-32 (105)
105 PF00301 Rubredoxin: Rubredoxi 76.5 1.2 2.6E-05 25.7 0.7 18 17-34 28-45 (47)
106 smart00709 Zpr1 Duplicated dom 76.4 4.1 9E-05 28.6 3.5 13 45-57 27-39 (160)
107 KOG2767|consensus 76.4 0.8 1.7E-05 36.7 -0.1 38 22-61 95-132 (400)
108 PRK00420 hypothetical protein; 76.4 2 4.3E-05 28.9 1.9 30 23-59 23-52 (112)
109 TIGR01562 FdhE formate dehydro 76.3 4.1 8.9E-05 31.5 3.8 36 23-58 224-263 (305)
110 COG1656 Uncharacterized conser 76.3 0.97 2.1E-05 32.4 0.3 31 24-57 98-140 (165)
111 PF10263 SprT-like: SprT-like 76.2 3.6 7.8E-05 27.3 3.1 33 22-58 122-154 (157)
112 PF05502 Dynactin_p62: Dynacti 76.1 3 6.5E-05 33.9 3.1 50 22-72 51-111 (483)
113 MTH00038 COX2 cytochrome c oxi 76.1 2.1 4.6E-05 31.4 2.1 50 30-80 177-228 (229)
114 PF08274 PhnA_Zn_Ribbon: PhnA 76.0 0.92 2E-05 24.0 0.1 25 25-56 4-28 (30)
115 PF05077 DUF678: Protein of un 74.8 2.4 5.3E-05 26.9 1.8 33 24-56 23-66 (74)
116 COG1998 RPS31 Ribosomal protei 74.7 1.9 4.1E-05 25.6 1.2 26 25-56 21-46 (51)
117 TIGR03830 CxxCG_CxxCG_HTH puta 74.4 4.1 9E-05 26.0 2.9 34 26-59 1-43 (127)
118 KOG1814|consensus 74.0 2.8 6.1E-05 34.2 2.4 52 22-79 367-418 (445)
119 PF15616 TerY-C: TerY-C metal 73.8 3.1 6.8E-05 28.7 2.3 35 25-59 79-117 (131)
120 smart00647 IBR In Between Ring 73.4 5.2 0.00011 22.4 2.9 34 22-59 17-52 (64)
121 PF01485 IBR: IBR domain; Int 72.4 1.8 4E-05 24.3 0.8 34 22-59 17-52 (64)
122 COG5415 Predicted integral mem 70.6 1.9 4.1E-05 32.6 0.7 22 19-41 211-233 (251)
123 COG2835 Uncharacterized conser 70.6 5.8 0.00013 24.2 2.7 40 19-64 4-45 (60)
124 cd00729 rubredoxin_SM Rubredox 69.6 6.1 0.00013 21.0 2.4 25 23-55 2-26 (34)
125 PF01807 zf-CHC2: CHC2 zinc fi 69.6 7.3 0.00016 24.7 3.2 32 23-57 33-64 (97)
126 MTH00129 COX2 cytochrome c oxi 69.5 3.8 8.2E-05 30.1 2.1 50 30-80 177-228 (230)
127 TIGR02996 rpt_mate_G_obs repea 69.4 2.1 4.5E-05 24.4 0.6 13 66-78 17-29 (42)
128 cd00350 rubredoxin_like Rubred 68.7 2.2 4.7E-05 22.4 0.5 13 22-34 16-28 (33)
129 PF09538 FYDLN_acid: Protein o 68.6 2.8 6.1E-05 27.9 1.1 36 18-60 4-39 (108)
130 KOG2907|consensus 68.4 3.6 7.8E-05 28.1 1.7 36 24-59 75-114 (116)
131 PF01927 Mut7-C: Mut7-C RNAse 68.4 6.4 0.00014 26.7 2.9 31 24-57 92-134 (147)
132 PLN00209 ribosomal protein S27 68.3 8.1 0.00018 25.1 3.2 37 17-58 27-66 (86)
133 MTH00008 COX2 cytochrome c oxi 68.3 4.7 0.0001 29.6 2.4 49 30-79 177-227 (228)
134 PRK00750 lysK lysyl-tRNA synth 67.2 12 0.00027 30.4 4.8 38 25-63 177-215 (510)
135 COG1198 PriA Primosomal protei 67.1 4.6 0.0001 34.7 2.4 29 22-56 443-471 (730)
136 PF14122 YokU: YokU-like prote 67.0 4.7 0.0001 26.3 1.9 35 25-59 1-47 (87)
137 PF10058 DUF2296: Predicted in 66.7 3.5 7.6E-05 24.2 1.2 14 19-32 40-53 (54)
138 MTH00185 COX2 cytochrome c oxi 66.6 4 8.8E-05 30.0 1.8 48 32-80 179-228 (230)
139 KOG2703|consensus 66.4 2.7 5.9E-05 34.3 0.9 13 20-32 65-77 (460)
140 PF10083 DUF2321: Uncharacteri 66.0 1.7 3.6E-05 31.1 -0.3 54 22-80 38-97 (158)
141 KOG2593|consensus 65.9 1.8 3.8E-05 35.3 -0.3 38 21-58 126-164 (436)
142 TIGR01433 CyoA cytochrome o ub 65.6 5.2 0.00011 29.3 2.2 48 30-78 176-225 (226)
143 PF01667 Ribosomal_S27e: Ribos 65.4 9.6 0.00021 22.7 2.9 30 25-59 9-38 (55)
144 KOG1296|consensus 65.3 5.9 0.00013 28.4 2.3 33 23-55 64-107 (161)
145 MTH00139 COX2 cytochrome c oxi 65.1 4.6 0.0001 29.4 1.8 47 30-77 177-225 (226)
146 MTH00117 COX2 cytochrome c oxi 64.9 6 0.00013 29.0 2.4 48 30-78 177-226 (227)
147 PF08996 zf-DNA_Pol: DNA Polym 64.4 1.5 3.2E-05 31.1 -0.9 38 21-58 16-56 (188)
148 MTH00154 COX2 cytochrome c oxi 64.1 5.9 0.00013 29.0 2.2 47 30-77 177-225 (227)
149 KOG1597|consensus 63.9 5.7 0.00012 31.1 2.2 42 25-75 2-43 (308)
150 MTH00051 COX2 cytochrome c oxi 63.7 6.2 0.00013 29.1 2.3 47 30-77 181-229 (234)
151 PF14206 Cys_rich_CPCC: Cystei 63.7 7.1 0.00015 24.7 2.2 28 24-56 2-29 (78)
152 COG1241 MCM2 Predicted ATPase 63.6 6.8 0.00015 33.5 2.8 46 22-69 128-176 (682)
153 smart00714 LITAF Possible memb 63.4 5.2 0.00011 23.7 1.5 18 21-38 1-18 (67)
154 PF13909 zf-H2C2_5: C2H2-type 63.0 3.5 7.6E-05 19.5 0.6 8 24-31 1-8 (24)
155 PRK12495 hypothetical protein; 62.9 4.8 0.0001 30.3 1.6 32 19-58 38-69 (226)
156 PF09332 Mcm10: Mcm10 replicat 62.4 4.1 8.9E-05 32.1 1.2 32 19-56 281-312 (344)
157 PTZ00083 40S ribosomal protein 62.3 16 0.00036 23.6 3.8 38 17-59 26-66 (85)
158 PF03604 DNA_RNApol_7kD: DNA d 61.5 4.2 9E-05 21.7 0.8 25 25-56 2-26 (32)
159 PF00096 zf-C2H2: Zinc finger, 61.4 3.5 7.5E-05 19.1 0.4 11 49-59 2-12 (23)
160 KOG1812|consensus 60.8 5.7 0.00012 31.3 1.7 29 23-58 306-334 (384)
161 COG1503 eRF1 Peptide chain rel 60.6 4.3 9.4E-05 32.8 1.0 43 22-69 326-368 (411)
162 PF13878 zf-C2H2_3: zinc-finge 60.1 3.6 7.9E-05 22.7 0.4 16 45-60 11-26 (41)
163 MTH00080 COX2 cytochrome c oxi 60.1 7.3 0.00016 28.8 2.1 48 30-78 180-229 (231)
164 COG3058 FdhE Uncharacterized p 60.0 4.9 0.00011 31.4 1.2 33 21-53 183-217 (308)
165 KOG2846|consensus 57.7 5.4 0.00012 31.5 1.1 14 21-34 240-253 (328)
166 TIGR00373 conserved hypothetic 57.2 4.9 0.00011 27.9 0.7 12 20-31 125-136 (158)
167 TIGR01432 QOXA cytochrome aa3 56.3 10 0.00022 27.3 2.3 48 30-78 167-216 (217)
168 PF11781 RRN7: RNA polymerase 56.3 12 0.00025 20.2 2.0 27 23-56 8-34 (36)
169 PF12322 T4_baseplate: T4 bact 56.2 15 0.00033 26.7 3.2 53 18-71 73-128 (205)
170 PRK12380 hydrogenase nickel in 56.2 11 0.00025 24.7 2.3 30 18-55 65-94 (113)
171 MTH00076 COX2 cytochrome c oxi 56.1 11 0.00024 27.6 2.5 50 30-80 177-228 (228)
172 PRK03824 hypA hydrogenase nick 56.0 5.5 0.00012 27.0 0.8 16 19-34 66-81 (135)
173 PF14768 RPA_interact_C: Repli 56.0 14 0.0003 23.0 2.6 32 26-65 2-33 (82)
174 TIGR01391 dnaG DNA primase, ca 56.0 11 0.00023 29.8 2.5 30 23-56 34-64 (415)
175 TIGR02866 CoxB cytochrome c ox 55.7 8.6 0.00019 27.3 1.8 46 30-76 154-201 (201)
176 PF01921 tRNA-synt_1f: tRNA sy 55.4 12 0.00026 29.7 2.7 39 25-63 176-215 (360)
177 MTH00023 COX2 cytochrome c oxi 55.3 10 0.00022 28.1 2.2 47 30-77 188-236 (240)
178 PHA02942 putative transposase; 55.3 6.8 0.00015 30.8 1.3 47 22-78 324-370 (383)
179 PF00628 PHD: PHD-finger; Int 55.1 13 0.00028 20.3 2.1 29 26-63 2-30 (51)
180 COG3809 Uncharacterized protei 54.9 14 0.0003 24.0 2.5 28 25-56 3-30 (88)
181 PRK06266 transcription initiat 54.1 6.2 0.00013 28.0 0.8 12 20-31 133-144 (178)
182 PF07191 zinc-ribbons_6: zinc- 54.1 11 0.00025 23.5 1.9 28 24-59 2-29 (70)
183 PF10813 DUF2733: Protein of u 53.8 3.8 8.2E-05 22.1 -0.2 26 49-74 4-29 (32)
184 PF03119 DNA_ligase_ZBD: NAD-d 53.7 3.8 8.2E-05 21.0 -0.2 7 25-31 1-7 (28)
185 PRK05667 dnaG DNA primase; Val 53.2 13 0.00029 30.8 2.7 30 23-56 36-66 (580)
186 PRK00241 nudC NADH pyrophospha 53.2 15 0.00033 27.3 2.8 26 26-57 102-127 (256)
187 MTH00168 COX2 cytochrome c oxi 52.8 9.5 0.00021 27.8 1.7 43 33-76 180-224 (225)
188 COG2260 Predicted Zn-ribbon RN 52.8 8.8 0.00019 23.4 1.3 26 49-74 19-44 (59)
189 KOG2462|consensus 52.7 6.7 0.00015 30.3 0.9 35 21-58 159-198 (279)
190 PF10122 Mu-like_Com: Mu-like 52.6 10 0.00022 22.4 1.5 42 22-67 3-45 (51)
191 PF08209 Sgf11: Sgf11 (transcr 52.5 7.2 0.00016 20.9 0.8 10 22-31 3-12 (33)
192 TIGR00595 priA primosomal prot 52.3 13 0.00028 30.1 2.5 30 23-58 222-251 (505)
193 PF13912 zf-C2H2_6: C2H2-type 51.7 5.6 0.00012 19.1 0.2 12 48-59 2-13 (27)
194 PF13451 zf-trcl: Probable zin 51.5 11 0.00025 21.9 1.6 16 47-62 4-19 (49)
195 MTH00027 COX2 cytochrome c oxi 51.4 12 0.00025 28.3 2.0 47 30-77 211-259 (262)
196 PTZ00047 cytochrome c oxidase 51.3 12 0.00026 26.8 1.9 46 33-79 113-160 (162)
197 PF10601 zf-LITAF-like: LITAF- 51.3 11 0.00024 22.6 1.5 13 20-32 4-16 (73)
198 smart00249 PHD PHD zinc finger 51.1 11 0.00024 19.3 1.3 26 26-60 2-27 (47)
199 PHA02611 51 baseplate hub asse 50.9 12 0.00027 28.4 2.1 25 18-42 77-101 (249)
200 PHA00616 hypothetical protein 50.7 5.3 0.00011 22.8 0.0 8 24-31 2-9 (44)
201 cd00674 LysRS_core_class_I cat 50.7 35 0.00075 26.8 4.6 37 25-62 171-207 (353)
202 PRK14811 formamidopyrimidine-D 50.6 12 0.00026 27.9 2.0 28 25-56 237-264 (269)
203 PRK14810 formamidopyrimidine-D 50.5 13 0.00029 27.7 2.2 26 25-54 246-271 (272)
204 PF09297 zf-NADH-PPase: NADH p 50.5 9.8 0.00021 19.5 1.1 26 26-57 6-31 (32)
205 KOG2691|consensus 50.2 15 0.00033 24.9 2.2 47 26-74 7-58 (113)
206 KOG3113|consensus 49.5 6.6 0.00014 30.5 0.4 53 21-73 109-177 (293)
207 PF04690 YABBY: YABBY protein; 49.3 12 0.00025 26.9 1.6 42 23-64 12-53 (170)
208 TIGR02300 FYDLN_acid conserved 49.2 8.6 0.00019 26.7 0.9 35 18-59 4-38 (129)
209 MTH00098 COX2 cytochrome c oxi 48.6 13 0.00028 27.3 1.8 47 30-77 177-225 (227)
210 smart00731 SprT SprT homologue 48.5 34 0.00073 23.0 3.7 33 23-58 112-144 (146)
211 COG2023 RPR2 RNase P subunit R 48.4 28 0.00061 23.3 3.2 39 22-62 55-97 (105)
212 smart00400 ZnF_CHCC zinc finge 48.0 21 0.00045 20.2 2.3 30 25-57 4-33 (55)
213 TIGR00100 hypA hydrogenase nic 46.5 8 0.00017 25.5 0.4 30 18-55 65-94 (115)
214 PRK01103 formamidopyrimidine/5 45.9 17 0.00038 27.0 2.2 27 25-55 247-273 (274)
215 PF12773 DZR: Double zinc ribb 45.8 7.3 0.00016 21.4 0.1 24 26-56 15-38 (50)
216 PF14690 zf-ISL3: zinc-finger 45.4 13 0.00029 20.0 1.1 11 23-33 2-12 (47)
217 PRK04011 peptide chain release 45.3 15 0.00032 29.2 1.8 50 23-79 328-377 (411)
218 COG5349 Uncharacterized protei 44.5 6.1 0.00013 27.3 -0.4 31 24-59 22-52 (126)
219 COG3877 Uncharacterized protei 44.4 21 0.00045 24.5 2.2 24 23-56 6-29 (122)
220 COG4049 Uncharacterized protei 44.3 9.2 0.0002 23.5 0.4 14 18-31 12-25 (65)
221 PRK13945 formamidopyrimidine-D 44.2 18 0.0004 27.0 2.1 26 25-54 256-281 (282)
222 PF10609 ParA: ParA/MinD ATPas 44.0 11 0.00023 24.0 0.7 10 22-31 64-73 (81)
223 PRK10445 endonuclease VIII; Pr 43.7 19 0.00042 26.7 2.1 26 25-54 237-262 (263)
224 PF04032 Rpr2: RNAse P Rpr2/Rp 43.4 52 0.0011 19.6 3.7 33 22-54 45-84 (85)
225 TIGR00577 fpg formamidopyrimid 43.3 19 0.00042 26.8 2.1 26 25-54 247-272 (272)
226 PF04135 Nop10p: Nucleolar RNA 43.2 20 0.00044 21.2 1.7 30 45-74 13-44 (53)
227 PF13824 zf-Mss51: Zinc-finger 43.1 13 0.00029 22.2 1.0 15 18-32 9-23 (55)
228 PHA00732 hypothetical protein 42.8 2.7 5.9E-05 26.3 -2.2 47 23-69 1-49 (79)
229 COG1655 Uncharacterized protei 42.8 11 0.00023 29.0 0.6 11 21-31 17-27 (267)
230 PF06827 zf-FPG_IleRS: Zinc fi 42.7 25 0.00054 17.6 1.9 26 25-54 3-28 (30)
231 TIGR00319 desulf_FeS4 desulfof 42.3 36 0.00079 17.5 2.5 25 22-51 6-30 (34)
232 KOG3022|consensus 42.1 13 0.00029 29.0 1.1 13 22-34 221-233 (300)
233 COG0333 RpmF Ribosomal protein 42.0 16 0.00036 21.9 1.3 27 18-55 22-48 (57)
234 COG3357 Predicted transcriptio 41.3 11 0.00023 25.1 0.4 30 47-76 58-88 (97)
235 PF13408 Zn_ribbon_recom: Reco 41.3 16 0.00035 20.1 1.1 15 45-59 3-17 (58)
236 PF09779 Ima1_N: Ima1 N-termin 40.5 18 0.00039 24.4 1.4 10 46-55 19-28 (131)
237 COG4306 Uncharacterized protei 40.4 6.5 0.00014 27.8 -0.8 48 21-68 37-89 (160)
238 PF14447 Prok-RING_4: Prokaryo 39.8 14 0.0003 22.1 0.7 15 18-32 34-48 (55)
239 TIGR00467 lysS_arch lysyl-tRNA 39.8 56 0.0012 26.9 4.4 36 25-62 170-205 (515)
240 PRK00762 hypA hydrogenase nick 39.7 19 0.00042 24.0 1.5 9 24-32 93-101 (124)
241 KOG2893|consensus 39.5 11 0.00024 29.3 0.3 31 26-56 13-43 (341)
242 PF09334 tRNA-synt_1g: tRNA sy 39.5 8.7 0.00019 30.1 -0.3 34 45-78 164-198 (391)
243 cd00974 DSRD Desulforedoxin (D 38.9 44 0.00096 17.2 2.5 25 22-51 3-27 (34)
244 MTH00140 COX2 cytochrome c oxi 38.8 33 0.00071 25.0 2.7 48 30-78 177-226 (228)
245 PRK04023 DNA polymerase II lar 38.3 18 0.00038 32.8 1.3 13 66-78 679-691 (1121)
246 PRK15338 type III secretion sy 38.0 15 0.00032 29.5 0.7 18 62-79 195-212 (372)
247 TIGR00622 ssl1 transcription f 37.6 15 0.00033 24.8 0.7 10 49-58 57-66 (112)
248 KOG4080|consensus 37.5 16 0.00035 26.5 0.9 15 18-32 88-102 (176)
249 PF10276 zf-CHCC: Zinc-finger 37.4 55 0.0012 18.1 2.9 22 34-57 18-39 (40)
250 PF01396 zf-C4_Topoisom: Topoi 37.3 70 0.0015 17.2 3.4 28 25-56 3-33 (39)
251 PF13913 zf-C2HC_2: zinc-finge 37.2 16 0.00035 17.9 0.6 11 48-58 3-13 (25)
252 PF04161 Arv1: Arv1-like famil 37.0 24 0.00051 25.3 1.6 33 24-56 1-33 (208)
253 COG1571 Predicted DNA-binding 36.9 15 0.00032 29.9 0.7 28 25-59 352-379 (421)
254 COG1675 TFA1 Transcription ini 36.6 15 0.00033 26.4 0.6 10 22-31 131-140 (176)
255 PF06677 Auto_anti-p27: Sjogre 35.8 35 0.00076 19.0 1.9 24 24-54 18-41 (41)
256 PF09151 DUF1936: Domain of un 35.6 77 0.0017 17.2 3.4 27 25-52 3-29 (36)
257 PRK14873 primosome assembly pr 35.5 30 0.00066 29.3 2.3 29 22-56 391-419 (665)
258 TIGR00627 tfb4 transcription f 35.3 15 0.00032 28.1 0.4 29 19-57 251-279 (279)
259 PRK05580 primosome assembly pr 35.3 29 0.00063 29.1 2.1 29 23-57 390-418 (679)
260 PHA00733 hypothetical protein 35.3 5.9 0.00013 26.6 -1.6 40 21-60 71-112 (128)
261 PF02591 DUF164: Putative zinc 35.2 21 0.00046 20.3 1.0 11 21-31 44-54 (56)
262 COG3529 Predicted nucleic-acid 34.8 4.9 0.00011 24.9 -1.8 31 25-57 12-42 (66)
263 PF12480 DUF3699: Protein of u 34.8 84 0.0018 19.5 3.7 38 40-78 23-61 (77)
264 PF05280 FlhC: Flagellar trans 34.6 16 0.00035 26.0 0.5 12 20-31 151-162 (175)
265 PF05495 zf-CHY: CHY zinc fing 34.5 8.2 0.00018 23.4 -0.9 36 21-58 17-52 (71)
266 PF14952 zf-tcix: Putative tre 34.5 20 0.00044 20.6 0.8 30 19-58 7-38 (44)
267 KOG3277|consensus 34.4 40 0.00086 24.3 2.4 53 17-71 73-129 (165)
268 PF14311 DUF4379: Domain of un 34.2 24 0.00051 20.0 1.1 22 43-64 24-45 (55)
269 PRK14715 DNA polymerase II lar 33.9 26 0.00057 32.8 1.7 45 22-79 673-717 (1627)
270 PF12874 zf-met: Zinc-finger o 33.8 17 0.00036 17.0 0.3 12 49-60 2-13 (25)
271 PF05907 DUF866: Eukaryotic pr 33.5 26 0.00057 24.5 1.4 34 21-54 62-106 (161)
272 COG1773 Rubredoxin [Energy pro 33.2 27 0.00058 20.9 1.2 22 17-38 30-51 (55)
273 PF14446 Prok-RING_1: Prokaryo 33.2 32 0.0007 20.4 1.5 25 25-57 7-31 (54)
274 smart00782 PhnA_Zn_Ribbon PhnA 32.7 54 0.0012 18.7 2.4 31 25-55 9-44 (47)
275 PF06397 Desulfoferrod_N: Desu 32.7 68 0.0015 17.5 2.7 25 21-50 4-28 (36)
276 PF02891 zf-MIZ: MIZ/SP-RING z 32.1 20 0.00043 20.4 0.5 9 23-31 41-49 (50)
277 TIGR00320 dfx_rbo desulfoferro 32.0 47 0.001 22.4 2.4 30 21-57 5-34 (125)
278 PF01155 HypA: Hydrogenase exp 31.9 31 0.00067 22.5 1.5 12 20-31 67-78 (113)
279 PRK00564 hypA hydrogenase nick 31.7 22 0.00048 23.5 0.8 31 18-55 66-96 (117)
280 PF06170 DUF983: Protein of un 31.6 17 0.00037 23.1 0.2 12 48-59 9-20 (86)
281 COG1592 Rubrerythrin [Energy p 31.6 21 0.00047 25.4 0.7 10 22-31 148-157 (166)
282 PRK10525 cytochrome o ubiquino 31.3 39 0.00086 26.3 2.2 49 30-79 188-239 (315)
283 smart00355 ZnF_C2H2 zinc finge 31.3 23 0.00049 15.7 0.6 9 50-58 3-11 (26)
284 PF13901 DUF4206: Domain of un 31.2 24 0.00051 25.3 0.9 33 22-58 151-183 (202)
285 PHA02893 hypothetical protein; 31.1 40 0.00087 22.0 1.8 11 46-56 68-78 (88)
286 COG4311 SoxD Sarcosine oxidase 31.0 23 0.00051 23.5 0.8 9 23-31 3-11 (97)
287 KOG2324|consensus 31.0 21 0.00046 29.2 0.6 32 21-56 225-256 (457)
288 PF02701 zf-Dof: Dof domain, z 31.0 33 0.00071 21.1 1.3 37 21-57 3-40 (63)
289 PRK04351 hypothetical protein; 30.8 59 0.0013 22.5 2.8 34 22-59 111-144 (149)
290 smart00350 MCM minichromosome 30.8 22 0.00047 28.7 0.7 33 22-56 36-70 (509)
291 PF07295 DUF1451: Protein of u 30.7 58 0.0013 22.6 2.7 31 21-57 110-140 (146)
292 COG1107 Archaea-specific RecJ- 30.6 59 0.0013 28.2 3.2 40 19-58 47-91 (715)
293 cd03019 DsbA_DsbA DsbA family, 30.5 18 0.00039 23.7 0.2 11 22-32 23-33 (178)
294 KOG3507|consensus 30.2 33 0.00071 21.0 1.2 30 20-56 17-46 (62)
295 COG1439 Predicted nucleic acid 30.1 33 0.00073 24.8 1.5 7 26-32 156-162 (177)
296 TIGR00686 phnA alkylphosphonat 30.0 23 0.00049 23.9 0.6 15 20-34 16-30 (109)
297 PF14169 YdjO: Cold-inducible 29.4 32 0.0007 20.8 1.1 19 19-37 35-53 (59)
298 PRK15103 paraquat-inducible me 29.3 49 0.0011 26.4 2.5 32 22-57 9-40 (419)
299 PRK12722 transcriptional activ 29.0 24 0.00052 25.7 0.6 12 20-31 151-162 (187)
300 PF04423 Rad50_zn_hook: Rad50 28.8 19 0.00041 20.4 0.0 7 25-31 22-28 (54)
301 TIGR00155 pqiA_fam integral me 28.8 67 0.0014 25.5 3.1 35 19-57 9-43 (403)
302 smart00734 ZnF_Rad18 Rad18-lik 28.5 26 0.00056 17.5 0.5 8 24-31 2-9 (26)
303 PRK07111 anaerobic ribonucleos 28.5 27 0.00059 29.9 0.9 21 24-55 681-701 (735)
304 PF12677 DUF3797: Domain of un 28.4 27 0.00058 20.5 0.6 12 21-32 11-22 (49)
305 PRK08332 ribonucleotide-diphos 28.0 49 0.0011 31.5 2.5 28 25-56 1706-1735(1740)
306 PF05191 ADK_lid: Adenylate ki 28.0 42 0.0009 18.0 1.3 14 48-61 2-15 (36)
307 PF05741 zf-nanos: Nanos RNA b 28.0 27 0.00059 20.7 0.6 12 21-32 31-42 (55)
308 TIGR01374 soxD sarcosine oxida 27.8 27 0.00058 22.4 0.6 8 24-31 2-9 (84)
309 PRK10220 hypothetical protein; 27.4 30 0.00066 23.4 0.8 18 19-36 16-33 (111)
310 cd05468 pVHL von Hippel-Landau 27.3 14 0.00029 25.2 -0.9 16 60-77 13-28 (141)
311 PF11648 RIG-I_C-RD: C-termina 27.1 48 0.001 22.1 1.8 15 43-57 56-70 (123)
312 PF04981 NMD3: NMD3 family ; 26.9 35 0.00076 24.8 1.1 16 43-58 31-46 (236)
313 COG5319 Uncharacterized protei 26.8 19 0.00041 25.3 -0.3 9 23-31 32-40 (142)
314 TIGR00354 polC DNA polymerase, 26.8 40 0.00086 30.6 1.6 45 22-79 624-668 (1095)
315 PRK08351 DNA-directed RNA poly 26.7 35 0.00076 20.7 0.9 9 25-33 17-25 (61)
316 COG1499 NMD3 NMD protein affec 26.3 61 0.0013 25.7 2.5 16 42-57 38-53 (355)
317 PF13597 NRDD: Anaerobic ribon 26.1 37 0.0008 27.9 1.3 11 23-33 504-514 (546)
318 PF06676 DUF1178: Protein of u 26.1 40 0.00086 23.7 1.3 10 22-31 31-40 (148)
319 PRK06393 rpoE DNA-directed RNA 26.1 37 0.0008 20.8 1.0 9 25-33 19-27 (64)
320 PF01197 Ribosomal_L31: Riboso 26.1 43 0.00093 20.3 1.3 16 45-60 11-26 (69)
321 KOG3309|consensus 26.1 27 0.00058 25.1 0.4 34 46-79 83-117 (159)
322 PF03470 zf-XS: XS zinc finger 25.9 39 0.00084 19.3 1.0 7 26-32 1-7 (43)
323 PRK12860 transcriptional activ 25.6 34 0.00073 25.0 0.9 13 19-31 150-162 (189)
324 PF04267 SoxD: Sarcosine oxida 25.4 21 0.00045 22.9 -0.2 7 25-31 3-9 (84)
325 PRK09502 iscA iron-sulfur clus 25.3 24 0.00052 22.6 0.0 12 46-58 95-106 (107)
326 CHL00136 rpl31 ribosomal prote 25.2 60 0.0013 19.9 1.8 34 21-58 13-46 (68)
327 PRK03681 hypA hydrogenase nick 25.0 52 0.0011 21.6 1.6 31 18-55 65-95 (114)
328 cd03023 DsbA_Com1_like DsbA fa 24.8 22 0.00048 22.3 -0.2 11 22-32 13-23 (154)
329 PF13397 DUF4109: Domain of un 24.8 43 0.00093 22.4 1.2 15 19-33 46-60 (105)
330 PF07450 HycH: Formate hydroge 24.5 38 0.00082 23.5 0.9 30 42-80 34-63 (131)
331 PF08772 NOB1_Zn_bind: Nin one 24.3 60 0.0013 20.2 1.7 19 20-39 22-40 (73)
332 PF09416 UPF1_Zn_bind: RNA hel 24.1 1.4E+02 0.0029 21.2 3.6 36 19-54 55-94 (152)
333 COG0819 TenA Putative transcri 24.1 32 0.00069 25.3 0.5 14 66-79 153-166 (218)
334 PF09788 Tmemb_55A: Transmembr 24.0 72 0.0016 24.5 2.4 30 23-56 65-94 (256)
335 TIGR03676 aRF1/eRF1 peptide ch 24.0 61 0.0013 25.8 2.1 33 23-57 320-352 (403)
336 PRK05452 anaerobic nitric oxid 23.7 37 0.00079 27.4 0.8 18 17-34 452-469 (479)
337 COG5082 AIR1 Arginine methyltr 23.6 31 0.00067 25.3 0.3 8 48-55 98-105 (190)
338 COG2093 DNA-directed RNA polym 23.5 39 0.00085 20.8 0.7 10 24-33 19-28 (64)
339 PTZ00293 thymidine kinase; Pro 23.4 71 0.0015 23.4 2.2 30 25-54 139-176 (211)
340 TIGR00120 ArgJ glutamate N-ace 23.3 76 0.0017 25.7 2.5 33 31-63 367-400 (404)
341 COG2816 NPY1 NTP pyrophosphohy 23.1 70 0.0015 24.7 2.2 26 26-57 114-139 (279)
342 TIGR00558 pdxH pyridoxamine-ph 23.1 33 0.00071 24.9 0.4 15 65-79 28-42 (217)
343 KOG3352|consensus 23.1 40 0.00086 24.0 0.8 11 21-31 131-141 (153)
344 COG1996 RPC10 DNA-directed RNA 23.0 53 0.0011 19.1 1.2 30 22-57 5-34 (49)
345 PF10825 DUF2752: Protein of u 23.0 37 0.0008 19.4 0.5 14 22-35 8-21 (52)
346 PF15135 UPF0515: Uncharacteri 22.9 70 0.0015 24.8 2.2 42 17-58 106-166 (278)
347 PF07491 PPI_Ypi1: Protein pho 22.7 38 0.00081 20.6 0.5 7 1-7 31-37 (60)
348 PF06221 zf-C2HC5: Putative zi 22.7 42 0.00092 20.0 0.8 9 23-31 35-43 (57)
349 PLN00162 transport protein sec 22.5 45 0.00097 28.6 1.1 15 22-36 74-88 (761)
350 PRK10954 periplasmic protein d 22.4 26 0.00055 24.6 -0.3 13 22-34 45-57 (207)
351 PHA02768 hypothetical protein; 22.4 33 0.00072 20.4 0.3 37 23-59 5-43 (55)
352 smart00154 ZnF_AN1 AN1-like Zi 22.3 47 0.001 18.0 0.8 9 23-31 12-20 (39)
353 PRK14714 DNA polymerase II lar 22.2 62 0.0013 30.1 2.0 10 23-32 667-676 (1337)
354 cd01675 RNR_III Class III ribo 21.9 48 0.001 27.3 1.1 11 23-33 532-542 (555)
355 PRK11823 DNA repair protein Ra 21.8 78 0.0017 25.2 2.3 24 22-55 6-29 (446)
356 PRK15084 formate hydrogenlyase 21.8 45 0.00098 23.2 0.9 29 43-80 37-65 (133)
357 PF14634 zf-RING_5: zinc-RING 21.8 48 0.001 17.8 0.8 10 21-30 34-43 (44)
358 PF14913 DPCD: DPCD protein fa 21.7 30 0.00065 25.5 -0.0 24 54-77 95-118 (194)
359 COG0266 Nei Formamidopyrimidin 21.6 72 0.0016 24.5 2.0 26 25-54 247-272 (273)
360 cd07153 Fur_like Ferric uptake 21.6 56 0.0012 20.4 1.2 17 46-62 72-88 (116)
361 PF14369 zf-RING_3: zinc-finge 21.4 1.4E+02 0.003 15.8 2.6 31 24-59 3-33 (35)
362 KOG3456|consensus 21.3 61 0.0013 22.2 1.4 25 30-58 91-115 (120)
363 PRK09504 sufA iron-sulfur clus 21.3 31 0.00068 22.8 -0.0 12 46-58 110-121 (122)
364 PRK14559 putative protein seri 21.3 44 0.00095 28.4 0.9 25 25-59 29-53 (645)
365 PRK08270 anaerobic ribonucleos 20.9 64 0.0014 27.4 1.7 10 23-32 639-648 (656)
366 PF01599 Ribosomal_S27: Riboso 20.9 31 0.00067 19.9 -0.1 27 23-55 18-46 (47)
367 PF14375 Cys_rich_CWC: Cystein 20.9 53 0.0012 18.5 0.9 10 26-35 1-10 (50)
368 TIGR00308 TRM1 tRNA(guanine-26 20.6 86 0.0019 24.6 2.3 44 18-66 228-275 (374)
369 PRK04860 hypothetical protein; 20.6 59 0.0013 22.8 1.2 33 23-59 119-155 (160)
370 KOG1598|consensus 20.4 59 0.0013 27.3 1.4 27 25-56 2-28 (521)
371 PRK11088 rrmA 23S rRNA methylt 20.4 46 0.001 24.1 0.7 26 23-57 2-27 (272)
372 PF01783 Ribosomal_L32p: Ribos 20.1 35 0.00076 19.8 0.0 24 20-54 23-46 (56)
No 1
>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=100.00 E-value=1.2e-43 Score=225.86 Aligned_cols=79 Identities=56% Similarity=0.978 Sum_probs=45.8
Q ss_pred CCCCcCCC-CCCCCCCCCCCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhhhhcCC
Q psy3498 2 GRRKSKRK-PPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVP 80 (81)
Q Consensus 2 GkRK~~~k-~~~kkk~~~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~WiD~c~~ 80 (81)
||||++++ +++++ ++++|||.|+||||||++||+|+||++.++|+|+|++||++|+++|++|+||||||++|||+|+|
T Consensus 1 GkRK~~~k~~~~kk-~~~~l~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~~L~epiDVY~~wiD~~~~ 79 (81)
T PF05129_consen 1 GKRKKKRKKPPKKK-KKPKLPKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKINPLSEPIDVYSEWIDACEE 79 (81)
T ss_dssp --------------------SS----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE--SS--TTHHHHHHHHHHH-
T ss_pred CCCcccCCCCCccC-cCCCCCceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccCccCcccchhHHHHHHHHh
Confidence 89998888 44444 48999999999999999999999999999999999999999999999999999999999999987
Q ss_pred C
Q psy3498 81 S 81 (81)
Q Consensus 81 ~ 81 (81)
.
