Query 034528
Match_columns 92
No_of_seqs 104 out of 188
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 03:49:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034528.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034528hhsearch_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 5.3E-44 1.2E-48 234.1 6.5 80 2-81 1-81 (81)
2 KOG3214 Uncharacterized Zn rib 100.0 1.7E-43 3.8E-48 241.7 3.8 90 1-90 1-91 (109)
3 COG4888 Uncharacterized Zn rib 100.0 1.8E-38 4E-43 216.4 8.1 82 1-82 1-82 (104)
4 PRK14892 putative transcriptio 100.0 1.7E-34 3.8E-39 195.7 6.5 77 1-81 1-77 (99)
5 TIGR03655 anti_R_Lar restricti 97.2 0.00032 6.9E-09 42.0 2.8 34 24-58 3-38 (53)
6 PF14354 Lar_restr_allev: Rest 97.0 0.0011 2.4E-08 39.9 3.7 33 21-54 2-37 (61)
7 TIGR01206 lysW lysine biosynth 96.7 0.0027 5.9E-08 39.0 3.8 37 22-62 2-39 (54)
8 PRK09710 lar restriction allev 96.3 0.0055 1.2E-07 39.1 3.5 34 19-55 3-36 (64)
9 COG1327 Predicted transcriptio 96.3 0.0024 5.2E-08 46.8 1.7 35 24-58 2-40 (156)
10 PF01096 TFIIS_C: Transcriptio 96.2 0.011 2.4E-07 33.6 4.1 35 23-57 1-39 (39)
11 TIGR00244 transcriptional regu 96.2 0.0047 1E-07 44.8 3.1 36 24-59 2-41 (147)
12 PF08271 TF_Zn_Ribbon: TFIIB z 96.2 0.0045 9.8E-08 35.4 2.4 32 23-59 1-32 (43)
13 TIGR02098 MJ0042_CXXC MJ0042 f 96.1 0.0025 5.5E-08 35.3 1.0 34 22-57 2-36 (38)
14 TIGR00280 L37a ribosomal prote 95.5 0.038 8.3E-07 37.3 4.9 44 21-70 34-77 (91)
15 PTZ00255 60S ribosomal protein 95.5 0.038 8.2E-07 37.2 4.8 45 20-70 34-78 (90)
16 PRK00398 rpoP DNA-directed RNA 95.4 0.034 7.5E-07 32.1 3.9 34 21-60 2-35 (46)
17 smart00440 ZnF_C2C2 C2C2 Zinc 95.4 0.045 9.7E-07 31.3 4.3 34 23-56 1-38 (40)
18 PF14255 Cys_rich_CPXG: Cystei 95.2 0.037 8E-07 33.7 3.7 48 23-70 1-50 (52)
19 PRK03976 rpl37ae 50S ribosomal 95.1 0.058 1.3E-06 36.3 4.8 44 21-70 35-78 (90)
20 PRK12286 rpmF 50S ribosomal pr 94.9 0.031 6.7E-07 34.5 2.9 28 17-55 22-49 (57)
21 PRK00464 nrdR transcriptional 94.8 0.042 9.2E-07 39.8 3.8 35 24-58 2-40 (154)
22 PF01780 Ribosomal_L37ae: Ribo 94.8 0.018 3.9E-07 38.8 1.7 42 21-68 34-75 (90)
23 PF13719 zinc_ribbon_5: zinc-r 94.7 0.024 5.1E-07 31.8 1.9 33 23-57 3-36 (37)
24 PF13717 zinc_ribbon_4: zinc-r 94.5 0.016 3.5E-07 32.5 0.8 34 22-56 2-35 (36)
25 PF14353 CpXC: CpXC protein 94.4 0.049 1.1E-06 37.0 3.1 39 23-61 2-53 (128)
26 PRK09678 DNA-binding transcrip 94.1 0.049 1.1E-06 35.2 2.5 44 23-67 2-53 (72)
27 smart00778 Prim_Zn_Ribbon Zinc 94.1 0.038 8.2E-07 31.6 1.7 29 24-54 5-33 (37)
28 PF09855 DUF2082: Nucleic-acid 94.0 0.13 2.8E-06 32.5 4.3 48 23-70 1-62 (64)
29 PF12760 Zn_Tnp_IS1595: Transp 93.3 0.076 1.6E-06 30.7 2.2 32 18-54 14-45 (46)
30 COG1997 RPL43A Ribosomal prote 93.1 0.088 1.9E-06 35.5 2.5 32 21-58 34-65 (89)
31 PF08792 A2L_zn_ribbon: A2L zi 92.9 0.12 2.6E-06 28.7 2.5 30 23-58 4-33 (33)
32 PF02150 RNA_POL_M_15KD: RNA p 92.2 0.3 6.4E-06 27.2 3.6 28 25-57 4-31 (35)
33 PHA00626 hypothetical protein 92.1 0.18 3.9E-06 31.7 2.8 34 24-58 2-35 (59)
34 TIGR03829 YokU_near_AblA uncha 91.8 0.29 6.2E-06 32.9 3.7 35 24-58 1-47 (89)
35 PF04216 FdhE: Protein involve 91.7 0.4 8.6E-06 36.9 4.9 49 22-70 211-262 (290)
36 PF04606 Ogr_Delta: Ogr/Delta- 91.1 0.44 9.6E-06 27.7 3.6 36 24-59 1-40 (47)
37 PRK00432 30S ribosomal protein 90.8 0.15 3.3E-06 30.5 1.5 26 24-56 22-47 (50)
38 smart00834 CxxC_CXXC_SSSS Puta 90.8 0.13 2.8E-06 28.2 1.1 31 22-55 5-35 (41)
39 PF04216 FdhE: Protein involve 90.6 0.31 6.8E-06 37.4 3.5 36 23-58 173-209 (290)
40 PF13240 zinc_ribbon_2: zinc-r 90.6 0.093 2E-06 26.9 0.3 21 25-55 2-22 (23)
41 PF09986 DUF2225: Uncharacteri 90.3 0.43 9.4E-06 35.6 3.8 44 20-65 3-68 (214)
42 PRK13130 H/ACA RNA-protein com 90.2 0.25 5.4E-06 30.6 2.1 45 22-78 5-49 (56)
43 PF09723 Zn-ribbon_8: Zinc rib 90.0 0.16 3.4E-06 29.1 1.0 30 22-54 5-34 (42)
44 PRK03988 translation initiatio 89.8 0.5 1.1E-05 33.7 3.7 33 21-56 101-133 (138)
45 TIGR00311 aIF-2beta translatio 89.8 0.49 1.1E-05 33.5 3.6 34 21-57 96-129 (133)
46 PF14803 Nudix_N_2: Nudix N-te 89.4 0.41 8.8E-06 26.7 2.3 29 25-55 3-31 (34)
47 smart00661 RPOL9 RNA polymeras 89.3 0.4 8.7E-06 27.5 2.4 28 25-56 3-30 (52)
48 TIGR01384 TFS_arch transcripti 89.3 1.2 2.5E-05 29.2 4.9 40 18-57 57-101 (104)
49 PF13453 zf-TFIIB: Transcripti 89.1 0.7 1.5E-05 26.0 3.3 27 24-54 1-27 (41)
50 COG3478 Predicted nucleic-acid 88.8 0.62 1.3E-05 30.0 3.2 45 20-64 2-60 (68)
51 PF06044 DRP: Dam-replacing fa 88.7 0.37 7.9E-06 37.9 2.5 60 22-83 31-94 (254)
52 COG3677 Transposase and inacti 88.5 0.44 9.5E-06 33.4 2.6 41 23-65 31-73 (129)
53 PF14205 Cys_rich_KTR: Cystein 87.7 0.65 1.4E-05 28.8 2.7 38 23-60 5-42 (55)
54 PF08273 Prim_Zn_Ribbon: Zinc- 87.6 0.37 7.9E-06 27.9 1.4 29 24-53 5-33 (40)
55 smart00653 eIF2B_5 domain pres 86.9 1 2.3E-05 30.8 3.6 32 21-55 79-110 (110)
56 smart00659 RPOLCX RNA polymera 86.8 0.34 7.4E-06 28.3 1.0 31 22-59 2-32 (44)
57 COG2051 RPS27A Ribosomal prote 86.6 1.1 2.3E-05 28.9 3.3 30 24-58 21-50 (67)
58 smart00531 TFIIE Transcription 86.4 0.2 4.4E-06 35.2 -0.1 40 20-59 97-136 (147)
59 PF05605 zf-Di19: Drought indu 86.3 0.31 6.7E-06 28.8 0.7 32 22-55 2-40 (54)
60 PF01873 eIF-5_eIF-2B: Domain 86.2 0.73 1.6E-05 32.2 2.6 32 21-55 92-123 (125)
61 TIGR02605 CxxC_CxxC_SSSS putat 86.1 0.38 8.1E-06 27.9 1.0 30 22-54 5-34 (52)
62 PF09526 DUF2387: Probable met 86.1 1.8 3.8E-05 27.7 4.2 36 24-61 10-45 (71)
63 TIGR03831 YgiT_finger YgiT-typ 86.1 1.7 3.7E-05 23.9 3.7 12 47-58 33-44 (46)
64 PF10571 UPF0547: Uncharacteri 85.9 0.35 7.5E-06 25.5 0.7 24 24-57 2-25 (26)
65 TIGR01385 TFSII transcription 85.7 1.4 3.1E-05 34.9 4.3 40 18-57 254-297 (299)
66 COG1405 SUA7 Transcription ini 85.5 0.45 9.8E-06 37.4 1.4 41 24-75 3-43 (285)
67 TIGR02443 conserved hypothetic 85.3 1.6 3.5E-05 27.4 3.5 33 24-58 11-43 (59)
68 KOG0478 DNA replication licens 85.1 0.41 8.9E-06 42.6 1.1 37 20-58 262-298 (804)
69 COG1645 Uncharacterized Zn-fin 85.1 0.74 1.6E-05 32.9 2.2 27 22-56 28-54 (131)
70 PF09862 DUF2089: Protein of u 85.0 1.1 2.3E-05 31.2 2.9 44 25-81 1-49 (113)
71 PRK14890 putative Zn-ribbon RN 84.7 0.51 1.1E-05 29.6 1.1 34 20-54 23-56 (59)
72 PF13248 zf-ribbon_3: zinc-rib 84.5 0.45 9.7E-06 24.6 0.7 22 24-55 4-25 (26)
73 PRK00423 tfb transcription ini 84.4 0.79 1.7E-05 35.8 2.3 32 22-58 11-42 (310)
74 PF07754 DUF1610: Domain of un 84.3 0.55 1.2E-05 24.6 1.0 12 18-29 12-23 (24)
75 PRK03564 formate dehydrogenase 84.1 0.9 2E-05 36.3 2.5 38 20-57 185-223 (309)
76 COG1779 C4-type Zn-finger prot 83.8 1.3 2.8E-05 33.8 3.2 38 18-57 10-54 (201)
77 PRK12336 translation initiatio 83.8 1.5 3.3E-05 32.6 3.5 35 21-58 97-131 (201)
78 PRK05978 hypothetical protein; 83.4 0.52 1.1E-05 34.1 0.9 31 23-58 34-64 (148)
79 PF05180 zf-DNL: DNL zinc fing 83.4 1.4 3E-05 28.1 2.7 35 22-58 4-41 (66)
80 PRK03564 formate dehydrogenase 83.4 3.6 7.8E-05 32.9 5.7 60 22-81 226-292 (309)
