Query 035653
Match_columns 87
No_of_seqs 103 out of 190
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 05:01:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035653.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035653hhsearch_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 4.5E-44 9.8E-49 231.3 6.6 80 2-85 1-81 (81)
2 KOG3214 Uncharacterized Zn rib 100.0 4E-43 8.7E-48 236.3 3.6 84 1-87 1-84 (109)
3 COG4888 Uncharacterized Zn rib 100.0 1.1E-37 2.4E-42 209.4 7.7 82 1-86 1-82 (104)
4 PRK14892 putative transcriptio 100.0 2.6E-34 5.5E-39 192.2 6.0 76 1-84 1-76 (99)
5 TIGR03655 anti_R_Lar restricti 97.3 0.00023 5E-09 42.1 2.7 34 28-62 3-38 (53)
6 PF14354 Lar_restr_allev: Rest 97.0 0.00097 2.1E-08 39.6 3.6 33 25-58 2-37 (61)
7 TIGR01206 lysW lysine biosynth 96.8 0.0017 3.6E-08 39.3 3.0 34 26-63 2-35 (54)
8 PRK09710 lar restriction allev 96.4 0.0047 1E-07 38.8 3.6 50 23-76 3-52 (64)
9 PTZ00255 60S ribosomal protein 96.4 0.0076 1.7E-07 40.0 4.8 53 24-82 34-87 (90)
10 TIGR00280 L37a ribosomal prote 96.4 0.009 2E-07 39.7 5.1 55 25-85 34-89 (91)
11 PF08271 TF_Zn_Ribbon: TFIIB z 96.3 0.004 8.6E-08 35.2 2.6 32 27-63 1-32 (43)
12 PF01096 TFIIS_C: Transcriptio 96.3 0.0084 1.8E-07 33.6 3.9 34 27-60 1-38 (39)
13 COG1327 Predicted transcriptio 96.2 0.0023 5.1E-08 46.2 1.5 36 28-63 2-41 (156)
14 TIGR00244 transcriptional regu 96.2 0.0044 9.5E-08 44.3 2.8 36 28-63 2-41 (147)
15 TIGR02098 MJ0042_CXXC MJ0042 f 96.1 0.0022 4.8E-08 35.0 0.5 34 26-61 2-36 (38)
16 PRK03976 rpl37ae 50S ribosomal 95.8 0.022 4.9E-07 37.8 4.6 44 25-74 35-78 (90)
17 PRK00398 rpoP DNA-directed RNA 95.6 0.024 5.2E-07 32.3 3.8 34 25-64 2-35 (46)
18 smart00440 ZnF_C2C2 C2C2 Zinc 95.6 0.035 7.5E-07 31.3 4.2 34 27-60 1-38 (40)
19 PF14255 Cys_rich_CPXG: Cystei 95.4 0.025 5.4E-07 34.0 3.4 47 27-73 1-49 (52)
20 PRK00464 nrdR transcriptional 95.3 0.017 3.8E-07 41.2 2.9 36 28-63 2-41 (154)
21 PF01780 Ribosomal_L37ae: Ribo 95.1 0.014 3.1E-07 38.7 1.7 45 24-74 33-77 (90)
22 PF13719 zinc_ribbon_5: zinc-r 94.9 0.029 6.2E-07 31.0 2.5 33 27-61 3-36 (37)
23 PF14353 CpXC: CpXC protein 94.8 0.036 7.8E-07 37.2 3.1 40 27-66 2-54 (128)
24 PF09855 DUF2082: Nucleic-acid 94.7 0.095 2.1E-06 32.6 4.6 47 27-74 1-62 (64)
25 smart00778 Prim_Zn_Ribbon Zinc 94.3 0.028 6.1E-07 31.6 1.5 29 28-58 5-33 (37)
26 PF13717 zinc_ribbon_4: zinc-r 94.2 0.016 3.4E-07 32.0 0.4 34 26-60 2-35 (36)
27 PRK09678 DNA-binding transcrip 94.1 0.065 1.4E-06 34.1 3.1 44 27-71 2-53 (72)
28 PF08792 A2L_zn_ribbon: A2L zi 93.0 0.12 2.5E-06 28.3 2.4 31 26-62 3-33 (33)
29 PF12760 Zn_Tnp_IS1595: Transp 92.9 0.086 1.9E-06 30.1 2.0 32 22-58 14-45 (46)
30 TIGR03829 YokU_near_AblA uncha 92.7 0.2 4.3E-06 33.2 3.8 36 28-63 1-48 (89)
31 COG1997 RPL43A Ribosomal prote 92.7 0.11 2.4E-06 34.5 2.5 32 25-62 34-65 (89)
32 PHA00626 hypothetical protein 92.5 0.16 3.5E-06 31.4 2.9 34 28-62 2-35 (59)
33 smart00834 CxxC_CXXC_SSSS Puta 92.3 0.076 1.6E-06 28.8 1.2 31 26-59 5-35 (41)
34 PF02150 RNA_POL_M_15KD: RNA p 92.1 0.31 6.8E-06 26.7 3.5 28 29-61 4-31 (35)
35 PF04216 FdhE: Protein involve 91.8 0.32 6.9E-06 36.9 4.4 49 26-74 211-262 (290)
36 PRK14890 putative Zn-ribbon RN 91.7 0.087 1.9E-06 32.6 1.0 34 24-58 23-56 (59)
37 PF04606 Ogr_Delta: Ogr/Delta- 91.1 0.4 8.6E-06 27.5 3.4 36 28-63 1-40 (47)
38 PF09723 Zn-ribbon_8: Zinc rib 91.1 0.1 2.2E-06 29.4 0.9 30 26-58 5-34 (42)
39 PF06044 DRP: Dam-replacing fa 91.0 0.2 4.3E-06 38.7 2.6 57 26-84 31-91 (254)
40 PF13240 zinc_ribbon_2: zinc-r 90.8 0.08 1.7E-06 26.7 0.2 21 29-59 2-22 (23)
41 PRK13130 H/ACA RNA-protein com 90.8 0.19 4.2E-06 30.6 1.9 44 26-81 5-48 (56)
42 PRK00432 30S ribosomal protein 90.8 0.14 3.1E-06 30.2 1.3 26 28-60 22-47 (50)
43 PF13453 zf-TFIIB: Transcripti 90.6 0.48 1E-05 26.3 3.3 27 28-58 1-27 (41)
44 PF09986 DUF2225: Uncharacteri 90.6 0.46 1E-05 35.0 4.1 44 24-69 3-68 (214)
45 PF04216 FdhE: Protein involve 90.1 0.39 8.4E-06 36.4 3.5 36 27-62 173-209 (290)
46 COG2888 Predicted Zn-ribbon RN 90.1 0.11 2.4E-06 32.3 0.4 34 24-58 25-58 (61)
47 PF01807 zf-CHC2: CHC2 zinc fi 90.0 0.78 1.7E-05 29.8 4.4 48 26-84 33-85 (97)
48 PF14803 Nudix_N_2: Nudix N-te 89.8 0.31 6.8E-06 26.8 2.1 29 29-59 3-31 (34)
49 TIGR01384 TFS_arch transcripti 89.4 1 2.2E-05 29.1 4.6 40 22-61 57-101 (104)
50 COG3478 Predicted nucleic-acid 89.4 0.6 1.3E-05 29.6 3.3 45 24-68 2-60 (68)
51 TIGR00311 aIF-2beta translatio 88.6 0.69 1.5E-05 32.3 3.6 35 24-61 95-129 (133)
52 PRK03988 translation initiatio 88.6 0.7 1.5E-05 32.4 3.6 34 24-60 100-133 (138)
53 TIGR03831 YgiT_finger YgiT-typ 88.3 1.2 2.6E-05 24.2 3.9 11 51-61 33-43 (46)
54 PF14205 Cys_rich_KTR: Cystein 88.2 0.57 1.2E-05 28.6 2.6 36 27-62 5-40 (55)
55 TIGR02605 CxxC_CxxC_SSSS putat 88.1 0.24 5.2E-06 28.4 0.9 30 26-58 5-34 (52)
56 PF05605 zf-Di19: Drought indu 87.8 0.23 4.9E-06 29.0 0.6 32 26-59 2-40 (54)
57 smart00531 TFIIE Transcription 87.6 0.14 3E-06 35.5 -0.4 40 24-63 97-136 (147)
58 COG1405 SUA7 Transcription ini 87.6 0.32 7E-06 37.7 1.6 40 28-78 3-42 (285)
59 KOG0402 60S ribosomal protein 87.6 0.3 6.6E-06 32.5 1.2 32 25-62 35-66 (92)
60 smart00659 RPOLCX RNA polymera 87.5 0.3 6.6E-06 28.1 1.1 31 26-63 2-32 (44)
61 PF09526 DUF2387: Probable met 87.4 1.6 3.4E-05 27.6 4.3 36 28-65 10-45 (71)
62 TIGR02443 conserved hypothetic 87.3 1.3 2.8E-05 27.4 3.8 33 28-62 11-43 (59)
63 KOG0478 DNA replication licens 87.1 0.25 5.5E-06 43.2 0.8 41 24-66 262-303 (804)
64 PF10571 UPF0547: Uncharacteri 87.0 0.27 5.8E-06 25.5 0.6 24 28-61 2-25 (26)
65 TIGR01385 TFSII transcription 86.9 1.1 2.5E-05 34.9 4.3 41 22-62 254-298 (299)
66 PF08273 Prim_Zn_Ribbon: Zinc- 86.9 0.28 6.1E-06 27.9 0.7 29 28-57 5-33 (40)
67 PF01873 eIF-5_eIF-2B: Domain 86.6 0.93 2E-05 31.2 3.3 33 24-59 91-123 (125)
68 COG3677 Transposase and inacti 86.4 0.62 1.3E-05 32.1 2.3 41 27-69 31-73 (129)
69 PRK00420 hypothetical protein; 86.0 0.58 1.2E-05 32.0 2.0 30 26-62 23-52 (112)
70 COG2051 RPS27A Ribosomal prote 85.6 1.7 3.8E-05 27.5 3.8 30 28-62 21-50 (67)
71 PF07282 OrfB_Zn_ribbon: Putat 85.5 0.42 9E-06 28.7 1.0 36 24-65 26-61 (69)
72 PF13248 zf-ribbon_3: zinc-rib 85.2 0.38 8.3E-06 24.5 0.6 22 28-59 4-25 (26)
73 PF07754 DUF1610: Domain of un 85.1 0.49 1.1E-05 24.4 1.0 12 22-33 12-23 (24)
74 PF13465 zf-H2C2_2: Zinc-finge 85.0 0.36 7.8E-06 24.4 0.4 11 24-34 12-22 (26)
75 PRK00423 tfb transcription ini 84.9 0.81 1.7E-05 35.3 2.6 32 26-62 11-42 (310)
76 PRK05978 hypothetical protein; 84.8 0.38 8.3E-06 34.3 0.6 32 27-63 34-65 (148)
77 smart00653 eIF2B_5 domain pres 84.2 1.1 2.4E-05 30.3 2.7 33 24-59 78-110 (110)
78 smart00661 RPOL9 RNA polymeras 84.0 0.96 2.1E-05 25.5 2.0 28 29-60 3-30 (52)
79 COG1645 Uncharacterized Zn-fin 83.7 1 2.2E-05 31.7 2.4 27 26-60 28-54 (131)
80 TIGR02159 PA_CoA_Oxy4 phenylac 83.7 0.22 4.9E-06 35.1 -0.9 36 26-61 105-141 (146)
81 PF09862 DUF2089: Protein of u 83.7 1.3 2.9E-05 30.3 3.0 24 29-62 1-24 (113)
82 PF05876 Terminase_GpA: Phage 83.6 1 2.2E-05 37.6 2.7 36 26-61 200-240 (557)
83 PRK12286 rpmF 50S ribosomal pr 83.4 1.3 2.8E-05 26.8 2.5 27 22-59 23-49 (57)
84 PRK03564 formate dehydrogenase 83.0 1 2.2E-05 35.5 2.4 38 24-61 185-223 (309)
85 PRK03564 formate dehydrogenase 82.8 2.2 4.8E-05 33.6 4.2 56 26-81 226-288 (309)
86 PHA02998 RNA polymerase subuni 82.7 2.5 5.4E-05 31.6 4.2 38 25-62 142-183 (195)
87 TIGR01562 FdhE formate dehydro 82.7 1.9 4E-05 33.9 3.7 37 26-62 224-264 (305)
88 PF05180 zf-DNL: DNL zinc fing 82.6 2 4.3E-05 27.0 3.2 35 26-62 4-41 (66)
89 COG1779 C4-type Zn-finger prot 82.6 1.7 3.8E-05 32.6 3.4 38 22-61 10-54 (201)
90 COG0675 Transposase and inacti 82.1 0.83 1.8E-05 33.2 1.5 34 22-66 305-338 (364)
91 PF03811 Zn_Tnp_IS1: InsA N-te 82.1 1.5 3.2E-05 24.3 2.2 30 27-57 6-36 (36)
92 PHA02540 61 DNA primase; Provi 81.8 1.6 3.5E-05 34.7 3.1 42 25-68 26-78 (337)
93 PF03367 zf-ZPR1: ZPR1 zinc-fi 81.7 2.8 6.1E-05 29.8 4.1 34 28-61 3-41 (161)
94 COG1326 Uncharacterized archae 81.6 0.52 1.1E-05 35.4 0.3 34 26-60 6-40 (201)
95 PF03966 Trm112p: Trm112p-like 81.0 0.35 7.6E-06 29.5 -0.7 18 45-62 48-65 (68)
96 PF05502 Dynactin_p62: Dynacti 80.9 1.6 3.6E-05 35.9 3.0 48 25-75 51-111 (483)
97 PRK12336 translation initiatio 80.3 1.8 3.9E-05 31.8 2.7 36 24-62 96-131 (201)
98 PF00301 Rubredoxin: Rubredoxi 79.6 0.93 2E-05 26.5 0.9 18 20-37 28-45 (47)
99 COG2835 Uncharacterized conser 79.4 3.4 7.3E-05 25.6 3.4 41 22-68 4-46 (60)
100 TIGR01562 FdhE formate dehydro 79.1 1.1 2.4E-05 35.2 1.4 36 26-61 184-221 (305)
101 TIGR00340 zpr1_rel ZPR1-relate 79.1 2.5 5.4E-05 30.4 3.1 31 29-60 1-38 (163)
102 cd00730 rubredoxin Rubredoxin; 79.1 0.96 2.1E-05 26.7 0.8 18 20-37 28-45 (50)
103 PF13894 zf-C2H2_4: C2H2-type 78.1 0.9 1.9E-05 21.0 0.4 8 27-34 1-8 (24)
104 COG1594 RPB9 DNA-directed RNA 77.3 5.6 0.00012 26.9 4.3 41 21-61 66-111 (113)
105 PF04810 zf-Sec23_Sec24: Sec23 76.8 0.76 1.7E-05 25.6 -0.1 14 25-38 23-36 (40)
106 TIGR00310 ZPR1_znf ZPR1 zinc f 76.8 4.5 9.9E-05 29.7 4.0 33 28-60 2-40 (192)
107 PRK00415 rps27e 30S ribosomal 76.2 4.1 9E-05 25.1 3.1 28 28-60 13-40 (59)
108 TIGR03830 CxxCG_CxxCG_HTH puta 76.1 3.5 7.6E-05 26.8 3.0 34 29-62 1-43 (127)
109 PRK11827 hypothetical protein; 74.7 2.3 4.9E-05 26.2 1.6 39 23-67 5-45 (60)
110 PF09538 FYDLN_acid: Protein o 74.5 1.7 3.6E-05 29.4 1.1 36 21-63 4-39 (108)
111 smart00709 Zpr1 Duplicated dom 73.8 6 0.00013 28.2 3.9 13 48-60 27-39 (160)
112 COG1241 MCM2 Predicted ATPase 73.7 3.1 6.7E-05 36.1 2.8 47 25-73 128-177 (682)
113 PF08274 PhnA_Zn_Ribbon: PhnA 73.4 1.1 2.3E-05 24.1 -0.0 25 28-59 4-28 (30)
114 KOG1812 Predicted E3 ubiquitin 72.5 2.4 5.3E-05 33.9 1.8 30 26-62 306-335 (384)
115 cd00350 rubredoxin_like Rubred 72.4 1.6 3.4E-05 23.3 0.5 13 25-37 16-28 (33)
116 COG1594 RPB9 DNA-directed RNA 72.4 4.1 9E-05 27.5 2.6 29 29-61 5-33 (113)
117 KOG1814 Predicted E3 ubiquitin 72.3 2.3 5.1E-05 35.2 1.7 50 25-80 367-416 (445)
118 cd00729 rubredoxin_SM Rubredox 72.1 2.2 4.7E-05 23.1 1.0 26 26-59 2-27 (34)
119 PF14206 Cys_rich_CPCC: Cystei 71.4 3.7 8E-05 26.4 2.1 28 27-59 2-29 (78)
120 smart00400 ZnF_CHCC zinc finge 71.3 4.9 0.00011 23.2 2.5 38 28-76 4-41 (55)
121 PLN00209 ribosomal protein S27 71.1 10 0.00022 25.0 4.2 41 17-62 24-67 (86)
122 PF15616 TerY-C: TerY-C metal 71.0 4.9 0.00011 28.2 2.8 36 28-63 79-118 (131)
123 PF14122 YokU: YokU-like prote 70.7 4 8.7E-05 27.0 2.2 36 28-63 1-48 (87)
124 PRK00750 lysK lysyl-tRNA synth 70.3 10 0.00022 31.3 5.0 38 28-66 177-215 (510)
125 PF10122 Mu-like_Com: Mu-like 70.1 3 6.4E-05 25.1 1.4 43 25-71 3-46 (51)
126 KOG2593 Transcription initiati 69.9 1.2 2.5E-05 36.9 -0.6 56 24-79 126-184 (436)
127 PF07191 zinc-ribbons_6: zinc- 69.6 4 8.7E-05 25.9 2.0 29 27-63 2-30 (70)
128 PTZ00083 40S ribosomal protein 69.5 11 0.00025 24.8 4.1 41 17-62 23-66 (85)
129 TIGR01391 dnaG DNA primase, ca 69.2 7.7 0.00017 31.1 4.0 30 26-59 34-64 (415)
130 KOG2767 Translation initiation 69.2 1.4 3.1E-05 35.9 -0.2 38 25-64 95-132 (400)
131 COG1656 Uncharacterized conser 68.9 1.8 4E-05 31.5 0.3 32 26-60 97-140 (165)
132 KOG1296 Uncharacterized conser 68.4 4.5 9.8E-05 29.4 2.3 32 26-57 64-106 (161)
133 PF10276 zf-CHCC: Zinc-finger 68.3 7.5 0.00016 22.0 2.7 25 33-60 15-39 (40)
134 TIGR01031 rpmF_bact ribosomal 68.2 7.1 0.00015 23.3 2.8 27 21-58 21-47 (55)
135 KOG2703 C4-type Zn-finger prot 67.6 2.3 5E-05 35.3 0.7 18 22-40 64-81 (460)
136 COG3809 Uncharacterized protei 67.0 6.5 0.00014 25.9 2.6 27 28-58 3-29 (88)
137 KOG2906 RNA polymerase III sub 66.0 9.7 0.00021 26.0 3.4 53 24-76 19-95 (105)
138 COG1998 RPS31 Ribosomal protei 65.9 3.6 7.8E-05 24.8 1.1 26 28-59 21-46 (51)
139 KOG1597 Transcription initiati 65.9 5 0.00011 31.9 2.2 42 28-78 2-43 (308)
140 PF10263 SprT-like: SprT-like 64.2 8.2 0.00018 26.0 2.8 33 25-61 122-154 (157)
141 KOG3113 Uncharacterized conser 64.1 4.4 9.5E-05 31.9 1.6 55 24-78 109-179 (293)
142 KOG2907 RNA polymerase I trans 64.0 4.3 9.4E-05 28.1 1.4 36 27-62 75-114 (116)
143 PF00096 zf-C2H2: Zinc finger, 63.8 2.7 5.8E-05 19.8 0.2 11 52-62 2-12 (23)
144 PRK12495 hypothetical protein; 63.6 4.4 9.5E-05 31.0 1.5 34 21-62 37-70 (226)
145 KOG2906 RNA polymerase III sub 63.2 17 0.00037 24.8 4.2 31 28-62 3-33 (105)
146 PRK03824 hypA hydrogenase nick 63.0 3.2 7E-05 28.6 0.6 16 22-37 66-81 (135)
147 COG2260 Predicted Zn-ribbon RN 62.6 4.8 0.0001 24.9 1.3 30 52-81 19-48 (59)
148 PF13909 zf-H2C2_5: C2H2-type 62.5 3.2 6.9E-05 20.0 0.4 8 27-34 1-8 (24)
149 TIGR02996 rpt_mate_G_obs repea 62.4 3.8 8.3E-05 23.7 0.8 13 69-81 17-29 (42)
150 PF09297 zf-NADH-PPase: NADH p 62.4 4.7 0.0001 21.1 1.1 26 29-60 6-31 (32)
151 PF10083 DUF2321: Uncharacteri 62.3 2.1 4.6E-05 31.1 -0.4 54 25-85 38-99 (158)
152 PF01927 Mut7-C: Mut7-C RNAse 61.9 9.7 0.00021 26.2 2.9 31 27-60 92-134 (147)
153 COG2023 RPR2 RNase P subunit R 61.8 14 0.0003 25.2 3.5 48 18-65 45-97 (105)
154 COG5415 Predicted integral mem 61.5 3.4 7.5E-05 31.7 0.6 19 26-44 214-233 (251)
155 PF03119 DNA_ligase_ZBD: NAD-d 61.2 2.5 5.3E-05 22.1 -0.2 8 28-35 1-8 (28)
156 PF14768 RPA_interact_C: Repli 61.2 7.5 0.00016 24.6 2.0 34 29-70 2-35 (82)
157 smart00714 LITAF Possible memb 60.8 6.8 0.00015 23.5 1.7 20 24-45 1-20 (67)
158 COG1198 PriA Primosomal protei 60.7 6.9 0.00015 34.2 2.3 29 25-59 443-471 (730)
159 PRK12380 hydrogenase nickel in 60.6 4.6 9.9E-05 27.1 1.0 30 21-58 65-94 (113)
160 PF10058 DUF2296: Predicted in 60.2 4.6 9.9E-05 24.1 0.9 14 22-35 40-53 (54)
161 smart00647 IBR In Between Ring 60.1 11 0.00024 21.4 2.5 35 25-63 17-53 (64)
162 TIGR00373 conserved hypothetic 59.2 4.4 9.6E-05 28.5 0.8 11 24-34 126-136 (158)
163 PF08996 zf-DNA_Pol: DNA Polym 59.2 3.5 7.5E-05 29.7 0.3 38 24-61 16-56 (188)
164 PHA00616 hypothetical protein 59.0 3.4 7.4E-05 24.0 0.2 9 26-34 1-9 (44)
165 PF01921 tRNA-synt_1f: tRNA sy 58.9 11 0.00024 30.4 3.1 39 28-66 176-215 (360)
166 PRK00241 nudC NADH pyrophospha 58.8 9.9 0.00022 28.7 2.7 28 28-61 101-128 (256)
167 PF12322 T4_baseplate: T4 bact 58.8 14 0.00031 27.3 3.5 55 21-76 73-130 (205)
168 PF10601 zf-LITAF-like: LITAF- 58.7 8.2 0.00018 23.5 1.9 23 22-46 3-25 (73)
169 PF05077 DUF678: Protein of un 58.3 8.9 0.00019 24.7 2.0 12 48-59 55-66 (74)
170 PRK04011 peptide chain release 57.7 12 0.00025 30.3 3.1 53 26-85 328-380 (411)
171 PF00628 PHD: PHD-finger; Int 57.7 5.8 0.00013 22.1 1.0 28 29-65 2-29 (51)
172 TIGR02300 FYDLN_acid conserved 57.6 5.1 0.00011 28.2 0.9 36 21-63 4-39 (129)
173 PF13878 zf-C2H2_3: zinc-finge 57.4 4.4 9.5E-05 22.7 0.4 16 48-63 11-26 (41)
174 PRK04023 DNA polymerase II lar 57.4 8.5 0.00018 35.3 2.4 19 67-85 677-695 (1121)
175 PF03604 DNA_RNApol_7kD: DNA d 57.3 3.7 8.1E-05 22.2 0.1 25 28-59 2-26 (32)
176 PF01667 Ribosomal_S27e: Ribos 57.1 16 0.00034 22.1 2.9 31 28-63 9-39 (55)
177 PF09332 Mcm10: Mcm10 replicat 57.0 3.4 7.3E-05 33.1 -0.1 32 22-59 281-312 (344)
178 KOG2893 Zn finger protein [Gen 56.6 2.7 5.9E-05 33.1 -0.7 33 49-82 33-66 (341)
179 PF11781 RRN7: RNA polymerase 56.5 12 0.00026 20.5 2.1 26 26-58 8-33 (36)
180 KOG2462 C2H2-type Zn-finger pr 55.9 4.9 0.00011 31.6 0.6 36 24-62 159-199 (279)
181 PHA02611 51 baseplate hub asse 55.3 9.5 0.00021 29.5 2.1 25 21-45 77-101 (249)
182 PRK06266 transcription initiat 55.2 5.7 0.00012 28.6 0.8 9 25-33 116-124 (178)
183 PRK03681 hypA hydrogenase nick 55.0 6.7 0.00015 26.3 1.1 31 21-58 65-95 (114)
184 TIGR00595 priA primosomal prot 55.0 9.9 0.00021 31.3 2.3 30 26-61 222-251 (505)
185 PHA02942 putative transposase; 54.4 6.4 0.00014 31.4 1.1 47 25-81 324-370 (383)
186 cd00674 LysRS_core_class_I cat 54.2 30 0.00066 27.5 4.8 37 28-65 171-207 (353)
187 COG5349 Uncharacterized protei 53.8 4 8.7E-05 28.7 -0.2 31 27-62 22-52 (126)
188 COG1503 eRF1 Peptide chain rel 53.5 5.3 0.00012 32.8 0.5 38 25-67 326-363 (411)
189 PRK14715 DNA polymerase II lar 53.0 13 0.00027 35.3 2.8 48 25-85 673-720 (1627)
190 KOG2846 Predicted membrane pro 52.7 5.9 0.00013 31.7 0.6 13 24-36 240-252 (328)
191 PF14311 DUF4379: Domain of un 52.6 5.1 0.00011 23.2 0.2 10 26-35 28-37 (55)
192 PF10813 DUF2733: Protein of u 51.6 4.5 9.8E-05 22.2 -0.1 26 52-77 4-29 (32)
193 COG5216 Uncharacterized conser 51.6 15 0.00033 23.0 2.2 32 26-60 22-54 (67)
194 PF13824 zf-Mss51: Zinc-finger 51.5 9.8 0.00021 23.1 1.3 13 22-34 10-22 (55)
195 PF09334 tRNA-synt_1g: tRNA sy 50.9 9.7 0.00021 30.3 1.6 38 48-85 164-202 (391)
196 smart00249 PHD PHD zinc finger 50.6 9 0.0002 19.9 1.0 27 28-63 1-27 (47)
197 PF14446 Prok-RING_1: Prokaryo 50.0 11 0.00023 22.8 1.3 25 28-60 7-31 (54)
198 smart00731 SprT SprT homologue 49.2 20 0.00044 24.4 2.8 34 25-61 111-144 (146)
199 PF04161 Arv1: Arv1-like famil 49.2 14 0.00031 26.9 2.1 31 27-59 1-33 (208)
200 PF08209 Sgf11: Sgf11 (transcr 49.1 7.4 0.00016 21.2 0.5 10 25-34 3-12 (33)
201 PF04690 YABBY: YABBY protein; 49.0 13 0.00029 27.1 1.9 42 27-68 13-54 (170)
202 TIGR00100 hypA hydrogenase nic 48.8 6.6 0.00014 26.3 0.3 30 21-58 65-94 (115)
203 PRK05667 dnaG DNA primase; Val 48.8 14 0.0003 31.2 2.3 31 25-59 35-66 (580)
204 PF09151 DUF1936: Domain of un 48.4 43 0.00093 18.5 3.4 27 28-55 3-29 (36)
205 COG3058 FdhE Uncharacterized p 48.0 9.4 0.0002 30.4 1.1 21 24-44 183-203 (308)
206 PF04135 Nop10p: Nucleolar RNA 47.6 15 0.00033 22.0 1.7 27 52-78 19-45 (53)
207 PF01485 IBR: IBR domain; Int 47.6 7.5 0.00016 22.1 0.4 36 24-63 16-53 (64)
208 PF06677 Auto_anti-p27: Sjogre 47.3 12 0.00026 21.2 1.2 24 27-57 18-41 (41)
209 KOG3456 NADH:ubiquinone oxidor 46.7 11 0.00024 26.2 1.1 27 31-61 89-115 (120)
210 PF14690 zf-ISL3: zinc-finger 46.5 14 0.00031 20.2 1.4 11 26-36 2-12 (47)
211 PF13451 zf-trcl: Probable zin 45.3 18 0.00039 21.4 1.8 16 50-65 4-19 (49)
212 PF12480 DUF3699: Protein of u 45.2 68 0.0015 20.2 4.6 39 43-82 23-62 (77)
213 PF12773 DZR: Double zinc ribb 45.1 6.9 0.00015 21.9 -0.1 24 29-59 15-38 (50)
214 PF13912 zf-C2H2_6: C2H2-type 45.1 7.2 0.00016 19.0 0.0 11 52-62 3-13 (27)
215 COG4306 Uncharacterized protei 45.1 8 0.00017 27.7 0.3 43 24-68 37-86 (160)
216 KOG4080 Mitochondrial ribosoma 44.9 11 0.00024 27.8 1.0 14 22-35 89-102 (176)
217 PRK14811 formamidopyrimidine-D 44.8 20 0.00043 27.2 2.4 28 28-59 237-264 (269)
218 PF04032 Rpr2: RNAse P Rpr2/Rp 43.9 67 0.0015 19.4 4.3 33 25-57 45-84 (85)
219 PRK14810 formamidopyrimidine-D 43.9 22 0.00049 26.9 2.5 26 28-57 246-271 (272)
220 KOG2691 RNA polymerase II subu 43.6 19 0.00041 24.9 1.9 47 29-77 7-58 (113)
221 PF14447 Prok-RING_4: Prokaryo 43.3 12 0.00025 22.8 0.7 16 20-35 33-48 (55)
222 PF10609 ParA: ParA/MinD ATPas 43.2 9.6 0.00021 24.6 0.4 11 25-35 64-74 (81)
223 COG1655 Uncharacterized protei 43.0 10 0.00022 29.6 0.5 11 24-34 17-27 (267)
224 PHA00733 hypothetical protein 42.6 3.3 7.3E-05 28.3 -1.9 40 24-63 71-112 (128)
225 KOG3277 Uncharacterized conser 42.5 36 0.00079 24.9 3.3 64 17-83 70-137 (165)
226 COG1592 Rubrerythrin [Energy p 42.2 12 0.00027 27.1 0.9 11 25-35 148-158 (166)
227 KOG3022 Predicted ATPase, nucl 41.7 15 0.00032 29.2 1.3 13 25-37 221-233 (300)
228 TIGR00467 lysS_arch lysyl-tRNA 41.6 50 0.0011 27.7 4.4 36 28-65 170-205 (515)
229 PRK14714 DNA polymerase II lar 41.1 26 0.00055 32.9 2.8 59 26-85 667-741 (1337)
230 TIGR00354 polC DNA polymerase, 41.1 24 0.00051 32.5 2.6 48 25-85 624-671 (1095)
231 COG1571 Predicted DNA-binding 40.7 11 0.00023 31.2 0.4 29 28-63 352-380 (421)
232 PF01396 zf-C4_Topoisom: Topoi 40.7 57 0.0012 17.8 3.3 28 28-59 3-33 (39)
233 COG3877 Uncharacterized protei 40.6 27 0.00057 24.3 2.3 23 27-59 7-29 (122)
234 PRK01103 formamidopyrimidine/5 40.0 28 0.00062 26.2 2.6 27 28-58 247-273 (274)
235 cd01237 Unc112 Unc-112 pleckst 40.0 19 0.0004 24.4 1.4 15 72-86 90-104 (106)
236 PRK14873 primosome assembly pr 39.9 23 0.00049 30.5 2.2 29 25-59 391-419 (665)
237 PRK00762 hypA hydrogenase nick 39.7 15 0.00032 25.0 0.9 9 27-35 93-101 (124)
238 PRK00564 hypA hydrogenase nick 39.6 14 0.0003 24.8 0.8 31 21-58 66-96 (117)
239 PF13408 Zn_ribbon_recom: Reco 39.4 16 0.00034 20.5 0.9 16 48-63 3-18 (58)
240 COG1675 TFA1 Transcription ini 38.9 14 0.0003 27.1 0.7 10 25-34 131-140 (176)
241 PHA00732 hypothetical protein 38.8 3 6.6E-05 26.5 -2.4 46 26-72 1-49 (79)
242 TIGR00319 desulf_FeS4 desulfof 38.8 38 0.00082 17.7 2.3 26 24-54 5-30 (34)
243 PRK10445 endonuclease VIII; Pr 37.9 32 0.00068 26.0 2.5 26 28-57 237-262 (263)
244 TIGR00577 fpg formamidopyrimid 37.7 31 0.00066 26.1 2.4 26 28-57 247-272 (272)
245 PRK13945 formamidopyrimidine-D 37.5 31 0.00068 26.2 2.5 26 28-57 256-281 (282)
246 PF01155 HypA: Hydrogenase exp 37.4 29 0.00063 23.0 2.0 12 23-34 67-78 (113)
247 PF02891 zf-MIZ: MIZ/SP-RING z 37.3 15 0.00031 21.3 0.5 8 27-34 42-49 (50)
248 PRK15338 type III secretion sy 37.0 17 0.00038 29.5 1.1 20 65-84 195-214 (372)
249 COG3529 Predicted nucleic-acid 36.6 4.8 0.0001 25.3 -1.7 30 28-59 12-41 (66)
250 PF13913 zf-C2HC_2: zinc-finge 36.2 17 0.00037 18.1 0.6 10 51-60 3-12 (25)
251 PF06397 Desulfoferrod_N: Desu 36.1 25 0.00054 19.5 1.3 28 24-58 4-31 (36)
252 PF11793 FANCL_C: FANCL C-term 35.8 6.1 0.00013 24.3 -1.4 16 24-41 53-68 (70)
253 PF02591 DUF164: Putative zinc 35.7 20 0.00043 20.8 0.9 11 24-34 44-54 (56)
254 PF06827 zf-FPG_IleRS: Zinc fi 35.6 64 0.0014 16.3 3.6 26 28-57 3-28 (30)
255 cd00974 DSRD Desulforedoxin (D 35.6 47 0.001 17.4 2.3 25 25-54 3-27 (34)
256 COG3357 Predicted transcriptio 35.2 15 0.00033 24.7 0.4 29 51-79 59-88 (97)
257 COG4311 SoxD Sarcosine oxidase 35.2 17 0.00037 24.5 0.7 9 26-34 3-11 (97)
258 smart00355 ZnF_C2H2 zinc finge 35.1 19 0.00041 16.2 0.6 8 53-60 3-10 (26)
259 PF05280 FlhC: Flagellar trans 34.8 16 0.00035 26.5 0.5 12 23-34 151-162 (175)
260 TIGR00558 pdxH pyridoxamine-ph 34.8 23 0.0005 26.1 1.3 18 68-85 28-45 (217)
261 PF14369 zf-RING_3: zinc-finge 34.7 51 0.0011 17.8 2.4 31 27-62 3-33 (35)
262 COG1773 Rubredoxin [Energy pro 34.2 22 0.00048 21.6 1.0 21 20-40 30-50 (55)
263 PRK07111 anaerobic ribonucleos 33.9 20 0.00042 31.3 0.9 35 27-73 681-719 (735)
264 KOG2164 Predicted E3 ubiquitin 33.7 9.7 0.00021 32.2 -0.9 33 24-60 184-216 (513)
265 COG2816 NPY1 NTP pyrophosphohy 33.6 36 0.00078 26.7 2.3 27 29-61 114-140 (279)
266 cd03019 DsbA_DsbA DsbA family, 33.5 16 0.00034 24.4 0.3 11 25-35 23-33 (178)
267 PF02701 zf-Dof: Dof domain, z 32.7 30 0.00064 21.7 1.4 37 24-60 3-40 (63)
268 PF06170 DUF983: Protein of un 32.6 16 0.00034 23.7 0.1 11 52-62 10-20 (86)
269 TIGR03676 aRF1/eRF1 peptide ch 32.3 52 0.0011 26.6 3.1 52 26-84 320-371 (403)
270 PRK04351 hypothetical protein; 32.2 49 0.0011 23.3 2.6 34 25-62 111-144 (149)
271 smart00734 ZnF_Rad18 Rad18-lik 32.0 22 0.00047 18.1 0.6 8 27-34 2-9 (26)
272 KOG2324 Prolyl-tRNA synthetase 31.3 21 0.00046 29.7 0.7 32 24-59 225-256 (457)
273 PF01363 FYVE: FYVE zinc finge 31.2 43 0.00094 19.6 1.9 28 26-61 9-36 (69)
274 PF05495 zf-CHY: CHY zinc fing 31.0 11 0.00025 23.1 -0.7 36 24-61 17-52 (71)
275 PF04423 Rad50_zn_hook: Rad50 31.0 17 0.00038 20.9 0.1 7 28-34 22-28 (54)
276 TIGR00120 ArgJ glutamate N-ace 30.9 49 0.0011 27.2 2.7 33 34-66 367-400 (404)
277 PF03470 zf-XS: XS zinc finger 30.9 28 0.0006 20.2 1.0 7 29-35 1-7 (43)
278 PTZ00293 thymidine kinase; Pro 30.9 43 0.00092 25.0 2.2 31 28-58 139-177 (211)
279 COG1439 Predicted nucleic acid 30.7 33 0.00072 25.3 1.6 7 29-35 156-162 (177)
280 PRK06260 threonine synthase; V 30.5 33 0.00072 27.0 1.7 8 27-34 4-11 (397)
281 PF05907 DUF866: Eukaryotic pr 30.5 30 0.00066 24.6 1.3 34 24-57 62-106 (161)
282 TIGR00622 ssl1 transcription f 30.5 20 0.00043 24.6 0.4 9 53-61 58-66 (112)
283 TIGR00320 dfx_rbo desulfoferro 30.5 47 0.001 22.7 2.2 30 24-60 5-34 (125)
284 PRK05580 primosome assembly pr 30.5 35 0.00077 29.1 1.9 30 26-61 390-419 (679)
285 smart00782 PhnA_Zn_Ribbon PhnA 30.3 52 0.0011 19.1 2.1 31 28-58 9-44 (47)
286 PF14169 YdjO: Cold-inducible 30.2 31 0.00066 21.2 1.1 19 22-40 35-53 (59)
287 PF12898 Stc1: Stc1 domain; I 30.2 57 0.0012 20.7 2.4 37 20-76 31-67 (84)
288 PF12647 RNHCP: RNHCP domain; 30.2 20 0.00044 23.8 0.4 39 25-67 3-41 (92)
289 smart00350 MCM minichromosome 30.2 35 0.00077 27.9 1.8 33 25-59 36-70 (509)
290 KOG3309 Ferredoxin [Energy pro 30.0 24 0.00052 25.7 0.7 37 49-85 83-120 (159)
291 PF12677 DUF3797: Domain of un 30.0 25 0.00053 21.0 0.7 13 24-36 11-23 (49)
292 MTH00129 COX2 cytochrome c oxi 29.9 51 0.0011 24.6 2.5 50 33-83 177-228 (230)
293 COG1499 NMD3 NMD protein affec 29.9 44 0.00096 26.9 2.3 31 28-58 8-51 (355)
294 KOG2463 Predicted RNA-binding 29.9 52 0.0011 26.9 2.6 43 21-65 253-303 (376)
295 TIGR01374 soxD sarcosine oxida 29.8 24 0.00052 23.1 0.6 8 27-34 2-9 (84)
296 PRK12722 transcriptional activ 29.4 24 0.00052 26.1 0.7 13 23-35 151-163 (187)
297 PF04981 NMD3: NMD3 family ; 29.2 27 0.00059 25.8 0.9 17 46-62 31-47 (236)
298 TIGR01433 CyoA cytochrome o ub 29.1 50 0.0011 24.6 2.3 47 33-80 176-224 (226)
299 PF05741 zf-nanos: Nanos RNA b 28.6 27 0.00058 21.1 0.7 14 22-35 29-42 (55)
300 PF09416 UPF1_Zn_bind: RNA hel 28.5 44 0.00095 24.0 1.9 37 21-57 54-94 (152)
301 cd01412 SIRT5_Af1_CobB SIRT5_A 28.5 45 0.00098 24.0 2.0 55 26-85 109-163 (224)
302 PF05191 ADK_lid: Adenylate ki 28.5 33 0.00071 18.7 1.0 15 51-65 2-16 (36)
303 MTH00038 COX2 cytochrome c oxi 28.3 55 0.0012 24.3 2.4 50 33-83 177-228 (229)
304 cd03023 DsbA_Com1_like DsbA fa 28.1 19 0.0004 23.1 -0.1 11 25-35 13-23 (154)
305 COG4391 Uncharacterized protei 28.1 56 0.0012 20.3 2.0 35 24-62 22-60 (62)
306 TIGR00686 phnA alkylphosphonat 27.9 25 0.00053 24.2 0.5 15 23-37 16-30 (109)
307 PRK05452 anaerobic nitric oxid 27.7 27 0.00059 28.5 0.8 18 20-37 452-469 (479)
308 PF13132 DUF3950: Domain of un 27.6 41 0.00089 18.2 1.2 10 74-83 17-27 (30)
309 TIGR02866 CoxB cytochrome c ox 27.3 41 0.0009 24.1 1.6 46 33-79 154-201 (201)
310 PF06676 DUF1178: Protein of u 27.3 39 0.00085 24.1 1.4 11 25-35 31-41 (148)
311 KOG3352 Cytochrome c oxidase, 27.1 31 0.00067 25.0 0.9 11 24-34 131-141 (153)
312 PHA02768 hypothetical protein; 26.9 24 0.00053 21.3 0.3 38 26-63 5-44 (55)
313 PF13397 DUF4109: Domain of un 26.9 36 0.00078 23.1 1.1 16 21-36 45-60 (105)
314 PF04267 SoxD: Sarcosine oxida 26.8 19 0.00041 23.5 -0.2 7 28-34 3-9 (84)
315 COG1107 Archaea-specific RecJ- 26.7 78 0.0017 27.9 3.3 45 18-62 43-92 (715)
316 PF09452 Mvb12: ESCRT-I subuni 26.6 32 0.0007 22.9 0.8 25 61-85 27-51 (91)
317 TIGR00627 tfb4 transcription f 26.5 21 0.00045 27.7 -0.1 29 22-60 251-279 (279)
318 PRK08351 DNA-directed RNA poly 26.5 35 0.00077 21.0 0.9 9 28-36 17-25 (61)
319 PF14319 Zn_Tnp_IS91: Transpos 26.2 29 0.00063 23.1 0.6 31 25-61 41-71 (111)
320 PRK12860 transcriptional activ 26.1 35 0.00075 25.3 1.0 14 22-35 150-163 (189)
321 PRK14559 putative protein seri 26.0 30 0.00065 29.8 0.7 26 28-63 29-54 (645)
322 KOG3507 DNA-directed RNA polym 25.8 35 0.00077 21.2 0.8 31 22-59 16-46 (62)
323 TIGR00308 TRM1 tRNA(guanine-26 25.4 88 0.0019 25.0 3.2 54 19-82 226-283 (374)
324 PF14634 zf-RING_5: zinc-RING 25.3 40 0.00087 18.4 1.0 11 24-34 34-44 (44)
325 PRK11088 rrmA 23S rRNA methylt 25.2 33 0.00071 25.3 0.7 25 26-58 2-26 (272)
326 PF06524 NOA36: NOA36 protein; 25.1 44 0.00095 26.6 1.4 21 22-42 205-225 (314)
327 PF07295 DUF1451: Protein of u 25.0 59 0.0013 22.9 2.0 32 24-61 110-141 (146)
328 PRK10220 hypothetical protein; 25.0 33 0.00072 23.6 0.7 16 22-37 16-31 (111)
329 PHA02893 hypothetical protein; 24.9 67 0.0015 21.3 2.1 11 49-59 68-78 (88)
330 PRK08332 ribonucleotide-diphos 24.9 52 0.0011 31.8 2.1 30 28-59 1706-1735(1740)