T Consensus 80 ~ 80 (81)
T PF05129_consen 80 G 80 (81)
T ss_dssp -
T ss_pred c
Confidence 3
No 2
>KOG3214|consensus
Probab=100.00 E-value=1.4e-42 Score=230.24 Aligned_cols=80 Identities=61% Similarity=1.090 Sum_probs=76.9
Q ss_pred CCCCCcCCCCCCCCCCCCCCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhhhhcCC
Q psy3498 1 MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVP 80 (81)
Q Consensus 1 MGkRK~~~k~~~kkk~~~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~WiD~c~~ 80 (81)
|||||+|++.++|.+++++|+|.|+||||||+++|+|+||++.++|.++|++|+++||+.||+|++||||||+|||+|++
T Consensus 1 MgkRk~K~k~~~k~r~~~~ldt~FnClfcnHek~v~~~~Dk~~~iG~~sC~iC~esFqt~it~LsepIDVYSdWiDaCe~ 80 (109)
T KOG3214|consen 1 MGKRKSKRKEPPKERRVEPLDTQFNCLFCNHEKSVSCTLDKKHNIGKASCRICEESFQTTITALSEPIDVYSDWIDACEA 80 (109)
T ss_pred CCcccccccCCchhhhccchheeeccCccccccceeeeehhhcCcceeeeeehhhhhccchHhhccchHHHHHHHHHHHH
Confidence 99999999988885569999999999999999999999999999999999999999999999999999999999999975
No 3
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=100.00 E-value=6.8e-39 Score=212.11 Aligned_cols=79 Identities=39% Similarity=0.681 Sum_probs=75.9
Q ss_pred CCCCCcCCCCCCCCCCCCCCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhhhhcCC
Q psy3498 1 MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVP 80 (81)
Q Consensus 1 MGkRK~~~k~~~kkk~~~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~WiD~c~~ 80 (81)
|||||++++.++|++ .++|||.|+||||||+++++|.++++.++|.++|++||++|++.||.|++||||||+|||+|+|
T Consensus 1 MG~rr~krr~~ik~~-~~~L~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l~~~vDvYs~wvDay~e 79 (104)
T COG4888 1 MGRRRRKRRKIIKRR-PQVLPKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPELSEPVDVYSAWVDAYLE 79 (104)
T ss_pred CCcccccccccCccc-CccCCceEecCccCCeeeeEEEEEecCceeEEEcccCcceEEEeccccccchhHHHHHHHHHHh
Confidence 999999988888887 6889999999999999999999999999999999999999999999999999999999999986
No 4
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=100.00 E-value=9.9e-35 Score=191.28 Aligned_cols=75 Identities=36% Similarity=0.562 Sum_probs=68.7
Q ss_pred CCCCCcCCCCCCCCCCCCCCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhhhhcCC
Q psy3498 1 MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVP 80 (81)
Q Consensus 1 MGkRK~~~k~~~kkk~~~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~WiD~c~~ 80 (81)
|||||++++++ +|+ +.++|+.|+|||||+ .+|.|+|++ +++++.|.+||+.|.+.|++|++||||||+|||+|+|
T Consensus 1 MGkRk~~~k~~-~k~-k~klpt~f~CP~Cge-~~v~v~~~k--~~~h~~C~~CG~y~~~~V~~l~epIDVY~~wiD~~~e 75 (99)
T PRK14892 1 MGRRRKKRKKI-IRP-KPKLPKIFECPRCGK-VSISVKIKK--NIAIITCGNCGLYTEFEVPSVYDEVDVYNKFIDLYLE 75 (99)
T ss_pred CCCccccCCCC-ccc-ccCCCcEeECCCCCC-eEeeeecCC--CcceEECCCCCCccCEECCccccchhhHHHHHHHHHh
Confidence 99999998744 444 589999999999995 899999987 8999999999999999999999999999999999986
No 5
>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=97.35 E-value=0.00026 Score=41.17 Aligned_cols=46 Identities=26% Similarity=0.456 Sum_probs=29.3
Q ss_pred cCCCCCCCCceEEE--eecCCceEEEEcccccceeEeccCCCCchhhhhh
Q psy3498 25 NCPFCNHEKSCEVK--MDKGRNSARIACRVCLEDFQTTINFLSEAIDVYN 72 (81)
Q Consensus 25 ~CPfC~~~~sV~v~--i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs 72 (81)
.|||||.+ .+.+. .+-....+...|..||.+... .....++|+.++
T Consensus 3 PCPfCGg~-~~~~~~~~~~~~~~~~~~C~~Cga~~~~-~~~~~~Ai~~WN 50 (53)
T TIGR03655 3 PCPFCGGA-DVYLRRGFDPLDLSHYFECSTCGASGPV-EEDEAEAIEAWN 50 (53)
T ss_pred CCCCCCCc-ceeeEeccCCCCCEEEEECCCCCCCccc-ccCHHHHHHHHh
Confidence 59999984 44343 344456666799999998664 334445555443
No 6
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=97.02 E-value=0.0013 Score=38.43 Aligned_cols=32 Identities=25% Similarity=0.608 Sum_probs=22.1
Q ss_pred eecCCCCCCCCceEEEeecCCce---EEEEcccccc
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNS---ARIACRVCLE 55 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~---g~l~C~~C~~ 55 (81)
.-.|||||. ..+.+.-+..... ..+.|..||.
T Consensus 3 LkPCPFCG~-~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGS-ADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCC-cceEeecccCCCCCCEEEEEcCCCCC
Confidence 446999987 5555555433222 7899999998
No 7
>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=96.95 E-value=0.0011 Score=39.51 Aligned_cols=33 Identities=24% Similarity=0.703 Sum_probs=25.7
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
.|.||.||. ++.+.....-..+.|..||+.|+-
T Consensus 2 ~~~CP~CG~----~iev~~~~~GeiV~Cp~CGaeleV 34 (54)
T TIGR01206 2 QFECPDCGA----EIELENPELGELVICDECGAELEV 34 (54)
T ss_pred ccCCCCCCC----EEecCCCccCCEEeCCCCCCEEEE
Confidence 589999998 455554444458899999999985
No 8
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=96.51 E-value=0.0046 Score=38.21 Aligned_cols=50 Identities=28% Similarity=0.380 Sum_probs=34.0
Q ss_pred CCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhh
Q psy3498 20 LDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYND 73 (81)
Q Consensus 20 l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~ 73 (81)
.+++=.|||||- ++|.++- ..+...+.|..|++.-...-.. -++||+|+.
T Consensus 3 ~d~lKPCPFCG~-~~~~v~~--~~g~~~v~C~~CgA~~~~~~te-~~Aie~WN~ 52 (64)
T PRK09710 3 YDNVKPCPFCGC-PSVTVKA--ISGYYRAKCNGCESRTGYGGSE-KEALERWNK 52 (64)
T ss_pred cccccCCCCCCC-ceeEEEe--cCceEEEEcCCCCcCcccccCH-HHHHHHHHh
Confidence 466778999997 5666665 4677889999999864322111 157777654
No 9
>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=96.41 E-value=0.0036 Score=34.86 Aligned_cols=31 Identities=19% Similarity=0.616 Sum_probs=22.4
Q ss_pred ecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
|.||.|++.. +..| ...|.+.|..||+--+.
T Consensus 1 m~Cp~Cg~~~---~~~D--~~~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 1 MKCPNCGSKE---IVFD--PERGELVCPNCGLVLEE 31 (43)
T ss_dssp ESBTTTSSSE---EEEE--TTTTEEEETTT-BBEE-
T ss_pred CCCcCCcCCc---eEEc--CCCCeEECCCCCCEeec
Confidence 6899999943 4555 45588899999987664
No 10
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=96.36 E-value=0.0075 Score=33.30 Aligned_cols=35 Identities=17% Similarity=0.493 Sum_probs=24.6
Q ss_pred ecCCCCCCCCceEEEeecC----CceEEEEcccccceeE
Q psy3498 24 FNCPFCNHEKSCEVKMDKG----RNSARIACRVCLEDFQ 58 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~----~~~g~l~C~~C~~~~~ 58 (81)
|+||.|||.+++-..+.-. .+.-...|..||..|.
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence 6899999999888866442 3567888999998763
No 11
>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=96.35 E-value=0.0016 Score=35.03 Aligned_cols=32 Identities=19% Similarity=0.609 Sum_probs=22.8
Q ss_pred eecCCCCCCCCceEEEeecC---CceEEEEcccccceeE
Q psy3498 23 QFNCPFCNHEKSCEVKMDKG---RNSARIACRVCLEDFQ 58 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~---~~~g~l~C~~C~~~~~ 58 (81)
.+.||.|+.. ..++.. ...+.+.|.+||..|.
T Consensus 2 ~~~CP~C~~~----~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 2 RIQCPNCKTS----FRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCE----EEeCHHHcCCCCCEEECCCCCCEEE
Confidence 4789999983 444432 2334899999999875
No 12
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=96.13 E-value=0.0052 Score=43.27 Aligned_cols=36 Identities=31% Similarity=0.647 Sum_probs=24.5
Q ss_pred cCCCCCCCCceEEEe-ecCCceE---EEEcccccceeEec
Q psy3498 25 NCPFCNHEKSCEVKM-DKGRNSA---RIACRVCLEDFQTT 60 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i-~k~~~~g---~l~C~~C~~~~~~~ 60 (81)
.||||||+++-.+.= .-+++.+ .=.|..||.+|+|-
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTy 41 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTF 41 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcccee
Confidence 599999987744332 1134433 35799999999873
No 13
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=96.05 E-value=0.017 Score=32.48 Aligned_cols=34 Identities=21% Similarity=0.492 Sum_probs=25.1
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEecc
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTI 61 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i 61 (81)
..|.||.||. .+.++... ..+.|..||..+....
T Consensus 2 ~~y~C~~CG~----~~~~~~~~--~~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 2 AEYKCARCGR----EVELDEYG--TGVRCPYCGYRILFKE 35 (46)
T ss_pred CEEECCCCCC----EEEECCCC--CceECCCCCCeEEEcc
Confidence 4799999998 55555433 3789999998876543
No 14
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=96.04 E-value=0.0039 Score=44.35 Aligned_cols=34 Identities=38% Similarity=0.829 Sum_probs=23.5
Q ss_pred cCCCCCCCCceEEEeecC--CceE---EEEcccccceeEe
Q psy3498 25 NCPFCNHEKSCEVKMDKG--RNSA---RIACRVCLEDFQT 59 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~--~~~g---~l~C~~C~~~~~~ 59 (81)
.||||||+.|=.+. .+. .|-+ .-.|..||.+|+|
T Consensus 2 ~CPfC~~~~tkViD-SR~~edg~aIRRRReC~~C~~RFTT 40 (156)
T COG1327 2 KCPFCGHEDTKVID-SRPAEEGNAIRRRRECLECGERFTT 40 (156)
T ss_pred CCCCCCCCCCeeee-cccccccchhhhhhcccccccccch
Confidence 59999998884432 222 2222 4579999999987
No 15
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=95.94 E-value=0.009 Score=32.58 Aligned_cols=32 Identities=19% Similarity=0.615 Sum_probs=23.6
Q ss_pred eecCCCCCCCCceEEEeecC---CceEEEEcccccceeE
Q psy3498 23 QFNCPFCNHEKSCEVKMDKG---RNSARIACRVCLEDFQ 58 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~---~~~g~l~C~~C~~~~~ 58 (81)
..+||.|+. .-+|+.+ .+.+.+.|..|+..|.
T Consensus 2 ~i~CP~C~~----~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 2 IITCPNCQT----RFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EEECCCCCc----eEEcCHHHcccCCcEEECCCCCcEee
Confidence 358999998 3344332 4567999999999875
No 16
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=95.42 E-value=0.039 Score=30.60 Aligned_cols=34 Identities=15% Similarity=0.427 Sum_probs=26.2
Q ss_pred ecCCCCCCCCceEEEeecC----CceEEEEccccccee
Q psy3498 24 FNCPFCNHEKSCEVKMDKG----RNSARIACRVCLEDF 57 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~----~~~g~l~C~~C~~~~ 57 (81)
|.||.|||.+++-..+.-. .+.-...|..||-.+
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w 38 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRW 38 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEe
Confidence 6899999999987776432 346688999999765
No 17
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=95.19 E-value=0.0093 Score=32.48 Aligned_cols=34 Identities=18% Similarity=0.457 Sum_probs=23.2
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
.++||.|+..-.|.-..-. ...+.+.|..||..|
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip-~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIP-PKGRKVRCSKCGHVF 35 (36)
T ss_pred EEECCCCCCEEeCCHHHCC-CCCcEEECCCCCCEe
Confidence 4689999985443333211 455689999999876
No 18
>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=95.13 E-value=0.031 Score=36.62 Aligned_cols=33 Identities=30% Similarity=0.763 Sum_probs=25.8
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEec
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~ 60 (81)
..+.||||+.. + ++ ...+|+-.|+.|+..|.--
T Consensus 34 a~y~CpfCgk~-~--vk---R~a~GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 34 AKYVCPFCGKK-T--VK---RGSTGIWTCRKCGAKFAGG 66 (91)
T ss_pred cCccCCCCCCC-c--eE---EEeeEEEEcCCCCCEEeCC
Confidence 67899999973 2 22 2688999999999998643
No 19
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=95.11 E-value=0.031 Score=36.49 Aligned_cols=40 Identities=23% Similarity=0.443 Sum_probs=28.2
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCch
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEA 67 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~ep 67 (81)
..+.||||+.. .++ ...+|+-.|+.|+..|.--.-.++.|
T Consensus 35 a~y~CpfCgk~---~vk---R~a~GIW~C~~C~~~~AGGAy~~~T~ 74 (90)
T PRK03976 35 AKHVCPVCGRP---KVK---RVGTGIWECRKCGAKFAGGAYTPETP 74 (90)
T ss_pred cCccCCCCCCC---ceE---EEEEEEEEcCCCCCEEeCCccccccc
Confidence 67899999863 222 26889999999999986533333333
No 20
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=95.10 E-value=0.028 Score=33.22 Aligned_cols=46 Identities=22% Similarity=0.521 Sum_probs=30.1
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccc--eeEeccCCCCchhhh
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLE--DFQTTINFLSEAIDV 70 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~--~~~~~i~~L~epIDV 70 (81)
+||+||+...+.+..........--|.+|-. .+...+.....-|.|
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI~~~v~~d~~~~~v~v 49 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPIEVQVTVDEDEPSVSV 49 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCCccEEEEEECCCCCEEEE
Confidence 7999999766666555555566788999986 444445444333333
No 21
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=94.98 E-value=0.035 Score=36.25 Aligned_cols=33 Identities=24% Similarity=0.642 Sum_probs=25.7
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEec
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~ 60 (81)
..+.||||+.. + ++ ...+|+-.|+.|+..|.--
T Consensus 35 a~y~CpfCgk~-~--vk---R~a~GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 35 AKYFCPFCGKH-A--VK---RQAVGIWRCKGCKKTVAGG 67 (90)
T ss_pred CCccCCCCCCC-c--ee---eeeeEEEEcCCCCCEEeCC
Confidence 67999999973 2 22 2577999999999998643
No 22
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=94.70 E-value=0.049 Score=38.30 Aligned_cols=35 Identities=29% Similarity=0.658 Sum_probs=22.6
Q ss_pred cCCCCCCCCceEEEeec-CCc--e-EEEEcccccceeEe
Q psy3498 25 NCPFCNHEKSCEVKMDK-GRN--S-ARIACRVCLEDFQT 59 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k-~~~--~-g~l~C~~C~~~~~~ 59 (81)
.||+||++.+-.+.=.- ..| + -.-.|..||-+|++
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~ 40 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTT 40 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceE
Confidence 69999997743332221 111 2 24789999999976
No 23
>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=94.68 E-value=0.03 Score=36.60 Aligned_cols=41 Identities=24% Similarity=0.535 Sum_probs=27.5
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchh
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAI 68 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epI 68 (81)
..+.||||+... ++. ..+|+-.|+.|+..|.--.-.++.|.
T Consensus 34 ~ky~Cp~Cgk~~---vkR---~a~GIW~C~~C~~~~AGGAy~~~T~~ 74 (90)
T PF01780_consen 34 AKYTCPFCGKTS---VKR---VATGIWKCKKCGKKFAGGAYTPSTPA 74 (90)
T ss_dssp S-BEESSSSSSE---EEE---EETTEEEETTTTEEEE-BSSSSS-HH
T ss_pred CCCcCCCCCCce---eEE---eeeEEeecCCCCCEEeCCCccccchH
Confidence 578999999842 332 56788999999999876444444443
No 24
>PF14353 CpXC: CpXC protein
Probab=94.35 E-value=0.049 Score=35.98 Aligned_cols=40 Identities=25% Similarity=0.513 Sum_probs=27.2
Q ss_pred ecCCCCCCCCceEEEeec-------------CCceEEEEcccccceeEeccCC
Q psy3498 24 FNCPFCNHEKSCEVKMDK-------------GRNSARIACRVCLEDFQTTINF 63 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k-------------~~~~g~l~C~~C~~~~~~~i~~ 63 (81)
-+||.|+|+..+++--.- ........|..||..+....+-
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~ 54 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPL 54 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCE
Confidence 379999997666553211 1245689999999988754443
No 25
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=94.30 E-value=0.087 Score=32.27 Aligned_cols=48 Identities=19% Similarity=0.458 Sum_probs=31.4
Q ss_pred ecCCCCCCCCceEEEe-----------ecC-CceEEEEcccccc--eeEeccCCCCchhhhh
Q psy3498 24 FNCPFCNHEKSCEVKM-----------DKG-RNSARIACRVCLE--DFQTTINFLSEAIDVY 71 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i-----------~k~-~~~g~l~C~~C~~--~~~~~i~~L~epIDVY 71 (81)
+.||-||++..-.=.+ |-. +..-.++|..||- -|....+.|.+-+|.+
T Consensus 1 y~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYTE~Y~~~~~~~~~i~D~~ 62 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYTEFYKAKTSNGSNILDFF 62 (64)
T ss_pred CCCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCEEEEeecCcccchhhhhh
Confidence 4799999964322121 211 1234789999994 4667888888887764
No 26
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=93.77 E-value=0.072 Score=28.67 Aligned_cols=30 Identities=17% Similarity=0.410 Sum_probs=22.6
Q ss_pred ecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
-.|+-|||+.-+. ...+...|..||.+|++
T Consensus 4 ~~C~~C~~~~i~~------~~~~~~~C~~Cg~~~~~ 33 (33)
T PF08792_consen 4 KKCSKCGGNGIVN------KEDDYEVCIFCGSSFPY 33 (33)
T ss_pred eEcCCCCCCeEEE------ecCCeEEcccCCcEeeC
Confidence 4699999965332 34478999999999874
No 27
>PHA00626 hypothetical protein
Probab=93.69 E-value=0.073 Score=32.41 Aligned_cols=34 Identities=24% Similarity=0.408 Sum_probs=24.8
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
.||.||+.+-+-+.+-++ ....-.|..||-.|+-
T Consensus 2 ~CP~CGS~~Ivrcg~cr~-~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRG-WSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCceeeeeceecc-cCcceEcCCCCCeech
Confidence 599999976665555443 2467789999998863
No 28
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=93.59 E-value=0.054 Score=29.98 Aligned_cols=29 Identities=24% Similarity=0.567 Sum_probs=24.9
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
.||.|+-..... ++.+.+.|...|..|+.
T Consensus 5 pCP~CGG~DrFr--~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 5 PCPNCGGSDRFR--FDDKDGRGTWFCSVCGA 33 (37)
T ss_pred CCCCCCCccccc--cccCCCCcCEEeCCCCC
Confidence 599999988877 66678889999999985
No 29
>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=93.28 E-value=0.07 Score=29.98 Aligned_cols=31 Identities=26% Similarity=0.741 Sum_probs=21.3
Q ss_pred CCceecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 20 LDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 20 l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
-+.-|.||+||+.+ ...+ ...+.-.|..|+.
T Consensus 15 W~~g~~CP~Cg~~~--~~~~---~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 15 WPDGFVCPHCGSTK--HYRL---KTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCCCee--eEEe---CCCCeEECCCCCC
Confidence 45669999999952 2222 2267889999974
No 30
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=93.26 E-value=0.11 Score=32.58 Aligned_cols=43 Identities=21% Similarity=0.519 Sum_probs=25.4
Q ss_pred ecCCCCCCCCceEEEeec-CC--ceEEEEcc--cccceeEecc---CCCCch
Q psy3498 24 FNCPFCNHEKSCEVKMDK-GR--NSARIACR--VCLEDFQTTI---NFLSEA 67 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k-~~--~~g~l~C~--~C~~~~~~~i---~~L~ep 67 (81)
|.||+||+.. ...+=.. .. ..-.-.|. .||.+|.+.. +.|+.|
T Consensus 2 m~CP~Cg~~a-~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~es~s~tis~p 52 (72)
T PRK09678 2 FHCPLCQHAA-HARTSRYITDTTKERYHQCQNVNCSATFITYESVQRYIVKP 52 (72)
T ss_pred ccCCCCCCcc-EEEEChhcChhhheeeeecCCCCCCCEEEEEEEEEEEEcCC
Confidence 7899999954 2222111 12 22456788 7999997632 245544
No 31
>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=92.75 E-value=0.24 Score=26.77 Aligned_cols=28 Identities=36% Similarity=0.621 Sum_probs=20.5
Q ss_pred CCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 26 CPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
||.||+ ....+-++...+ .|+.|+-.++
T Consensus 4 Cp~C~n--lL~p~~~~~~~~---~C~~C~Y~~~ 31 (35)
T PF02150_consen 4 CPECGN--LLYPKEDKEKRV---ACRTCGYEEP 31 (35)
T ss_dssp ETTTTS--BEEEEEETTTTE---EESSSS-EEE
T ss_pred CCCCCc--cceEcCCCccCc---CCCCCCCccC
Confidence 899996 566666665555 9999997665
No 32
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=92.60 E-value=0.11 Score=33.90 Aligned_cols=31 Identities=32% Similarity=0.710 Sum_probs=24.5
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
....||+|+.. .|+ -...|+-.|+.||..|.
T Consensus 34 ~~~~Cp~C~~~---~Vk---R~a~GIW~C~kCg~~fA 64 (89)
T COG1997 34 AKHVCPFCGRT---TVK---RIATGIWKCRKCGAKFA 64 (89)
T ss_pred cCCcCCCCCCc---cee---eeccCeEEcCCCCCeec
Confidence 56899999984 332 25779999999999885
No 33
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=92.15 E-value=0.053 Score=26.95 Aligned_cols=21 Identities=29% Similarity=0.615 Sum_probs=13.3
Q ss_pred CCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 26 CPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
||.||++..-.. .-|..||..
T Consensus 2 Cp~CG~~~~~~~----------~fC~~CG~~ 22 (23)
T PF13240_consen 2 CPNCGAEIEDDA----------KFCPNCGTP 22 (23)
T ss_pred CcccCCCCCCcC----------cchhhhCCc
Confidence 899998644322 238888763
No 34
>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=91.78 E-value=0.11 Score=27.68 Aligned_cols=31 Identities=23% Similarity=0.516 Sum_probs=21.5
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
.|.|+.||+.-.+...+ .. -..+.|-.||..
T Consensus 5 ~y~C~~Cg~~fe~~~~~--~~-~~~~~CP~Cg~~ 35 (41)
T smart00834 5 EYRCEDCGHTFEVLQKI--SD-DPLATCPECGGD 35 (41)
T ss_pred EEEcCCCCCEEEEEEec--CC-CCCCCCCCCCCc
Confidence 68999999953333333 22 467889999984
No 35
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=91.74 E-value=0.21 Score=29.84 Aligned_cols=26 Identities=19% Similarity=0.405 Sum_probs=21.1
Q ss_pred CCCceecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
.++....||.||+- ...+-.|..||.
T Consensus 23 ~~~~l~~C~~CG~~-----------~~~H~vC~~CG~ 48 (57)
T PRK12286 23 KAPGLVECPNCGEP-----------KLPHRVCPSCGY 48 (57)
T ss_pred cCCcceECCCCCCc-----------cCCeEECCCCCc
Confidence 46889999999982 346889999995
No 36
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=91.47 E-value=0.12 Score=29.99 Aligned_cols=26 Identities=23% Similarity=0.423 Sum_probs=18.1
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
-||.||++ -.. . ..+...|+.||..+
T Consensus 22 fCP~Cg~~-~m~---~---~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSG-FMA---E---HLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCCCcc-hhe---c---cCCcEECCCcCCEE
Confidence 79999984 111 1 12688999999765
No 37
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=91.45 E-value=0.31 Score=27.57 Aligned_cols=36 Identities=17% Similarity=0.436 Sum_probs=22.3
Q ss_pred cCCCCCCCCceEEEeecCC--ceEEEEccc--ccceeEec
Q psy3498 25 NCPFCNHEKSCEVKMDKGR--NSARIACRV--CLEDFQTT 60 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~--~~g~l~C~~--C~~~~~~~ 60 (81)
.||+||+...+.-.-.... ......|.+ ||.+|.+.
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFVAN 40 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEEEE
Confidence 4999999543332222222 234667888 99999764
No 38
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=91.17 E-value=0.38 Score=26.29 Aligned_cols=27 Identities=22% Similarity=0.529 Sum_probs=21.0
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
+||.|++ ......+ ..+..-.|..||=
T Consensus 1 ~CP~C~~-~l~~~~~---~~~~id~C~~C~G 27 (41)
T PF13453_consen 1 KCPRCGT-ELEPVRL---GDVEIDVCPSCGG 27 (41)
T ss_pred CcCCCCc-ccceEEE---CCEEEEECCCCCe
Confidence 5999999 5666666 5577888999984
No 39
>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=90.75 E-value=0.24 Score=37.69 Aligned_cols=36 Identities=25% Similarity=0.634 Sum_probs=15.1
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEcccccceeEec
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~ 60 (81)
-.-||.||+...- .+....-+|-..|..|++.||.+
T Consensus 31 n~yCP~Cg~~~L~--~f~NN~PVaDF~C~~C~eeyELK 66 (254)
T PF06044_consen 31 NMYCPNCGSKPLS--KFENNRPVADFYCPNCNEEYELK 66 (254)
T ss_dssp H---TTT--SS-E--E--------EEE-TTT--EEEEE
T ss_pred CCcCCCCCChhHh--hccCCCccceeECCCCchHHhhh
Confidence 4679999996443 33445678999999999999864
No 40
>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=90.64 E-value=0.14 Score=28.41 Aligned_cols=30 Identities=20% Similarity=0.571 Sum_probs=23.5
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
.|.|+-|||.-.+...+.. ...+.|-.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~---~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISE---DDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEcCC---CCCCcCCCCCC
Confidence 5999999997655555543 67889999998
No 41
>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=90.61 E-value=0.29 Score=36.55 Aligned_cols=35 Identities=20% Similarity=0.490 Sum_probs=19.1
Q ss_pred ecCCCCCCCCceEEEeecCC-ceEEEEcccccceeE
Q psy3498 24 FNCPFCNHEKSCEVKMDKGR-NSARIACRVCLEDFQ 58 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~~-~~g~l~C~~C~~~~~ 58 (81)
=.||.||..-++++...... |.=.+.|..||..+.
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~ 208 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWR 208 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeee
Confidence 47999999777776665543 667999999998764
No 42
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=90.30 E-value=0.16 Score=30.94 Aligned_cols=34 Identities=18% Similarity=0.414 Sum_probs=20.4
Q ss_pred CceecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
-..|.||.||.+.-..|.-=++.+ ..-.|..||.
T Consensus 23 ~~~F~CPnCG~~~I~RC~~CRk~~-~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEVIIYRCEKCRKQS-NPYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCeeEeechhHHhcC-CceECCCCCC
Confidence 378999999983233333323332 3457877775
No 43
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=90.07 E-value=0.36 Score=31.45 Aligned_cols=35 Identities=26% Similarity=0.639 Sum_probs=23.9
Q ss_pred cCCCCCCCC----ceEEEeecCC--------ceEEEEcccccceeEe
Q psy3498 25 NCPFCNHEK----SCEVKMDKGR--------NSARIACRVCLEDFQT 59 (81)
Q Consensus 25 ~CPfC~~~~----sV~v~i~k~~--------~~g~l~C~~C~~~~~~ 59 (81)
.|+.|++.. .+++..+..+ .+-.+.|..||+.|.+
T Consensus 1 ~C~~C~~~~~~~~~tTv~~el~~G~~~IvIknVPa~~C~~CGe~y~~ 47 (89)
T TIGR03829 1 KCRWCEEEKAIARTTTVYWELPDGTKAIEIKETPSISCSHCGMEYQD 47 (89)
T ss_pred CCcccCCCceecceEEEEEEecCCceEEEEecCCcccccCCCcEeec
Confidence 499997633 4455555533 3446799999999975
No 44
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=89.62 E-value=0.32 Score=33.06 Aligned_cols=36 Identities=25% Similarity=0.523 Sum_probs=26.4
Q ss_pred ecCCCCCCCCceEEEeecCCceEEEEcccccceeEec
Q psy3498 24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~ 60 (81)
=.||+|++.+ |...=....+...-.|..|+-+|+-.
T Consensus 31 ~~cP~C~s~~-~~k~g~~~~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 31 VNCPRCKSSN-VVKIGGIRRGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred CcCCCCCccc-eeeECCccccccccccCCcCcceeee
Confidence 4799999988 33332233457888999999999753
No 45
>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=89.53 E-value=0.51 Score=35.22 Aligned_cols=49 Identities=14% Similarity=0.298 Sum_probs=26.7
Q ss_pred eecCCCCCCCCceEEEee---cCCceEEEEcccccceeEeccCCCCchhhhh
Q psy3498 23 QFNCPFCNHEKSCEVKMD---KGRNSARIACRVCLEDFQTTINFLSEAIDVY 71 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~---k~~~~g~l~C~~C~~~~~~~i~~L~epIDVY 71 (81)
...||+||+++....... -..+.-.-.|..|+...-+--...+..+|.+
T Consensus 211 R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd~~~~~~~~~~ 262 (290)
T PF04216_consen 211 RIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVDREKDPELDPV 262 (290)
T ss_dssp TTS-TTT---SS-EEE--------SEEEEEETTTTEEEEEEETTT-TT--HH
T ss_pred CCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHhhhhCcccchh
Confidence 457999999998877765 3456778899999987665335566666655
No 46
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=89.32 E-value=0.59 Score=32.29 Aligned_cols=34 Identities=18% Similarity=0.343 Sum_probs=26.6
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
..=.||.|+...+.-++ +..+-.+.|..||+...
T Consensus 101 ~yVlC~~C~spdT~l~k---~~r~~~l~C~ACGa~~~ 134 (138)
T PRK03988 101 EYVICPECGSPDTKLIK---EGRIWVLKCEACGAETP 134 (138)
T ss_pred hcEECCCCCCCCcEEEE---cCCeEEEEcccCCCCCc
Confidence 44579999998876554 46688999999998644
No 47
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=89.29 E-value=0.54 Score=32.32 Aligned_cols=35 Identities=17% Similarity=0.331 Sum_probs=26.7
Q ss_pred CceecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
...=.||.|+...+.-++ +..+-.+.|..||+...
T Consensus 95 ~~yVlC~~C~sPdT~l~k---~~r~~~l~C~ACGa~~~ 129 (133)
T TIGR00311 95 RKYVICRECNRPDTRIIK---EGRVSLLKCEACGAKAP 129 (133)
T ss_pred hheEECCCCCCCCcEEEE---eCCeEEEecccCCCCCc
Confidence 345579999999886554 45667899999998654
No 48
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=89.23 E-value=0.52 Score=29.41 Aligned_cols=43 Identities=21% Similarity=0.458 Sum_probs=27.2
Q ss_pred CceecCCCCCCCCceEEEeecC------------CceEEEEcccccce--eEeccCC
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKG------------RNSARIACRVCLED--FQTTINF 63 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~------------~~~g~l~C~~C~~~--~~~~i~~ 63 (81)
...|.||-||..+-.+=.|.-. +..-.+.|.+||-+ |+..+..
T Consensus 2 ~~~~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYtEfY~a~~st 58 (68)
T COG3478 2 KNAFKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYTEFYSAKIST 58 (68)
T ss_pred CccccCCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCchhheeccccc
Confidence 3468899999876655444332 23357899999942 4444443
No 49
>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=89.11 E-value=1.1 Score=28.46 Aligned_cols=40 Identities=18% Similarity=0.419 Sum_probs=29.2
Q ss_pred CCCc-eecCCCCCCCCceEEEeecC----CceEEEEcccccceeE
Q psy3498 19 PLDI-QFNCPFCNHEKSCEVKMDKG----RNSARIACRVCLEDFQ 58 (81)
Q Consensus 19 ~l~~-~F~CPfC~~~~sV~v~i~k~----~~~g~l~C~~C~~~~~ 58 (81)
.+|+ ...||.|||..++-..+.-. .+.-.-.|-.||..+.
T Consensus 57 ~~~~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 57 TLPTTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred CCCcccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeE
Confidence 4443 79999999999888776442 2455778999997654
No 50
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=88.77 E-value=0.36 Score=28.94 Aligned_cols=40 Identities=20% Similarity=0.370 Sum_probs=32.1
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhh
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDW 74 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~W 74 (81)
.-.|+.||. .+. ...|.+||.......++-..|.|-|++.
T Consensus 5 mr~C~~Cgv---YTL---------k~~CP~CG~~t~~~~P~rfSp~D~y~~y 44 (56)
T PRK13130 5 IRKCPKCGV---YTL---------KEICPVCGGKTKNPHPPRFSPEDKYGKY 44 (56)
T ss_pred ceECCCCCC---EEc---------cccCcCCCCCCCCCCCCCCCCCCccHHH
Confidence 346888886 222 3479999999999999999999999975
No 51
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=88.76 E-value=0.48 Score=28.53 Aligned_cols=36 Identities=17% Similarity=0.487 Sum_probs=26.8
Q ss_pred ecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
--||.||...-+.+.-|-...-.-+.|..|.++.-.
T Consensus 5 i~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI 40 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKNFPLYCPKCKQETLI 40 (55)
T ss_pred EECCCCCCccceeeecCceeccccccCCCCCceEEE
Confidence 359999987667666665556678899999987643
No 52
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=88.69 E-value=0.7 Score=28.81 Aligned_cols=29 Identities=24% Similarity=0.665 Sum_probs=22.8
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
.||-|+| .++.+++. .-.+.|.+||..--
T Consensus 21 kCpdC~N---~q~vFsha--st~V~C~~CG~~l~ 49 (67)
T COG2051 21 KCPDCGN---EQVVFSHA--STVVTCLICGTTLA 49 (67)
T ss_pred ECCCCCC---EEEEeccC--ceEEEecccccEEE
Confidence 7999999 46677664 47899999998654
No 53
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=88.53 E-value=0.79 Score=33.23 Aligned_cols=46 Identities=20% Similarity=0.263 Sum_probs=27.6
Q ss_pred CceecCCCCCCCCceEEEeecCC--------------c-----eEEEEcccccceeEe-ccCCCCc
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKGR--------------N-----SARIACRVCLEDFQT-TINFLSE 66 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~~--------------~-----~g~l~C~~C~~~~~~-~i~~L~e 66 (81)
++..+||+|+++-...-...... + --...|..||-.+.. ..+.|+.
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~F~~l~~ 68 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEEDFEKLSP 68 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccccccccCCH
Confidence 57789999998644332221111 0 137899999976643 3555543
No 54
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=88.19 E-value=0.67 Score=25.07 Aligned_cols=28 Identities=29% Similarity=0.739 Sum_probs=17.0
Q ss_pred CCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 26 CPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
||.||+. ++..|-..+..-.+.|..||.
T Consensus 3 C~~CG~~--l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 3 CPQCGGP--LERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -TTT--B---EEE--TT-SS-EEEETTTTE
T ss_pred cccccCh--hhhhcCCCCCccceECCCCCC
Confidence 9999984 777777667888999999996
No 55
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=87.86 E-value=0.57 Score=26.54 Aligned_cols=28 Identities=21% Similarity=0.538 Sum_probs=20.6
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
.|.|..||++ ++++ ..+.+.|..||-+-
T Consensus 2 ~Y~C~~Cg~~----~~~~---~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRE----NEIK---SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCE----eecC---CCCceECCCCCceE
Confidence 4889999994 3343 34779999999754
No 56
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=87.84 E-value=0.18 Score=34.46 Aligned_cols=42 Identities=17% Similarity=0.366 Sum_probs=26.3
Q ss_pred CceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccC
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTIN 62 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~ 62 (81)
...|.||+|+..=+..--+......|...|..||..-...-|
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn 138 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEEDDN 138 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEcCc
Confidence 468999999974332211111123577999999987654333
No 57
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=87.53 E-value=0.61 Score=25.98 Aligned_cols=29 Identities=31% Similarity=0.677 Sum_probs=16.5
Q ss_pred CCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 26 CPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
||.||+ .+..+ .........|..||..+.