81 PHA02540 61 DNA primase; Provi 83.1 1.4 3.1E-05 35.5 3.3 50 21-77 26-86 (337)
82 PF07282 OrfB_Zn_ribbon: Putat 83.1 0.61 1.3E-05 28.3 1.0 36 19-60 25-60 (69)
83 PF03811 Zn_Tnp_IS1: InsA N-te 82.2 1.8 3.8E-05 24.4 2.6 30 23-53 6-36 (36)
84 KOG0402 60S ribosomal protein 82.1 0.6 1.3E-05 31.5 0.7 31 21-57 35-65 (92)
85 KOG1814 Predicted E3 ubiquitin 82.0 0.94 2E-05 38.0 2.0 55 21-81 367-421 (445)
86 COG1326 Uncharacterized archae 81.9 0.59 1.3E-05 35.6 0.7 34 22-56 6-40 (201)
87 PF03367 zf-ZPR1: ZPR1 zinc-fi 81.7 2.2 4.8E-05 30.8 3.6 34 24-57 3-41 (161)
88 PF03966 Trm112p: Trm112p-like 81.6 0.38 8.1E-06 29.8 -0.4 24 35-58 42-65 (68)
89 PF13465 zf-H2C2_2: Zinc-finge 81.5 0.58 1.3E-05 24.0 0.4 11 20-30 12-22 (26)
90 PF05876 Terminase_GpA: Phage 81.5 1.4 3E-05 37.3 2.8 33 23-55 201-238 (557)
91 PF05502 Dynactin_p62: Dynacti 81.5 1.5 3.3E-05 36.7 3.0 48 21-71 51-111 (483)
92 PF10083 DUF2321: Uncharacteri 81.0 0.27 5.9E-06 36.2 -1.3 60 21-87 38-105 (158)
93 TIGR01562 FdhE formate dehydro 80.6 2.5 5.4E-05 33.7 3.9 59 22-80 224-291 (305)
94 COG2888 Predicted Zn-ribbon RN 80.2 0.72 1.6E-05 29.2 0.5 34 20-54 25-58 (61)
95 TIGR01562 FdhE formate dehydro 80.2 1 2.2E-05 35.9 1.5 36 22-57 184-221 (305)
96 TIGR01031 rpmF_bact ribosomal 79.6 2.5 5.3E-05 25.7 2.8 27 17-54 21-47 (55)
97 PF05077 DUF678: Protein of un 79.2 1.6 3.4E-05 28.6 1.9 33 23-55 23-66 (74)
98 PHA02998 RNA polymerase subuni 79.1 3.6 7.9E-05 31.2 4.1 38 21-58 142-183 (195)
99 PRK00420 hypothetical protein; 78.5 1.6 3.5E-05 30.3 1.9 29 23-58 24-52 (112)
100 COG0675 Transposase and inacti 78.1 1.3 2.9E-05 32.5 1.5 34 18-62 305-338 (364)
101 TIGR00340 zpr1_rel ZPR1-relate 77.7 2.7 5.9E-05 30.7 3.0 31 25-56 1-38 (163)
102 TIGR00310 ZPR1_znf ZPR1 zinc f 76.8 4.1 8.9E-05 30.4 3.8 33 24-56 2-40 (192)
103 PF04810 zf-Sec23_Sec24: Sec23 76.5 0.72 1.6E-05 26.1 -0.2 14 21-34 23-36 (40)
104 TIGR02159 PA_CoA_Oxy4 phenylac 76.5 0.64 1.4E-05 33.2 -0.5 36 22-57 105-141 (146)
105 cd00730 rubredoxin Rubredoxin; 76.1 1.3 2.8E-05 26.6 0.8 18 16-33 28-45 (50)
106 PF00301 Rubredoxin: Rubredoxi 76.1 1.2 2.7E-05 26.4 0.7 18 16-33 28-45 (47)
107 PRK00415 rps27e 30S ribosomal 75.2 4.3 9.4E-05 25.4 3.0 28 24-56 13-40 (59)
108 COG2835 Uncharacterized conser 74.5 4 8.7E-05 25.7 2.7 41 18-64 4-46 (60)
109 PF13894 zf-C2H2_4: C2H2-type 74.4 1.3 2.8E-05 20.7 0.4 8 23-30 1-8 (24)
110 TIGR03830 CxxCG_CxxCG_HTH puta 74.4 4 8.6E-05 26.9 2.9 34 25-58 1-43 (127)
111 smart00709 Zpr1 Duplicated dom 74.4 5.2 0.00011 28.9 3.7 10 46-55 29-38 (160)
112 COG1998 RPS31 Ribosomal protei 74.0 2.1 4.6E-05 26.2 1.4 26 24-55 21-46 (51)
113 COG0333 RpmF Ribosomal protein 72.3 2.6 5.6E-05 26.2 1.5 29 16-55 21-49 (57)
114 PRK11827 hypothetical protein; 72.1 2.9 6.3E-05 26.1 1.7 39 19-63 5-45 (60)
115 PF01807 zf-CHC2: CHC2 zinc fi 71.7 5.1 0.00011 26.3 2.9 32 22-56 33-64 (97)
116 PRK00750 lysK lysyl-tRNA synth 71.2 9.4 0.0002 32.0 5.0 38 24-62 177-215 (510)
117 smart00400 ZnF_CHCC zinc finge 70.7 5.4 0.00012 23.4 2.6 38 24-72 4-41 (55)
118 COG1241 MCM2 Predicted ATPase 70.4 4.2 9.2E-05 35.8 2.9 47 21-69 128-177 (682)
119 KOG2593 Transcription initiati 70.4 1.2 2.7E-05 37.3 -0.3 38 20-57 126-164 (436)
120 PF08274 PhnA_Zn_Ribbon: PhnA 69.5 1.5 3.2E-05 23.9 -0.0 25 24-55 4-28 (30)
121 PRK01110 rpmF 50S ribosomal pr 69.2 4.1 8.9E-05 25.2 1.9 28 17-56 22-49 (60)
122 COG3809 Uncharacterized protei 68.3 5.4 0.00012 26.7 2.5 27 24-54 3-29 (88)
123 COG1594 RPB9 DNA-directed RNA 68.1 7 0.00015 26.8 3.1 30 24-57 4-33 (113)
124 KOG1812 Predicted E3 ubiquitin 67.9 3.5 7.5E-05 33.5 1.8 30 22-58 306-335 (384)
125 PF10276 zf-CHCC: Zinc-finger 67.9 8.8 0.00019 22.1 3.0 25 29-56 15-39 (40)
126 PF14122 YokU: YokU-like prote 67.9 4.6 9.9E-05 27.2 2.0 35 24-58 1-47 (87)
127 COG1656 Uncharacterized conser 67.6 2.1 4.4E-05 31.8 0.4 32 22-56 97-140 (165)
128 PF15616 TerY-C: TerY-C metal 66.3 6.4 0.00014 28.0 2.7 35 24-58 79-117 (131)
129 cd00350 rubredoxin_like Rubred 66.2 2.5 5.4E-05 22.8 0.5 13 21-33 16-28 (33)
130 KOG1597 Transcription initiati 65.6 4.9 0.00011 32.5 2.2 44 24-76 2-45 (308)
131 PF14206 Cys_rich_CPCC: Cystei 65.2 6.1 0.00013 25.8 2.2 28 23-55 2-29 (78)
132 PF01927 Mut7-C: Mut7-C RNAse 64.3 8.3 0.00018 26.9 2.9 32 22-56 91-134 (147)
133 KOG1296 Uncharacterized conser 64.2 6.5 0.00014 29.0 2.4 60 22-81 64-145 (161)
134 PF10263 SprT-like: SprT-like 62.9 8.7 0.00019 26.2 2.8 33 21-57 122-154 (157)
135 KOG2703 C4-type Zn-finger prot 62.1 3.4 7.3E-05 34.9 0.7 18 18-36 64-81 (460)
136 PRK12495 hypothetical protein; 62.0 5 0.00011 31.1 1.6 34 17-58 37-70 (226)
137 KOG2906 RNA polymerase III sub 61.7 18 0.0004 25.0 4.1 31 24-58 3-33 (105)
138 PF07191 zinc-ribbons_6: zinc- 61.4 6.5 0.00014 25.4 1.8 28 23-58 2-29 (70)
139 COG2260 Predicted Zn-ribbon RN 61.1 5.5 0.00012 25.0 1.4 31 48-78 19-49 (59)
140 PF13878 zf-C2H2_3: zinc-finge 61.1 2.8 6E-05 23.9 0.0 16 44-59 11-26 (41)
141 PF09538 FYDLN_acid: Protein o 61.1 4.9 0.00011 27.5 1.3 36 17-59 4-39 (108)
142 PF04690 YABBY: YABBY protein; 60.9 6.6 0.00014 29.1 2.0 42 23-64 13-54 (170)
143 COG5415 Predicted integral mem 60.8 3.7 7.9E-05 32.1 0.6 19 22-40 214-233 (251)
144 PF03604 DNA_RNApol_7kD: DNA d 60.5 4.6 0.0001 22.2 0.9 25 24-55 2-26 (32)
145 PF12322 T4_baseplate: T4 bact 60.4 15 0.00032 27.6 3.8 62 17-79 73-137 (205)
146 PRK03824 hypA hydrogenase nick 60.1 3.9 8.5E-05 28.6 0.6 15 18-32 66-80 (135)
147 smart00647 IBR In Between Ring 59.9 13 0.00027 21.5 2.8 35 21-59 17-53 (64)
148 COG1198 PriA Primosomal protei 59.9 7.3 0.00016 34.6 2.4 29 21-55 443-471 (730)
149 PF08996 zf-DNA_Pol: DNA Polym 59.8 3.9 8.4E-05 29.8 0.6 38 20-57 16-56 (188)
150 PF13909 zf-H2C2_5: C2H2-type 59.7 3.8 8.3E-05 20.0 0.4 8 23-30 1-8 (24)
151 PLN00209 ribosomal protein S27 59.6 14 0.0003 24.8 3.2 38 16-58 27-67 (86)
152 KOG2767 Translation initiation 59.0 3 6.4E-05 34.6 -0.1 38 21-60 95-132 (400)
153 KOG2907 RNA polymerase I trans 58.8 6.4 0.00014 27.7 1.5 36 23-58 75-114 (116)
154 PF09332 Mcm10: Mcm10 replicat 58.6 4.4 9.6E-05 32.9 0.8 32 18-55 281-312 (344)
155 PF14768 RPA_interact_C: Repli 57.6 9.1 0.0002 24.5 2.0 34 25-66 2-35 (82)
156 PF00096 zf-C2H2: Zinc finger, 57.6 3.9 8.5E-05 19.5 0.2 10 48-57 2-11 (23)
157 PRK00241 nudC NADH pyrophospha 57.4 11 0.00023 28.9 2.7 27 25-57 102-128 (256)
158 PF01921 tRNA-synt_1f: tRNA sy 57.3 12 0.00026 30.6 3.1 39 24-62 176-215 (360)
159 PTZ00083 40S ribosomal protein 57.2 16 0.00035 24.4 3.2 38 16-58 26-66 (85)
160 TIGR02996 rpt_mate_G_obs repea 57.1 5.5 0.00012 23.4 0.8 13 65-77 17-29 (42)
161 PF10058 DUF2296: Predicted in 56.8 6.9 0.00015 23.7 1.3 15 17-31 39-53 (54)
162 PF01667 Ribosomal_S27e: Ribos 56.4 18 0.00039 22.2 3.1 31 24-59 9-39 (55)
163 PF11781 RRN7: RNA polymerase 56.4 12 0.00026 20.9 2.1 27 22-55 8-34 (36)
164 smart00714 LITAF Possible memb 56.3 8.2 0.00018 23.5 1.6 20 20-41 1-20 (67)