331 PF04641 Rtf2: Rtf2 RING-finge 24.9 1.6E+02 0.0035 22.0 4.4 58 23-80 110-184 (260)
332 CHL00136 rpl31 ribosomal prote 24.6 71 0.0015 19.9 2.1 34 24-61 13-46 (68)
333 PRK12496 hypothetical protein; 24.6 37 0.00079 24.1 0.9 9 26-34 127-135 (164)
334 PF13901 DUF4206: Domain of un 24.3 31 0.00067 25.1 0.4 34 25-62 151-184 (202)
335 PRK06393 rpoE DNA-directed RNA 24.1 41 0.0009 20.9 0.9 9 28-36 19-27 (64)
336 KOG3053 Uncharacterized conser 24.1 33 0.0007 27.2 0.6 22 47-68 68-89 (293)
337 PF06221 zf-C2HC5: Putative zi 23.9 39 0.00085 20.5 0.8 10 26-35 35-44 (57)
338 PF13597 NRDD: Anaerobic ribon 23.8 52 0.0011 27.6 1.7 35 28-74 493-531 (546)
339 smart00154 ZnF_AN1 AN1-like Zi 23.6 41 0.00089 18.5 0.8 9 26-34 12-20 (39)
340 PF10825 DUF2752: Protein of u 23.4 37 0.00081 19.7 0.6 14 25-38 8-21 (52)
341 PF12874 zf-met: Zinc-finger o 23.3 51 0.0011 15.4 1.0 12 52-63 2-13 (25)
342 PF14471 DUF4428: Domain of un 23.3 31 0.00067 20.2 0.2 30 28-60 1-30 (51)
343 cd01675 RNR_III Class III ribo 23.3 43 0.00093 28.1 1.2 11 26-36 532-542 (555)
344 PRK10954 periplasmic protein d 23.2 25 0.00054 25.0 -0.2 13 25-37 45-57 (207)
345 TIGR03844 cysteate_syn cysteat 23.1 47 0.001 26.6 1.3 10 26-35 2-11 (398)
346 PRK08270 anaerobic ribonucleos 23.0 56 0.0012 28.1 1.8 10 26-35 639-648 (656)
347 PRK08197 threonine synthase; V 23.0 61 0.0013 25.5 1.9 27 26-61 7-33 (394)
348 KOG1598 Transcription initiati 22.9 43 0.00093 28.5 1.1 27 28-59 2-28 (521)
349 COG1364 ArgJ N-acetylglutamate 22.9 54 0.0012 27.1 1.6 32 36-67 369-401 (404)
350 PF15135 UPF0515: Uncharacteri 22.9 42 0.0009 26.4 0.9 43 19-61 105-166 (278)
351 PRK11823 DNA repair protein Ra 22.6 71 0.0015 25.9 2.3 26 24-59 5-30 (446)
352 PF01599 Ribosomal_S27: Riboso 22.3 71 0.0015 18.7 1.7 27 27-59 19-47 (47)
353 cd05468 pVHL von Hippel-Landau 22.3 17 0.00037 25.1 -1.2 16 63-80 13-28 (141)
354 cd07153 Fur_like Ferric uptake 22.3 44 0.00095 21.2 0.8 16 49-64 72-87 (116)
355 COG2093 DNA-directed RNA polym 22.0 44 0.00095 21.0 0.8 11 26-36 18-28 (64)
356 PF11648 RIG-I_C-RD: C-termina 22.0 74 0.0016 21.5 1.9 14 47-60 57-70 (123)
357 PF01197 Ribosomal_L31: Riboso 21.9 54 0.0012 20.2 1.2 28 48-75 11-40 (69)
358 PF09237 GAGA: GAGA factor; I 21.9 57 0.0012 19.8 1.2 17 18-34 16-32 (54)
359 cd05133 RasGAP_IQGAP1 IQGAP1 i 21.8 57 0.0012 26.2 1.5 17 68-84 77-93 (360)
360 PF11672 DUF3268: Protein of u 21.7 1.2E+02 0.0026 20.3 2.9 33 27-60 3-41 (102)
361 PF13806 Rieske_2: Rieske-like 21.6 60 0.0013 21.1 1.4 46 28-74 42-92 (104)
362 PF02257 RFX_DNA_binding: RFX 21.6 60 0.0013 21.0 1.4 14 72-85 28-41 (85)
363 MTH00117 COX2 cytochrome c oxi 21.2 86 0.0019 23.3 2.3 48 33-81 177-226 (227)
364 PRK11788 tetratricopeptide rep 21.2 96 0.0021 23.0 2.6 37 22-68 350-387 (389)
365 PF00265 TK: Thymidine kinase; 21.2 1E+02 0.0022 21.8 2.6 29 28-56 139-175 (176)
366 PF09889 DUF2116: Uncharacteri 21.1 48 0.001 20.2 0.8 23 28-60 5-28 (59)
367 PRK08402 replication factor A; 21.1 66 0.0014 25.7 1.8 27 26-58 212-238 (355)
368 COG0819 TenA Putative transcri 21.1 42 0.00091 25.0 0.6 13 69-81 153-165 (218)
369 PRK08271 anaerobic ribonucleos 21.1 49 0.0011 28.5 1.1 22 27-58 567-588 (623)
370 PF07491 PPI_Ypi1: Protein pho 21.0 41 0.00089 20.8 0.5 8 1-8 31-38 (60)
371 PRK12366 replication factor A; 20.7 48 0.001 28.3 1.0 26 26-59 532-557 (637)
372 PF02489 Herpes_glycop_H: Herp 20.6 1.3E+02 0.0028 25.4 3.5 25 23-50 558-582 (657)
373 PRK08329 threonine synthase; V 20.5 93 0.002 24.1 2.5 26 27-62 2-27 (347)
374 PF14940 TMEM219: Transmembran 20.2 99 0.0021 23.4 2.5 27 58-85 28-54 (223)
375 cd02972 DsbA_family DsbA famil 20.2 29 0.00064 19.9 -0.3 8 27-34 7-14 (98)
376 PF11023 DUF2614: Protein of u 20.2 46 0.00099 23.0 0.6 25 26-58 69-93 (114)
377 COG5082 AIR1 Arginine methyltr 20.2 39 0.00084 25.2 0.3 9 51-59 98-106 (190)
378 cd05131 RasGAP_IQGAP2 IQGAP2 i 20.1 66 0.0014 25.3 1.6 17 68-84 77-93 (339)
379 KOG2879 Predicted E3 ubiquitin 20.1 48 0.001 26.4 0.8 22 22-43 235-256 (298)
380 COG1180 PflA Pyruvate-formate 20.1 48 0.001 24.9 0.8 14 26-39 46-59 (260)
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=4.5e-44 Score=231.25 Aligned_cols=80 Identities=50% Similarity=0.904 Sum_probs=45.9
Q ss_pred Cccccccc-cCCCcccccCCCCCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhhhhhHHH
Q 035653 2 GKRKSRKA-KAVGVKKTKGMEKLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIYAEWIDE 80 (87)
Q Consensus 2 GkRK~k~k-~~~~~~~kk~~~kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVYs~wiD~ 80 (87)
||||++++ +++ +|++++||+.|+||||||++||+|+||++.++|+|+|++||+.|+++|++|+||||||++|||+
T Consensus 1 GkRK~~~k~~~~----kk~~~~l~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~~L~epiDVY~~wiD~ 76 (81)
T PF05129_consen 1 GKRKKKRKKPPK----KKKKPKLPKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKINPLSEPIDVYSEWIDA 76 (81)
T ss_dssp -----------------------SS----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE--SS--TTHHHHHHHHH
T ss_pred CCCcccCCCCCc----cCcCCCCCceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccCccCcccchhHHHHHH
Confidence 89998887 555 7889999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhh
Q 035653 81 CERAN 85 (87)
Q Consensus 81 ~e~~n 85 (87)
|+++|
T Consensus 77 ~~~~n 81 (81)
T PF05129_consen 77 CEEGN 81 (81)
T ss_dssp HH---
T ss_pred HHhcC
Confidence 99998
No 2
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=100.00 E-value=4e-43 Score=236.34 Aligned_cols=84 Identities=54% Similarity=0.986 Sum_probs=80.3
Q ss_pred CCccccccccCCCcccccCCCCCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhhhhhHHH
Q 035653 1 MGKRKSRKAKAVGVKKTKGMEKLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIYAEWIDE 80 (87)
Q Consensus 1 MGkRK~k~k~~~~~~~kk~~~kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVYs~wiD~ 80 (87)
|||||+|++++++ .|...+|++.|+||||||+++|+|+||++.++|.++|++|+++|++.|++|++||||||+|||+
T Consensus 1 MgkRk~K~k~~~k---~r~~~~ldt~FnClfcnHek~v~~~~Dk~~~iG~~sC~iC~esFqt~it~LsepIDVYSdWiDa 77 (109)
T KOG3214|consen 1 MGKRKSKRKEPPK---ERRVEPLDTQFNCLFCNHEKSVSCTLDKKHNIGKASCRICEESFQTTITALSEPIDVYSDWIDA 77 (109)
T ss_pred CCcccccccCCch---hhhccchheeeccCccccccceeeeehhhcCcceeeeeehhhhhccchHhhccchHHHHHHHHH
Confidence 9999999987762 4889999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhCC
Q 035653 81 CERANNS 87 (87)
Q Consensus 81 ~e~~n~~ 87 (87)
|+++|++
T Consensus 78 Ce~vn~a 84 (109)
T KOG3214|consen 78 CEAVNNA 84 (109)
T ss_pred HHHhhcc
Confidence 9999974
No 3
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=100.00 E-value=1.1e-37 Score=209.44 Aligned_cols=82 Identities=33% Similarity=0.784 Sum_probs=77.8
Q ss_pred CCccccccccCCCcccccCCCCCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhhhhhHHH
Q 035653 1 MGKRKSRKAKAVGVKKTKGMEKLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIYAEWIDE 80 (87)
Q Consensus 1 MGkRK~k~k~~~~~~~kk~~~kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVYs~wiD~ 80 (87)
|||||++++.++ +++.++||+.|+||||||+++++|.++++.++|.+.|++||++|++.||+|++||||||+|||+
T Consensus 1 MG~rr~krr~~i----k~~~~~L~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l~~~vDvYs~wvDa 76 (104)
T COG4888 1 MGRRRRKRRKII----KRRPQVLPKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPELSEPVDVYSAWVDA 76 (104)
T ss_pred CCcccccccccC----cccCccCCceEecCccCCeeeeEEEEEecCceeEEEcccCcceEEEeccccccchhHHHHHHHH
Confidence 999999988777 6777889999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhC
Q 035653 81 CERANN 86 (87)
Q Consensus 81 ~e~~n~ 86 (87)
|+|.+.
T Consensus 77 y~eg~~ 82 (104)
T COG4888 77 YLEGRG 82 (104)
T ss_pred HHhccc
Confidence 999763
No 4
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=100.00 E-value=2.6e-34 Score=192.21 Aligned_cols=76 Identities=29% Similarity=0.573 Sum_probs=70.2
Q ss_pred CCccccccccCCCcccccCCCCCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhhhhhHHH
Q 035653 1 MGKRKSRKAKAVGVKKTKGMEKLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIYAEWIDE 80 (87)
Q Consensus 1 MGkRK~k~k~~~~~~~kk~~~kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVYs~wiD~ 80 (87)
|||||++++++ +|++.++|+.|+|||||+ .+|.|+|++ +++++.|.+||..|.++|++|+|||||||+|||+
T Consensus 1 MGkRk~~~k~~-----~k~k~klpt~f~CP~Cge-~~v~v~~~k--~~~h~~C~~CG~y~~~~V~~l~epIDVY~~wiD~ 72 (99)
T PRK14892 1 MGRRRKKRKKI-----IRPKPKLPKIFECPRCGK-VSISVKIKK--NIAIITCGNCGLYTEFEVPSVYDEVDVYNKFIDL 72 (99)
T ss_pred CCCccccCCCC-----cccccCCCcEeECCCCCC-eEeeeecCC--CcceEECCCCCCccCEECCccccchhhHHHHHHH
Confidence 99999997744 577899999999999995 799999987 8999999999999999999999999999999999
Q ss_pred HHHh
Q 035653 81 CERA 84 (87)
Q Consensus 81 ~e~~ 84 (87)
|++-
T Consensus 73 ~~eg 76 (99)
T PRK14892 73 YLEG 76 (99)
T ss_pred HHhc
Confidence 9973
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=97.30 E-value=0.00023 Score=42.08 Aligned_cols=34 Identities=29% Similarity=0.396 Sum_probs=24.4
Q ss_pred cCCCCCCCCeEEEE--EeccCcEEEEEcCcccceeEe
Q 035653 28 QCPFCGHGTSVECR--IDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 28 ~CPfC~~~~sV~v~--idk~~~~g~~~C~~C~~~~~~ 62 (87)
.|||||.. .+.+. .+.....+...|..||.+...
T Consensus 3 PCPfCGg~-~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGA-DVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCc-ceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 59999984 45454 444556677799999987654
No 6
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=97.04 E-value=0.00097 Score=39.62 Aligned_cols=33 Identities=30% Similarity=0.556 Sum_probs=23.1
Q ss_pred ccccCCCCCCCCeEEEEEeccCcE---EEEEcCcccc
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQI---GEAFCWNCLE 58 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~---g~~~C~~C~~ 58 (87)
+.-.|||||. ..+.+.-+..... ..|.|..||.
T Consensus 2 ~LkPCPFCG~-~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGS-ADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCC-cceEeecccCCCCCCEEEEEcCCCCC
Confidence 3446999987 4566665443322 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=96.75 E-value=0.0017 Score=39.33 Aligned_cols=34 Identities=26% Similarity=0.515 Sum_probs=25.1
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEee
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQ 63 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~ 63 (87)
.|.||.||. ++++ .....-.++.|..||..|+--
T Consensus 2 ~~~CP~CG~--~iev--~~~~~GeiV~Cp~CGaeleVv 35 (54)
T TIGR01206 2 QFECPDCGA--EIEL--ENPELGELVICDECGAELEVV 35 (54)
T ss_pred ccCCCCCCC--EEec--CCCccCCEEeCCCCCCEEEEE
Confidence 589999998 3444 433334588999999999763
No 8
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=96.44 E-value=0.0047 Score=38.76 Aligned_cols=50 Identities=26% Similarity=0.419 Sum_probs=33.5
Q ss_pred CCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhhhh
Q 035653 23 LDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIYAE 76 (87)
Q Consensus 23 l~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVYs~ 76 (87)
.|++=.|||||- ++|.++- ..+...+.|..||..-...-.. -++||+|+.
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 5677765 4778889999999863222111 146666654
No 9
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=96.44 E-value=0.0076 Score=39.99 Aligned_cols=53 Identities=25% Similarity=0.504 Sum_probs=35.0
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhh-hhhHHHHH
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIY-AEWIDECE 82 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVY-s~wiD~~e 82 (87)
-..+.||||+... | +...+|+-.|+.|+..|.--.-.++.|.-+. ..=|..+.
T Consensus 34 ~a~y~CpfCgk~~-v-----kR~a~GIW~C~~C~~~~AGGAy~~~T~~~~t~~~~irr~~ 87 (90)
T PTZ00255 34 HAKYFCPFCGKHA-V-----KRQAVGIWRCKGCKKTVAGGAWTLSTPAASTVRSTIRRLR 87 (90)
T ss_pred hCCccCCCCCCCc-e-----eeeeeEEEEcCCCCCEEeCCccccccchhHHHHHHHHHHH
Confidence 3679999999743 2 2356899999999999977544444444443 33444333
No 10
>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=96.43 E-value=0.009 Score=39.73 Aligned_cols=55 Identities=24% Similarity=0.448 Sum_probs=37.2
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhh-hhhHHHHHHhh
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIY-AEWIDECERAN 85 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVY-s~wiD~~e~~n 85 (87)
..+.||||+... | +...+|+-.|+.|+..|.--.-.++.|.-+. ..=|..+.|..
T Consensus 34 a~y~CpfCgk~~---v---kR~a~GIW~C~~C~~~~AGGAy~p~T~~~~t~~~~irrl~e~~ 89 (91)
T TIGR00280 34 AKYVCPFCGKKT---V---KRGSTGIWTCRKCGAKFAGGAYTPVTPAGKTVRKTIRRIVEMK 89 (91)
T ss_pred cCccCCCCCCCc---e---EEEeeEEEEcCCCCCEEeCCccccccchhHHHHHHHHHHHHhh
Confidence 578999999743 2 2367899999999999977644445554444 44555554443
No 11
>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=96.33 E-value=0.004 Score=35.20 Aligned_cols=32 Identities=31% Similarity=0.588 Sum_probs=22.5
Q ss_pred ccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEee
Q 035653 27 FQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQ 63 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~ 63 (87)
|.||.||+.. +..| ...|.+.|..||.--+..
T Consensus 1 m~Cp~Cg~~~---~~~D--~~~g~~vC~~CG~Vl~e~ 32 (43)
T PF08271_consen 1 MKCPNCGSKE---IVFD--PERGELVCPNCGLVLEEN 32 (43)
T ss_dssp ESBTTTSSSE---EEEE--TTTTEEEETTT-BBEE-T
T ss_pred CCCcCCcCCc---eEEc--CCCCeEECCCCCCEeecc
Confidence 6899999943 4455 445888999999876654
No 12
>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=96.33 E-value=0.0084 Score=33.60 Aligned_cols=34 Identities=32% Similarity=0.659 Sum_probs=23.4
Q ss_pred ccCCCCCCCCeEEEEEecc----CcEEEEEcCccccee
Q 035653 27 FQCPFCGHGTSVECRIDKK----IQIGEAFCWNCLERF 60 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk~----~~~g~~~C~~C~~~~ 60 (87)
|+||.|||...+-..+.-. ...-...|..||..|
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCee
Confidence 6899999998888866432 236678899999876
No 13
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=96.22 E-value=0.0023 Score=46.15 Aligned_cols=36 Identities=33% Similarity=0.627 Sum_probs=24.0
Q ss_pred cCCCCCCCCeEEEEEecc-CcEE---EEEcCcccceeEee
Q 035653 28 QCPFCGHGTSVECRIDKK-IQIG---EAFCWNCLERFCTQ 63 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~-~~~g---~~~C~~C~~~~~~~ 63 (87)
.||||||+.|=.+.=-.. +|-+ .=.|..||.+|.|-
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTf 41 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTF 41 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchh
Confidence 599999998755532111 2222 25799999999773
No 14
>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=96.20 E-value=0.0044 Score=44.34 Aligned_cols=36 Identities=31% Similarity=0.540 Sum_probs=25.2
Q ss_pred cCCCCCCCCeEEEEEec-cCcEEE---EEcCcccceeEee
Q 035653 28 QCPFCGHGTSVECRIDK-KIQIGE---AFCWNCLERFCTQ 63 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk-~~~~g~---~~C~~C~~~~~~~ 63 (87)
.||||||+++=.+.=-. .+|.++ =.|..||.+|.|-
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTy 41 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTF 41 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcccee
Confidence 59999998876553221 234333 5799999999885
No 15
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=96.05 E-value=0.0022 Score=35.04 Aligned_cols=34 Identities=21% Similarity=0.426 Sum_probs=22.3
Q ss_pred cccCCCCCCCCeEEEEEecc-CcEEEEEcCcccceeE
Q 035653 26 QFQCPFCGHGTSVECRIDKK-IQIGEAFCWNCLERFC 61 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~-~~~g~~~C~~C~~~~~ 61 (87)
.++||.|+.. ..+.-+.. ...+.+.|.+||..|.
T Consensus 2 ~~~CP~C~~~--~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 2 RIQCPNCKTS--FRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCE--EEeCHHHcCCCCCEEECCCCCCEEE
Confidence 3789999984 33322221 2234899999998875
No 16
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=95.79 E-value=0.022 Score=37.75 Aligned_cols=44 Identities=25% Similarity=0.516 Sum_probs=31.7
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhh
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIY 74 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVY 74 (87)
..+.||||+... | +...+|+-.|+.|+..|.--.-.++.|.-+.
T Consensus 35 a~y~CpfCgk~~-v-----kR~a~GIW~C~~C~~~~AGGAy~~~T~~~~t 78 (90)
T PRK03976 35 AKHVCPVCGRPK-V-----KRVGTGIWECRKCGAKFAGGAYTPETPAGKT 78 (90)
T ss_pred cCccCCCCCCCc-e-----EEEEEEEEEcCCCCCEEeCCccccccchhhh
Confidence 579999998742 2 2467899999999999877644455554444
No 17
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=95.62 E-value=0.024 Score=32.29 Aligned_cols=34 Identities=21% Similarity=0.425 Sum_probs=24.1
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeec
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQI 64 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i 64 (87)
..|.||.||.. ++++... ..+.|..||..+....
T Consensus 2 ~~y~C~~CG~~----~~~~~~~--~~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 2 AEYKCARCGRE----VELDEYG--TGVRCPYCGYRILFKE 35 (46)
T ss_pred CEEECCCCCCE----EEECCCC--CceECCCCCCeEEEcc
Confidence 36899999983 3334333 3789999998876653
No 18
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=95.57 E-value=0.035 Score=31.27 Aligned_cols=34 Identities=21% Similarity=0.462 Sum_probs=25.5
Q ss_pred ccCCCCCCCCeEEEEEecc----CcEEEEEcCccccee
Q 035653 27 FQCPFCGHGTSVECRIDKK----IQIGEAFCWNCLERF 60 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk~----~~~g~~~C~~C~~~~ 60 (87)
|.||.|||..++-..+... ...-...|..||-.+
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 6899999999887776332 235578899999765
No 19
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=95.40 E-value=0.025 Score=33.95 Aligned_cols=47 Identities=17% Similarity=0.317 Sum_probs=28.4
Q ss_pred ccCCCCCCCCeEEEEEeccCcEEEEEcCcccce--eEeecCCCCchhhh
Q 035653 27 FQCPFCGHGTSVECRIDKKIQIGEAFCWNCLER--FCTQIHALTEPIDI 73 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~--~~~~i~~L~epiDV 73 (87)
.+||+||+..++.+..........--|.+|-.- +...+.....-|.|
T Consensus 1 i~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI~~~v~~d~~~~~v~v 49 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPIEVQVTVDEDEPSVSV 49 (52)
T ss_pred CCCCCCCCeeEEEEecCCCCeeEEeehhhcCCccEEEEEECCCCCEEEE
Confidence 379999996544444433334567789999864 44445544444433
No 20
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=95.30 E-value=0.017 Score=41.22 Aligned_cols=36 Identities=33% Similarity=0.637 Sum_probs=23.2
Q ss_pred cCCCCCCCCeEEEEEec-cCc--E-EEEEcCcccceeEee
Q 035653 28 QCPFCGHGTSVECRIDK-KIQ--I-GEAFCWNCLERFCTQ 63 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk-~~~--~-g~~~C~~C~~~~~~~ 63 (87)
.||+||++.+-.+.=.- ..| + -.-.|..||-+|.+-
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~ 41 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTF 41 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEe
Confidence 69999998743333221 121 2 237899999999774
No 21
>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=95.05 E-value=0.014 Score=38.70 Aligned_cols=45 Identities=24% Similarity=0.612 Sum_probs=29.9
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhh
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIY 74 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVY 74 (87)
-..+.|||||.. + |+ ...+|+-.|+.|+..|.--.-.++.|.-+.
T Consensus 33 ~~ky~Cp~Cgk~-~--vk---R~a~GIW~C~~C~~~~AGGAy~~~T~~~~t 77 (90)
T PF01780_consen 33 HAKYTCPFCGKT-S--VK---RVATGIWKCKKCGKKFAGGAYTPSTPAAKT 77 (90)
T ss_dssp HS-BEESSSSSS-E--EE---EEETTEEEETTTTEEEE-BSSSSS-HHHHH
T ss_pred hCCCcCCCCCCc-e--eE---EeeeEEeecCCCCCEEeCCCccccchHHHH
Confidence 357899999984 2 22 245788999999999987655555554443
No 22
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=94.91 E-value=0.029 Score=31.01 Aligned_cols=33 Identities=24% Similarity=0.382 Sum_probs=23.4
Q ss_pred ccCCCCCCCCeEEEEEec-cCcEEEEEcCcccceeE
Q 035653 27 FQCPFCGHGTSVECRIDK-KIQIGEAFCWNCLERFC 61 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk-~~~~g~~~C~~C~~~~~ 61 (87)
.+||.|+.. ..|.-++ ..+.+.+.|..|+..|.
T Consensus 3 i~CP~C~~~--f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTR--FRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCce--EEcCHHHcccCCcEEECCCCCcEee
Confidence 589999984 4443332 24567999999999874
No 23
>PF14353 CpXC: CpXC protein
Probab=94.76 E-value=0.036 Score=37.20 Aligned_cols=40 Identities=23% Similarity=0.422 Sum_probs=27.1
Q ss_pred ccCCCCCCCCeEEEEEec-------------cCcEEEEEcCcccceeEeecCC
Q 035653 27 FQCPFCGHGTSVECRIDK-------------KIQIGEAFCWNCLERFCTQIHA 66 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk-------------~~~~g~~~C~~C~~~~~~~i~~ 66 (87)
-+||.|||+..+++--.- ........|..||..+....+-
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 479999997655553211 1235689999999998665443
No 24
>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=94.67 E-value=0.095 Score=32.61 Aligned_cols=47 Identities=21% Similarity=0.485 Sum_probs=31.5
Q ss_pred ccCCCCCCCCeEEEEE------------eccC-cEEEEEcCcccce--eEeecCCCCchhhhh
Q 035653 27 FQCPFCGHGTSVECRI------------DKKI-QIGEAFCWNCLER--FCTQIHALTEPIDIY 74 (87)
Q Consensus 27 F~CPfC~~~~sV~v~i------------dk~~-~~g~~~C~~C~~~--~~~~i~~L~epiDVY 74 (87)
+.||.||++. .+..- |-.. .--.++|.+||-+ |..+.+.+.+-+|.+
T Consensus 1 y~C~KCg~~~-~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYTE~Y~~~~~~~~~i~D~~ 62 (64)
T PF09855_consen 1 YKCPKCGNEE-YESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYTEFYKAKTSNGSNILDFF 62 (64)
T ss_pred CCCCCCCCcc-eecceEEccCCeeEEEEEecCcEEEEEECCCCCCEEEEeecCcccchhhhhh
Confidence 5799999964 32221 2111 1335899999954 787888888888865
No 25
>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=94.29 E-value=0.028 Score=31.60 Aligned_cols=29 Identities=34% Similarity=0.671 Sum_probs=25.3
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
.||.|+-..... ++.+++.|...|+.|+.
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 699999988887 67788899999999975
No 26
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=94.21 E-value=0.016 Score=32.04 Aligned_cols=34 Identities=18% Similarity=0.310 Sum_probs=22.3
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCccccee
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERF 60 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~ 60 (87)
.++||.|+..-.|.=+.- ....+.+.|..||..|
T Consensus 2 ~i~Cp~C~~~y~i~d~~i-p~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKI-PPKGRKVRCSKCGHVF 35 (36)
T ss_pred EEECCCCCCEEeCCHHHC-CCCCcEEECCCCCCEe
Confidence 368999998533322211 1345689999999876
No 27
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=94.14 E-value=0.065 Score=34.08 Aligned_cols=44 Identities=25% Similarity=0.443 Sum_probs=26.9
Q ss_pred ccCCCCCCCCeEEEEEec-cC--cEEEEEcC--cccceeEee---cCCCCchh
Q 035653 27 FQCPFCGHGTSVECRIDK-KI--QIGEAFCW--NCLERFCTQ---IHALTEPI 71 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk-~~--~~g~~~C~--~C~~~~~~~---i~~L~epi 71 (87)
|.||+||+.. ...+=.. .. ..-.-.|. .||.+|.+. .+.|+.|.
T Consensus 2 m~CP~Cg~~a-~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~es~s~tis~p~ 53 (72)
T PRK09678 2 FHCPLCQHAA-HARTSRYITDTTKERYHQCQNVNCSATFITYESVQRYIVKPG 53 (72)
T ss_pred ccCCCCCCcc-EEEEChhcChhhheeeeecCCCCCCCEEEEEEEEEEEEcCCC
Confidence 7899999954 2222111 11 23456788 999999775 33555553
No 28
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=92.98 E-value=0.12 Score=28.29 Aligned_cols=31 Identities=23% Similarity=0.353 Sum_probs=22.7
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
.-.|+.|||+.-+. ...+...|..||..|++
T Consensus 3 ~~~C~~C~~~~i~~------~~~~~~~C~~Cg~~~~~ 33 (33)
T PF08792_consen 3 LKKCSKCGGNGIVN------KEDDYEVCIFCGSSFPY 33 (33)
T ss_pred ceEcCCCCCCeEEE------ecCCeEEcccCCcEeeC
Confidence 34699999975221 33478899999999874
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=92.93 E-value=0.086 Score=30.08 Aligned_cols=32 Identities=28% Similarity=0.671 Sum_probs=21.7
Q ss_pred CCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 22 KLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 22 kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
.-+.-|.||+||+.+ ...| ...+.-.|..|+.
T Consensus 14 RW~~g~~CP~Cg~~~--~~~~---~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 14 RWPDGFVCPHCGSTK--HYRL---KTRGRYRCKACRK 45 (46)
T ss_pred cCCCCCCCCCCCCee--eEEe---CCCCeEECCCCCC
Confidence 345669999999952 2222 2267889999974
No 30
>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=92.74 E-value=0.2 Score=33.18 Aligned_cols=36 Identities=11% Similarity=0.295 Sum_probs=24.6
Q ss_pred cCCCCCCC----CeEEEEEeccCc--------EEEEEcCcccceeEee
Q 035653 28 QCPFCGHG----TSVECRIDKKIQ--------IGEAFCWNCLERFCTQ 63 (87)
Q Consensus 28 ~CPfC~~~----~sV~v~idk~~~--------~g~~~C~~C~~~~~~~ 63 (87)
.|+.|+++ ..+++..+..+| +--+.|..||+.|.+.
T Consensus 1 ~C~~C~~~~~~~~~tTv~~el~~G~~~IvIknVPa~~C~~CGe~y~~d 48 (89)
T TIGR03829 1 KCRWCEEEKAIARTTTVYWELPDGTKAIEIKETPSISCSHCGMEYQDD 48 (89)
T ss_pred CCcccCCCceecceEEEEEEecCCceEEEEecCCcccccCCCcEeecH
Confidence 49999763 345555556443 3457999999998763
No 31
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=92.68 E-value=0.11 Score=34.51 Aligned_cols=32 Identities=31% Similarity=0.798 Sum_probs=25.0
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
....||+|+.. .|+ ..+.|+-.|+.||..|.-
T Consensus 34 ~~~~Cp~C~~~---~Vk---R~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGRT---TVK---RIATGIWKCRKCGAKFAG 65 (89)
T ss_pred cCCcCCCCCCc---cee---eeccCeEEcCCCCCeecc
Confidence 46899999985 333 356789999999999854
No 32
>PHA00626 hypothetical protein
Probab=92.48 E-value=0.16 Score=31.37 Aligned_cols=34 Identities=21% Similarity=0.467 Sum_probs=24.2
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
.||.||+.+-+-+.+-++ ....-.|..||..|+-
T Consensus 2 ~CP~CGS~~Ivrcg~cr~-~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRG-WSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCceeeeeceecc-cCcceEcCCCCCeech
Confidence 599999976665555433 1355689999988864
No 33
>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=92.35 E-value=0.076 Score=28.80 Aligned_cols=31 Identities=29% Similarity=0.457 Sum_probs=21.5
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
.|.||.||+.-.+...+ .. ...+.|..||..
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 34
>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=92.14 E-value=0.31 Score=26.69 Aligned_cols=28 Identities=29% Similarity=0.547 Sum_probs=20.6
Q ss_pred CCCCCCCCeEEEEEeccCcEEEEEcCcccceeE
Q 035653 29 CPFCGHGTSVECRIDKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 29 CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~ 61 (87)
||.||+ -+.++=++...+ .|+.|+-.++
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 999997 466666666655 9999997654
No 35
>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=91.75 E-value=0.32 Score=36.91 Aligned_cols=49 Identities=16% Similarity=0.303 Sum_probs=27.1
Q ss_pred cccCCCCCCCCeEEEEEe---ccCcEEEEEcCcccceeEeecCCCCchhhhh
Q 035653 26 QFQCPFCGHGTSVECRID---KKIQIGEAFCWNCLERFCTQIHALTEPIDIY 74 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~id---k~~~~g~~~C~~C~~~~~~~i~~L~epiDVY 74 (87)
...||+||+++......- -..+.-.-.|..|+...-+--...+..+|.+
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 457999999988877764 3445777899999987665445666666655
No 36
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=91.67 E-value=0.087 Score=32.59 Aligned_cols=34 Identities=26% Similarity=0.474 Sum_probs=21.2
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
-..|.||.||.+--..|.-=++.+. .-.|..||.