T Consensus 3 Cp~Cg~--~l~~~--~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 3 CPKCGN--MLIPK--EGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCC--ccccc--cCCCCCEEECCcCCCeEE
Confidence 888887 22222 111123778999996543
No 58
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=87.40 E-value=0.37 Score=24.46 Aligned_cols=11 Identities=36% Similarity=1.059 Sum_probs=9.6
Q ss_pred CCceecCCCCC
Q psy3498 20 LDIQFNCPFCN 30 (81)
Q Consensus 20 l~~~F~CPfC~ 30 (81)
....|.||.||
T Consensus 13 ~~v~f~CPnCG 23 (24)
T PF07754_consen 13 QAVPFPCPNCG 23 (24)
T ss_pred cCceEeCCCCC
Confidence 46899999998
No 59
>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=87.35 E-value=0.76 Score=31.19 Aligned_cols=32 Identities=19% Similarity=0.388 Sum_probs=24.8
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
+.-.||.|+...+.-++- ...-.+.|..||++
T Consensus 92 ~yVlC~~C~spdT~l~k~---~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 92 EYVLCPECGSPDTELIKE---GRLIFLKCKACGAS 123 (125)
T ss_dssp HHSSCTSTSSSSEEEEEE---TTCCEEEETTTSCE
T ss_pred HEEEcCCCCCCccEEEEc---CCEEEEEecccCCc
Confidence 445799999988754443 66789999999985
No 60
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=87.05 E-value=0.35 Score=27.23 Aligned_cols=30 Identities=23% Similarity=0.547 Sum_probs=21.6
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
.|.|+.||+.-.+...++. ...+.|-.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~---~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSD---DPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecCC---CCCCCCCCCCC
Confidence 5899999996555444432 45678999997
No 61
>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=86.95 E-value=0.29 Score=25.03 Aligned_cols=24 Identities=33% Similarity=0.701 Sum_probs=14.5
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
+||.|+++- ..+...|..||-.|+
T Consensus 2 ~CP~C~~~V----------~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEV----------PESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCc----------hhhcCcCCCCCCCCc
Confidence 477777742 234446777776664
No 62
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=86.66 E-value=0.46 Score=26.62 Aligned_cols=29 Identities=28% Similarity=0.631 Sum_probs=18.0
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEccccc
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCL 54 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~ 54 (81)
.||.|+-..-..+--|+ .+.|.-.|+.|+
T Consensus 5 pCP~CGG~DrFri~~d~-~~~G~~~C~~C~ 33 (40)
T PF08273_consen 5 PCPICGGKDRFRIFDDK-DGRGTWICRQCG 33 (40)
T ss_dssp --TTTT-TTTEEEETT-----S-EEETTTT
T ss_pred CCCCCcCccccccCcCc-ccCCCEECCCCC
Confidence 69999998888776665 566999999994
No 63
>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=86.60 E-value=0.36 Score=28.50 Aligned_cols=35 Identities=23% Similarity=0.546 Sum_probs=25.1
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccC
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTIN 62 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~ 62 (81)
|.=.||.||+...- ........|..||..+.-.+|
T Consensus 27 TSq~C~~CG~~~~~------~~~~r~~~C~~Cg~~~~rD~n 61 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK------RRSGRVFTCPNCGFEMDRDVN 61 (69)
T ss_pred CccCccCccccccc------ccccceEEcCCCCCEECcHHH
Confidence 66679999993221 345678999999998765544
No 64
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=86.48 E-value=0.29 Score=28.08 Aligned_cols=34 Identities=24% Similarity=0.677 Sum_probs=19.9
Q ss_pred eecCCCCCCCCceEEEeec------CCceEEEEccccccee
Q psy3498 23 QFNCPFCNHEKSCEVKMDK------GRNSARIACRVCLEDF 57 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k------~~~~g~l~C~~C~~~~ 57 (81)
.|.||||+.+-++. .+-. ......+.|.+|...+
T Consensus 2 ~f~CP~C~~~~~~~-~L~~H~~~~H~~~~~~v~CPiC~~~~ 41 (54)
T PF05605_consen 2 SFTCPYCGKGFSES-SLVEHCEDEHRSESKNVVCPICSSRV 41 (54)
T ss_pred CcCCCCCCCccCHH-HHHHHHHhHCcCCCCCccCCCchhhh
Confidence 59999999832211 1100 1223368999998643
No 65
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=86.46 E-value=1.2 Score=23.85 Aligned_cols=12 Identities=25% Similarity=0.786 Sum_probs=9.1
Q ss_pred EEEcccccceeE
Q psy3498 47 RIACRVCLEDFQ 58 (81)
Q Consensus 47 ~l~C~~C~~~~~ 58 (81)
-..|..||+.|-
T Consensus 32 ~~~C~~CGE~~~ 43 (46)
T TIGR03831 32 ALVCPQCGEEYL 43 (46)
T ss_pred ccccccCCCEee
Confidence 346999999774
No 66
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=86.33 E-value=1.2 Score=29.58 Aligned_cols=32 Identities=19% Similarity=0.366 Sum_probs=24.3
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
..=.||.|+...+.-++ ++..-.+.|..||+.
T Consensus 79 ~yVlC~~C~spdT~l~k---~~r~~~l~C~aCGa~ 110 (110)
T smart00653 79 EYVLCPECGSPDTELIK---ENRLFFLKCEACGAR 110 (110)
T ss_pred hcEECCCCCCCCcEEEE---eCCeEEEEccccCCC
Confidence 44579999998764433 467889999999973
No 67
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=86.13 E-value=0.32 Score=29.81 Aligned_cols=34 Identities=18% Similarity=0.390 Sum_probs=20.5
Q ss_pred CceecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
-..|.||.||.+.-..+..-++ .-..-.|.+||.
T Consensus 25 ~v~F~CPnCGe~~I~Rc~~CRk-~g~~Y~Cp~CGF 58 (61)
T COG2888 25 AVKFPCPNCGEVEIYRCAKCRK-LGNPYRCPKCGF 58 (61)
T ss_pred eeEeeCCCCCceeeehhhhHHH-cCCceECCCcCc
Confidence 3789999999732222222222 234567888885
No 68
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=86.13 E-value=0.95 Score=27.95 Aligned_cols=35 Identities=17% Similarity=0.448 Sum_probs=23.1
Q ss_pred eecCCCCCCCCceEEEeecC---CceEEEEcccccceeEe
Q psy3498 23 QFNCPFCNHEKSCEVKMDKG---RNSARIACRVCLEDFQT 59 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~---~~~g~l~C~~C~~~~~~ 59 (81)
.|+|..|++..+ =.|.+. .|+-.+.|..|+..+-.
T Consensus 4 ~FTC~~C~~Rs~--~~~sk~aY~~GvViv~C~gC~~~HlI 41 (66)
T PF05180_consen 4 TFTCNKCGTRSA--KMFSKQAYHKGVVIVQCPGCKNRHLI 41 (66)
T ss_dssp EEEETTTTEEEE--EEEEHHHHHTSEEEEE-TTS--EEES
T ss_pred EEEcCCCCCccc--eeeCHHHHhCCeEEEECCCCcceeee
Confidence 699999998322 233332 68999999999997753
No 69
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=85.98 E-value=1.4 Score=33.84 Aligned_cols=40 Identities=15% Similarity=0.406 Sum_probs=29.8
Q ss_pred CCceecCCCCCCCCceEEEeecC----CceEEEEcccccceeEe
Q psy3498 20 LDIQFNCPFCNHEKSCEVKMDKG----RNSARIACRVCLEDFQT 59 (81)
Q Consensus 20 l~~~F~CPfC~~~~sV~v~i~k~----~~~g~l~C~~C~~~~~~ 59 (81)
....|.||.|+|.+++--.+.-. .+.-...|..||..+.+
T Consensus 255 ~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~f 298 (299)
T TIGR01385 255 VTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWKF 298 (299)
T ss_pred CcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeeee
Confidence 44679999999998887666332 24667899999987653
No 70
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=85.72 E-value=0.38 Score=35.50 Aligned_cols=36 Identities=17% Similarity=0.427 Sum_probs=24.6
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
...||.|+.+...+--|.....-..+.|..||.-+.
T Consensus 6 y~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~~ 41 (201)
T COG1326 6 YIECPSCGSEEVSHEVIKERGREPLVRCEECGTVHP 41 (201)
T ss_pred EEECCCCCcchhhHHHHHhcCCceEEEccCCCcEee
Confidence 568999995444333333334447999999999883
No 71
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=85.62 E-value=0.37 Score=24.20 Aligned_cols=22 Identities=27% Similarity=0.588 Sum_probs=15.0
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
.||.||++. ..+...|..||+.
T Consensus 4 ~Cp~Cg~~~----------~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 4 FCPNCGAEI----------DPDAKFCPNCGAK 25 (26)
T ss_pred CCcccCCcC----------CcccccChhhCCC
Confidence 599999842 2245578888864
No 72
>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=85.54 E-value=2.1 Score=26.53 Aligned_cols=36 Identities=14% Similarity=0.234 Sum_probs=28.0
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccceeEeccC
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTIN 62 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~ 62 (81)
.||.|+.-.++..-. .+++-.+.|-.||-+.+.+..
T Consensus 10 ~CP~C~~~D~i~~~~--e~~ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWR--ENGVEYVECVECGYTERQPDQ 45 (71)
T ss_pred cCCCCcCccEEEEEE--eCCceEEEecCCCCeeccCCc
Confidence 699999988665554 557999999999987765443
No 73
>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=85.38 E-value=1.5 Score=26.71 Aligned_cols=33 Identities=24% Similarity=0.443 Sum_probs=26.8
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
.||-|+.-.++..- +.+++-.+.|-.||-+-+.
T Consensus 11 ~CP~C~~~Dtl~~~--~e~~~e~vECv~Cg~~~~~ 43 (59)
T TIGR02443 11 VCPACSAQDTLAMW--KENNIELVECVECGYQEQQ 43 (59)
T ss_pred cCCCCcCccEEEEE--EeCCceEEEeccCCCcccc
Confidence 69999998887544 5678899999999976643
No 74
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=85.24 E-value=1 Score=30.38 Aligned_cols=23 Identities=30% Similarity=0.834 Sum_probs=18.0
Q ss_pred CCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 26 CPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
||.||++ -.+-.+.|..|+...+
T Consensus 1 CPvCg~~----------l~vt~l~C~~C~t~i~ 23 (113)
T PF09862_consen 1 CPVCGGE----------LVVTRLKCPSCGTEIE 23 (113)
T ss_pred CCCCCCc----------eEEEEEEcCCCCCEEE
Confidence 9999983 3456889999998653
No 75
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=84.83 E-value=1 Score=30.03 Aligned_cols=29 Identities=24% Similarity=0.602 Sum_probs=18.7
Q ss_pred CCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 26 CPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
||-||. -....++...+.+.|+.||-.++
T Consensus 5 Cp~Cgs----ll~p~~~~~~~~l~C~kCgye~~ 33 (113)
T COG1594 5 CPKCGS----LLYPKKDDEGGKLVCRKCGYEEE 33 (113)
T ss_pred cCCccC----eeEEeEcCCCcEEECCCCCcchh
Confidence 888886 22223333445899999997654
No 76
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=84.80 E-value=1.1 Score=32.34 Aligned_cols=35 Identities=20% Similarity=0.302 Sum_probs=26.8
Q ss_pred CceecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
...=.||.|+...+--+ ++...-.+.|..||+...
T Consensus 96 ~~yV~C~~C~~pdT~l~---k~~~~~~l~C~aCGa~~~ 130 (201)
T PRK12336 96 DEYVICSECGLPDTRLV---KEDRVLMLRCDACGAHRP 130 (201)
T ss_pred HheEECCCCCCCCcEEE---EcCCeEEEEcccCCCCcc
Confidence 34557999999877544 345778899999999764
No 77
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=84.54 E-value=0.83 Score=34.62 Aligned_cols=31 Identities=23% Similarity=0.536 Sum_probs=22.6
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
.-.||.||. . .+..|. ..|.+.|..||.-.+
T Consensus 11 ~~~Cp~Cg~-~--~iv~d~--~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 11 KLVCPECGS-D--KLIYDY--ERGEIVCADCGLVIE 41 (310)
T ss_pred CCcCcCCCC-C--CeeEEC--CCCeEeecccCCccc
Confidence 346999997 3 344443 569999999998654
No 78
>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=83.42 E-value=1.8 Score=25.56 Aligned_cols=26 Identities=19% Similarity=0.390 Sum_probs=19.7
Q ss_pred CCCceecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
+.+..-.||.||. -...+-.|..||.
T Consensus 22 ~~p~l~~C~~cG~-----------~~~~H~vc~~cG~ 47 (55)
T TIGR01031 22 TAPTLVVCPNCGE-----------FKLPHRVCPSCGY 47 (55)
T ss_pred cCCcceECCCCCC-----------cccCeeECCccCe
Confidence 4578888999997 2346778888883
No 79
>KOG0478|consensus
Probab=83.37 E-value=0.54 Score=40.56 Aligned_cols=36 Identities=31% Similarity=0.649 Sum_probs=27.2
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
..|.|..|||+ +.+.+++..-.--..|..|+.++++
T Consensus 263 afFrC~vC~~~--~~ve~drg~i~eP~~C~~C~~~~~~ 298 (804)
T KOG0478|consen 263 AFFRCSVCGHE--IAVESDRGRIKEPMLCKECGTTNSF 298 (804)
T ss_pred HhhhhhhcCce--EEEEeecCccCCCcccccccCcccc
Confidence 68999999996 5666666444456789999987765
No 80
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=82.79 E-value=0.82 Score=34.92 Aligned_cols=40 Identities=23% Similarity=0.507 Sum_probs=28.6
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhh
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWV 75 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~Wi 75 (81)
.||.||.. .+..+..-|.+.|..||+--+ +.+||-..+|-
T Consensus 3 ~CpeCg~~-----~~~~d~~~ge~VC~~CG~Vi~------~~~id~gpewr 42 (285)
T COG1405 3 SCPECGST-----NIITDYERGEIVCADCGLVLE------DSLIDPGPEWR 42 (285)
T ss_pred CCCCCCCc-----cceeeccCCeEEeccCCEEec------cccccCCCCcc
Confidence 69999984 333344479999999998543 24677777775
No 81
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=82.69 E-value=1.2 Score=34.55 Aligned_cols=37 Identities=16% Similarity=0.531 Sum_probs=25.7
Q ss_pred CceecCCCCCCCCceEE-EeecCCceEEEEccccccee
Q psy3498 21 DIQFNCPFCNHEKSCEV-KMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v-~i~k~~~~g~l~C~~C~~~~ 57 (81)
+..=.||.||..-..++ .+.-..|.-.+.|..|+...
T Consensus 185 ~~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW 222 (309)
T PRK03564 185 EQRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEW 222 (309)
T ss_pred cCCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcc
Confidence 45678999999775554 33334566788888888754
No 82
>PHA02540 61 DNA primase; Provisional
Probab=82.62 E-value=1.6 Score=34.11 Aligned_cols=41 Identities=20% Similarity=0.406 Sum_probs=28.7
Q ss_pred ceecCCCCCCCC------ceEEEeecCCceEEEEcccccce-----eEeccCCC
Q psy3498 22 IQFNCPFCNHEK------SCEVKMDKGRNSARIACRVCLED-----FQTTINFL 64 (81)
Q Consensus 22 ~~F~CPfC~~~~------sV~v~i~k~~~~g~l~C~~C~~~-----~~~~i~~L 64 (81)
=.|.|||||..+ |..|.-++. .+.-+|-.||++ |-+.+..|
T Consensus 26 ~~~~CPf~~ds~~~~~kpsF~V~p~k~--~~~yhCFgCGa~Gd~i~Flme~e~l 77 (337)
T PHA02540 26 YNFRCPICGDSQKDKNKARGWIYEKKD--GGVFKCHNCGYHRPFGNFLKDYEPD 77 (337)
T ss_pred EEecCCCCCCccccCcCCcEEEeccCC--ceEEEecCCCCCCCHHHHHHHhcCC
Confidence 478999999743 566665553 568899999985 44455554
No 83
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=82.58 E-value=0.56 Score=23.33 Aligned_cols=11 Identities=27% Similarity=1.301 Sum_probs=8.8
Q ss_pred CceecCCCCCC
Q psy3498 21 DIQFNCPFCNH 31 (81)
Q Consensus 21 ~~~F~CPfC~~ 31 (81)
++.|.||.|+.
T Consensus 12 ~k~~~C~~C~k 22 (26)
T PF13465_consen 12 EKPYKCPYCGK 22 (26)
T ss_dssp SSSEEESSSSE
T ss_pred CCCCCCCCCcC
Confidence 46799999984
No 84
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=82.56 E-value=1.9 Score=30.25 Aligned_cols=34 Identities=15% Similarity=0.353 Sum_probs=18.8
Q ss_pred cCCCCCCCCceEEEeec-----CCceEEEEcccccceeE
Q psy3498 25 NCPFCNHEKSCEVKMDK-----GRNSARIACRVCLEDFQ 58 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k-----~~~~g~l~C~~C~~~~~ 58 (81)
.||.|+++......+.. +-.+-...|..||-++.
T Consensus 3 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ 41 (161)
T PF03367_consen 3 LCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNN 41 (161)
T ss_dssp E-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEE
T ss_pred cCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEee
Confidence 59999986544333322 23566789999998763
No 85
>PRK05978 hypothetical protein; Provisional
Probab=82.34 E-value=0.61 Score=32.72 Aligned_cols=31 Identities=29% Similarity=0.488 Sum_probs=22.0
Q ss_pred ecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
=.||.||..+... .-..-.-+|..||+.|+.
T Consensus 34 grCP~CG~G~LF~-----g~Lkv~~~C~~CG~~~~~ 64 (148)
T PRK05978 34 GRCPACGEGKLFR-----AFLKPVDHCAACGEDFTH 64 (148)
T ss_pred CcCCCCCCCcccc-----cccccCCCccccCCcccc
Confidence 4699999865432 333345689999999874
No 86
>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=82.32 E-value=1.3 Score=36.22 Aligned_cols=34 Identities=38% Similarity=0.780 Sum_probs=26.4
Q ss_pred ecCCCCCCCCceE---EEeecC--CceEEEEccccccee
Q psy3498 24 FNCPFCNHEKSCE---VKMDKG--RNSARIACRVCLEDF 57 (81)
Q Consensus 24 F~CPfC~~~~sV~---v~i~k~--~~~g~l~C~~C~~~~ 57 (81)
..||+|||.+.+. ++.+.. ...+...|..||...
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i 239 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEI 239 (557)
T ss_pred ccCCCCCCCccccccceeecCCCCccceEEECCCCcCCC
Confidence 4799999998876 555443 467899999999754
No 87
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=81.77 E-value=1.3 Score=30.76 Aligned_cols=27 Identities=22% Similarity=0.529 Sum_probs=20.4
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
.-+||-||.. +.+ ..|.+.|-+||..+
T Consensus 28 ~~hCp~Cg~P------LF~--KdG~v~CPvC~~~~ 54 (131)
T COG1645 28 AKHCPKCGTP------LFR--KDGEVFCPVCGYRE 54 (131)
T ss_pred HhhCcccCCc------cee--eCCeEECCCCCceE
Confidence 4589999983 333 56999999999544
No 88
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=81.76 E-value=2 Score=23.40 Aligned_cols=30 Identities=27% Similarity=0.617 Sum_probs=18.1
Q ss_pred ecCCCCCCCCceEEEeec-CCceEEEEccccc
Q psy3498 24 FNCPFCNHEKSCEVKMDK-GRNSARIACRVCL 54 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k-~~~~g~l~C~~C~ 54 (81)
-.||+|+...+| ++--+ ..+.-.-.|..|.
T Consensus 6 v~CP~C~s~~~v-~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 6 VHCPRCQSTEGV-KKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeCCCCCCCCcc-eeCCCCCCCCEeEecCcCC
Confidence 479999986543 22222 2345567777773
No 89
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=81.68 E-value=0.91 Score=32.44 Aligned_cols=34 Identities=24% Similarity=0.479 Sum_probs=25.4
Q ss_pred CCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCC
Q psy3498 19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINF 63 (81)
Q Consensus 19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~ 63 (81)
+-.|.=.||.||+ .......|..||..+.-.+|+
T Consensus 305 ~~~tS~~C~~cg~-----------~~~r~~~C~~cg~~~~rD~na 338 (364)
T COG0675 305 PYYTSKTCPCCGH-----------LSGRLFKCPRCGFVHDRDVNA 338 (364)
T ss_pred CCCCcccccccCC-----------ccceeEECCCCCCeehhhHHH
Confidence 3456667999999 335788999999987665554
No 90
>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=81.14 E-value=0.98 Score=34.90 Aligned_cols=35 Identities=14% Similarity=0.475 Sum_probs=24.4
Q ss_pred eecCCCCCCCCceEEEeec--CCceEEEEccccccee
Q psy3498 23 QFNCPFCNHEKSCEVKMDK--GRNSARIACRVCLEDF 57 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k--~~~~g~l~C~~C~~~~ 57 (81)
.=.||.||..-..++.... ++|.-.++|..|+..+
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW 220 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEW 220 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcc
Confidence 4489999997766654442 4666678888887654
No 91
>KOG0402|consensus
Probab=80.39 E-value=0.72 Score=30.20 Aligned_cols=30 Identities=20% Similarity=0.654 Sum_probs=23.2
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
..++|+|||.. + + +...+|+-.|+.|...+
T Consensus 35 aky~CsfCGK~-~----v-KR~AvGiW~C~~C~kv~ 64 (92)
T KOG0402|consen 35 AKYTCSFCGKK-T----V-KRKAVGIWKCGSCKKVV 64 (92)
T ss_pred hhhhhhhcchh-h----h-hhhceeEEecCCcccee
Confidence 56899999983 2 2 23678999999998765
No 92
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=80.36 E-value=2.6 Score=25.55 Aligned_cols=28 Identities=25% Similarity=0.667 Sum_probs=21.5
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
.||-|++ .++.+++.. -.+.|.+||..-
T Consensus 13 kCp~C~n---~q~vFsha~--t~V~C~~Cg~~L 40 (59)
T PRK00415 13 KCPDCGN---EQVVFSHAS--TVVRCLVCGKTL 40 (59)
T ss_pred ECCCCCC---eEEEEecCC--cEEECcccCCCc
Confidence 6999999 466676543 688999999754
No 93
>PHA02998 RNA polymerase subunit; Provisional
Probab=80.00 E-value=3.6 Score=30.30 Aligned_cols=37 Identities=24% Similarity=0.578 Sum_probs=29.2
Q ss_pred ceecCCCCCCCCceEEEeecC----CceEEEEcccccceeE
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKG----RNSARIACRVCLEDFQ 58 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~----~~~g~l~C~~C~~~~~ 58 (81)
+.-.||.|+|.++.-..+.-. -+.-...|..||-.|.
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccC
Confidence 567899999999886666542 2567889999998875
No 94
>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=79.77 E-value=0.45 Score=28.55 Aligned_cols=18 Identities=11% Similarity=0.388 Sum_probs=14.3
Q ss_pred CCceEEEEcccccceeEe
Q psy3498 42 GRNSARIACRVCLEDFQT 59 (81)
Q Consensus 42 ~~~~g~l~C~~C~~~~~~ 59 (81)
.-.-|.+.|..||..|..
T Consensus 48 ~i~eg~L~Cp~c~r~YPI 65 (68)
T PF03966_consen 48 EIVEGELICPECGREYPI 65 (68)
T ss_dssp ETTTTEEEETTTTEEEEE
T ss_pred cccCCEEEcCCCCCEEeC
Confidence 335599999999998863
No 95
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=79.05 E-value=0.53 Score=32.64 Aligned_cols=36 Identities=25% Similarity=0.529 Sum_probs=26.3
Q ss_pred eecCCCCCCCCceEEEeecCC-ceEEEEcccccceeE
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGR-NSARIACRVCLEDFQ 58 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~-~~g~l~C~~C~~~~~ 58 (81)
.-.||+||+.++..+...-.. =.+...|..|.+-|+
T Consensus 105 ~~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~epf~ 141 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFGPTACKALYRCRACKEPFE 141 (146)
T ss_pred CCcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCcHh
Confidence 469999999888776554422 356788888987664
No 96
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=78.79 E-value=0.59 Score=25.62 Aligned_cols=14 Identities=21% Similarity=0.686 Sum_probs=9.1
Q ss_pred ceecCCCCCCCCce
Q psy3498 22 IQFNCPFCNHEKSC 35 (81)
Q Consensus 22 ~~F~CPfC~~~~sV 35 (81)
+.+.|+||++.+.|
T Consensus 23 ~~w~C~~C~~~N~l 36 (40)
T PF04810_consen 23 KTWICNFCGTKNPL 36 (40)
T ss_dssp TEEEETTT--EEE-
T ss_pred CEEECcCCCCcCCC
Confidence 68999999996554
No 97
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=78.69 E-value=2.5 Score=29.91 Aligned_cols=14 Identities=14% Similarity=0.159 Sum_probs=8.7
Q ss_pred ceEEEEccccccee
Q psy3498 44 NSARIACRVCLEDF 57 (81)
Q Consensus 44 ~~g~l~C~~C~~~~ 57 (81)
.+-...|..||.++
T Consensus 25 ii~sf~C~~CGyr~ 38 (163)
T TIGR00340 25 MLSTYICEKCGYRS 38 (163)
T ss_pred EEEEEECCCCCCch
Confidence 34466777777654
No 98
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=78.00 E-value=4 Score=31.66 Aligned_cols=55 Identities=18% Similarity=0.267 Sum_probs=31.9
Q ss_pred eecCCCCCCCCceEEE-eecC-CceEEEEcccccceeEec---cCCCCchh--hhhhhhhhh
Q psy3498 23 QFNCPFCNHEKSCEVK-MDKG-RNSARIACRVCLEDFQTT---INFLSEAI--DVYNDWVDA 77 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~-i~k~-~~~g~l~C~~C~~~~~~~---i~~L~epI--DVYs~WiD~ 77 (81)
.-.||+||....+..- ++-. ..+-.-.|..|+...-+- .++..+|+ |+-+--+|.
T Consensus 226 R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~~~~~~d~~~~p~adDlatL~LDl 287 (309)
T PRK03564 226 RVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYLKILYQEKDPKVEAVADDLASLVLDA 287 (309)
T ss_pred CccCCCCCCCCceeeeeecCCCcceEeeecccccccceecccccCCCCCcchhHHhhhHhHH
Confidence 4579999987766543 4433 345567899999865442 22223343 555555553
No 99
>PRK11827 hypothetical protein; Provisional
Probab=77.72 E-value=2.6 Score=25.53 Aligned_cols=34 Identities=21% Similarity=0.451 Sum_probs=24.0
Q ss_pred CCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 20 LDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 20 l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
|-..--||.|..+ ...+.. ...+.|..|++.|..
T Consensus 5 LLeILaCP~ckg~----L~~~~~--~~~Lic~~~~laYPI 38 (60)
T PRK11827 5 LLEIIACPVCNGK----LWYNQE--KQELICKLDNLAFPL 38 (60)
T ss_pred HHhheECCCCCCc----CeEcCC--CCeEECCccCeeccc
Confidence 4456789999872 334432 247889999999964
No 100
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=77.36 E-value=1.1 Score=20.34 Aligned_cols=8 Identities=50% Similarity=1.676 Sum_probs=3.2
Q ss_pred ecCCCCCC
Q psy3498 24 FNCPFCNH 31 (81)
Q Consensus 24 F~CPfC~~ 31 (81)
|.|+.|+.
T Consensus 1 ~~C~~C~~ 8 (24)
T PF13894_consen 1 FQCPICGK 8 (24)
T ss_dssp EE-SSTS-
T ss_pred CCCcCCCC
Confidence 45555554
No 101
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=77.04 E-value=1.2 Score=25.90 Aligned_cols=18 Identities=33% Similarity=0.720 Sum_probs=14.9
Q ss_pred CCCCCceecCCCCCCCCc
Q psy3498 17 IEPLDIQFNCPFCNHEKS 34 (81)
Q Consensus 17 ~~~l~~~F~CPfC~~~~s 34 (81)
-..||-.|.||.|+..++
T Consensus 28 f~~Lp~~w~CP~C~a~K~ 45 (50)
T cd00730 28 FEDLPDDWVCPVCGAGKD 45 (50)
T ss_pred HhHCCCCCCCCCCCCcHH
Confidence 456899999999998764
No 102
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=76.86 E-value=3.9 Score=29.58 Aligned_cols=33 Identities=21% Similarity=0.348 Sum_probs=18.9
Q ss_pred cCCCCCCCCceEEEeec------CCceEEEEccccccee
Q psy3498 25 NCPFCNHEKSCEVKMDK------GRNSARIACRVCLEDF 57 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k------~~~~g~l~C~~C~~~~ 57 (81)
+||.||.+......+-. .-.+-...|..||-++
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~ 40 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRS 40 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCcc
Confidence 58888765443333222 2234577788888765
No 103
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=76.80 E-value=2.7 Score=31.05 Aligned_cols=38 Identities=13% Similarity=0.213 Sum_probs=25.3
Q ss_pred CCceecCCCCCCCCceEEEeec------CCceEEEEcccccceeE
Q psy3498 20 LDIQFNCPFCNHEKSCEVKMDK------GRNSARIACRVCLEDFQ 58 (81)
Q Consensus 20 l~~~F~CPfC~~~~sV~v~i~k------~~~~g~l~C~~C~~~~~ 58 (81)
..+.-+||.||+ ........- .-.+-...|..||-++.
T Consensus 11 ~~~~~~CPvCg~-~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 11 FETRIDCPVCGG-TLKAHMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred eeeeecCCcccc-eeeEEEeeecCCccceEEEEEEEccccCCccc
Confidence 457779999999 332222221 12567899999998764
No 104
>KOG2906|consensus
Probab=76.66 E-value=5.4 Score=26.78 Aligned_cols=30 Identities=30% Similarity=0.779 Sum_probs=22.5
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
=||-||+ ...+......-.++|+.|+-.|.
T Consensus 3 FCP~Cgn----~Live~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 3 FCPTCGN----MLIVESGESCNRFSCRTCPYVFP 32 (105)
T ss_pred ccCCCCC----EEEEecCCeEeeEEcCCCCceee
Confidence 4999997 44455555578999999997664
No 105
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=76.54 E-value=1.2 Score=25.65 Aligned_cols=18 Identities=39% Similarity=0.757 Sum_probs=12.1
Q ss_pred CCCCCceecCCCCCCCCc
Q psy3498 17 IEPLDIQFNCPFCNHEKS 34 (81)
Q Consensus 17 ~~~l~~~F~CPfC~~~~s 34 (81)
-..||.-|.||.|++.++
T Consensus 28 F~~Lp~~w~CP~C~a~K~ 45 (47)
T PF00301_consen 28 FEDLPDDWVCPVCGAPKS 45 (47)
T ss_dssp GGGS-TT-B-TTTSSBGG
T ss_pred HHHCCCCCcCcCCCCccc
Confidence 467999999999998654
No 106
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=76.38 E-value=4.1 Score=28.60 Aligned_cols=13 Identities=15% Similarity=0.238 Sum_probs=7.3
Q ss_pred eEEEEccccccee
Q psy3498 45 SARIACRVCLEDF 57 (81)
Q Consensus 45 ~g~l~C~~C~~~~ 57 (81)
+-...|..||-++
T Consensus 27 i~sf~C~~CGyk~ 39 (160)
T smart00709 27 IMSFECEHCGYRN 39 (160)
T ss_pred EEEEECCCCCCcc
Confidence 3455666666543
No 107
>KOG2767|consensus
Probab=76.37 E-value=0.8 Score=36.73 Aligned_cols=38 Identities=18% Similarity=0.460 Sum_probs=28.9
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEecc
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTI 61 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i 61 (81)
+.-.||+|+++.+ .+.|.+++++ ...|.-||.+..+..
T Consensus 95 KFVlC~~C~NPET-el~itk~q~i-~~~CkACG~r~~~d~ 132 (400)
T KOG2767|consen 95 KFVLCPSCENPET-ELIITKKQTI-SLKCKACGFRSDMDL 132 (400)
T ss_pred HheeCcCCCCCce-eEEecccchh-hhHHHHcCCcccccc
Confidence 4567999999776 6666665544 569999999887765
No 108
>PRK00420 hypothetical protein; Validated
Probab=76.37 E-value=2 Score=28.92 Aligned_cols=30 Identities=17% Similarity=0.438 Sum_probs=21.7
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
.-.||.||.+ +.+ ...|...|-+||..+..
T Consensus 23 ~~~CP~Cg~p------Lf~-lk~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 23 SKHCPVCGLP------LFE-LKDGEVVCPVHGKVYIV 52 (112)
T ss_pred cCCCCCCCCc------cee-cCCCceECCCCCCeeee
Confidence 3689999983 111 14579999999997753
No 109
>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=76.30 E-value=4.1 Score=31.51 Aligned_cols=36 Identities=14% Similarity=0.442 Sum_probs=22.8
Q ss_pred eecCCCCCCCCceE-EEeec---CCceEEEEcccccceeE
Q psy3498 23 QFNCPFCNHEKSCE-VKMDK---GRNSARIACRVCLEDFQ 58 (81)
Q Consensus 23 ~F~CPfC~~~~sV~-v~i~k---~~~~g~l~C~~C~~~~~ 58 (81)
.-.||+||+.+.+. ..++- ...+-.-.|..|+...-
T Consensus 224 R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK 263 (305)
T TIGR01562 224 RVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYLK 263 (305)
T ss_pred CccCCCCCCCCceeeEeecCCCCCcceEEeeccccccchh
Confidence 45799999877654 33433 12344558999997543
No 110
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=76.30 E-value=0.97 Score=32.44 Aligned_cols=31 Identities=23% Similarity=0.414 Sum_probs=21.7
Q ss_pred ecCCCCCCCCceEEEeecCCceE------------EEEccccccee
Q psy3498 24 FNCPFCNHEKSCEVKMDKGRNSA------------RIACRVCLEDF 57 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~~~~g------------~l~C~~C~~~~ 57 (81)
=.||.||. .-+++.+..-.+ ...|.+||.-|
T Consensus 98 ~RCp~CN~---~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 98 SRCPECNG---ELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred ccCcccCC---EeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 36999998 466666655333 33499999876
No 111
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=76.20 E-value=3.6 Score=27.33 Aligned_cols=33 Identities=24% Similarity=0.567 Sum_probs=23.9
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
-.+.|+.|+.+ +...++.......|+.|+..+.
T Consensus 122 ~~~~C~~C~~~----~~r~~~~~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 122 YVYRCPSCGRE----YKRHRRSKRKRYRCGRCGGPLV 154 (157)
T ss_pred eEEEcCCCCCE----eeeecccchhhEECCCCCCEEE
Confidence 47899999983 3444444666789999997664
No 112
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=76.09 E-value=3 Score=33.87 Aligned_cols=50 Identities=18% Similarity=0.397 Sum_probs=29.4
Q ss_pred ceecCCCCCCCCceEEEee----------cCCceEEEEcccccceeEeccCC-CCchhhhhh
Q psy3498 22 IQFNCPFCNHEKSCEVKMD----------KGRNSARIACRVCLEDFQTTINF-LSEAIDVYN 72 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~----------k~~~~g~l~C~~C~~~~~~~i~~-L~epIDVYs 72 (81)
.-|+||.|.+.=+|...-. ...+...+.|.-|.=+.. .|+- .+.|=+++.
T Consensus 51 ~Cf~CP~C~~~L~~~~~~~~~~~~~~~~~~~~~~~~l~C~~C~Wss~-~igi~Fdkpt~l~~ 111 (483)
T PF05502_consen 51 NCFDCPICFSPLSVRASDTPPSPPDPSSDSGGKPYYLSCSYCRWSSR-DIGIKFDKPTGLRA 111 (483)
T ss_pred ccccCCCCCCcceeEecccccccccccccCCCCCEEEECCCceeecc-ccCccccCchhHHH
Confidence 5699999998544332221 124677999999986532 2333 244444443
No 113
>MTH00038 COX2 cytochrome c oxidase subunit II; Provisional
Probab=76.08 E-value=2.1 Score=31.40 Aligned_cols=50 Identities=12% Similarity=0.248 Sum_probs=36.1
Q ss_pred CCCCceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhhhcCC
Q psy3498 30 NHEKSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVDASVP 80 (81)
Q Consensus 30 ~~~~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD~c~~ 80 (81)
|..+.+....++ .|+....|.. ||..+. |++.--..+-|.|.+|+++..|
T Consensus 177 G~~~~~~~~~~~-~G~~~g~Cse~CG~~Hs~M~~~v~vv~~~~f~~W~~~~~~ 228 (229)
T MTH00038 177 GRLNQTTFFISR-TGLFYGQCSEICGANHSFMPIVIESVPFNTFENWVSNFLE 228 (229)
T ss_pred CceEEEEEEcCC-CEEEEEEcccccCcCcCCCeEEEEEeCHHHHHHHHHHhhc
Confidence 445556666654 6788899998 999876 4655555677889999987655
No 114
>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=75.96 E-value=0.92 Score=23.98 Aligned_cols=25 Identities=24% Similarity=0.782 Sum_probs=11.2
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
.||.|+.+.+. ..-..+.|..|+-.