165 PF10122 Mu-like_Com: Mu-like 55.9 9.3 0.0002 23.3 1.7 42 21-66 3-45 (51)
166 MTH00038 COX2 cytochrome c oxi 55.9 11 0.00025 28.4 2.6 50 29-79 177-228 (229)
167 TIGR00373 conserved hypothetic 55.5 5.5 0.00012 28.5 0.8 11 20-30 126-136 (158)
168 COG4306 Uncharacterized protei 55.1 3.2 6.9E-05 30.3 -0.5 46 20-67 37-89 (160)
169 TIGR01391 dnaG DNA primase, ca 54.9 11 0.00024 30.6 2.5 30 22-55 34-64 (415)
170 COG2023 RPR2 RNase P subunit R 54.8 21 0.00045 24.7 3.5 41 21-61 55-97 (105)
171 PF10601 zf-LITAF-like: LITAF- 54.7 8.5 0.00018 23.8 1.5 22 18-41 3-24 (73)
172 KOG2846 Predicted membrane pro 54.3 5.3 0.00012 32.5 0.6 13 20-32 240-252 (328)
173 PRK04023 DNA polymerase II lar 54.3 11 0.00024 35.1 2.6 23 62-84 676-698 (1121)
174 KOG3113 Uncharacterized conser 54.0 8.1 0.00018 30.9 1.6 57 20-76 109-182 (293)
175 cd00674 LysRS_core_class_I cat 53.8 30 0.00066 27.9 4.9 37 24-61 171-207 (353)
176 KOG3277 Uncharacterized conser 53.8 19 0.00042 26.7 3.4 66 13-81 70-139 (165)
177 PHA02611 51 baseplate hub asse 53.6 9.9 0.00022 29.8 2.0 25 17-41 77-101 (249)
178 PF03119 DNA_ligase_ZBD: NAD-d 53.6 3.7 8.1E-05 21.7 -0.3 7 24-30 1-7 (28)
179 TIGR00595 priA primosomal prot 53.5 11 0.00023 31.6 2.2 30 22-57 222-251 (505)
180 PF01485 IBR: IBR domain; Int 53.4 6.9 0.00015 22.5 0.8 34 21-58 17-52 (64)
181 COG1503 eRF1 Peptide chain rel 53.0 5.5 0.00012 33.2 0.5 31 21-54 326-356 (411)
182 PF00628 PHD: PHD-finger; Int 52.1 14 0.0003 20.8 2.0 30 25-63 2-31 (51)
183 PHA02942 putative transposase; 52.0 13 0.00028 30.1 2.5 51 20-80 323-373 (383)
184 PRK14715 DNA polymerase II lar 51.9 14 0.0003 35.6 2.9 49 21-82 673-721 (1627)
185 PRK12380 hydrogenase nickel in 51.6 5.7 0.00012 27.0 0.3 30 17-54 65-94 (113)
186 KOG2462 C2H2-type Zn-finger pr 51.4 7.3 0.00016 31.1 0.9 35 20-57 159-198 (279)
187 PRK06266 transcription initiat 51.1 7.2 0.00016 28.5 0.8 9 21-29 116-124 (178)
188 PF10813 DUF2733: Protein of u 50.6 5 0.00011 22.4 -0.1 26 48-73 4-29 (32)
189 PHA00616 hypothetical protein 50.5 5.6 0.00012 23.5 0.1 9 22-30 1-9 (44)
190 PRK04011 peptide chain release 50.1 19 0.0004 29.5 3.1 53 22-81 328-380 (411)
191 PRK05667 dnaG DNA primase; Val 50.0 15 0.00032 31.5 2.6 30 22-55 36-66 (580)
192 cd00729 rubredoxin_SM Rubredox 49.9 7.1 0.00015 21.3 0.5 11 23-33 19-29 (34)
193 PF08209 Sgf11: Sgf11 (transcr 49.3 7.2 0.00016 21.6 0.4 10 21-30 3-12 (33)
194 PF09297 zf-NADH-PPase: NADH p 49.1 11 0.00023 20.0 1.1 26 25-56 6-31 (32)
195 smart00249 PHD PHD zinc finger 48.9 9.4 0.0002 20.1 0.9 26 25-59 2-27 (47)
196 COG5216 Uncharacterized conser 48.6 19 0.0004 23.0 2.3 31 22-55 22-53 (67)
197 PF14311 DUF4379: Domain of un 48.2 6.9 0.00015 23.0 0.3 8 23-30 29-36 (55)
198 smart00731 SprT SprT homologue 48.0 22 0.00048 24.6 2.9 33 22-57 112-144 (146)
199 PF09334 tRNA-synt_1g: tRNA sy 47.5 12 0.00027 30.1 1.7 39 44-82 164-203 (391)
200 COG3877 Uncharacterized protei 46.3 19 0.00041 25.4 2.3 24 22-55 6-29 (122)
201 PF13912 zf-C2H2_6: C2H2-type 46.0 6.7 0.00014 19.4 -0.0 12 47-58 2-13 (27)
202 PF04135 Nop10p: Nucleolar RNA 45.9 16 0.00036 22.2 1.7 28 48-75 19-46 (53)
203 PHA00732 hypothetical protein 45.3 2.6 5.6E-05 27.2 -2.0 48 22-69 1-50 (79)
204 KOG3456 NADH:ubiquinone oxidor 44.9 13 0.00029 26.2 1.3 26 28-57 90-115 (120)
205 COG4049 Uncharacterized protei 44.8 8.8 0.00019 24.3 0.4 13 18-30 13-25 (65)
206 KOG2691 RNA polymerase II subu 44.8 23 0.00049 24.9 2.5 48 25-74 7-59 (113)
207 TIGR01433 CyoA cytochrome o ub 44.7 20 0.00043 27.1 2.3 47 29-76 176-224 (226)
208 TIGR00100 hypA hydrogenase nic 43.8 8.5 0.00019 26.1 0.2 29 18-54 66-94 (115)
209 COG1571 Predicted DNA-binding 43.8 10 0.00022 31.8 0.7 29 24-59 352-380 (421)
210 COG5349 Uncharacterized protei 43.4 7.9 0.00017 27.6 0.0 31 23-58 22-52 (126)
211 PF13824 zf-Mss51: Zinc-finger 43.3 14 0.00029 22.8 1.1 15 17-31 9-23 (55)
212 TIGR00467 lysS_arch lysyl-tRNA 43.3 46 0.001 28.3 4.5 36 24-61 170-205 (515)
213 MTH00129 COX2 cytochrome c oxi 43.2 23 0.00051 26.8 2.5 49 29-78 177-227 (230)
214 PF13451 zf-trcl: Probable zin 43.0 19 0.00042 21.6 1.7 16 46-61 4-19 (49)
215 TIGR02300 FYDLN_acid conserved 42.5 12 0.00027 26.7 0.9 36 17-59 4-39 (129)
216 COG1655 Uncharacterized protei 42.4 10 0.00022 30.0 0.5 11 20-30 17-27 (267)
217 PF09151 DUF1936: Domain of un 42.1 62 0.0013 18.2 3.5 27 24-51 3-29 (36)
218 MTH00080 COX2 cytochrome c oxi 41.8 26 0.00056 26.7 2.6 48 29-77 180-229 (231)
219 PHA00733 hypothetical protein 40.6 4.5 9.7E-05 28.1 -1.6 40 20-59 71-112 (128)
220 PF12773 DZR: Double zinc ribb 40.1 9.5 0.00021 21.6 0.0 11 45-55 28-38 (50)
221 PF04032 Rpr2: RNAse P Rpr2/Rp 40.0 84 0.0018 19.2 4.4 33 21-53 45-84 (85)
222 PF14690 zf-ISL3: zinc-finger 39.8 20 0.00043 19.8 1.3 11 22-32 2-12 (47)
223 PF01396 zf-C4_Topoisom: Topoi 39.7 62 0.0013 18.0 3.4 28 24-55 3-33 (39)
224 PF12480 DUF3699: Protein of u 39.4 1E+02 0.0022 19.7 5.3 47 39-86 23-70 (77)
225 TIGR00354 polC DNA polymerase, 39.4 27 0.00059 32.6 2.7 49 21-82 624-672 (1095)
226 PF10609 ParA: ParA/MinD ATPas 39.4 12 0.00025 24.5 0.3 11 21-31 64-74 (81)
227 COG3058 FdhE Uncharacterized p 39.3 23 0.0005 28.7 2.0 32 20-51 183-216 (308)
228 MTH00117 COX2 cytochrome c oxi 39.2 28 0.0006 26.3 2.4 48 29-77 177-226 (227)
229 PRK14873 primosome assembly pr 39.0 23 0.0005 30.9 2.2 29 21-55 391-419 (665)
230 MTH00154 COX2 cytochrome c oxi 38.9 29 0.00063 26.2 2.5 47 29-76 177-225 (227)
231 MTH00185 COX2 cytochrome c oxi 38.8 32 0.00068 26.1 2.7 47 32-79 180-228 (230)
232 PRK14714 DNA polymerase II lar 37.8 36 0.00077 32.5 3.3 25 60-84 720-744 (1337)
233 PF13408 Zn_ribbon_recom: Reco 37.6 20 0.00043 20.3 1.1 15 44-58 3-17 (58)
234 PRK00762 hypA hydrogenase nick 37.1 22 0.00048 24.4 1.5 9 23-31 93-101 (124)
235 MTH00139 COX2 cytochrome c oxi 36.9 27 0.00058 26.2 2.0 47 29-76 177-225 (226)
236 KOG3022 Predicted ATPase, nucl 36.5 19 0.00041 29.0 1.2 12 21-32 221-232 (300)
237 TIGR00120 ArgJ glutamate N-ace 36.4 35 0.00076 28.5 2.7 33 30-62 367-400 (404)
238 MTH00051 COX2 cytochrome c oxi 36.3 39 0.00084 25.6 2.8 46 30-76 182-229 (234)
239 KOG4080 Mitochondrial ribosoma 36.1 18 0.00039 27.1 0.9 25 18-53 89-113 (176)
240 PF13913 zf-C2HC_2: zinc-finge 35.7 18 0.00039 18.4 0.6 11 47-57 3-13 (25)
241 PRK14810 formamidopyrimidine-D 35.7 31 0.00067 26.5 2.2 26 24-53 246-271 (272)
242 PF06397 Desulfoferrod_N: Desu 35.5 24 0.00051 19.9 1.2 26 19-49 3-28 (36)
243 PRK14811 formamidopyrimidine-D 35.5 29 0.00063 26.7 2.0 28 24-55 237-264 (269)
244 PF04161 Arv1: Arv1-like famil 35.5 25 0.00055 25.9 1.7 33 23-55 1-33 (208)
245 KOG1598 Transcription initiati 35.3 24 0.00051 30.5 1.6 27 24-55 2-28 (521)
246 TIGR00319 desulf_FeS4 desulfof 35.1 43 0.00093 17.8 2.2 26 20-50 5-30 (34)
247 COG1675 TFA1 Transcription ini 35.0 17 0.00037 27.0 0.7 10 21-30 131-140 (176)