T Consensus 23 ~~~F~CPnCG~~~I~RC~~CRk~~~-~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEVIIYRCEKCRKQSN-PYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCeeEeechhHHhcCC-ceECCCCCC
Confidence 3789999999843333333333333 347888885
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=91.14 E-value=0.4 Score=27.54 Aligned_cols=36 Identities=22% Similarity=0.477 Sum_probs=22.5
Q ss_pred cCCCCCCCCeEEEEEeccC--cEEEEEcCc--ccceeEee
Q 035653 28 QCPFCGHGTSVECRIDKKI--QIGEAFCWN--CLERFCTQ 63 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~--~~g~~~C~~--C~~~~~~~ 63 (87)
.||+||+.-.+.-.-.... ......|.+ ||.+|.+.
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 4999999543322222222 245678888 99999775
No 38
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=91.13 E-value=0.1 Score=29.44 Aligned_cols=30 Identities=27% Similarity=0.478 Sum_probs=23.3
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
.|.|+-|||.-.+...| .+ ...+.|..||.
T Consensus 5 ey~C~~Cg~~fe~~~~~--~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSI--SE-DDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEc--CC-CCCCcCCCCCC
Confidence 59999999965555555 44 67889999998
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=90.96 E-value=0.2 Score=38.74 Aligned_cols=57 Identities=21% Similarity=0.520 Sum_probs=24.2
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecC--CCCchh--hhhhhhHHHHHHh
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIH--ALTEPI--DIYAEWIDECERA 84 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~--~L~epi--DVYs~wiD~~e~~ 84 (87)
.+-||.||+..-- .+.-..-+|-..|..|++.||.+-. .|+.-| -.|+--|+.+...
T Consensus 31 n~yCP~Cg~~~L~--~f~NN~PVaDF~C~~C~eeyELKSk~~~l~~~I~dGAY~Tmi~Ri~s~ 91 (254)
T PF06044_consen 31 NMYCPNCGSKPLS--KFENNRPVADFYCPNCNEEYELKSKKKKLSNKINDGAYHTMIERITSD 91 (254)
T ss_dssp H---TTT--SS-E--E--------EEE-TTT--EEEEEEEESS--SEEEEEEHHHHHHHHHTT
T ss_pred CCcCCCCCChhHh--hccCCCccceeECCCCchHHhhhhhccccCCcccCccHHHHHHHhhcc
Confidence 4679999996422 3344566899999999999998632 232222 2466666655544
No 40
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=90.81 E-value=0.08 Score=26.69 Aligned_cols=21 Identities=38% Similarity=0.830 Sum_probs=13.3
Q ss_pred CCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 29 CPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 29 CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
||.||++..- +...|..||..
T Consensus 2 Cp~CG~~~~~----------~~~fC~~CG~~ 22 (23)
T PF13240_consen 2 CPNCGAEIED----------DAKFCPNCGTP 22 (23)
T ss_pred CcccCCCCCC----------cCcchhhhCCc
Confidence 8999985322 22348888863
No 41
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=90.80 E-value=0.19 Score=30.60 Aligned_cols=44 Identities=20% Similarity=0.350 Sum_probs=34.5
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhhhhhHHHH
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIYAEWIDEC 81 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVYs~wiD~~ 81 (87)
.-.||.||. .+. ...|.+||.......++-..|.|-|++.-=++
T Consensus 5 mr~C~~Cgv---YTL---------k~~CP~CG~~t~~~~P~rfSp~D~y~~yR~~~ 48 (56)
T PRK13130 5 IRKCPKCGV---YTL---------KEICPVCGGKTKNPHPPRFSPEDKYGKYRRAL 48 (56)
T ss_pred ceECCCCCC---EEc---------cccCcCCCCCCCCCCCCCCCCCCccHHHHHHH
Confidence 346888886 333 33899999999999999999999999865433
No 42
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=90.79 E-value=0.14 Score=30.19 Aligned_cols=26 Identities=27% Similarity=0.552 Sum_probs=18.1
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCccccee
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERF 60 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~ 60 (87)
-||.||++ +-. ... +...|+.||.++
T Consensus 22 fCP~Cg~~--~m~--~~~---~r~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSG--FMA--EHL---DRWHCGKCGYTE 47 (50)
T ss_pred cCcCCCcc--hhe--ccC---CcEECCCcCCEE
Confidence 79999984 211 111 678999999765
No 43
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=90.61 E-value=0.48 Score=26.30 Aligned_cols=27 Identities=26% Similarity=0.588 Sum_probs=20.2
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
+||.|++ .-....+ .++..-.|..||=
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 5999998 4455555 5678888999984
No 44
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=90.58 E-value=0.46 Score=35.00 Aligned_cols=44 Identities=18% Similarity=0.394 Sum_probs=27.4
Q ss_pred CccccCCCCCCCCeEEEEEeccCc---------------------EEEEEcCcccceeEee-cCCCCc
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQ---------------------IGEAFCWNCLERFCTQ-IHALTE 69 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~---------------------~g~~~C~~C~~~~~~~-i~~L~e 69 (87)
++..+||+|+++ ...+.-+... --...|..||-.+... .+.|++
T Consensus 3 ~k~~~CPvC~~~--F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~F~~l~~ 68 (214)
T PF09986_consen 3 DKKITCPVCGKE--FKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEEDFEKLSP 68 (214)
T ss_pred CCceECCCCCCe--eeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccccccccCCH
Confidence 577899999985 3333222211 1358999999776443 555553
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=90.14 E-value=0.39 Score=36.44 Aligned_cols=36 Identities=17% Similarity=0.248 Sum_probs=18.5
Q ss_pred ccCCCCCCCCeEEEEEeccC-cEEEEEcCcccceeEe
Q 035653 27 FQCPFCGHGTSVECRIDKKI-QIGEAFCWNCLERFCT 62 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk~~-~~g~~~C~~C~~~~~~ 62 (87)
=.||.||..-++++-..... |.=.+.|..||..+.+
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~ 209 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRF 209 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE-
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeee
Confidence 48999999766666554332 6678999999987655
No 46
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=90.07 E-value=0.11 Score=32.33 Aligned_cols=34 Identities=26% Similarity=0.539 Sum_probs=21.5
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
-..|.||.||.+.-..+..=++.+ ..-.|..||.
T Consensus 25 ~v~F~CPnCGe~~I~Rc~~CRk~g-~~Y~Cp~CGF 58 (61)
T COG2888 25 AVKFPCPNCGEVEIYRCAKCRKLG-NPYRCPKCGF 58 (61)
T ss_pred eeEeeCCCCCceeeehhhhHHHcC-CceECCCcCc
Confidence 468999999974333333333333 3447888885
No 47
>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=89.99 E-value=0.78 Score=29.78 Aligned_cols=48 Identities=17% Similarity=0.370 Sum_probs=25.2
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhhhh-----hHHHHHHh
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIYAE-----WIDECERA 84 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVYs~-----wiD~~e~~ 84 (87)
...||||+. ++=+..|+.+.+ .-.|-.||... +.||.+.+ |.++++..
T Consensus 33 ~~~CPfH~d-~~pS~~i~~~k~--~~~Cf~Cg~~G--------d~i~~v~~~~~~~f~eAv~~l 85 (97)
T PF01807_consen 33 RCLCPFHDD-KTPSFSINPDKN--RFKCFGCGKGG--------DVIDFVMKYEGCSFKEAVKWL 85 (97)
T ss_dssp EE--SSS---SS--EEEETTTT--EEEETTT--EE---------HHHHHHHHHT--HHHHHHHH
T ss_pred EEECcCCCC-CCCceEEECCCC--eEEECCCCCCC--------cHHhHHHHHhCCCHHHHHHHH
Confidence 577999995 444555555543 67899999764 55666644 66666554
No 48
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=89.79 E-value=0.31 Score=26.77 Aligned_cols=29 Identities=31% Similarity=0.496 Sum_probs=17.5
Q ss_pred CCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 29 CPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 29 CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
||.||+. ++..|-..++.-...|..||.-
T Consensus 3 C~~CG~~--l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 3 CPQCGGP--LERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -TTT--B---EEE--TT-SS-EEEETTTTEE
T ss_pred cccccCh--hhhhcCCCCCccceECCCCCCE
Confidence 9999985 7887776777888999999964
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=89.36 E-value=1 Score=29.11 Aligned_cols=40 Identities=23% Similarity=0.411 Sum_probs=28.4
Q ss_pred CCCc-cccCCCCCCCCeEEEEEecc----CcEEEEEcCcccceeE
Q 035653 22 KLDT-QFQCPFCGHGTSVECRIDKK----IQIGEAFCWNCLERFC 61 (87)
Q Consensus 22 kl~~-~F~CPfC~~~~sV~v~idk~----~~~g~~~C~~C~~~~~ 61 (87)
.+|+ ...||.|||...+-..+... ...-.-.|-.||..+.
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 4444 79999999998887776432 1344678999997653
No 50
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=89.36 E-value=0.6 Score=29.60 Aligned_cols=45 Identities=24% Similarity=0.447 Sum_probs=28.0
Q ss_pred CccccCCCCCCCCeEEEEEecc-----------C-cEEEEEcCcccce--eEeecCCCC
Q 035653 24 DTQFQCPFCGHGTSVECRIDKK-----------I-QIGEAFCWNCLER--FCTQIHALT 68 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~-----------~-~~g~~~C~~C~~~--~~~~i~~L~ 68 (87)
...|+||-||..+-.+=+|.-. . .--.++|.+||-+ |+-++..+.
T Consensus 2 ~~~~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYtEfY~a~~st~~ 60 (68)
T COG3478 2 KNAFKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYTEFYSAKISTTG 60 (68)
T ss_pred CccccCCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCchhheeccccccc
Confidence 3467899999865544444322 2 2346899999954 565555443
No 51
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=88.57 E-value=0.69 Score=32.29 Aligned_cols=35 Identities=14% Similarity=0.178 Sum_probs=26.4
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeE
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~ 61 (87)
...=.||.|+.+.+.-+ ++..+-.+.|..||....
T Consensus 95 ~~yVlC~~C~sPdT~l~---k~~r~~~l~C~ACGa~~~ 129 (133)
T TIGR00311 95 RKYVICRECNRPDTRII---KEGRVSLLKCEACGAKAP 129 (133)
T ss_pred hheEECCCCCCCCcEEE---EeCCeEEEecccCCCCCc
Confidence 34557999999887644 346677899999998643
No 52
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=88.56 E-value=0.7 Score=32.43 Aligned_cols=34 Identities=24% Similarity=0.310 Sum_probs=26.3
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCccccee
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERF 60 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~ 60 (87)
...=.||.|+.+.+.-+ ++..+-.+.|..||...
T Consensus 100 ~~yVlC~~C~spdT~l~---k~~r~~~l~C~ACGa~~ 133 (138)
T PRK03988 100 KEYVICPECGSPDTKLI---KEGRIWVLKCEACGAET 133 (138)
T ss_pred HhcEECCCCCCCCcEEE---EcCCeEEEEcccCCCCC
Confidence 34557999999886554 35668899999999864
No 53
>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=88.31 E-value=1.2 Score=24.22 Aligned_cols=11 Identities=27% Similarity=0.630 Sum_probs=8.8
Q ss_pred EEcCcccceeE
Q 035653 51 AFCWNCLERFC 61 (87)
Q Consensus 51 ~~C~~C~~~~~ 61 (87)
..|..||+.|-
T Consensus 33 ~~C~~CGE~~~ 43 (46)
T TIGR03831 33 LVCPQCGEEYL 43 (46)
T ss_pred cccccCCCEee
Confidence 46999999874
No 54
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=88.20 E-value=0.57 Score=28.63 Aligned_cols=36 Identities=25% Similarity=0.567 Sum_probs=25.3
Q ss_pred ccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 27 FQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
--||.||+..-+.+.=|-...-.-+.|..|.++.-.
T Consensus 5 i~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI 40 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKNFPLYCPKCKQETLI 40 (55)
T ss_pred EECCCCCCccceeeecCceeccccccCCCCCceEEE
Confidence 359999987656665554445567899999987533
No 55
>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=88.10 E-value=0.24 Score=28.36 Aligned_cols=30 Identities=27% Similarity=0.495 Sum_probs=21.5
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
.|.|+.||+.-.+...++ + ...+.|..||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~--~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMS--D-DPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecC--C-CCCCCCCCCCC
Confidence 589999999644444443 2 35678999997
No 56
>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=87.81 E-value=0.23 Score=29.00 Aligned_cols=32 Identities=28% Similarity=0.820 Sum_probs=19.4
Q ss_pred cccCCCCCCCCeEEEE-E------eccCcEEEEEcCcccce
Q 035653 26 QFQCPFCGHGTSVECR-I------DKKIQIGEAFCWNCLER 59 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~-i------dk~~~~g~~~C~~C~~~ 59 (87)
.|.||||+.+ ++.. + .-......+.|.+|...
T Consensus 2 ~f~CP~C~~~--~~~~~L~~H~~~~H~~~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 2 SFTCPYCGKG--FSESSLVEHCEDEHRSESKNVVCPICSSR 40 (54)
T ss_pred CcCCCCCCCc--cCHHHHHHHHHhHCcCCCCCccCCCchhh
Confidence 5999999973 3221 1 00122346899999864
No 57
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=87.65 E-value=0.14 Score=35.54 Aligned_cols=40 Identities=18% Similarity=0.262 Sum_probs=24.8
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEee
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQ 63 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~ 63 (87)
...|.||.|+..=+..=-+...+..|...|..||..-...
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEED 136 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEc
Confidence 4689999999743221111111235679999999876554
No 58
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=87.62 E-value=0.32 Score=37.72 Aligned_cols=40 Identities=33% Similarity=0.571 Sum_probs=28.9
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhhhhhH
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIYAEWI 78 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVYs~wi 78 (87)
.||.||.. .+..+..-|.+.|..||+--+ +.+||-..+|-
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 69999974 333344479999999998543 34677777775
No 59
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=87.60 E-value=0.3 Score=32.45 Aligned_cols=32 Identities=31% Similarity=0.727 Sum_probs=24.2
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
..++|+|||... | +...+|+-.|+.|+..+.-
T Consensus 35 aky~CsfCGK~~-v-----KR~AvGiW~C~~C~kv~ag 66 (92)
T KOG0402|consen 35 AKYTCSFCGKKT-V-----KRKAVGIWKCGSCKKVVAG 66 (92)
T ss_pred hhhhhhhcchhh-h-----hhhceeEEecCCccceecc
Confidence 568999999842 2 3467899999999876543
No 60
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=87.48 E-value=0.3 Score=28.10 Aligned_cols=31 Identities=26% Similarity=0.466 Sum_probs=21.7
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEee
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQ 63 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~ 63 (87)
.|.|..||++ ++ ++ ..+.+.|..||-+--++
T Consensus 2 ~Y~C~~Cg~~--~~--~~---~~~~irC~~CG~rIlyK 32 (44)
T smart00659 2 IYICGECGRE--NE--IK---SKDVVRCRECGYRILYK 32 (44)
T ss_pred EEECCCCCCE--ee--cC---CCCceECCCCCceEEEE
Confidence 4789999985 33 33 34678999999774443
No 61
>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=87.37 E-value=1.6 Score=27.59 Aligned_cols=36 Identities=14% Similarity=0.169 Sum_probs=28.2
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecC
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIH 65 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~ 65 (87)
.||.|+.-+++.. -..+++-.+.|-.||...+.+-.
T Consensus 10 ~CP~C~~~D~i~~--~~e~~ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 10 VCPKCQAMDTIMM--WRENGVEYVECVECGYTERQPDQ 45 (71)
T ss_pred cCCCCcCccEEEE--EEeCCceEEEecCCCCeeccCCc
Confidence 6999999886555 44667999999999987665544
No 62
>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=87.27 E-value=1.3 Score=27.42 Aligned_cols=33 Identities=21% Similarity=0.314 Sum_probs=26.9
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
.||-|+.-+++.. -+.+++-.+.|-.||-.-+.
T Consensus 11 ~CP~C~~~Dtl~~--~~e~~~e~vECv~Cg~~~~~ 43 (59)
T TIGR02443 11 VCPACSAQDTLAM--WKENNIELVECVECGYQEQQ 43 (59)
T ss_pred cCCCCcCccEEEE--EEeCCceEEEeccCCCcccc
Confidence 6999999888754 46788899999999976544
No 63
>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]
Probab=87.06 E-value=0.25 Score=43.20 Aligned_cols=41 Identities=24% Similarity=0.552 Sum_probs=30.8
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEee-cCC
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQ-IHA 66 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~-i~~ 66 (87)
...|.|..|||+ +.+++++..----..|..|+.++++. |+.
T Consensus 262 ~afFrC~vC~~~--~~ve~drg~i~eP~~C~~C~~~~~~~Lihn 303 (804)
T KOG0478|consen 262 EAFFRCSVCGHE--IAVESDRGRIKEPMLCKECGTTNSFQLLHN 303 (804)
T ss_pred hHhhhhhhcCce--EEEEeecCccCCCcccccccCcccceeehh
Confidence 368999999995 77777755444457899999988776 443
No 64
>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=87.01 E-value=0.27 Score=25.54 Aligned_cols=24 Identities=33% Similarity=0.717 Sum_probs=15.2
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccceeE
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~ 61 (87)
+||.|+++- ..+...|..||-.|+
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 588888742 234447888887664
No 65
>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=86.91 E-value=1.1 Score=34.92 Aligned_cols=41 Identities=15% Similarity=0.302 Sum_probs=29.4
Q ss_pred CCCccccCCCCCCCCeEEEEEecc----CcEEEEEcCcccceeEe
Q 035653 22 KLDTQFQCPFCGHGTSVECRIDKK----IQIGEAFCWNCLERFCT 62 (87)
Q Consensus 22 kl~~~F~CPfC~~~~sV~v~idk~----~~~g~~~C~~C~~~~~~ 62 (87)
.....|.||.|+|.+.+-..+.-. ...-...|..||..+.+
T Consensus 254 ~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~f 298 (299)
T TIGR01385 254 AVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWKF 298 (299)
T ss_pred CCcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeeee
Confidence 345679999999988776665332 23556789999987653
No 66
>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=86.89 E-value=0.28 Score=27.93 Aligned_cols=29 Identities=31% Similarity=0.575 Sum_probs=17.2
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCccc
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCL 57 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~ 57 (87)
.||.|+-..-..|--|+ .+.|.-.|+.|+
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 69999998877765444 566899999994
No 67
>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=86.65 E-value=0.93 Score=31.24 Aligned_cols=33 Identities=21% Similarity=0.308 Sum_probs=25.1
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
.+.-.||.|+.+.+.-+ ++..+-.+.|..||..
T Consensus 91 ~~yVlC~~C~spdT~l~---k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 91 KEYVLCPECGSPDTELI---KEGRLIFLKCKACGAS 123 (125)
T ss_dssp CHHSSCTSTSSSSEEEE---EETTCCEEEETTTSCE
T ss_pred HHEEEcCCCCCCccEEE---EcCCEEEEEecccCCc
Confidence 34568999999875443 3377789999999985
No 68
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=86.40 E-value=0.62 Score=32.15 Aligned_cols=41 Identities=20% Similarity=0.432 Sum_probs=28.3
Q ss_pred ccCCCCCCCCeEEEEEec-cCcEEEEEcCcccceeEeec-CCCCc
Q 035653 27 FQCPFCGHGTSVECRIDK-KIQIGEAFCWNCLERFCTQI-HALTE 69 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk-~~~~g~~~C~~C~~~~~~~i-~~L~e 69 (87)
=.||+|++.. .+++-. ..+...-.|..|+-.|+-.. .++..
T Consensus 31 ~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~~~~~~~~~ 73 (129)
T COG3677 31 VNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTVETGSPLSK 73 (129)
T ss_pred CcCCCCCccc--eeeECCccccccccccCCcCcceeeeccCcccc
Confidence 4799999987 333322 23477889999999998763 33433
No 69
>PRK00420 hypothetical protein; Validated
Probab=86.02 E-value=0.58 Score=32.03 Aligned_cols=30 Identities=23% Similarity=0.445 Sum_probs=21.9
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
.-+||.||.+- .+ ...|.+.|.+||..+..
T Consensus 23 ~~~CP~Cg~pL------f~-lk~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 23 SKHCPVCGLPL------FE-LKDGEVVCPVHGKVYIV 52 (112)
T ss_pred cCCCCCCCCcc------ee-cCCCceECCCCCCeeee
Confidence 37899999852 22 14478999999997654
No 70
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=85.56 E-value=1.7 Score=27.46 Aligned_cols=30 Identities=20% Similarity=0.515 Sum_probs=22.3
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
.||-|+|+ ++.+... .-.+.|.+||..--.
T Consensus 21 kCpdC~N~---q~vFsha--st~V~C~~CG~~l~~ 50 (67)
T COG2051 21 KCPDCGNE---QVVFSHA--STVVTCLICGTTLAE 50 (67)
T ss_pred ECCCCCCE---EEEeccC--ceEEEecccccEEEe
Confidence 79999995 4556444 467899999986544
No 71
>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=85.48 E-value=0.42 Score=28.69 Aligned_cols=36 Identities=28% Similarity=0.427 Sum_probs=25.2
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecC
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIH 65 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~ 65 (87)
-|.=.||.||+... .........|..||..+.-.++
T Consensus 26 ~TSq~C~~CG~~~~------~~~~~r~~~C~~Cg~~~~rD~n 61 (69)
T PF07282_consen 26 YTSQTCPRCGHRNK------KRRSGRVFTCPNCGFEMDRDVN 61 (69)
T ss_pred CCccCccCcccccc------cccccceEEcCCCCCEECcHHH
Confidence 36678999999431 1345568899999988655443
No 72
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=85.17 E-value=0.38 Score=24.51 Aligned_cols=22 Identities=36% Similarity=0.824 Sum_probs=15.2
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
.||.||++. ..+...|..||..
T Consensus 4 ~Cp~Cg~~~----------~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 4 FCPNCGAEI----------DPDAKFCPNCGAK 25 (26)
T ss_pred CCcccCCcC----------CcccccChhhCCC
Confidence 599999842 2235588888864
No 73
>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=85.10 E-value=0.49 Score=24.36 Aligned_cols=12 Identities=42% Similarity=1.110 Sum_probs=10.0
Q ss_pred CCCccccCCCCC
Q 035653 22 KLDTQFQCPFCG 33 (87)
Q Consensus 22 kl~~~F~CPfC~ 33 (87)
..-..|.||.||
T Consensus 12 ~~~v~f~CPnCG 23 (24)
T PF07754_consen 12 EQAVPFPCPNCG 23 (24)
T ss_pred ccCceEeCCCCC
Confidence 446799999998
No 74
>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=85.02 E-value=0.36 Score=24.43 Aligned_cols=11 Identities=36% Similarity=1.576 Sum_probs=9.0
Q ss_pred CccccCCCCCC
Q 035653 24 DTQFQCPFCGH 34 (87)
Q Consensus 24 ~~~F~CPfC~~ 34 (87)
++.|.||.|+.
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 56799999985
No 75
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=84.95 E-value=0.81 Score=35.26 Aligned_cols=32 Identities=28% Similarity=0.571 Sum_probs=23.0
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
.-.||.||. . .+..| ..-|.+.|..||.-.+.
T Consensus 11 ~~~Cp~Cg~-~--~iv~d--~~~Ge~vC~~CG~Vl~e 42 (310)
T PRK00423 11 KLVCPECGS-D--KLIYD--YERGEIVCADCGLVIEE 42 (310)
T ss_pred CCcCcCCCC-C--CeeEE--CCCCeEeecccCCcccc
Confidence 347999996 3 33334 35799999999986554
No 76
>PRK05978 hypothetical protein; Provisional
Probab=84.78 E-value=0.38 Score=34.30 Aligned_cols=32 Identities=28% Similarity=0.574 Sum_probs=22.0
Q ss_pred ccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEee
Q 035653 27 FQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQ 63 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~ 63 (87)
=.||.||..+-.. .--.-.-.|.+||+.|+..
T Consensus 34 grCP~CG~G~LF~-----g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 34 GRCPACGEGKLFR-----AFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred CcCCCCCCCcccc-----cccccCCCccccCCccccC
Confidence 3699999865332 2223345899999998754
No 77
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=84.24 E-value=1.1 Score=30.29 Aligned_cols=33 Identities=24% Similarity=0.388 Sum_probs=24.6
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
+..=.||.|+.+.+. |.+++.+-.+.|..||..
T Consensus 78 ~~yVlC~~C~spdT~---l~k~~r~~~l~C~aCGa~ 110 (110)
T smart00653 78 KEYVLCPECGSPDTE---LIKENRLFFLKCEACGAR 110 (110)
T ss_pred HhcEECCCCCCCCcE---EEEeCCeEEEEccccCCC
Confidence 344579999998754 334477889999999973
No 78
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=83.99 E-value=0.96 Score=25.55 Aligned_cols=28 Identities=21% Similarity=0.392 Sum_probs=15.8
Q ss_pred CCCCCCCCeEEEEEeccCcEEEEEcCccccee
Q 035653 29 CPFCGHGTSVECRIDKKIQIGEAFCWNCLERF 60 (87)
Q Consensus 29 CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~ 60 (87)
||.||+- +..+- ........|..||..+
T Consensus 3 Cp~Cg~~--l~~~~--~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 3 CPKCGNM--LIPKE--GKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCc--ccccc--CCCCCEEECCcCCCeE
Confidence 8888872 32221 1112367888888554
No 79
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=83.74 E-value=1 Score=31.75 Aligned_cols=27 Identities=37% Similarity=0.631 Sum_probs=20.2
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCccccee
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERF 60 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~ 60 (87)
--+||-||.+- .+ ..|.+.|.+||-.+
T Consensus 28 ~~hCp~Cg~PL------F~--KdG~v~CPvC~~~~ 54 (131)
T COG1645 28 AKHCPKCGTPL------FR--KDGEVFCPVCGYRE 54 (131)
T ss_pred HhhCcccCCcc------ee--eCCeEECCCCCceE
Confidence 45899999852 33 45999999999544
No 80
>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=83.73 E-value=0.22 Score=35.06 Aligned_cols=36 Identities=28% Similarity=0.448 Sum_probs=25.9
Q ss_pred cccCCCCCCCCeEEEEEeccCc-EEEEEcCcccceeE
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQ-IGEAFCWNCLERFC 61 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~-~g~~~C~~C~~~~~ 61 (87)
.-.||+||..++-.+...-... .+...|..|.+-|+
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 4699999998877665543332 56788999987654
No 81
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=83.72 E-value=1.3 Score=30.30 Aligned_cols=24 Identities=25% Similarity=0.639 Sum_probs=18.4
Q ss_pred CCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 29 CPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 29 CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
||.||++ -.+-.+.|..|+...+-
T Consensus 1 CPvCg~~----------l~vt~l~C~~C~t~i~G 24 (113)
T PF09862_consen 1 CPVCGGE----------LVVTRLKCPSCGTEIEG 24 (113)
T ss_pred CCCCCCc----------eEEEEEEcCCCCCEEEe
Confidence 9999984 33467899999987543
No 82
>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=83.64 E-value=1 Score=37.56 Aligned_cols=36 Identities=25% Similarity=0.498 Sum_probs=26.8
Q ss_pred cccCCCCCCCCeEE---EEEec--cCcEEEEEcCcccceeE
Q 035653 26 QFQCPFCGHGTSVE---CRIDK--KIQIGEAFCWNCLERFC 61 (87)
Q Consensus 26 ~F~CPfC~~~~sV~---v~idk--~~~~g~~~C~~C~~~~~ 61 (87)
...||.|||.+.+. ++.+. ....+...|..||...+
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIE 240 (557)
T ss_pred EccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCC
Confidence 34799999998876 55543 24578999999997543
No 83
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=83.43 E-value=1.3 Score=26.81 Aligned_cols=27 Identities=26% Similarity=0.567 Sum_probs=21.7
Q ss_pred CCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 22 KLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 22 kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
.++....||.||+. ...+-.|..||..
T Consensus 23 ~~~~l~~C~~CG~~-----------~~~H~vC~~CG~Y 49 (57)
T PRK12286 23 KAPGLVECPNCGEP-----------KLPHRVCPSCGYY 49 (57)
T ss_pred cCCcceECCCCCCc-----------cCCeEECCCCCcC
Confidence 56889999999983 2358899999964
No 84
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=82.97 E-value=1 Score=35.54 Aligned_cols=38 Identities=18% Similarity=0.423 Sum_probs=25.0
Q ss_pred CccccCCCCCCCCeEEE-EEeccCcEEEEEcCcccceeE
Q 035653 24 DTQFQCPFCGHGTSVEC-RIDKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v-~idk~~~~g~~~C~~C~~~~~ 61 (87)
+..=.||.||..-.+++ .+.-..|.-+++|..|+..+.
T Consensus 185 ~~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~ 223 (309)
T PRK03564 185 EQRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWH 223 (309)
T ss_pred cCCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCccc
Confidence 45678999999765553 333345666777777776543
No 85
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=82.82 E-value=2.2 Score=33.64 Aligned_cols=56 Identities=14% Similarity=0.311 Sum_probs=34.4
Q ss_pred cccCCCCCCCCeEEEE-Eecc-CcEEEEEcCcccceeEee---cCCCCchh--hhhhhhHHHH
Q 035653 26 QFQCPFCGHGTSVECR-IDKK-IQIGEAFCWNCLERFCTQ---IHALTEPI--DIYAEWIDEC 81 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~-idk~-~~~g~~~C~~C~~~~~~~---i~~L~epi--DVYs~wiD~~ 81 (87)
.-.||+||+.+.+..- ++-. ..+-.-.|..|+...-+- .++..+|+ |+-+--+|..
T Consensus 226 R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~~~~~~d~~~~p~adDlatL~LDl~ 288 (309)
T PRK03564 226 RVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYLKILYQEKDPKVEAVADDLASLVLDAR 288 (309)
T ss_pred CccCCCCCCCCceeeeeecCCCcceEeeecccccccceecccccCCCCCcchhHHhhhHhHHH
Confidence 3479999987766643 4433 245557999999875553 23333444 5556566654
No 86
>PHA02998 RNA polymerase subunit; Provisional
Probab=82.71 E-value=2.5 Score=31.57 Aligned_cols=38 Identities=18% Similarity=0.427 Sum_probs=28.8
Q ss_pred ccccCCCCCCCCeEEEEEecc--C--cEEEEEcCcccceeEe
Q 035653 25 TQFQCPFCGHGTSVECRIDKK--I--QIGEAFCWNCLERFCT 62 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~--~--~~g~~~C~~C~~~~~~ 62 (87)
+.-.||.|+|.++.-..+.-. + ..-...|..||-.|.-
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 567899999999886666442 2 3667899999988754
No 87
>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=82.68 E-value=1.9 Score=33.94 Aligned_cols=37 Identities=14% Similarity=0.416 Sum_probs=22.9
Q ss_pred cccCCCCCCCCeEE-EEEec---cCcEEEEEcCcccceeEe
Q 035653 26 QFQCPFCGHGTSVE-CRIDK---KIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 26 ~F~CPfC~~~~sV~-v~idk---~~~~g~~~C~~C~~~~~~ 62 (87)
.-.||+||+.+.+. ..++- ..++-.-.|..|+...-+
T Consensus 224 R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~ 264 (305)
T TIGR01562 224 RVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYLKI 264 (305)
T ss_pred CccCCCCCCCCceeeEeecCCCCCcceEEeeccccccchhh
Confidence 34799999877664 33433 123444589999976443
No 88
>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=82.60 E-value=2 Score=26.95 Aligned_cols=35 Identities=23% Similarity=0.435 Sum_probs=23.1
Q ss_pred cccCCCCCCCCeEEEEEecc---CcEEEEEcCcccceeEe
Q 035653 26 QFQCPFCGHGTSVECRIDKK---IQIGEAFCWNCLERFCT 62 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~---~~~g~~~C~~C~~~~~~ 62 (87)
.|+|..|++.. . =.|.+. .|+-.+.|..|+..+-.
T Consensus 4 ~FTC~~C~~Rs-~-~~~sk~aY~~GvViv~C~gC~~~HlI 41 (66)
T PF05180_consen 4 TFTCNKCGTRS-A-KMFSKQAYHKGVVIVQCPGCKNRHLI 41 (66)
T ss_dssp EEEETTTTEEE-E-EEEEHHHHHTSEEEEE-TTS--EEES
T ss_pred EEEcCCCCCcc-c-eeeCHHHHhCCeEEEECCCCcceeee
Confidence 69999999843 2 233443 78999999999987643
No 89
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=82.56 E-value=1.7 Score=32.59 Aligned_cols=38 Identities=24% Similarity=0.601 Sum_probs=25.8
Q ss_pred CCCccccCCCCCCCCeEEEEEecc-------CcEEEEEcCcccceeE
Q 035653 22 KLDTQFQCPFCGHGTSVECRIDKK-------IQIGEAFCWNCLERFC 61 (87)
Q Consensus 22 kl~~~F~CPfC~~~~sV~v~idk~-------~~~g~~~C~~C~~~~~ 61 (87)
-..+.-+||.||+ .+...+... -.+-...|..||-++.
T Consensus 10 ~~~~~~~CPvCg~--~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 10 EFETRIDCPVCGG--TLKAHMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred eeeeeecCCcccc--eeeEEEeeecCCccceEEEEEEEccccCCccc
Confidence 3456779999999 343333222 2367899999998764
No 90
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=82.08 E-value=0.83 Score=33.17 Aligned_cols=34 Identities=26% Similarity=0.389 Sum_probs=25.3
Q ss_pred CCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCC
Q 035653 22 KLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHA 66 (87)
Q Consensus 22 kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~ 66 (87)
+-.|.=.||.||+ .......|..||..+.-.+|+
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 4456678999999 335778999999887665554
No 91
>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=82.05 E-value=1.5 Score=24.32 Aligned_cols=30 Identities=23% Similarity=0.472 Sum_probs=17.1
Q ss_pred ccCCCCCCCCeEEEEEec-cCcEEEEEcCccc
Q 035653 27 FQCPFCGHGTSVECRIDK-KIQIGEAFCWNCL 57 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk-~~~~g~~~C~~C~ 57 (87)
-.||+|+...+|. +--+ ..|.-.-.|..|.
T Consensus 6 v~CP~C~s~~~v~-k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 6 VHCPRCQSTEGVK-KNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeCCCCCCCCcce-eCCCCCCCCEeEecCcCC
Confidence 4799999865332 1111 2344556777773
No 92
>PHA02540 61 DNA primase; Provisional
Probab=81.81 E-value=1.6 Score=34.74 Aligned_cols=42 Identities=24% Similarity=0.378 Sum_probs=28.7
Q ss_pred ccccCCCCCCCC------eEEEEEeccCcEEEEEcCcccce-----eEeecCCCC
Q 035653 25 TQFQCPFCGHGT------SVECRIDKKIQIGEAFCWNCLER-----FCTQIHALT 68 (87)
Q Consensus 25 ~~F~CPfC~~~~------sV~v~idk~~~~g~~~C~~C~~~-----~~~~i~~L~ 68 (87)
=.|.|||||..+ |..|.=+ .+...-+|-.||.. |-++...|+
T Consensus 26 ~~~~CPf~~ds~~~~~kpsF~V~p~--k~~~~yhCFgCGa~Gd~i~Flme~e~ls 78 (337)
T PHA02540 26 YNFRCPICGDSQKDKNKARGWIYEK--KDGGVFKCHNCGYHRPFGNFLKDYEPDL 78 (337)
T ss_pred EEecCCCCCCccccCcCCcEEEecc--CCceEEEecCCCCCCCHHHHHHHhcCCC
Confidence 579999999743 4665443 33568899999986 445555553
No 93
>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=81.71 E-value=2.8 Score=29.81 Aligned_cols=34 Identities=21% Similarity=0.409 Sum_probs=18.4
Q ss_pred cCCCCCCCCeEEEEEec-----cCcEEEEEcCcccceeE
Q 035653 28 QCPFCGHGTSVECRIDK-----KIQIGEAFCWNCLERFC 61 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk-----~~~~g~~~C~~C~~~~~ 61 (87)
.||.||+.....+.+.. .--+-...|..||.++.
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 59999986544333221 23466789999997763
No 94
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=81.61 E-value=0.52 Score=35.36 Aligned_cols=34 Identities=24% Similarity=0.398 Sum_probs=23.1
Q ss_pred cccCCCCCCCCeEEEEEecc-CcEEEEEcCccccee
Q 035653 26 QFQCPFCGHGTSVECRIDKK-IQIGEAFCWNCLERF 60 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~-~~~g~~~C~~C~~~~ 60 (87)
...||-|+.+. |.=++-+. ..-..+.|..||.-+
T Consensus 6 y~~Cp~Cg~ee-v~hEVik~~g~~~lvrC~eCG~V~ 40 (201)
T COG1326 6 YIECPSCGSEE-VSHEVIKERGREPLVRCEECGTVH 40 (201)
T ss_pred EEECCCCCcch-hhHHHHHhcCCceEEEccCCCcEe
Confidence 46899999543 42133333 445789999999988
No 95
>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=80.95 E-value=0.35 Score=29.48 Aligned_cols=18 Identities=28% Similarity=0.514 Sum_probs=14.2
Q ss_pred cCcEEEEEcCcccceeEe
Q 035653 45 KIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 45 ~~~~g~~~C~~C~~~~~~ 62 (87)
.-.-|.+.|..||..|-.
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 444589999999998853
No 96
>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=80.90 E-value=1.6 Score=35.95 Aligned_cols=48 Identities=21% Similarity=0.309 Sum_probs=31.3
Q ss_pred ccccCCCCCCCCeEEEEEecc------------CcEEEEEcCcccceeEeecCC-CCchhhhhh
Q 035653 25 TQFQCPFCGHGTSVECRIDKK------------IQIGEAFCWNCLERFCTQIHA-LTEPIDIYA 75 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~------------~~~g~~~C~~C~~~~~~~i~~-L~epiDVYs 75 (87)
.-|+||.|.+. +++..... .+...+.|.-|.=++. .|.- .+.|=+++.
T Consensus 51 ~Cf~CP~C~~~--L~~~~~~~~~~~~~~~~~~~~~~~~l~C~~C~Wss~-~igi~Fdkpt~l~~ 111 (483)
T PF05502_consen 51 NCFDCPICFSP--LSVRASDTPPSPPDPSSDSGGKPYYLSCSYCRWSSR-DIGIKFDKPTGLRA 111 (483)
T ss_pred ccccCCCCCCc--ceeEecccccccccccccCCCCCEEEECCCceeecc-ccCccccCchhHHH
Confidence 57999999985 55554332 4577899999986532 3433 255555554
No 97
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=80.31 E-value=1.8 Score=31.79 Aligned_cols=36 Identities=19% Similarity=0.207 Sum_probs=27.1
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
...=.||.|+.+.+--+ ++..+-.+.|..||.....