T Consensus 4 ~Cp~C~se~~y-------~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCPLCGSEYTY-------EDGELLVCPECGHE 28 (30)
T ss_dssp --TTT-----E-------E-SSSEEETTTTEE
T ss_pred CCCCCCCccee-------ccCCEEeCCccccc
Confidence 58899887766 22245678888754
No 115
>PF05077 DUF678: Protein of unknown function (DUF678); InterPro: IPR007769 This family contains poxvirus proteins belonging to the A19 family. The proteins are of unknown function.
Probab=74.83 E-value=2.4 Score=26.86 Aligned_cols=33 Identities=21% Similarity=0.459 Sum_probs=19.5
Q ss_pred ecCCCCCCCCceEEEeecC-----------CceEEEEcccccce
Q psy3498 24 FNCPFCNHEKSCEVKMDKG-----------RNSARIACRVCLED 56 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~-----------~~~g~l~C~~C~~~ 56 (81)
-+|+-|..=+|=-|+|.-- ...+.|+|..||..
T Consensus 23 d~c~tCSsC~SkLV~~Sdvtk~sl~~~~~~g~~~tLsCsACGS~ 66 (74)
T PF05077_consen 23 DDCTTCSSCQSKLVKFSDVTKVSLDEYKVAGKGNTLSCSACGSE 66 (74)
T ss_pred CCccchhhhhhheeeeecccceehhhhcccCCCCeEeehhcccc
Confidence 5666665544444444321 12368999999964
No 116
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=74.72 E-value=1.9 Score=25.57 Aligned_cols=26 Identities=31% Similarity=0.532 Sum_probs=16.3
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
.||.||. .+ -|- .-.-...|+.||-.
T Consensus 21 ~CPrCG~-gv---fmA--~H~dR~~CGkCgyT 46 (51)
T COG1998 21 FCPRCGP-GV---FMA--DHKDRWACGKCGYT 46 (51)
T ss_pred cCCCCCC-cc---hhh--hcCceeEeccccce
Confidence 4999996 22 221 11128999999953
No 117
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=74.41 E-value=4.1 Score=26.01 Aligned_cols=34 Identities=21% Similarity=0.467 Sum_probs=19.3
Q ss_pred CCCCCCCCceEEEeec----CC-----ceEEEEcccccceeEe
Q psy3498 26 CPFCNHEKSCEVKMDK----GR-----NSARIACRVCLEDFQT 59 (81)
Q Consensus 26 CPfC~~~~sV~v~i~k----~~-----~~g~l~C~~C~~~~~~ 59 (81)
||+|+....+....+. +. .+....|..||..|-+
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~~~ 43 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEELLD 43 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEEEc
Confidence 9999964443222221 11 2235579999987643
No 118
>KOG1814|consensus
Probab=73.97 E-value=2.8 Score=34.19 Aligned_cols=52 Identities=15% Similarity=0.337 Sum_probs=42.9
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhhhhcC
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASV 79 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~WiD~c~ 79 (81)
..=+||-|.- -|.|.+|--.-+|..||+.|-.--..+..|.|.|.-|-|..-
T Consensus 367 N~krCP~C~v------~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~~nPYkHF~e~~s 418 (445)
T KOG1814|consen 367 NSKRCPKCKV------VIERSEGCNKMHCTKCGTYFCWICAELLYPENPYKHFSEPGS 418 (445)
T ss_pred cCCCCCcccc------eeecCCCccceeeccccccceeehhhhcCCCChhhhhcCCcC
Confidence 4457999974 466677888999999999999999999999999998877643
No 119
>PF15616 TerY-C: TerY-C metal binding domain
Probab=73.83 E-value=3.1 Score=28.71 Aligned_cols=35 Identities=20% Similarity=0.451 Sum_probs=22.8
Q ss_pred cCCCCCCCCceEEE-eec---CCceEEEEcccccceeEe
Q psy3498 25 NCPFCNHEKSCEVK-MDK---GRNSARIACRVCLEDFQT 59 (81)
Q Consensus 25 ~CPfC~~~~sV~v~-i~k---~~~~g~l~C~~C~~~~~~ 59 (81)
.||.||+...+.+- =-+ =.+-+.+.|.-||.+-.+
T Consensus 79 gCP~CGn~~~fa~C~CGkl~Ci~g~~~~~CPwCg~~g~~ 117 (131)
T PF15616_consen 79 GCPHCGNQYAFAVCGCGKLFCIDGEGEVTCPWCGNEGSF 117 (131)
T ss_pred CCCCCcChhcEEEecCCCEEEeCCCCCEECCCCCCeeee
Confidence 69999998444432 111 134568999999986554
No 120
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=73.40 E-value=5.2 Score=22.45 Aligned_cols=34 Identities=21% Similarity=0.402 Sum_probs=22.3
Q ss_pred ceecCC--CCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 22 IQFNCP--FCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 22 ~~F~CP--fC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
+.--|| .|+. .+..+...+...+.|..||..|-+
T Consensus 17 ~~~~CP~~~C~~----~~~~~~~~~~~~v~C~~C~~~fC~ 52 (64)
T smart00647 17 DLKWCPAPDCSA----AIIVTEEEGCNRVTCPKCGFSFCF 52 (64)
T ss_pred CccCCCCCCCcc----eEEecCCCCCCeeECCCCCCeECC
Confidence 444699 9976 222322335568999999988854
No 121
>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=72.37 E-value=1.8 Score=24.32 Aligned_cols=34 Identities=29% Similarity=0.528 Sum_probs=17.1
Q ss_pred ceecCCC--CCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 22 IQFNCPF--CNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 22 ~~F~CPf--C~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
..-.||. |++ .+.++.......+.|..|+..|-+
T Consensus 17 ~~~~Cp~~~C~~----~~~~~~~~~~~~~~C~~C~~~fC~ 52 (64)
T PF01485_consen 17 NIRWCPNPDCEY----IIEKDDGCNSPIVTCPSCGTEFCF 52 (64)
T ss_dssp -CC--TTSST-------ECS-SSTTS--CCTTSCCSEECS
T ss_pred CccCCCCCCCcc----cEEecCCCCCCeeECCCCCCcCcc
Confidence 4458988 987 444444444446899999988854
No 122
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=70.62 E-value=1.9 Score=32.61 Aligned_cols=22 Identities=36% Similarity=0.906 Sum_probs=15.6
Q ss_pred CCCceecCCCCCCCC-ceEEEeec
Q psy3498 19 PLDIQFNCPFCNHEK-SCEVKMDK 41 (81)
Q Consensus 19 ~l~~~F~CPfC~~~~-sV~v~i~k 41 (81)
++. .|-||||||.+ .|.-.+|.
T Consensus 211 ~~~-efiC~~Cn~~n~~~~~~~ds 233 (251)
T COG5415 211 PII-EFICPHCNHKNDEVKEREDS 233 (251)
T ss_pred cch-heecccchhhcCcccccccc
Confidence 344 79999999987 55555554
No 123
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=70.60 E-value=5.8 Score=24.18 Aligned_cols=40 Identities=23% Similarity=0.509 Sum_probs=28.0
Q ss_pred CCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEe--ccCCC
Q psy3498 19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT--TINFL 64 (81)
Q Consensus 19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~--~i~~L 64 (81)
+|--..-||.|.+. ...+... ..+.|..|++-|-. .|+-|
T Consensus 4 ~LLeiLaCP~~kg~----L~~~~~~--~~L~c~~~~~aYpI~dGIPvl 45 (60)
T COG2835 4 RLLEILACPVCKGP----LVYDEEK--QELICPRCKLAYPIRDGIPVL 45 (60)
T ss_pred hhheeeeccCcCCc----ceEeccC--CEEEecccCceeecccCcccc
Confidence 35567789999995 3333333 49999999999964 35544
No 124
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=69.63 E-value=6.1 Score=20.95 Aligned_cols=25 Identities=24% Similarity=0.599 Sum_probs=15.4
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
.+.|+.||+. ..-+. +--.|-+||+
T Consensus 2 ~~~C~~CG~i----~~g~~----~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYI----HEGEE----APEKCPICGA 26 (34)
T ss_pred eEECCCCCCE----eECCc----CCCcCcCCCC
Confidence 5788899882 11111 2338888887
No 125
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 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 CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=69.55 E-value=7.3 Score=24.75 Aligned_cols=32 Identities=19% Similarity=0.472 Sum_probs=16.2
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
...||||+.. +=+..++.+. +.-.|-.||...
T Consensus 33 ~~~CPfH~d~-~pS~~i~~~k--~~~~Cf~Cg~~G 64 (97)
T PF01807_consen 33 RCLCPFHDDK-TPSFSINPDK--NRFKCFGCGKGG 64 (97)
T ss_dssp EE--SSS--S-S--EEEETTT--TEEEETTT--EE
T ss_pred EEECcCCCCC-CCceEEECCC--CeEEECCCCCCC
Confidence 5789999954 3345554433 468999999865
No 126
>MTH00129 COX2 cytochrome c oxidase subunit II; Provisional
Probab=69.51 E-value=3.8 Score=30.13 Aligned_cols=50 Identities=8% Similarity=0.201 Sum_probs=36.0
Q ss_pred CCCCceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhhhcCC
Q psy3498 30 NHEKSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVDASVP 80 (81)
Q Consensus 30 ~~~~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD~c~~ 80 (81)
|..+.+....++ .|+....|.. ||..+. +++.-...+.+.|.+|+..-+|
T Consensus 177 G~~~~~~~~~~~-~G~~~g~C~e~CG~~H~~M~~~v~vv~~~~f~~Wl~~~~~ 228 (230)
T MTH00129 177 GRLNQTAFIASR-PGVFYGQCSEICGANHSFMPIVVEAVPLEHFENWSSLMLE 228 (230)
T ss_pred CceEEEEEEeCC-ceEEEEEChhhccccccCCcEEEEEECHHHHHHHHHHhhh
Confidence 444555555554 5677888988 999775 4666666778999999987655
No 127
>TIGR02996 rpt_mate_G_obs repeat-companion domain TIGR02996. This model describes an abundant paralogous domain of Gemmata obscuriglobus UQM 2246, a member of the Planctomycetes. The domain also occurs, although rarely, in Myxococcus xanthus DK 1622 and related species. Most member proteins have extensive repeats similar to the leucine-rich repeat, or another repeat class or region of low-complexity sequence. This domain is not repeated, and in Gemmata is usually found at the protein N-terminus.
Probab=69.36 E-value=2.1 Score=24.41 Aligned_cols=13 Identities=38% Similarity=0.767 Sum_probs=9.6
Q ss_pred chhhhhhhhhhhc
Q psy3498 66 EAIDVYNDWVDAS 78 (81)
Q Consensus 66 epIDVYs~WiD~c 78 (81)
.|==||.+|+|+-
T Consensus 17 t~RLvYADWL~e~ 29 (42)
T TIGR02996 17 TPRLVYADWLDEH 29 (42)
T ss_pred chHHHHHHHHHHc
Confidence 3444999999963
No 128
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=68.72 E-value=2.2 Score=22.39 Aligned_cols=13 Identities=31% Similarity=0.869 Sum_probs=10.3
Q ss_pred ceecCCCCCCCCc
Q psy3498 22 IQFNCPFCNHEKS 34 (81)
Q Consensus 22 ~~F~CPfC~~~~s 34 (81)
..+.||.||+.++
T Consensus 16 ~~~~CP~Cg~~~~ 28 (33)
T cd00350 16 APWVCPVCGAPKD 28 (33)
T ss_pred CCCcCcCCCCcHH
Confidence 5789999998654
No 129
>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=68.61 E-value=2.8 Score=27.85 Aligned_cols=36 Identities=25% Similarity=0.495 Sum_probs=25.6
Q ss_pred CCCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEec
Q psy3498 18 EPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60 (81)
Q Consensus 18 ~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~ 60 (81)
+-|=|-..||.||.. .-..+.--|.|-.||..|...
T Consensus 4 pelGtKR~Cp~CG~k-------FYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 4 PELGTKRTCPSCGAK-------FYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCcccCCCCcch-------hccCCCCCccCCCCCCccCcc
Confidence 457778889999972 223344667899999988754
No 130
>KOG2907|consensus
Probab=68.45 E-value=3.6 Score=28.08 Aligned_cols=36 Identities=22% Similarity=0.509 Sum_probs=25.5
Q ss_pred ecCCCCCCCCceEEEeecC----CceEEEEcccccceeEe
Q psy3498 24 FNCPFCNHEKSCEVKMDKG----RNSARIACRVCLEDFQT 59 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~----~~~g~l~C~~C~~~~~~ 59 (81)
-.||-|||+...-=++... ...-.-.|-+|+-.|.+
T Consensus 75 ~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred ccCcccCCchhhhhhhhcccccCCceEEEEcCccceeeec
Confidence 3699999997765555442 23457789999988764
No 131
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=68.37 E-value=6.4 Score=26.69 Aligned_cols=31 Identities=23% Similarity=0.358 Sum_probs=20.8
Q ss_pred ecCCCCCCCCceEEEeecCCc------------eEEEEccccccee
Q psy3498 24 FNCPFCNHEKSCEVKMDKGRN------------SARIACRVCLEDF 57 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~~~------------~g~l~C~~C~~~~ 57 (81)
=.|+.||. .-..+++... --.-.|..||.-|
T Consensus 92 sRC~~CN~---~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 92 SRCPKCNG---PLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CccCCCCc---EeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 36999998 3444455422 1267899999877
No 132
>PLN00209 ribosomal protein S27; Provisional
Probab=68.31 E-value=8.1 Score=25.10 Aligned_cols=37 Identities=14% Similarity=0.388 Sum_probs=26.9
Q ss_pred CCCCCcee---cCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 17 IEPLDIQF---NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 17 ~~~l~~~F---~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
++...+.| .||-|++ +++.++. ..-.+.|.+||....
T Consensus 27 v~~PnS~Fm~VkCp~C~n---~q~VFSh--A~t~V~C~~Cg~~L~ 66 (86)
T PLN00209 27 VQSPNSFFMDVKCQGCFN---ITTVFSH--SQTVVVCGSCQTVLC 66 (86)
T ss_pred ecCCCCEEEEEECCCCCC---eeEEEec--CceEEEccccCCEee
Confidence 44455666 7999999 4666755 347889999998654
No 133
>MTH00008 COX2 cytochrome c oxidase subunit II; Validated
Probab=68.27 E-value=4.7 Score=29.59 Aligned_cols=49 Identities=10% Similarity=0.202 Sum_probs=34.8
Q ss_pred CCCCceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhhhcC
Q psy3498 30 NHEKSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVDASV 79 (81)
Q Consensus 30 ~~~~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD~c~ 79 (81)
|.-+.+....++ .|+....|.. ||..+. +++.-...+.+.|.+|+.+.-
T Consensus 177 G~~~~~~~~~~~-~G~~~g~Cse~CG~~Hs~M~~~v~vv~~~~f~~Wl~~~~ 227 (228)
T MTH00008 177 GRLNQIGFTITR-PGVFYGQCSEICGANHSFMPIVLEAVDTKSFMKWVSSFA 227 (228)
T ss_pred CceEEEEEEeCC-CEEEEEEChhhcCcCccCceeEEEEECHHHHHHHHHhcC
Confidence 344455555544 5777899987 999876 466666677889999997653
No 134
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=67.20 E-value=12 Score=30.36 Aligned_cols=38 Identities=18% Similarity=0.405 Sum_probs=28.6
Q ss_pred cCCCCCCCCceEE-EeecCCceEEEEcccccceeEeccCC
Q psy3498 25 NCPFCNHEKSCEV-KMDKGRNSARIACRVCLEDFQTTINF 63 (81)
Q Consensus 25 ~CPfC~~~~sV~v-~i~k~~~~g~l~C~~C~~~~~~~i~~ 63 (81)
-||.||.-.++.+ ..|-..+.-.-.|. ||-..+..|..
T Consensus 177 ic~~cg~~~~~~~~~~d~~~~~v~y~~~-cG~~~~~~~~~ 215 (510)
T PRK00750 177 ICPKCGKVLTTPVISYDAEAGTVTYDCE-CGHEGEVPVTG 215 (510)
T ss_pred eCCCCCccceEEEEEEeCCCCEEEEEcC-CCCEEEEecCC
Confidence 4999999988776 67666655555675 99988887764
No 135
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=67.13 E-value=4.6 Score=34.69 Aligned_cols=29 Identities=21% Similarity=0.622 Sum_probs=20.5
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
.+|.||+|+. ..++.+.. +.+.|.-||-.
T Consensus 443 ~v~~Cp~Cd~----~lt~H~~~--~~L~CH~Cg~~ 471 (730)
T COG1198 443 YIAECPNCDS----PLTLHKAT--GQLRCHYCGYQ 471 (730)
T ss_pred CcccCCCCCc----ceEEecCC--CeeEeCCCCCC
Confidence 5788999986 44554433 78888888865
No 136
>PF14122 YokU: YokU-like protein
Probab=66.95 E-value=4.7 Score=26.26 Aligned_cols=35 Identities=23% Similarity=0.550 Sum_probs=22.7
Q ss_pred cCCCCCCCCceEEEeec----C--------CceEEEEcccccceeEe
Q psy3498 25 NCPFCNHEKSCEVKMDK----G--------RNSARIACRVCLEDFQT 59 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k----~--------~~~g~l~C~~C~~~~~~ 59 (81)
.|-.|+..+++...-.- - ...-.+.|..||..|+.
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~ 47 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQD 47 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEeh
Confidence 47888876555433211 1 23457899999999975
No 137
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=66.67 E-value=3.5 Score=24.21 Aligned_cols=14 Identities=36% Similarity=0.968 Sum_probs=11.1
Q ss_pred CCCceecCCCCCCC
Q psy3498 19 PLDIQFNCPFCNHE 32 (81)
Q Consensus 19 ~l~~~F~CPfC~~~ 32 (81)
.-+..|.||+||+-
T Consensus 40 ~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 40 FEEIQYRCPYCGAL 53 (54)
T ss_pred CCceEEEcCCCCCc
Confidence 34569999999984
No 138
>MTH00185 COX2 cytochrome c oxidase subunit II; Provisional
Probab=66.55 E-value=4 Score=30.01 Aligned_cols=48 Identities=8% Similarity=0.224 Sum_probs=33.4
Q ss_pred CCceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhhhcCC
Q psy3498 32 EKSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVDASVP 80 (81)
Q Consensus 32 ~~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD~c~~ 80 (81)
.+.+....++ .|+....|.. ||..+. +++.-...+-|.|.+|+++..|
T Consensus 179 ~~~~~~~~~~-~G~~~g~Cse~CG~~Hs~M~~~v~vv~~~~f~~W~~~~~~ 228 (230)
T MTH00185 179 LNQATFIISR-PGLYYGQCSEICGANHSFMPIVVEAVPLEHFENWSSLMLE 228 (230)
T ss_pred eEEEEEEeCC-cEEEEEEchhhcCcCcCCCeEEEEEECHHHHHHHHHHHHh
Confidence 3444444443 4667788987 999775 4666555678899999988655
No 139
>KOG2703|consensus
Probab=66.45 E-value=2.7 Score=34.30 Aligned_cols=13 Identities=38% Similarity=1.196 Sum_probs=10.8
Q ss_pred CCceecCCCCCCC
Q psy3498 20 LDIQFNCPFCNHE 32 (81)
Q Consensus 20 l~~~F~CPfC~~~ 32 (81)
+--.|.||+|||.
T Consensus 65 VimSF~CpHCG~k 77 (460)
T KOG2703|consen 65 VIMSFECPHCGHK 77 (460)
T ss_pred eeEEeecCccCCc
Confidence 4468999999994
No 140
>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=66.00 E-value=1.7 Score=31.10 Aligned_cols=54 Identities=20% Similarity=0.369 Sum_probs=31.1
Q ss_pred ceecCCCCCCCCc----e--EEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhhhhcCC
Q psy3498 22 IQFNCPFCNHEKS----C--EVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVP 80 (81)
Q Consensus 22 ~~F~CPfC~~~~s----V--~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~WiD~c~~ 80 (81)
++=.||.|++.-- | .+.+. ....+--.|.+||..|....+.| +.+.+-+++.+|
T Consensus 38 tI~~Cp~C~~~IrG~y~v~gv~~~g-~~~~~PsYC~~CGkpyPWt~~~L----~aa~el~ee~ee 97 (158)
T PF10083_consen 38 TITSCPNCSTPIRGDYHVEGVFGLG-GHYEAPSYCHNCGKPYPWTENAL----EAANELIEEDEE 97 (158)
T ss_pred HHHHCcCCCCCCCCceecCCeeeeC-CCCCCChhHHhCCCCCchHHHHH----HHHHHHHHHhhc
Confidence 4568999998311 0 00110 12223448999999987766554 555666665544
No 141
>KOG2593|consensus
Probab=65.92 E-value=1.8 Score=35.29 Aligned_cols=38 Identities=16% Similarity=0.385 Sum_probs=23.9
Q ss_pred CceecCCCCCCCCc-eEEEeecCCceEEEEcccccceeE
Q psy3498 21 DIQFNCPFCNHEKS-CEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 21 ~~~F~CPfC~~~~s-V~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
..-|-||+|+..=+ +.+---.....|...|..||-.-.
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelv 164 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELV 164 (436)
T ss_pred cccccCCccccchhhhHHHHhhcccCceEEEecCCCchh
Confidence 35799999998522 111111123468999999997543
No 142
>TIGR01433 CyoA cytochrome o ubiquinol oxidase subunit II. This enzyme catalyzes the oxidation of ubiquinol with the concomitant reduction of molecular oxygen to water. This acts as the terminal electron acceptor in the respiratory chain. Subunit II is responsible for binding and oxidation of the ubiquinone substrate. This sequence is closely related to QoxA, which oxidizes quinol in gram positive bacteria but which is in complex with subunits which utilize cytochromes a in the reduction of molecular oxygen. Slightly more distantly related is subunit II of cytochrome c oxidase which uses cyt. c as the oxidant.
Probab=65.64 E-value=5.2 Score=29.34 Aligned_cols=48 Identities=6% Similarity=0.119 Sum_probs=34.3
Q ss_pred CCCCceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhhhc
Q psy3498 30 NHEKSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVDAS 78 (81)
Q Consensus 30 ~~~~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD~c 78 (81)
|+.+.+..+.++ .|.....|.. ||..|. |.+.-.-.+-|-|.+|+++.
T Consensus 176 G~~n~~~~~~~~-~G~y~g~CaE~CG~~Ha~M~~~V~v~~~~~F~~Wl~~~ 225 (226)
T TIGR01433 176 GMQTKLHLIANE-PGVYDGISANYSGPGFSGMKFKAIATDRAAFDQWVAKV 225 (226)
T ss_pred CceEEEEEEeCC-CEEEEEEchhhcCcCccCCeEEEEEECHHHHHHHHHhc
Confidence 455566666665 6788899998 999775 44444445678999999763
No 143
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=65.37 E-value=9.6 Score=22.70 Aligned_cols=30 Identities=20% Similarity=0.553 Sum_probs=18.6
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
.||-|++ +++.+++.. -.+.|.+||..-..
T Consensus 9 kCp~C~~---~q~vFSha~--t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 9 KCPGCYN---IQTVFSHAQ--TVVKCVVCGTVLAQ 38 (55)
T ss_dssp E-TTT-S---EEEEETT-S--S-EE-SSSTSEEEE
T ss_pred ECCCCCC---eeEEEecCC--eEEEcccCCCEecC
Confidence 6999999 466676644 67899999986543
No 144
>KOG1296|consensus
Probab=65.35 E-value=5.9 Score=28.36 Aligned_cols=33 Identities=21% Similarity=0.446 Sum_probs=25.1
Q ss_pred eecCCCCCCCCceEEEeecC-----------CceEEEEcccccc
Q psy3498 23 QFNCPFCNHEKSCEVKMDKG-----------RNSARIACRVCLE 55 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~-----------~~~g~l~C~~C~~ 55 (81)
+-.|-||+.++||++.-+.. .-+...-|+-|..
T Consensus 64 v~KCK~C~Rensv~iv~~~~~pyt~ed~e~~~~i~vfdCRG~Ep 107 (161)
T KOG1296|consen 64 VMKCKFCSRENSVTIVAFEDKPYTAEDSEKFKTIVVFDCRGLEP 107 (161)
T ss_pred hhhhhhhcccCcEEEecCCCCcccccccccccceEEEeccCCcc
Confidence 45799999999999876553 2466888988864
No 145
>MTH00139 COX2 cytochrome c oxidase subunit II; Provisional
Probab=65.09 E-value=4.6 Score=29.40 Aligned_cols=47 Identities=9% Similarity=0.181 Sum_probs=33.5
Q ss_pred CCCCceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhhh
Q psy3498 30 NHEKSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVDA 77 (81)
Q Consensus 30 ~~~~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD~ 77 (81)
|..+.+..+.++ .|+....|.. ||..+. +++.--..+-+.|.+|+++
T Consensus 177 G~~n~~~~~~~~-~G~y~g~CsE~CG~~Hs~M~~~v~vv~~~~f~~Wl~~ 225 (226)
T MTH00139 177 GRLNQVGFFINR-PGVFYGQCSEICGANHSFMPIVVEAISPKFFLEWILE 225 (226)
T ss_pred CcEEEEEEEcCC-CEEEEEEChhhcCcCcCCCeEEEEEeCHHHHHHHHhh
Confidence 555556666554 5788999998 999775 4555444567899999974
No 146
>MTH00117 COX2 cytochrome c oxidase subunit II; Provisional
Probab=64.88 E-value=6 Score=28.98 Aligned_cols=48 Identities=10% Similarity=0.187 Sum_probs=33.1
Q ss_pred CCCCceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhhhc
Q psy3498 30 NHEKSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVDAS 78 (81)
Q Consensus 30 ~~~~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD~c 78 (81)
|..+.+....++ .|+....|.. ||+.+. |++.--..+.+-|.+|+++.
T Consensus 177 G~~n~~~~~~~~-~G~y~g~CsE~CG~~Hs~M~~~v~vv~~~~f~~Wl~~~ 226 (227)
T MTH00117 177 GRLNQTSFITTR-PGVFYGQCSEICGANHSFMPIVVESVPLKHFENWSSLL 226 (227)
T ss_pred CceEEEEEEEcc-cceEEEEeccccccCccCCeEEEEEcCHHHHHHHHHhc
Confidence 344555666554 5677889988 999876 35555445668899999864
No 147
>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=64.36 E-value=1.5 Score=31.12 Aligned_cols=38 Identities=16% Similarity=0.492 Sum_probs=17.0
Q ss_pred CceecCCCCCCCCceEEEeecCC---ceEEEEcccccceeE
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKGR---NSARIACRVCLEDFQ 58 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~~---~~g~l~C~~C~~~~~ 58 (81)
|=.|.||.|+++..+.=.+.... ....+.|.+|+..+.
T Consensus 16 ~l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~~~~ 56 (188)
T PF08996_consen 16 PLKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCSTPLS 56 (188)
T ss_dssp -EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--B--
T ss_pred ceEeECCCCCCCccccccccCCccccccCcCcCCCCCCcCC
Confidence 34899999999544332222111 233789999998554
No 148
>MTH00154 COX2 cytochrome c oxidase subunit II; Provisional
Probab=64.07 E-value=5.9 Score=29.04 Aligned_cols=47 Identities=11% Similarity=0.257 Sum_probs=35.1
Q ss_pred CCCCceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhhh
Q psy3498 30 NHEKSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVDA 77 (81)
Q Consensus 30 ~~~~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD~ 77 (81)
|..+.+....++ .|+....|.. ||..+. +++.-.-.+-+.|.+|+.+
T Consensus 177 G~~~~~~~~~~~-~G~y~g~Cse~CG~~H~~M~~~v~vv~~~~f~~Wl~~ 225 (227)
T MTH00154 177 GRLNQLNFLINR-PGLFFGQCSEICGANHSFMPIVIESVSVNNFINWIKN 225 (227)
T ss_pred CceEEEEEEEcC-ceEEEEEeechhCcCccCCeEEEEEeCHHHHHHHHHh
Confidence 555666666665 5788999988 999876 4666555678889999965
No 149
>KOG1597|consensus
Probab=63.89 E-value=5.7 Score=31.10 Aligned_cols=42 Identities=21% Similarity=0.530 Sum_probs=29.5
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhh
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWV 75 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~Wi 75 (81)
.||-|....- .+.-| ..-|...|..||+.++. -.||+-|+|-
T Consensus 2 ~c~~C~~~~~-~~V~d--~~~gdtvC~~CGlVl~~------r~Id~~sEwr 43 (308)
T KOG1597|consen 2 TCPDCKRHPE-NLVED--HSAGDTVCSECGLVLED------RIIDEGSEWR 43 (308)
T ss_pred CCCCCCCCCC-Ceeee--ccCCceecccCCeeecc------cccccccccc
Confidence 4788876655 33333 35588899999998874 4578888884
No 150
>MTH00051 COX2 cytochrome c oxidase subunit II; Provisional
Probab=63.71 E-value=6.2 Score=29.06 Aligned_cols=47 Identities=15% Similarity=0.285 Sum_probs=33.7
Q ss_pred CCCCceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhhh
Q psy3498 30 NHEKSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVDA 77 (81)
Q Consensus 30 ~~~~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD~ 77 (81)
|..+.+....++ .|+....|.. ||..++ |++.--..+-+-|.+|+++
T Consensus 181 G~~~~~~~~~~~-~G~y~g~Cse~CG~~Hs~M~i~v~vv~~~~f~~Wl~~ 229 (234)
T MTH00051 181 GRLNQTSFFIKR-PGVFYGQCSEICGANHSFMPIVIEGVSLDKYINWVAT 229 (234)
T ss_pred CceEeEEEEeCC-CEEEEEEChhhcCcccccCeeEEEEECHHHHHHHHHH
Confidence 344455555554 5677888987 999876 4666666778999999975
No 151
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=63.66 E-value=7.1 Score=24.72 Aligned_cols=28 Identities=21% Similarity=0.682 Sum_probs=18.3
Q ss_pred ecCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
|.||-||+ -+++.......-.|.+|+=.
T Consensus 2 ~~CPCCg~-----~Tl~~~~~~~ydIC~VC~WE 29 (78)
T PF14206_consen 2 YPCPCCGY-----YTLEERGEGTYDICPVCFWE 29 (78)
T ss_pred ccCCCCCc-----EEeccCCCcCceECCCCCcc
Confidence 78999998 23333333236789999843
No 152
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=63.65 E-value=6.8 Score=33.48 Aligned_cols=46 Identities=30% Similarity=0.447 Sum_probs=28.3
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccc---cceeEeccCCCCchhh
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVC---LEDFQTTINFLSEAID 69 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C---~~~~~~~i~~L~epID 69 (81)
-.|.|+.|||. +.+.++.....-...|..| +...-..++..++.+|
T Consensus 128 ~~~~C~~Cg~~--~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~s~f~d 176 (682)
T COG1241 128 AVFECPKCGRE--VEVEQSEFRVEPPRECENCGKFGKGPLKLVPRKSEFID 176 (682)
T ss_pred EEEEcCCCCCE--EEEEeccccccCCccCCCccccCCCceEEecCcceeee
Confidence 58999999995 4444443334456679999 2222334555666665
No 153
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=63.37 E-value=5.2 Score=23.68 Aligned_cols=18 Identities=28% Similarity=0.643 Sum_probs=12.0
Q ss_pred CceecCCCCCCCCceEEE
Q psy3498 21 DIQFNCPFCNHEKSCEVK 38 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~ 38 (81)
|..+.||+||+...-.++
T Consensus 1 p~~i~Cp~C~~~~~T~v~ 18 (67)
T smart00714 1 PYQLFCPRCQNNVTTRVE 18 (67)
T ss_pred CcceECCCCCCEEEEEEE
Confidence 457899999985333333
No 154
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=62.96 E-value=3.5 Score=19.49 Aligned_cols=8 Identities=38% Similarity=1.460 Sum_probs=4.4
Q ss_pred ecCCCCCC
Q psy3498 24 FNCPFCNH 31 (81)
Q Consensus 24 F~CPfC~~ 31 (81)
|.|++|+-
T Consensus 1 y~C~~C~y 8 (24)
T PF13909_consen 1 YKCPHCSY 8 (24)
T ss_dssp EE-SSSS-
T ss_pred CCCCCCCC
Confidence 67777775
No 155
>PRK12495 hypothetical protein; Provisional
Probab=62.93 E-value=4.8 Score=30.28 Aligned_cols=32 Identities=16% Similarity=0.353 Sum_probs=25.1
Q ss_pred CCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
.-...|.|+.||..-- ...|.+.|-+|+..+.
T Consensus 38 atmsa~hC~~CG~PIp--------a~pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 38 ATMTNAHCDECGDPIF--------RHDGQEFCPTCQQPVT 69 (226)
T ss_pred cccchhhcccccCccc--------CCCCeeECCCCCCccc
Confidence 3457899999998522 3479999999998765
No 156
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=62.39 E-value=4.1 Score=32.13 Aligned_cols=32 Identities=16% Similarity=0.561 Sum_probs=15.4
Q ss_pred CCCceecCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
.+-..|.|+.||. . ++.+++ +-.-.|..||..
T Consensus 281 a~KRFFkC~~C~~-R--t~sl~r---~P~~~C~~Cg~~ 312 (344)
T PF09332_consen 281 AVKRFFKCKDCGN-R--TISLER---LPKKHCSNCGSS 312 (344)
T ss_dssp EE-EEEE-T-TS--E--EEESSS---S--S--TTT-S-
T ss_pred eeeeeEECCCCCC-e--eeeccc---CCCCCCCcCCcC
Confidence 3457899999998 3 445554 344699999973
No 157
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=62.30 E-value=16 Score=23.62 Aligned_cols=38 Identities=16% Similarity=0.468 Sum_probs=27.3
Q ss_pred CCCCCcee---cCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 17 IEPLDIQF---NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 17 ~~~l~~~F---~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
++...+.| .||-|++ +++.++.. .-.+.|.+||.....
T Consensus 26 v~~PnS~Fm~VkCp~C~n---~q~VFShA--~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 26 VQGPNSYFMDVKCPGCSQ---ITTVFSHA--QTVVLCGGCSSQLCQ 66 (85)
T ss_pred ecCCCCeEEEEECCCCCC---eeEEEecC--ceEEEccccCCEeec
Confidence 44445666 7999999 56667654 478899999986543
No 158
>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=61.54 E-value=4.2 Score=21.65 Aligned_cols=25 Identities=28% Similarity=0.585 Sum_probs=13.1
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
.|..||++.. +.... .+.|..||-+
T Consensus 2 ~C~~Cg~~~~----~~~~~---~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAEVE----LKPGD---PIRCPECGHR 26 (32)
T ss_dssp BESSSSSSE-----BSTSS---TSSBSSSS-S
T ss_pred CCCcCCCeeE----cCCCC---cEECCcCCCe
Confidence 4777777422 33333 2477777753
No 159
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=61.40 E-value=3.5 Score=19.09 Aligned_cols=11 Identities=27% Similarity=0.933 Sum_probs=6.4
Q ss_pred EcccccceeEe
Q psy3498 49 ACRVCLEDFQT 59 (81)
Q Consensus 49 ~C~~C~~~~~~ 59 (81)
.|..|+..|..
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 36666666643
No 160
>KOG1812|consensus
Probab=60.76 E-value=5.7 Score=31.34 Aligned_cols=29 Identities=24% Similarity=0.665 Sum_probs=22.2
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
-=+||-|+| . |.+..|=.++.|+ ||..|-
T Consensus 306 wr~CpkC~~----~--ie~~~GCnhm~Cr-C~~~fc 334 (384)
T KOG1812|consen 306 WRQCPKCKF----M--IELSEGCNHMTCR-CGHQFC 334 (384)
T ss_pred cCcCcccce----e--eeecCCcceEEee-ccccch
Confidence 457999998 2 3556678899999 997663
No 161
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=60.65 E-value=4.3 Score=32.82 Aligned_cols=43 Identities=19% Similarity=0.369 Sum_probs=26.2
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhh
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAID 69 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epID 69 (81)
-.|.||.||.++..+.+= ...... .|..||. ++.+-.-+.-||
T Consensus 326 ~~~~c~~~~~e~~~t~~~--~~~~~~-~~~~~~~--e~~~v~~~d~vd 368 (411)
T COG1503 326 VTYKCPTCGYENLKSKRE--FEQKRF-RCPECGS--EMEEVEVSDLVD 368 (411)
T ss_pred eeecCCCcchhhhhcccc--cccccc-cCccccc--cccchhhhhHHH
Confidence 379999999976544322 122234 9999998 544444333343
No 162
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=60.09 E-value=3.6 Score=22.69 Aligned_cols=16 Identities=13% Similarity=0.274 Sum_probs=13.0
Q ss_pred eEEEEcccccceeEec
Q psy3498 45 SARIACRVCLEDFQTT 60 (81)
Q Consensus 45 ~g~l~C~~C~~~~~~~ 60 (81)
.|...|..||..|...