248 COG3357 Predicted transcriptio 34.6 16 0.00034 25.0 0.4 29 47-75 59-88 (97)
249 PF05280 FlhC: Flagellar trans 34.4 16 0.00035 26.8 0.5 12 19-30 151-162 (175)
250 PF06677 Auto_anti-p27: Sjogre 34.3 36 0.00077 19.5 1.8 24 23-53 18-41 (41)
251 PHA02893 hypothetical protein; 34.3 34 0.00073 23.0 1.9 11 45-55 68-78 (88)
252 TIGR00622 ssl1 transcription f 33.8 19 0.00042 25.0 0.7 23 23-55 2-24 (112)
253 COG1592 Rubrerythrin [Energy p 33.5 20 0.00043 26.4 0.8 11 21-31 148-158 (166)
254 PF14913 DPCD: DPCD protein fa 33.5 21 0.00047 27.1 1.0 24 53-76 95-118 (194)
255 COG4311 SoxD Sarcosine oxidase 33.4 19 0.00041 24.7 0.6 9 22-30 3-11 (97)
256 COG3529 Predicted nucleic-acid 33.3 7.7 0.00017 24.8 -1.2 30 24-55 12-41 (66)
257 smart00350 MCM minichromosome 32.5 25 0.00054 29.2 1.3 34 20-55 35-70 (509)
258 PF02891 zf-MIZ: MIZ/SP-RING z 32.4 19 0.00042 21.1 0.5 8 23-30 42-49 (50)
259 PF02701 zf-Dof: Dof domain, z 32.3 30 0.00066 22.0 1.4 37 20-56 3-40 (63)
260 MTH00008 COX2 cytochrome c oxi 32.2 33 0.00072 25.9 1.9 47 29-76 177-225 (228)
261 PF02591 DUF164: Putative zinc 32.0 24 0.00052 20.7 0.8 11 20-30 44-54 (56)
262 cd00974 DSRD Desulforedoxin (D 31.9 54 0.0012 17.4 2.2 25 21-50 3-27 (34)
263 PF05495 zf-CHY: CHY zinc fing 31.8 11 0.00024 23.6 -0.7 36 20-57 17-52 (71)
264 PTZ00047 cytochrome c oxidase 31.7 50 0.0011 24.3 2.7 46 32-78 113-160 (162)
265 PRK00564 hypA hydrogenase nick 31.5 19 0.00041 24.5 0.4 30 18-54 67-96 (117)
266 cd03019 DsbA_DsbA DsbA family, 31.3 18 0.00039 24.4 0.3 11 21-31 23-33 (178)
267 PRK01103 formamidopyrimidine/5 31.2 41 0.00089 25.7 2.3 27 24-54 247-273 (274)
268 PF06827 zf-FPG_IleRS: Zinc fi 31.0 82 0.0018 16.1 3.4 26 24-53 3-28 (30)
269 smart00355 ZnF_C2H2 zinc finge 30.9 24 0.00053 16.0 0.7 8 49-56 3-10 (26)
270 PRK04351 hypothetical protein; 30.8 50 0.0011 23.6 2.5 34 21-58 111-144 (149)
271 TIGR02866 CoxB cytochrome c ox 30.8 35 0.00075 24.9 1.7 45 29-74 154-200 (201)
272 PRK07111 anaerobic ribonucleos 30.7 24 0.00053 31.2 1.0 21 23-54 681-701 (735)
273 PRK15338 type III secretion sy 30.6 25 0.00055 29.1 1.0 22 60-81 194-215 (372)
274 COG1364 ArgJ N-acetylglutamate 30.6 32 0.0007 28.8 1.7 32 32-63 369-401 (404)
275 PF14446 Prok-RING_1: Prokaryo 30.4 37 0.0008 20.8 1.5 25 24-56 7-31 (54)
276 COG1773 Rubredoxin [Energy pro 30.4 30 0.00066 21.3 1.1 23 15-37 29-51 (55)
277 PF12898 Stc1: Stc1 domain; I 30.2 58 0.0013 21.0 2.5 37 16-72 31-67 (84)
278 TIGR03676 aRF1/eRF1 peptide ch 30.2 59 0.0013 26.6 3.1 53 22-81 320-372 (403)
279 PF05907 DUF866: Eukaryotic pr 30.1 31 0.00068 24.9 1.4 34 20-53 62-106 (161)
280 PRK13945 formamidopyrimidine-D 29.8 43 0.00093 25.8 2.1 26 24-53 256-281 (282)
281 MTH00023 COX2 cytochrome c oxi 29.7 49 0.0011 25.2 2.4 46 30-76 189-236 (240)
282 PF04981 NMD3: NMD3 family ; 29.7 28 0.00061 26.0 1.1 17 42-58 31-47 (236)
283 PF01155 HypA: Hydrogenase exp 29.6 38 0.00083 22.8 1.6 11 20-30 68-78 (113)
284 PRK10445 endonuclease VIII; Pr 29.6 45 0.00097 25.5 2.2 26 24-53 237-262 (263)
285 COG1499 NMD3 NMD protein affec 29.4 71 0.0015 26.1 3.4 56 24-79 8-77 (355)
286 TIGR00577 fpg formamidopyrimid 29.2 44 0.00096 25.6 2.1 26 24-53 247-272 (272)
287 PF11793 FANCL_C: FANCL C-term 29.1 15 0.00031 22.9 -0.5 17 20-38 53-69 (70)
288 PF14369 zf-RING_3: zinc-finge 29.1 81 0.0018 17.3 2.6 32 22-58 2-33 (35)
289 KOG2923 Uncharacterized conser 28.9 33 0.00071 22.0 1.1 33 22-57 22-55 (67)
290 PF13901 DUF4206: Domain of un 28.8 27 0.00058 25.8 0.8 34 21-58 151-184 (202)
291 TIGR00627 tfb4 transcription f 28.8 20 0.00044 28.2 0.2 29 18-56 251-279 (279)
292 KOG2463 Predicted RNA-binding 28.8 79 0.0017 26.3 3.6 43 17-61 253-303 (376)
293 COG1107 Archaea-specific RecJ- 28.5 69 0.0015 28.6 3.3 42 17-58 46-92 (715)
294 KOG2186 Cell growth-regulating 28.5 16 0.00035 29.1 -0.4 35 22-58 3-41 (276)
295 TIGR00320 dfx_rbo desulfoferro 28.5 49 0.0011 23.0 2.1 30 20-56 5-34 (125)
296 PF06170 DUF983: Protein of un 28.3 21 0.00045 23.4 0.1 11 48-58 10-20 (86)
297 PRK12722 transcriptional activ 28.3 26 0.00056 26.3 0.7 13 19-31 151-163 (187)
298 MTH00168 COX2 cytochrome c oxi 28.2 43 0.00093 25.2 1.9 43 32-75 180-224 (225)
299 smart00734 ZnF_Rad18 Rad18-lik 28.1 28 0.0006 17.9 0.6 8 23-30 2-9 (26)
300 KOG2324 Prolyl-tRNA synthetase 28.1 27 0.00058 29.5 0.8 32 20-55 225-256 (457)
301 COG2816 NPY1 NTP pyrophosphohy 28.1 49 0.0011 26.4 2.2 27 25-57 114-140 (279)
302 smart00782 PhnA_Zn_Ribbon PhnA 27.9 66 0.0014 19.0 2.3 31 24-54 9-44 (47)
303 PF14952 zf-tcix: Putative tre 27.9 30 0.00064 20.6 0.7 30 18-57 7-38 (44)
304 TIGR01432 QOXA cytochrome aa3 27.8 57 0.0012 24.2 2.5 47 29-76 167-215 (217)
305 TIGR00308 TRM1 tRNA(guanine-26 27.7 75 0.0016 25.7 3.3 54 17-80 228-285 (374)
306 KOG2805 tRNA (5-methylaminomet 27.7 37 0.0008 28.2 1.5 22 67-88 81-102 (377)
307 TIGR00558 pdxH pyridoxamine-ph 27.6 37 0.0008 25.4 1.4 19 64-82 28-46 (217)
308 PRK05580 primosome assembly pr 27.5 48 0.001 28.7 2.3 30 22-57 390-419 (679)
309 PF10932 DUF2783: Protein of u 27.5 30 0.00066 21.7 0.8 26 61-86 5-30 (60)
310 PF04423 Rad50_zn_hook: Rad50 27.3 21 0.00045 20.9 0.0 7 24-30 22-28 (54)
311 CHL00136 rpl31 ribosomal prote 27.2 63 0.0014 20.4 2.2 34 20-57 13-46 (68)
312 KOG2164 Predicted E3 ubiquitin 27.2 14 0.00031 31.7 -1.0 33 20-56 184-216 (513)
313 TIGR00686 phnA alkylphosphonat 27.1 26 0.00056 24.5 0.4 15 19-33 16-30 (109)
314 PF03470 zf-XS: XS zinc finger 26.9 36 0.00077 20.0 1.0 7 25-31 1-7 (43)
315 COG1439 Predicted nucleic acid 26.7 42 0.00091 25.1 1.5 7 25-31 156-162 (177)
316 KOG3507 DNA-directed RNA polym 26.5 34 0.00074 21.7 0.9 31 18-55 16-46 (62)
317 cd03023 DsbA_Com1_like DsbA fa 26.3 21 0.00046 23.1 -0.1 11 21-31 13-23 (154)
318 TIGR01374 soxD sarcosine oxida 26.2 30 0.00065 22.9 0.6 8 23-30 2-9 (84)
319 KOG3309 Ferredoxin [Energy pro 26.1 32 0.00069 25.4 0.8 38 45-82 83-121 (159)
320 MTH00027 COX2 cytochrome c oxi 26.0 52 0.0011 25.6 2.0 46 29-75 211-258 (262)
321 PF05191 ADK_lid: Adenylate ki 25.9 36 0.00078 18.9 0.8 15 47-61 2-16 (36)
322 PF12874 zf-met: Zinc-finger o 25.9 41 0.0009 16.0 1.0 12 48-59 2-13 (25)
323 PF05741 zf-nanos: Nanos RNA b 25.8 34 0.00073 21.0 0.8 15 18-32 29-43 (55)
324 KOG2893 Zn finger protein [Gen 25.8 20 0.00044 28.8 -0.3 31 25-55 13-43 (341)
325 PRK12860 transcriptional activ 25.7 34 0.00075 25.7 0.9 13 18-30 150-162 (189)
326 COG1622 CyoA Heme/copper-type 25.3 45 0.00098 25.7 1.6 38 41-80 185-226 (247)
327 PF13397 DUF4109: Domain of un 25.2 39 0.00085 23.3 1.1 15 17-31 45-59 (105)
328 PF01599 Ribosomal_S27: Riboso 25.0 69 0.0015 19.1 2.0 27 23-55 19-47 (47)
329 PF12677 DUF3797: Domain of un 24.9 34 0.00075 20.7 0.7 13 20-32 11-23 (49)
330 PF06676 DUF1178: Protein of u 24.9 46 0.00099 24.1 1.4 11 21-31 31-41 (148)
331 PRK08332 ribonucleotide-diphos 24.7 51 0.0011 32.3 2.0 30 24-55 1706-1735(1740)