T Consensus 96 ~~yV~C~~C~~pdT~l~---k~~~~~~l~C~aCGa~~~v 131 (201)
T PRK12336 96 DEYVICSECGLPDTRLV---KEDRVLMLRCDACGAHRPV 131 (201)
T ss_pred HheEECCCCCCCCcEEE---EcCCeEEEEcccCCCCccc
Confidence 34557999999875443 4467888999999987644
No 98
>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=79.58 E-value=0.93 Score=26.51 Aligned_cols=18 Identities=39% Similarity=0.911 Sum_probs=12.1
Q ss_pred CCCCCccccCCCCCCCCe
Q 035653 20 MEKLDTQFQCPFCGHGTS 37 (87)
Q Consensus 20 ~~kl~~~F~CPfC~~~~s 37 (87)
-..||..|.||.|++.++
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 457899999999998753
No 99
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=79.45 E-value=3.4 Score=25.61 Aligned_cols=41 Identities=24% Similarity=0.438 Sum_probs=28.9
Q ss_pred CCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEee--cCCCC
Q 035653 22 KLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQ--IHALT 68 (87)
Q Consensus 22 kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~--i~~L~ 68 (87)
+|=-.--||.|.+. ...+... ..+.|..|++.|-.. |+-|-
T Consensus 4 ~LLeiLaCP~~kg~----L~~~~~~--~~L~c~~~~~aYpI~dGIPvlL 46 (60)
T COG2835 4 RLLEILACPVCKGP----LVYDEEK--QELICPRCKLAYPIRDGIPVLL 46 (60)
T ss_pred hhheeeeccCcCCc----ceEeccC--CEEEecccCceeecccCccccC
Confidence 34456789999996 3334433 499999999999664 66653
No 100
>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=79.10 E-value=1.1 Score=35.22 Aligned_cols=36 Identities=17% Similarity=0.348 Sum_probs=23.0
Q ss_pred cccCCCCCCCCeEEEEEec--cCcEEEEEcCcccceeE
Q 035653 26 QFQCPFCGHGTSVECRIDK--KIQIGEAFCWNCLERFC 61 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk--~~~~g~~~C~~C~~~~~ 61 (87)
.=.||.||..-.+++-... ..|.-+++|..|+..+.
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~ 221 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWH 221 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCccc
Confidence 4489999997655543332 45666777777766543
No 101
>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=79.09 E-value=2.5 Score=30.41 Aligned_cols=31 Identities=29% Similarity=0.613 Sum_probs=17.8
Q ss_pred CCCCCCCCeEEEEEe-------ccCcEEEEEcCccccee
Q 035653 29 CPFCGHGTSVECRID-------KKIQIGEAFCWNCLERF 60 (87)
Q Consensus 29 CPfC~~~~sV~v~id-------k~~~~g~~~C~~C~~~~ 60 (87)
||.||++ ++...+. +.--+-...|..||.++
T Consensus 1 CP~Cg~~-~~~~~~~~~~IP~F~evii~sf~C~~CGyr~ 38 (163)
T TIGR00340 1 CPVCGSR-TLKAVTYDYDIPYFGKIMLSTYICEKCGYRS 38 (163)
T ss_pred CCCCCCc-ceEeeeEeccCCCcceEEEEEEECCCCCCch
Confidence 7888874 3333321 12234567788888765
No 102
>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=79.05 E-value=0.96 Score=26.73 Aligned_cols=18 Identities=39% Similarity=1.031 Sum_probs=14.7
Q ss_pred CCCCCccccCCCCCCCCe
Q 035653 20 MEKLDTQFQCPFCGHGTS 37 (87)
Q Consensus 20 ~~kl~~~F~CPfC~~~~s 37 (87)
-..||-.|.||.|+..++
T Consensus 28 f~~Lp~~w~CP~C~a~K~ 45 (50)
T cd00730 28 FEDLPDDWVCPVCGAGKD 45 (50)
T ss_pred HhHCCCCCCCCCCCCcHH
Confidence 346899999999998764
No 103
>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=78.12 E-value=0.9 Score=21.00 Aligned_cols=8 Identities=75% Similarity=2.016 Sum_probs=3.5
Q ss_pred ccCCCCCC
Q 035653 27 FQCPFCGH 34 (87)
Q Consensus 27 F~CPfC~~ 34 (87)
|.||+|+.
T Consensus 1 ~~C~~C~~ 8 (24)
T PF13894_consen 1 FQCPICGK 8 (24)
T ss_dssp EE-SSTS-
T ss_pred CCCcCCCC
Confidence 45666654
No 104
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=77.32 E-value=5.6 Score=26.85 Aligned_cols=41 Identities=22% Similarity=0.418 Sum_probs=25.9
Q ss_pred CCCCc-cccCCCCCCCCeEEEEEecc----CcEEEEEcCcccceeE
Q 035653 21 EKLDT-QFQCPFCGHGTSVECRIDKK----IQIGEAFCWNCLERFC 61 (87)
Q Consensus 21 ~kl~~-~F~CPfC~~~~sV~v~idk~----~~~g~~~C~~C~~~~~ 61 (87)
..+++ .|.||-|||....---+... ...-.-.|-.||-.+.
T Consensus 66 ~~~~~~~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 66 KTLPTAKEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred cccccccccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEee
Confidence 34555 49999999966444433221 1234578999997764
No 105
>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=76.84 E-value=0.76 Score=25.57 Aligned_cols=14 Identities=29% Similarity=0.923 Sum_probs=9.0
Q ss_pred ccccCCCCCCCCeE
Q 035653 25 TQFQCPFCGHGTSV 38 (87)
Q Consensus 25 ~~F~CPfC~~~~sV 38 (87)
+.+.|+||++.+.|
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 57999999996644
No 106
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=76.81 E-value=4.5 Score=29.73 Aligned_cols=33 Identities=21% Similarity=0.460 Sum_probs=19.5
Q ss_pred cCCCCCCCCeEEEEEec------cCcEEEEEcCccccee
Q 035653 28 QCPFCGHGTSVECRIDK------KIQIGEAFCWNCLERF 60 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk------~~~~g~~~C~~C~~~~ 60 (87)
+||.||........+-. .--+-...|..||.++
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~ 40 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRS 40 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCcc
Confidence 58888875443333322 1234567888888765
No 107
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=76.20 E-value=4.1 Score=25.09 Aligned_cols=28 Identities=21% Similarity=0.558 Sum_probs=20.4
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCccccee
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERF 60 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~ 60 (87)
.||-|+++ .+.+++. .-.+.|.+||..-
T Consensus 13 kCp~C~n~---q~vFsha--~t~V~C~~Cg~~L 40 (59)
T PRK00415 13 KCPDCGNE---QVVFSHA--STVVRCLVCGKTL 40 (59)
T ss_pred ECCCCCCe---EEEEecC--CcEEECcccCCCc
Confidence 69999994 4555444 3678999999653
No 108
>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=76.13 E-value=3.5 Score=26.79 Aligned_cols=34 Identities=32% Similarity=0.581 Sum_probs=18.8
Q ss_pred CCCCCCCCeEEEEEe----ccC-----cEEEEEcCcccceeEe
Q 035653 29 CPFCGHGTSVECRID----KKI-----QIGEAFCWNCLERFCT 62 (87)
Q Consensus 29 CPfC~~~~sV~v~id----k~~-----~~g~~~C~~C~~~~~~ 62 (87)
||+|+....+....+ .+. .+....|..||+.|-+
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~~~ 43 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEELLD 43 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEEEc
Confidence 999996433322111 111 1234679999987644
No 109
>PRK11827 hypothetical protein; Provisional
Probab=74.74 E-value=2.3 Score=26.20 Aligned_cols=39 Identities=23% Similarity=0.308 Sum_probs=25.9
Q ss_pred CCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEee--cCCC
Q 035653 23 LDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQ--IHAL 67 (87)
Q Consensus 23 l~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~--i~~L 67 (87)
|-..--||.|..+ +. .+.. ...+.|..|+..|... |+-|
T Consensus 5 LLeILaCP~ckg~--L~--~~~~--~~~Lic~~~~laYPI~dgIPVl 45 (60)
T PRK11827 5 LLEIIACPVCNGK--LW--YNQE--KQELICKLDNLAFPLRDGIPVL 45 (60)
T ss_pred HHhheECCCCCCc--Ce--EcCC--CCeEECCccCeeccccCCcccc
Confidence 3345689999874 32 3332 3468899999999764 5543
No 110
>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=74.49 E-value=1.7 Score=29.38 Aligned_cols=36 Identities=25% Similarity=0.489 Sum_probs=25.7
Q ss_pred CCCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEee
Q 035653 21 EKLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQ 63 (87)
Q Consensus 21 ~kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~ 63 (87)
+-|=+-..||.||.. .-..+.--|.|..||..|...
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 456677889999973 223334567899999988765
No 111
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=73.82 E-value=6 Score=28.23 Aligned_cols=13 Identities=31% Similarity=0.230 Sum_probs=8.0
Q ss_pred EEEEEcCccccee
Q 035653 48 IGEAFCWNCLERF 60 (87)
Q Consensus 48 ~g~~~C~~C~~~~ 60 (87)
+-...|..||.++
T Consensus 27 i~sf~C~~CGyk~ 39 (160)
T smart00709 27 IMSFECEHCGYRN 39 (160)
T ss_pred EEEEECCCCCCcc
Confidence 4456677777654
No 112
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=73.71 E-value=3.1 Score=36.10 Aligned_cols=47 Identities=28% Similarity=0.384 Sum_probs=31.1
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcc---cceeEeecCCCCchhhh
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNC---LERFCTQIHALTEPIDI 73 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C---~~~~~~~i~~L~epiDV 73 (87)
-.|.|+.|||. +.+.++.....-...|..| +......++..++.+|.
T Consensus 128 ~~~~C~~Cg~~--~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~s~f~d~ 177 (682)
T COG1241 128 AVFECPKCGRE--VEVEQSEFRVEPPRECENCGKFGKGPLKLVPRKSEFIDF 177 (682)
T ss_pred EEEEcCCCCCE--EEEEeccccccCCccCCCccccCCCceEEecCcceeeec
Confidence 57999999995 6666655554456779999 22233445666776663
No 113
>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=73.44 E-value=1.1 Score=24.08 Aligned_cols=25 Identities=24% Similarity=0.567 Sum_probs=11.2
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
.||.|+.+.+. ..-..+.|..|+-.
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 58999987766 12245678888754
No 114
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.49 E-value=2.4 Score=33.93 Aligned_cols=30 Identities=30% Similarity=0.586 Sum_probs=23.7
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
--+||-|+|. |.+..|-.+++|+ ||..|..
T Consensus 306 wr~CpkC~~~------ie~~~GCnhm~Cr-C~~~fcy 335 (384)
T KOG1812|consen 306 WRQCPKCKFM------IELSEGCNHMTCR-CGHQFCY 335 (384)
T ss_pred cCcCccccee------eeecCCcceEEee-ccccchh
Confidence 5689999982 3678889999999 9976543
No 115
>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=72.41 E-value=1.6 Score=23.31 Aligned_cols=13 Identities=31% Similarity=0.974 Sum_probs=10.4
Q ss_pred ccccCCCCCCCCe
Q 035653 25 TQFQCPFCGHGTS 37 (87)
Q Consensus 25 ~~F~CPfC~~~~s 37 (87)
..+.||.||+.++
T Consensus 16 ~~~~CP~Cg~~~~ 28 (33)
T cd00350 16 APWVCPVCGAPKD 28 (33)
T ss_pred CCCcCcCCCCcHH
Confidence 5789999998653
No 116
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=72.38 E-value=4.1 Score=27.48 Aligned_cols=29 Identities=28% Similarity=0.492 Sum_probs=17.4
Q ss_pred CCCCCCCCeEEEEEeccCcEEEEEcCcccceeE
Q 035653 29 CPFCGHGTSVECRIDKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 29 CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~ 61 (87)
||-||. -+..+ ++...+.+.|+.||-.++
T Consensus 5 Cp~Cgs--ll~p~--~~~~~~~l~C~kCgye~~ 33 (113)
T COG1594 5 CPKCGS--LLYPK--KDDEGGKLVCRKCGYEEE 33 (113)
T ss_pred cCCccC--eeEEe--EcCCCcEEECCCCCcchh
Confidence 888886 23322 223334888999986544
No 117
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.27 E-value=2.3 Score=35.20 Aligned_cols=50 Identities=22% Similarity=0.455 Sum_probs=42.1
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhhhhhHHH
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIYAEWIDE 80 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVYs~wiD~ 80 (87)
..=+||-|.- .|.+.+|--.-+|..||..|..--..+..|.|.|.-|-|.
T Consensus 367 N~krCP~C~v------~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~~nPYkHF~e~ 416 (445)
T KOG1814|consen 367 NSKRCPKCKV------VIERSEGCNKMHCTKCGTYFCWICAELLYPENPYKHFSEP 416 (445)
T ss_pred cCCCCCcccc------eeecCCCccceeeccccccceeehhhhcCCCChhhhhcCC
Confidence 3457999974 4678888899999999999999989999999999887654
No 118
>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=72.13 E-value=2.2 Score=23.09 Aligned_cols=26 Identities=23% Similarity=0.455 Sum_probs=15.3
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
.+.|+.||+. . + ...+--.|.+||..
T Consensus 2 ~~~C~~CG~i---~---~--g~~~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYI---H---E--GEEAPEKCPICGAP 27 (34)
T ss_pred eEECCCCCCE---e---E--CCcCCCcCcCCCCc
Confidence 5778888872 1 1 11123388888863
No 119
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=71.37 E-value=3.7 Score=26.42 Aligned_cols=28 Identities=21% Similarity=0.570 Sum_probs=18.6
Q ss_pred ccCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 27 FQCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
|.||-||+. +|+.......-.|.+|+=.
T Consensus 2 ~~CPCCg~~-----Tl~~~~~~~ydIC~VC~WE 29 (78)
T PF14206_consen 2 YPCPCCGYY-----TLEERGEGTYDICPVCFWE 29 (78)
T ss_pred ccCCCCCcE-----EeccCCCcCceECCCCCcc
Confidence 789999982 2333333236789999844
No 120
>smart00400 ZnF_CHCC zinc finger.
Probab=71.33 E-value=4.9 Score=23.25 Aligned_cols=38 Identities=18% Similarity=0.394 Sum_probs=25.8
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhhhh
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIYAE 76 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVYs~ 76 (87)
.|||++- ++=+..|+.+. ....|..||+.. ..||.|.+
T Consensus 4 ~cPfh~d-~~pSf~v~~~k--n~~~Cf~cg~gG--------d~i~fv~~ 41 (55)
T smart00400 4 LCPFHGE-KTPSFSVSPDK--QFFHCFGCGAGG--------NVISFLMK 41 (55)
T ss_pred cCcCCCC-CCCCEEEECCC--CEEEEeCCCCCC--------CHHHHHHH
Confidence 4999984 55566665443 568999998643 56666665
No 121
>PLN00209 ribosomal protein S27; Provisional
Probab=71.05 E-value=10 Score=25.03 Aligned_cols=41 Identities=15% Similarity=0.349 Sum_probs=27.9
Q ss_pred ccCCCCCCccc---cCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 17 TKGMEKLDTQF---QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 17 kk~~~kl~~~F---~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
++-.+...+.| .||-|+++ .+.+... .-.+.|.+||.....
T Consensus 24 k~Lv~~PnS~Fm~VkCp~C~n~---q~VFShA--~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 24 KRLVQSPNSFFMDVKCQGCFNI---TTVFSHS--QTVVVCGSCQTVLCQ 67 (86)
T ss_pred eeeecCCCCEEEEEECCCCCCe---eEEEecC--ceEEEccccCCEeec
Confidence 34455556677 69999994 4555443 467899999976543
No 122
>PF15616 TerY-C: TerY-C metal binding domain
Probab=70.96 E-value=4.9 Score=28.18 Aligned_cols=36 Identities=25% Similarity=0.345 Sum_probs=23.3
Q ss_pred cCCCCCCCCeEEEE-Eec---cCcEEEEEcCcccceeEee
Q 035653 28 QCPFCGHGTSVECR-IDK---KIQIGEAFCWNCLERFCTQ 63 (87)
Q Consensus 28 ~CPfC~~~~sV~v~-idk---~~~~g~~~C~~C~~~~~~~ 63 (87)
.||.||+...+.+- =-+ =++-+.+.|.-||..-.+.
T Consensus 79 gCP~CGn~~~fa~C~CGkl~Ci~g~~~~~CPwCg~~g~~~ 118 (131)
T PF15616_consen 79 GCPHCGNQYAFAVCGCGKLFCIDGEGEVTCPWCGNEGSFG 118 (131)
T ss_pred CCCCCcChhcEEEecCCCEEEeCCCCCEECCCCCCeeeec
Confidence 69999997555443 100 1345678999999875543
No 123
>PF14122 YokU: YokU-like protein
Probab=70.74 E-value=4 Score=27.01 Aligned_cols=36 Identities=19% Similarity=0.433 Sum_probs=23.0
Q ss_pred cCCCCCCCCeEEEEEe----ccC--------cEEEEEcCcccceeEee
Q 035653 28 QCPFCGHGTSVECRID----KKI--------QIGEAFCWNCLERFCTQ 63 (87)
Q Consensus 28 ~CPfC~~~~sV~v~id----k~~--------~~g~~~C~~C~~~~~~~ 63 (87)
+|-.|+..+++...-. .-+ .+-.+.|..||..|+..
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~d 48 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQDD 48 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEehh
Confidence 4788887655543321 111 23468999999999764
No 124
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=70.26 E-value=10 Score=31.34 Aligned_cols=38 Identities=18% Similarity=0.274 Sum_probs=29.0
Q ss_pred cCCCCCCCCeEEE-EEeccCcEEEEEcCcccceeEeecCC
Q 035653 28 QCPFCGHGTSVEC-RIDKKIQIGEAFCWNCLERFCTQIHA 66 (87)
Q Consensus 28 ~CPfC~~~~sV~v-~idk~~~~g~~~C~~C~~~~~~~i~~ 66 (87)
-||.||...++.+ ..|-..+.-.-.|. ||-..+..|..
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 67766664455676 99988888764
No 125
>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=70.09 E-value=3 Score=25.12 Aligned_cols=43 Identities=16% Similarity=0.289 Sum_probs=26.7
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEee-cCCCCchh
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQ-IHALTEPI 71 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~-i~~L~epi 71 (87)
+.+.|+.||.- -.+. ..-....|.|..|+.-.... ..+..+|-
T Consensus 3 ~eiRC~~Cnkl---La~~-g~~~~leIKCpRC~tiN~~~a~~~~~~p~ 46 (51)
T PF10122_consen 3 KEIRCGHCNKL---LAKA-GEVIELEIKCPRCKTINHVRATSPEPEPL 46 (51)
T ss_pred cceeccchhHH---Hhhh-cCccEEEEECCCCCccceEeccCCCCCch
Confidence 46889999972 1110 01124688999999877665 45555553
No 126
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=69.90 E-value=1.2 Score=36.92 Aligned_cols=56 Identities=21% Similarity=0.341 Sum_probs=31.1
Q ss_pred CccccCCCCCCCC-eEEEEEeccCcEEEEEcCcccceeEeecCCC--CchhhhhhhhHH
Q 035653 24 DTQFQCPFCGHGT-SVECRIDKKIQIGEAFCWNCLERFCTQIHAL--TEPIDIYAEWID 79 (87)
Q Consensus 24 ~~~F~CPfC~~~~-sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L--~epiDVYs~wiD 79 (87)
..-|-||+|+..= ++.+---.....|...|.+||-.-...-+.+ -+-.+-++.+.+
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelveDe~~~~~~e~~~~l~~~~~ 184 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVEDENKLPSKESRTALNRLME 184 (436)
T ss_pred cccccCCccccchhhhHHHHhhcccCceEEEecCCCchhcccccCchHHHHHHHHHHHH
Confidence 4579999999841 1211111123468999999997654433322 233344554433
No 127
>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=69.63 E-value=4 Score=25.92 Aligned_cols=29 Identities=21% Similarity=0.565 Sum_probs=16.1
Q ss_pred ccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEee
Q 035653 27 FQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQ 63 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~ 63 (87)
..||-|+++ |+... +...|..|+..|...
T Consensus 2 ~~CP~C~~~------L~~~~--~~~~C~~C~~~~~~~ 30 (70)
T PF07191_consen 2 NTCPKCQQE------LEWQG--GHYHCEACQKDYKKE 30 (70)
T ss_dssp -B-SSS-SB------EEEET--TEEEETTT--EEEEE
T ss_pred CcCCCCCCc------cEEeC--CEEECccccccceec
Confidence 368999885 33333 677888888887654
No 128
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=69.51 E-value=11 Score=24.76 Aligned_cols=41 Identities=17% Similarity=0.489 Sum_probs=28.0
Q ss_pred ccCCCCCCccc---cCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 17 TKGMEKLDTQF---QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 17 kk~~~kl~~~F---~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
++-++...+.| .||-|+++ ++.+... .-.+.|.+||.....
T Consensus 23 k~Lv~~PnS~Fm~VkCp~C~n~---q~VFShA--~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 23 KRLVQGPNSYFMDVKCPGCSQI---TTVFSHA--QTVVLCGGCSSQLCQ 66 (85)
T ss_pred eeEecCCCCeEEEEECCCCCCe---eEEEecC--ceEEEccccCCEeec
Confidence 34455556677 69999994 4555444 467899999976543
No 129
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=69.17 E-value=7.7 Score=31.06 Aligned_cols=30 Identities=23% Similarity=0.358 Sum_probs=20.6
Q ss_pred cccCCCCCCCC-eEEEEEeccCcEEEEEcCcccce
Q 035653 26 QFQCPFCGHGT-SVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 26 ~F~CPfC~~~~-sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
..-||||+... |..|. .. .+.-.|-.||..
T Consensus 34 ~~~CPfh~ek~pSf~v~--~~--k~~~~Cf~Cg~~ 64 (415)
T TIGR01391 34 VGLCPFHHEKTPSFSVS--PE--KQFYHCFGCGAG 64 (415)
T ss_pred EeeCCCCCCCCCeEEEE--cC--CCcEEECCCCCC
Confidence 45799998643 45553 33 356899999985
No 130
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=69.16 E-value=1.4 Score=35.91 Aligned_cols=38 Identities=29% Similarity=0.392 Sum_probs=28.0
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeec
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQI 64 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i 64 (87)
+.-.||+|+++.+ .+.|.++..+ ...|..||.+..+..
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 4568999999864 5556554444 459999999887766
No 131
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=68.85 E-value=1.8 Score=31.53 Aligned_cols=32 Identities=16% Similarity=0.274 Sum_probs=20.6
Q ss_pred cccCCCCCCCCeEEEEEeccCcEE------------EEEcCccccee
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIG------------EAFCWNCLERF 60 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g------------~~~C~~C~~~~ 60 (87)
.=.||.||. .-+++.+..-.+ ...|.+||.-|
T Consensus 97 ~~RCp~CN~---~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 97 FSRCPECNG---ELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred cccCcccCC---EeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 346999997 344555544222 24599999876
No 132
>KOG1296 consensus Uncharacterized conserved protein [Function unknown]
Probab=68.41 E-value=4.5 Score=29.39 Aligned_cols=32 Identities=22% Similarity=0.277 Sum_probs=24.1
Q ss_pred cccCCCCCCCCeEEEEEecc-----------CcEEEEEcCccc
Q 035653 26 QFQCPFCGHGTSVECRIDKK-----------IQIGEAFCWNCL 57 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~-----------~~~g~~~C~~C~ 57 (87)
+-.|-||+.++||++-=+.. .-+...-||-|.
T Consensus 64 v~KCK~C~Rensv~iv~~~~~pyt~ed~e~~~~i~vfdCRG~E 106 (161)
T KOG1296|consen 64 VMKCKFCSRENSVTIVAFEDKPYTAEDSEKFKTIVVFDCRGLE 106 (161)
T ss_pred hhhhhhhcccCcEEEecCCCCcccccccccccceEEEeccCCc
Confidence 45799999999999865442 136778899886
No 133
>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=68.27 E-value=7.5 Score=22.03 Aligned_cols=25 Identities=28% Similarity=0.501 Sum_probs=17.6
Q ss_pred CCCCeEEEEEeccCcEEEEEcCccccee
Q 035653 33 GHGTSVECRIDKKIQIGEAFCWNCLERF 60 (87)
Q Consensus 33 ~~~~sV~v~idk~~~~g~~~C~~C~~~~ 60 (87)
+|+. |-+.|+...+ .+.|.=||..|
T Consensus 15 gHPr-Vyl~l~~~~~--~~~CpYCg~~y 39 (40)
T PF10276_consen 15 GHPR-VYLNLDDEPG--PVVCPYCGTRY 39 (40)
T ss_dssp CCCC-EEEE-TTTTC--EEEETTTTEEE
T ss_pred CCCe-EEEecCCCCC--eEECCCCCCEE
Confidence 5654 7777766544 78999999887
No 134
>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=68.22 E-value=7.1 Score=23.31 Aligned_cols=27 Identities=26% Similarity=0.477 Sum_probs=20.4
Q ss_pred CCCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 21 EKLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 21 ~kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
.+.+..-.||.||.. ...+-.|..||.
T Consensus 21 l~~p~l~~C~~cG~~-----------~~~H~vc~~cG~ 47 (55)
T TIGR01031 21 LTAPTLVVCPNCGEF-----------KLPHRVCPSCGY 47 (55)
T ss_pred ccCCcceECCCCCCc-----------ccCeeECCccCe
Confidence 355788899999972 246778999984
No 135
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=67.57 E-value=2.3 Score=35.25 Aligned_cols=18 Identities=39% Similarity=0.885 Sum_probs=12.7
Q ss_pred CCCccccCCCCCCCCeEEE
Q 035653 22 KLDTQFQCPFCGHGTSVEC 40 (87)
Q Consensus 22 kl~~~F~CPfC~~~~sV~v 40 (87)
.+=-.|.||+|||. ++++
T Consensus 64 vVimSF~CpHCG~k-N~ei 81 (460)
T KOG2703|consen 64 VVIMSFECPHCGHK-NNEI 81 (460)
T ss_pred eeeEEeecCccCCc-cccc
Confidence 34457999999994 3444
No 136
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.02 E-value=6.5 Score=25.94 Aligned_cols=27 Identities=26% Similarity=0.687 Sum_probs=20.8
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
-||.||. +..+....+|-+-.|..|+-
T Consensus 3 lCP~C~v----~l~~~~rs~vEiD~CPrCrG 29 (88)
T COG3809 3 LCPICGV----ELVMSVRSGVEIDYCPRCRG 29 (88)
T ss_pred ccCcCCc----eeeeeeecCceeeeCCcccc
Confidence 4999995 45555567888899999974
No 137
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=66.02 E-value=9.7 Score=25.96 Aligned_cols=53 Identities=21% Similarity=0.350 Sum_probs=40.0
Q ss_pred CccccCCCCCCCCeEEEEEeccCc--------------------EEEEEcCcccce----eEeecCCCCchhhhhhh
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQ--------------------IGEAFCWNCLER----FCTQIHALTEPIDIYAE 76 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~--------------------~g~~~C~~C~~~----~~~~i~~L~epiDVYs~ 76 (87)
-..|.|+-|...-.|+.+|.+... .-...|..||-. +|.++.+-+||--.|-+
T Consensus 19 ~~rf~C~tCpY~~~I~~ei~~r~~~~~Kevd~vlgg~~a~~nv~~t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYk 95 (105)
T KOG2906|consen 19 CNRFSCRTCPYVFPISREISSRKYPKLKEVDDVLGGDEAWENVDQTEATCPTCGHERAYFMQLQTRSADEPMTTFYK 95 (105)
T ss_pred EeeEEcCCCCceeeEeeeeeccccCchhhhhhhcCCcccccchhhccCcCCCCCCCceEEEEeeeccCCCcHhHhhh
Confidence 357999999998888888866421 123689999944 47789999999877654
No 138
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=65.90 E-value=3.6 Score=24.78 Aligned_cols=26 Identities=35% Similarity=0.643 Sum_probs=16.4
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
.||.||.. ++-- +.+ -...|+.||-+
T Consensus 21 ~CPrCG~g-vfmA--~H~---dR~~CGkCgyT 46 (51)
T COG1998 21 FCPRCGPG-VFMA--DHK---DRWACGKCGYT 46 (51)
T ss_pred cCCCCCCc-chhh--hcC---ceeEeccccce
Confidence 59999962 2211 112 27899999964
No 139
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=65.89 E-value=5 Score=31.93 Aligned_cols=42 Identities=26% Similarity=0.460 Sum_probs=29.5
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhhhhhH
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIYAEWI 78 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVYs~wi 78 (87)
.||.|....- .+.-| ..-|...|..||+.++. -+||+-|+|-
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 4888877654 23333 34578899999998775 4578888885
No 140
>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=64.24 E-value=8.2 Score=25.98 Aligned_cols=33 Identities=18% Similarity=0.494 Sum_probs=23.1
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeE
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~ 61 (87)
-.+.|+-|+.+ + .-..+.......|+.|+..+.
T Consensus 122 ~~~~C~~C~~~--~--~r~~~~~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 122 YVYRCPSCGRE--Y--KRHRRSKRKRYRCGRCGGPLV 154 (157)
T ss_pred eEEEcCCCCCE--e--eeecccchhhEECCCCCCEEE
Confidence 47899999984 3 223333566789999997653
No 141
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=64.13 E-value=4.4 Score=31.91 Aligned_cols=55 Identities=18% Similarity=0.497 Sum_probs=40.1
Q ss_pred CccccCCCCCCCCeEE----------EEEecc--CcEEEEEcCcccceeEee----cCCCCchhhhhhhhH
Q 035653 24 DTQFQCPFCGHGTSVE----------CRIDKK--IQIGEAFCWNCLERFCTQ----IHALTEPIDIYAEWI 78 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~----------v~idk~--~~~g~~~C~~C~~~~~~~----i~~L~epiDVYs~wi 78 (87)
...|.||.=|++.+=. |.+.-. ..+..-+|.+||+-|+.. ||+-.|-+|+|..-+
T Consensus 109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeikas~C~~C~a~y~~~dvIvlNg~~E~~dllk~rm 179 (293)
T KOG3113|consen 109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIKASVCHVCGAAYQEDDVIVLNGTEEDVDLLKTRM 179 (293)
T ss_pred cceeecccccceecceEEEEEEeccceeccHHHHHHhhhccccccCCcccccCeEeeCCCHHHHHHHHHHH
Confidence 4689999988875422 233221 346677999999999764 899999999998743
No 142
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=64.02 E-value=4.3 Score=28.14 Aligned_cols=36 Identities=25% Similarity=0.418 Sum_probs=23.5
Q ss_pred ccCCCCCCCCeEEEEEec---c-CcEEEEEcCcccceeEe
Q 035653 27 FQCPFCGHGTSVECRIDK---K-IQIGEAFCWNCLERFCT 62 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk---~-~~~g~~~C~~C~~~~~~ 62 (87)
-.||-|||+.-.-=++.. + ...-.-+|..|+-.|.+
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 369999998644333322 1 12456799999988764
No 143
>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=63.85 E-value=2.7 Score=19.82 Aligned_cols=11 Identities=27% Similarity=0.519 Sum_probs=5.7
Q ss_pred EcCcccceeEe
Q 035653 52 FCWNCLERFCT 62 (87)
Q Consensus 52 ~C~~C~~~~~~ 62 (87)
.|..|+..|..
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 35555555543
No 144
>PRK12495 hypothetical protein; Provisional
Probab=63.65 E-value=4.4 Score=30.98 Aligned_cols=34 Identities=24% Similarity=0.421 Sum_probs=26.0
Q ss_pred CCCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 21 EKLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 21 ~kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
..-...|.|+.||.+- . ...|.+.|-+|+..+.-
T Consensus 37 gatmsa~hC~~CG~PI------p--a~pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 37 GATMTNAHCDECGDPI------F--RHDGQEFCPTCQQPVTE 70 (226)
T ss_pred hcccchhhcccccCcc------c--CCCCeeECCCCCCcccc
Confidence 3456789999999863 1 33699999999987653
No 145
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=63.25 E-value=17 Score=24.76 Aligned_cols=31 Identities=23% Similarity=0.442 Sum_probs=22.0
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
=||-||+ -+.|+ .....-.++|+.|+-.|..
T Consensus 3 FCP~Cgn--~Live--~g~~~~rf~C~tCpY~~~I 33 (105)
T KOG2906|consen 3 FCPTCGN--MLIVE--SGESCNRFSCRTCPYVFPI 33 (105)
T ss_pred ccCCCCC--EEEEe--cCCeEeeEEcCCCCceeeE
Confidence 4999997 24443 3444788999999976643
No 146
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=62.97 E-value=3.2 Score=28.63 Aligned_cols=16 Identities=25% Similarity=0.592 Sum_probs=12.0
Q ss_pred CCCccccCCCCCCCCe
Q 035653 22 KLDTQFQCPFCGHGTS 37 (87)
Q Consensus 22 kl~~~F~CPfC~~~~s 37 (87)
..|-.+.|+.||+.-+
T Consensus 66 ~~p~~~~C~~CG~~~~ 81 (135)
T PRK03824 66 EEEAVLKCRNCGNEWS 81 (135)
T ss_pred ecceEEECCCCCCEEe
Confidence 5567899999997533
No 147
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=62.64 E-value=4.8 Score=24.89 Aligned_cols=30 Identities=20% Similarity=0.170 Sum_probs=26.2
Q ss_pred EcCcccceeEeecCCCCchhhhhhhhHHHH
Q 035653 52 FCWNCLERFCTQIHALTEPIDIYAEWIDEC 81 (87)
Q Consensus 52 ~C~~C~~~~~~~i~~L~epiDVYs~wiD~~ 81 (87)
.|.+||..-...+++-..|.|=|++.--+.
T Consensus 19 ~Cp~CG~~t~~~~PprFSPeD~y~kYR~~l 48 (59)
T COG2260 19 KCPVCGGDTKVPHPPRFSPEDKYGKYRREL 48 (59)
T ss_pred cCCCCCCccccCCCCCCCccchHHHHHHHH
Confidence 699999999999999999999999865443
No 148
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=62.51 E-value=3.2 Score=19.96 Aligned_cols=8 Identities=38% Similarity=1.468 Sum_probs=4.3
Q ss_pred ccCCCCCC
Q 035653 27 FQCPFCGH 34 (87)
Q Consensus 27 F~CPfC~~ 34 (87)
|.|++|+-
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 56777774
No 149
>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=62.41 E-value=3.8 Score=23.70 Aligned_cols=13 Identities=46% Similarity=1.053 Sum_probs=9.7
Q ss_pred chhhhhhhhHHHH
Q 035653 69 EPIDIYAEWIDEC 81 (87)
Q Consensus 69 epiDVYs~wiD~~ 81 (87)
.|==||.+|+|+-
T Consensus 17 t~RLvYADWL~e~ 29 (42)
T TIGR02996 17 TPRLVYADWLDEH 29 (42)
T ss_pred chHHHHHHHHHHc
Confidence 3445999999874
No 150
>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=62.36 E-value=4.7 Score=21.11 Aligned_cols=26 Identities=23% Similarity=0.277 Sum_probs=11.5
Q ss_pred CCCCCCCCeEEEEEeccCcEEEEEcCccccee
Q 035653 29 CPFCGHGTSVECRIDKKIQIGEAFCWNCLERF 60 (87)
Q Consensus 29 CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~ 60 (87)
||.||.+. + ...+--...|..||..+
T Consensus 6 C~~CG~~t-~-----~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 6 CGRCGAPT-K-----PAPGGWARRCPSCGHEH 31 (32)
T ss_dssp -TTT--BE-E-----E-SSSS-EEESSSS-EE
T ss_pred cCcCCccc-c-----CCCCcCEeECCCCcCEe
Confidence 88888852 1 12222345788888653
No 151
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=62.25 E-value=2.1 Score=31.07 Aligned_cols=54 Identities=20% Similarity=0.399 Sum_probs=32.6
Q ss_pred ccccCCCCCCCCeEEEEEeccCcE--------EEEEcCcccceeEeecCCCCchhhhhhhhHHHHHHhh
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQI--------GEAFCWNCLERFCTQIHALTEPIDIYAEWIDECERAN 85 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~--------g~~~C~~C~~~~~~~i~~L~epiDVYs~wiD~~e~~n 85 (87)
+.-.||.|++. +.=.-. -.++ +--.|.+||..|--..+ .++.+.+-+++.++.+
T Consensus 38 tI~~Cp~C~~~--IrG~y~-v~gv~~~g~~~~~PsYC~~CGkpyPWt~~----~L~aa~el~ee~eeLs 99 (158)
T PF10083_consen 38 TITSCPNCSTP--IRGDYH-VEGVFGLGGHYEAPSYCHNCGKPYPWTEN----ALEAANELIEEDEELS 99 (158)
T ss_pred HHHHCcCCCCC--CCCcee-cCCeeeeCCCCCCChhHHhCCCCCchHHH----HHHHHHHHHHHhhcCC
Confidence 45589999984 211100 1122 33489999998855444 4477777777766653
No 152
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=61.87 E-value=9.7 Score=26.21 Aligned_cols=31 Identities=19% Similarity=0.256 Sum_probs=20.1
Q ss_pred ccCCCCCCCCeEEEEEeccCc------------EEEEEcCccccee
Q 035653 27 FQCPFCGHGTSVECRIDKKIQ------------IGEAFCWNCLERF 60 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk~~~------------~g~~~C~~C~~~~ 60 (87)
=.||.||. .-..+++..- --.-.|..||.-|
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 2333444321 1257899999877
No 153
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=61.83 E-value=14 Score=25.20 Aligned_cols=48 Identities=15% Similarity=0.103 Sum_probs=32.2
Q ss_pred cCCCCCC---ccccCCCCCCC--CeEEEEEeccCcEEEEEcCcccceeEeecC
Q 035653 18 KGMEKLD---TQFQCPFCGHG--TSVECRIDKKIQIGEAFCWNCLERFCTQIH 65 (87)
Q Consensus 18 k~~~kl~---~~F~CPfC~~~--~sV~v~idk~~~~g~~~C~~C~~~~~~~i~ 65 (87)
|-+-.|| +.+-|+.|+.. --+.+.+-..++.-.++|..||...-+++.