T Consensus 11 ~~~~~C~~CgM~Y~~~ 26 (41)
T PF13878_consen 11 FGATTCPTCGMLYSPG 26 (41)
T ss_pred cCCcCCCCCCCEECCC
Confidence 4678999999999743
No 163
>MTH00080 COX2 cytochrome c oxidase subunit II; Provisional
Probab=60.07 E-value=7.3 Score=28.80 Aligned_cols=48 Identities=10% Similarity=0.162 Sum_probs=35.8
Q ss_pred CCCCceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhhhc
Q psy3498 30 NHEKSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVDAS 78 (81)
Q Consensus 30 ~~~~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD~c 78 (81)
|.-+.+....++ .|+....|.. ||..+. |++.--..+-+-|.+|+..+
T Consensus 180 Gr~n~~~~~~~~-~G~y~g~CsE~CG~~Hs~M~~~v~vv~~~~f~~Wl~~~ 229 (231)
T MTH00080 180 GILSTLCYSFPM-PGVFYGQCSEICGANHSFMPIAVEVTLLDNFKEWCKLL 229 (231)
T ss_pred CceEEEEEEEcC-ceEEEEEehhhcCcCccCCEEEEEEECHHHHHHHHHHh
Confidence 555666666655 5788899987 999876 46665556778999999765
No 164
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=60.04 E-value=4.9 Score=31.41 Aligned_cols=33 Identities=15% Similarity=0.424 Sum_probs=23.5
Q ss_pred CceecCCCCCCCCceEEEeecCC--ceEEEEcccc
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKGR--NSARIACRVC 53 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~~--~~g~l~C~~C 53 (81)
+.+--||.||..-++++.++-.. |--.++|..|
T Consensus 183 e~~~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC 217 (308)
T COG3058 183 ESRQYCPVCGSMPVASMVQIGETEQGLRYLHCSLC 217 (308)
T ss_pred cccccCCCcCCCCcceeeeecCccccchhhhhhhH
Confidence 77888999999998888887733 3334554444
No 165
>KOG2846|consensus
Probab=57.67 E-value=5.4 Score=31.47 Aligned_cols=14 Identities=43% Similarity=0.961 Sum_probs=11.4
Q ss_pred CceecCCCCCCCCc
Q psy3498 21 DIQFNCPFCNHEKS 34 (81)
Q Consensus 21 ~~~F~CPfC~~~~s 34 (81)
...|-||||||-+.
T Consensus 240 yi~F~C~~Cn~LN~ 253 (328)
T KOG2846|consen 240 YITFRCPHCNALNP 253 (328)
T ss_pred ceEEECccccccCC
Confidence 47899999999543
No 166
>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=57.17 E-value=4.9 Score=27.88 Aligned_cols=12 Identities=33% Similarity=1.207 Sum_probs=9.6
Q ss_pred CCceecCCCCCC
Q psy3498 20 LDIQFNCPFCNH 31 (81)
Q Consensus 20 l~~~F~CPfC~~ 31 (81)
++.-|.||.||.
T Consensus 125 ~~~~F~Cp~Cg~ 136 (158)
T TIGR00373 125 MELNFTCPRCGA 136 (158)
T ss_pred HHcCCcCCCCCC
Confidence 345799999998
No 167
>TIGR01432 QOXA cytochrome aa3 quinol oxidase, subunit II. This enzyme catalyzes the oxidation of quinol with the concomitant reduction of molecular oxygen to water. This acts as the terminal electron acceptor in the respiratory chain. This subunit contains two transmembrane helices and a large external domain responsible for the binding and oxidation of quinol. QuoX is (presently) only found in gram positive bacteria of the Bacillus/Staphylococcus group. Like CyoA, the ubiquinol oxidase found in proteobacteria, the residues responsible for the ligation of Cu(a) and cytochrome c (found in the related cyt. c oxidases) are absent. Unlike CyoA, QoxA is in complex with a subunit I which contains cytochromes a similar to the cyt. c oxidases (as opposed to cytochromes b).
Probab=56.33 E-value=10 Score=27.32 Aligned_cols=48 Identities=15% Similarity=0.182 Sum_probs=33.0
Q ss_pred CCCCceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhhhc
Q psy3498 30 NHEKSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVDAS 78 (81)
Q Consensus 30 ~~~~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD~c 78 (81)
|..+.+..+.++ .|.....|.. ||..|. |.+.-.-.+-+-|.+|+++.
T Consensus 167 G~~~~~~~~~~~-~G~y~g~Cae~CG~~Hs~M~~~v~v~~~~~f~~W~~~~ 216 (217)
T TIGR01432 167 GMTMNWYLQADQ-VGTYRGRNANFNGEGFADQTFDVNAVSEKDFDKWVKET 216 (217)
T ss_pred CceEEEEEEeCC-CEEEEEEehhhcCccccCCeEEEEEeCHHHHHHHHHhc
Confidence 445556666554 5788999998 999875 34444334557899999764
No 168
>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=56.25 E-value=12 Score=20.24 Aligned_cols=27 Identities=19% Similarity=0.426 Sum_probs=18.2
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
.|.|+.|+. + ... ..-|...|..||-.
T Consensus 8 ~~~C~~C~~---~--~~~--~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 8 NEPCPVCGS---R--WFY--SDDGFYYCDRCGHQ 34 (36)
T ss_pred CCcCCCCCC---e--EeE--ccCCEEEhhhCceE
Confidence 466999997 2 222 23478889888853
No 169
>PF12322 T4_baseplate: T4 bacteriophage base plate protein; InterPro: IPR024364 Proteins in this family are found in T4-like viruses. They have a single completely conserved residue S that may be functionally important. The family includes the two base plate proteins from bacteriophage T4: Gp51 and Gp26, encoded by late genes []. Gp26 is a structural component of central hub of the baseplate. It associates with Gp25 (tail lysozyme) in the assembly process. Gp51 is essential for the formation of the central hub of the phage baseplate, playing a catalytic role for the central hub formation. It may be also a structural component of the hub.
Probab=56.23 E-value=15 Score=26.68 Aligned_cols=53 Identities=19% Similarity=0.293 Sum_probs=30.4
Q ss_pred CCCCceecCCCCCCCCceEEEeecCCc---eEEEEcccccceeEeccCCCCchhhhh
Q psy3498 18 EPLDIQFNCPFCNHEKSCEVKMDKGRN---SARIACRVCLEDFQTTINFLSEAIDVY 71 (81)
Q Consensus 18 ~~l~~~F~CPfC~~~~sV~v~i~k~~~---~g~l~C~~C~~~~~~~i~~L~epIDVY 71 (81)
.+++-.|.||-||++..+.+.++...- ...+. -.=|..-.++.|.|++--|++
T Consensus 73 ~~v~~~~~C~~cg~~~~~~i~l~~~~l~~~~~~~~-~~~~i~i~~ryP~~~~~~~~~ 128 (205)
T PF12322_consen 73 TKVPVNYTCPDCGEEVKVPINLDQIKLTDGKNEIK-LSDGIKIKMRYPSLFEFDDVF 128 (205)
T ss_pred ccceEEEECCCCCcEEEEEecchhcccCCCCcceE-ecCCEEEEEeCCcccccCCHH
Confidence 348899999999997777666665432 22111 112233455566665544444
No 170
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=56.21 E-value=11 Score=24.72 Aligned_cols=30 Identities=17% Similarity=0.225 Sum_probs=18.9
Q ss_pred CCCCceecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 18 EPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 18 ~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
..+|-.+.|+.||++-. ++. ....|..||.
T Consensus 65 ~~vp~~~~C~~Cg~~~~----~~~----~~~~CP~Cgs 94 (113)
T PRK12380 65 VYKPAQAWCWDCSQVVE----IHQ----HDAQCPHCHG 94 (113)
T ss_pred EeeCcEEEcccCCCEEe----cCC----cCccCcCCCC
Confidence 45677889999997322 211 2234999984
No 171
>MTH00076 COX2 cytochrome c oxidase subunit II; Provisional
Probab=56.09 E-value=11 Score=27.62 Aligned_cols=50 Identities=8% Similarity=0.200 Sum_probs=33.1
Q ss_pred CCCCceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhhhcCC
Q psy3498 30 NHEKSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVDASVP 80 (81)
Q Consensus 30 ~~~~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD~c~~ 80 (81)
|..+.+....++ .|+....|.. ||..+. +++.--..+-|.|.+|+++-.|
T Consensus 177 G~~n~~~~~~~~-~G~~~g~C~e~CG~~Hs~M~~~v~vv~~~~f~~wl~~~~~ 228 (228)
T MTH00076 177 GRLNQTSFIASR-PGVYYGQCSEICGANHSFMPIVVEATPLNNFLNWSSSMLE 228 (228)
T ss_pred CcceeEEEEeCC-cEEEEEEChhhcCccccCCceEEEEeCHHHHHHHHHhccC
Confidence 334445555544 5667788987 999876 3555444566889999987543
No 172
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.03 E-value=5.5 Score=27.04 Aligned_cols=16 Identities=25% Similarity=0.476 Sum_probs=12.1
Q ss_pred CCCceecCCCCCCCCc
Q psy3498 19 PLDIQFNCPFCNHEKS 34 (81)
Q Consensus 19 ~l~~~F~CPfC~~~~s 34 (81)
..|-.+.|+.||+.-+
T Consensus 66 ~~p~~~~C~~CG~~~~ 81 (135)
T PRK03824 66 EEEAVLKCRNCGNEWS 81 (135)
T ss_pred ecceEEECCCCCCEEe
Confidence 5677899999997433
No 173
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=56.03 E-value=14 Score=22.96 Aligned_cols=32 Identities=31% Similarity=0.613 Sum_probs=21.3
Q ss_pred CCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCC
Q psy3498 26 CPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLS 65 (81)
Q Consensus 26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~ 65 (81)
||.|...+. .. ..+.+.| .||+++.+.-..++
T Consensus 2 CPVC~~~~L-~~------~~~~i~C-~Cgl~l~~~~~~~t 33 (82)
T PF14768_consen 2 CPVCQKGNL-RE------NSNVISC-SCGLRLNTQQDELT 33 (82)
T ss_pred CCccCCCcc-cc------cCCeEEC-CCccEEecCCCCCC
Confidence 899998433 22 4477999 56688877644443
No 174
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=56.00 E-value=11 Score=29.81 Aligned_cols=30 Identities=23% Similarity=0.343 Sum_probs=21.0
Q ss_pred eecCCCCCCCC-ceEEEeecCCceEEEEcccccce
Q psy3498 23 QFNCPFCNHEK-SCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 23 ~F~CPfC~~~~-sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
..-||||+.+. |..|..+ .+.-.|-.||..
T Consensus 34 ~~~CPfh~ek~pSf~v~~~----k~~~~Cf~Cg~~ 64 (415)
T TIGR01391 34 VGLCPFHHEKTPSFSVSPE----KQFYHCFGCGAG 64 (415)
T ss_pred EeeCCCCCCCCCeEEEEcC----CCcEEECCCCCC
Confidence 45799998653 4555443 357899999985
No 175
>TIGR02866 CoxB cytochrome c oxidase, subunit II. Cytochrome c oxidase is the terminal electron acceptor of mitochondria (and one of several possible acceptors in prokaryotes) in the electron transport chain of aerobic respiration. The enzyme couples the oxidation of reduced cytochrome c with the reduction of molecular oxygen to water. This process results in the pumping of four protons across the membrane which are used in the proton gradient powered synthesis of ATP. The oxidase contains two heme a cofactors and three copper atoms as well as other bound ions.
Probab=55.74 E-value=8.6 Score=27.26 Aligned_cols=46 Identities=7% Similarity=0.143 Sum_probs=31.5
Q ss_pred CCCCceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhh
Q psy3498 30 NHEKSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVD 76 (81)
Q Consensus 30 ~~~~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD 76 (81)
|..+.+..+.++ .|.....|.. ||..|. |.+.-.-.|-+-|.+|++
T Consensus 154 G~~~~~~~~~~~-~G~y~~~c~e~cG~~h~~M~~~v~v~~~~~f~~Wl~ 201 (201)
T TIGR02866 154 GQYNALWFNADE-PGVYYGYCAELCGAGHSLMLFKVVVVEREEFDAYIE 201 (201)
T ss_pred CcEEEEEEEeCC-CEEEEEEehhhCCcCccCCeEEEEEECHHHHHHHhC
Confidence 344555665554 5778899998 999875 344444455678999984
No 176
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=55.41 E-value=12 Score=29.72 Aligned_cols=39 Identities=15% Similarity=0.314 Sum_probs=24.6
Q ss_pred cCCCCCC-CCceEEEeecCCceEEEEcccccceeEeccCC
Q psy3498 25 NCPFCNH-EKSCEVKMDKGRNSARIACRVCLEDFQTTINF 63 (81)
Q Consensus 25 ~CPfC~~-~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~ 63 (81)
-|+.||. ..+.....|-..+.-.-.|..||..-+..+..
T Consensus 176 iC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~~~i~~ 215 (360)
T PF01921_consen 176 ICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGEVDITG 215 (360)
T ss_dssp EETTTEE--EEEEEEE--SSSEEEEE--TTS---EEETTT
T ss_pred eccccCCcccceeeEeecCCCEEEEEecCCCCEEEEecCC
Confidence 4999999 45555677777888999999999988877664
No 177
>MTH00023 COX2 cytochrome c oxidase subunit II; Validated
Probab=55.29 E-value=10 Score=28.07 Aligned_cols=47 Identities=13% Similarity=0.248 Sum_probs=32.4
Q ss_pred CCCCceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhhh
Q psy3498 30 NHEKSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVDA 77 (81)
Q Consensus 30 ~~~~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD~ 77 (81)
|..+.+....++ .|+....|.. ||..++ +++.--..+.+.|.+|+.+
T Consensus 188 G~~n~~~~~~~~-~G~y~g~C~e~CG~~Hs~M~~~v~vv~~~~f~~Wl~~ 236 (240)
T MTH00023 188 GRLNQTGFFIKR-PGVFYGQCSEICGANHSFMPIVIEAVSLDKYINWLLS 236 (240)
T ss_pred CcceeEEEEcCC-CEEEEEEchhhcCcCccCCeEEEEEECHHHHHHHHHH
Confidence 344455555544 5777889987 999876 3555545667899999865
No 178
>PHA02942 putative transposase; Provisional
Probab=55.29 E-value=6.8 Score=30.76 Aligned_cols=47 Identities=13% Similarity=0.246 Sum_probs=30.4
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhhhhc
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDAS 78 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~WiD~c 78 (81)
|.=.||.|||... ......-.|..||....-.+| .++.++..+++..
T Consensus 324 TSq~Cs~CG~~~~-------~l~~r~f~C~~CG~~~drD~n---AA~NI~~rg~~~~ 370 (383)
T PHA02942 324 SSVSCPKCGHKMV-------EIAHRYFHCPSCGYENDRDVI---AIMNLNGRGSLTL 370 (383)
T ss_pred CCccCCCCCCccC-------cCCCCEEECCCCCCEeCcHHH---HHHHHHHHHHHHh
Confidence 5567999999431 223347899999987765554 3455665555443
No 179
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=55.13 E-value=13 Score=20.28 Aligned_cols=29 Identities=21% Similarity=0.555 Sum_probs=21.2
Q ss_pred CCCCCCCCceEEEeecCCceEEEEcccccceeEeccCC
Q psy3498 26 CPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINF 63 (81)
Q Consensus 26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~ 63 (81)
|++|+. .......|.|..|+..|-..--.
T Consensus 2 C~vC~~---------~~~~~~~i~C~~C~~~~H~~C~~ 30 (51)
T PF00628_consen 2 CPVCGQ---------SDDDGDMIQCDSCNRWYHQECVG 30 (51)
T ss_dssp BTTTTS---------SCTTSSEEEBSTTSCEEETTTST
T ss_pred CcCCCC---------cCCCCCeEEcCCCChhhCcccCC
Confidence 778886 23455789999999999765333
No 180
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.90 E-value=14 Score=24.04 Aligned_cols=28 Identities=25% Similarity=0.451 Sum_probs=21.2
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
-||.||. +..+.-..++-+-.|..|+-.
T Consensus 3 lCP~C~v----~l~~~~rs~vEiD~CPrCrGV 30 (88)
T COG3809 3 LCPICGV----ELVMSVRSGVEIDYCPRCRGV 30 (88)
T ss_pred ccCcCCc----eeeeeeecCceeeeCCccccE
Confidence 4999996 455555578889999999753
No 181
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=54.12 E-value=6.2 Score=28.01 Aligned_cols=12 Identities=33% Similarity=1.107 Sum_probs=9.5
Q ss_pred CCceecCCCCCC
Q psy3498 20 LDIQFNCPFCNH 31 (81)
Q Consensus 20 l~~~F~CPfC~~ 31 (81)
++.-|.||.||.
T Consensus 133 ~~~~F~Cp~Cg~ 144 (178)
T PRK06266 133 MEYGFRCPQCGE 144 (178)
T ss_pred hhcCCcCCCCCC
Confidence 345799999997
No 182
>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=54.08 E-value=11 Score=23.49 Aligned_cols=28 Identities=25% Similarity=0.765 Sum_probs=14.9
Q ss_pred ecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
..||-|+++ |+... +...|..|+..|..
T Consensus 2 ~~CP~C~~~------L~~~~--~~~~C~~C~~~~~~ 29 (70)
T PF07191_consen 2 NTCPKCQQE------LEWQG--GHYHCEACQKDYKK 29 (70)
T ss_dssp -B-SSS-SB------EEEET--TEEEETTT--EEEE
T ss_pred CcCCCCCCc------cEEeC--CEEECcccccccee
Confidence 368888884 22222 67788888887754
No 183
>PF10813 DUF2733: Protein of unknown function (DUF2733); InterPro: IPR024360 The UL11 gene product of herpes simplex virus is a membrane-associated tegument protein that is incorporated into the HSV virion and functions in viral envelopment []. UL11 is acylated, which is crucial for lipid raft association [].
Probab=53.82 E-value=3.8 Score=22.14 Aligned_cols=26 Identities=15% Similarity=0.414 Sum_probs=18.0
Q ss_pred EcccccceeEeccCCCCchhhhhhhh
Q psy3498 49 ACRVCLEDFQTTINFLSEAIDVYNDW 74 (81)
Q Consensus 49 ~C~~C~~~~~~~i~~L~epIDVYs~W 74 (81)
.|+.|.-+..+-...=-+|||||.+|
T Consensus 4 ~~s~Ckrr~n~l~Dv~G~~Inl~~dF 29 (32)
T PF10813_consen 4 LLSMCKRRHNPLKDVKGNPINLYKDF 29 (32)
T ss_pred eeeeeeccCCcccccCCCEEechhcc
Confidence 46677776655444446899999876
No 184
>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=53.66 E-value=3.8 Score=21.02 Aligned_cols=7 Identities=43% Similarity=1.493 Sum_probs=3.4
Q ss_pred cCCCCCC
Q psy3498 25 NCPFCNH 31 (81)
Q Consensus 25 ~CPfC~~ 31 (81)
+||.||+
T Consensus 1 ~CP~C~s 7 (28)
T PF03119_consen 1 TCPVCGS 7 (28)
T ss_dssp B-TTT--
T ss_pred CcCCCCC
Confidence 5999998
No 185
>PRK05667 dnaG DNA primase; Validated
Probab=53.23 E-value=13 Score=30.83 Aligned_cols=30 Identities=27% Similarity=0.407 Sum_probs=21.3
Q ss_pred eecCCCCCCCC-ceEEEeecCCceEEEEcccccce
Q psy3498 23 QFNCPFCNHEK-SCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 23 ~F~CPfC~~~~-sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
...||||+... |..|..+ .+.-.|-.||..
T Consensus 36 ~~~CPfH~ektpSf~V~~~----k~~~~CF~Cg~~ 66 (580)
T PRK05667 36 KGLCPFHDEKTPSFTVSPD----KQFYHCFGCGAG 66 (580)
T ss_pred eecCCCCCCCCCceEEECC----CCeEEECCCCCC
Confidence 45799999653 5555543 367899999984
No 186
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=53.20 E-value=15 Score=27.26 Aligned_cols=26 Identities=23% Similarity=0.651 Sum_probs=16.7
Q ss_pred CCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 26 CPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
||.||+...+ ...+ -...|..||..+
T Consensus 102 C~~CG~~~~~-----~~~~-~~~~C~~c~~~~ 127 (256)
T PRK00241 102 CGYCGHPMHP-----SKTE-WAMLCPHCRERY 127 (256)
T ss_pred ccccCCCCee-----cCCc-eeEECCCCCCEE
Confidence 9999985332 1233 346799999654
No 187
>MTH00168 COX2 cytochrome c oxidase subunit II; Provisional
Probab=52.80 E-value=9.5 Score=27.83 Aligned_cols=43 Identities=16% Similarity=0.285 Sum_probs=30.3
Q ss_pred CceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhh
Q psy3498 33 KSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVD 76 (81)
Q Consensus 33 ~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD 76 (81)
+.+....++ .|+....|.. ||..+. +++.-.-.+-+.|.+|++
T Consensus 180 n~~~~~~~~-~G~~~g~CsE~CG~~Hs~M~~~v~vv~~~~f~~W~~ 224 (225)
T MTH00168 180 NQLAFLSSR-PGSFYGQCSEICGANHSFMPIVVEFVPWETFENWVD 224 (225)
T ss_pred EEEEEEcCC-CEEEEEEcccccCcCcCCCeEEEEEeCHHHHHHHHh
Confidence 445555543 5777889987 999876 465555566788999985
No 188
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=52.78 E-value=8.8 Score=23.36 Aligned_cols=26 Identities=23% Similarity=0.331 Sum_probs=23.4
Q ss_pred EcccccceeEeccCCCCchhhhhhhh
Q psy3498 49 ACRVCLEDFQTTINFLSEAIDVYNDW 74 (81)
Q Consensus 49 ~C~~C~~~~~~~i~~L~epIDVYs~W 74 (81)
.|.+||..-...+++-..|.|=|++.
T Consensus 19 ~Cp~CG~~t~~~~PprFSPeD~y~kY 44 (59)
T COG2260 19 KCPVCGGDTKVPHPPRFSPEDKYGKY 44 (59)
T ss_pred cCCCCCCccccCCCCCCCccchHHHH
Confidence 59999998888999999999999875
No 189
>KOG2462|consensus
Probab=52.69 E-value=6.7 Score=30.33 Aligned_cols=35 Identities=23% Similarity=0.594 Sum_probs=20.1
Q ss_pred CceecCCCCCCCCceEEEeecC-----CceEEEEcccccceeE
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKG-----RNSARIACRVCLEDFQ 58 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~-----~~~g~l~C~~C~~~~~ 58 (81)
.+.|.|+.|+. +-|.|--. ...---.|.+||..|+
T Consensus 159 ~ka~~C~~C~K---~YvSmpALkMHirTH~l~c~C~iCGKaFS 198 (279)
T KOG2462|consen 159 KKAFSCKYCGK---VYVSMPALKMHIRTHTLPCECGICGKAFS 198 (279)
T ss_pred cccccCCCCCc---eeeehHHHhhHhhccCCCccccccccccc
Confidence 35677777776 45554322 1223456778887775
No 190
>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=52.64 E-value=10 Score=22.41 Aligned_cols=42 Identities=19% Similarity=0.249 Sum_probs=25.0
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEec-cCCCCch
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT-INFLSEA 67 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~-i~~L~ep 67 (81)
..+.|+.||.- -.+.. .-...+|.|..|+.-...+ ..+..+|
T Consensus 3 ~eiRC~~Cnkl---La~~g-~~~~leIKCpRC~tiN~~~a~~~~~~p 45 (51)
T PF10122_consen 3 KEIRCGHCNKL---LAKAG-EVIELEIKCPRCKTINHVRATSPEPEP 45 (51)
T ss_pred cceeccchhHH---Hhhhc-CccEEEEECCCCCccceEeccCCCCCc
Confidence 46889999971 11110 1224689999999866543 3333344
No 191
>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=52.51 E-value=7.2 Score=20.93 Aligned_cols=10 Identities=30% Similarity=0.840 Sum_probs=6.8
Q ss_pred ceecCCCCCC
Q psy3498 22 IQFNCPFCNH 31 (81)
Q Consensus 22 ~~F~CPfC~~ 31 (81)
..|.||.|+.
T Consensus 3 ~~~~C~nC~R 12 (33)
T PF08209_consen 3 PYVECPNCGR 12 (33)
T ss_dssp -EEE-TTTSS
T ss_pred CeEECCCCcC
Confidence 4689999986
No 192
>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=52.34 E-value=13 Score=30.13 Aligned_cols=30 Identities=20% Similarity=0.536 Sum_probs=18.3
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
+..||+|+. ..+..+. .+.+.|.-||.+..
T Consensus 222 ~~~C~~C~~----~l~~h~~--~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 222 ILCCPNCDV----SLTYHKK--EGKLRCHYCGYQEP 251 (505)
T ss_pred ccCCCCCCC----ceEEecC--CCeEEcCCCcCcCC
Confidence 345777764 3444443 35788888886543
No 193
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=51.70 E-value=5.6 Score=19.07 Aligned_cols=12 Identities=25% Similarity=0.758 Sum_probs=8.8
Q ss_pred EEcccccceeEe
Q psy3498 48 IACRVCLEDFQT 59 (81)
Q Consensus 48 l~C~~C~~~~~~ 59 (81)
..|..|+..|.+
T Consensus 2 ~~C~~C~~~F~~ 13 (27)
T PF13912_consen 2 FECDECGKTFSS 13 (27)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCccCCccCC
Confidence 368888888864
No 194
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=51.52 E-value=11 Score=21.90 Aligned_cols=16 Identities=25% Similarity=0.619 Sum_probs=13.1
Q ss_pred EEEcccccceeEeccC
Q psy3498 47 RIACRVCLEDFQTTIN 62 (81)
Q Consensus 47 ~l~C~~C~~~~~~~i~ 62 (81)
.|.|..||..|.+.+.
T Consensus 4 ~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 4 TLTCKDCGAEFVFTAG 19 (49)
T ss_pred eEEcccCCCeEEEehh
Confidence 6899999999987654
No 195
>MTH00027 COX2 cytochrome c oxidase subunit II; Provisional
Probab=51.37 E-value=12 Score=28.33 Aligned_cols=47 Identities=15% Similarity=0.268 Sum_probs=33.3
Q ss_pred CCCCceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhhh
Q psy3498 30 NHEKSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVDA 77 (81)
Q Consensus 30 ~~~~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD~ 77 (81)
|+-+.+....++ .|+....|.. ||..+. |++.--..+-+.|.+|++.
T Consensus 211 Gr~n~~~~~~~~-~G~y~g~CsE~CG~~Hs~Mpi~v~vv~~~~f~~Wl~~ 259 (262)
T MTH00027 211 GRINETGFLIKR-PGIFYGQCSEICGANHSFMPIVVESVSLSKYIDWIGR 259 (262)
T ss_pred CceeeEEEEcCC-cEEEEEEcchhcCcCcCCCeEEEEEECHHHHHHHHcc
Confidence 444555666554 5777889987 999886 4666555667899999854
No 196
>PTZ00047 cytochrome c oxidase subunit II; Provisional
Probab=51.28 E-value=12 Score=26.76 Aligned_cols=46 Identities=9% Similarity=0.027 Sum_probs=32.1
Q ss_pred CceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhhhcC
Q psy3498 33 KSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVDASV 79 (81)
Q Consensus 33 ~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD~c~ 79 (81)
+.+....++ .|+....|.. ||..+. |++.-...+-+.|..|+...+
T Consensus 113 n~l~~~~~~-~G~y~gqCsElCG~gHs~M~~~V~vvs~~~F~~w~~~~~ 160 (162)
T PTZ00047 113 HKINTFILR-EGVFYGQCSEMCGTLHGFMPIVVEAVSPEAYAAHAKKYY 160 (162)
T ss_pred EEEEEecCC-CeEEEEEcchhcCcCccCceEEEEEeCHHHHHHHHHHHh
Confidence 344444443 6778899987 999876 455555456788999997654
No 197
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=51.25 E-value=11 Score=22.57 Aligned_cols=13 Identities=23% Similarity=1.025 Sum_probs=10.9
Q ss_pred CCceecCCCCCCC
Q psy3498 20 LDIQFNCPFCNHE 32 (81)
Q Consensus 20 l~~~F~CPfC~~~ 32 (81)
-|....||+||+.
T Consensus 4 ~p~~~~CP~C~~~ 16 (73)
T PF10601_consen 4 EPVRIYCPYCQQQ 16 (73)
T ss_pred CceeeECCCCCCE
Confidence 4678999999984
No 198
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PHA02611 51 baseplate hub assembly protein; Provisional
Probab=50.93 E-value=12 Score=28.44 Aligned_cols=25 Identities=24% Similarity=0.681 Sum_probs=20.2
Q ss_pred CCCCceecCCCCCCCCceEEEeecC
Q psy3498 18 EPLDIQFNCPFCNHEKSCEVKMDKG 42 (81)
Q Consensus 18 ~~l~~~F~CPfC~~~~sV~v~i~k~ 42 (81)
.+++..|.||-||++..|...++..
T Consensus 77 ~~v~~~~tCp~Cg~e~~v~~~l~~~ 101 (249)
T PHA02611 77 TKIPVTFTCPKCKKEKTVLFNLKQE 101 (249)
T ss_pred ceeeEEEECCCCCCceeEEEEeehh
Confidence 3468899999999998888777654
No 200
>PHA00616 hypothetical protein
Probab=50.72 E-value=5.3 Score=22.84 Aligned_cols=8 Identities=25% Similarity=0.928 Sum_probs=6.0
Q ss_pred ecCCCCCC
Q psy3498 24 FNCPFCNH 31 (81)
Q Consensus 24 F~CPfC~~ 31 (81)
|+||.||.
T Consensus 2 YqC~~CG~ 9 (44)
T PHA00616 2 YQCLRCGG 9 (44)
T ss_pred CccchhhH
Confidence 67888874
No 201
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=50.67 E-value=35 Score=26.79 Aligned_cols=37 Identities=16% Similarity=0.398 Sum_probs=26.5
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccceeEeccC
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTIN 62 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~ 62 (81)
-||.||--.+..+.+|-+.+.-.-.|. ||-.-++.|.
T Consensus 171 ~c~~cg~~~~~v~~~d~~~~~v~y~c~-cG~~g~~~~~ 207 (353)
T cd00674 171 YCEKCGKDTTTVEAYDAKAGTVTYKCE-CGHEETVDIR 207 (353)
T ss_pred ecCCcCcceeEEEEEeCCCCeEEEEcC-CCCEEEEeec
Confidence 499999655444467766776677894 9988877764
No 202
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=50.63 E-value=12 Score=27.91 Aligned_cols=28 Identities=18% Similarity=0.355 Sum_probs=20.7
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
.||.||+. +...+-.+.++-.|..|+..
T Consensus 237 pC~~Cg~~----I~~~~~~gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 237 PCPRCGTP----IEKIVVGGRGTHFCPQCQPL 264 (269)
T ss_pred CCCcCCCe----eEEEEECCCCcEECCCCcCC
Confidence 69999983 33333457889999999864
No 203
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=50.53 E-value=13 Score=27.70 Aligned_cols=26 Identities=15% Similarity=0.354 Sum_probs=18.9
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEccccc
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCL 54 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~ 54 (81)
.||.||+ .+...+-.+.++-.|..|+
T Consensus 246 pCprCG~----~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 246 PCLNCKT----PIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred cCCCCCC----eeEEEEECCCccEECcCCc
Confidence 7999997 2333333567889999997
No 204
>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=50.46 E-value=9.8 Score=19.54 Aligned_cols=26 Identities=19% Similarity=0.387 Sum_probs=10.9
Q ss_pred CCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 26 CPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
||.||++ . .+. .+--...|..||..+
T Consensus 6 C~~CG~~---t-~~~--~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 6 CGRCGAP---T-KPA--PGGWARRCPSCGHEH 31 (32)
T ss_dssp -TTT--B---E-EE---SSSS-EEESSSS-EE
T ss_pred cCcCCcc---c-cCC--CCcCEeECCCCcCEe
Confidence 7888873 1 111 122345788888653
No 205
>KOG2691|consensus
Probab=50.24 E-value=15 Score=24.94 Aligned_cols=47 Identities=30% Similarity=0.326 Sum_probs=34.7
Q ss_pred CCCCCCCCceEEEeecCCceEEEEcccccceeE-----eccCCCCchhhhhhhh
Q psy3498 26 CPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ-----TTINFLSEAIDVYNDW 74 (81)
Q Consensus 26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~-----~~i~~L~epIDVYs~W 74 (81)
|+-||+ .+-=+=|+.+.+-.++|++|.-.++ ..+|.|...+|=...-
T Consensus 7 C~eCNN--mLYPkEDked~~L~laCrnCd~ve~A~s~~vY~~~~~~e~dE~t~i 58 (113)
T KOG2691|consen 7 CRECNN--MLYPKEDKEDRILLLACRNCDYVEEADSSRVYVNELSHEHDELTQI 58 (113)
T ss_pred hhhhhc--cccccccccccEEEEEecCCcceEecCCcceEcCCcccchhhHHHH
Confidence 788885 4555667778899999999997664 3578888777755443
No 206
>KOG3113|consensus
Probab=49.47 E-value=6.6 Score=30.46 Aligned_cols=53 Identities=23% Similarity=0.500 Sum_probs=38.5
Q ss_pred CceecCCCCCCCCc----------eEEEeecC--CceEEEEcccccceeEe----ccCCCCchhhhhhh
Q psy3498 21 DIQFNCPFCNHEKS----------CEVKMDKG--RNSARIACRVCLEDFQT----TINFLSEAIDVYND 73 (81)
Q Consensus 21 ~~~F~CPfC~~~~s----------V~v~i~k~--~~~g~l~C~~C~~~~~~----~i~~L~epIDVYs~ 73 (81)
...|.||.=|++-+ ..|.+.-. ..+..-+|-+||+-|+. .||+-.|-+|+|..
T Consensus 109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeikas~C~~C~a~y~~~dvIvlNg~~E~~dllk~ 177 (293)
T KOG3113|consen 109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIKASVCHVCGAAYQEDDVIVLNGTEEDVDLLKT 177 (293)
T ss_pred cceeecccccceecceEEEEEEeccceeccHHHHHHhhhccccccCCcccccCeEeeCCCHHHHHHHHH
Confidence 36899998887644 22333321 34667799999999974 68999999999975
No 207
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=49.32 E-value=12 Score=26.95 Aligned_cols=42 Identities=19% Similarity=0.414 Sum_probs=31.0
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCC
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFL 64 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L 64 (81)
+=+|-|||.-=.|+|=-..--.+-++.||-|.-=.+-.+.++
T Consensus 12 YVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~~ 53 (170)
T PF04690_consen 12 YVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRAL 53 (170)
T ss_pred EEEcCCcCeEEEEecchhhhhhhhceeccCccceeeeecccc
Confidence 347999998777777666666888999999996555444443
No 208
>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=49.20 E-value=8.6 Score=26.67 Aligned_cols=35 Identities=17% Similarity=0.116 Sum_probs=23.9
Q ss_pred CCCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 18 EPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 18 ~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
+-|-|-..||.||.. .-..+.--+.|-.||..|..
T Consensus 4 ~elGtKr~Cp~cg~k-------FYDLnk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 4 PDLGTKRICPNTGSK-------FYDLNRRPAVSPYTGEQFPP 38 (129)
T ss_pred hhhCccccCCCcCcc-------ccccCCCCccCCCcCCccCc
Confidence 346677889988872 22334467788888888754
No 209
>MTH00098 COX2 cytochrome c oxidase subunit II; Validated
Probab=48.57 E-value=13 Score=27.31 Aligned_cols=47 Identities=9% Similarity=0.197 Sum_probs=32.3
Q ss_pred CCCCceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhhh
Q psy3498 30 NHEKSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVDA 77 (81)
Q Consensus 30 ~~~~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD~ 77 (81)
|..+.+....++ .|+....|.. ||..+. +++.--..+-|.|.+|+-.
T Consensus 177 G~~~~~~~~~~~-~G~~~g~Cse~CG~~H~~M~~~v~v~~~~~f~~W~~~ 225 (227)
T MTH00098 177 GRLNQTTLMSTR-PGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSAS 225 (227)
T ss_pred CceEEEEEecCC-cEEEEEECccccCcCcCCceEEEEEeCHHHHHHHHHh
Confidence 444555555554 4667788987 999876 4666555677899999853
No 210
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=48.53 E-value=34 Score=22.95 Aligned_cols=33 Identities=18% Similarity=0.558 Sum_probs=24.9
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
.+.|.-|+... ...-+-..+....|+.||..+.