332 PF13132 DUF3950: Domain of un 24.5 50 0.0011 18.1 1.2 10 70-79 17-27 (30)
333 PRK14559 putative protein seri 24.5 35 0.00076 29.9 0.9 13 45-57 40-52 (645)
334 PRK10220 hypothetical protein; 24.2 34 0.00075 23.9 0.7 17 18-34 16-32 (111)
335 PRK05452 anaerobic nitric oxid 24.2 34 0.00074 28.4 0.8 18 16-33 452-469 (479)
336 cd01237 Unc112 Unc-112 pleckst 24.2 49 0.0011 22.7 1.4 15 68-82 90-104 (106)
337 KOG3352 Cytochrome c oxidase, 24.1 38 0.00081 24.9 0.9 11 20-30 131-141 (153)
338 PRK08351 DNA-directed RNA poly 24.1 42 0.0009 21.0 1.0 9 24-32 17-25 (61)
339 MTH00076 COX2 cytochrome c oxi 24.0 59 0.0013 24.5 1.9 46 30-76 178-225 (228)
340 COG0777 AccD Acetyl-CoA carbox 23.9 56 0.0012 26.4 1.8 60 23-87 29-112 (294)
341 PF13597 NRDD: Anaerobic ribon 23.9 40 0.00086 28.6 1.1 11 22-32 504-514 (546)
342 PRK03681 hypA hydrogenase nick 23.9 56 0.0012 22.1 1.6 31 17-54 65-95 (114)
343 PF04267 SoxD: Sarcosine oxida 23.8 23 0.0005 23.5 -0.3 6 24-29 3-8 (84)
344 PTZ00293 thymidine kinase; Pro 23.7 69 0.0015 24.2 2.3 31 24-54 139-177 (211)
345 PF03833 PolC_DP2: DNA polymer 23.7 26 0.00057 32.1 0.0 61 21-82 654-725 (900)
346 PF01197 Ribosomal_L31: Riboso 23.4 48 0.001 20.8 1.2 18 44-61 11-28 (69)
347 PRK09502 iscA iron-sulfur clus 22.9 29 0.00062 22.9 0.1 12 45-57 95-106 (107)
348 PF07450 HycH: Formate hydroge 22.8 35 0.00075 24.5 0.5 31 41-80 34-64 (131)
349 PF10825 DUF2752: Protein of u 22.8 39 0.00084 20.0 0.6 13 21-33 8-20 (52)
350 PF14634 zf-RING_5: zinc-RING 22.8 47 0.001 18.4 0.9 11 20-30 34-44 (44)
351 PRK06260 threonine synthase; V 22.7 65 0.0014 25.7 2.1 9 23-31 4-12 (397)
352 cd02152 OAT Ornithine acetyltr 22.7 89 0.0019 26.0 2.9 32 32-63 355-387 (390)
353 PF06221 zf-C2HC5: Putative zi 22.6 43 0.00093 20.6 0.8 9 22-30 35-43 (57)
354 PF09416 UPF1_Zn_bind: RNA hel 22.4 69 0.0015 23.4 2.0 37 17-53 54-94 (152)
355 PRK15103 paraquat-inducible me 22.3 68 0.0015 26.4 2.1 33 20-56 8-40 (419)
356 PRK12496 hypothetical protein; 22.2 43 0.00092 24.1 0.8 8 23-30 128-135 (164)
357 PHA02768 hypothetical protein; 21.8 35 0.00076 20.9 0.3 38 22-59 5-44 (55)
358 PF14940 TMEM219: Transmembran 21.8 89 0.0019 24.0 2.5 28 54-82 28-55 (223)
359 PF02146 SIR2: Sir2 family; I 21.7 6.8 0.00015 27.7 -3.4 57 22-80 105-161 (178)
360 PRK10954 periplasmic protein d 21.7 28 0.00061 25.1 -0.2 13 21-33 45-57 (207)
361 smart00154 ZnF_AN1 AN1-like Zi 21.6 67 0.0015 17.9 1.4 9 22-30 12-20 (39)
362 COG4391 Uncharacterized protei 21.5 91 0.002 19.7 2.1 35 20-58 22-60 (62)
363 PRK06393 rpoE DNA-directed RNA 21.4 50 0.0011 20.9 1.0 9 24-32 19-27 (64)
364 PRK08402 replication factor A; 21.4 58 0.0012 26.4 1.5 26 23-54 213-238 (355)
365 PF09082 DUF1922: Domain of un 21.2 46 0.00099 21.4 0.7 29 22-58 3-31 (68)
366 cd01675 RNR_III Class III ribo 21.2 50 0.0011 28.0 1.2 11 22-32 532-542 (555)
367 MTH00098 COX2 cytochrome c oxi 21.1 74 0.0016 24.0 2.0 46 29-75 177-224 (227)
368 PRK15084 formate hydrogenlyase 21.0 41 0.00088 24.2 0.5 31 41-80 36-66 (133)
369 PRK11088 rrmA 23S rRNA methylt 21.0 44 0.00096 24.9 0.7 25 22-54 2-26 (272)
370 PRK04860 hypothetical protein; 20.9 51 0.0011 23.8 1.0 34 22-59 119-156 (160)
371 PRK11788 tetratricopeptide rep 20.8 94 0.002 23.3 2.5 37 18-64 350-387 (389)
372 PF14319 Zn_Tnp_IS91: Transpos 20.6 74 0.0016 21.4 1.7 31 21-57 41-71 (111)
373 KOG3002 Zn finger protein [Gen 20.5 36 0.00079 27.1 0.2 35 18-55 44-78 (299)
374 TIGR01908 cas_CXXC_CXXC CRISPR 20.4 61 0.0013 25.7 1.4 22 19-40 2-23 (309)
375 PRK11823 DNA repair protein Ra 20.1 83 0.0018 25.9 2.2 26 20-55 5-30 (446)
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=5.3e-44 Score=234.07 Aligned_cols=80 Identities=59% Similarity=1.065 Sum_probs=45.9
Q ss_pred CCCccCCC-CCCCCCCCCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhh
Q 034528 2 GKRKSRAK-PPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERV 80 (92)
Q Consensus 2 GkRK~k~k-~~~kk~~~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~ 80 (92)
||||++++ ++++|++++|||.|+||||||++||+|+||++.++|+|+|++||++|+++|++|++||||||+|||+|+++
T Consensus 1 GkRK~~~k~~~~kk~~~~l~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~~L~epiDVY~~wiD~~~~~ 80 (81)
T PF05129_consen 1 GKRKKKRKKPPKKKKKPKLPKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKINPLSEPIDVYSEWIDACEEG 80 (81)
T ss_dssp -------------------SS----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE--SS--TTHHHHHHHHHHH--
T ss_pred CCCcccCCCCCccCcCCCCCceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccCccCcccchhHHHHHHHHhc
Confidence 89998887 67788899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred c
Q 034528 81 N 81 (92)
Q Consensus 81 n 81 (92)
|
T Consensus 81 n 81 (81)
T PF05129_consen 81 N 81 (81)
T ss_dssp -
T ss_pred C
Confidence 7
No 2
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=100.00 E-value=1.7e-43 Score=241.69 Aligned_cols=90 Identities=66% Similarity=1.134 Sum_probs=84.4
Q ss_pred CCCCccCCCCCCC-CCCCCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHh
Q 034528 1 MGKRKSRAKPPPK-KRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECER 79 (92)
Q Consensus 1 MGkRK~k~k~~~k-k~~~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~ 79 (92)
|||||+|++++++ |...+|+|.|+||||||+++|+|+||++.++|.++|++|+++|++.|++|++||||||+|||+|++
T Consensus 1 MgkRk~K~k~~~k~r~~~~ldt~FnClfcnHek~v~~~~Dk~~~iG~~sC~iC~esFqt~it~LsepIDVYSdWiDaCe~ 80 (109)
T KOG3214|consen 1 MGKRKSKRKEPPKERRVEPLDTQFNCLFCNHEKSVSCTLDKKHNIGKASCRICEESFQTTITALSEPIDVYSDWIDACEA 80 (109)
T ss_pred CCcccccccCCchhhhccchheeeccCccccccceeeeehhhcCcceeeeeehhhhhccchHhhccchHHHHHHHHHHHH
Confidence 9999999887766 789999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCccccchhh
Q 034528 80 VNNLEDDGAYE 90 (92)
Q Consensus 80 ~n~~~~~~~~~ 90 (92)
+|.-+.+++++
T Consensus 81 vn~a~~~~vd~ 91 (109)
T KOG3214|consen 81 VNNAEDDVVDE 91 (109)
T ss_pred hhccccchhhh
Confidence 99866666553
No 3
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=100.00 E-value=1.8e-38 Score=216.39 Aligned_cols=82 Identities=33% Similarity=0.725 Sum_probs=78.7
Q ss_pred CCCCccCCCCCCCCCCCCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhh
Q 034528 1 MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERV 80 (92)
Q Consensus 1 MGkRK~k~k~~~kk~~~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~ 80 (92)
|||||++++.+.+++.++|||.|+||||||+++++|.++++.++|.++|++||++|++.||.|++||||||+|||+|+|+
T Consensus 1 MG~rr~krr~~ik~~~~~L~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l~~~vDvYs~wvDay~eg 80 (104)
T COG4888 1 MGRRRRKRRKIIKRRPQVLPKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPELSEPVDVYSAWVDAYLEG 80 (104)
T ss_pred CCcccccccccCcccCccCCceEecCccCCeeeeEEEEEecCceeEEEcccCcceEEEeccccccchhHHHHHHHHHHhc
Confidence 99999888777778888899999999999999999999999999999999999999999999999999999999999999
Q ss_pred cC
Q 034528 81 NN 82 (92)
Q Consensus 81 n~ 82 (92)
+.