T Consensus 45 K~rv~lp~~iKR~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~p~~ 97 (105)
T COG2023 45 KYRVRLPREIKRTICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRYPYG 97 (105)
T ss_pred hhccccCHHHHHHhccccCcccccCcceEEEEcCCeEEEEecCCCcEEEeccc
Confidence 4444555 66789999982 224444444556688999999987766654
No 154
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=61.53 E-value=3.4 Score=31.74 Aligned_cols=19 Identities=42% Similarity=0.906 Sum_probs=13.5
Q ss_pred cccCCCCCCCC-eEEEEEec
Q 035653 26 QFQCPFCGHGT-SVECRIDK 44 (87)
Q Consensus 26 ~F~CPfC~~~~-sV~v~idk 44 (87)
.|-||||||.+ .+.=.+|.
T Consensus 214 efiC~~Cn~~n~~~~~~~ds 233 (251)
T COG5415 214 EFICPHCNHKNDEVKEREDS 233 (251)
T ss_pred heecccchhhcCcccccccc
Confidence 79999999976 45444443
No 155
>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=61.25 E-value=2.5 Score=22.07 Aligned_cols=8 Identities=50% Similarity=1.497 Sum_probs=3.8
Q ss_pred cCCCCCCC
Q 035653 28 QCPFCGHG 35 (87)
Q Consensus 28 ~CPfC~~~ 35 (87)
+||.||++
T Consensus 1 ~CP~C~s~ 8 (28)
T PF03119_consen 1 TCPVCGSK 8 (28)
T ss_dssp B-TTT--B
T ss_pred CcCCCCCE
Confidence 59999983
No 156
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=61.21 E-value=7.5 Score=24.59 Aligned_cols=34 Identities=32% Similarity=0.578 Sum_probs=23.3
Q ss_pred CCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCch
Q 035653 29 CPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEP 70 (87)
Q Consensus 29 CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~ep 70 (87)
||.|...+ +.. ..+.+.| .||+++.+.-..++..
T Consensus 2 CPVC~~~~-L~~------~~~~i~C-~Cgl~l~~~~~~~tl~ 35 (82)
T PF14768_consen 2 CPVCQKGN-LRE------NSNVISC-SCGLRLNTQQDELTLE 35 (82)
T ss_pred CCccCCCc-ccc------cCCeEEC-CCccEEecCCCCCCHH
Confidence 99999843 433 4467999 5668888875555543
No 157
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=60.81 E-value=6.8 Score=23.54 Aligned_cols=20 Identities=30% Similarity=0.702 Sum_probs=13.4
Q ss_pred CccccCCCCCCCCeEEEEEecc
Q 035653 24 DTQFQCPFCGHGTSVECRIDKK 45 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~ 45 (87)
|..+.||+||+. +.-.++..
T Consensus 1 p~~i~Cp~C~~~--~~T~v~~~ 20 (67)
T smart00714 1 PYQLFCPRCQNN--VTTRVETE 20 (67)
T ss_pred CcceECCCCCCE--EEEEEEEE
Confidence 457899999984 44444444
No 158
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=60.72 E-value=6.9 Score=34.23 Aligned_cols=29 Identities=24% Similarity=0.509 Sum_probs=18.8
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
.+|.||+|+.. .++.+. .+.+.|.-||-.
T Consensus 443 ~v~~Cp~Cd~~----lt~H~~--~~~L~CH~Cg~~ 471 (730)
T COG1198 443 YIAECPNCDSP----LTLHKA--TGQLRCHYCGYQ 471 (730)
T ss_pred CcccCCCCCcc----eEEecC--CCeeEeCCCCCC
Confidence 57889999863 333333 377778777754
No 159
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=60.60 E-value=4.6 Score=27.06 Aligned_cols=30 Identities=20% Similarity=0.254 Sum_probs=19.0
Q ss_pred CCCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 21 EKLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 21 ~kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
..+|-.+.|+.||++-.+. . ....|..||.
T Consensus 65 ~~vp~~~~C~~Cg~~~~~~------~--~~~~CP~Cgs 94 (113)
T PRK12380 65 VYKPAQAWCWDCSQVVEIH------Q--HDAQCPHCHG 94 (113)
T ss_pred EeeCcEEEcccCCCEEecC------C--cCccCcCCCC
Confidence 4567788999999742221 1 2234999984
No 160
>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=60.20 E-value=4.6 Score=24.09 Aligned_cols=14 Identities=36% Similarity=1.009 Sum_probs=11.0
Q ss_pred CCCccccCCCCCCC
Q 035653 22 KLDTQFQCPFCGHG 35 (87)
Q Consensus 22 kl~~~F~CPfC~~~ 35 (87)
.-+..|.||+||+-
T Consensus 40 ~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 40 FEEIQYRCPYCGAL 53 (54)
T ss_pred CCceEEEcCCCCCc
Confidence 44569999999973
No 161
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=60.07 E-value=11 Score=21.40 Aligned_cols=35 Identities=20% Similarity=0.414 Sum_probs=22.6
Q ss_pred ccccCC--CCCCCCeEEEEEeccCcEEEEEcCcccceeEee
Q 035653 25 TQFQCP--FCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQ 63 (87)
Q Consensus 25 ~~F~CP--fC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~ 63 (87)
+.--|| .|+.. +.. +...+...+.|..||..|-..
T Consensus 17 ~~~~CP~~~C~~~--~~~--~~~~~~~~v~C~~C~~~fC~~ 53 (64)
T smart00647 17 DLKWCPAPDCSAA--IIV--TEEEGCNRVTCPKCGFSFCFR 53 (64)
T ss_pred CccCCCCCCCcce--EEe--cCCCCCCeeECCCCCCeECCC
Confidence 445699 99762 222 213355688999999888654
No 162
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=59.21 E-value=4.4 Score=28.54 Aligned_cols=11 Identities=45% Similarity=1.280 Sum_probs=9.1
Q ss_pred CccccCCCCCC
Q 035653 24 DTQFQCPFCGH 34 (87)
Q Consensus 24 ~~~F~CPfC~~ 34 (87)
+.-|.||.||.
T Consensus 126 ~~~F~Cp~Cg~ 136 (158)
T TIGR00373 126 ELNFTCPRCGA 136 (158)
T ss_pred HcCCcCCCCCC
Confidence 35799999997
No 163
>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=59.16 E-value=3.5 Score=29.68 Aligned_cols=38 Identities=18% Similarity=0.383 Sum_probs=16.3
Q ss_pred CccccCCCCCCCCeEEEEEeccC---cEEEEEcCcccceeE
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKI---QIGEAFCWNCLERFC 61 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~---~~g~~~C~~C~~~~~ 61 (87)
|=.|.||.|+++..+.=.++... ....+.|.+|+..+.
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 45799999999643322112111 123589999998443
No 164
>PHA00616 hypothetical protein
Probab=58.95 E-value=3.4 Score=23.99 Aligned_cols=9 Identities=44% Similarity=1.091 Sum_probs=6.8
Q ss_pred cccCCCCCC
Q 035653 26 QFQCPFCGH 34 (87)
Q Consensus 26 ~F~CPfC~~ 34 (87)
.|+||.||.
T Consensus 1 pYqC~~CG~ 9 (44)
T PHA00616 1 MYQCLRCGG 9 (44)
T ss_pred CCccchhhH
Confidence 378888885
No 165
>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=58.95 E-value=11 Score=30.42 Aligned_cols=39 Identities=21% Similarity=0.235 Sum_probs=24.2
Q ss_pred cCCCCCC-CCeEEEEEeccCcEEEEEcCcccceeEeecCC
Q 035653 28 QCPFCGH-GTSVECRIDKKIQIGEAFCWNCLERFCTQIHA 66 (87)
Q Consensus 28 ~CPfC~~-~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~ 66 (87)
-|+.||. ..+-.+..|...+.-.-.|..||..-+..+..
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 44444577777888888999999988887764
No 166
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=58.84 E-value=9.9 Score=28.67 Aligned_cols=28 Identities=32% Similarity=0.787 Sum_probs=17.7
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccceeE
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~ 61 (87)
=||.||+...+ ...+. ...|..||..+-
T Consensus 101 fC~~CG~~~~~-----~~~~~-~~~C~~c~~~~y 128 (256)
T PRK00241 101 FCGYCGHPMHP-----SKTEW-AMLCPHCRERYY 128 (256)
T ss_pred cccccCCCCee-----cCCce-eEECCCCCCEEC
Confidence 39999985322 12333 467999997543
No 167
>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=58.82 E-value=14 Score=27.26 Aligned_cols=55 Identities=20% Similarity=0.276 Sum_probs=31.8
Q ss_pred CCCCccccCCCCCCCCeEEEEEeccCc---EEEEEcCcccceeEeecCCCCchhhhhhh
Q 035653 21 EKLDTQFQCPFCGHGTSVECRIDKKIQ---IGEAFCWNCLERFCTQIHALTEPIDIYAE 76 (87)
Q Consensus 21 ~kl~~~F~CPfC~~~~sV~v~idk~~~---~g~~~C~~C~~~~~~~i~~L~epiDVYs~ 76 (87)
.+++-.|.||-||++..+.+.++...- ...+. -.=|..-.++.|.|++--|++.-
T Consensus 73 ~~v~~~~~C~~cg~~~~~~i~l~~~~l~~~~~~~~-~~~~i~i~~ryP~~~~~~~~~~m 130 (205)
T PF12322_consen 73 TKVPVNYTCPDCGEEVKVPINLDQIKLTDGKNEIK-LSDGIKIKMRYPSLFEFDDVFEM 130 (205)
T ss_pred ccceEEEECCCCCcEEEEEecchhcccCCCCcceE-ecCCEEEEEeCCcccccCCHHHH
Confidence 457889999999997666666554321 11111 12233455666666654455544
No 168
>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=58.70 E-value=8.2 Score=23.50 Aligned_cols=23 Identities=26% Similarity=0.667 Sum_probs=14.9
Q ss_pred CCCccccCCCCCCCCeEEEEEeccC
Q 035653 22 KLDTQFQCPFCGHGTSVECRIDKKI 46 (87)
Q Consensus 22 kl~~~F~CPfC~~~~sV~v~idk~~ 46 (87)
+-|....||+||+. +.=.+..+.
T Consensus 3 ~~p~~~~CP~C~~~--~~T~v~~~~ 25 (73)
T PF10601_consen 3 PEPVRIYCPYCQQQ--VQTRVEYKS 25 (73)
T ss_pred CCceeeECCCCCCE--EEEEEEEEe
Confidence 34678999999984 444444443
No 169
>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=58.33 E-value=8.9 Score=24.69 Aligned_cols=12 Identities=17% Similarity=0.207 Sum_probs=9.8
Q ss_pred EEEEEcCcccce
Q 035653 48 IGEAFCWNCLER 59 (87)
Q Consensus 48 ~g~~~C~~C~~~ 59 (87)
.+.|+|..||..
T Consensus 55 ~~tLsCsACGS~ 66 (74)
T PF05077_consen 55 GNTLSCSACGSE 66 (74)
T ss_pred CCeEeehhcccc
Confidence 368999999964
No 170
>PRK04011 peptide chain release factor 1; Provisional
Probab=57.71 E-value=12 Score=30.26 Aligned_cols=53 Identities=23% Similarity=0.442 Sum_probs=35.2
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhhhhhHHHHHHhh
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIYAEWIDECERAN 85 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVYs~wiD~~e~~n 85 (87)
.|.||.||+.....++- ....-.-.|..||...+. .+..|.+-.+++.+++.+
T Consensus 328 ~~~c~~c~~~~~~~~~~--~~~~~~~~c~~~~~~~~~-----~~~~~~v~~l~e~a~~~g 380 (411)
T PRK04011 328 TYKCPNCGYEEEKTVKR--REELPEKTCPKCGSELEI-----VEEEDIIEELSELAEQSG 380 (411)
T ss_pred EEEcCCCCcceeeeccc--ccccccccCcccCccccc-----chhhhHHHHHHHHHHHcC
Confidence 68899999976444433 333444689999975332 355677777777777644
No 171
>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=57.70 E-value=5.8 Score=22.06 Aligned_cols=28 Identities=21% Similarity=0.516 Sum_probs=21.4
Q ss_pred CCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecC
Q 035653 29 CPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIH 65 (87)
Q Consensus 29 CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~ 65 (87)
|++|+. .......|.|..|+..|-..--
T Consensus 2 C~vC~~---------~~~~~~~i~C~~C~~~~H~~C~ 29 (51)
T PF00628_consen 2 CPVCGQ---------SDDDGDMIQCDSCNRWYHQECV 29 (51)
T ss_dssp BTTTTS---------SCTTSSEEEBSTTSCEEETTTS
T ss_pred CcCCCC---------cCCCCCeEEcCCCChhhCcccC
Confidence 788886 2345568899999999988733
No 172
>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=57.64 E-value=5.1 Score=28.25 Aligned_cols=36 Identities=22% Similarity=0.182 Sum_probs=23.7
Q ss_pred CCCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEee
Q 035653 21 EKLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQ 63 (87)
Q Consensus 21 ~kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~ 63 (87)
+-|=+-..||.||.. .-..+.--+.|..||..|...
T Consensus 4 ~elGtKr~Cp~cg~k-------FYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 4 PDLGTKRICPNTGSK-------FYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred hhhCccccCCCcCcc-------ccccCCCCccCCCcCCccCcc
Confidence 456677788888873 223334567888888877543
No 173
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=57.42 E-value=4.4 Score=22.71 Aligned_cols=16 Identities=19% Similarity=0.422 Sum_probs=12.8
Q ss_pred EEEEEcCcccceeEee
Q 035653 48 IGEAFCWNCLERFCTQ 63 (87)
Q Consensus 48 ~g~~~C~~C~~~~~~~ 63 (87)
.|...|..||..|...
T Consensus 11 ~~~~~C~~CgM~Y~~~ 26 (41)
T PF13878_consen 11 FGATTCPTCGMLYSPG 26 (41)
T ss_pred cCCcCCCCCCCEECCC
Confidence 4568999999998654
No 174
>PRK04023 DNA polymerase II large subunit; Validated
Probab=57.42 E-value=8.5 Score=35.27 Aligned_cols=19 Identities=16% Similarity=0.107 Sum_probs=13.7
Q ss_pred CCchhhhhhhhHHHHHHhh
Q 035653 67 LTEPIDIYAEWIDECERAN 85 (87)
Q Consensus 67 L~epiDVYs~wiD~~e~~n 85 (87)
-..-||+=..|-++.+.+.
T Consensus 677 s~~~i~l~~~~~~A~~~lg 695 (1121)
T PRK04023 677 SKRKIDLKELYDRALENLG 695 (1121)
T ss_pred ceEEecHHHHHHHHHHHhC
Confidence 3456788888888887754
No 175
>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=57.34 E-value=3.7 Score=22.18 Aligned_cols=25 Identities=28% Similarity=0.495 Sum_probs=12.6
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
.|..||++. + |...+ .+.|..||-+
T Consensus 2 ~C~~Cg~~~--~--~~~~~---~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAEV--E--LKPGD---PIRCPECGHR 26 (32)
T ss_dssp BESSSSSSE-----BSTSS---TSSBSSSS-S
T ss_pred CCCcCCCee--E--cCCCC---cEECCcCCCe
Confidence 466777652 2 32222 2477777754
No 176
>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=57.15 E-value=16 Score=22.12 Aligned_cols=31 Identities=16% Similarity=0.285 Sum_probs=18.1
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEee
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQ 63 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~ 63 (87)
.||-|+++ ++.++.. .-.+.|.+||..-..+
T Consensus 9 kCp~C~~~---q~vFSha--~t~V~C~~Cg~~L~~P 39 (55)
T PF01667_consen 9 KCPGCYNI---QTVFSHA--QTVVKCVVCGTVLAQP 39 (55)
T ss_dssp E-TTT-SE---EEEETT---SS-EE-SSSTSEEEEE
T ss_pred ECCCCCCe---eEEEecC--CeEEEcccCCCEecCC
Confidence 69999984 4446444 3678999999876543
No 177
>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=57.02 E-value=3.4 Score=33.12 Aligned_cols=32 Identities=22% Similarity=0.699 Sum_probs=15.1
Q ss_pred CCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 22 KLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 22 kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
.+-..|.|+.||. .+|+ +++ +-.-.|..||..
T Consensus 281 a~KRFFkC~~C~~-Rt~s--l~r---~P~~~C~~Cg~~ 312 (344)
T PF09332_consen 281 AVKRFFKCKDCGN-RTIS--LER---LPKKHCSNCGSS 312 (344)
T ss_dssp EE-EEEE-T-TS--EEEE--SSS---S--S--TTT-S-
T ss_pred eeeeeEECCCCCC-eeee--ccc---CCCCCCCcCCcC
Confidence 4456999999998 4454 343 344699999974
No 178
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=56.64 E-value=2.7 Score=33.14 Aligned_cols=33 Identities=18% Similarity=0.284 Sum_probs=15.7
Q ss_pred EEEEcCcccce-eEeecCCCCchhhhhhhhHHHHH
Q 035653 49 GEAFCWNCLER-FCTQIHALTEPIDIYAEWIDECE 82 (87)
Q Consensus 49 g~~~C~~C~~~-~~~~i~~L~epiDVYs~wiD~~e 82 (87)
-+..|.+|+.. |+-.=-++ .-.-|.-+-||++-
T Consensus 33 khfkchichkkl~sgpglsi-hcmqvhketid~ip 66 (341)
T KOG2893|consen 33 KHFKCHICHKKLFSGPGLSI-HCMQVHKETIDKIP 66 (341)
T ss_pred ccceeeeehhhhccCCCcee-ehhhhhhhhhhccc
Confidence 35778888765 32221111 22345555555543
No 179
>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=56.49 E-value=12 Score=20.50 Aligned_cols=26 Identities=27% Similarity=0.578 Sum_probs=17.6
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
.|.|+.|+.. .. ...-|...|..||-
T Consensus 8 ~~~C~~C~~~-----~~--~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 8 NEPCPVCGSR-----WF--YSDDGFYYCDRCGH 33 (36)
T ss_pred CCcCCCCCCe-----Ee--EccCCEEEhhhCce
Confidence 4669999972 22 23347888988885
No 180
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=55.89 E-value=4.9 Score=31.57 Aligned_cols=36 Identities=22% Similarity=0.537 Sum_probs=21.9
Q ss_pred CccccCCCCCCCCeEEEEEec-----cCcEEEEEcCcccceeEe
Q 035653 24 DTQFQCPFCGHGTSVECRIDK-----KIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk-----~~~~g~~~C~~C~~~~~~ 62 (87)
.+.|.|+.||. +-|.|-- ....---.|.+||..|+-
T Consensus 159 ~ka~~C~~C~K---~YvSmpALkMHirTH~l~c~C~iCGKaFSR 199 (279)
T KOG2462|consen 159 KKAFSCKYCGK---VYVSMPALKMHIRTHTLPCECGICGKAFSR 199 (279)
T ss_pred cccccCCCCCc---eeeehHHHhhHhhccCCCcccccccccccc
Confidence 46788888876 4455422 122234578888888763
No 181
>PHA02611 51 baseplate hub assembly protein; Provisional
Probab=55.34 E-value=9.5 Score=29.51 Aligned_cols=25 Identities=24% Similarity=0.612 Sum_probs=20.2
Q ss_pred CCCCccccCCCCCCCCeEEEEEecc
Q 035653 21 EKLDTQFQCPFCGHGTSVECRIDKK 45 (87)
Q Consensus 21 ~kl~~~F~CPfC~~~~sV~v~idk~ 45 (87)
.+.|..|+||-||+++.|...++..
T Consensus 77 ~~v~~~~tCp~Cg~e~~v~~~l~~~ 101 (249)
T PHA02611 77 TKIPVTFTCPKCKKEKTVLFNLKQE 101 (249)
T ss_pred ceeeEEEECCCCCCceeEEEEeehh
Confidence 4578899999999998788777553
No 182
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=55.15 E-value=5.7 Score=28.63 Aligned_cols=9 Identities=44% Similarity=1.010 Sum_probs=5.2
Q ss_pred ccccCCCCC
Q 035653 25 TQFQCPFCG 33 (87)
Q Consensus 25 ~~F~CPfC~ 33 (87)
..|.||.|+
T Consensus 116 ~~Y~Cp~C~ 124 (178)
T PRK06266 116 MFFFCPNCH 124 (178)
T ss_pred CEEECCCCC
Confidence 455666664
No 183
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=55.00 E-value=6.7 Score=26.29 Aligned_cols=31 Identities=19% Similarity=0.305 Sum_probs=18.8
Q ss_pred CCCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 21 EKLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 21 ~kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
..+|-.|.|+-||+. +... ......|..||.
T Consensus 65 ~~~p~~~~C~~Cg~~--~~~~-----~~~~~~CP~Cgs 95 (114)
T PRK03681 65 EEQEAECWCETCQQY--VTLL-----TQRVRRCPQCHG 95 (114)
T ss_pred EeeCcEEEcccCCCe--eecC-----CccCCcCcCcCC
Confidence 456778889999862 2211 112246888884
No 184
>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=54.99 E-value=9.9 Score=31.28 Aligned_cols=30 Identities=27% Similarity=0.412 Sum_probs=17.8
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeE
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~ 61 (87)
...||.|+.. .+..+. .+.+.|.-||....
T Consensus 222 ~~~C~~C~~~----l~~h~~--~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 222 ILCCPNCDVS----LTYHKK--EGKLRCHYCGYQEP 251 (505)
T ss_pred ccCCCCCCCc----eEEecC--CCeEEcCCCcCcCC
Confidence 3467777642 333333 34788888886654
No 185
>PHA02942 putative transposase; Provisional
Probab=54.41 E-value=6.4 Score=31.42 Aligned_cols=47 Identities=17% Similarity=0.260 Sum_probs=30.3
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhhhhhHHHH
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIYAEWIDEC 81 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVYs~wiD~~ 81 (87)
|.=.||.|||... ......-.|..||....-.++ .++.++..+++.+
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 6667999999531 123346899999987655554 3456666655544
No 186
>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=54.17 E-value=30 Score=27.54 Aligned_cols=37 Identities=24% Similarity=0.317 Sum_probs=26.5
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecC
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIH 65 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~ 65 (87)
-||.||--.+..+.+|-..+.-.-.|. ||-.-++.|.
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 499999654444467776776666894 9988888774
No 187
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.78 E-value=4 Score=28.67 Aligned_cols=31 Identities=23% Similarity=0.419 Sum_probs=20.1
Q ss_pred ccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 27 FQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
=.||.||..+ +.+.--.-.-.|..||+.|..
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 3699999754 222222233479999998854
No 188
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=53.48 E-value=5.3 Score=32.83 Aligned_cols=38 Identities=21% Similarity=0.274 Sum_probs=23.7
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCC
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHAL 67 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L 67 (87)
-.|.||.||.+...+.+= ...... .|.-||. ++.+-.-
T Consensus 326 ~~~~c~~~~~e~~~t~~~--~~~~~~-~~~~~~~--e~~~v~~ 363 (411)
T COG1503 326 VTYKCPTCGYENLKSKRE--FEQKRF-RCPECGS--EMEEVEV 363 (411)
T ss_pred eeecCCCcchhhhhcccc--cccccc-cCccccc--cccchhh
Confidence 379999999976443321 222344 9999998 5444333
No 189
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=52.97 E-value=13 Score=35.33 Aligned_cols=48 Identities=23% Similarity=0.304 Sum_probs=34.4
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhhhhhHHHHHHhh
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIYAEWIDECERAN 85 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVYs~wiD~~e~~n 85 (87)
-.|.||.||+.. -...|..||..-+. -++-..-||+=..|-++.+.+.
T Consensus 673 ~~~~Cp~Cg~~~------------~~~~Cp~CG~~~~~-~~~~~~~i~~~~~~~~A~~~v~ 720 (1627)
T PRK14715 673 AFFKCPKCGKVG------------LYHVCPFCGTRVEL-KPYARREIPPKDYWYAALENLK 720 (1627)
T ss_pred EeeeCCCCCCcc------------ccccCcccCCcccC-CCccceecCHHHHHHHHHHHhC
Confidence 468999999842 34589999987332 2334457899899999988763
No 190
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=52.70 E-value=5.9 Score=31.74 Aligned_cols=13 Identities=31% Similarity=0.802 Sum_probs=10.9
Q ss_pred CccccCCCCCCCC
Q 035653 24 DTQFQCPFCGHGT 36 (87)
Q Consensus 24 ~~~F~CPfC~~~~ 36 (87)
...|-||||||-+
T Consensus 240 yi~F~C~~Cn~LN 252 (328)
T KOG2846|consen 240 YITFRCPHCNALN 252 (328)
T ss_pred ceEEECccccccC
Confidence 5789999999954
No 191
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=52.59 E-value=5.1 Score=23.20 Aligned_cols=10 Identities=50% Similarity=1.381 Sum_probs=6.3
Q ss_pred cccCCCCCCC
Q 035653 26 QFQCPFCGHG 35 (87)
Q Consensus 26 ~F~CPfC~~~ 35 (87)
-+.||.|||+
T Consensus 28 ~W~C~~Cgh~ 37 (55)
T PF14311_consen 28 WWKCPKCGHE 37 (55)
T ss_pred EEECCCCCCe
Confidence 3667777663
No 192
>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=51.65 E-value=4.5 Score=22.18 Aligned_cols=26 Identities=19% Similarity=0.418 Sum_probs=18.3
Q ss_pred EcCcccceeEeecCCCCchhhhhhhh
Q 035653 52 FCWNCLERFCTQIHALTEPIDIYAEW 77 (87)
Q Consensus 52 ~C~~C~~~~~~~i~~L~epiDVYs~w 77 (87)
.|+.|.-+..+-...=-+|||||.+|
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 46667766655555557899999876
No 193
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=51.57 E-value=15 Score=23.04 Aligned_cols=32 Identities=25% Similarity=0.522 Sum_probs=23.1
Q ss_pred cccCCCCCCCCeEEEEEe-ccCcEEEEEcCccccee
Q 035653 26 QFQCPFCGHGTSVECRID-KKIQIGEAFCWNCLERF 60 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~id-k~~~~g~~~C~~C~~~~ 60 (87)
.|.|| ||. -.+|.++ ...|--.+.|..|.+--
T Consensus 22 tyPCP-CGD--RFeIsLeDl~~GE~VArCPSCSLiv 54 (67)
T COG5216 22 TYPCP-CGD--RFEISLEDLRNGEVVARCPSCSLIV 54 (67)
T ss_pred EecCC-CCC--EeEEEHHHhhCCceEEEcCCceEEE
Confidence 56788 775 4777774 35677788999998753
No 194
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=51.48 E-value=9.8 Score=23.10 Aligned_cols=13 Identities=38% Similarity=0.986 Sum_probs=8.1
Q ss_pred CCCccccCCCCCC
Q 035653 22 KLDTQFQCPFCGH 34 (87)
Q Consensus 22 kl~~~F~CPfC~~ 34 (87)
+..-.|+||.||-
T Consensus 10 ~~~v~~~Cp~cGi 22 (55)
T PF13824_consen 10 PAHVNFECPDCGI 22 (55)
T ss_pred ccccCCcCCCCCC
Confidence 4455667777665
No 195
>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=50.89 E-value=9.7 Score=30.32 Aligned_cols=38 Identities=11% Similarity=0.089 Sum_probs=24.8
Q ss_pred EEEEEcCcccceeEee-cCCCCchhhhhhhhHHHHHHhh
Q 035653 48 IGEAFCWNCLERFCTQ-IHALTEPIDIYAEWIDECERAN 85 (87)
Q Consensus 48 ~g~~~C~~C~~~~~~~-i~~L~epiDVYs~wiD~~e~~n 85 (87)
.-...|..||..-+.+ ...+.=++.-|.+|+.+..+.+
T Consensus 164 l~~p~~~~~g~~~~~r~e~~~ff~L~~~~~~L~~~l~~~ 202 (391)
T PF09334_consen 164 LINPVCKICGSPPEVREEENYFFKLSKFRDQLREWLESN 202 (391)
T ss_dssp SECEEETTTS-B-EEEEEEEEEE-GGGGHHHHHHHHHHS
T ss_pred ccCCccccccccCccccceEEEEehHHhHHHHHHHHhcC
Confidence 3456788888776655 6666667777888888777655
No 196
>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 PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=49.97 E-value=11 Score=22.85 Aligned_cols=25 Identities=28% Similarity=0.612 Sum_probs=17.5
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCccccee
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERF 60 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~ 60 (87)
.|+.||-. .+.+-.++.|..||.-|
T Consensus 7 ~C~~Cg~~--------~~~~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 7 KCPVCGKK--------FKDGDDIVVCPECGAPY 31 (54)
T ss_pred cChhhCCc--------ccCCCCEEECCCCCCcc
Confidence 58888862 23455678899998865
No 198
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=49.16 E-value=20 Score=24.43 Aligned_cols=34 Identities=18% Similarity=0.530 Sum_probs=25.7
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeE
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~ 61 (87)
=.+.|.-|+... . ...+...+....|+.||..+.
T Consensus 111 ~~y~C~~C~~~~-~--~~rr~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 111 YPYRCTGCGQRY-L--RVRRSNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEEECCCCCCCC-c--eEccccCcceEEcCCCCCEEE
Confidence 378999999743 3 445556678999999998765
No 199
>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=49.15 E-value=14 Score=26.91 Aligned_cols=31 Identities=32% Similarity=0.449 Sum_probs=21.3
Q ss_pred ccCCCCCCCCeEEE--EEeccCcEEEEEcCcccce
Q 035653 27 FQCPFCGHGTSVEC--RIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 27 F~CPfC~~~~sV~v--~idk~~~~g~~~C~~C~~~ 59 (87)
|-|-.||++ |.- +.=..+++-...|.+||.-
T Consensus 1 miCIeCg~~--v~~Ly~~Ys~~~irLt~C~~C~~v 33 (208)
T PF04161_consen 1 MICIECGHP--VKSLYRQYSPGNIRLTKCPNCGKV 33 (208)
T ss_pred CEeccCCCc--chhhhhccCCCcEEEeeccccCCc
Confidence 568999996 321 2223456888899999963
No 200
>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=49.11 E-value=7.4 Score=21.22 Aligned_cols=10 Identities=40% Similarity=1.162 Sum_probs=6.8
Q ss_pred ccccCCCCCC
Q 035653 25 TQFQCPFCGH 34 (87)
Q Consensus 25 ~~F~CPfC~~ 34 (87)
..|.||.|+.
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 3689999986
No 201
>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=49.00 E-value=13 Score=27.08 Aligned_cols=42 Identities=19% Similarity=0.411 Sum_probs=31.0
Q ss_pred ccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCC
Q 035653 27 FQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALT 68 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~ 68 (87)
=+|-|||.-=.|+|=-..--.+-.+.||-|.-=.+..+.++.
T Consensus 13 VhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~~~ 54 (170)
T PF04690_consen 13 VHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRALL 54 (170)
T ss_pred EEcCCcCeEEEEecchhhhhhhhceeccCccceeeeeccccc
Confidence 479999987666666566667889999999966665555443
No 202
>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=48.83 E-value=6.6 Score=26.29 Aligned_cols=30 Identities=27% Similarity=0.414 Sum_probs=18.5
Q ss_pred CCCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 21 EKLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 21 ~kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
..+|-.+.|+.||+.-++. - ....|..||.
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 3456778888888643221 0 1356888885
No 203
>PRK05667 dnaG DNA primase; Validated
Probab=48.80 E-value=14 Score=31.19 Aligned_cols=31 Identities=23% Similarity=0.364 Sum_probs=21.1
Q ss_pred ccccCCCCCCCC-eEEEEEeccCcEEEEEcCcccce
Q 035653 25 TQFQCPFCGHGT-SVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 25 ~~F~CPfC~~~~-sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
-...||||+... |++|. .. .+.-.|..||..
T Consensus 35 ~~~~CPfH~ektpSf~V~--~~--k~~~~CF~Cg~~ 66 (580)
T PRK05667 35 YKGLCPFHDEKTPSFTVS--PD--KQFYHCFGCGAG 66 (580)
T ss_pred eeecCCCCCCCCCceEEE--CC--CCeEEECCCCCC
Confidence 345799999643 55554 33 456899999984
No 204
>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=48.43 E-value=43 Score=18.52 Aligned_cols=27 Identities=33% Similarity=0.487 Sum_probs=17.1
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCc
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWN 55 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~ 55 (87)
-||.||- ..+.-..+.+..|-...|.+
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 5999997 44555667777788888875
No 205
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=47.95 E-value=9.4 Score=30.36 Aligned_cols=21 Identities=19% Similarity=0.393 Sum_probs=18.1
Q ss_pred CccccCCCCCCCCeEEEEEec
Q 035653 24 DTQFQCPFCGHGTSVECRIDK 44 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk 44 (87)
+..--||.||..-++++.++-
T Consensus 183 e~~~~CPvCGS~PvaSmV~~g 203 (308)
T COG3058 183 ESRQYCPVCGSMPVASMVQIG 203 (308)
T ss_pred cccccCCCcCCCCcceeeeec
Confidence 788899999998888888766
No 206
>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=47.63 E-value=15 Score=22.01 Aligned_cols=27 Identities=22% Similarity=0.210 Sum_probs=22.7
Q ss_pred EcCcccceeEeecCCCCchhhhhhhhH
Q 035653 52 FCWNCLERFCTQIHALTEPIDIYAEWI 78 (87)
Q Consensus 52 ~C~~C~~~~~~~i~~L~epiDVYs~wi 78 (87)
.|..||..-...-++=..|-|-|++.-
T Consensus 19 ~cp~cG~~T~~ahPaRFSPdDky~~yR 45 (53)
T PF04135_consen 19 KCPPCGGPTESAHPARFSPDDKYSKYR 45 (53)
T ss_dssp BBTTTSSBSEESSSSSS-TTTTTCHHH
T ss_pred ccCCCCCCCcCCcCCCCCCCCccHHHH
Confidence 499999988888999999999999854
No 207
>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=47.58 E-value=7.5 Score=22.06 Aligned_cols=36 Identities=22% Similarity=0.347 Sum_probs=16.1
Q ss_pred CccccCCC--CCCCCeEEEEEeccCcEEEEEcCcccceeEee
Q 035653 24 DTQFQCPF--CGHGTSVECRIDKKIQIGEAFCWNCLERFCTQ 63 (87)
Q Consensus 24 ~~~F~CPf--C~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~ 63 (87)
+..-.||. |+.. +.++.......+.|..|+..|-..
T Consensus 16 ~~~~~Cp~~~C~~~----~~~~~~~~~~~~~C~~C~~~fC~~ 53 (64)
T PF01485_consen 16 PNIRWCPNPDCEYI----IEKDDGCNSPIVTCPSCGTEFCFK 53 (64)
T ss_dssp --CC--TTSST-------ECS-SSTTS--CCTTSCCSEECSS
T ss_pred CCccCCCCCCCccc----EEecCCCCCCeeECCCCCCcCccc
Confidence 34458988 8872 222223333358899998887654
No 208
>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=47.30 E-value=12 Score=21.22 Aligned_cols=24 Identities=42% Similarity=0.863 Sum_probs=14.8
Q ss_pred ccCCCCCCCCeEEEEEeccCcEEEEEcCccc
Q 035653 27 FQCPFCGHGTSVECRIDKKIQIGEAFCWNCL 57 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~ 57 (87)
-.||.|+.+ -.+ ++ -|.+.|-+|+
T Consensus 18 ~~Cp~C~~P---L~~-~k---~g~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTP---LMR-DK---DGKIYCVSCG 41 (41)
T ss_pred CccCCCCCe---eEE-ec---CCCEECCCCC
Confidence 369999752 222 22 3467898885
No 209
>KOG3456 consensus NADH:ubiquinone oxidoreductase, NDUFS6/13 kDa subunit [Energy production and conversion]
Probab=46.69 E-value=11 Score=26.16 Aligned_cols=27 Identities=33% Similarity=0.432 Sum_probs=20.2
Q ss_pred CCCCCCeEEEEEeccCcEEEEEcCcccceeE
Q 035653 31 FCGHGTSVECRIDKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 31 fC~~~~sV~v~idk~~~~g~~~C~~C~~~~~ 61 (87)
-=||++ |-|.+|+... ..|+-||++|-
T Consensus 89 aLGHPk-vyInLDk~~~---~~CgYCGlrf~ 115 (120)
T KOG3456|consen 89 ALGHPK-VYINLDKPGP---HICGYCGLRFV 115 (120)
T ss_pred CCCCCe-EEEEcCCCCC---cccccchhhhh
Confidence 336765 7788887643 68999999884
No 210
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=46.47 E-value=14 Score=20.17 Aligned_cols=11 Identities=36% Similarity=1.038 Sum_probs=8.8
Q ss_pred cccCCCCCCCC
Q 035653 26 QFQCPFCGHGT 36 (87)
Q Consensus 26 ~F~CPfC~~~~ 36 (87)
...||.||...
T Consensus 2 ~~~Cp~Cg~~~ 12 (47)
T PF14690_consen 2 PPRCPHCGSPS 12 (47)
T ss_pred CccCCCcCCCc
Confidence 56899999864
No 211
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=45.25 E-value=18 Score=21.41 Aligned_cols=16 Identities=19% Similarity=0.351 Sum_probs=12.9
Q ss_pred EEEcCcccceeEeecC
Q 035653 50 EAFCWNCLERFCTQIH 65 (87)
Q Consensus 50 ~~~C~~C~~~~~~~i~ 65 (87)
.|.|..||..|.+...
T Consensus 4 ~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 4 TLTCKDCGAEFVFTAG 19 (49)
T ss_pred eEEcccCCCeEEEehh
Confidence 5789999999887653
No 212
>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=45.24 E-value=68 Score=20.22 Aligned_cols=39 Identities=21% Similarity=0.214 Sum_probs=30.0
Q ss_pred eccCcEEEEEcCcccceeEee-cCCCCchhhhhhhhHHHHH
Q 035653 43 DKKIQIGEAFCWNCLERFCTQ-IHALTEPIDIYAEWIDECE 82 (87)
Q Consensus 43 dk~~~~g~~~C~~C~~~~~~~-i~~L~epiDVYs~wiD~~e 82 (87)
|.......+.|.. |..|..+ .++.++|=+++..|+....
T Consensus 23 ~~~~~~l~lk~~t-~r~~yl~L~~~~~~~~~~F~~w~~lv~ 62 (77)
T PF12480_consen 23 DLEKQQLKLKLVT-GRPFYLQLCAPADKPETLFGEWIRLVS 62 (77)
T ss_pred cCcccEEEEEEcc-CCEEEEEEeCcccCcchhHHHHHHHHH
Confidence 4455677788777 4556666 8889999999999998765
No 213
>PF12773 DZR: Double zinc ribbon
Probab=45.12 E-value=6.9 Score=21.89 Aligned_cols=24 Identities=29% Similarity=0.696 Sum_probs=13.0
Q ss_pred CCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 29 CPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 29 CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
||.||..-. ......+.|..||..