T Consensus 112 ~y~C~~C~~~~---~~~rr~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 112 PYRCTGCGQRY---LRVRRSNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEECCCCCCCC---ceEccccCcceEEcCCCCCEEE
Confidence 78999999853 2444455669999999998775
No 211
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=48.36 E-value=28 Score=23.31 Aligned_cols=39 Identities=15% Similarity=0.307 Sum_probs=28.2
Q ss_pred ceecCCCCCCC----CceEEEeecCCceEEEEcccccceeEeccC
Q psy3498 22 IQFNCPFCNHE----KSCEVKMDKGRNSARIACRVCLEDFQTTIN 62 (81)
Q Consensus 22 ~~F~CPfC~~~----~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~ 62 (81)
+.+-|+.|+.- ....|.+ .++.-.+.|..||...-+++.
T Consensus 55 KR~~CkkC~t~Lvpg~n~rvR~--~~~~v~vtC~~CG~~~R~p~~ 97 (105)
T COG2023 55 KRTICKKCYTPLVPGKNARVRL--RKGRVVVTCLECGTIRRYPYG 97 (105)
T ss_pred HHHhccccCcccccCcceEEEE--cCCeEEEEecCCCcEEEeccc
Confidence 67889999983 3445555 445589999999987665544
No 212
>smart00400 ZnF_CHCC zinc finger.
Probab=47.96 E-value=21 Score=20.18 Aligned_cols=30 Identities=20% Similarity=0.336 Sum_probs=20.4
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
.|||++- ++=+..++.. .....|-.||...
T Consensus 4 ~cPfh~d-~~pSf~v~~~--kn~~~Cf~cg~gG 33 (55)
T smart00400 4 LCPFHGE-KTPSFSVSPD--KQFFHCFGCGAGG 33 (55)
T ss_pred cCcCCCC-CCCCEEEECC--CCEEEEeCCCCCC
Confidence 4999985 4445666543 3668999998654
No 213
>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=46.46 E-value=8 Score=25.49 Aligned_cols=30 Identities=27% Similarity=0.445 Sum_probs=18.7
Q ss_pred CCCCceecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 18 EPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 18 ~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
..+|-.+.|+.||+.-.+. . ....|..||.
T Consensus 65 ~~~p~~~~C~~Cg~~~~~~----~----~~~~CP~Cgs 94 (115)
T TIGR00100 65 EDEPVECECEDCSEEVSPE----I----DLYRCPKCHG 94 (115)
T ss_pred EeeCcEEEcccCCCEEecC----C----cCccCcCCcC
Confidence 3456788888888732221 1 1356888885
No 214
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=45.92 E-value=17 Score=26.95 Aligned_cols=27 Identities=19% Similarity=0.463 Sum_probs=19.2
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
.||.||.. +...+-.+.++--|..|+.
T Consensus 247 pC~~Cg~~----I~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 247 PCRRCGTP----IEKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCe----eEEEEECCCCcEECcCCCC
Confidence 49999973 3333335778899999974
No 215
>PF12773 DZR: Double zinc ribbon
Probab=45.80 E-value=7.3 Score=21.45 Aligned_cols=24 Identities=21% Similarity=0.659 Sum_probs=13.0
Q ss_pred CCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 26 CPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
||.||+.-. ......+.|..||..
T Consensus 15 C~~CG~~l~-------~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 15 CPHCGTPLP-------PPDQSKKICPNCGAE 38 (50)
T ss_pred ChhhcCChh-------hccCCCCCCcCCcCC
Confidence 666665322 223345567777763
No 216
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=45.41 E-value=13 Score=19.99 Aligned_cols=11 Identities=27% Similarity=0.806 Sum_probs=8.7
Q ss_pred eecCCCCCCCC
Q psy3498 23 QFNCPFCNHEK 33 (81)
Q Consensus 23 ~F~CPfC~~~~ 33 (81)
...||.||...
T Consensus 2 ~~~Cp~Cg~~~ 12 (47)
T PF14690_consen 2 PPRCPHCGSPS 12 (47)
T ss_pred CccCCCcCCCc
Confidence 46799999854
No 217
>PRK04011 peptide chain release factor 1; Provisional
Probab=45.28 E-value=15 Score=29.18 Aligned_cols=50 Identities=20% Similarity=0.452 Sum_probs=31.8
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhhhhcC
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASV 79 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~WiD~c~ 79 (81)
.|.||.||++....++- ....-.-.|..||...+. .+..|.+-.+++.++
T Consensus 328 ~~~c~~c~~~~~~~~~~--~~~~~~~~c~~~~~~~~~-----~~~~~~v~~l~e~a~ 377 (411)
T PRK04011 328 TYKCPNCGYEEEKTVKR--REELPEKTCPKCGSELEI-----VEEEDIIEELSELAE 377 (411)
T ss_pred EEEcCCCCcceeeeccc--ccccccccCcccCccccc-----chhhhHHHHHHHHHH
Confidence 68999999975544443 233445689999976442 344566666666554
No 218
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.48 E-value=6.1 Score=27.33 Aligned_cols=31 Identities=26% Similarity=0.511 Sum_probs=20.6
Q ss_pred ecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
=.||.||.-+ +.+.-..-.-.|..||+.|..
T Consensus 22 grCP~CGeGr-----LF~gFLK~~p~C~aCG~dyg~ 52 (126)
T COG5349 22 GRCPRCGEGR-----LFRGFLKVVPACEACGLDYGF 52 (126)
T ss_pred CCCCCCCCch-----hhhhhcccCchhhhccccccC
Confidence 4699999753 333223334579999998753
No 219
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.44 E-value=21 Score=24.45 Aligned_cols=24 Identities=21% Similarity=0.602 Sum_probs=18.3
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
.-.||.||.+ --+-.+.|.+|+..
T Consensus 6 ~~~cPvcg~~----------~iVTeL~c~~~etT 29 (122)
T COG3877 6 INRCPVCGRK----------LIVTELKCSNCETT 29 (122)
T ss_pred CCCCCccccc----------ceeEEEecCCCCce
Confidence 3469999973 34568999999975
No 220
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=44.30 E-value=9.2 Score=23.48 Aligned_cols=14 Identities=21% Similarity=0.513 Sum_probs=10.9
Q ss_pred CCCCceecCCCCCC
Q psy3498 18 EPLDIQFNCPFCNH 31 (81)
Q Consensus 18 ~~l~~~F~CPfC~~ 31 (81)
+-=+..|.||.|+.
T Consensus 12 RDGE~~lrCPRC~~ 25 (65)
T COG4049 12 RDGEEFLRCPRCGM 25 (65)
T ss_pred cCCceeeeCCchhH
Confidence 34468899999986
No 221
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=44.20 E-value=18 Score=27.04 Aligned_cols=26 Identities=19% Similarity=0.362 Sum_probs=18.9
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEccccc
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCL 54 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~ 54 (81)
.||.||.. |....-.+.++-.|..|+
T Consensus 256 pC~~Cg~~----I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 256 PCRKCGTP----IERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred CCCcCCCe----eEEEEECCCccEECCCCc
Confidence 79999973 223333577889999997
No 222
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=44.00 E-value=11 Score=24.00 Aligned_cols=10 Identities=40% Similarity=1.085 Sum_probs=5.6
Q ss_pred ceecCCCCCC
Q psy3498 22 IQFNCPFCNH 31 (81)
Q Consensus 22 ~~F~CPfC~~ 31 (81)
..|.||.||+
T Consensus 64 s~~~Cp~Cg~ 73 (81)
T PF10609_consen 64 SYFVCPHCGE 73 (81)
T ss_dssp -EEE-TTT--
T ss_pred CccCCCCCCC
Confidence 5799999998
No 223
>PRK10445 endonuclease VIII; Provisional
Probab=43.72 E-value=19 Score=26.68 Aligned_cols=26 Identities=15% Similarity=0.314 Sum_probs=18.3
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEccccc
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCL 54 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~ 54 (81)
.||.||.. +...+-.+.++-.|-.|+
T Consensus 237 ~Cp~Cg~~----I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 237 ACERCGGI----IEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCE----eEEEEECCCCcEECCCCc
Confidence 49999972 233333577888999996
No 224
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=43.35 E-value=52 Score=19.62 Aligned_cols=33 Identities=24% Similarity=0.494 Sum_probs=20.6
Q ss_pred ceecCCCCCC----CCceEEEeec---CCceEEEEccccc
Q psy3498 22 IQFNCPFCNH----EKSCEVKMDK---GRNSARIACRVCL 54 (81)
Q Consensus 22 ~~F~CPfC~~----~~sV~v~i~k---~~~~g~l~C~~C~ 54 (81)
+..-|..|+. ..++.+.|.+ ....-...|..||
T Consensus 45 kr~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~ 84 (85)
T PF04032_consen 45 KRTICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCG 84 (85)
T ss_dssp CCTB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTT
T ss_pred hcccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccC
Confidence 5667999997 2356777763 3566789999997
No 225
>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=43.29 E-value=19 Score=26.79 Aligned_cols=26 Identities=19% Similarity=0.394 Sum_probs=18.2
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEccccc
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCL 54 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~ 54 (81)
.||.||++ |...+-.+.++-.|..|+
T Consensus 247 pC~~Cg~~----I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 247 PCRRCGTP----IEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCe----eEEEEECCCCCEECCCCC
Confidence 69999983 333333567788898885
No 226
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=43.24 E-value=20 Score=21.16 Aligned_cols=30 Identities=13% Similarity=0.197 Sum_probs=23.5
Q ss_pred eEEE--EcccccceeEeccCCCCchhhhhhhh
Q psy3498 45 SARI--ACRVCLEDFQTTINFLSEAIDVYNDW 74 (81)
Q Consensus 45 ~g~l--~C~~C~~~~~~~i~~L~epIDVYs~W 74 (81)
+.+| .|..||..-...-++-..|-|-|++.
T Consensus 13 ~YTLk~~cp~cG~~T~~ahPaRFSPdDky~~y 44 (53)
T PF04135_consen 13 VYTLKDKCPPCGGPTESAHPARFSPDDKYSKY 44 (53)
T ss_dssp EEESSSBBTTTSSBSEESSSSSS-TTTTTCHH
T ss_pred cEeCCCccCCCCCCCcCCcCCCCCCCCccHHH
Confidence 4444 49999998888889999999999874
No 227
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=43.05 E-value=13 Score=22.16 Aligned_cols=15 Identities=33% Similarity=0.877 Sum_probs=11.9
Q ss_pred CCCCceecCCCCCCC
Q psy3498 18 EPLDIQFNCPFCNHE 32 (81)
Q Consensus 18 ~~l~~~F~CPfC~~~ 32 (81)
.+..-.|+||.||-.
T Consensus 9 ~~~~v~~~Cp~cGip 23 (55)
T PF13824_consen 9 LPAHVNFECPDCGIP 23 (55)
T ss_pred cccccCCcCCCCCCc
Confidence 356789999999964
No 228
>PHA00732 hypothetical protein
Probab=42.79 E-value=2.7 Score=26.30 Aligned_cols=47 Identities=17% Similarity=0.466 Sum_probs=24.5
Q ss_pred eecCCCCCCCCceEEEeecCCc--eEEEEcccccceeEeccCCCCchhh
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRN--SARIACRVCLEDFQTTINFLSEAID 69 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~--~g~l~C~~C~~~~~~~i~~L~epID 69 (81)
.|.|+.|+..-.-.-.+..-.. -..-.|..||..|.........--|
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~~l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYRRLNQHFYSQYD 49 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeCChhhhhcccCC
Confidence 3789999864321111111000 0012799999999865555444444
No 229
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.77 E-value=11 Score=28.97 Aligned_cols=11 Identities=36% Similarity=1.044 Sum_probs=9.6
Q ss_pred CceecCCCCCC
Q psy3498 21 DIQFNCPFCNH 31 (81)
Q Consensus 21 ~~~F~CPfC~~ 31 (81)
.+.|+||+||.
T Consensus 17 kk~ieCPvC~t 27 (267)
T COG1655 17 KKTIECPVCNT 27 (267)
T ss_pred hceeccCcccc
Confidence 57899999996
No 230
>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=42.68 E-value=25 Score=17.59 Aligned_cols=26 Identities=19% Similarity=0.558 Sum_probs=13.7
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEccccc
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCL 54 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~ 54 (81)
.||.|++. ...+.+ .+...--|..|.
T Consensus 3 ~C~rC~~~-~~~~~~---~~r~~~~C~rCq 28 (30)
T PF06827_consen 3 KCPRCWNY-IEDIGI---NGRSTYLCPRCQ 28 (30)
T ss_dssp B-TTT--B-BEEEEE---TTEEEEE-TTTC
T ss_pred cCccCCCc-ceEeEe---cCCCCeECcCCc
Confidence 59999983 333333 566777888875
No 231
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=42.32 E-value=36 Score=17.51 Aligned_cols=25 Identities=12% Similarity=0.503 Sum_probs=15.7
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcc
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACR 51 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~ 51 (81)
++|.|..||+ +...++ .+-+.+.|-
T Consensus 6 ~~ykC~~Cgn---iv~v~~--~~~~~l~Cc 30 (34)
T TIGR00319 6 QVYKCEVCGN---IVEVLH--AGGGQLVCC 30 (34)
T ss_pred cEEEcCCCCc---EEEEEE--CCCcceecc
Confidence 6899999998 333333 333456663
No 232
>KOG3022|consensus
Probab=42.14 E-value=13 Score=29.00 Aligned_cols=13 Identities=38% Similarity=0.945 Sum_probs=10.7
Q ss_pred ceecCCCCCCCCc
Q psy3498 22 IQFNCPFCNHEKS 34 (81)
Q Consensus 22 ~~F~CPfC~~~~s 34 (81)
+.|.||.|+|...
T Consensus 221 s~f~Cp~C~~~~~ 233 (300)
T KOG3022|consen 221 SGFVCPKCGHSTN 233 (300)
T ss_pred ccccCCCCCCcce
Confidence 6899999999533
No 233
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=42.00 E-value=16 Score=21.87 Aligned_cols=27 Identities=19% Similarity=0.289 Sum_probs=20.5
Q ss_pred CCCCceecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 18 EPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 18 ~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
-++++.=.||.||. ....+-.|..||.
T Consensus 22 l~~~~~~~c~~cG~-----------~~l~Hrvc~~cg~ 48 (57)
T COG0333 22 LKAPTLSVCPNCGE-----------YKLPHRVCLKCGY 48 (57)
T ss_pred hhCccceeccCCCC-----------cccCceEcCCCCC
Confidence 45678888999997 3456778888884
No 234
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=41.35 E-value=11 Score=25.05 Aligned_cols=30 Identities=20% Similarity=0.516 Sum_probs=19.5
Q ss_pred EEEcccccceeEe-ccCCCCchhhhhhhhhh
Q psy3498 47 RIACRVCLEDFQT-TINFLSEAIDVYNDWVD 76 (81)
Q Consensus 47 ~l~C~~C~~~~~~-~i~~L~epIDVYs~WiD 76 (81)
-+.|+.||..|.. +|+.-|--=--=|+||.
T Consensus 58 Pa~CkkCGfef~~~~ik~pSRCP~CKSE~Ie 88 (97)
T COG3357 58 PARCKKCGFEFRDDKIKKPSRCPKCKSEWIE 88 (97)
T ss_pred ChhhcccCccccccccCCcccCCcchhhccc
Confidence 4579999988865 56644443345667775
No 235
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=41.33 E-value=16 Score=20.11 Aligned_cols=15 Identities=20% Similarity=0.454 Sum_probs=11.5
Q ss_pred eEEEEcccccceeEe
Q psy3498 45 SARIACRVCLEDFQT 59 (81)
Q Consensus 45 ~g~l~C~~C~~~~~~ 59 (81)
.|.|.|+.||..+..
T Consensus 3 ~g~l~C~~CG~~m~~ 17 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTR 17 (58)
T ss_pred CCcEEcccCCcEeEE
Confidence 477889999987654
No 236
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=40.55 E-value=18 Score=24.36 Aligned_cols=10 Identities=20% Similarity=0.640 Sum_probs=5.6
Q ss_pred EEEEcccccc
Q psy3498 46 ARIACRVCLE 55 (81)
Q Consensus 46 g~l~C~~C~~ 55 (81)
..-.|..|++
T Consensus 19 ~~w~C~~C~q 28 (131)
T PF09779_consen 19 SNWTCPHCEQ 28 (131)
T ss_pred CeeECCCCCC
Confidence 3455666665
No 237
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.44 E-value=6.5 Score=27.78 Aligned_cols=48 Identities=21% Similarity=0.353 Sum_probs=25.8
Q ss_pred CceecCCCCCCCCc----eEEEeecC-CceEEEEcccccceeEeccCCCCchh
Q psy3498 21 DIQFNCPFCNHEKS----CEVKMDKG-RNSARIACRVCLEDFQTTINFLSEAI 68 (81)
Q Consensus 21 ~~~F~CPfC~~~~s----V~v~i~k~-~~~g~l~C~~C~~~~~~~i~~L~epI 68 (81)
.|+-+||.|+..-- |+=.+... +..---.|.+||..|...-..|..++
T Consensus 37 ati~qcp~csasirgd~~vegvlglg~dye~psfchncgs~fpwterkiaga~ 89 (160)
T COG4306 37 ATITQCPICSASIRGDYYVEGVLGLGGDYEPPSFCHNCGSRFPWTERKIAGAV 89 (160)
T ss_pred HHHhcCCccCCcccccceeeeeeccCCCCCCcchhhcCCCCCCcHHHHHhHHH
Confidence 46789999997311 11111100 00113469999999976544444333
No 238
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=39.80 E-value=14 Score=22.14 Aligned_cols=15 Identities=33% Similarity=0.720 Sum_probs=10.9
Q ss_pred CCCCceecCCCCCCC
Q psy3498 18 EPLDIQFNCPFCNHE 32 (81)
Q Consensus 18 ~~l~~~F~CPfC~~~ 32 (81)
-+++..=-||||+..
T Consensus 34 f~~~rYngCPfC~~~ 48 (55)
T PF14447_consen 34 FPGERYNGCPFCGTP 48 (55)
T ss_pred cChhhccCCCCCCCc
Confidence 355666679999973
No 239
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=39.76 E-value=56 Score=26.92 Aligned_cols=36 Identities=19% Similarity=0.394 Sum_probs=26.0
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccceeEeccC
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTIN 62 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~ 62 (81)
-||.||.-.+-.+..+-.. .-.-.|. ||...++.|.
T Consensus 170 ic~~cGrv~~~~~~~~~~~-~v~Y~c~-cG~~g~~~~~ 205 (515)
T TIGR00467 170 FCENCGRDTTTVNNYDNEY-SIEYSCE-CGNQESVDIY 205 (515)
T ss_pred ecCCcCccCceEEEecCCc-eEEEEcC-CCCEEEEeec
Confidence 4999999877666666544 4455785 9988887763
No 240
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.66 E-value=19 Score=23.98 Aligned_cols=9 Identities=33% Similarity=1.309 Sum_probs=7.3
Q ss_pred ecCCCCCCC
Q psy3498 24 FNCPFCNHE 32 (81)
Q Consensus 24 F~CPfC~~~ 32 (81)
|.||.||..
T Consensus 93 ~~CP~Cgs~ 101 (124)
T PRK00762 93 IECPVCGNK 101 (124)
T ss_pred CcCcCCCCC
Confidence 689999963
No 241
>KOG2893|consensus
Probab=39.54 E-value=11 Score=29.32 Aligned_cols=31 Identities=23% Similarity=0.589 Sum_probs=15.2
Q ss_pred CCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 26 CPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
|=+||.+--=+=.+..-++--+..|.+|+..
T Consensus 13 cwycnrefddekiliqhqkakhfkchichkk 43 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAKHFKCHICHKK 43 (341)
T ss_pred eeecccccchhhhhhhhhhhccceeeeehhh
Confidence 7777764221111111123346778887753
No 242
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=39.53 E-value=8.7 Score=30.07 Aligned_cols=34 Identities=9% Similarity=0.117 Sum_probs=18.2
Q ss_pred eEEEEcccccceeEec-cCCCCchhhhhhhhhhhc
Q psy3498 45 SARIACRVCLEDFQTT-INFLSEAIDVYNDWVDAS 78 (81)
Q Consensus 45 ~g~l~C~~C~~~~~~~-i~~L~epIDVYs~WiD~c 78 (81)
.-...|..||..-+.+ ...+.=++.-|.+|+.+.
T Consensus 164 l~~p~~~~~g~~~~~r~e~~~ff~L~~~~~~L~~~ 198 (391)
T PF09334_consen 164 LINPVCKICGSPPEVREEENYFFKLSKFRDQLREW 198 (391)
T ss_dssp SECEEETTTS-B-EEEEEEEEEE-GGGGHHHHHHH
T ss_pred ccCCccccccccCccccceEEEEehHHhHHHHHHH
Confidence 3456788888765543 455555555566655543
No 243
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=38.92 E-value=44 Score=17.21 Aligned_cols=25 Identities=12% Similarity=0.488 Sum_probs=15.5
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcc
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACR 51 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~ 51 (81)
++|.|..||+ +...+. .+-+.+.|-
T Consensus 3 ~~ykC~~CGn---iv~v~~--~~~~~l~Cc 27 (34)
T cd00974 3 EVYKCEICGN---IVEVLN--VGGGTLVCC 27 (34)
T ss_pred cEEEcCCCCc---EEEEEE--CCCcceeec
Confidence 5899999998 333332 344556664
No 244
>MTH00140 COX2 cytochrome c oxidase subunit II; Provisional
Probab=38.81 E-value=33 Score=24.99 Aligned_cols=48 Identities=8% Similarity=0.201 Sum_probs=33.9
Q ss_pred CCCCceEEEeecCCceEEEEccc-ccceeE-eccCCCCchhhhhhhhhhhc
Q psy3498 30 NHEKSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEAIDVYNDWVDAS 78 (81)
Q Consensus 30 ~~~~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~epIDVYs~WiD~c 78 (81)
|..+.+....++ .|.....|.. ||..+. |++.-.-.+-+-|.+|+..-
T Consensus 177 g~~~~~~~~~~~-~g~y~~~C~e~CG~~H~~M~~~v~v~~~~~f~~W~~~~ 226 (228)
T MTH00140 177 GRLNQLSFEPKR-PGVFYGQCSEICGANHSFMPIVVEAVPLEDFVKWLELM 226 (228)
T ss_pred CcceeEEEEeCC-CEEEEEECccccCcCcCCCeEEEEEECHHHHHHHHHhc
Confidence 444556666554 5677899988 999775 46666666778899998653
No 245
>PRK04023 DNA polymerase II large subunit; Validated
Probab=38.25 E-value=18 Score=32.82 Aligned_cols=13 Identities=23% Similarity=0.169 Sum_probs=6.7
Q ss_pred chhhhhhhhhhhc
Q psy3498 66 EAIDVYNDWVDAS 78 (81)
Q Consensus 66 epIDVYs~WiD~c 78 (81)
.-||+=..|-+|.
T Consensus 679 ~~i~l~~~~~~A~ 691 (1121)
T PRK04023 679 RKIDLKELYDRAL 691 (1121)
T ss_pred EEecHHHHHHHHH
Confidence 4455555555543
No 246
>PRK15338 type III secretion system regulator InvE; Provisional
Probab=37.96 E-value=15 Score=29.51 Aligned_cols=18 Identities=22% Similarity=0.610 Sum_probs=14.2
Q ss_pred CCCCchhhhhhhhhhhcC
Q psy3498 62 NFLSEAIDVYNDWVDASV 79 (81)
Q Consensus 62 ~~L~epIDVYs~WiD~c~ 79 (81)
..=..++++|.+||+.+.
T Consensus 195 ~~d~~~~~iY~~Wieeyg 212 (372)
T PRK15338 195 QSESHEVEIYSDWIASYG 212 (372)
T ss_pred hccCcHHHHHHHHHHHhC
Confidence 334578999999999874
No 247
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.57 E-value=15 Score=24.77 Aligned_cols=10 Identities=30% Similarity=0.597 Sum_probs=5.5
Q ss_pred EcccccceeE
Q psy3498 49 ACRVCLEDFQ 58 (81)
Q Consensus 49 ~C~~C~~~~~ 58 (81)
.|..|+..|.
T Consensus 57 ~C~~C~~~f~ 66 (112)
T TIGR00622 57 FCFGCQGPFP 66 (112)
T ss_pred cccCcCCCCC
Confidence 3555555554
No 248
>KOG4080|consensus
Probab=37.54 E-value=16 Score=26.52 Aligned_cols=15 Identities=40% Similarity=0.809 Sum_probs=11.1
Q ss_pred CCCCceecCCCCCCC
Q psy3498 18 EPLDIQFNCPFCNHE 32 (81)
Q Consensus 18 ~~l~~~F~CPfC~~~ 32 (81)
....-.=.||-|||-
T Consensus 88 k~k~nl~~CP~CGh~ 102 (176)
T KOG4080|consen 88 KPKDNLNTCPACGHI 102 (176)
T ss_pred cchhccccCcccCcc
Confidence 344557889999993
No 249
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=37.39 E-value=55 Score=18.12 Aligned_cols=22 Identities=14% Similarity=0.456 Sum_probs=15.3
Q ss_pred ceEEEeecCCceEEEEccccccee
Q psy3498 34 SCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 34 sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
-|-+.|+...+ .+.|.=||..|
T Consensus 18 rVyl~l~~~~~--~~~CpYCg~~y 39 (40)
T PF10276_consen 18 RVYLNLDDEPG--PVVCPYCGTRY 39 (40)
T ss_dssp CEEEE-TTTTC--EEEETTTTEEE
T ss_pred eEEEecCCCCC--eEECCCCCCEE
Confidence 46677766443 88999999887
No 250
>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=37.29 E-value=70 Score=17.19 Aligned_cols=28 Identities=21% Similarity=0.520 Sum_probs=17.4
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEccc---ccce
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRV---CLED 56 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~---C~~~ 56 (81)
.||.||+ .+..+..+.. -.+.|.. |...
T Consensus 3 ~CP~Cg~--~lv~r~~k~g--~F~~Cs~yP~C~~~ 33 (39)
T PF01396_consen 3 KCPKCGG--PLVLRRGKKG--KFLGCSNYPECKYT 33 (39)
T ss_pred CCCCCCc--eeEEEECCCC--CEEECCCCCCcCCe
Confidence 6999995 3444443333 5678887 6643
No 251
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=37.25 E-value=16 Score=17.95 Aligned_cols=11 Identities=27% Similarity=0.993 Sum_probs=7.6
Q ss_pred EEcccccceeE
Q psy3498 48 IACRVCLEDFQ 58 (81)
Q Consensus 48 l~C~~C~~~~~ 58 (81)
+.|..||.+|.
T Consensus 3 ~~C~~CgR~F~ 13 (25)
T PF13913_consen 3 VPCPICGRKFN 13 (25)
T ss_pred CcCCCCCCEEC
Confidence 45777777774
No 252
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=37.01 E-value=24 Score=25.34 Aligned_cols=33 Identities=18% Similarity=0.246 Sum_probs=22.0
Q ss_pred ecCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
|-|-.||++..---+.=..+.+-...|.+||+-
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~v 33 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKV 33 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCCc
Confidence 468899996221112223567888999999974
No 253
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=36.93 E-value=15 Score=29.89 Aligned_cols=28 Identities=21% Similarity=0.595 Sum_probs=19.7
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
-||+||. .|..+ |.+-..|..||..+..
T Consensus 352 ~Cp~Cg~------~m~S~-G~~g~rC~kCg~~~~~ 379 (421)
T COG1571 352 VCPRCGG------RMKSA-GRNGFRCKKCGTRARE 379 (421)
T ss_pred CCCccCC------chhhc-CCCCcccccccccCCc
Confidence 5999997 34333 2226799999998865
No 254
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=36.60 E-value=15 Score=26.43 Aligned_cols=10 Identities=40% Similarity=1.245 Sum_probs=8.6
Q ss_pred ceecCCCCCC
Q psy3498 22 IQFNCPFCNH 31 (81)
Q Consensus 22 ~~F~CPfC~~ 31 (81)
..|.||-||.
T Consensus 131 ~~F~Cp~Cg~ 140 (176)
T COG1675 131 LGFTCPKCGE 140 (176)
T ss_pred hCCCCCCCCc
Confidence 4699999997
No 255
>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=35.80 E-value=35 Score=18.97 Aligned_cols=24 Identities=33% Similarity=0.707 Sum_probs=14.6
Q ss_pred ecCCCCCCCCceEEEeecCCceEEEEccccc
Q psy3498 24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCL 54 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~ 54 (81)
-.||.|+. .-.. ++ .|.+.|-+|+
T Consensus 18 ~~Cp~C~~---PL~~-~k---~g~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGT---PLMR-DK---DGKIYCVSCG 41 (41)
T ss_pred CccCCCCC---eeEE-ec---CCCEECCCCC
Confidence 36999975 2222 22 3467888885
No 256
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=35.62 E-value=77 Score=17.21 Aligned_cols=27 Identities=19% Similarity=0.332 Sum_probs=15.7
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEccc
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRV 52 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~ 52 (81)
-||-||- ..+.=..+.+..|-...|.+
T Consensus 3 lcpkcgv-gvl~pvy~~kgeikvfrcsn 29 (36)
T PF09151_consen 3 LCPKCGV-GVLEPVYNQKGEIKVFRCSN 29 (36)
T ss_dssp B-TTTSS-SBEEEEE-TTS-EEEEEES-
T ss_pred cCCccCc-eEEEEeecCCCcEEEEEcCC
Confidence 4999997 44444556666777777775
No 257
>PRK14873 primosome assembly protein PriA; Provisional
Probab=35.49 E-value=30 Score=29.28 Aligned_cols=29 Identities=17% Similarity=0.446 Sum_probs=18.0
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
..+.||+|+. ...+.+ ..+.+.|.-||..
T Consensus 391 ~~~~C~~C~~----~L~~h~--~~~~l~Ch~CG~~ 419 (665)
T PRK14873 391 TPARCRHCTG----PLGLPS--AGGTPRCRWCGRA 419 (665)
T ss_pred CeeECCCCCC----ceeEec--CCCeeECCCCcCC
Confidence 4567777775 233333 3357888888864
No 258
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.35 E-value=15 Score=28.06 Aligned_cols=29 Identities=24% Similarity=0.614 Sum_probs=21.0
Q ss_pred CCCceecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
..+.-|-||.|.. +-|++. ..|.+||..|
T Consensus 251 ~v~~GyvCs~Cls---i~C~~p-------~~C~~Cgt~f 279 (279)
T TIGR00627 251 LVSIGFVCSVCLS---VLCQYT-------PICKTCKTAF 279 (279)
T ss_pred cccceEECCCccC---CcCCCC-------CCCCCCCCCC
Confidence 3556699999986 555553 3899999876
No 259
>PRK05580 primosome assembly protein PriA; Validated
Probab=35.31 E-value=29 Score=29.13 Aligned_cols=29 Identities=21% Similarity=0.597 Sum_probs=16.8
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
.+.||.|+- .....+ ....+.|.-||...
T Consensus 390 ~~~C~~C~~----~l~~h~--~~~~l~Ch~Cg~~~ 418 (679)
T PRK05580 390 VAECPHCDA----SLTLHR--FQRRLRCHHCGYQE 418 (679)
T ss_pred ccCCCCCCC----ceeEEC--CCCeEECCCCcCCC
Confidence 455666664 333333 34577888888654
No 260
>PHA00733 hypothetical protein
Probab=35.28 E-value=5.9 Score=26.64 Aligned_cols=40 Identities=25% Similarity=0.530 Sum_probs=22.5
Q ss_pred CceecCCCCCCCCceEEEeecCCc--eEEEEcccccceeEec
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKGRN--SARIACRVCLEDFQTT 60 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~~~--~g~l~C~~C~~~~~~~ 60 (81)
.+.|.|+.|+..-+-...+..-.. .....|..|+..|...
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~ 112 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNT 112 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCH
Confidence 467999999963221111111000 1246999999988643
No 261
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=35.19 E-value=21 Score=20.33 Aligned_cols=11 Identities=36% Similarity=0.776 Sum_probs=9.3
Q ss_pred CceecCCCCCC
Q psy3498 21 DIQFNCPFCNH 31 (81)
Q Consensus 21 ~~~F~CPfC~~ 31 (81)
+.+..||.||.
T Consensus 44 ~~i~~Cp~CgR 54 (56)
T PF02591_consen 44 DEIVFCPNCGR 54 (56)
T ss_pred CCeEECcCCCc
Confidence 67899999985
No 262
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=34.84 E-value=4.9 Score=24.86 Aligned_cols=31 Identities=23% Similarity=0.542 Sum_probs=23.5
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
.||-|+...++. +=+.+++-++.|-.||-.-
T Consensus 12 ~CP~C~~~Dtl~--mW~En~ve~vECV~CG~~~ 42 (66)
T COG3529 12 VCPACQAQDTLA--MWRENNVEIVECVKCGHHM 42 (66)
T ss_pred CCcccchhhHHH--HHHhcCCceEehhhcchHh
Confidence 699999866543 3446789999999999643
No 263
>PF12480 DUF3699: Protein of unknown function (DUF3699) ; InterPro: IPR022168 This domain family is found in eukaryotes, and is approximately 80 amino acids in length.
Probab=34.80 E-value=84 Score=19.48 Aligned_cols=38 Identities=8% Similarity=0.190 Sum_probs=28.5
Q ss_pred ecCCceEEEEcccccceeEe-ccCCCCchhhhhhhhhhhc
Q psy3498 40 DKGRNSARIACRVCLEDFQT-TINFLSEAIDVYNDWVDAS 78 (81)
Q Consensus 40 ~k~~~~g~l~C~~C~~~~~~-~i~~L~epIDVYs~WiD~c 78 (81)
+.......+.|.. |..|.. -.++.++|=+++..|+...
T Consensus 23 ~~~~~~l~lk~~t-~r~~yl~L~~~~~~~~~~F~~w~~lv 61 (77)
T PF12480_consen 23 DLEKQQLKLKLVT-GRPFYLQLCAPADKPETLFGEWIRLV 61 (77)
T ss_pred cCcccEEEEEEcc-CCEEEEEEeCcccCcchhHHHHHHHH
Confidence 4456777888877 445555 4888999999999999754
No 264
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=34.56 E-value=16 Score=26.04 Aligned_cols=12 Identities=42% Similarity=1.038 Sum_probs=3.2
Q ss_pred CCceecCCCCCC
Q psy3498 20 LDIQFNCPFCNH 31 (81)
Q Consensus 20 l~~~F~CPfC~~ 31 (81)
+..-|.||||+-
T Consensus 151 ~~~~~~Cp~C~~ 162 (175)
T PF05280_consen 151 PRHSFVCPFCQP 162 (175)
T ss_dssp -SS----TT---
T ss_pred CCcCcCCCCCCC
Confidence 457899999994
No 265
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=34.51 E-value=8.2 Score=23.44 Aligned_cols=36 Identities=22% Similarity=0.562 Sum_probs=17.9
Q ss_pred CceecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
.+.|.|.+|..+.+ .=.+++. .+..+.|+.|+....
T Consensus 17 ~~~y~C~~CHde~~-~H~~~~~-~~~~v~Cg~C~~~~~ 52 (71)
T PF05495_consen 17 GKYYPCRFCHDELE-DHPFDRW-PVKRVICGKCRTEQP 52 (71)
T ss_dssp TEEESSHHHHHHCS-SS---TT-T--EEEETTT--EEE
T ss_pred cCeecHHHHHHHhc-cCccccc-cccCeECCCCCCccC
Confidence 46777777765544 2233332 233788888886554
No 266
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=34.50 E-value=20 Score=20.61 Aligned_cols=30 Identities=23% Similarity=0.583 Sum_probs=19.7
Q ss_pred CCCceecCCCCCCCCceEEEeecCCceEEEEccc--ccceeE
Q psy3498 19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRV--CLEDFQ 58 (81)
Q Consensus 19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~--C~~~~~ 58 (81)
.|--+-.||.||..+ +.-.+.|++ |++.|.