T Consensus 81 ~~ 82 (104)
T COG4888 81 RG 82 (104)
T ss_pred cc
Confidence 96
No 4
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=100.00 E-value=1.7e-34 Score=195.72 Aligned_cols=77 Identities=25% Similarity=0.505 Sum_probs=71.9
Q ss_pred CCCCccCCCCCCCCCCCCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhh
Q 034528 1 MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERV 80 (92)
Q Consensus 1 MGkRK~k~k~~~kk~~~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~ 80 (92)
|||||++++ +++|++.++|+.|+|||||+ .+|.|+|++ +++++.|.+||.+|.+.|++|++||||||+|||+|+++
T Consensus 1 MGkRk~~~k-~~~k~k~klpt~f~CP~Cge-~~v~v~~~k--~~~h~~C~~CG~y~~~~V~~l~epIDVY~~wiD~~~eg 76 (99)
T PRK14892 1 MGRRRKKRK-KIIRPKPKLPKIFECPRCGK-VSISVKIKK--NIAIITCGNCGLYTEFEVPSVYDEVDVYNKFIDLYLEG 76 (99)
T ss_pred CCCccccCC-CCcccccCCCcEeECCCCCC-eEeeeecCC--CcceEECCCCCCccCEECCccccchhhHHHHHHHHHhc
Confidence 999999976 44677899999999999995 799999987 89999999999999999999999999999999999999
Q ss_pred c
Q 034528 81 N 81 (92)
Q Consensus 81 n 81 (92)
.
T Consensus 77 ~ 77 (99)
T PRK14892 77 K 77 (99)
T ss_pred C
Confidence 8
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=97.23 E-value=0.00032 Score=42.04 Aligned_cols=34 Identities=32% Similarity=0.570 Sum_probs=24.5
Q ss_pred cCCCCCCCCeEEEE--eecCCceEEEEcCccCCeeEe
Q 034528 24 SCPFCNHGTSVECR--IDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 24 ~CPfC~~~~sV~vk--idk~~~~g~l~C~~Cg~~~~~ 58 (92)
.|||||.. .+.+. .+-....+...|..||.+...
T Consensus 3 PCPfCGg~-~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGA-DVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCc-ceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 69999984 45454 444556677799999987654
No 6
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=97.01 E-value=0.0011 Score=39.93 Aligned_cols=33 Identities=27% Similarity=0.437 Sum_probs=23.2
Q ss_pred ccccCCCCCCCCeEEEEeecCCce---EEEEcCccCC
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLI---GEAICNICQE 54 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~---g~l~C~~Cg~ 54 (92)
++-.|||||. ..+.+.-+..... ..|.|..||.
T Consensus 2 ~LkPCPFCG~-~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGS-ADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCC-cceEeecccCCCCCCEEEEEcCCCCC
Confidence 3457999987 4566665443222 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=96.72 E-value=0.0027 Score=38.97 Aligned_cols=37 Identities=24% Similarity=0.596 Sum_probs=26.5
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe-ecCC
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST-TITA 62 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~-~i~~ 62 (92)
.|.||.||. ++++ .....-.++.|..||..|+- ..++
T Consensus 2 ~~~CP~CG~--~iev--~~~~~GeiV~Cp~CGaeleVv~~~p 39 (54)
T TIGR01206 2 QFECPDCGA--EIEL--ENPELGELVICDECGAELEVVSLDP 39 (54)
T ss_pred ccCCCCCCC--EEec--CCCccCCEEeCCCCCCEEEEEeCCC
Confidence 589999997 3444 33333458899999999986 4444
No 8
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=96.33 E-value=0.0055 Score=39.07 Aligned_cols=34 Identities=35% Similarity=0.631 Sum_probs=27.3
Q ss_pred CCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 19 LDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 19 l~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
.+++=.|||||- ++|.++- ..+...+.|..||..
T Consensus 3 ~d~lKPCPFCG~-~~~~v~~--~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 3 YDNVKPCPFCGC-PSVTVKA--ISGYYRAKCNGCESR 36 (64)
T ss_pred cccccCCCCCCC-ceeEEEe--cCceEEEEcCCCCcC
Confidence 466778999997 5677765 577888999999986
No 9
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=96.25 E-value=0.0024 Score=46.81 Aligned_cols=35 Identities=29% Similarity=0.543 Sum_probs=24.0
Q ss_pred cCCCCCCCCeEEEEeecC-CceE---EEEcCccCCeeEe
Q 034528 24 SCPFCNHGTSVECRIDMK-NLIG---EAICNICQESFST 58 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~-~~~g---~l~C~~Cg~~~~~ 58 (92)
.||||+|+.|=.+.=-.. .|-+ .=.|..||.+|+|
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTT 40 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTT 40 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccch
Confidence 599999998755443222 2222 2579999999987
No 10
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=96.23 E-value=0.011 Score=33.59 Aligned_cols=35 Identities=23% Similarity=0.556 Sum_probs=24.1
Q ss_pred ccCCCCCCCCeEEEEeecC----CceEEEEcCccCCeeE
Q 034528 23 FSCPFCNHGTSVECRIDMK----NLIGEAICNICQESFS 57 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~----~~~g~l~C~~Cg~~~~ 57 (92)
|+||.|||.+.+-..+.-. .+.-...|..||..|.
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence 6899999998888766332 3567789999998763
No 11
>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=96.22 E-value=0.0047 Score=44.85 Aligned_cols=36 Identities=28% Similarity=0.574 Sum_probs=25.5
Q ss_pred cCCCCCCCCeEEEEeec-CCceEE---EEcCccCCeeEee
Q 034528 24 SCPFCNHGTSVECRIDM-KNLIGE---AICNICQESFSTT 59 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk-~~~~g~---l~C~~Cg~~~~~~ 59 (92)
.||||||+++=.+.=-. .+|.++ =.|..||.+|+|-
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTy 41 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTF 41 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcccee
Confidence 59999998876554322 344443 5799999999873
No 12
>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=96.21 E-value=0.0045 Score=35.44 Aligned_cols=32 Identities=25% Similarity=0.562 Sum_probs=22.5
Q ss_pred ccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee
Q 034528 23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT 59 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~ 59 (92)
|.||.|++.. +..| ...|.+.|..||.--+..
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 6899999843 4555 445888999999876653
No 13
>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=96.10 E-value=0.0025 Score=35.28 Aligned_cols=34 Identities=18% Similarity=0.382 Sum_probs=22.7
Q ss_pred cccCCCCCCCCeEEEEeecC-CceEEEEcCccCCeeE
Q 034528 22 VFSCPFCNHGTSVECRIDMK-NLIGEAICNICQESFS 57 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~-~~~g~l~C~~Cg~~~~ 57 (92)
.+.||.|+.. ..|.-+.. ...+.+.|.+||..|.
T Consensus 2 ~~~CP~C~~~--~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 2 RIQCPNCKTS--FRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCE--EEeCHHHcCCCCCEEECCCCCCEEE
Confidence 3789999974 33333222 2234899999998875
No 14
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=95.50 E-value=0.038 Score=37.29 Aligned_cols=44 Identities=23% Similarity=0.534 Sum_probs=31.6
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhh
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIY 70 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVY 70 (92)
..+.||||+... |+ ...+|+-.|+.||..|.--.-.++.|.-+.
T Consensus 34 a~y~CpfCgk~~---vk---R~a~GIW~C~~C~~~~AGGAy~p~T~~~~t 77 (91)
T TIGR00280 34 AKYVCPFCGKKT---VK---RGSTGIWTCRKCGAKFAGGAYTPVTPAGKT 77 (91)
T ss_pred cCccCCCCCCCc---eE---EEeeEEEEcCCCCCEEeCCccccccchhHH
Confidence 578999999732 22 367899999999999986544445554444
No 15
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=95.48 E-value=0.038 Score=37.25 Aligned_cols=45 Identities=20% Similarity=0.536 Sum_probs=31.2
Q ss_pred CccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhh
Q 034528 20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIY 70 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVY 70 (92)
-..+.||||+... |+ ...+|+-.|+.|+..|.--.-.++.|.-+.
T Consensus 34 ~a~y~CpfCgk~~---vk---R~a~GIW~C~~C~~~~AGGAy~~~T~~~~t 78 (90)
T PTZ00255 34 HAKYFCPFCGKHA---VK---RQAVGIWRCKGCKKTVAGGAWTLSTPAAST 78 (90)
T ss_pred hCCccCCCCCCCc---ee---eeeeEEEEcCCCCCEEeCCccccccchhHH
Confidence 3679999999642 22 356799999999999886444444444433
No 16
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=95.37 E-value=0.034 Score=32.09 Aligned_cols=34 Identities=15% Similarity=0.352 Sum_probs=24.2
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeec
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i 60 (92)
..|.||.||.. +.++... ..+.|..||..+.+..
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 46899999973 3444333 3789999998877643
No 17
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=95.37 E-value=0.045 Score=31.27 Aligned_cols=34 Identities=15% Similarity=0.479 Sum_probs=25.9
Q ss_pred ccCCCCCCCCeEEEEeecC----CceEEEEcCccCCee
Q 034528 23 FSCPFCNHGTSVECRIDMK----NLIGEAICNICQESF 56 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~----~~~g~l~C~~Cg~~~ 56 (92)
|.||.|||..++-..+... .+.-...|..||-.+
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 6899999998887766321 346678999999765
No 18
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=95.20 E-value=0.037 Score=33.70 Aligned_cols=48 Identities=13% Similarity=0.346 Sum_probs=29.8
Q ss_pred ccCCCCCCCCeEEEEeecCCceEEEEcCccCC--eeEeecCCCCcchhhh
Q 034528 23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQE--SFSTTITALTEPIDIY 70 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~--~~~~~i~~L~epVDVY 70 (92)
.+||+||+...+.+.......-..--|.+|-. .+...+.....-|.|+
T Consensus 1 i~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI~~~v~~d~~~~~v~v~ 50 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPIEVQVTVDEDEPSVSVR 50 (52)
T ss_pred CCCCCCCCeeEEEEecCCCCeeEEeehhhcCCccEEEEEECCCCCEEEEE
Confidence 37999999655544444444456788999986 4455555554444443
No 19
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=95.10 E-value=0.058 Score=36.33 Aligned_cols=44 Identities=18% Similarity=0.375 Sum_probs=31.2
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhh
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIY 70 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVY 70 (92)
..+.||||+.. .|+ ...+|+-.|+.|+..|.--.-.++.|.-+.