T Consensus 15 C~~CG~~l~-------~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 15 CPHCGTPLP-------PPDQSKKICPNCGAE 38 (50)
T ss_pred ChhhcCChh-------hccCCCCCCcCCcCC
Confidence 666666422 223345567777763
No 214
>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=45.09 E-value=7.2 Score=18.97 Aligned_cols=11 Identities=27% Similarity=0.607 Sum_probs=7.9
Q ss_pred EcCcccceeEe
Q 035653 52 FCWNCLERFCT 62 (87)
Q Consensus 52 ~C~~C~~~~~~ 62 (87)
.|..|+..|.+
T Consensus 3 ~C~~C~~~F~~ 13 (27)
T PF13912_consen 3 ECDECGKTFSS 13 (27)
T ss_dssp EETTTTEEESS
T ss_pred CCCccCCccCC
Confidence 57788877754
No 215
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.08 E-value=8 Score=27.75 Aligned_cols=43 Identities=28% Similarity=0.616 Sum_probs=23.8
Q ss_pred CccccCCCCCCCCeEEEEE--eccCcEE-----EEEcCcccceeEeecCCCC
Q 035653 24 DTQFQCPFCGHGTSVECRI--DKKIQIG-----EAFCWNCLERFCTQIHALT 68 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~i--dk~~~~g-----~~~C~~C~~~~~~~i~~L~ 68 (87)
.++-+||.|+.. +.=.. .---+.| --.|.+||..|--.-..|.
T Consensus 37 ati~qcp~csas--irgd~~vegvlglg~dye~psfchncgs~fpwterkia 86 (160)
T COG4306 37 ATITQCPICSAS--IRGDYYVEGVLGLGGDYEPPSFCHNCGSRFPWTERKIA 86 (160)
T ss_pred HHHhcCCccCCc--ccccceeeeeeccCCCCCCcchhhcCCCCCCcHHHHHh
Confidence 467799999973 21111 0001111 2479999999865444433
No 216
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=44.92 E-value=11 Score=27.78 Aligned_cols=14 Identities=43% Similarity=0.814 Sum_probs=10.5
Q ss_pred CCCccccCCCCCCC
Q 035653 22 KLDTQFQCPFCGHG 35 (87)
Q Consensus 22 kl~~~F~CPfC~~~ 35 (87)
...-.=.||-|||-
T Consensus 89 ~k~nl~~CP~CGh~ 102 (176)
T KOG4080|consen 89 PKDNLNTCPACGHI 102 (176)
T ss_pred chhccccCcccCcc
Confidence 34457789999994
No 217
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=44.79 E-value=20 Score=27.22 Aligned_cols=28 Identities=29% Similarity=0.490 Sum_probs=20.4
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
.||.||+. |....-.+.+.-.|..|+..
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 69999974 23333457788999999864
No 218
>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=43.91 E-value=67 Score=19.41 Aligned_cols=33 Identities=33% Similarity=0.567 Sum_probs=20.7
Q ss_pred ccccCCCCCC----CCeEEEEEec---cCcEEEEEcCccc
Q 035653 25 TQFQCPFCGH----GTSVECRIDK---KIQIGEAFCWNCL 57 (87)
Q Consensus 25 ~~F~CPfC~~----~~sV~v~idk---~~~~g~~~C~~C~ 57 (87)
+..-|..|+. ..++++.|.+ ..+.-.+.|..||
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 3356777763 3456788999998
No 219
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=43.91 E-value=22 Score=26.91 Aligned_cols=26 Identities=19% Similarity=0.409 Sum_probs=18.6
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCccc
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCL 57 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~ 57 (87)
.||.||++ | ...+-.+.+.-.|..|+
T Consensus 246 pCprCG~~--I--~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 246 PCLNCKTP--I--RRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred cCCCCCCe--e--EEEEECCCccEECcCCc
Confidence 79999973 2 22333567888999997
No 220
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=43.61 E-value=19 Score=24.85 Aligned_cols=47 Identities=21% Similarity=0.236 Sum_probs=35.1
Q ss_pred CCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe-----ecCCCCchhhhhhhh
Q 035653 29 CPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT-----QIHALTEPIDIYAEW 77 (87)
Q Consensus 29 CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~-----~i~~L~epiDVYs~w 77 (87)
|+-||+ -+--+=|+.+.+-.++|++|.-.++- .+|.|.-.+|=...-
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 888886 36666688888999999999976543 378888877755443
No 221
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=43.34 E-value=12 Score=22.85 Aligned_cols=16 Identities=31% Similarity=0.609 Sum_probs=11.6
Q ss_pred CCCCCccccCCCCCCC
Q 035653 20 MEKLDTQFQCPFCGHG 35 (87)
Q Consensus 20 ~~kl~~~F~CPfC~~~ 35 (87)
--+++..=-|||||..
T Consensus 33 ~f~~~rYngCPfC~~~ 48 (55)
T PF14447_consen 33 CFPGERYNGCPFCGTP 48 (55)
T ss_pred ccChhhccCCCCCCCc
Confidence 3456667779999974
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=43.16 E-value=9.6 Score=24.58 Aligned_cols=11 Identities=45% Similarity=1.265 Sum_probs=6.0
Q ss_pred ccccCCCCCCC
Q 035653 25 TQFQCPFCGHG 35 (87)
Q Consensus 25 ~~F~CPfC~~~ 35 (87)
..|.||.||+.
T Consensus 64 s~~~Cp~Cg~~ 74 (81)
T PF10609_consen 64 SYFVCPHCGER 74 (81)
T ss_dssp -EEE-TTT--E
T ss_pred CccCCCCCCCe
Confidence 57999999984
No 223
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.02 E-value=10 Score=29.59 Aligned_cols=11 Identities=27% Similarity=1.032 Sum_probs=9.5
Q ss_pred CccccCCCCCC
Q 035653 24 DTQFQCPFCGH 34 (87)
Q Consensus 24 ~~~F~CPfC~~ 34 (87)
++.|+||+||.
T Consensus 17 kk~ieCPvC~t 27 (267)
T COG1655 17 KKTIECPVCNT 27 (267)
T ss_pred hceeccCcccc
Confidence 57899999996
No 224
>PHA00733 hypothetical protein
Probab=42.58 E-value=3.3 Score=28.30 Aligned_cols=40 Identities=20% Similarity=0.416 Sum_probs=22.6
Q ss_pred CccccCCCCCCCCeEEEEEeccC--cEEEEEcCcccceeEee
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKI--QIGEAFCWNCLERFCTQ 63 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~--~~g~~~C~~C~~~~~~~ 63 (87)
.+.|.|+.|+..-+-...+..-. ......|..|+..|...
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 56899999996321111110000 01236999999988654
No 225
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=42.52 E-value=36 Score=24.90 Aligned_cols=64 Identities=11% Similarity=0.171 Sum_probs=42.8
Q ss_pred ccCCCCCCccccCCCCCCCCeEEEEEec---cCcEEEEEcCcccceeEeec-CCCCchhhhhhhhHHHHHH
Q 035653 17 TKGMEKLDTQFQCPFCGHGTSVECRIDK---KIQIGEAFCWNCLERFCTQI-HALTEPIDIYAEWIDECER 83 (87)
Q Consensus 17 kk~~~kl~~~F~CPfC~~~~sV~v~idk---~~~~g~~~C~~C~~~~~~~i-~~L~epiDVYs~wiD~~e~ 83 (87)
+..++.+.-.|+|-.||.-.+= .|.+ ..|+-.+.|.-|....-.-= -.|....|+|. =|+++..
T Consensus 70 ~~~kp~m~l~yTCkvCntRs~k--tisk~AY~~GvVivqC~gC~~~HliaDnL~~F~d~~~~~-nied~l~ 137 (165)
T KOG3277|consen 70 KVPKPRMQLAYTCKVCNTRSTK--TISKQAYEKGVVIVQCPGCKNHHLIADNLGWFHDLKGKR-NIEDILA 137 (165)
T ss_pred cCCCcceEEEEEeeccCCcccc--ccChhhhhCceEEEECCCCccceeehhhhcccccccccc-cHHHHHH
Confidence 4556778889999999987653 3333 36889999999998765531 12455667774 2444433
No 226
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=42.23 E-value=12 Score=27.10 Aligned_cols=11 Identities=36% Similarity=0.933 Sum_probs=5.6
Q ss_pred ccccCCCCCCC
Q 035653 25 TQFQCPFCGHG 35 (87)
Q Consensus 25 ~~F~CPfC~~~ 35 (87)
.+-.||.||+.
T Consensus 148 ~P~~CPiCga~ 158 (166)
T COG1592 148 APEVCPICGAP 158 (166)
T ss_pred CCCcCCCCCCh
Confidence 34455555553
No 227
>KOG3022 consensus Predicted ATPase, nucleotide-binding [Cell cycle control, cell division, chromosome partitioning]
Probab=41.70 E-value=15 Score=29.25 Aligned_cols=13 Identities=54% Similarity=1.272 Sum_probs=10.7
Q ss_pred ccccCCCCCCCCe
Q 035653 25 TQFQCPFCGHGTS 37 (87)
Q Consensus 25 ~~F~CPfC~~~~s 37 (87)
+.|.||.|+|..+
T Consensus 221 s~f~Cp~C~~~~~ 233 (300)
T KOG3022|consen 221 SGFVCPKCGHSTN 233 (300)
T ss_pred ccccCCCCCCcce
Confidence 6899999999643
No 228
>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=41.57 E-value=50 Score=27.65 Aligned_cols=36 Identities=25% Similarity=0.352 Sum_probs=25.7
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecC
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIH 65 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~ 65 (87)
-||.||.-.+-.+..|-.. .-.-.|. ||...++.|.
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 4999999877555666554 3444785 9998888774
No 229
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=41.14 E-value=26 Score=32.94 Aligned_cols=59 Identities=20% Similarity=0.263 Sum_probs=31.9
Q ss_pred cccCCCCCCCCeEEEEEeccC--cEEEEEcCcccceeE--------------eecCCCCchhhhhhhhHHHHHHhh
Q 035653 26 QFQCPFCGHGTSVECRIDKKI--QIGEAFCWNCLERFC--------------TQIHALTEPIDIYAEWIDECERAN 85 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~--~~g~~~C~~C~~~~~--------------~~i~~L~epiDVYs~wiD~~e~~n 85 (87)
.|.||.||++. ....=..-. ......|..||.... -.+.+-..-||+=..|-++.+.+.
T Consensus 667 ~rkCPkCG~~t-~~~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGtplv~~~~~~i~~~~~~~~A~~~~g 741 (1337)
T PRK14714 667 RRRCPSCGTET-YENRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELTPYQRRTINVKEEYRSALENVG 741 (1337)
T ss_pred EEECCCCCCcc-ccccCcccCCcCCCceeCccCCCccCCCccccccCCCCCCcccccceEEecHHHHHHHHHHHhC
Confidence 48888888742 111000000 012336777776431 113444557888888888888763
No 230
>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=41.06 E-value=24 Score=32.45 Aligned_cols=48 Identities=19% Similarity=0.218 Sum_probs=33.6
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhhhhhHHHHHHhh
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIYAEWIDECERAN 85 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVYs~wiD~~e~~n 85 (87)
-.|.||-||+. .-...|..||..- ..+.+-..-||+=..|-++.+.+.
T Consensus 624 ~~RKCPkCG~y------------Tlk~rCP~CG~~T-e~~~pc~~~i~l~~~~~~A~~~lg 671 (1095)
T TIGR00354 624 AIRKCPQCGKE------------SFWLKCPVCGELT-EQLYYGKRKVDLRELYEEAIANLG 671 (1095)
T ss_pred EEEECCCCCcc------------cccccCCCCCCcc-ccccceeEEecHHHHHHHHHHHhC
Confidence 45788888873 1345899999863 334444668899899998888763
No 231
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=40.71 E-value=11 Score=31.24 Aligned_cols=29 Identities=28% Similarity=0.487 Sum_probs=20.5
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEee
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQ 63 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~ 63 (87)
-||+||. .|+.+... -..|..||..+...
T Consensus 352 ~Cp~Cg~------~m~S~G~~-g~rC~kCg~~~~~~ 380 (421)
T COG1571 352 VCPRCGG------RMKSAGRN-GFRCKKCGTRARET 380 (421)
T ss_pred CCCccCC------chhhcCCC-CcccccccccCCcc
Confidence 5999997 33443333 56999999988654
No 232
>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=40.68 E-value=57 Score=17.83 Aligned_cols=28 Identities=36% Similarity=0.527 Sum_probs=17.7
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCc---ccce
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWN---CLER 59 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~---C~~~ 59 (87)
.||-||+ .+..+..+.. -.+.|.. |...
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 2544444433 5678877 6643
No 233
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.55 E-value=27 Score=24.32 Aligned_cols=23 Identities=35% Similarity=0.834 Sum_probs=17.8
Q ss_pred ccCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 27 FQCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
-.||.||.+ --+-.+.|.+|+.+
T Consensus 7 ~~cPvcg~~----------~iVTeL~c~~~etT 29 (122)
T COG3877 7 NRCPVCGRK----------LIVTELKCSNCETT 29 (122)
T ss_pred CCCCccccc----------ceeEEEecCCCCce
Confidence 469999974 23467899999976
No 234
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=39.98 E-value=28 Score=26.24 Aligned_cols=27 Identities=26% Similarity=0.503 Sum_probs=19.0
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
.||.||.. | ....-.+.+.-.|..|+.
T Consensus 247 pC~~Cg~~--I--~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 247 PCRRCGTP--I--EKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCe--e--EEEEECCCCcEECcCCCC
Confidence 49999973 2 223335678889999974
No 235
>cd01237 Unc112 Unc-112 pleckstrin homology (PH) domain. Unc-112 pleckstrin homology (PH) domain. Unc-112 and related proteins contain two FERM domains with a PH domain between them. Both the PH and FERM domains have a PH-like fold. The FERM domains are likely responsible for the role of Unc-112 in organizing beta-integrin. The specific role of the Unc-112 PH domain is not known, but it is predicted to be involved in mediating membrane interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=39.97 E-value=19 Score=24.42 Aligned_cols=15 Identities=33% Similarity=0.893 Sum_probs=12.6
Q ss_pred hhhhhhHHHHHHhhC
Q 035653 72 DIYAEWIDECERANN 86 (87)
Q Consensus 72 DVYs~wiD~~e~~n~ 86 (87)
.-|.+|+++|..|.+
T Consensus 90 eqya~Wmaa~rlas~ 104 (106)
T cd01237 90 KQYAKWMAACRLASK 104 (106)
T ss_pred HHHHHHHHHHHHhhC
Confidence 568999999998864
No 236
>PRK14873 primosome assembly protein PriA; Provisional
Probab=39.88 E-value=23 Score=30.51 Aligned_cols=29 Identities=21% Similarity=0.400 Sum_probs=17.6
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
..+.||.|+.. ++ +.+ ..+.+.|.-||..
T Consensus 391 ~~~~C~~C~~~--L~--~h~--~~~~l~Ch~CG~~ 419 (665)
T PRK14873 391 TPARCRHCTGP--LG--LPS--AGGTPRCRWCGRA 419 (665)
T ss_pred CeeECCCCCCc--ee--Eec--CCCeeECCCCcCC
Confidence 45677777753 22 222 2357888888864
No 237
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.75 E-value=15 Score=24.97 Aligned_cols=9 Identities=44% Similarity=1.483 Sum_probs=7.6
Q ss_pred ccCCCCCCC
Q 035653 27 FQCPFCGHG 35 (87)
Q Consensus 27 F~CPfC~~~ 35 (87)
|.||.||..
T Consensus 93 ~~CP~Cgs~ 101 (124)
T PRK00762 93 IECPVCGNK 101 (124)
T ss_pred CcCcCCCCC
Confidence 689999964
No 238
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.64 E-value=14 Score=24.83 Aligned_cols=31 Identities=16% Similarity=0.411 Sum_probs=18.3
Q ss_pred CCCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 21 EKLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 21 ~kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
...|-.|.|+-||+.-++. ......|..||.
T Consensus 66 e~vp~~~~C~~Cg~~~~~~-------~~~~~~CP~Cgs 96 (117)
T PRK00564 66 VDEKVELECKDCSHVFKPN-------ALDYGVCEKCHS 96 (117)
T ss_pred EecCCEEEhhhCCCccccC-------CccCCcCcCCCC
Confidence 3456778888888643221 123345888885
No 239
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=39.40 E-value=16 Score=20.47 Aligned_cols=16 Identities=19% Similarity=0.391 Sum_probs=12.2
Q ss_pred EEEEEcCcccceeEee
Q 035653 48 IGEAFCWNCLERFCTQ 63 (87)
Q Consensus 48 ~g~~~C~~C~~~~~~~ 63 (87)
.|.|.|+.||..+...
T Consensus 3 ~g~l~C~~CG~~m~~~ 18 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTRR 18 (58)
T ss_pred CCcEEcccCCcEeEEE
Confidence 4678999999876553
No 240
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=38.90 E-value=14 Score=27.08 Aligned_cols=10 Identities=50% Similarity=1.298 Sum_probs=8.3
Q ss_pred ccccCCCCCC
Q 035653 25 TQFQCPFCGH 34 (87)
Q Consensus 25 ~~F~CPfC~~ 34 (87)
..|.||-||.
T Consensus 131 ~~F~Cp~Cg~ 140 (176)
T COG1675 131 LGFTCPKCGE 140 (176)
T ss_pred hCCCCCCCCc
Confidence 4599999997
No 241
>PHA00732 hypothetical protein
Probab=38.83 E-value=3 Score=26.50 Aligned_cols=46 Identities=20% Similarity=0.411 Sum_probs=23.8
Q ss_pred cccCCCCCCCCeEEEEEec--c-CcEEEEEcCcccceeEeecCCCCchhh
Q 035653 26 QFQCPFCGHGTSVECRIDK--K-IQIGEAFCWNCLERFCTQIHALTEPID 72 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk--~-~~~g~~~C~~C~~~~~~~i~~L~epiD 72 (87)
.|.|+.|+..-+-.-.+.. . .-.+ -.|..||..|.........--|
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~-~~C~~CgKsF~~l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL-TKCPVCNKSYRRLNQHFYSQYD 49 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC-CccCCCCCEeCChhhhhcccCC
Confidence 4789999864211110100 0 0011 2799999999865544444333
No 242
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=38.78 E-value=38 Score=17.72 Aligned_cols=26 Identities=19% Similarity=0.595 Sum_probs=15.9
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcC
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCW 54 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~ 54 (87)
-+.|.|..||+ +...++ .+-+.+.|-
T Consensus 5 ~~~ykC~~Cgn---iv~v~~--~~~~~l~Cc 30 (34)
T TIGR00319 5 GQVYKCEVCGN---IVEVLH--AGGGQLVCC 30 (34)
T ss_pred CcEEEcCCCCc---EEEEEE--CCCcceecc
Confidence 35899999998 333332 334456663
No 243
>PRK10445 endonuclease VIII; Provisional
Probab=37.95 E-value=32 Score=25.98 Aligned_cols=26 Identities=19% Similarity=0.303 Sum_probs=18.2
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCccc
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCL 57 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~ 57 (87)
.||.||.. -..+ +-.+.+.-.|..|+
T Consensus 237 ~Cp~Cg~~-I~~~---~~~gR~t~~CP~CQ 262 (263)
T PRK10445 237 ACERCGGI-IEKT---TLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCE-eEEE---EECCCCcEECCCCc
Confidence 59999973 2222 33567888999996
No 244
>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=37.68 E-value=31 Score=26.13 Aligned_cols=26 Identities=31% Similarity=0.570 Sum_probs=18.0
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCccc
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCL 57 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~ 57 (87)
.||.||++ | ....-.+...-.|..|+
T Consensus 247 pC~~Cg~~--I--~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 247 PCRRCGTP--I--EKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCe--e--EEEEECCCCCEECCCCC
Confidence 69999974 2 22333567788999985
No 245
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=37.46 E-value=31 Score=26.21 Aligned_cols=26 Identities=27% Similarity=0.524 Sum_probs=18.7
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCccc
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCL 57 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~ 57 (87)
.||.||.. | ....-.+.+.-.|..|+
T Consensus 256 pC~~Cg~~--I--~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 256 PCRKCGTP--I--ERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred CCCcCCCe--e--EEEEECCCccEECCCCc
Confidence 79999973 2 22233667888999996
No 246
>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=37.38 E-value=29 Score=23.02 Aligned_cols=12 Identities=33% Similarity=0.905 Sum_probs=5.1
Q ss_pred CCccccCCCCCC
Q 035653 23 LDTQFQCPFCGH 34 (87)
Q Consensus 23 l~~~F~CPfC~~ 34 (87)
.|-.|.|+.||+
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 344555666665
No 247
>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=37.25 E-value=15 Score=21.29 Aligned_cols=8 Identities=38% Similarity=1.568 Sum_probs=3.9
Q ss_pred ccCCCCCC
Q 035653 27 FQCPFCGH 34 (87)
Q Consensus 27 F~CPfC~~ 34 (87)
+.||.|+.
T Consensus 42 W~CPiC~~ 49 (50)
T PF02891_consen 42 WKCPICNK 49 (50)
T ss_dssp -B-TTT--
T ss_pred eECcCCcC
Confidence 89999985
No 248
>PRK15338 type III secretion system regulator InvE; Provisional
Probab=37.00 E-value=17 Score=29.54 Aligned_cols=20 Identities=20% Similarity=0.619 Sum_probs=15.2
Q ss_pred CCCCchhhhhhhhHHHHHHh
Q 035653 65 HALTEPIDIYAEWIDECERA 84 (87)
Q Consensus 65 ~~L~epiDVYs~wiD~~e~~ 84 (87)
..=..++++|.+||+.+...
T Consensus 195 ~~d~~~~~iY~~Wieeyg~~ 214 (372)
T PRK15338 195 QSESHEVEIYSDWIASYGYQ 214 (372)
T ss_pred hccCcHHHHHHHHHHHhCcc
Confidence 33457899999999998543
No 249
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=36.56 E-value=4.8 Score=25.29 Aligned_cols=30 Identities=17% Similarity=0.445 Sum_probs=23.1
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
.||-|+..+++. |=+.+++-++.|-.||-.
T Consensus 12 ~CP~C~~~Dtl~--mW~En~ve~vECV~CG~~ 41 (66)
T COG3529 12 VCPACQAQDTLA--MWRENNVEIVECVKCGHH 41 (66)
T ss_pred CCcccchhhHHH--HHHhcCCceEehhhcchH
Confidence 699999876443 345678999999999954
No 250
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=36.20 E-value=17 Score=18.15 Aligned_cols=10 Identities=30% Similarity=0.574 Sum_probs=6.5
Q ss_pred EEcCccccee
Q 035653 51 AFCWNCLERF 60 (87)
Q Consensus 51 ~~C~~C~~~~ 60 (87)
+.|..||..|
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 3566777666
No 251
>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=36.11 E-value=25 Score=19.54 Aligned_cols=28 Identities=32% Similarity=0.633 Sum_probs=13.4
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
-.+|.|..||+ -|+|.- .+-|.+.| ||+
T Consensus 4 ~~~YkC~~CGn--iVev~~---~g~g~lvC--CGe 31 (36)
T PF06397_consen 4 GEFYKCEHCGN--IVEVVH---DGGGPLVC--CGE 31 (36)
T ss_dssp TEEEE-TTT----EEEEEE-----SS-EEE--TTE
T ss_pred ccEEEccCCCC--EEEEEE---CCCCCEEe--CCc
Confidence 45899999998 244432 33456666 554
No 252
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=35.80 E-value=6.1 Score=24.30 Aligned_cols=16 Identities=19% Similarity=0.605 Sum_probs=7.9
Q ss_pred CccccCCCCCCCCeEEEE
Q 035653 24 DTQFQCPFCGHGTSVECR 41 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~ 41 (87)
+..=+||+|..+ |+++
T Consensus 53 ~~~G~CP~C~~~--i~~~ 68 (70)
T PF11793_consen 53 PIFGECPYCSSP--ISWS 68 (70)
T ss_dssp --EEE-TTT-SE--EEGG
T ss_pred ccccCCcCCCCe--eeEe
Confidence 444579999974 5443
No 253
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=35.65 E-value=20 Score=20.78 Aligned_cols=11 Identities=45% Similarity=1.057 Sum_probs=9.6
Q ss_pred CccccCCCCCC
Q 035653 24 DTQFQCPFCGH 34 (87)
Q Consensus 24 ~~~F~CPfC~~ 34 (87)
+....||.||.
T Consensus 44 ~~i~~Cp~CgR 54 (56)
T PF02591_consen 44 DEIVFCPNCGR 54 (56)
T ss_pred CCeEECcCCCc
Confidence 77899999985
No 254
>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=35.65 E-value=64 Score=16.27 Aligned_cols=26 Identities=23% Similarity=0.432 Sum_probs=14.4
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCccc
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCL 57 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~ 57 (87)
.||.|++. ...+.+ .+...-.|..|.
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 59999984 344444 556777888885
No 255
>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=35.64 E-value=47 Score=17.40 Aligned_cols=25 Identities=28% Similarity=0.764 Sum_probs=15.4
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcC
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCW 54 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~ 54 (87)
..|.|..||+. |.+ ++ .+-+.+.|-
T Consensus 3 ~~ykC~~CGni--v~v-~~--~~~~~l~Cc 27 (34)
T cd00974 3 EVYKCEICGNI--VEV-LN--VGGGTLVCC 27 (34)
T ss_pred cEEEcCCCCcE--EEE-EE--CCCcceeec
Confidence 47999999982 333 32 344556663
No 256
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=35.23 E-value=15 Score=24.73 Aligned_cols=29 Identities=28% Similarity=0.448 Sum_probs=16.8
Q ss_pred EEcCcccceeEe-ecCCCCchhhhhhhhHH
Q 035653 51 AFCWNCLERFCT-QIHALTEPIDIYAEWID 79 (87)
Q Consensus 51 ~~C~~C~~~~~~-~i~~L~epiDVYs~wiD 79 (87)
+.|+.||..|.. +|+.-|--=--=|+||.
T Consensus 59 a~CkkCGfef~~~~ik~pSRCP~CKSE~Ie 88 (97)
T COG3357 59 ARCKKCGFEFRDDKIKKPSRCPKCKSEWIE 88 (97)
T ss_pred hhhcccCccccccccCCcccCCcchhhccc
Confidence 578888877754 45543333334556664
No 257
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=35.22 E-value=17 Score=24.47 Aligned_cols=9 Identities=44% Similarity=1.549 Sum_probs=6.8
Q ss_pred cccCCCCCC
Q 035653 26 QFQCPFCGH 34 (87)
Q Consensus 26 ~F~CPfC~~ 34 (87)
.+.||+||-
T Consensus 3 LI~CP~Cg~ 11 (97)
T COG4311 3 LIPCPYCGE 11 (97)
T ss_pred eecCCCCCC
Confidence 467888886
No 258
>smart00355 ZnF_C2H2 zinc finger.
Probab=35.13 E-value=19 Score=16.19 Aligned_cols=8 Identities=38% Similarity=0.862 Sum_probs=3.9
Q ss_pred cCccccee
Q 035653 53 CWNCLERF 60 (87)
Q Consensus 53 C~~C~~~~ 60 (87)
|..|+..|
T Consensus 3 C~~C~~~f 10 (26)
T smart00355 3 CPECGKVF 10 (26)
T ss_pred CCCCcchh
Confidence 44555444
No 259
>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=34.82 E-value=16 Score=26.46 Aligned_cols=12 Identities=42% Similarity=1.063 Sum_probs=3.2
Q ss_pred CCccccCCCCCC
Q 035653 23 LDTQFQCPFCGH 34 (87)
Q Consensus 23 l~~~F~CPfC~~ 34 (87)
+-.-|.||||+-
T Consensus 151 ~~~~~~Cp~C~~ 162 (175)
T PF05280_consen 151 PRHSFVCPFCQP 162 (175)
T ss_dssp -SS----TT---
T ss_pred CCcCcCCCCCCC
Confidence 456899999995
No 260
>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=34.77 E-value=23 Score=26.10 Aligned_cols=18 Identities=33% Similarity=0.853 Sum_probs=15.6
Q ss_pred CchhhhhhhhHHHHHHhh
Q 035653 68 TEPIDIYAEWIDECERAN 85 (87)
Q Consensus 68 ~epiDVYs~wiD~~e~~n 85 (87)
.+|+|++..|+++..+++
T Consensus 28 ~~P~~~f~~W~~~a~~~~ 45 (217)
T TIGR00558 28 DDPIDLFEIWFNEAIEAR 45 (217)
T ss_pred CCHHHHHHHHHHHHHhcC
Confidence 599999999999887654
No 261
>PF14369 zf-RING_3: zinc-finger
Probab=34.73 E-value=51 Score=17.80 Aligned_cols=31 Identities=19% Similarity=0.431 Sum_probs=17.0
Q ss_pred ccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 27 FQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
|=|-.|+. .|.+...... .+.|..|+-.|-.
T Consensus 3 ywCh~C~~--~V~~~~~~~~---~~~CP~C~~gFvE 33 (35)
T PF14369_consen 3 YWCHQCNR--FVRIAPSPDS---DVACPRCHGGFVE 33 (35)
T ss_pred EeCccCCC--EeEeCcCCCC---CcCCcCCCCcEeE
Confidence 44666765 4555433222 2368888777643
No 262
>COG1773 Rubredoxin [Energy production and conversion]
Probab=34.24 E-value=22 Score=21.55 Aligned_cols=21 Identities=33% Similarity=0.640 Sum_probs=16.2
Q ss_pred CCCCCccccCCCCCCCCeEEE
Q 035653 20 MEKLDTQFQCPFCGHGTSVEC 40 (87)
Q Consensus 20 ~~kl~~~F~CPfC~~~~sV~v 40 (87)
-.-||-.+.||.||..++.-.
T Consensus 30 fedlPd~w~CP~Cg~~K~~F~ 50 (55)
T COG1773 30 FEDLPDDWVCPECGVGKKDFE 50 (55)
T ss_pred hhhCCCccCCCCCCCCHhHee
Confidence 467899999999998665433
No 263
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=33.86 E-value=20 Score=31.30 Aligned_cols=35 Identities=29% Similarity=0.467 Sum_probs=20.4
Q ss_pred ccCCCCCCCCeEEEEEeccCcEEEEEcCcccc----eeEeecCCCCchhhh
Q 035653 27 FQCPFCGHGTSVECRIDKKIQIGEAFCWNCLE----RFCTQIHALTEPIDI 73 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~----~~~~~i~~L~epiDV 73 (87)
=.|+-||+.... .-.|..||. .+.--+.+| .||+=
T Consensus 681 ~~C~~CG~~~~~-----------~~~CP~CG~~~~~~~~Ri~GYl-~~v~~ 719 (735)
T PRK07111 681 DRCPVCGYLGVI-----------EDKCPKCGSTNIQRIRRITGYL-GTLDR 719 (735)
T ss_pred eecCCCCCCCCc-----------CccCcCCCCccceeeehhhhhc-cchhh
Confidence 358888874321 158999984 222234555 66654
No 264
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.68 E-value=9.7 Score=32.22 Aligned_cols=33 Identities=36% Similarity=0.833 Sum_probs=27.3
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCccccee
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERF 60 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~ 60 (87)
+|.-+||+|=++.+|.+.+. -|++.|..|-+.|
T Consensus 184 ~t~~~CPICL~~~~~p~~t~----CGHiFC~~CiLqy 216 (513)
T KOG2164|consen 184 STDMQCPICLEPPSVPVRTN----CGHIFCGPCILQY 216 (513)
T ss_pred CcCCcCCcccCCCCcccccc----cCceeeHHHHHHH
Confidence 34689999999999988764 6999999998765
No 265
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=33.59 E-value=36 Score=26.70 Aligned_cols=27 Identities=22% Similarity=0.332 Sum_probs=17.8
Q ss_pred CCCCCCCCeEEEEEeccCcEEEEEcCcccceeE
Q 035653 29 CPFCGHGTSVECRIDKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 29 CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~ 61 (87)
|+.||++. ....+--...|..||..+-
T Consensus 114 Cg~CG~~~------~~~~~g~~~~C~~cg~~~f 140 (279)
T COG2816 114 CGRCGTKT------YPREGGWARVCPKCGHEHF 140 (279)
T ss_pred CCCCCCcC------ccccCceeeeCCCCCCccC
Confidence 78888743 4444445568999987653
No 266
>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=33.51 E-value=16 Score=24.38 Aligned_cols=11 Identities=27% Similarity=0.745 Sum_probs=8.5
Q ss_pred ccccCCCCCCC
Q 035653 25 TQFQCPFCGHG 35 (87)
Q Consensus 25 ~~F~CPfC~~~ 35 (87)
.-|.||+|-+-
T Consensus 23 ~D~~Cp~C~~~ 33 (178)
T cd03019 23 FSYGCPHCYNF 33 (178)
T ss_pred ECCCCcchhhh
Confidence 45899999863
No 267
>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=32.74 E-value=30 Score=21.65 Aligned_cols=37 Identities=19% Similarity=0.508 Sum_probs=20.8
Q ss_pred CccccCCCCCCCCeEEEEEeccC-cEEEEEcCccccee
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKI-QIGEAFCWNCLERF 60 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~-~~g~~~C~~C~~~~ 60 (87)
+..-.||.|+..++==|=..... .--.-.|..|...+
T Consensus 3 ~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~ryw 40 (63)
T PF02701_consen 3 EQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYW 40 (63)
T ss_pred ccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHH
Confidence 45678999998665433332211 12344677776543
No 268
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=32.57 E-value=16 Score=23.66 Aligned_cols=11 Identities=18% Similarity=0.407 Sum_probs=9.0
Q ss_pred EcCcccceeEe
Q 035653 52 FCWNCLERFCT 62 (87)
Q Consensus 52 ~C~~C~~~~~~ 62 (87)
+|..||+.|+.
T Consensus 10 ~C~~CG~d~~~ 20 (86)
T PF06170_consen 10 RCPHCGLDYSH 20 (86)
T ss_pred cccccCCcccc
Confidence 79999998865
No 269
>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=32.34 E-value=52 Score=26.60 Aligned_cols=52 Identities=23% Similarity=0.401 Sum_probs=29.3
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhhhhhHHHHHHh
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIYAEWIDECERA 84 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVYs~wiD~~e~~ 84 (87)
.|.||.||++..+.++ .......-.|..||...+ +.+..|++-..++.+++.
T Consensus 320 ~~rc~~c~~~~~~~~~--~~~~~~~~~~~~~~~~~~-----~~~~~~~ve~L~e~a~~~ 371 (403)
T TIGR03676 320 TFKCPNCGYEEEKTVK--PEEGDKSEACPKCGSELE-----IVEEEDIIEELSELAEES 371 (403)
T ss_pred EEEcCCCCcceeeecc--cccccccccCcccCcccc-----cchhhhHHHHHHHHHHHc
Confidence 5999999996544442 222222245888887522 223445555556665554
No 270
>PRK04351 hypothetical protein; Provisional
Probab=32.19 E-value=49 Score=23.26 Aligned_cols=34 Identities=21% Similarity=0.484 Sum_probs=23.1
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
=.+.|.-||+. .... +..+...-.|+.|+..+..
T Consensus 111 y~Y~C~~Cg~~---~~r~-Rr~n~~~yrCg~C~g~L~~ 144 (149)
T PRK04351 111 YLYECQSCGQQ---YLRK-RRINTKRYRCGKCRGKLKL 144 (149)
T ss_pred EEEECCCCCCE---eeee-eecCCCcEEeCCCCcEeee
Confidence 45899999973 2333 3445677899999976643
No 271
>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=32.05 E-value=22 Score=18.06 Aligned_cols=8 Identities=50% Similarity=1.202 Sum_probs=4.9
Q ss_pred ccCCCCCC
Q 035653 27 FQCPFCGH 34 (87)
Q Consensus 27 F~CPfC~~ 34 (87)
+.||.|+.
T Consensus 2 v~CPiC~~ 9 (26)
T smart00734 2 VQCPVCFR 9 (26)
T ss_pred CcCCCCcC
Confidence 45666665
No 272
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=31.28 E-value=21 Score=29.67 Aligned_cols=32 Identities=31% Similarity=0.502 Sum_probs=20.7
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
|+...||.|+-++-- ..-+..+.++|..|...
T Consensus 225 D~l~~C~~C~~s~n~----e~~~~sk~~~Cp~C~~~ 256 (457)
T KOG2324|consen 225 DTLMSCPSCGYSKNS----EDLDLSKIASCPKCNEG 256 (457)
T ss_pred cceeecCcCCccCch----hhhcCCccccCCcccCC
Confidence 678899999754311 11123345899999985
No 273
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=31.16 E-value=43 Score=19.63 Aligned_cols=28 Identities=29% Similarity=0.613 Sum_probs=9.8
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeE
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~ 61 (87)
.=.|..|+..=++ ..-.-+|+.||..|-
T Consensus 9 ~~~C~~C~~~F~~--------~~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 9 ASNCMICGKKFSL--------FRRRHHCRNCGRVVC 36 (69)
T ss_dssp -SB-TTT--B-BS--------SS-EEE-TTT--EEE
T ss_pred CCcCcCcCCcCCC--------ceeeEccCCCCCEEC
Confidence 3467778764222 233446666666553
No 274
>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=31.02 E-value=11 Score=23.14 Aligned_cols=36 Identities=17% Similarity=0.446 Sum_probs=16.8
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeE
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~ 61 (87)
.+.|.|.+|..+.+ .=.|++.. +..+.|+.|+....
T Consensus 17 ~~~y~C~~CHde~~-~H~~~~~~-~~~v~Cg~C~~~~~ 52 (71)
T PF05495_consen 17 GKYYPCRFCHDELE-DHPFDRWP-VKRVICGKCRTEQP 52 (71)
T ss_dssp TEEESSHHHHHHCS-SS---TTT---EEEETTT--EEE
T ss_pred cCeecHHHHHHHhc-cCcccccc-ccCeECCCCCCccC
Confidence 45677777765433 22233322 33777888876543
No 275
>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=30.95 E-value=17 Score=20.87 Aligned_cols=7 Identities=57% Similarity=1.777 Sum_probs=3.6
Q ss_pred cCCCCCC
Q 035653 28 QCPFCGH 34 (87)
Q Consensus 28 ~CPfC~~ 34 (87)
.||.|+.
T Consensus 22 ~CPlC~r 28 (54)
T PF04423_consen 22 CCPLCGR 28 (54)
T ss_dssp E-TTT--
T ss_pred cCCCCCC
Confidence 7999987
No 276
>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=30.90 E-value=49 Score=27.17 Aligned_cols=33 Identities=21% Similarity=0.379 Sum_probs=29.5
Q ss_pred CCCeEEEEEeccCcEEEEEcCcccceeEe-ecCC
Q 035653 34 HGTSVECRIDKKIQIGEAFCWNCLERFCT-QIHA 66 (87)
Q Consensus 34 ~~~sV~v~idk~~~~g~~~C~~C~~~~~~-~i~~ 66 (87)
|+..|.|.+|...|.+...-+.|.++|++ +||.