T Consensus 7 TlRGirkCp~CGt~N----------G~R~~~CKN~~C~~~~~ 38 (44)
T PF14952_consen 7 TLRGIRKCPKCGTYN----------GTRGLSCKNKSCPQVFN 38 (44)
T ss_pred hHhccccCCcCcCcc----------CcccccccCCccchhhh
Confidence 344566799999843 333477876 777654
No 267
>KOG3277|consensus
Probab=34.37 E-value=40 Score=24.31 Aligned_cols=53 Identities=13% Similarity=0.307 Sum_probs=37.1
Q ss_pred CCCCCceecCCCCCCCCceEEEeec---CCceEEEEcccccceeEeccC-CCCchhhhh
Q psy3498 17 IEPLDIQFNCPFCNHEKSCEVKMDK---GRNSARIACRVCLEDFQTTIN-FLSEAIDVY 71 (81)
Q Consensus 17 ~~~l~~~F~CPfC~~~~sV~v~i~k---~~~~g~l~C~~C~~~~~~~i~-~L~epIDVY 71 (81)
.+.+.-.|+|-.||.-.+ =.|.+ ..|+-.+.|.-|...+-..=| .|....|+|
T Consensus 73 kp~m~l~yTCkvCntRs~--ktisk~AY~~GvVivqC~gC~~~HliaDnL~~F~d~~~~ 129 (165)
T KOG3277|consen 73 KPRMQLAYTCKVCNTRST--KTISKQAYEKGVVIVQCPGCKNHHLIADNLGWFHDLKGK 129 (165)
T ss_pred CcceEEEEEeeccCCccc--cccChhhhhCceEEEECCCCccceeehhhhccccccccc
Confidence 456778999999999666 33444 368899999999987754211 244556666
No 268
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=34.23 E-value=24 Score=19.99 Aligned_cols=22 Identities=14% Similarity=0.365 Sum_probs=14.4
Q ss_pred CceEEEEcccccceeEeccCCC
Q psy3498 43 RNSARIACRVCLEDFQTTINFL 64 (81)
Q Consensus 43 ~~~g~l~C~~C~~~~~~~i~~L 64 (81)
...+-=.|..||-+|+..|+.-
T Consensus 24 ~~~v~W~C~~Cgh~w~~~v~~R 45 (55)
T PF14311_consen 24 NKKVWWKCPKCGHEWKASVNDR 45 (55)
T ss_pred CCEEEEECCCCCCeeEccHhhh
Confidence 3445567777777777766543
No 269
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=33.94 E-value=26 Score=32.83 Aligned_cols=45 Identities=20% Similarity=0.409 Sum_probs=29.3
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhhhhcC
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASV 79 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~WiD~c~ 79 (81)
-.|.||.||+. .-...|..||..-+. -++-..-||+=..|-+|.+
T Consensus 673 ~~~~Cp~Cg~~------------~~~~~Cp~CG~~~~~-~~~~~~~i~~~~~~~~A~~ 717 (1627)
T PRK14715 673 AFFKCPKCGKV------------GLYHVCPFCGTRVEL-KPYARREIPPKDYWYAALE 717 (1627)
T ss_pred EeeeCCCCCCc------------cccccCcccCCcccC-CCccceecCHHHHHHHHHH
Confidence 46889999983 235689999987332 2223356777777776654
No 270
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=33.79 E-value=17 Score=16.96 Aligned_cols=12 Identities=25% Similarity=0.858 Sum_probs=8.6
Q ss_pred EcccccceeEec
Q psy3498 49 ACRVCLEDFQTT 60 (81)
Q Consensus 49 ~C~~C~~~~~~~ 60 (81)
.|.+|+..|...
T Consensus 2 ~C~~C~~~f~s~ 13 (25)
T PF12874_consen 2 YCDICNKSFSSE 13 (25)
T ss_dssp EETTTTEEESSH
T ss_pred CCCCCCCCcCCH
Confidence 588888877643
No 271
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=33.48 E-value=26 Score=24.47 Aligned_cols=34 Identities=26% Similarity=0.527 Sum_probs=21.1
Q ss_pred CceecCCCCCCCCceEEEeecC-----------CceEEEEccccc
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKG-----------RNSARIACRVCL 54 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~-----------~~~g~l~C~~C~ 54 (81)
.=++.|.+|+++.++.+.-... ..+..+.|+-|.
T Consensus 62 Nfv~KCk~C~re~si~i~~~~~~~~~~e~~~~~~~i~~fdCRG~e 106 (161)
T PF05907_consen 62 NFVMKCKFCKRESSIDIIPGKGKPYTAEDSGKFVPILAFDCRGLE 106 (161)
T ss_dssp SEEE--SSSS--EEEEEE--TTTEEEGGGTTS-EEEEEEEEESEE
T ss_pred EeEecCcCcCCccEEEEEecCccccccccccCCceEEEEECCCcE
Confidence 4578999999999998865431 246788999985
No 272
>COG1773 Rubredoxin [Energy production and conversion]
Probab=33.15 E-value=27 Score=20.86 Aligned_cols=22 Identities=27% Similarity=0.348 Sum_probs=16.7
Q ss_pred CCCCCceecCCCCCCCCceEEE
Q psy3498 17 IEPLDIQFNCPFCNHEKSCEVK 38 (81)
Q Consensus 17 ~~~l~~~F~CPfC~~~~sV~v~ 38 (81)
-.-||-.+.||.|+..++.-..
T Consensus 30 fedlPd~w~CP~Cg~~K~~F~~ 51 (55)
T COG1773 30 FEDLPDDWVCPECGVGKKDFEM 51 (55)
T ss_pred hhhCCCccCCCCCCCCHhHeee
Confidence 4679999999999976654433
No 273
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=33.15 E-value=32 Score=20.43 Aligned_cols=25 Identities=20% Similarity=0.740 Sum_probs=17.0
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
.|+.||-. | +.+-..+.|..||+-|
T Consensus 7 ~C~~Cg~~------~--~~~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 7 KCPVCGKK------F--KDGDDIVVCPECGAPY 31 (54)
T ss_pred cChhhCCc------c--cCCCCEEECCCCCCcc
Confidence 57888751 1 2355678899999865
No 274
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised 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 characterised phosphonoacetate hydrolase designated PhnA.
Probab=32.70 E-value=54 Score=18.71 Aligned_cols=31 Identities=16% Similarity=0.553 Sum_probs=20.2
Q ss_pred cCCCCCCCCceEE-Eeec----CCceEEEEcccccc
Q psy3498 25 NCPFCNHEKSCEV-KMDK----GRNSARIACRVCLE 55 (81)
Q Consensus 25 ~CPfC~~~~sV~v-~i~k----~~~~g~l~C~~C~~ 55 (81)
.|.+|+++..+.+ .+-- ...-+.+.|..|..
T Consensus 9 kCELC~a~~~L~vy~Vpp~~~~~~d~~iliC~tC~~ 44 (47)
T smart00782 9 KCELCGSDSPLVVYAVPPSSDVTADNSVMLCDTCHS 44 (47)
T ss_pred cccCcCCCCCceEEecCCCCCCCccceeeechHHHH
Confidence 4999999887655 3322 12346788888864
No 275
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=32.69 E-value=68 Score=17.45 Aligned_cols=25 Identities=20% Similarity=0.578 Sum_probs=11.7
Q ss_pred CceecCCCCCCCCceEEEeecCCceEEEEc
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKGRNSARIAC 50 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C 50 (81)
-.+|.|..||+ -|++. . .+.|.+.|
T Consensus 4 ~~~YkC~~CGn--iVev~--~-~g~g~lvC 28 (36)
T PF06397_consen 4 GEFYKCEHCGN--IVEVV--H-DGGGPLVC 28 (36)
T ss_dssp TEEEE-TTT----EEEEE--E---SS-EEE
T ss_pred ccEEEccCCCC--EEEEE--E-CCCCCEEe
Confidence 36899999997 23332 2 34456666
No 276
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=32.14 E-value=20 Score=20.39 Aligned_cols=9 Identities=44% Similarity=1.549 Sum_probs=3.8
Q ss_pred eecCCCCCC
Q psy3498 23 QFNCPFCNH 31 (81)
Q Consensus 23 ~F~CPfC~~ 31 (81)
.+.||.|+.
T Consensus 41 ~W~CPiC~~ 49 (50)
T PF02891_consen 41 KWKCPICNK 49 (50)
T ss_dssp --B-TTT--
T ss_pred CeECcCCcC
Confidence 389999985
No 277
>TIGR00320 dfx_rbo desulfoferrodoxin. This protein is described in some articles as rubredoxin oxidoreductase (rbo), and its gene shares an operon with the rubredoxin gene in Desulfovibrio vulgaris Hildenborough.
Probab=32.03 E-value=47 Score=22.39 Aligned_cols=30 Identities=13% Similarity=0.519 Sum_probs=19.1
Q ss_pred CceecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
-+.|.|+.||. |...+. .+-+.++| ||+..
T Consensus 5 ~~fYkC~~CGn---iv~v~~--~g~~~l~C--Cge~m 34 (125)
T TIGR00320 5 LQVYKCEVCGN---IVEVLN--AGIGQLVC--CNQPM 34 (125)
T ss_pred CcEEECCCCCc---EEEEEE--CCCcceee--CCccc
Confidence 36999999998 333343 34466777 46544
No 278
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=31.90 E-value=31 Score=22.50 Aligned_cols=12 Identities=25% Similarity=0.661 Sum_probs=5.3
Q ss_pred CCceecCCCCCC
Q psy3498 20 LDIQFNCPFCNH 31 (81)
Q Consensus 20 l~~~F~CPfC~~ 31 (81)
+|-.|.|+.||+
T Consensus 67 ~p~~~~C~~Cg~ 78 (113)
T PF01155_consen 67 VPARARCRDCGH 78 (113)
T ss_dssp E--EEEETTTS-
T ss_pred cCCcEECCCCCC
Confidence 344566666665
No 279
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.75 E-value=22 Score=23.46 Aligned_cols=31 Identities=16% Similarity=0.339 Sum_probs=18.7
Q ss_pred CCCCceecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 18 EPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 18 ~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
...|-.|.|+.||+.-++. ......|..||.
T Consensus 66 e~vp~~~~C~~Cg~~~~~~-------~~~~~~CP~Cgs 96 (117)
T PRK00564 66 VDEKVELECKDCSHVFKPN-------ALDYGVCEKCHS 96 (117)
T ss_pred EecCCEEEhhhCCCccccC-------CccCCcCcCCCC
Confidence 3456788888888643221 113345888885
No 280
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=31.61 E-value=17 Score=23.13 Aligned_cols=12 Identities=25% Similarity=0.539 Sum_probs=9.3
Q ss_pred EEcccccceeEe
Q psy3498 48 IACRVCLEDFQT 59 (81)
Q Consensus 48 l~C~~C~~~~~~ 59 (81)
-+|..||+.|+.
T Consensus 9 ~~C~~CG~d~~~ 20 (86)
T PF06170_consen 9 PRCPHCGLDYSH 20 (86)
T ss_pred CcccccCCcccc
Confidence 379999998864
No 281
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=31.59 E-value=21 Score=25.45 Aligned_cols=10 Identities=30% Similarity=0.803 Sum_probs=5.1
Q ss_pred ceecCCCCCC
Q psy3498 22 IQFNCPFCNH 31 (81)
Q Consensus 22 ~~F~CPfC~~ 31 (81)
.+-.||.|||
T Consensus 148 ~P~~CPiCga 157 (166)
T COG1592 148 APEVCPICGA 157 (166)
T ss_pred CCCcCCCCCC
Confidence 3445555555
No 282
>PRK10525 cytochrome o ubiquinol oxidase subunit II; Provisional
Probab=31.34 E-value=39 Score=26.26 Aligned_cols=49 Identities=6% Similarity=0.133 Sum_probs=31.6
Q ss_pred CCCCceEEEeecCCceEEEEccc-ccceeE-eccCCCCch-hhhhhhhhhhcC
Q psy3498 30 NHEKSCEVKMDKGRNSARIACRV-CLEDFQ-TTINFLSEA-IDVYNDWVDASV 79 (81)
Q Consensus 30 ~~~~sV~v~i~k~~~~g~l~C~~-C~~~~~-~~i~~L~ep-IDVYs~WiD~c~ 79 (81)
|..+.+....++ .|.....|.. ||..|. |.+.-...+ -|-|.+|+++-.
T Consensus 188 G~~n~l~~~a~~-~G~Y~G~CaEyCG~gHs~M~f~v~v~~~~~~F~~Wv~~~~ 239 (315)
T PRK10525 188 GMQTRLHLIANE-PGTYDGISASYSGPGFSGMKFKAIATPDRAEFDQWVAKAK 239 (315)
T ss_pred CceeEEEEEcCC-CEEEEEEChhhcCccccCCeEEEEEECCHHHHHHHHHHHh
Confidence 334455555544 6778899998 999885 444433332 356999998643
No 283
>smart00355 ZnF_C2H2 zinc finger.
Probab=31.34 E-value=23 Score=15.65 Aligned_cols=9 Identities=33% Similarity=0.837 Sum_probs=4.8
Q ss_pred cccccceeE
Q psy3498 50 CRVCLEDFQ 58 (81)
Q Consensus 50 C~~C~~~~~ 58 (81)
|..|+..|.
T Consensus 3 C~~C~~~f~ 11 (26)
T smart00355 3 CPECGKVFK 11 (26)
T ss_pred CCCCcchhC
Confidence 555555553
No 284
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=31.18 E-value=24 Score=25.31 Aligned_cols=33 Identities=21% Similarity=0.587 Sum_probs=22.0
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
+-|-|.+|+++ ++...- +......|..|+.-|-
T Consensus 151 kGfiCe~C~~~---~~IfPF-~~~~~~~C~~C~~v~H 183 (202)
T PF13901_consen 151 KGFICEICNSD---DIIFPF-QIDTTVRCPKCKSVFH 183 (202)
T ss_pred CCCCCccCCCC---CCCCCC-CCCCeeeCCcCccccc
Confidence 45889999874 222222 2247889999998774
No 285
>PHA02893 hypothetical protein; Provisional
Probab=31.13 E-value=40 Score=21.98 Aligned_cols=11 Identities=27% Similarity=0.667 Sum_probs=9.0
Q ss_pred EEEEcccccce
Q psy3498 46 ARIACRVCLED 56 (81)
Q Consensus 46 g~l~C~~C~~~ 56 (81)
..|+|.-||..
T Consensus 68 ~tL~CaACGS~ 78 (88)
T PHA02893 68 SNIKCIACGSS 78 (88)
T ss_pred Cceeehhhchh
Confidence 57999999964
No 286
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=31.00 E-value=23 Score=23.46 Aligned_cols=9 Identities=33% Similarity=1.294 Sum_probs=7.1
Q ss_pred eecCCCCCC
Q psy3498 23 QFNCPFCNH 31 (81)
Q Consensus 23 ~F~CPfC~~ 31 (81)
.+.||+||-
T Consensus 3 LI~CP~Cg~ 11 (97)
T COG4311 3 LIPCPYCGE 11 (97)
T ss_pred eecCCCCCC
Confidence 467999986
No 287
>KOG2324|consensus
Probab=30.99 E-value=21 Score=29.21 Aligned_cols=32 Identities=31% Similarity=0.549 Sum_probs=20.8
Q ss_pred CceecCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
++...||.|+.++--+ . -...+.++|..|..+
T Consensus 225 D~l~~C~~C~~s~n~e-~---~~~sk~~~Cp~C~~~ 256 (457)
T KOG2324|consen 225 DTLMSCPSCGYSKNSE-D---LDLSKIASCPKCNEG 256 (457)
T ss_pred cceeecCcCCccCchh-h---hcCCccccCCcccCC
Confidence 6788999997532211 1 123345899999985
No 288
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=30.98 E-value=33 Score=21.13 Aligned_cols=37 Identities=16% Similarity=0.432 Sum_probs=23.4
Q ss_pred CceecCCCCCCCCceEEEeecC-CceEEEEccccccee
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKG-RNSARIACRVCLEDF 57 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~-~~~g~l~C~~C~~~~ 57 (81)
+....||.|+..++==|=.... ...-.-.|..|...+
T Consensus 3 ~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~ryw 40 (63)
T PF02701_consen 3 EQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYW 40 (63)
T ss_pred ccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHH
Confidence 3566899999977655544432 233456777777654
No 289
>PRK04351 hypothetical protein; Provisional
Probab=30.84 E-value=59 Score=22.51 Aligned_cols=34 Identities=18% Similarity=0.546 Sum_probs=23.1
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
=.+.|.-||+.. ... +.-+...-.|+.|+..+..
T Consensus 111 y~Y~C~~Cg~~~---~r~-Rr~n~~~yrCg~C~g~L~~ 144 (149)
T PRK04351 111 YLYECQSCGQQY---LRK-RRINTKRYRCGKCRGKLKL 144 (149)
T ss_pred EEEECCCCCCEe---eee-eecCCCcEEeCCCCcEeee
Confidence 368999999732 232 3445677899999977653
No 290
>smart00350 MCM minichromosome maintenance proteins.
Probab=30.82 E-value=22 Score=28.66 Aligned_cols=33 Identities=24% Similarity=0.602 Sum_probs=21.3
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEccc--ccce
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRV--CLED 56 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~--C~~~ 56 (81)
-.|.|..||+...+.+. ...-.--..|.. |+..
T Consensus 36 ~~f~C~~C~~~~~~~~~--~~~~~~p~~C~~~~C~~~ 70 (509)
T smart00350 36 ASFTCEKCGATLGPEIQ--SGRETEPTVCPPRECQSP 70 (509)
T ss_pred EEEEecCCCCEEeEEec--CCcccCCCcCCCCcCCCC
Confidence 68999999997555543 222222347877 8864
No 291
>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=30.74 E-value=58 Score=22.61 Aligned_cols=31 Identities=23% Similarity=0.412 Sum_probs=20.2
Q ss_pred CceecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
+-.|.|-.||| .+.+.... -...|..||-..
T Consensus 110 ~G~l~C~~Cg~----~~~~~~~~--~l~~Cp~C~~~~ 140 (146)
T PF07295_consen 110 PGTLVCENCGH----EVELTHPE--RLPPCPKCGHTE 140 (146)
T ss_pred CceEecccCCC----EEEecCCC--cCCCCCCCCCCe
Confidence 35688888888 44554432 366788888543
No 292
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=30.56 E-value=59 Score=28.15 Aligned_cols=40 Identities=20% Similarity=0.405 Sum_probs=30.4
Q ss_pred CCCcee--cCCCCCCCCceEEEeecC--CceE-EEEcccccceeE
Q psy3498 19 PLDIQF--NCPFCNHEKSCEVKMDKG--RNSA-RIACRVCLEDFQ 58 (81)
Q Consensus 19 ~l~~~F--~CPfC~~~~sV~v~i~k~--~~~g-~l~C~~C~~~~~ 58 (81)
.+.-.| .||+|.-..+|.+-.... .+.| .+.|.+||..+-
T Consensus 47 D~~~~~~~pc~~c~gkG~V~v~~~c~~c~G~gkv~~c~~cG~~~~ 91 (715)
T COG1107 47 DLFASFEIPCPKCRGKGTVTVYDTCPECGGTGKVLTCDICGDIIV 91 (715)
T ss_pred cccccCCCCCCeeccceeEEEEeecccCCCceeEEeeccccceec
Confidence 444455 799999999999987765 3544 789999998664
No 293
>cd03019 DsbA_DsbA DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol oxidant known, due to the unusual stability of the thiolate anion form of the first cysteine in the CXXC motif. The highly unstable oxidized form of DsbA directly donates disulfide bonds to reduced proteins secreted into the bacterial periplasm. This rapid and unidirectional process helps to catalyze the folding of newly-synthesized polypeptides. To regain catalytic activity, reduced DsbA is then reoxidized by the membrane protein DsbB, which generates its disulfides from oxidized quinones, which in turn are reoxidized by the electron transport chain.
Probab=30.46 E-value=18 Score=23.68 Aligned_cols=11 Identities=27% Similarity=1.002 Sum_probs=8.4
Q ss_pred ceecCCCCCCC
Q psy3498 22 IQFNCPFCNHE 32 (81)
Q Consensus 22 ~~F~CPfC~~~ 32 (81)
.-|.||+|-+-
T Consensus 23 ~D~~Cp~C~~~ 33 (178)
T cd03019 23 FSYGCPHCYNF 33 (178)
T ss_pred ECCCCcchhhh
Confidence 45889999863
No 294
>KOG3507|consensus
Probab=30.18 E-value=33 Score=21.05 Aligned_cols=30 Identities=23% Similarity=0.504 Sum_probs=22.2
Q ss_pred CCceecCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 20 LDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 20 l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
-+-.+-|--|+.++++ . ..-.+.|+.||-+
T Consensus 17 ~~miYiCgdC~~en~l----k---~~D~irCReCG~R 46 (62)
T KOG3507|consen 17 ATMIYICGDCGQENTL----K---RGDVIRCRECGYR 46 (62)
T ss_pred ccEEEEeccccccccc----c---CCCcEehhhcchH
Confidence 3458999999998764 2 2346799999964
No 295
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=30.06 E-value=33 Score=24.84 Aligned_cols=7 Identities=43% Similarity=1.488 Sum_probs=6.5
Q ss_pred CCCCCCC
Q psy3498 26 CPFCNHE 32 (81)
Q Consensus 26 CPfC~~~ 32 (81)
||.|||+
T Consensus 156 Cp~CG~~ 162 (177)
T COG1439 156 CPICGSP 162 (177)
T ss_pred CCCCCCc
Confidence 9999995
No 296
>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=30.04 E-value=23 Score=23.95 Aligned_cols=15 Identities=33% Similarity=0.468 Sum_probs=11.6
Q ss_pred CCceecCCCCCCCCc
Q psy3498 20 LDIQFNCPFCNHEKS 34 (81)
Q Consensus 20 l~~~F~CPfC~~~~s 34 (81)
-...|-||-|+||=+
T Consensus 16 dg~~~iCpeC~~EW~ 30 (109)
T TIGR00686 16 DGTQLICPSCLYEWN 30 (109)
T ss_pred cCCeeECcccccccc
Confidence 345799999999754
No 297
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=29.36 E-value=32 Score=20.77 Aligned_cols=19 Identities=16% Similarity=0.487 Sum_probs=12.4
Q ss_pred CCCceecCCCCCCCCceEE
Q psy3498 19 PLDIQFNCPFCNHEKSCEV 37 (81)
Q Consensus 19 ~l~~~F~CPfC~~~~sV~v 37 (81)
..+..=.||+|+++-.-+.
T Consensus 35 s~~~~p~CPlC~s~M~~~~ 53 (59)
T PF14169_consen 35 SFEEEPVCPLCKSPMVSGT 53 (59)
T ss_pred ccCCCccCCCcCCccccce
Confidence 3455567999998644333
No 298
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=29.34 E-value=49 Score=26.42 Aligned_cols=32 Identities=22% Similarity=0.525 Sum_probs=20.3
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
..=.||.|+. .+....-..-..+.|..||..-
T Consensus 9 ~~~~C~~Cd~----l~~~~~l~~g~~a~CpRCg~~L 40 (419)
T PRK15103 9 KHILCPQCDM----LVALPRLEHGQKAACPRCGTTL 40 (419)
T ss_pred CcccCCCCCc----eeecCCCCCCCeeECCCCCCCC
Confidence 3455999997 2333332333468899999754
No 299
>PRK12722 transcriptional activator FlhC; Provisional
Probab=29.03 E-value=24 Score=25.69 Aligned_cols=12 Identities=25% Similarity=0.509 Sum_probs=10.1
Q ss_pred CCceecCCCCCC
Q psy3498 20 LDIQFNCPFCNH 31 (81)
Q Consensus 20 l~~~F~CPfC~~ 31 (81)
+-..|.||+|+-
T Consensus 151 ~~~~f~CplC~~ 162 (187)
T PRK12722 151 PVGSFVCGLCQP 162 (187)
T ss_pred cCCCCcCCCCCC
Confidence 456899999997
No 300
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=28.84 E-value=19 Score=20.41 Aligned_cols=7 Identities=43% Similarity=1.512 Sum_probs=3.5
Q ss_pred cCCCCCC
Q psy3498 25 NCPFCNH 31 (81)
Q Consensus 25 ~CPfC~~ 31 (81)
.||.|+.
T Consensus 22 ~CPlC~r 28 (54)
T PF04423_consen 22 CCPLCGR 28 (54)
T ss_dssp E-TTT--
T ss_pred cCCCCCC
Confidence 7999986
No 301
>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=28.76 E-value=67 Score=25.52 Aligned_cols=35 Identities=20% Similarity=0.466 Sum_probs=21.7
Q ss_pred CCCceecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
+....=.||.|+.- +.+..-..-..+.|..||..-
T Consensus 9 ~~~~~~~C~~Cd~l----~~~~~l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 9 PAAKHILCSQCDML----VALPRIESGQKAACPRCGTTL 43 (403)
T ss_pred CCCCeeeCCCCCCc----ccccCCCCCCeeECCCCCCCC
Confidence 33445569999972 233332333478899999754
No 302
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=28.55 E-value=26 Score=17.46 Aligned_cols=8 Identities=38% Similarity=1.207 Sum_probs=4.5
Q ss_pred ecCCCCCC
Q psy3498 24 FNCPFCNH 31 (81)
Q Consensus 24 F~CPfC~~ 31 (81)
..||.|+.
T Consensus 2 v~CPiC~~ 9 (26)
T smart00734 2 VQCPVCFR 9 (26)
T ss_pred CcCCCCcC
Confidence 35666654
No 303
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=28.52 E-value=27 Score=29.94 Aligned_cols=21 Identities=24% Similarity=0.494 Sum_probs=13.7
Q ss_pred ecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
=.|+.||+.... .-.|..||.
T Consensus 681 ~~C~~CG~~~~~-----------~~~CP~CG~ 701 (735)
T PRK07111 681 DRCPVCGYLGVI-----------EDKCPKCGS 701 (735)
T ss_pred eecCCCCCCCCc-----------CccCcCCCC
Confidence 358888874321 158888984
No 304
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=28.35 E-value=27 Score=20.52 Aligned_cols=12 Identities=25% Similarity=0.833 Sum_probs=9.9
Q ss_pred CceecCCCCCCC
Q psy3498 21 DIQFNCPFCNHE 32 (81)
Q Consensus 21 ~~~F~CPfC~~~ 32 (81)
.+.=.||.||++
T Consensus 11 ~kY~~Cp~CGN~ 22 (49)
T PF12677_consen 11 NKYCKCPKCGND 22 (49)
T ss_pred hhhccCcccCCc
Confidence 467799999985
No 305
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=28.04 E-value=49 Score=31.47 Aligned_cols=28 Identities=29% Similarity=0.660 Sum_probs=20.2
Q ss_pred cCCCCCCCC--ceEEEeecCCceEEEEcccccce
Q psy3498 25 NCPFCNHEK--SCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 25 ~CPfC~~~~--sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
.||.|+... .|++.+ .. |=+.|..||-+
T Consensus 1706 ~cp~c~~~~~~~~~~~~--~~--gc~~c~~cg~s 1735 (1740)
T PRK08332 1706 YCPVCYEKEGKLVELRM--ES--GCATCPVCGWS 1735 (1740)
T ss_pred CCCCCCCCCCcceeeEe--cC--CceeCCCCCCc
Confidence 399999873 555555 33 67799999964
No 306
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=28.01 E-value=42 Score=18.01 Aligned_cols=14 Identities=14% Similarity=0.382 Sum_probs=10.7
Q ss_pred EEcccccceeEecc
Q psy3498 48 IACRVCLEDFQTTI 61 (81)
Q Consensus 48 l~C~~C~~~~~~~i 61 (81)
..|..||..|....
T Consensus 2 r~C~~Cg~~Yh~~~ 15 (36)
T PF05191_consen 2 RICPKCGRIYHIEF 15 (36)
T ss_dssp EEETTTTEEEETTT
T ss_pred cCcCCCCCcccccc
Confidence 47999999987543
No 307
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=27.99 E-value=27 Score=20.73 Aligned_cols=12 Identities=25% Similarity=0.808 Sum_probs=4.7
Q ss_pred CceecCCCCCCC
Q psy3498 21 DIQFNCPFCNHE 32 (81)
Q Consensus 21 ~~~F~CPfC~~~ 32 (81)
-..+.||.||+.
T Consensus 31 Lr~y~Cp~CgAt 42 (55)
T PF05741_consen 31 LRKYVCPICGAT 42 (55)
T ss_dssp GGG---TTT---
T ss_pred HhcCcCCCCcCc
Confidence 367899999984
No 308
>TIGR01374 soxD sarcosine oxidase, delta subunit family, heterotetrameric form. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) form
Probab=27.84 E-value=27 Score=22.45 Aligned_cols=8 Identities=38% Similarity=1.460 Sum_probs=5.9
Q ss_pred ecCCCCCC
Q psy3498 24 FNCPFCNH 31 (81)
Q Consensus 24 F~CPfC~~ 31 (81)
-+||+||-
T Consensus 2 I~CP~CG~ 9 (84)
T TIGR01374 2 IPCPYCGP 9 (84)
T ss_pred ccCCCCCC
Confidence 36888884
No 309
>PRK10220 hypothetical protein; Provisional
Probab=27.36 E-value=30 Score=23.44 Aligned_cols=18 Identities=28% Similarity=0.458 Sum_probs=13.0
Q ss_pred CCCceecCCCCCCCCceE
Q psy3498 19 PLDIQFNCPFCNHEKSCE 36 (81)
Q Consensus 19 ~l~~~F~CPfC~~~~sV~ 36 (81)
.-...|-||-|+||=+-.
T Consensus 16 ~d~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 16 EDNGMYICPECAHEWNDA 33 (111)
T ss_pred cCCCeEECCcccCcCCcc
Confidence 344679999999985433
No 310
>cd05468 pVHL von Hippel-Landau (pVHL) tumor suppressor protein. von Hippel-Landau (pVHL) protein, the gene product of VHL, is a critical regulator of the ubiquitous oxygen-sensing pathway. It is conserved throughout evolution, as its homologs are found in organisms ranging from mammals to the Drosophila melanogaster, Anopheles gambiae insects and the Caenorhabditis elegans nematode. pVHL acts as the substrate recognition component of an E3 ubiquitin ligase complex. Several proteins have been identified as pVHL-binding proteins that are subject to ubiquitin-mediated proteolysis; the best characterized putative substrates are the alpha subunits of the hypoxia-inducible factor (HIF1alpha, HIF2alpha, and HIF3alpha). In addition to HIF degradation, pVHL has been implicated to be involved in HIF independent cellular processes. Germline VHL mutations cause renal cell carcinomas, hemangioblastomas and pheochromocytomas in humans. pVHL can bind to and direct the proper deposition of fibronecti
Probab=27.25 E-value=14 Score=25.22 Aligned_cols=16 Identities=25% Similarity=0.762 Sum_probs=13.0
Q ss_pred ccCCCCchhhhhhhhhhh
Q psy3498 60 TINFLSEAIDVYNDWVDA 77 (81)
Q Consensus 60 ~i~~L~epIDVYs~WiD~ 77 (81)
=+|....+|||| |||.
T Consensus 13 F~N~t~~~v~~~--Wid~ 28 (141)
T cd05468 13 FVNRTDRPVELY--WIDY 28 (141)
T ss_pred EEeCCCCeEEEE--EECC
Confidence 378888999998 8874
No 311
>PF11648 RIG-I_C-RD: C-terminal domain of RIG-I; InterPro: IPR021673 This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependent dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity []. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2RQB_A 3GA3_A 2W4R_D 3EQT_A 2RQA_A 2RMJ_A 3NCU_A 2QFD_C 2QFB_D 3TMI_A ....
Probab=27.11 E-value=48 Score=22.08 Aligned_cols=15 Identities=27% Similarity=0.798 Sum_probs=11.8
Q ss_pred CceEEEEccccccee
Q psy3498 43 RNSARIACRVCLEDF 57 (81)
Q Consensus 43 ~~~g~l~C~~C~~~~ 57 (81)
...|.+.|+.||+..
T Consensus 56 ~~~~~I~C~~C~~~w 70 (123)
T PF11648_consen 56 EPNGKIHCKNCGQDW 70 (123)
T ss_dssp EEEEEEEETSTSBEE
T ss_pred EeCCEEEcCCCChHh
Confidence 356899999999853
No 312
>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=26.86 E-value=35 Score=24.78 Aligned_cols=16 Identities=13% Similarity=0.071 Sum_probs=12.2
Q ss_pred CceEEEEcccccceeE
Q psy3498 43 RNSARIACRVCLEDFQ 58 (81)
Q Consensus 43 ~~~g~l~C~~C~~~~~ 58 (81)
..+-...|..||..+.
T Consensus 31 ~~i~v~~C~~Cg~~~~ 46 (236)
T PF04981_consen 31 DRIEVTICPKCGRYRI 46 (236)
T ss_pred CccCceECCCCCCEEC
Confidence 3456789999998764
No 313
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.84 E-value=19 Score=25.32 Aligned_cols=9 Identities=33% Similarity=1.106 Sum_probs=7.8
Q ss_pred eecCCCCCC
Q psy3498 23 QFNCPFCNH 31 (81)
Q Consensus 23 ~F~CPfC~~ 31 (81)
.-+||.|||
T Consensus 32 Lv~CPvCgs 40 (142)
T COG5319 32 LVTCPVCGS 40 (142)
T ss_pred ceeCCCCCc
Confidence 468999998
No 314
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized 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.
Probab=26.83 E-value=40 Score=30.58 Aligned_cols=45 Identities=24% Similarity=0.439 Sum_probs=27.2
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhhhhcC
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASV 79 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~WiD~c~ 79 (81)
-.|.||-||+. .-...|..||..- ..+.+-..-||+=..|-+|.+
T Consensus 624 ~~RKCPkCG~y------------Tlk~rCP~CG~~T-e~~~pc~~~i~l~~~~~~A~~ 668 (1095)
T TIGR00354 624 AIRKCPQCGKE------------SFWLKCPVCGELT-EQLYYGKRKVDLRELYEEAIA 668 (1095)
T ss_pred EEEECCCCCcc------------cccccCCCCCCcc-ccccceeEEecHHHHHHHHHH
Confidence 35778888872 2355788888752 223333556777766666543
No 315
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=26.65 E-value=35 Score=20.68 Aligned_cols=9 Identities=33% Similarity=1.187 Sum_probs=7.5
Q ss_pred cCCCCCCCC
Q psy3498 25 NCPFCNHEK 33 (81)
Q Consensus 25 ~CPfC~~~~ 33 (81)
.||.||...
T Consensus 17 ~CP~Cgs~~ 25 (61)
T PRK08351 17 RCPVCGSRD 25 (61)
T ss_pred cCCCCcCCc
Confidence 699999854
No 316
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=26.27 E-value=61 Score=25.65 Aligned_cols=16 Identities=19% Similarity=0.177 Sum_probs=12.0
Q ss_pred CCceEEEEccccccee
Q psy3498 42 GRNSARIACRVCLEDF 57 (81)
Q Consensus 42 ~~~~g~l~C~~C~~~~ 57 (81)
...+....|..||+.+
T Consensus 38 p~~~~v~~C~~Cga~~ 53 (355)
T COG1499 38 PDEVNVEVCRHCGAYR 53 (355)
T ss_pred CCceEEEECCcCCCcc
Confidence 3467789999999433
No 317
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=26.12 E-value=37 Score=27.94 Aligned_cols=11 Identities=36% Similarity=0.824 Sum_probs=4.9
Q ss_pred eecCCCCCCCC
Q psy3498 23 QFNCPFCNHEK 33 (81)
Q Consensus 23 ~F~CPfC~~~~ 33 (81)
.+.||.||.++
T Consensus 504 ~~~CP~CGs~~ 514 (546)
T PF13597_consen 504 GDKCPKCGSEN 514 (546)
T ss_dssp EEE-CCC----
T ss_pred CCCCCCCCCcc
Confidence 67888888865
No 318
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=26.09 E-value=40 Score=23.65 Aligned_cols=10 Identities=30% Similarity=0.859 Sum_probs=8.3
Q ss_pred ceecCCCCCC
Q psy3498 22 IQFNCPFCNH 31 (81)
Q Consensus 22 ~~F~CPfC~~ 31 (81)
...+||.||.
T Consensus 31 glv~CP~Cgs 40 (148)
T PF06676_consen 31 GLVSCPVCGS 40 (148)
T ss_pred CCccCCCCCC
Confidence 4578999998
No 319
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=26.07 E-value=37 Score=20.83 Aligned_cols=9 Identities=44% Similarity=0.962 Sum_probs=7.8
Q ss_pred cCCCCCCCC
Q psy3498 25 NCPFCNHEK 33 (81)
Q Consensus 25 ~CPfC~~~~ 33 (81)
.||.||.+.
T Consensus 19 ~Cp~Cgs~~ 27 (64)
T PRK06393 19 TCPVHGDEK 27 (64)
T ss_pred cCCCCCCCc
Confidence 899999964
No 320
>PF01197 Ribosomal_L31: Ribosomal protein L31; InterPro: IPR002150 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 L31 is one of the proteins from the large ribosomal subunit. L31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3D5D_4 3PYO_1 3D5B_4 3PYV_1 3PYT_1 3MRZ_1 3MS1_1 3PYR_1 3F1F_4 3F1H_4 ....