T Consensus 35 a~y~CpfCgk~---~vk---R~a~GIW~C~~C~~~~AGGAy~~~T~~~~t 78 (90)
T PRK03976 35 AKHVCPVCGRP---KVK---RVGTGIWECRKCGAKFAGGAYTPETPAGKT 78 (90)
T ss_pred cCccCCCCCCC---ceE---EEEEEEEEcCCCCCEEeCCccccccchhhh
Confidence 57899999863 222 367899999999999876544444554443
No 20
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=94.91 E-value=0.031 Score=34.49 Aligned_cols=28 Identities=21% Similarity=0.497 Sum_probs=22.4
Q ss_pred CCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 17 DKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 17 ~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
-.+|.+..||.||+. ...+-.|..||..
T Consensus 22 l~~~~l~~C~~CG~~-----------~~~H~vC~~CG~Y 49 (57)
T PRK12286 22 LKAPGLVECPNCGEP-----------KLPHRVCPSCGYY 49 (57)
T ss_pred ccCCcceECCCCCCc-----------cCCeEECCCCCcC
Confidence 467899999999973 3468899999954
No 21
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=94.82 E-value=0.042 Score=39.80 Aligned_cols=35 Identities=29% Similarity=0.602 Sum_probs=22.7
Q ss_pred cCCCCCCCCeEEEEeec-CCc--e-EEEEcCccCCeeEe
Q 034528 24 SCPFCNHGTSVECRIDM-KNL--I-GEAICNICQESFST 58 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk-~~~--~-g~l~C~~Cg~~~~~ 58 (92)
.||+||++.+-.+.=.- ..| + -.-.|..||-+|.+
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~ 40 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTT 40 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceE
Confidence 69999997743333221 111 1 23789999999986
No 22
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=94.79 E-value=0.018 Score=38.78 Aligned_cols=42 Identities=24% Similarity=0.565 Sum_probs=28.3
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchh
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPID 68 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVD 68 (92)
..+.||||+.. + |+- ..+|+-.|+.|+..|.--.-.++.|.-
T Consensus 34 ~ky~Cp~Cgk~-~--vkR---~a~GIW~C~~C~~~~AGGAy~~~T~~~ 75 (90)
T PF01780_consen 34 AKYTCPFCGKT-S--VKR---VATGIWKCKKCGKKFAGGAYTPSTPAA 75 (90)
T ss_dssp S-BEESSSSSS-E--EEE---EETTEEEETTTTEEEE-BSSSSS-HHH
T ss_pred CCCcCCCCCCc-e--eEE---eeeEEeecCCCCCEEeCCCccccchHH
Confidence 56899999984 2 332 456889999999999875555555543
No 23
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=94.74 E-value=0.024 Score=31.82 Aligned_cols=33 Identities=21% Similarity=0.423 Sum_probs=23.8
Q ss_pred ccCCCCCCCCeEEEEeec-CCceEEEEcCccCCeeE
Q 034528 23 FSCPFCNHGTSVECRIDM-KNLIGEAICNICQESFS 57 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk-~~~~g~l~C~~Cg~~~~ 57 (92)
.+||.|+.. ..|.-++ ..+.+.+.|..|+..|.
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 589999973 4444432 24567999999999874
No 24
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=94.52 E-value=0.016 Score=32.48 Aligned_cols=34 Identities=18% Similarity=0.435 Sum_probs=22.5
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESF 56 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~ 56 (92)
.+.||.|+..-.|.=..- ......+.|..||..|
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 368999998533322221 2445689999999876
No 25
>PF14353 CpXC: CpXC protein
Probab=94.39 E-value=0.049 Score=37.03 Aligned_cols=39 Identities=21% Similarity=0.496 Sum_probs=26.5
Q ss_pred ccCCCCCCCCeEEEEe--ec-----------CCceEEEEcCccCCeeEeecC
Q 034528 23 FSCPFCNHGTSVECRI--DM-----------KNLIGEAICNICQESFSTTIT 61 (92)
Q Consensus 23 F~CPfC~~~~sV~vki--dk-----------~~~~g~l~C~~Cg~~~~~~i~ 61 (92)
-+||.|+|+..+++-- +- ...+....|..||..+....+
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p 53 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYP 53 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCC
Confidence 4799999976555432 21 135568999999998765433
No 26
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=94.06 E-value=0.049 Score=35.18 Aligned_cols=44 Identities=23% Similarity=0.458 Sum_probs=26.6
Q ss_pred ccCCCCCCCCeEEEEeec-C--CceEEEEcC--ccCCeeEeec---CCCCcch
Q 034528 23 FSCPFCNHGTSVECRIDM-K--NLIGEAICN--ICQESFSTTI---TALTEPI 67 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk-~--~~~g~l~C~--~Cg~~~~~~i---~~L~epV 67 (92)
|.||+||+.. ...+=.. . ...-.-.|. .||.+|.+.. +.|+.|.
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 7899999854 2222211 1 223456788 7999998742 3455553
No 27
>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=94.06 E-value=0.038 Score=31.55 Aligned_cols=29 Identities=28% Similarity=0.676 Sum_probs=25.2
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQE 54 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~ 54 (92)
.||.|+-..... ++.+.+.|...|+.|+.
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 699999988777 77788899999999975
No 28
>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=94.05 E-value=0.13 Score=32.48 Aligned_cols=48 Identities=15% Similarity=0.470 Sum_probs=31.2
Q ss_pred ccCCCCCCCCeEEEE-----------eecC-CceEEEEcCccCCe--eEeecCCCCcchhhh
Q 034528 23 FSCPFCNHGTSVECR-----------IDMK-NLIGEAICNICQES--FSTTITALTEPIDIY 70 (92)
Q Consensus 23 F~CPfC~~~~sV~vk-----------idk~-~~~g~l~C~~Cg~~--~~~~i~~L~epVDVY 70 (92)
+.||-||++.--.=. +|-. +..-.++|..||-+ |....+.|++-+|.+
T Consensus 1 y~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYTE~Y~~~~~~~~~i~D~~ 62 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYTEFYKAKTSNGSNILDFF 62 (64)
T ss_pred CCCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCEEEEeecCcccchhhhhh
Confidence 579999996422111 1211 23346899999954 667888888887764
No 29
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=93.31 E-value=0.076 Score=30.74 Aligned_cols=32 Identities=25% Similarity=0.691 Sum_probs=21.9
Q ss_pred CCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528 18 KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQE 54 (92)
Q Consensus 18 kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~ 54 (92)
.-+.-|.||+||+.+ ...| ...+.-.|..|+.
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 345669999999852 2222 2267889999974
No 30
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=93.07 E-value=0.088 Score=35.51 Aligned_cols=32 Identities=25% Similarity=0.588 Sum_probs=25.0
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
....||+|+.. .|+- ...|+-.|+.||..|.-
T Consensus 34 ~~~~Cp~C~~~---~VkR---~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGRT---TVKR---IATGIWKCRKCGAKFAG 65 (89)
T ss_pred cCCcCCCCCCc---ceee---eccCeEEcCCCCCeecc
Confidence 46899999984 3333 56799999999999864
No 31
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=92.89 E-value=0.12 Score=28.65 Aligned_cols=30 Identities=23% Similarity=0.451 Sum_probs=22.4
Q ss_pred ccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
-.|+-|||+.-+. ...+...|..||.+|++
T Consensus 4 ~~C~~C~~~~i~~------~~~~~~~C~~Cg~~~~~ 33 (33)
T PF08792_consen 4 KKCSKCGGNGIVN------KEDDYEVCIFCGSSFPY 33 (33)
T ss_pred eEcCCCCCCeEEE------ecCCeEEcccCCcEeeC
Confidence 4699999975221 33478999999999874
No 32
>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=92.24 E-value=0.3 Score=27.18 Aligned_cols=28 Identities=21% Similarity=0.516 Sum_probs=21.2
Q ss_pred CCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528 25 CPFCNHGTSVECRIDMKNLIGEAICNICQESFS 57 (92)
Q Consensus 25 CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~ 57 (92)
||.||+ -+.++=++...+ .|+.|+-.++
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 999996 577777776666 9999997654
No 33
>PHA00626 hypothetical protein
Probab=92.12 E-value=0.18 Score=31.69 Aligned_cols=34 Identities=24% Similarity=0.425 Sum_probs=24.0
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
.||.||+.+-+-+.+-++ ....-.|..||-.|+-
T Consensus 2 ~CP~CGS~~Ivrcg~cr~-~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRG-WSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCceeeeeceecc-cCcceEcCCCCCeech
Confidence 599999976565555333 1356789999988864
No 34
>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=91.77 E-value=0.29 Score=32.90 Aligned_cols=35 Identities=11% Similarity=0.456 Sum_probs=23.8
Q ss_pred cCCCCCCC----CeEEEEeecCC--------ceEEEEcCccCCeeEe
Q 034528 24 SCPFCNHG----TSVECRIDMKN--------LIGEAICNICQESFST 58 (92)
Q Consensus 24 ~CPfC~~~----~sV~vkidk~~--------~~g~l~C~~Cg~~~~~ 58 (92)
.|+.|++. ..+++..+..+ ++-.+.|..||+.|.+
T Consensus 1 ~C~~C~~~~~~~~~tTv~~el~~G~~~IvIknVPa~~C~~CGe~y~~ 47 (89)
T TIGR03829 1 KCRWCEEEKAIARTTTVYWELPDGTKAIEIKETPSISCSHCGMEYQD 47 (89)
T ss_pred CCcccCCCceecceEEEEEEecCCceEEEEecCCcccccCCCcEeec
Confidence 49999663 34455555543 3345899999999875
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=91.71 E-value=0.4 Score=36.88 Aligned_cols=49 Identities=14% Similarity=0.300 Sum_probs=27.3
Q ss_pred cccCCCCCCCCeEEEEee---cCCceEEEEcCccCCeeEeecCCCCcchhhh
Q 034528 22 VFSCPFCNHGTSVECRID---MKNLIGEAICNICQESFSTTITALTEPIDIY 70 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkid---k~~~~g~l~C~~Cg~~~~~~i~~L~epVDVY 70 (92)
...||+||+++......- -..+.-.-.|..|+.+.-+--...+..+|.+
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 3456778899999997766335666666655
No 36
>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=91.11 E-value=0.44 Score=27.73 Aligned_cols=36 Identities=17% Similarity=0.462 Sum_probs=22.7
Q ss_pred cCCCCCCCCeEEEEeecC--CceEEEEcCc--cCCeeEee
Q 034528 24 SCPFCNHGTSVECRIDMK--NLIGEAICNI--CQESFSTT 59 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~--~~~g~l~C~~--Cg~~~~~~ 59 (92)
.||+||+.-.+.-.-... .......|.+ ||.+|.+.
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 499999854332222222 2334678888 99999875
No 37
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=90.83 E-value=0.15 Score=30.53 Aligned_cols=26 Identities=23% Similarity=0.487 Sum_probs=18.1
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESF 56 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~ 56 (92)
-||.||++ +- .... +...|+.||.++
T Consensus 22 fCP~Cg~~--~m--~~~~---~r~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSG--FM--AEHL---DRWHCGKCGYTE 47 (50)
T ss_pred cCcCCCcc--hh--eccC---CcEECCCcCCEE
Confidence 79999973 21 1111 688999999865
No 38
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=90.80 E-value=0.13 Score=28.23 Aligned_cols=31 Identities=26% Similarity=0.465 Sum_probs=21.4
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
.|.|+.||+.-.+...+ .. -..+.|-.||..