T Consensus 367 ~~~ei~I~vdLg~G~~~~~~w~cDLt~eYV~INa 400 (404)
T TIGR00120 367 ESDEIEIVVDLGTGDGAGTAWGCDLSYDYVRINA 400 (404)
T ss_pred CCCEEEEEEEeCCCCceEEEEcccCCccceeECC
Confidence 56789999999999999999999999988 4776
No 277
>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=30.90 E-value=28 Score=20.18 Aligned_cols=7 Identities=57% Similarity=1.592 Sum_probs=5.7
Q ss_pred CCCCCCC
Q 035653 29 CPFCGHG 35 (87)
Q Consensus 29 CPfC~~~ 35 (87)
||||...
T Consensus 1 CP~C~~k 7 (43)
T PF03470_consen 1 CPFCPGK 7 (43)
T ss_pred CCCCCCC
Confidence 8999874
No 278
>PTZ00293 thymidine kinase; Provisional
Probab=30.87 E-value=43 Score=24.97 Aligned_cols=31 Identities=35% Similarity=0.605 Sum_probs=23.8
Q ss_pred cCCCCCCCCeEEEEEeccCc--------EEEEEcCcccc
Q 035653 28 QCPFCGHGTSVECRIDKKIQ--------IGEAFCWNCLE 58 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~--------~g~~~C~~C~~ 58 (87)
-|.+||.+-+.+.++..... .....|+.|-.
T Consensus 139 iC~~CG~~A~~t~R~~~~~~~v~IGg~e~Y~a~CR~c~~ 177 (211)
T PTZ00293 139 VCMFCGKEASFSKRIVQSEQIELIGGEDKYIATCRKCFR 177 (211)
T ss_pred EchhhCCcceeEEEEcCCCCEEEECCcccEEehhhhhhh
Confidence 49999999999988865322 24788999983
No 279
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=30.70 E-value=33 Score=25.27 Aligned_cols=7 Identities=57% Similarity=1.730 Sum_probs=6.6
Q ss_pred CCCCCCC
Q 035653 29 CPFCGHG 35 (87)
Q Consensus 29 CPfC~~~ 35 (87)
||.|||+
T Consensus 156 Cp~CG~~ 162 (177)
T COG1439 156 CPICGSP 162 (177)
T ss_pred CCCCCCc
Confidence 9999996
No 280
>PRK06260 threonine synthase; Validated
Probab=30.55 E-value=33 Score=27.03 Aligned_cols=8 Identities=38% Similarity=1.132 Sum_probs=4.5
Q ss_pred ccCCCCCC
Q 035653 27 FQCPFCGH 34 (87)
Q Consensus 27 F~CPfC~~ 34 (87)
|.|+.||+
T Consensus 4 ~~C~~cg~ 11 (397)
T PRK06260 4 LKCIECGK 11 (397)
T ss_pred EEECCCCC
Confidence 55555555
No 281
>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=30.54 E-value=30 Score=24.56 Aligned_cols=34 Identities=21% Similarity=0.364 Sum_probs=20.6
Q ss_pred CccccCCCCCCCCeEEEEEecc-----------CcEEEEEcCccc
Q 035653 24 DTQFQCPFCGHGTSVECRIDKK-----------IQIGEAFCWNCL 57 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~-----------~~~g~~~C~~C~ 57 (87)
.=++.|.+|+++.|+++.=... .-+..+.||-|.
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 4578999999999988754321 126788999985
No 282
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.48 E-value=20 Score=24.57 Aligned_cols=9 Identities=33% Similarity=1.021 Sum_probs=4.6
Q ss_pred cCcccceeE
Q 035653 53 CWNCLERFC 61 (87)
Q Consensus 53 C~~C~~~~~ 61 (87)
|..|+..|.
T Consensus 58 C~~C~~~f~ 66 (112)
T TIGR00622 58 CFGCQGPFP 66 (112)
T ss_pred ccCcCCCCC
Confidence 555555543
No 283
>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=30.47 E-value=47 Score=22.74 Aligned_cols=30 Identities=23% Similarity=0.717 Sum_probs=18.8
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCccccee
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERF 60 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~ 60 (87)
-+.|.|+.||+ |...+. .+-+.++| ||+..
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 35899999998 333332 44466777 45543
No 284
>PRK05580 primosome assembly protein PriA; Validated
Probab=30.47 E-value=35 Score=29.09 Aligned_cols=30 Identities=17% Similarity=0.372 Sum_probs=16.8
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeE
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~ 61 (87)
.+.||.|+- .....+ ....+.|..||..+.
T Consensus 390 ~~~C~~C~~----~l~~h~--~~~~l~Ch~Cg~~~~ 419 (679)
T PRK05580 390 VAECPHCDA----SLTLHR--FQRRLRCHHCGYQEP 419 (679)
T ss_pred ccCCCCCCC----ceeEEC--CCCeEECCCCcCCCC
Confidence 456666664 222333 235678888886543
No 285
>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=30.31 E-value=52 Score=19.07 Aligned_cols=31 Identities=16% Similarity=0.531 Sum_probs=20.1
Q ss_pred cCCCCCCCCeEEE-EEec----cCcEEEEEcCcccc
Q 035653 28 QCPFCGHGTSVEC-RIDK----KIQIGEAFCWNCLE 58 (87)
Q Consensus 28 ~CPfC~~~~sV~v-~idk----~~~~g~~~C~~C~~ 58 (87)
.|.+|+++..+++ .+-. ...-+.+.|..|..
T Consensus 9 kCELC~a~~~L~vy~Vpp~~~~~~d~~iliC~tC~~ 44 (47)
T smart00782 9 KCELCGSDSPLVVYAVPPSSDVTADNSVMLCDTCHS 44 (47)
T ss_pred cccCcCCCCCceEEecCCCCCCCccceeeechHHHH
Confidence 3999999887665 3311 12346788888864
No 286
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=30.23 E-value=31 Score=21.21 Aligned_cols=19 Identities=16% Similarity=0.473 Sum_probs=12.7
Q ss_pred CCCccccCCCCCCCCeEEE
Q 035653 22 KLDTQFQCPFCGHGTSVEC 40 (87)
Q Consensus 22 kl~~~F~CPfC~~~~sV~v 40 (87)
..+..=.||+|+++-.-+.
T Consensus 35 s~~~~p~CPlC~s~M~~~~ 53 (59)
T PF14169_consen 35 SFEEEPVCPLCKSPMVSGT 53 (59)
T ss_pred ccCCCccCCCcCCccccce
Confidence 4455568999999754333
No 287
>PF12898 Stc1: Stc1 domain; InterPro: IPR024630 The domain contains 8 conserved cysteines that may bind to zinc. In S. pombe, proteins containing the domain act as protein linkers, which link the chromatin modifying CLRC complex to RNAi by tethering it to the RITS complex. This domain has a slightly different arrangement of its CxxC pairs from the LIM domain, hence it is not part of that family []. The tandem zinc-finger structure could mediate protein-protein interactions.
Probab=30.22 E-value=57 Score=20.71 Aligned_cols=37 Identities=27% Similarity=0.646 Sum_probs=25.1
Q ss_pred CCCCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhhhh
Q 035653 20 MEKLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIYAE 76 (87)
Q Consensus 20 ~~kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVYs~ 76 (87)
..+....=.|..|..+..++ +.|..|+. +-|+|-||+
T Consensus 31 ~~~~~~~i~C~~ct~~q~~E-----------l~C~~C~~---------~k~ld~FSK 67 (84)
T PF12898_consen 31 VDPANSGIRCRECTGGQVVE-----------LTCSPCGK---------TKPLDEFSK 67 (84)
T ss_pred CccCCCCCCCccCCCCCcCc-----------CEeccCCC---------CcCHHHHhH
Confidence 34556677888888755444 48989986 466677664
No 288
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=30.19 E-value=20 Score=23.82 Aligned_cols=39 Identities=23% Similarity=0.376 Sum_probs=24.1
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCC
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHAL 67 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L 67 (87)
..|.|..||.. |. -+-..+.-.-+|..|-.+--..+.+-
T Consensus 3 ~~F~C~~CG~~--V~--p~~~g~~~RNHCP~CL~S~Hvd~~pG 41 (92)
T PF12647_consen 3 ESFTCVHCGLT--VS--PLAAGSAHRNHCPSCLSSLHVDIVPG 41 (92)
T ss_pred cccCccccCCC--cc--cCCCCCCccCcCcccccccccCCCCC
Confidence 47999999974 22 23334445568888887654444443
No 289
>smart00350 MCM minichromosome maintenance proteins.
Probab=30.17 E-value=35 Score=27.92 Aligned_cols=33 Identities=21% Similarity=0.448 Sum_probs=21.3
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCc--ccce
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWN--CLER 59 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~--C~~~ 59 (87)
-.|.|..||+...+.+ +...-.--..|.. |+..
T Consensus 36 ~~f~C~~C~~~~~~~~--~~~~~~~p~~C~~~~C~~~ 70 (509)
T smart00350 36 ASFTCEKCGATLGPEI--QSGRETEPTVCPPRECQSP 70 (509)
T ss_pred EEEEecCCCCEEeEEe--cCCcccCCCcCCCCcCCCC
Confidence 5899999999654543 3222122357988 9865
No 290
>KOG3309 consensus Ferredoxin [Energy production and conversion]
Probab=30.04 E-value=24 Score=25.69 Aligned_cols=37 Identities=22% Similarity=0.254 Sum_probs=29.3
Q ss_pred EEEEcCcccceeEee-cCCCCchhhhhhhhHHHHHHhh
Q 035653 49 GEAFCWNCLERFCTQ-IHALTEPIDIYAEWIDECERAN 85 (87)
Q Consensus 49 g~~~C~~C~~~~~~~-i~~L~epiDVYs~wiD~~e~~n 85 (87)
|++.|..|++.++.. ...|.||-|==.+-+|.....+
T Consensus 83 gslACSTCHViv~~~~yekl~ep~DeE~DmLDlA~gLt 120 (159)
T KOG3309|consen 83 GSLACSTCHVIVDEEYYEKLPEPEDEENDMLDLAFGLT 120 (159)
T ss_pred ccccccceEEEEcHHHHhcCCCCcchHHHHHHhhhccc
Confidence 789999999998765 6688999888777777665443
No 291
>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=30.03 E-value=25 Score=21.01 Aligned_cols=13 Identities=31% Similarity=0.938 Sum_probs=10.3
Q ss_pred CccccCCCCCCCC
Q 035653 24 DTQFQCPFCGHGT 36 (87)
Q Consensus 24 ~~~F~CPfC~~~~ 36 (87)
.++=.||.||++.
T Consensus 11 ~kY~~Cp~CGN~~ 23 (49)
T PF12677_consen 11 NKYCKCPKCGNDK 23 (49)
T ss_pred hhhccCcccCCcE
Confidence 4678999999853
No 292
>MTH00129 COX2 cytochrome c oxidase subunit II; Provisional
Probab=29.95 E-value=51 Score=24.56 Aligned_cols=50 Identities=12% Similarity=0.193 Sum_probs=32.9
Q ss_pred CCCCeEEEEEeccCcEEEEEcCc-cccee-EeecCCCCchhhhhhhhHHHHHH
Q 035653 33 GHGTSVECRIDKKIQIGEAFCWN-CLERF-CTQIHALTEPIDIYAEWIDECER 83 (87)
Q Consensus 33 ~~~~sV~v~idk~~~~g~~~C~~-C~~~~-~~~i~~L~epiDVYs~wiD~~e~ 83 (87)
|..+.+....++ .|+....|.. ||..+ .|++.-...+.+.|.+|++.-.|
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 444555555543 4566778864 99875 44555555677999999976544
No 293
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=29.91 E-value=44 Score=26.86 Aligned_cols=31 Identities=19% Similarity=0.441 Sum_probs=19.5
Q ss_pred cCCCCCCCCe-------------EEEEEeccCcEEEEEcCcccc
Q 035653 28 QCPFCGHGTS-------------VECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 28 ~CPfC~~~~s-------------V~v~idk~~~~g~~~C~~C~~ 58 (87)
-||.||.+.. ....+....++....|+.||+
T Consensus 8 ~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cga 51 (355)
T COG1499 8 LCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCGA 51 (355)
T ss_pred EeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCCC
Confidence 4889987541 011222245677899999994
No 294
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=29.87 E-value=52 Score=26.92 Aligned_cols=43 Identities=21% Similarity=0.424 Sum_probs=27.1
Q ss_pred CCCCccccCCCCCCCCe--EEEEEeccCcEEEEEcCc------ccceeEeecC
Q 035653 21 EKLDTQFQCPFCGHGTS--VECRIDKKIQIGEAFCWN------CLERFCTQIH 65 (87)
Q Consensus 21 ~kl~~~F~CPfC~~~~s--V~v~idk~~~~g~~~C~~------C~~~~~~~i~ 65 (87)
.-+++.| ||.|||..- |+|.++.+ |-++++|.- =|..|+-.-+
T Consensus 253 ~~m~k~F-Cp~CG~~TL~K~aVsv~~d-G~~~~h~k~r~~~n~RG~~YSlp~P 303 (376)
T KOG2463|consen 253 SEMPKDF-CPSCGHKTLTKCAVSVDED-GNGQTHFKKRFQWNNRGLQYSLPKP 303 (376)
T ss_pred Cccchhc-ccccCCCeeeEEEEEecCC-CceeEEeecccccccCcceeecCCC
Confidence 3456677 999999632 45666665 666677762 3666754433
No 295
>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=29.83 E-value=24 Score=23.06 Aligned_cols=8 Identities=50% Similarity=1.746 Sum_probs=5.8
Q ss_pred ccCCCCCC
Q 035653 27 FQCPFCGH 34 (87)
Q Consensus 27 F~CPfC~~ 34 (87)
-+||+||-
T Consensus 2 I~CP~CG~ 9 (84)
T TIGR01374 2 IPCPYCGP 9 (84)
T ss_pred ccCCCCCC
Confidence 36888884
No 296
>PRK12722 transcriptional activator FlhC; Provisional
Probab=29.44 E-value=24 Score=26.10 Aligned_cols=13 Identities=23% Similarity=0.490 Sum_probs=10.5
Q ss_pred CCccccCCCCCCC
Q 035653 23 LDTQFQCPFCGHG 35 (87)
Q Consensus 23 l~~~F~CPfC~~~ 35 (87)
+-..|.||+|+-+
T Consensus 151 ~~~~f~CplC~~p 163 (187)
T PRK12722 151 PVGSFVCGLCQPP 163 (187)
T ss_pred cCCCCcCCCCCCc
Confidence 4568999999974
No 297
>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=29.22 E-value=27 Score=25.77 Aligned_cols=17 Identities=18% Similarity=0.163 Sum_probs=12.7
Q ss_pred CcEEEEEcCcccceeEe
Q 035653 46 IQIGEAFCWNCLERFCT 62 (87)
Q Consensus 46 ~~~g~~~C~~C~~~~~~ 62 (87)
..+-...|+.||..+.-
T Consensus 31 ~~i~v~~C~~Cg~~~~~ 47 (236)
T PF04981_consen 31 DRIEVTICPKCGRYRIG 47 (236)
T ss_pred CccCceECCCCCCEECC
Confidence 44567899999987653
No 298
>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=29.06 E-value=50 Score=24.59 Aligned_cols=47 Identities=11% Similarity=0.218 Sum_probs=31.4
Q ss_pred CCCCeEEEEEeccCcEEEEEcC-ccccee-EeecCCCCchhhhhhhhHHH
Q 035653 33 GHGTSVECRIDKKIQIGEAFCW-NCLERF-CTQIHALTEPIDIYAEWIDE 80 (87)
Q Consensus 33 ~~~~sV~v~idk~~~~g~~~C~-~C~~~~-~~~i~~L~epiDVYs~wiD~ 80 (87)
|+.+.+....++ .|.....|. -||..+ .|.+.-.-.+-|-|.+|+++
T Consensus 176 G~~n~~~~~~~~-~G~y~g~CaE~CG~~Ha~M~~~V~v~~~~~F~~Wl~~ 224 (226)
T TIGR01433 176 GMQTKLHLIANE-PGVYDGISANYSGPGFSGMKFKAIATDRAAFDQWVAK 224 (226)
T ss_pred CceEEEEEEeCC-CEEEEEEchhhcCcCccCCeEEEEEECHHHHHHHHHh
Confidence 555666666654 567778886 499876 44444444456899999975
No 299
>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=28.61 E-value=27 Score=21.10 Aligned_cols=14 Identities=29% Similarity=0.914 Sum_probs=5.5
Q ss_pred CCCccccCCCCCCC
Q 035653 22 KLDTQFQCPFCGHG 35 (87)
Q Consensus 22 kl~~~F~CPfC~~~ 35 (87)
++-..+.||.||+.
T Consensus 29 PvLr~y~Cp~CgAt 42 (55)
T PF05741_consen 29 PVLRKYVCPICGAT 42 (55)
T ss_dssp TTGGG---TTT---
T ss_pred HHHhcCcCCCCcCc
Confidence 33467899999974
No 300
>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=28.51 E-value=44 Score=24.05 Aligned_cols=37 Identities=22% Similarity=0.381 Sum_probs=21.0
Q ss_pred CCC-CccccCCCCCCCCeEEEEEec--cCcEEEEEcCc-cc
Q 035653 21 EKL-DTQFQCPFCGHGTSVECRIDK--KIQIGEAFCWN-CL 57 (87)
Q Consensus 21 ~kl-~~~F~CPfC~~~~sV~v~idk--~~~~g~~~C~~-C~ 57 (87)
.+| ++++.|-.||..+-...-+-. .+.+-.|-||. |-
T Consensus 54 s~lgdt~leCy~Cg~~NvF~LGFipak~d~vvvllCR~pC~ 94 (152)
T PF09416_consen 54 SPLGDTVLECYNCGSRNVFLLGFIPAKSDSVVVLLCRQPCA 94 (152)
T ss_dssp STT-S-B---TTT----TTTEEEEEETTSCEEEEEETTTTT
T ss_pred CCCCCcEEEEEecCCCceeeEEEEEeccCCeEEEEeCCchh
Confidence 345 799999999998866655543 56788999998 76
No 301
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=28.48 E-value=45 Score=24.05 Aligned_cols=55 Identities=15% Similarity=0.242 Sum_probs=28.1
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEeecCCCCchhhhhhhhHHHHHHhh
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQIHALTEPIDIYAEWIDECERAN 85 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~i~~L~epiDVYs~wiD~~e~~n 85 (87)
..+|..|++.-...-.++ ....-.|..||..-.-.|-.-.|.++- +|-.+.++.+
T Consensus 109 ~~~C~~C~~~~~~~~~~~---~~~~p~C~~Cgg~lrp~Vv~fge~~p~--~~~~~~~~~~ 163 (224)
T cd01412 109 RVRCSSCGYVGENNEEIP---EEELPRCPKCGGLLRPGVVWFGESLPL--ALLEAVEALA 163 (224)
T ss_pred ccccCCCCCCCCcchhhh---ccCCCCCCCCCCccCCceEECCCCCHH--HHHHHHHHHH
Confidence 367999987532221111 112457999986544444444444433 4554544443
No 302
>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=28.45 E-value=33 Score=18.73 Aligned_cols=15 Identities=13% Similarity=0.443 Sum_probs=11.5
Q ss_pred EEcCcccceeEeecC
Q 035653 51 AFCWNCLERFCTQIH 65 (87)
Q Consensus 51 ~~C~~C~~~~~~~i~ 65 (87)
..|..||..|....+
T Consensus 2 r~C~~Cg~~Yh~~~~ 16 (36)
T PF05191_consen 2 RICPKCGRIYHIEFN 16 (36)
T ss_dssp EEETTTTEEEETTTB
T ss_pred cCcCCCCCccccccC
Confidence 479999999976543
No 303
>MTH00038 COX2 cytochrome c oxidase subunit II; Provisional
Probab=28.28 E-value=55 Score=24.32 Aligned_cols=50 Identities=14% Similarity=0.265 Sum_probs=32.8
Q ss_pred CCCCeEEEEEeccCcEEEEEcC-cccceeE-eecCCCCchhhhhhhhHHHHHH
Q 035653 33 GHGTSVECRIDKKIQIGEAFCW-NCLERFC-TQIHALTEPIDIYAEWIDECER 83 (87)
Q Consensus 33 ~~~~sV~v~idk~~~~g~~~C~-~C~~~~~-~~i~~L~epiDVYs~wiD~~e~ 83 (87)
|..+.+....++ .|+....|. .||..++ |++.--..+-|.|.+|+++..|
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 445556655543 567778886 5998764 4554444566889999976543
No 304
>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=28.06 E-value=19 Score=23.06 Aligned_cols=11 Identities=18% Similarity=0.791 Sum_probs=8.0
Q ss_pred ccccCCCCCCC
Q 035653 25 TQFQCPFCGHG 35 (87)
Q Consensus 25 ~~F~CPfC~~~ 35 (87)
.-|.||+|..-
T Consensus 13 ~D~~Cp~C~~~ 23 (154)
T cd03023 13 FDYNCGYCKKL 23 (154)
T ss_pred ECCCChhHHHh
Confidence 35789999763
No 305
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.05 E-value=56 Score=20.35 Aligned_cols=35 Identities=29% Similarity=0.423 Sum_probs=23.7
Q ss_pred CccccCCCC----CCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 24 DTQFQCPFC----GHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 24 ~~~F~CPfC----~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
+..|.||== +|+. |-+.| ...|++.|.=|+..|..
T Consensus 22 ~~~l~C~g~~~p~~HPr-V~L~m---g~~gev~CPYC~t~y~l 60 (62)
T COG4391 22 DLPLMCPGPEPPNDHPR-VFLDM---GDEGEVVCPYCSTRYRL 60 (62)
T ss_pred CeeEEcCCCCCCCCCCE-EEEEc---CCCCcEecCccccEEEe
Confidence 456666432 4543 66766 55689999999998853
No 306
>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=27.91 E-value=25 Score=24.17 Aligned_cols=15 Identities=33% Similarity=0.428 Sum_probs=11.5
Q ss_pred CCccccCCCCCCCCe
Q 035653 23 LDTQFQCPFCGHGTS 37 (87)
Q Consensus 23 l~~~F~CPfC~~~~s 37 (87)
-...|-||-|+||=+
T Consensus 16 dg~~~iCpeC~~EW~ 30 (109)
T TIGR00686 16 DGTQLICPSCLYEWN 30 (109)
T ss_pred cCCeeECcccccccc
Confidence 345789999999753
No 307
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=27.75 E-value=27 Score=28.53 Aligned_cols=18 Identities=28% Similarity=0.741 Sum_probs=14.4
Q ss_pred CCCCCccccCCCCCCCCe
Q 035653 20 MEKLDTQFQCPFCGHGTS 37 (87)
Q Consensus 20 ~~kl~~~F~CPfC~~~~s 37 (87)
-..||-.|.||.|+..++
T Consensus 452 ~~~lp~~~~cp~c~~~k~ 469 (479)
T PRK05452 452 WSEVPDNFLCPECSLGKD 469 (479)
T ss_pred hhhCCCCCcCcCCCCcHH
Confidence 356788889999998765
No 308
>PF13132 DUF3950: Domain of unknown function (DUF3950)
Probab=27.62 E-value=41 Score=18.17 Aligned_cols=10 Identities=40% Similarity=1.491 Sum_probs=6.9
Q ss_pred hhhhH-HHHHH
Q 035653 74 YAEWI-DECER 83 (87)
Q Consensus 74 Ys~wi-D~~e~ 83 (87)
||.|+ |+|.+
T Consensus 17 FSaWV~dACr~ 27 (30)
T PF13132_consen 17 FSAWVKDACRR 27 (30)
T ss_pred hHHHHHHHHHH
Confidence 67885 66665
No 309
>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=27.28 E-value=41 Score=24.14 Aligned_cols=46 Identities=11% Similarity=0.240 Sum_probs=29.3
Q ss_pred CCCCeEEEEEeccCcEEEEEcCc-ccceeE-eecCCCCchhhhhhhhHH
Q 035653 33 GHGTSVECRIDKKIQIGEAFCWN-CLERFC-TQIHALTEPIDIYAEWID 79 (87)
Q Consensus 33 ~~~~sV~v~idk~~~~g~~~C~~-C~~~~~-~~i~~L~epiDVYs~wiD 79 (87)
|..+++....++ .|.....|.. ||..++ |.+.-.-.|-+-|.+|++
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 444555665543 4677888986 998864 444444445577999973
No 310
>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=27.26 E-value=39 Score=24.07 Aligned_cols=11 Identities=36% Similarity=1.017 Sum_probs=8.8
Q ss_pred ccccCCCCCCC
Q 035653 25 TQFQCPFCGHG 35 (87)
Q Consensus 25 ~~F~CPfC~~~ 35 (87)
...+||+||..
T Consensus 31 glv~CP~Cgs~ 41 (148)
T PF06676_consen 31 GLVSCPVCGST 41 (148)
T ss_pred CCccCCCCCCC
Confidence 35789999984
No 311
>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]
Probab=27.15 E-value=31 Score=24.96 Aligned_cols=11 Identities=45% Similarity=1.156 Sum_probs=8.9
Q ss_pred CccccCCCCCC
Q 035653 24 DTQFQCPFCGH 34 (87)
Q Consensus 24 ~~~F~CPfC~~ 34 (87)
...|.||.|||
T Consensus 131 ge~~rc~eCG~ 141 (153)
T KOG3352|consen 131 GETQRCPECGH 141 (153)
T ss_pred CCcccCCcccc
Confidence 45788999998
No 312
>PHA02768 hypothetical protein; Provisional
Probab=26.91 E-value=24 Score=21.28 Aligned_cols=38 Identities=16% Similarity=0.265 Sum_probs=21.1
Q ss_pred cccCCCCCCCCeEEEEEeccCc--EEEEEcCcccceeEee
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQ--IGEAFCWNCLERFCTQ 63 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~--~g~~~C~~C~~~~~~~ 63 (87)
-|.||.||..=+..-.+..-.. .-...|..|+..|..+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~~~ 44 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISLRT 44 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcCCcccCCcccceeccc
Confidence 4899999974222211111000 0134899999988744
No 313
>PF13397 DUF4109: Domain of unknown function (DUF4109)
Probab=26.88 E-value=36 Score=23.15 Aligned_cols=16 Identities=25% Similarity=0.818 Sum_probs=12.8
Q ss_pred CCCCccccCCCCCCCC
Q 035653 21 EKLDTQFQCPFCGHGT 36 (87)
Q Consensus 21 ~kl~~~F~CPfC~~~~ 36 (87)
.-+|-+.+||+||.+-
T Consensus 45 AevP~~WeC~~cG~~A 60 (105)
T PF13397_consen 45 AEVPATWECPRCGLPA 60 (105)
T ss_pred CCCCCceeCCCCCCcc
Confidence 3578899999999863
No 314
>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=26.84 E-value=19 Score=23.49 Aligned_cols=7 Identities=57% Similarity=1.701 Sum_probs=4.5
Q ss_pred cCCCCCC
Q 035653 28 QCPFCGH 34 (87)
Q Consensus 28 ~CPfC~~ 34 (87)
.||+||-
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 315
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=26.70 E-value=78 Score=27.88 Aligned_cols=45 Identities=20% Similarity=0.244 Sum_probs=32.1
Q ss_pred cCCCCCCccc--cCCCCCCCCeEEEEEecc--CcEE-EEEcCcccceeEe
Q 035653 18 KGMEKLDTQF--QCPFCGHGTSVECRIDKK--IQIG-EAFCWNCLERFCT 62 (87)
Q Consensus 18 k~~~kl~~~F--~CPfC~~~~sV~v~idk~--~~~g-~~~C~~C~~~~~~ 62 (87)
+....+.-.| .||+|.-..+|++-..-. .|.| .+.|.+||..+--
T Consensus 43 ~~~~D~~~~~~~pc~~c~gkG~V~v~~~c~~c~G~gkv~~c~~cG~~~~~ 92 (715)
T COG1107 43 RETVDLFASFEIPCPKCRGKGTVTVYDTCPECGGTGKVLTCDICGDIIVP 92 (715)
T ss_pred hccccccccCCCCCCeeccceeEEEEeecccCCCceeEEeeccccceecC
Confidence 3334555556 799999999999877554 3554 5789999987643
No 316
>PF09452 Mvb12: ESCRT-I subunit Mvb12; InterPro: IPR019014 The endosomal sorting complex required for transport (ESCRT) complexes play a critical role in receptor down-regulation and retroviral budding. A new component of the ESCRT-I complex was identified [], multivesicular body sorting factor of 12 kDa (Mvb12), which binds to the coiled-coil domain of the ESCRT-I subunit vacuolar protein sorting 23 (Vps23) []. ; PDB: 2P22_D.
Probab=26.63 E-value=32 Score=22.90 Aligned_cols=25 Identities=16% Similarity=0.581 Sum_probs=14.8
Q ss_pred EeecCCCCchhhhhhhhHHHHHHhh
Q 035653 61 CTQIHALTEPIDIYAEWIDECERAN 85 (87)
Q Consensus 61 ~~~i~~L~epiDVYs~wiD~~e~~n 85 (87)
+..+++|...-+-+.-|+++|+++-
T Consensus 27 ~~~l~~~~~t~em~~~W~~ECd~i~ 51 (91)
T PF09452_consen 27 EIKLPPLQPTKEMFQPWYEECDQIV 51 (91)
T ss_dssp -------HHHHHHHHHHHHHHHHHH
T ss_pred cccCCCCCChHHHHHHHHHHHHHHH
Confidence 3457778766677999999999863
No 317
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.54 E-value=21 Score=27.72 Aligned_cols=29 Identities=28% Similarity=0.706 Sum_probs=18.9
Q ss_pred CCCccccCCCCCCCCeEEEEEeccCcEEEEEcCccccee
Q 035653 22 KLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERF 60 (87)
Q Consensus 22 kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~ 60 (87)
..+.-|-||.|.. +-|++- ..|.+||..|
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 3455588888875 455442 3888888765
No 318
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=26.52 E-value=35 Score=20.99 Aligned_cols=9 Identities=44% Similarity=1.390 Sum_probs=7.4
Q ss_pred cCCCCCCCC
Q 035653 28 QCPFCGHGT 36 (87)
Q Consensus 28 ~CPfC~~~~ 36 (87)
+||.||...
T Consensus 17 ~CP~Cgs~~ 25 (61)
T PRK08351 17 RCPVCGSRD 25 (61)
T ss_pred cCCCCcCCc
Confidence 699999854
No 319
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=26.22 E-value=29 Score=23.10 Aligned_cols=31 Identities=23% Similarity=0.530 Sum_probs=19.7
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeE
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~ 61 (87)
..+.|+-|||..-+- ..-..=.|..||..+.
T Consensus 41 ~~~~C~~Cg~~~~~~------~SCk~R~CP~C~~~~~ 71 (111)
T PF14319_consen 41 HRYRCEDCGHEKIVY------NSCKNRHCPSCQAKAT 71 (111)
T ss_pred ceeecCCCCceEEec------CcccCcCCCCCCChHH
Confidence 478999999954221 2223338889987653
No 320
>PRK12860 transcriptional activator FlhC; Provisional
Probab=26.07 E-value=35 Score=25.33 Aligned_cols=14 Identities=29% Similarity=0.710 Sum_probs=10.7
Q ss_pred CCCccccCCCCCCC
Q 035653 22 KLDTQFQCPFCGHG 35 (87)
Q Consensus 22 kl~~~F~CPfC~~~ 35 (87)
-+-..|.||+|+-+
T Consensus 150 e~~~~f~CplC~~p 163 (189)
T PRK12860 150 DLRHNFVCGLCQPP 163 (189)
T ss_pred ccCCCCcCCCCCCc
Confidence 34568999999953
No 321
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=26.03 E-value=30 Score=29.84 Aligned_cols=26 Identities=38% Similarity=0.763 Sum_probs=16.7
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEee
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCTQ 63 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~~ 63 (87)
.||.||++ ...+.-.|..||....+.
T Consensus 29 ~Cp~CG~~----------~~~~~~fC~~CG~~~~~~ 54 (645)
T PRK14559 29 PCPQCGTE----------VPVDEAHCPNCGAETGTI 54 (645)
T ss_pred cCCCCCCC----------CCcccccccccCCcccch
Confidence 37777764 234555888888776554
No 322
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=25.78 E-value=35 Score=21.23 Aligned_cols=31 Identities=19% Similarity=0.469 Sum_probs=22.6
Q ss_pred CCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 22 KLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 22 kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
.-+-.+-|--|+.++++ .+. -.+.|+.||-+
T Consensus 16 ~~~miYiCgdC~~en~l----k~~---D~irCReCG~R 46 (62)
T KOG3507|consen 16 TATMIYICGDCGQENTL----KRG---DVIRCRECGYR 46 (62)
T ss_pred cccEEEEeccccccccc----cCC---CcEehhhcchH
Confidence 34568999999998754 223 45799999965
No 323
>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=25.36 E-value=88 Score=25.01 Aligned_cols=54 Identities=22% Similarity=0.382 Sum_probs=31.6
Q ss_pred CCCCCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe----ecCCCCchhhhhhhhHHHHH
Q 035653 19 GMEKLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT----QIHALTEPIDIYAEWIDECE 82 (87)
Q Consensus 19 ~~~kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~----~i~~L~epiDVYs~wiD~~e 82 (87)
...++--++.|+.|++.+.+.-. . ...-.|..||..+.. .+.+|.++ +|++++.
T Consensus 226 ~~~~~g~v~~C~~c~~~~~~~~~-~----~~~~~C~~c~~~~~~~GPlW~G~l~d~-----~fl~~m~ 283 (374)
T TIGR00308 226 VMESTGYTYHCSRCLHNKPVNGI-S----QRKGRCKECGGEYHLAGPLYAGPLHDK-----EFIEEVL 283 (374)
T ss_pred HHHhceeEEECCCcccccccccc-c----CCCCCCCCCCCcceeecCcccCccCCH-----HHHHHHH
Confidence 34457779999999986543210 0 112369999987643 34445443 4555554
No 324
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=25.26 E-value=40 Score=18.37 Aligned_cols=11 Identities=27% Similarity=1.005 Sum_probs=8.4
Q ss_pred CccccCCCCCC
Q 035653 24 DTQFQCPFCGH 34 (87)
Q Consensus 24 ~~~F~CPfC~~ 34 (87)
.....||+|+.
T Consensus 34 ~~~~~CP~C~k 44 (44)
T PF14634_consen 34 GKSVKCPICRK 44 (44)
T ss_pred CCCCCCcCCCC
Confidence 56788999973
No 325
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=25.22 E-value=33 Score=25.31 Aligned_cols=25 Identities=20% Similarity=0.543 Sum_probs=17.0
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
.|.||.|+.+ ++. . -..+.|.+.+.
T Consensus 2 ~~~CP~C~~~--l~~----~--~~~~~C~~~h~ 26 (272)
T PRK11088 2 SYQCPLCHQP--LTL----E--ENSWICPQNHQ 26 (272)
T ss_pred cccCCCCCcc--hhc----C--CCEEEcCCCCC
Confidence 4999999974 322 1 14689998554
No 326
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=25.05 E-value=44 Score=26.61 Aligned_cols=21 Identities=24% Similarity=0.496 Sum_probs=14.7
Q ss_pred CCCccccCCCCCCCCeEEEEE
Q 035653 22 KLDTQFQCPFCGHGTSVECRI 42 (87)
Q Consensus 22 kl~~~F~CPfC~~~~sV~v~i 42 (87)
...+.+.||-|||+.+-+=.|
T Consensus 205 ~k~k~~PCPKCg~et~eTkdL 225 (314)
T PF06524_consen 205 EKGKPIPCPKCGYETQETKDL 225 (314)
T ss_pred ccCCCCCCCCCCCcccccccc
Confidence 334789999999986544333
No 327
>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=25.03 E-value=59 Score=22.93 Aligned_cols=32 Identities=25% Similarity=0.369 Sum_probs=20.0
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeE
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~ 61 (87)
+-.|.|-.|||. +.+ ... .-...|..||-.+-
T Consensus 110 ~G~l~C~~Cg~~--~~~--~~~--~~l~~Cp~C~~~~F 141 (146)
T PF07295_consen 110 PGTLVCENCGHE--VEL--THP--ERLPPCPKCGHTEF 141 (146)
T ss_pred CceEecccCCCE--EEe--cCC--CcCCCCCCCCCCee
Confidence 346888888884 333 332 23668888886543
No 328
>PRK10220 hypothetical protein; Provisional
Probab=24.98 E-value=33 Score=23.63 Aligned_cols=16 Identities=25% Similarity=0.632 Sum_probs=12.0
Q ss_pred CCCccccCCCCCCCCe
Q 035653 22 KLDTQFQCPFCGHGTS 37 (87)
Q Consensus 22 kl~~~F~CPfC~~~~s 37 (87)
.-...|-||-|+||=+
T Consensus 16 ~d~~~~vCpeC~hEW~ 31 (111)
T PRK10220 16 EDNGMYICPECAHEWN 31 (111)
T ss_pred cCCCeEECCcccCcCC
Confidence 3445799999999754
No 329
>PHA02893 hypothetical protein; Provisional
Probab=24.94 E-value=67 Score=21.26 Aligned_cols=11 Identities=18% Similarity=0.416 Sum_probs=8.9
Q ss_pred EEEEcCcccce
Q 035653 49 GEAFCWNCLER 59 (87)
Q Consensus 49 g~~~C~~C~~~ 59 (87)
..|+|..||..
T Consensus 68 ~tL~CaACGS~ 78 (88)
T PHA02893 68 SNIKCIACGSS 78 (88)
T ss_pred Cceeehhhchh
Confidence 57999999964
No 330
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=24.91 E-value=52 Score=31.78 Aligned_cols=30 Identities=23% Similarity=0.354 Sum_probs=20.2
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
.||.|+...---|++.... |=+.|..||-+
T Consensus 1706 ~cp~c~~~~~~~~~~~~~~--gc~~c~~cg~s 1735 (1740)
T PRK08332 1706 YCPVCYEKEGKLVELRMES--GCATCPVCGWS 1735 (1740)
T ss_pred CCCCCCCCCCcceeeEecC--CceeCCCCCCc
Confidence 3999998643334444454 55689999965
No 331
>PF04641 Rtf2: Rtf2 RING-finger
Probab=24.85 E-value=1.6e+02 Score=22.02 Aligned_cols=58 Identities=17% Similarity=0.336 Sum_probs=36.0
Q ss_pred CCccccCCCCCCCCe--EEEEEeccCc----------EE-EEEcCcccceeEee----cCCCCchhhhhhhhHHH
Q 035653 23 LDTQFQCPFCGHGTS--VECRIDKKIQ----------IG-EAFCWNCLERFCTQ----IHALTEPIDIYAEWIDE 80 (87)
Q Consensus 23 l~~~F~CPfC~~~~s--V~v~idk~~~----------~g-~~~C~~C~~~~~~~----i~~L~epiDVYs~wiD~ 80 (87)
-...|.||..+.+-+ ..+..-+.-| +. .-.|-+||..|... |++-.+.+....+-+..