Probab=26.05 E-value=43 Score=20.33 Aligned_cols=16 Identities=25% Similarity=0.750 Sum_probs=9.6
Q ss_pred eEEEEcccccceeEec
Q psy3498 45 SARIACRVCLEDFQTT 60 (81)
Q Consensus 45 ~g~l~C~~C~~~~~~~ 60 (81)
...+.|..||..|.+.
T Consensus 11 ~v~v~c~s~g~~~~~~ 26 (69)
T PF01197_consen 11 EVKVTCSSCGNTFETR 26 (69)
T ss_dssp EEEEEES-SSSCECEC
T ss_pred EEEEEEcCCCCEEEEE
Confidence 3466777777777654
No 321
>KOG3309|consensus
Probab=26.05 E-value=27 Score=25.07 Aligned_cols=34 Identities=26% Similarity=0.357 Sum_probs=27.3
Q ss_pred EEEEcccccceeEe-ccCCCCchhhhhhhhhhhcC
Q psy3498 46 ARIACRVCLEDFQT-TINFLSEAIDVYNDWVDASV 79 (81)
Q Consensus 46 g~l~C~~C~~~~~~-~i~~L~epIDVYs~WiD~c~ 79 (81)
|++.|..|++.++. ....|.+|-|==.+-+|...
T Consensus 83 gslACSTCHViv~~~~yekl~ep~DeE~DmLDlA~ 117 (159)
T KOG3309|consen 83 GSLACSTCHVIVDEEYYEKLPEPEDEENDMLDLAF 117 (159)
T ss_pred ccccccceEEEEcHHHHhcCCCCcchHHHHHHhhh
Confidence 69999999998875 46688899888777777643
No 322
>PF03470 zf-XS: XS zinc finger domain; InterPro: IPR005381 This domain is a putative nucleic acid binding zinc finger and is found at the N terminus of proteins that also contain an adjacent XS domain IPR005380 from INTERPRO and in some proteins a C-terminal XH domain IPR005379 from INTERPRO.
Probab=25.91 E-value=39 Score=19.25 Aligned_cols=7 Identities=57% Similarity=1.734 Sum_probs=5.6
Q ss_pred CCCCCCC
Q psy3498 26 CPFCNHE 32 (81)
Q Consensus 26 CPfC~~~ 32 (81)
||||...
T Consensus 1 CP~C~~k 7 (43)
T PF03470_consen 1 CPFCPGK 7 (43)
T ss_pred CCCCCCC
Confidence 8999864
No 323
>PRK12860 transcriptional activator FlhC; Provisional
Probab=25.62 E-value=34 Score=24.98 Aligned_cols=13 Identities=31% Similarity=0.751 Sum_probs=10.3
Q ss_pred CCCceecCCCCCC
Q psy3498 19 PLDIQFNCPFCNH 31 (81)
Q Consensus 19 ~l~~~F~CPfC~~ 31 (81)
-+-..|.||+|+-
T Consensus 150 e~~~~f~CplC~~ 162 (189)
T PRK12860 150 DLRHNFVCGLCQP 162 (189)
T ss_pred ccCCCCcCCCCCC
Confidence 3456899999994
No 324
>PF04267 SoxD: Sarcosine oxidase, delta subunit family ; InterPro: IPR006279 These sequences represent the delta subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Rhizobium loti (Mesorhizobium loti) and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate []. Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the heterotetrameric form.; GO: 0008115 sarcosine oxidase activity, 0046653 tetrahydrofolate metabolic process; PDB: 3AD7_D 1X31_D 1VRQ_D 3AD8_D 3ADA_D 3AD9_D 2GAG_D 2GAH_D.
Probab=25.37 E-value=21 Score=22.93 Aligned_cols=7 Identities=43% Similarity=1.374 Sum_probs=4.6
Q ss_pred cCCCCCC
Q psy3498 25 NCPFCNH 31 (81)
Q Consensus 25 ~CPfC~~ 31 (81)
.||+||-
T Consensus 3 ~CP~CG~ 9 (84)
T PF04267_consen 3 PCPHCGP 9 (84)
T ss_dssp EETTTEE
T ss_pred cCCCCCc
Confidence 5777763
No 325
>PRK09502 iscA iron-sulfur cluster assembly protein; Provisional
Probab=25.35 E-value=24 Score=22.59 Aligned_cols=12 Identities=33% Similarity=0.803 Sum_probs=9.7
Q ss_pred EEEEcccccceeE
Q psy3498 46 ARIACRVCLEDFQ 58 (81)
Q Consensus 46 g~l~C~~C~~~~~ 58 (81)
+..+|+ ||.+|+
T Consensus 95 a~~~Cg-CG~Sf~ 106 (107)
T PRK09502 95 VKDECG-CGESFH 106 (107)
T ss_pred CCCccC-CCCCee
Confidence 466899 999986
No 326
>CHL00136 rpl31 ribosomal protein L31; Validated
Probab=25.15 E-value=60 Score=19.88 Aligned_cols=34 Identities=6% Similarity=-0.135 Sum_probs=16.9
Q ss_pred CceecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 21 DIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
...+.| -|+.. ..+.-. ...+..-.|..|+--|+
T Consensus 13 ~~~v~c-~~~~~--~~~~ST-~~~i~vdv~s~~HPfyT 46 (68)
T CHL00136 13 ETKVYC-DGQLV--MTVGST-KPELNVDIWSGNHPFYT 46 (68)
T ss_pred eEEEEE-cCCCE--EEEeec-CCCEEEEeCCCCCccCc
Confidence 346667 46652 222211 23356666666765443
No 327
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.00 E-value=52 Score=21.60 Aligned_cols=31 Identities=19% Similarity=0.383 Sum_probs=19.9
Q ss_pred CCCCceecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 18 EPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 18 ~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
..+|-.+.|+.||+ ...+. ......|..||.
T Consensus 65 ~~~p~~~~C~~Cg~----~~~~~---~~~~~~CP~Cgs 95 (114)
T PRK03681 65 EEQEAECWCETCQQ----YVTLL---TQRVRRCPQCHG 95 (114)
T ss_pred EeeCcEEEcccCCC----eeecC---CccCCcCcCcCC
Confidence 45678899999997 23332 112256999994
No 328
>cd03023 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
Probab=24.81 E-value=22 Score=22.32 Aligned_cols=11 Identities=27% Similarity=1.087 Sum_probs=7.9
Q ss_pred ceecCCCCCCC
Q psy3498 22 IQFNCPFCNHE 32 (81)
Q Consensus 22 ~~F~CPfC~~~ 32 (81)
.-|.||+|..-
T Consensus 13 ~D~~Cp~C~~~ 23 (154)
T cd03023 13 FDYNCGYCKKL 23 (154)
T ss_pred ECCCChhHHHh
Confidence 34689999763
No 329
>PF13397 DUF4109: Domain of unknown function (DUF4109)
Probab=24.77 E-value=43 Score=22.41 Aligned_cols=15 Identities=20% Similarity=0.651 Sum_probs=12.4
Q ss_pred CCCceecCCCCCCCC
Q psy3498 19 PLDIQFNCPFCNHEK 33 (81)
Q Consensus 19 ~l~~~F~CPfC~~~~ 33 (81)
-+|-+.+||.||.+.
T Consensus 46 evP~~WeC~~cG~~A 60 (105)
T PF13397_consen 46 EVPATWECPRCGLPA 60 (105)
T ss_pred CCCCceeCCCCCCcc
Confidence 578899999999853
No 330
>PF07450 HycH: Formate hydrogenlyase maturation protein HycH; InterPro: IPR010005 This family contains the bacterial formate hydrogenlyase maturation protein HycH, which is approximately 140 residues long. This may be required for the conversion of a precursor form of the large subunit of hydrogenlyase 3 into a mature form [].
Probab=24.53 E-value=38 Score=23.53 Aligned_cols=30 Identities=20% Similarity=0.448 Sum_probs=22.4
Q ss_pred CCceEEEEcccccceeEeccCCCCchhhhhhhhhhhcCC
Q psy3498 42 GRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVP 80 (81)
Q Consensus 42 ~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~WiD~c~~ 80 (81)
...+|.+-|-.+ .|.=|.+.|.+||+...+
T Consensus 34 GHhvGvIDcle~---------~l~cp~~~y~~wi~~lp~ 63 (131)
T PF07450_consen 34 GHHVGVIDCLEK---------VLECPLEEYERWIAQLPE 63 (131)
T ss_pred ccccceEeechh---------hccCCHHHHHHHHHhCCc
Confidence 346778877665 356788999999998754
No 331
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=24.27 E-value=60 Score=20.19 Aligned_cols=19 Identities=32% Similarity=0.702 Sum_probs=6.9
Q ss_pred CCceecCCCCCCCCceEEEe
Q psy3498 20 LDIQFNCPFCNHEKSCEVKM 39 (81)
Q Consensus 20 l~~~F~CPfC~~~~sV~v~i 39 (81)
..+.| ||.||+....-|.+
T Consensus 22 ~~k~F-Cp~CGn~TL~rvsv 40 (73)
T PF08772_consen 22 MTKQF-CPKCGNATLKRVSV 40 (73)
T ss_dssp SS--S--SSS--S--EEEE-
T ss_pred CCcee-CcccCCCcceEEEE
Confidence 44556 99999976544433
No 332
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=24.14 E-value=1.4e+02 Score=21.20 Aligned_cols=36 Identities=25% Similarity=0.562 Sum_probs=20.3
Q ss_pred CC-CceecCCCCCCCCceEEEe--ecCCceEEEEccc-cc
Q psy3498 19 PL-DIQFNCPFCNHEKSCEVKM--DKGRNSARIACRV-CL 54 (81)
Q Consensus 19 ~l-~~~F~CPfC~~~~sV~v~i--~k~~~~g~l~C~~-C~ 54 (81)
+| ++++.|-.||..|....=+ -+.+.+-.|-|+. |-
T Consensus 55 ~lgdt~leCy~Cg~~NvF~LGFipak~d~vvvllCR~pC~ 94 (152)
T PF09416_consen 55 PLGDTVLECYNCGSRNVFLLGFIPAKSDSVVVLLCRQPCA 94 (152)
T ss_dssp TT-S-B---TTT----TTTEEEEEETTSCEEEEEETTTTT
T ss_pred CCCCcEEEEEecCCCceeeEEEEEeccCCeEEEEeCCchh
Confidence 45 6999999999988655444 3456788999998 86
No 333
>COG0819 TenA Putative transcription activator [Transcription]
Probab=24.07 E-value=32 Score=25.30 Aligned_cols=14 Identities=21% Similarity=0.648 Sum_probs=11.6
Q ss_pred chhhhhhhhhhhcC
Q psy3498 66 EAIDVYNDWVDASV 79 (81)
Q Consensus 66 epIDVYs~WiD~c~ 79 (81)
.|..+|.+|||-+-
T Consensus 153 ~~~~~Y~~Wi~~Y~ 166 (218)
T COG0819 153 SPNPPYQEWIDTYA 166 (218)
T ss_pred CCCCcHHHHHHHcC
Confidence 48899999999763
No 334
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=24.01 E-value=72 Score=24.46 Aligned_cols=30 Identities=20% Similarity=0.575 Sum_probs=23.9
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
.-+|-.|++ .+.|.-+...-.+.|.+|++.
T Consensus 65 ~v~CrVCq~----~I~i~gk~~QhVVkC~~CnEA 94 (256)
T PF09788_consen 65 VVTCRVCQS----LIDIEGKMHQHVVKCSVCNEA 94 (256)
T ss_pred eEEeecCCc----eecccCccceeeEECCCCCcc
Confidence 668999998 566666667788999999983
No 335
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=24.00 E-value=61 Score=25.78 Aligned_cols=33 Identities=30% Similarity=0.628 Sum_probs=20.2
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
.|.|+.||++..+.++ .......-.|..||...
T Consensus 320 ~~rc~~c~~~~~~~~~--~~~~~~~~~~~~~~~~~ 352 (403)
T TIGR03676 320 TFKCPNCGYEEEKTVK--PEEGDKSEACPKCGSEL 352 (403)
T ss_pred EEEcCCCCcceeeecc--cccccccccCcccCccc
Confidence 5999999996544442 22222224588888753
No 336
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=23.65 E-value=37 Score=27.35 Aligned_cols=18 Identities=28% Similarity=0.528 Sum_probs=14.8
Q ss_pred CCCCCceecCCCCCCCCc
Q psy3498 17 IEPLDIQFNCPFCNHEKS 34 (81)
Q Consensus 17 ~~~l~~~F~CPfC~~~~s 34 (81)
-..||-.|.||.|+..++
T Consensus 452 ~~~lp~~~~cp~c~~~k~ 469 (479)
T PRK05452 452 WSEVPDNFLCPECSLGKD 469 (479)
T ss_pred hhhCCCCCcCcCCCCcHH
Confidence 467888899999998765
No 337
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=23.59 E-value=31 Score=25.30 Aligned_cols=8 Identities=38% Similarity=0.654 Sum_probs=5.6
Q ss_pred EEcccccc
Q psy3498 48 IACRVCLE 55 (81)
Q Consensus 48 l~C~~C~~ 55 (81)
+.|.+||+
T Consensus 98 ~~C~~Cg~ 105 (190)
T COG5082 98 KKCYNCGE 105 (190)
T ss_pred cccccccc
Confidence 66777776
No 338
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=23.47 E-value=39 Score=20.84 Aligned_cols=10 Identities=30% Similarity=0.820 Sum_probs=7.9
Q ss_pred ecCCCCCCCC
Q psy3498 24 FNCPFCNHEK 33 (81)
Q Consensus 24 F~CPfC~~~~ 33 (81)
=.||.||.+.
T Consensus 19 e~CP~Cgs~~ 28 (64)
T COG2093 19 EICPVCGSTD 28 (64)
T ss_pred ccCCCCCCcc
Confidence 3599999864
No 339
>PTZ00293 thymidine kinase; Provisional
Probab=23.43 E-value=71 Score=23.40 Aligned_cols=30 Identities=27% Similarity=0.646 Sum_probs=23.1
Q ss_pred cCCCCCCCCceEEEeecCCc--------eEEEEccccc
Q psy3498 25 NCPFCNHEKSCEVKMDKGRN--------SARIACRVCL 54 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~--------~g~l~C~~C~ 54 (81)
-|.+||.+.+.+..+..... .....|+.|-
T Consensus 139 iC~~CG~~A~~t~R~~~~~~~v~IGg~e~Y~a~CR~c~ 176 (211)
T PTZ00293 139 VCMFCGKEASFSKRIVQSEQIELIGGEDKYIATCRKCF 176 (211)
T ss_pred EchhhCCcceeEEEEcCCCCEEEECCcccEEehhhhhh
Confidence 49999999998888865321 2488899998
No 340
>TIGR00120 ArgJ glutamate N-acetyltransferase/amino-acid acetyltransferase. This enzyme can acetylate Glu to N-acetyl-Glu by deacetylating N-2-acetyl-ornithine into ornithine; the two halves of this reaction represent the first and fifth steps in the synthesis of Arg (or citrulline) from Glu by way of ornithine (EC 2.3.1.35). In Bacillus stearothermophilus, but not in Thermus thermophilus HB27, the enzyme is bifunctional and can also use acetyl-CoA to acetylate Glu (EC 2.3.1.1).
Probab=23.26 E-value=76 Score=25.68 Aligned_cols=33 Identities=18% Similarity=0.233 Sum_probs=29.6
Q ss_pred CCCceEEEeecCCceEEEEcccccceeEe-ccCC
Q psy3498 31 HEKSCEVKMDKGRNSARIACRVCLEDFQT-TINF 63 (81)
Q Consensus 31 ~~~sV~v~i~k~~~~g~l~C~~C~~~~~~-~i~~ 63 (81)
|+..|.|.+|...+.+...--.|.++|++ +||.
T Consensus 367 ~~~ei~I~vdLg~G~~~~~~w~cDLt~eYV~INa 400 (404)
T TIGR00120 367 ESDEIEIVVDLGTGDGAGTAWGCDLSYDYVRINA 400 (404)
T ss_pred CCCEEEEEEEeCCCCceEEEEcccCCccceeECC
Confidence 57889999999999999999999999987 7886
No 341
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=23.13 E-value=70 Score=24.70 Aligned_cols=26 Identities=15% Similarity=0.363 Sum_probs=15.6
Q ss_pred CCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 26 CPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
|+.||++ +.-..+--...|..||..+
T Consensus 114 Cg~CG~~------~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 114 CGRCGTK------TYPREGGWARVCPKCGHEH 139 (279)
T ss_pred CCCCCCc------CccccCceeeeCCCCCCcc
Confidence 6777763 2333444566788888654
No 342
>TIGR00558 pdxH pyridoxamine-phosphate oxidase. This model is similar to Pyridox_oxidase from PFAM but is designed to find only true pyridoxamine-phosphate oxidase and to ignore the related protein PhzG involved in phenazine biosynthesis. This protein from E. coli was characterized as a homodimer with two FMN per dimer.
Probab=23.11 E-value=33 Score=24.88 Aligned_cols=15 Identities=20% Similarity=0.820 Sum_probs=13.1
Q ss_pred CchhhhhhhhhhhcC
Q psy3498 65 SEAIDVYNDWVDASV 79 (81)
Q Consensus 65 ~epIDVYs~WiD~c~ 79 (81)
.+|+|++..|+++..
T Consensus 28 ~~P~~~f~~W~~~a~ 42 (217)
T TIGR00558 28 DDPIDLFEIWFNEAI 42 (217)
T ss_pred CCHHHHHHHHHHHHH
Confidence 599999999998764
No 343
>KOG3352|consensus
Probab=23.06 E-value=40 Score=24.03 Aligned_cols=11 Identities=36% Similarity=0.854 Sum_probs=9.0
Q ss_pred CceecCCCCCC
Q psy3498 21 DIQFNCPFCNH 31 (81)
Q Consensus 21 ~~~F~CPfC~~ 31 (81)
...|.||.|||
T Consensus 131 ge~~rc~eCG~ 141 (153)
T KOG3352|consen 131 GETQRCPECGH 141 (153)
T ss_pred CCcccCCcccc
Confidence 35788999998
No 344
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=22.97 E-value=53 Score=19.13 Aligned_cols=30 Identities=23% Similarity=0.728 Sum_probs=18.3
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
..+.|-.||.+ +++ ......+.|.-||-.-
T Consensus 5 ~~Y~C~~Cg~~----~~~--~~~~~~irCp~Cg~rI 34 (49)
T COG1996 5 MEYKCARCGRE----VEL--DQETRGIRCPYCGSRI 34 (49)
T ss_pred EEEEhhhcCCe----eeh--hhccCceeCCCCCcEE
Confidence 46777888873 222 3344567788887654
No 345
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=22.96 E-value=37 Score=19.43 Aligned_cols=14 Identities=21% Similarity=0.617 Sum_probs=10.3
Q ss_pred ceecCCCCCCCCce
Q psy3498 22 IQFNCPFCNHEKSC 35 (81)
Q Consensus 22 ~~F~CPfC~~~~sV 35 (81)
|=+.||-||-..++
T Consensus 8 tG~~CPgCG~tRa~ 21 (52)
T PF10825_consen 8 TGIPCPGCGMTRAF 21 (52)
T ss_pred hCCCCCCCcHHHHH
Confidence 55789999976554
No 346
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=22.93 E-value=70 Score=24.78 Aligned_cols=42 Identities=33% Similarity=0.665 Sum_probs=26.1
Q ss_pred CCCCCceecCCCCCCC--------Cce----EEEe-------ecCCceEEEEcccccceeE
Q psy3498 17 IEPLDIQFNCPFCNHE--------KSC----EVKM-------DKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 17 ~~~l~~~F~CPfC~~~--------~sV----~v~i-------~k~~~~g~l~C~~C~~~~~ 58 (81)
.+..+..|-|.-|.+- +-| .|+. |+--|+|+-+|..|+-.|.
T Consensus 106 ip~~drqFaC~~Cd~~WwRrvp~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~ 166 (278)
T PF15135_consen 106 IPSVDRQFACSSCDHMWWRRVPQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFR 166 (278)
T ss_pred ccccceeeeccccchHHHhccCcccccccccccccccCCCccccccceeeeecccccccch
Confidence 4556778888888773 000 1111 2234788888888888774
No 347
>PF07491 PPI_Ypi1: Protein phosphatase inhibitor ; InterPro: IPR011107 These proteins include Ypi1, a novel Saccharomyces cerevisiae type 1 protein phosphatase inhibitor [] and ppp1r11/hcgv (O60927 from SWISSPROT), annotated as having protein phosphatase inhibitor activity [].
Probab=22.69 E-value=38 Score=20.58 Aligned_cols=7 Identities=71% Similarity=1.184 Sum_probs=5.2
Q ss_pred CCCCCcC
Q psy3498 1 MGRRKSK 7 (81)
Q Consensus 1 MGkRK~~ 7 (81)
|||+|++
T Consensus 31 mgkkkSK 37 (60)
T PF07491_consen 31 MGKKKSK 37 (60)
T ss_pred cccccCc
Confidence 7877766
No 348
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=22.66 E-value=42 Score=20.00 Aligned_cols=9 Identities=44% Similarity=1.110 Sum_probs=7.6
Q ss_pred eecCCCCCC
Q psy3498 23 QFNCPFCNH 31 (81)
Q Consensus 23 ~F~CPfC~~ 31 (81)
...|||||.
T Consensus 35 ~~pC~fCg~ 43 (57)
T PF06221_consen 35 LGPCPFCGT 43 (57)
T ss_pred cCcCCCCCC
Confidence 678999996
No 349
>PLN00162 transport protein sec23; Provisional
Probab=22.52 E-value=45 Score=28.61 Aligned_cols=15 Identities=27% Similarity=0.715 Sum_probs=12.8
Q ss_pred ceecCCCCCCCCceE
Q psy3498 22 IQFNCPFCNHEKSCE 36 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~ 36 (81)
+.|.||||+..|.+-
T Consensus 74 ~~W~C~~C~~~N~~P 88 (761)
T PLN00162 74 KIWICPFCFQRNHFP 88 (761)
T ss_pred CEEEccCCCCCCCCc
Confidence 689999999988764
No 350
>PRK10954 periplasmic protein disulfide isomerase I; Provisional
Probab=22.45 E-value=26 Score=24.58 Aligned_cols=13 Identities=31% Similarity=0.886 Sum_probs=9.6
Q ss_pred ceecCCCCCCCCc
Q psy3498 22 IQFNCPFCNHEKS 34 (81)
Q Consensus 22 ~~F~CPfC~~~~s 34 (81)
--|.||+|.+-..
T Consensus 45 fdy~CphC~~~~~ 57 (207)
T PRK10954 45 FSFYCPHCYQFEE 57 (207)
T ss_pred eCCCCccHHHhcc
Confidence 4578999998444
No 351
>PHA02768 hypothetical protein; Provisional
Probab=22.42 E-value=33 Score=20.38 Aligned_cols=37 Identities=14% Similarity=0.227 Sum_probs=21.3
Q ss_pred eecCCCCCCCCceEEEeecCCce--EEEEcccccceeEe
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNS--ARIACRVCLEDFQT 59 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~--g~l~C~~C~~~~~~ 59 (81)
-|.||.||..=+..-.+..-..+ -...|.+|+..|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~~ 43 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISLR 43 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcCCcccCCcccceecc
Confidence 48999999743332222111111 13489999998864
No 352
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=22.30 E-value=47 Score=17.98 Aligned_cols=9 Identities=33% Similarity=1.124 Sum_probs=8.0
Q ss_pred eecCCCCCC
Q psy3498 23 QFNCPFCNH 31 (81)
Q Consensus 23 ~F~CPfC~~ 31 (81)
.|.|.+|+.
T Consensus 12 ~f~C~~C~~ 20 (39)
T smart00154 12 GFKCRHCGN 20 (39)
T ss_pred CeECCccCC
Confidence 799999986
No 353
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=22.19 E-value=62 Score=30.09 Aligned_cols=10 Identities=40% Similarity=1.002 Sum_probs=7.7
Q ss_pred eecCCCCCCC
Q psy3498 23 QFNCPFCNHE 32 (81)
Q Consensus 23 ~F~CPfC~~~ 32 (81)
.|.||.||++
T Consensus 667 ~rkCPkCG~~ 676 (1337)
T PRK14714 667 RRRCPSCGTE 676 (1337)
T ss_pred EEECCCCCCc
Confidence 4888888874
No 354
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=21.86 E-value=48 Score=27.33 Aligned_cols=11 Identities=45% Similarity=1.162 Sum_probs=8.1
Q ss_pred eecCCCCCCCC
Q psy3498 23 QFNCPFCNHEK 33 (81)
Q Consensus 23 ~F~CPfC~~~~ 33 (81)
.+.||.||+++
T Consensus 532 ~~~CP~CGs~~ 542 (555)
T cd01675 532 GFKCPKCGSED 542 (555)
T ss_pred CCCCcCCCCcC
Confidence 57888888754
No 355
>PRK11823 DNA repair protein RadA; Provisional
Probab=21.81 E-value=78 Score=25.23 Aligned_cols=24 Identities=21% Similarity=0.396 Sum_probs=16.7
Q ss_pred ceecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
+.|.|..||++. ..=.-.|..|++
T Consensus 6 ~~y~C~~Cg~~~----------~~~~g~Cp~C~~ 29 (446)
T PRK11823 6 TAYVCQECGAES----------PKWLGRCPECGA 29 (446)
T ss_pred CeEECCcCCCCC----------cccCeeCcCCCC
Confidence 679999999832 223446888886
No 356
>PRK15084 formate hydrogenlyase maturation protein HycH; Provisional
Probab=21.78 E-value=45 Score=23.23 Aligned_cols=29 Identities=21% Similarity=0.399 Sum_probs=21.8
Q ss_pred CceEEEEcccccceeEeccCCCCchhhhhhhhhhhcCC
Q psy3498 43 RNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVP 80 (81)
Q Consensus 43 ~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~WiD~c~~ 80 (81)
..+|.+-|-.+ .|.=|.+.|.+||+...+
T Consensus 37 HhvGvIDcle~---------~L~~~~e~y~~wi~~l~~ 65 (133)
T PRK15084 37 HHVGVIDCLEA---------ALTCPLDEYLAWIATLEE 65 (133)
T ss_pred cccceEecchh---------hhcCCHHHHHHHHHhCCh
Confidence 45677777654 466789999999998744
No 357
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=21.78 E-value=48 Score=17.77 Aligned_cols=10 Identities=30% Similarity=1.032 Sum_probs=7.7
Q ss_pred CceecCCCCC
Q psy3498 21 DIQFNCPFCN 30 (81)
Q Consensus 21 ~~~F~CPfC~ 30 (81)
.....||+|+
T Consensus 34 ~~~~~CP~C~ 43 (44)
T PF14634_consen 34 GKSVKCPICR 43 (44)
T ss_pred CCCCCCcCCC
Confidence 3567899997
No 358
>PF14913 DPCD: DPCD protein family
Probab=21.66 E-value=30 Score=25.50 Aligned_cols=24 Identities=38% Similarity=0.333 Sum_probs=20.4
Q ss_pred cceeEeccCCCCchhhhhhhhhhh
Q psy3498 54 LEDFQTTINFLSEAIDVYNDWVDA 77 (81)
Q Consensus 54 ~~~~~~~i~~L~epIDVYs~WiD~ 77 (81)
..+|+.+|..|.=|.|||+-=+|.
T Consensus 95 k~~fqWRIRNLPYP~dvYsVtvd~ 118 (194)
T PF14913_consen 95 KTSFQWRIRNLPYPKDVYSVTVDE 118 (194)
T ss_pred ccceEEEEccCCCCccceEEEEcC
Confidence 357999999999999999976664
No 359
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=21.65 E-value=72 Score=24.46 Aligned_cols=26 Identities=27% Similarity=0.484 Sum_probs=18.8
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEccccc
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCL 54 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~ 54 (81)
.|+.||. +..++ +-.+.++--|..|+
T Consensus 247 pC~~CGt---~I~k~-~~~gR~t~~CP~CQ 272 (273)
T COG0266 247 PCRRCGT---PIEKI-KLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCccCC---EeEEE-EEcCCcCEeCCCCC
Confidence 5999997 34444 33677888999996
No 360
>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=21.60 E-value=56 Score=20.37 Aligned_cols=17 Identities=12% Similarity=0.214 Sum_probs=13.7
Q ss_pred EEEEcccccceeEeccC
Q psy3498 46 ARIACRVCLEDFQTTIN 62 (81)
Q Consensus 46 g~l~C~~C~~~~~~~i~ 62 (81)
.++.|..||.-++....
T Consensus 72 ~H~~C~~Cg~i~~~~~~ 88 (116)
T cd07153 72 HHLICTKCGKVIDFEDC 88 (116)
T ss_pred CceEeCCCCCEEEecCc
Confidence 58999999998886543
No 361
>PF14369 zf-RING_3: zinc-finger
Probab=21.39 E-value=1.4e+02 Score=15.79 Aligned_cols=31 Identities=23% Similarity=0.563 Sum_probs=15.4
Q ss_pred ecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
|=|-.|+. .|.+..... ..+.|..|+-.|-.
T Consensus 3 ywCh~C~~--~V~~~~~~~---~~~~CP~C~~gFvE 33 (35)
T PF14369_consen 3 YWCHQCNR--FVRIAPSPD---SDVACPRCHGGFVE 33 (35)
T ss_pred EeCccCCC--EeEeCcCCC---CCcCCcCCCCcEeE
Confidence 44666664 333332221 12367777776643
No 362
>KOG3456|consensus
Probab=21.34 E-value=61 Score=22.16 Aligned_cols=25 Identities=24% Similarity=0.405 Sum_probs=17.7
Q ss_pred CCCCceEEEeecCCceEEEEcccccceeE
Q psy3498 30 NHEKSCEVKMDKGRNSARIACRVCLEDFQ 58 (81)
Q Consensus 30 ~~~~sV~v~i~k~~~~g~l~C~~C~~~~~ 58 (81)
||. -|-+.+|+... ..|+-||++|-
T Consensus 91 GHP-kvyInLDk~~~---~~CgYCGlrf~ 115 (120)
T KOG3456|consen 91 GHP-KVYINLDKPGP---HICGYCGLRFV 115 (120)
T ss_pred CCC-eEEEEcCCCCC---cccccchhhhh
Confidence 553 35677776543 68999999884
No 363
>PRK09504 sufA iron-sulfur cluster assembly scaffold protein; Provisional
Probab=21.34 E-value=31 Score=22.79 Aligned_cols=12 Identities=42% Similarity=0.800 Sum_probs=9.6
Q ss_pred EEEEcccccceeE
Q psy3498 46 ARIACRVCLEDFQ 58 (81)
Q Consensus 46 g~l~C~~C~~~~~ 58 (81)
+..+|+ ||.+|.
T Consensus 110 a~~~Cg-CG~SF~ 121 (122)
T PRK09504 110 AQNECG-CGESFG 121 (122)
T ss_pred CCCCcC-CCCCee
Confidence 466899 999885
No 364
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=21.34 E-value=44 Score=28.40 Aligned_cols=25 Identities=28% Similarity=0.573 Sum_probs=15.5
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT 59 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~ 59 (81)
.||.||++ ...+.-.|..||..-.+
T Consensus 29 ~Cp~CG~~----------~~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 29 PCPQCGTE----------VPVDEAHCPNCGAETGT 53 (645)
T ss_pred cCCCCCCC----------CCcccccccccCCcccc
Confidence 36666664 23455578888876544
No 365
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.93 E-value=64 Score=27.36 Aligned_cols=10 Identities=40% Similarity=0.863 Sum_probs=7.4
Q ss_pred eecCCCCCCC
Q psy3498 23 QFNCPFCNHE 32 (81)
Q Consensus 23 ~F~CPfC~~~ 32 (81)
.|.||.||++
T Consensus 639 ~~~CP~CG~~ 648 (656)
T PRK08270 639 HEFCPKCGEE 648 (656)
T ss_pred CCCCcCCcCc
Confidence 4778888865
No 366
>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=20.88 E-value=31 Score=19.93 Aligned_cols=27 Identities=26% Similarity=0.493 Sum_probs=15.3
Q ss_pred eecCC--CCCCCCceEEEeecCCceEEEEcccccc
Q psy3498 23 QFNCP--FCNHEKSCEVKMDKGRNSARIACRVCLE 55 (81)
Q Consensus 23 ~F~CP--fC~~~~sV~v~i~k~~~~g~l~C~~C~~ 55 (81)
.=.|| .||.. . =|- +-.....|+.||.
T Consensus 18 rk~CP~~~CG~G-v---FMA--~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAG-V---FMA--EHKDRHYCGKCGY 46 (47)
T ss_dssp SEE-TSTTTTSS-S---EEE--E-SSEEEETTTSS
T ss_pred hhcCCCcccCCc-e---Eee--ecCCCccCCCccc
Confidence 34689 89972 2 121 1123778999986
No 367
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=20.85 E-value=53 Score=18.47 Aligned_cols=10 Identities=40% Similarity=1.162 Sum_probs=6.0
Q ss_pred CCCCCCCCce
Q psy3498 26 CPFCNHEKSC 35 (81)
Q Consensus 26 CPfC~~~~sV 35 (81)
||.||.++..
T Consensus 1 CP~Cg~~f~C 10 (50)
T PF14375_consen 1 CPRCGAPFEC 10 (50)
T ss_pred CCCCCCcCCC
Confidence 6777765443
No 368
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=20.63 E-value=86 Score=24.64 Aligned_cols=44 Identities=18% Similarity=0.411 Sum_probs=27.4
Q ss_pred CCCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeE----eccCCCCc
Q psy3498 18 EPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ----TTINFLSE 66 (81)
Q Consensus 18 ~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~----~~i~~L~e 66 (81)
.++--++.|+.|++.+.+.-.- .....|..||..+. +++.+|.+
T Consensus 228 ~~~g~v~~C~~c~~~~~~~~~~-----~~~~~C~~c~~~~~~~GPlW~G~l~d 275 (374)
T TIGR00308 228 ESTGYTYHCSRCLHNKPVNGIS-----QRKGRCKECGGEYHLAGPLYAGPLHD 275 (374)
T ss_pred HhceeEEECCCccccccccccc-----CCCCCCCCCCCcceeecCcccCccCC
Confidence 4567799999999865443110 11235999998764 35555554
No 369
>PRK04860 hypothetical protein; Provisional
Probab=20.58 E-value=59 Score=22.80 Aligned_cols=33 Identities=24% Similarity=0.599 Sum_probs=22.3
Q ss_pred eecCCCCCCCCceEEEeec----CCceEEEEcccccceeEe
Q psy3498 23 QFNCPFCNHEKSCEVKMDK----GRNSARIACRVCLEDFQT 59 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k----~~~~g~l~C~~C~~~~~~ 59 (81)
.|.|+ |+. ....+.+ ..+.....|+.|+..+..
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 69999 986 2332222 134567899999998865
No 370
>KOG1598|consensus
Probab=20.42 E-value=59 Score=27.29 Aligned_cols=27 Identities=15% Similarity=0.528 Sum_probs=20.9
Q ss_pred cCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498 25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLED 56 (81)
Q Consensus 25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~ 56 (81)
.|++||.. .++++...|-+.|.-||.-
T Consensus 2 ~C~~C~~s-----~fe~d~a~g~~~C~~CG~v 28 (521)
T KOG1598|consen 2 VCKNCGGS-----NFERDEATGNLYCTACGTV 28 (521)
T ss_pred cCCCCCCC-----CcccccccCCceeccccce
Confidence 48999973 3555667899999999963
No 371
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=20.42 E-value=46 Score=24.12 Aligned_cols=26 Identities=19% Similarity=0.653 Sum_probs=16.9
Q ss_pred eecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498 23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF 57 (81)
Q Consensus 23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~ 57 (81)
.|.||.|+..= .. . -..+.|.+.+ +|
T Consensus 2 ~~~CP~C~~~l----~~--~--~~~~~C~~~h-~f 27 (272)
T PRK11088 2 SYQCPLCHQPL----TL--E--ENSWICPQNH-QF 27 (272)
T ss_pred cccCCCCCcch----hc--C--CCEEEcCCCC-CC
Confidence 48999999742 11 1 2468998844 35
No 372
>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=20.13 E-value=35 Score=19.79 Aligned_cols=24 Identities=21% Similarity=0.488 Sum_probs=16.7
Q ss_pred CCceecCCCCCCCCceEEEeecCCceEEEEccccc
Q psy3498 20 LDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCL 54 (81)
Q Consensus 20 l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~ 54 (81)
.+..-.||.||+ . ...+-.|..||
T Consensus 23 ~~~l~~c~~cg~-----~------~~~H~vc~~cG 46 (56)
T PF01783_consen 23 APNLVKCPNCGE-----P------KLPHRVCPSCG 46 (56)
T ss_dssp TTSEEESSSSSS-----E------ESTTSBCTTTB
T ss_pred ccceeeeccCCC-----E------ecccEeeCCCC
Confidence 348899999996 1 22445688887
Done!