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k~~~~Cp~c~~~f~~~DiI~Lnp~~ee~~~l~~~~~~ 184 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELKKSKKCPVCGKPFTEEDIIPLNPPEEELEKLRERMEE 184 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhcccccccccCCccccCCEEEecCCccHHHHHHHHHHH
Confidence 577899999886531 2222222211 22 34699999999764 78887876666655433
No 332
>CHL00136 rpl31 ribosomal protein L31; Validated
Probab=24.60 E-value=71 Score=19.89 Aligned_cols=34 Identities=9% Similarity=0.004 Sum_probs=18.7
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeE
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~ 61 (87)
+..+.| -|+.. .++.-. ...+..-.|..|+--|.
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 332222 23366777888876554
No 333
>PRK12496 hypothetical protein; Provisional
Probab=24.59 E-value=37 Score=24.09 Aligned_cols=9 Identities=22% Similarity=0.497 Sum_probs=6.0
Q ss_pred cccCCCCCC
Q 035653 26 QFQCPFCGH 34 (87)
Q Consensus 26 ~F~CPfC~~ 34 (87)
.+.|+-|+.
T Consensus 127 ~~~C~gC~~ 135 (164)
T PRK12496 127 RKVCKGCKK 135 (164)
T ss_pred eEECCCCCc
Confidence 356777776
No 334
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=24.28 E-value=31 Score=25.11 Aligned_cols=34 Identities=18% Similarity=0.389 Sum_probs=22.0
Q ss_pred ccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 25 TQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 25 ~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
+-|-|.+|++. .|.--++. .....|..|+.-|-.
T Consensus 151 kGfiCe~C~~~-~~IfPF~~---~~~~~C~~C~~v~H~ 184 (202)
T PF13901_consen 151 KGFICEICNSD-DIIFPFQI---DTTVRCPKCKSVFHK 184 (202)
T ss_pred CCCCCccCCCC-CCCCCCCC---CCeeeCCcCccccch
Confidence 35888888874 23332322 367899999987744
No 335
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=24.11 E-value=41 Score=20.94 Aligned_cols=9 Identities=33% Similarity=0.896 Sum_probs=7.6
Q ss_pred cCCCCCCCC
Q 035653 28 QCPFCGHGT 36 (87)
Q Consensus 28 ~CPfC~~~~ 36 (87)
.||.||...
T Consensus 19 ~Cp~Cgs~~ 27 (64)
T PRK06393 19 TCPVHGDEK 27 (64)
T ss_pred cCCCCCCCc
Confidence 899999863
No 336
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.10 E-value=33 Score=27.17 Aligned_cols=22 Identities=14% Similarity=0.315 Sum_probs=19.1
Q ss_pred cEEEEEcCcccceeEeecCCCC
Q 035653 47 QIGEAFCWNCLERFCTQIHALT 68 (87)
Q Consensus 47 ~~g~~~C~~C~~~~~~~i~~L~ 68 (87)
..+.++|..|..+|....+.|.
T Consensus 68 ~~q~V~C~QCqTEYiiv~P~l~ 89 (293)
T KOG3053|consen 68 PLQTVSCPQCQTEYIIVFPQLG 89 (293)
T ss_pred CCceeechhhcchheeeccccC
Confidence 3788999999999999888873
No 337
>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=23.93 E-value=39 Score=20.47 Aligned_cols=10 Identities=50% Similarity=1.175 Sum_probs=8.1
Q ss_pred cccCCCCCCC
Q 035653 26 QFQCPFCGHG 35 (87)
Q Consensus 26 ~F~CPfC~~~ 35 (87)
...|||||.+
T Consensus 35 ~~pC~fCg~~ 44 (57)
T PF06221_consen 35 LGPCPFCGTP 44 (57)
T ss_pred cCcCCCCCCc
Confidence 6789999963
No 338
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=23.76 E-value=52 Score=27.56 Aligned_cols=35 Identities=23% Similarity=0.372 Sum_probs=14.4
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccce-eEe---ecCCCCchhhhh
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLER-FCT---QIHALTEPIDIY 74 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~-~~~---~i~~L~epiDVY 74 (87)
.|+-||+.. +. .-.|..||.. -+. -+.+|. ||.=+
T Consensus 493 ~C~~CG~~~----------~~-~~~CP~CGs~~~~~~~Rv~GYl~-~v~~~ 531 (546)
T PF13597_consen 493 ICPDCGYIG----------GE-GDKCPKCGSENIEVYSRVTGYLR-PVSRW 531 (546)
T ss_dssp EETTT---S-------------EEE-CCC----EEEEB-SSSS-B-TTS--
T ss_pred cccCCCcCC----------CC-CCCCCCCCCcccceEEEeecccc-Ccccc
Confidence 588888731 12 6679999976 222 256665 66553
No 339
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=23.55 E-value=41 Score=18.51 Aligned_cols=9 Identities=44% Similarity=1.379 Sum_probs=7.8
Q ss_pred cccCCCCCC
Q 035653 26 QFQCPFCGH 34 (87)
Q Consensus 26 ~F~CPfC~~ 34 (87)
.|.|.+|+.
T Consensus 12 ~f~C~~C~~ 20 (39)
T smart00154 12 GFKCRHCGN 20 (39)
T ss_pred CeECCccCC
Confidence 799999986
No 340
>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=23.37 E-value=37 Score=19.73 Aligned_cols=14 Identities=36% Similarity=0.783 Sum_probs=9.7
Q ss_pred ccccCCCCCCCCeE
Q 035653 25 TQFQCPFCGHGTSV 38 (87)
Q Consensus 25 ~~F~CPfC~~~~sV 38 (87)
+=+.||-||-..++
T Consensus 8 tG~~CPgCG~tRa~ 21 (52)
T PF10825_consen 8 TGIPCPGCGMTRAF 21 (52)
T ss_pred hCCCCCCCcHHHHH
Confidence 45789999875443
No 341
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=23.35 E-value=51 Score=15.43 Aligned_cols=12 Identities=25% Similarity=0.789 Sum_probs=8.4
Q ss_pred EcCcccceeEee
Q 035653 52 FCWNCLERFCTQ 63 (87)
Q Consensus 52 ~C~~C~~~~~~~ 63 (87)
.|.+|+..|..+
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 588888777543
No 342
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=23.33 E-value=31 Score=20.17 Aligned_cols=30 Identities=27% Similarity=0.664 Sum_probs=19.9
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCccccee
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLERF 60 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~ 60 (87)
.|+.||.+-.+--.+..++| -.|..|-...
T Consensus 1 ~C~iCg~kigl~~~~k~~DG---~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG---YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc---cchHHHHHHh
Confidence 59999997655444444554 3899887554
No 343
>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=23.31 E-value=43 Score=28.05 Aligned_cols=11 Identities=45% Similarity=1.222 Sum_probs=8.0
Q ss_pred cccCCCCCCCC
Q 035653 26 QFQCPFCGHGT 36 (87)
Q Consensus 26 ~F~CPfC~~~~ 36 (87)
.+.||.||+++
T Consensus 532 ~~~CP~CGs~~ 542 (555)
T cd01675 532 GFKCPKCGSED 542 (555)
T ss_pred CCCCcCCCCcC
Confidence 57888888654
No 344
>PRK10954 periplasmic protein disulfide isomerase I; Provisional
Probab=23.21 E-value=25 Score=25.02 Aligned_cols=13 Identities=31% Similarity=0.664 Sum_probs=9.8
Q ss_pred ccccCCCCCCCCe
Q 035653 25 TQFQCPFCGHGTS 37 (87)
Q Consensus 25 ~~F~CPfC~~~~s 37 (87)
--|.||+|.+-..
T Consensus 45 fdy~CphC~~~~~ 57 (207)
T PRK10954 45 FSFYCPHCYQFEE 57 (207)
T ss_pred eCCCCccHHHhcc
Confidence 4578999998544
No 345
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=23.07 E-value=47 Score=26.59 Aligned_cols=10 Identities=40% Similarity=1.085 Sum_probs=7.3
Q ss_pred cccCCCCCCC
Q 035653 26 QFQCPFCGHG 35 (87)
Q Consensus 26 ~F~CPfC~~~ 35 (87)
.|.|+.||++
T Consensus 2 ~l~C~~Cg~~ 11 (398)
T TIGR03844 2 TLRCPGCGEV 11 (398)
T ss_pred EEEeCCCCCc
Confidence 4678888874
No 346
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.98 E-value=56 Score=28.14 Aligned_cols=10 Identities=40% Similarity=0.939 Sum_probs=7.2
Q ss_pred cccCCCCCCC
Q 035653 26 QFQCPFCGHG 35 (87)
Q Consensus 26 ~F~CPfC~~~ 35 (87)
.|.||.||++
T Consensus 639 ~~~CP~CG~~ 648 (656)
T PRK08270 639 HEFCPKCGEE 648 (656)
T ss_pred CCCCcCCcCc
Confidence 4778888765
No 347
>PRK08197 threonine synthase; Validated
Probab=22.95 E-value=61 Score=25.51 Aligned_cols=27 Identities=19% Similarity=0.577 Sum_probs=17.5
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeE
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~ 61 (87)
.|.|+.||++-. .......| .||.-+.
T Consensus 7 ~~~C~~Cg~~~~--------~~~~~~~C-~cg~~l~ 33 (394)
T PRK08197 7 HLECSKCGETYD--------ADQVHNLC-KCGKPLL 33 (394)
T ss_pred EEEECCCCCCCC--------CCCcceec-CCCCeeE
Confidence 489999998632 22235679 7985543
No 348
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=22.91 E-value=43 Score=28.51 Aligned_cols=27 Identities=22% Similarity=0.633 Sum_probs=20.7
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
.|+.||.. .++++...|.+.|..||.-
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 49999974 2455667799999999964
No 349
>COG1364 ArgJ N-acetylglutamate synthase (N-acetylornithine aminotransferase) [Amino acid transport and metabolism]
Probab=22.91 E-value=54 Score=27.10 Aligned_cols=32 Identities=25% Similarity=0.430 Sum_probs=27.2
Q ss_pred CeEEEEEeccCcEEEEEcCcccceeEe-ecCCC
Q 035653 36 TSVECRIDKKIQIGEAFCWNCLERFCT-QIHAL 67 (87)
Q Consensus 36 ~sV~v~idk~~~~g~~~C~~C~~~~~~-~i~~L 67 (87)
.-|.|.+|...|.+...++.|.++|++ +||.-
T Consensus 369 ~ei~I~VdLg~G~~~at~wgCDLt~dYV~INa~ 401 (404)
T COG1364 369 DEITIRVDLGVGDGAATAWGCDLTYDYVRINAD 401 (404)
T ss_pred CcEEEEEEeccCCcceEEEeccCchhhEEeece
Confidence 348888999999999999999999987 47753
No 350
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=22.90 E-value=42 Score=26.42 Aligned_cols=43 Identities=37% Similarity=0.676 Sum_probs=26.5
Q ss_pred CCCCCCccccCCCCCCC--------CeE----EEEE-------eccCcEEEEEcCcccceeE
Q 035653 19 GMEKLDTQFQCPFCGHG--------TSV----ECRI-------DKKIQIGEAFCWNCLERFC 61 (87)
Q Consensus 19 ~~~kl~~~F~CPfC~~~--------~sV----~v~i-------dk~~~~g~~~C~~C~~~~~ 61 (87)
..+..+..|-|.-|.+- +-| .|+- |+--|+|+-.|..|+-.|.
T Consensus 105 ~ip~~drqFaC~~Cd~~WwRrvp~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~ 166 (278)
T PF15135_consen 105 LIPSVDRQFACSSCDHMWWRRVPQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFR 166 (278)
T ss_pred cccccceeeeccccchHHHhccCcccccccccccccccCCCccccccceeeeecccccccch
Confidence 34566788888888873 001 1111 2334688888888887774
No 351
>PRK11823 DNA repair protein RadA; Provisional
Probab=22.60 E-value=71 Score=25.88 Aligned_cols=26 Identities=23% Similarity=0.418 Sum_probs=18.4
Q ss_pred CccccCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 24 DTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 24 ~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
.+.|.|..||+.. .. =.-.|..|++.
T Consensus 5 ~~~y~C~~Cg~~~--------~~--~~g~Cp~C~~w 30 (446)
T PRK11823 5 KTAYVCQECGAES--------PK--WLGRCPECGAW 30 (446)
T ss_pred CCeEECCcCCCCC--------cc--cCeeCcCCCCc
Confidence 4679999999942 22 33479999875
No 352
>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=22.32 E-value=71 Score=18.70 Aligned_cols=27 Identities=26% Similarity=0.624 Sum_probs=14.7
Q ss_pred ccCC--CCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 27 FQCP--FCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 27 F~CP--fC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
=.|| .||..- +-- .-.....|+.||.+
T Consensus 19 k~CP~~~CG~Gv-FMA-----~H~dR~~CGKCg~T 47 (47)
T PF01599_consen 19 KECPSPRCGAGV-FMA-----EHKDRHYCGKCGYT 47 (47)
T ss_dssp EE-TSTTTTSSS-EEE-----E-SSEEEETTTSS-
T ss_pred hcCCCcccCCce-Eee-----ecCCCccCCCcccC
Confidence 4689 999732 111 11126689999863
No 353
>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=22.29 E-value=17 Score=25.14 Aligned_cols=16 Identities=31% Similarity=0.924 Sum_probs=12.5
Q ss_pred ecCCCCchhhhhhhhHHH
Q 035653 63 QIHALTEPIDIYAEWIDE 80 (87)
Q Consensus 63 ~i~~L~epiDVYs~wiD~ 80 (87)
=+|...++|||| |||.
T Consensus 13 F~N~t~~~v~~~--Wid~ 28 (141)
T cd05468 13 FVNRTDRPVELY--WIDY 28 (141)
T ss_pred EEeCCCCeEEEE--EECC
Confidence 368888999998 7763
No 354
>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=22.28 E-value=44 Score=21.20 Aligned_cols=16 Identities=13% Similarity=0.156 Sum_probs=13.3
Q ss_pred EEEEcCcccceeEeec
Q 035653 49 GEAFCWNCLERFCTQI 64 (87)
Q Consensus 49 g~~~C~~C~~~~~~~i 64 (87)
.++.|..||.-++...
T Consensus 72 ~H~~C~~Cg~i~~~~~ 87 (116)
T cd07153 72 HHLICTKCGKVIDFED 87 (116)
T ss_pred CceEeCCCCCEEEecC
Confidence 5799999999888653
No 355
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=22.05 E-value=44 Score=20.95 Aligned_cols=11 Identities=36% Similarity=0.914 Sum_probs=8.2
Q ss_pred cccCCCCCCCC
Q 035653 26 QFQCPFCGHGT 36 (87)
Q Consensus 26 ~F~CPfC~~~~ 36 (87)
.=.||.||.++
T Consensus 18 ~e~CP~Cgs~~ 28 (64)
T COG2093 18 TEICPVCGSTD 28 (64)
T ss_pred CccCCCCCCcc
Confidence 34699999863
No 356
>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=22.04 E-value=74 Score=21.52 Aligned_cols=14 Identities=29% Similarity=0.662 Sum_probs=11.1
Q ss_pred cEEEEEcCccccee
Q 035653 47 QIGEAFCWNCLERF 60 (87)
Q Consensus 47 ~~g~~~C~~C~~~~ 60 (87)
..|.|.|+.||+..
T Consensus 57 ~~~~I~C~~C~~~w 70 (123)
T PF11648_consen 57 PNGKIHCKNCGQDW 70 (123)
T ss_dssp EEEEEEETSTSBEE
T ss_pred eCCEEEcCCCChHh
Confidence 46889999999764
No 357
>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=21.94 E-value=54 Score=20.20 Aligned_cols=28 Identities=21% Similarity=0.239 Sum_probs=15.2
Q ss_pred EEEEEcCcccceeEeecCCCC--chhhhhh
Q 035653 48 IGEAFCWNCLERFCTQIHALT--EPIDIYA 75 (87)
Q Consensus 48 ~g~~~C~~C~~~~~~~i~~L~--epiDVYs 75 (87)
...+.|..||..|.+.-+... -.|||-|
T Consensus 11 ~v~v~c~s~g~~~~~~St~~~~~~~vdi~s 40 (69)
T PF01197_consen 11 EVKVTCSSCGNTFETRSTKEYPVIKVDICS 40 (69)
T ss_dssp EEEEEES-SSSCECECSSSSES-EEECSCS
T ss_pred EEEEEEcCCCCEEEEEECCcceEEEEeecC
Confidence 356677778877776543321 2355544
No 358
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=21.85 E-value=57 Score=19.81 Aligned_cols=17 Identities=29% Similarity=0.772 Sum_probs=8.0
Q ss_pred cCCCCCCccccCCCCCC
Q 035653 18 KGMEKLDTQFQCPFCGH 34 (87)
Q Consensus 18 k~~~kl~~~F~CPfC~~ 34 (87)
+....-+..-+||.|++
T Consensus 16 k~~~~S~~PatCP~C~a 32 (54)
T PF09237_consen 16 KSKSQSEQPATCPICGA 32 (54)
T ss_dssp CCCCTTS--EE-TTT--
T ss_pred HHhhccCCCCCCCcchh
Confidence 33445567789999997
No 359
>cd05133 RasGAP_IQGAP1 IQGAP1 is a homodimeric protein that is widely expressed among vertebrate cell types from early embryogenesis. Mammalian IQGAP1 protein is the best characterized member of the IQGAP family, and contains several protein-interacting domains. Human IQGAP1 is most similar to mouse Iqgap1 (94% identity) and has 62% identity to human IQGAP2. IQGAP1 binds and cross-links actin filaments in vitro and has been implicated in Ca2+/calmodulin signaling, E-cadherin-dependent cell adhesion, cell motility, and invasion. Yeast IQGAP homologues have a role in the recruitment of actin filaments, are components of the spindle pole body, and are required for actomyosin ring assembly and cytokinesis. Furthermore, IQGAP1 over-expression has also been detected in gastric and colorectal carcinomas and gastric cancer cell lines.
Probab=21.79 E-value=57 Score=26.18 Aligned_cols=17 Identities=41% Similarity=1.091 Sum_probs=14.4
Q ss_pred CchhhhhhhhHHHHHHh
Q 035653 68 TEPIDIYAEWIDECERA 84 (87)
Q Consensus 68 ~epiDVYs~wiD~~e~~ 84 (87)
++|+.||..||..-|..
T Consensus 77 ~dP~~Iy~~~in~~E~~ 93 (360)
T cd05133 77 TDPVDIYKSWVNQMESQ 93 (360)
T ss_pred CCHHHHHHHHHHHHHHh
Confidence 57999999999877764
No 360
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.68 E-value=1.2e+02 Score=20.30 Aligned_cols=33 Identities=18% Similarity=0.292 Sum_probs=18.6
Q ss_pred ccCCCCCCCCeEEEEEec------cCcEEEEEcCccccee
Q 035653 27 FQCPFCGHGTSVECRIDK------KIQIGEAFCWNCLERF 60 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk------~~~~g~~~C~~C~~~~ 60 (87)
=.||+||.. ++-+.=+. ..+.-.-.|..|+..-
T Consensus 3 ~~CpYCg~~-~~l~~~~~iYg~~~~~~~~~y~C~~C~AyV 41 (102)
T PF11672_consen 3 IICPYCGGP-AELVDGSEIYGHRYDDGPYLYVCTPCDAYV 41 (102)
T ss_pred cccCCCCCe-eEEcccchhcCccCCCCceeEECCCCCcee
Confidence 469999973 22222110 1223346899999863
No 361
>PF13806 Rieske_2: Rieske-like [2Fe-2S] domain; PDB: 2JO6_A 3C0D_A 3D89_A 2JZA_A.
Probab=21.63 E-value=60 Score=21.11 Aligned_cols=46 Identities=17% Similarity=0.112 Sum_probs=28.3
Q ss_pred cCCCCC-CCCeEEEEEeccCcEEEEEcCcccceeEee----cCCCCchhhhh
Q 035653 28 QCPFCG-HGTSVECRIDKKIQIGEAFCWNCLERFCTQ----IHALTEPIDIY 74 (87)
Q Consensus 28 ~CPfC~-~~~sV~v~idk~~~~g~~~C~~C~~~~~~~----i~~L~epiDVY 74 (87)
.||+++ ..-|=. .|....+.+.|.|.-.+..|... +..-..++.+|
T Consensus 42 ~Cph~~~~~Ls~G-~i~~~~g~~~V~CPlH~~~f~L~tG~~~~~~~~~l~~y 92 (104)
T PF13806_consen 42 RCPHSQAGPLSDG-LIGDGNGEPCVACPLHKWRFDLRTGECLEDPDVSLRTY 92 (104)
T ss_dssp BETTTTSSCGCGS-EEEECTTEEEEEETTTTEEEETTTTEESSECSEBSBEE
T ss_pred cCCccCCccccee-EEccCCCCEEEECCCCCCeEECCCcCcCCCCCCcEEeE
Confidence 588873 222222 23334677899999999999764 33334555555
No 362
>PF02257 RFX_DNA_binding: RFX DNA-binding domain; InterPro: IPR003150 RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1DP7_P 2KW3_A.
Probab=21.57 E-value=60 Score=21.03 Aligned_cols=14 Identities=36% Similarity=0.940 Sum_probs=12.5
Q ss_pred hhhhhhHHHHHHhh
Q 035653 72 DIYAEWIDECERAN 85 (87)
Q Consensus 72 DVYs~wiD~~e~~n 85 (87)
+||..|++.|++.+
T Consensus 28 ~lY~~Y~~~C~~~~ 41 (85)
T PF02257_consen 28 DLYAHYLSFCEKNG 41 (85)
T ss_dssp HHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHhC
Confidence 89999999999864
No 363
>MTH00117 COX2 cytochrome c oxidase subunit II; Provisional
Probab=21.24 E-value=86 Score=23.28 Aligned_cols=48 Identities=13% Similarity=0.178 Sum_probs=30.1
Q ss_pred CCCCeEEEEEeccCcEEEEEcC-ccccee-EeecCCCCchhhhhhhhHHHH
Q 035653 33 GHGTSVECRIDKKIQIGEAFCW-NCLERF-CTQIHALTEPIDIYAEWIDEC 81 (87)
Q Consensus 33 ~~~~sV~v~idk~~~~g~~~C~-~C~~~~-~~~i~~L~epiDVYs~wiD~~ 81 (87)
|.-+.+....++ .|+....|. .||..+ .|++.--..+.+-|.+|++++
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 444455555544 356677786 499876 345444444568899999764
No 364
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=21.21 E-value=96 Score=22.97 Aligned_cols=37 Identities=22% Similarity=0.384 Sum_probs=24.7
Q ss_pred CCCccccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe-ecCCCC
Q 035653 22 KLDTQFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT-QIHALT 68 (87)
Q Consensus 22 kl~~~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~-~i~~L~ 68 (87)
+.+-.|-|..||+. ...-...|..||.--+. .|..|+
T Consensus 350 ~~~p~~~c~~cg~~----------~~~~~~~c~~c~~~~~~~~~~~~~ 387 (389)
T PRK11788 350 KRKPRYRCRNCGFT----------ARTLYWHCPSCKAWETIKPIRGLD 387 (389)
T ss_pred hCCCCEECCCCCCC----------CccceeECcCCCCccCcCCcccCC
Confidence 45556899999993 33456789999974333 355554
No 365
>PF00265 TK: Thymidine kinase; InterPro: IPR001267 Thymidine kinase (TK) (2.7.1.21 from EC) is an ubiquitous enzyme that catalyzes the ATP-dependent phosphorylation of thymidine. Two different families of Thymidine kinase have been identified [, ] and are represented in this entry; one groups together Thymidine kinase from herpesviruses, as well as cytosolic thymidylate kinases and the second family groups Thymidine kinase from various sources that include, vertebrates, bacteria, the Bacteriophage T4, poxviruses, African swine fever virus (ASFV) and Fish lymphocystis disease virus (FLDV). The major capsid protein of insect iridescent viruses also belongs to this family.; GO: 0004797 thymidine kinase activity, 0005524 ATP binding; PDB: 1XX6_B 2J9R_A 2J87_B 3E2I_A 2JA1_A 2UZ3_B 2B8T_B 2WVJ_A 1W4R_F 1XBT_F ....
Probab=21.15 E-value=1e+02 Score=21.82 Aligned_cols=29 Identities=28% Similarity=0.587 Sum_probs=15.3
Q ss_pred cCCCCCCCCeEEEEEeccC--------cEEEEEcCcc
Q 035653 28 QCPFCGHGTSVECRIDKKI--------QIGEAFCWNC 56 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~--------~~g~~~C~~C 56 (87)
-|-.||.+-+.+..+.... ......|+.|
T Consensus 139 vC~~Cg~~A~~t~R~~~~~~~i~iGg~e~Y~~~Cr~c 175 (176)
T PF00265_consen 139 VCEVCGRKATFTQRIVDDGEQILIGGSEKYEPVCRKC 175 (176)
T ss_dssp E-TTTSSEE-EEEEEETTSSSS-TTSTTTEEEE-CTT
T ss_pred EECCCCCceeEEEEEcCCCCEEEECCCCeEEEechhh
Confidence 3677777766666666432 2345666665
No 366
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=21.14 E-value=48 Score=20.20 Aligned_cols=23 Identities=39% Similarity=1.110 Sum_probs=13.7
Q ss_pred cCCCCCCCCeEEEEEeccCcEEEEEcC-ccccee
Q 035653 28 QCPFCGHGTSVECRIDKKIQIGEAFCW-NCLERF 60 (87)
Q Consensus 28 ~CPfC~~~~sV~v~idk~~~~g~~~C~-~C~~~~ 60 (87)
.||+||.+ |. . ....|. .|++.|
T Consensus 5 HC~~CG~~--Ip--~------~~~fCS~~C~~~~ 28 (59)
T PF09889_consen 5 HCPVCGKP--IP--P------DESFCSPKCREEY 28 (59)
T ss_pred cCCcCCCc--CC--c------chhhhCHHHHHHH
Confidence 68999863 22 1 245674 676655
No 367
>PRK08402 replication factor A; Reviewed
Probab=21.14 E-value=66 Score=25.72 Aligned_cols=27 Identities=22% Similarity=0.348 Sum_probs=15.7
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
+=.||.||. ++..+.+-+.-.|..||.
T Consensus 212 y~aCp~CnK------kv~~~~~~~~~~Ce~~~~ 238 (355)
T PRK08402 212 YDACPECRR------KVDYDPATDTWICPEHGE 238 (355)
T ss_pred EecCCCCCe------EEEEecCCCCEeCCCCCC
Confidence 346888886 233233335557888874
No 368
>COG0819 TenA Putative transcription activator [Transcription]
Probab=21.09 E-value=42 Score=25.04 Aligned_cols=13 Identities=46% Similarity=0.902 Sum_probs=11.0
Q ss_pred chhhhhhhhHHHH
Q 035653 69 EPIDIYAEWIDEC 81 (87)
Q Consensus 69 epiDVYs~wiD~~ 81 (87)
.|..+|.+|||-+
T Consensus 153 ~~~~~Y~~Wi~~Y 165 (218)
T COG0819 153 SPNPPYQEWIDTY 165 (218)
T ss_pred CCCCcHHHHHHHc
Confidence 4889999999865
No 369
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=21.07 E-value=49 Score=28.50 Aligned_cols=22 Identities=23% Similarity=0.289 Sum_probs=14.4
Q ss_pred ccCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 27 FQCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
=-|+-||+.. .+. .-.|..||.
T Consensus 567 ~iC~~CG~~~---------~g~-~~~CP~CGs 588 (623)
T PRK08271 567 TICNDCHHID---------KRT-GKRCPICGS 588 (623)
T ss_pred ccCCCCCCcC---------CCC-CcCCcCCCC
Confidence 3599999841 111 358999985
No 370
>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=20.97 E-value=41 Score=20.75 Aligned_cols=8 Identities=63% Similarity=0.920 Sum_probs=6.0
Q ss_pred CCcccccc
Q 035653 1 MGKRKSRK 8 (87)
Q Consensus 1 MGkRK~k~ 8 (87)
|||+|++-
T Consensus 31 mgkkkSK~ 38 (60)
T PF07491_consen 31 MGKKKSKC 38 (60)
T ss_pred cccccCce
Confidence 78888773
No 371
>PRK12366 replication factor A; Reviewed
Probab=20.68 E-value=48 Score=28.26 Aligned_cols=26 Identities=38% Similarity=0.626 Sum_probs=17.4
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccce
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLER 59 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~ 59 (87)
.-.||.||.. |. .+-|.-.|..||..
T Consensus 532 y~aCp~CnkK--v~------~~~g~~~C~~c~~~ 557 (637)
T PRK12366 532 LYLCPNCRKR--VE------EVDGEYICEFCGEV 557 (637)
T ss_pred EecccccCeE--eE------cCCCcEECCCCCCC
Confidence 4579999862 32 13467789999875
No 372
>PF02489 Herpes_glycop_H: Herpesvirus glycoprotein H; InterPro: IPR003493 Herpesviruses are enveloped by a lipid bilayer that contains at least a dozen glycoproteins. The virion surface glycoproteins mediate recognition of susceptible cells and promote fusion of the viral envelope with the cell membrane, leading to virus entry. No single glycoprotein associated with the virion membrane has been identified as the fusogen []. Glycoprotein L (gL) forms a non-covalently linked heterodimer with glycoprotein H (gH). This heterodimer is essential for virus-cell and cell-cell fusion since the association of gH and gL is necessary for correct localisation of gH to the virion or cell surface. gH anchoring the heterodimer to the plasma membrane through its transmembrane domain. gL lacks a transmembrane domain and is secreted from cells when expressed in the absence of gH []. This entry represents Herpesvirus glycoprotein H (gH), which is a virion associated envelope glycoprotein []. Heterodimer formation between gH and gL has been demonstrated in both virions and infected cells []. Heterodimer formation between gL and gH is important for the proper folding of gH and its insertion into the membrane because the anti-gH conformation-dependent monoclonal antibodies (mAbs) 53S and LP11 bind gH only when gL is present [, ].; PDB: 3PHF_S 3M1C_A 2LQY_A 2XQY_A.
Probab=20.60 E-value=1.3e+02 Score=25.44 Aligned_cols=25 Identities=36% Similarity=0.639 Sum_probs=16.6
Q ss_pred CCccccCCCCCCCCeEEEEEeccCcEEE
Q 035653 23 LDTQFQCPFCGHGTSVECRIDKKIQIGE 50 (87)
Q Consensus 23 l~~~F~CPfC~~~~sV~v~idk~~~~g~ 50 (87)
+...++|+|||+ |-++=|-..|+-.
T Consensus 558 it~~~~C~~Cgs---v~l~Yde~~gi~~ 582 (657)
T PF02489_consen 558 ITPSKDCPFCGS---VFLRYDESGGIMS 582 (657)
T ss_dssp SSS-SS-STTT----EEEEEETTSSEEE
T ss_pred CCCCCCCCCCCc---EEEEEecCCCEEE
Confidence 335778999997 8888887776544
No 373
>PRK08329 threonine synthase; Validated
Probab=20.52 E-value=93 Score=24.08 Aligned_cols=26 Identities=19% Similarity=0.547 Sum_probs=15.0
Q ss_pred ccCCCCCCCCeEEEEEeccCcEEEEEcCcccceeEe
Q 035653 27 FQCPFCGHGTSVECRIDKKIQIGEAFCWNCLERFCT 62 (87)
Q Consensus 27 F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~~~~~ 62 (87)
+.|+.||++-. .. .. ..| .||-.+..
T Consensus 2 l~C~~Cg~~~~-------~~-~~-~~C-~c~~~l~~ 27 (347)
T PRK08329 2 LRCTKCGRTYE-------EK-FK-LRC-DCGGTLLV 27 (347)
T ss_pred cCcCCCCCCcC-------CC-Cc-eec-CCCCcEEE
Confidence 67888887531 11 12 578 68755433
No 374
>PF14940 TMEM219: Transmembrane 219
Probab=20.24 E-value=99 Score=23.42 Aligned_cols=27 Identities=19% Similarity=0.297 Sum_probs=22.3
Q ss_pred ceeEeecCCCCchhhhhhhhHHHHHHhh
Q 035653 58 ERFCTQIHALTEPIDIYAEWIDECERAN 85 (87)
Q Consensus 58 ~~~~~~i~~L~epiDVYs~wiD~~e~~n 85 (87)
+.|....+.|-.| ||+.+|-.-+.+.|
T Consensus 28 Lg~yi~~~~l~nP-Di~~DWN~fL~~ls 54 (223)
T PF14940_consen 28 LGYYIKRNELKNP-DIPQDWNTFLLSLS 54 (223)
T ss_pred eeeEecccCCCcc-cchhhHHHHHHhhc
Confidence 3455688999999 99999998887765
No 375
>cd02972 DsbA_family DsbA family; consists of DsbA and DsbA-like proteins, including DsbC, DsbG, glutathione (GSH) S-transferase kappa (GSTK), 2-hydroxychromene-2-carboxylate (HCCA) isomerase, an oxidoreductase (FrnE) presumed to be involved in frenolicin biosynthesis, a 27-kDa outer membrane protein, and similar proteins. Members of this family contain a redox active CXXC motif (except GSTK and HCCA isomerase) imbedded in a TRX fold, and an alpha helical insert of about 75 residues (shorter in DsbC and DsbG) relative to TRX. DsbA is involved in the oxidative protein folding pathway in prokaryotes, catalyzing disulfide bond formation of proteins secreted into the bacterial periplasm. DsbC and DsbG function as protein disulfide isomerases and chaperones to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins.
Probab=20.23 E-value=29 Score=19.93 Aligned_cols=8 Identities=38% Similarity=1.015 Sum_probs=5.9
Q ss_pred ccCCCCCC
Q 035653 27 FQCPFCGH 34 (87)
Q Consensus 27 F~CPfC~~ 34 (87)
|.||+|-.
T Consensus 7 ~~Cp~C~~ 14 (98)
T cd02972 7 PLCPYCYL 14 (98)
T ss_pred CCCHhHHh
Confidence 57888865
No 376
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=20.17 E-value=46 Score=23.04 Aligned_cols=25 Identities=36% Similarity=0.854 Sum_probs=15.4
Q ss_pred cccCCCCCCCCeEEEEEeccCcEEEEEcCcccc
Q 035653 26 QFQCPFCGHGTSVECRIDKKIQIGEAFCWNCLE 58 (87)
Q Consensus 26 ~F~CPfC~~~~sV~v~idk~~~~g~~~C~~C~~ 58 (87)
.-.||.|++.. ++ .|.. -.|--|++
T Consensus 69 ~V~CP~C~K~T----Km---LGr~-D~CM~C~~ 93 (114)
T PF11023_consen 69 QVECPNCGKQT----KM---LGRV-DACMHCKE 93 (114)
T ss_pred eeECCCCCChH----hh---hchh-hccCcCCC
Confidence 44699999852 11 1111 27888887
No 377
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=20.15 E-value=39 Score=25.18 Aligned_cols=9 Identities=44% Similarity=0.969 Sum_probs=6.3
Q ss_pred EEcCcccce
Q 035653 51 AFCWNCLER 59 (87)
Q Consensus 51 ~~C~~C~~~ 59 (87)
+.|.+||+.
T Consensus 98 ~~C~~Cg~~ 106 (190)
T COG5082 98 KKCYNCGET 106 (190)
T ss_pred ccccccccc
Confidence 677777764
No 378
>cd05131 RasGAP_IQGAP2 IQGAP2 is a member of the IQGAP family that contains a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeat, a single WW domain, four IQ motifs which mediate interactions with calmodulin, and a Ras-GTPase-activating protein (GAP)-related domain that binds Rho family GTPases. IQGAP2 and IQGAP3 play important roles in the regulation of the cytoskeleton for axon outgrowth in hippocampal neurons and are thought to stay in a common regulatory pathway. The results of RNA interference studies indicated that IQGAP3 partially compensates functions of IQGAP2, but has lesser ability than IQGAP2 to promote axon outgrowth in hippocampal neuron. Morevover, IQGAP2 is required for the cadherin-mediated cell-to-cell adhesion in Xenopus laevis embryos.
Probab=20.14 E-value=66 Score=25.33 Aligned_cols=17 Identities=35% Similarity=1.034 Sum_probs=13.9
Q ss_pred CchhhhhhhhHHHHHHh
Q 035653 68 TEPIDIYAEWIDECERA 84 (87)
Q Consensus 68 ~epiDVYs~wiD~~e~~ 84 (87)
++|+.||..||..-|..
T Consensus 77 ~dP~~Iy~~~i~~~e~~ 93 (339)
T cd05131 77 TNPVEVYKAWVNQLETA 93 (339)
T ss_pred CCHHHHHHHHHHHHHHh
Confidence 57999999999876643
No 379
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.10 E-value=48 Score=26.36 Aligned_cols=22 Identities=23% Similarity=0.587 Sum_probs=14.4
Q ss_pred CCCccccCCCCCCCCeEEEEEe
Q 035653 22 KLDTQFQCPFCGHGTSVECRID 43 (87)
Q Consensus 22 kl~~~F~CPfC~~~~sV~v~id 43 (87)
.-..-=+||+||-.-++--.|-
T Consensus 235 ~~t~~~~C~~Cg~~PtiP~~~~ 256 (298)
T KOG2879|consen 235 TGTSDTECPVCGEPPTIPHVIG 256 (298)
T ss_pred cccCCceeeccCCCCCCCeeec
Confidence 3345568999998766555443
No 380
>COG1180 PflA Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]
Probab=20.09 E-value=48 Score=24.93 Aligned_cols=14 Identities=21% Similarity=0.888 Sum_probs=10.9
Q ss_pred cccCCCCCCCCeEE
Q 035653 26 QFQCPFCGHGTSVE 39 (87)
Q Consensus 26 ~F~CPfC~~~~sV~ 39 (87)
.|.||+|++..+-.
T Consensus 46 nlrC~~C~N~~~~~ 59 (260)
T COG1180 46 NLRCPYCQNPEISQ 59 (260)
T ss_pred CCCCCCCCChhHhc
Confidence 48999999976544
Done!