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 58999999853333333 22 467889999983
No 39
>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=90.64 E-value=0.31 Score=37.45 Aligned_cols=36 Identities=14% Similarity=0.281 Sum_probs=18.6
Q ss_pred ccCCCCCCCCeEEEEeecCC-ceEEEEcCccCCeeEe
Q 034528 23 FSCPFCNHGTSVECRIDMKN-LIGEAICNICQESFST 58 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~~-~~g~l~C~~Cg~~~~~ 58 (92)
=.||.||..-++++-..... |.=.+.|..||..+.+
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 48999999766665554432 6788999999987654
No 40
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=90.58 E-value=0.093 Score=26.87 Aligned_cols=21 Identities=24% Similarity=0.672 Sum_probs=13.4
Q ss_pred CCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 25 CPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 25 CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
||.||++..- +..-|..||..
T Consensus 2 Cp~CG~~~~~----------~~~fC~~CG~~ 22 (23)
T PF13240_consen 2 CPNCGAEIED----------DAKFCPNCGTP 22 (23)
T ss_pred CcccCCCCCC----------cCcchhhhCCc
Confidence 8999986422 22348888863
No 41
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=90.31 E-value=0.43 Score=35.64 Aligned_cols=44 Identities=16% Similarity=0.345 Sum_probs=27.2
Q ss_pred CccccCCCCCCCCeEEEEeecCCc---------------------eEEEEcCccCCeeEe-ecCCCCc
Q 034528 20 DTVFSCPFCNHGTSVECRIDMKNL---------------------IGEAICNICQESFST-TITALTE 65 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~~~---------------------~g~l~C~~Cg~~~~~-~i~~L~e 65 (92)
++..+||+|+++ ...+.-+... --...|..||-.+.. ..+.|+.
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 578899999985 3333222111 135899999977654 3555553
No 42
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=90.25 E-value=0.25 Score=30.57 Aligned_cols=45 Identities=20% Similarity=0.462 Sum_probs=35.5
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHH
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECE 78 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~ 78 (92)
.-.|+.||. .+. ...|.+||.......++-+.|.|-|++.-=++.
T Consensus 5 mr~C~~Cgv---YTL---------k~~CP~CG~~t~~~~P~rfSp~D~y~~yR~~~k 49 (56)
T PRK13130 5 IRKCPKCGV---YTL---------KEICPVCGGKTKNPHPPRFSPEDKYGKYRRALK 49 (56)
T ss_pred ceECCCCCC---EEc---------cccCcCCCCCCCCCCCCCCCCCCccHHHHHHHH
Confidence 346888885 222 348999999999999999999999998765543
No 43
>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=89.96 E-value=0.16 Score=29.08 Aligned_cols=30 Identities=23% Similarity=0.447 Sum_probs=23.3
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQE 54 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~ 54 (92)
.|.|+-|||.-.+...| .+ ...+.|-.||.
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 58999999965555555 33 67889999998
No 44
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=89.81 E-value=0.5 Score=33.66 Aligned_cols=33 Identities=18% Similarity=0.358 Sum_probs=26.1
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESF 56 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~ 56 (92)
..=.||.|+.+++.-++ +..+-.+.|..||...
T Consensus 101 ~yVlC~~C~spdT~l~k---~~r~~~l~C~ACGa~~ 133 (138)
T PRK03988 101 EYVICPECGSPDTKLIK---EGRIWVLKCEACGAET 133 (138)
T ss_pred hcEECCCCCCCCcEEEE---cCCeEEEEcccCCCCC
Confidence 34579999998876554 5678899999999864
No 45
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=89.79 E-value=0.49 Score=33.52 Aligned_cols=34 Identities=15% Similarity=0.333 Sum_probs=26.2
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFS 57 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~ 57 (92)
..=.||.|+.+.+.-++ +..+-.+.|..||....
T Consensus 96 ~yVlC~~C~sPdT~l~k---~~r~~~l~C~ACGa~~~ 129 (133)
T TIGR00311 96 KYVICRECNRPDTRIIK---EGRVSLLKCEACGAKAP 129 (133)
T ss_pred heEECCCCCCCCcEEEE---eCCeEEEecccCCCCCc
Confidence 44579999998876554 46677899999998643
No 46
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=89.36 E-value=0.41 Score=26.73 Aligned_cols=29 Identities=28% Similarity=0.523 Sum_probs=17.4
Q ss_pred CCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 25 CPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 25 CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
||.||+. ++..|-..+..-...|..||.-
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 9999984 7888876677889999999963
No 47
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=89.31 E-value=0.4 Score=27.53 Aligned_cols=28 Identities=18% Similarity=0.400 Sum_probs=16.6
Q ss_pred CCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528 25 CPFCNHGTSVECRIDMKNLIGEAICNICQESF 56 (92)
Q Consensus 25 CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~ 56 (92)
||.||+ -+..+-+ .......|..||..+
T Consensus 3 Cp~Cg~--~l~~~~~--~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 3 CPKCGN--MLIPKEG--KEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCC--ccccccC--CCCCEEECCcCCCeE
Confidence 899987 2333221 111378899999544
No 48
>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=89.27 E-value=1.2 Score=29.21 Aligned_cols=40 Identities=20% Similarity=0.361 Sum_probs=28.8
Q ss_pred CCCc-cccCCCCCCCCeEEEEeecC----CceEEEEcCccCCeeE
Q 034528 18 KLDT-VFSCPFCNHGTSVECRIDMK----NLIGEAICNICQESFS 57 (92)
Q Consensus 18 kl~~-~F~CPfC~~~~sV~vkidk~----~~~g~l~C~~Cg~~~~ 57 (92)
.+|+ ...||.|||...+-..+... .+.-.-.|-.||..+.
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 79999999998877766332 2445678999997653
No 49
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=89.13 E-value=0.7 Score=25.98 Aligned_cols=27 Identities=22% Similarity=0.591 Sum_probs=20.1
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQE 54 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~ 54 (92)
+||.|++ .-....+ .++..-.|..||=
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 3445555 5678888999984
No 50
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=88.80 E-value=0.62 Score=30.00 Aligned_cols=45 Identities=24% Similarity=0.473 Sum_probs=27.7
Q ss_pred CccccCCCCCCCCeEEEEeec-----------C-CceEEEEcCccCCe--eEeecCCCC
Q 034528 20 DTVFSCPFCNHGTSVECRIDM-----------K-NLIGEAICNICQES--FSTTITALT 64 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk-----------~-~~~g~l~C~~Cg~~--~~~~i~~L~ 64 (92)
...|.||-||..+-.+=.|.- . +..-.++|.+||-+ |+-.+..+.
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 346889999986544433322 1 23456999999954 454554433
No 51
>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=88.72 E-value=0.37 Score=37.86 Aligned_cols=60 Identities=20% Similarity=0.431 Sum_probs=25.5
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeec--CCCCcch--hhhhhHHHHHHhhcCc
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI--TALTEPI--DIYSEWIDECERVNNL 83 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i--~~L~epV--DVYs~WiD~~~~~n~~ 83 (92)
.+-||.||+.. --.+.-..-++-..|..|++.||.+- ..|+.-| -.|+--|+.+...+.+
T Consensus 31 n~yCP~Cg~~~--L~~f~NN~PVaDF~C~~C~eeyELKSk~~~l~~~I~dGAY~Tmi~Ri~s~~NP 94 (254)
T PF06044_consen 31 NMYCPNCGSKP--LSKFENNRPVADFYCPNCNEEYELKSKKKKLSNKINDGAYHTMIERITSDNNP 94 (254)
T ss_dssp H---TTT--SS---EE--------EEE-TTT--EEEEEEEESS--SEEEEEEHHHHHHHHHTT---
T ss_pred CCcCCCCCChh--HhhccCCCccceeECCCCchHHhhhhhccccCCcccCccHHHHHHHhhccCCC
Confidence 46799999853 23445567789999999999999743 3333332 2577777766655443
No 52
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=88.53 E-value=0.44 Score=33.38 Aligned_cols=41 Identities=20% Similarity=0.503 Sum_probs=28.8
Q ss_pred ccCCCCCCCCeEEEEeec-CCceEEEEcCccCCeeEeec-CCCCc
Q 034528 23 FSCPFCNHGTSVECRIDM-KNLIGEAICNICQESFSTTI-TALTE 65 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk-~~~~g~l~C~~Cg~~~~~~i-~~L~e 65 (92)
=.||+|++.. .+++.. ..+...-.|..|+-+|+-.. .+|..
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 334433 34578899999999998743 33443
No 53
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=87.70 E-value=0.65 Score=28.83 Aligned_cols=38 Identities=21% Similarity=0.402 Sum_probs=27.1
Q ss_pred ccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeec
Q 034528 23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i 60 (92)
--||.||+..-+.+.-|-...-.-+.|..|.+..-..|
T Consensus 5 i~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI~v 42 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKNFPLYCPKCKQETLIDV 42 (55)
T ss_pred EECCCCCCccceeeecCceeccccccCCCCCceEEEEe
Confidence 35999998765666665555667799999998654433
No 54
>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=87.58 E-value=0.37 Score=27.87 Aligned_cols=29 Identities=28% Similarity=0.553 Sum_probs=17.7
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccC
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQ 53 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg 53 (92)
.||.|+-..-..|--|+ .+.|.-.|+.|+
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 69999998877766655 556999999994
No 55
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=86.94 E-value=1 Score=30.85 Aligned_cols=32 Identities=19% Similarity=0.329 Sum_probs=24.2
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
..=-||.|+.+.+.-+ +++++-.+.|..||..
T Consensus 79 ~yVlC~~C~spdT~l~---k~~r~~~l~C~aCGa~ 110 (110)
T smart00653 79 EYVLCPECGSPDTELI---KENRLFFLKCEACGAR 110 (110)
T ss_pred hcEECCCCCCCCcEEE---EeCCeEEEEccccCCC
Confidence 3457999999875443 3477889999999973
No 56
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=86.84 E-value=0.34 Score=28.30 Aligned_cols=31 Identities=19% Similarity=0.383 Sum_probs=21.8
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT 59 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~ 59 (92)
.|.|..||++ ++ ++ ..+.+.|..||-+--++
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 34779999999765443
No 57
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=86.56 E-value=1.1 Score=28.89 Aligned_cols=30 Identities=20% Similarity=0.541 Sum_probs=22.6
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
.||-|+|+ .+.+.+. .-.+.|.+||..--.
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 5666554 367899999986544
No 58
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=86.43 E-value=0.2 Score=35.19 Aligned_cols=40 Identities=18% Similarity=0.462 Sum_probs=24.9
Q ss_pred CccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee
Q 034528 20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT 59 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~ 59 (92)
...|.||+|+..=+..=-+......|...|..||..-...
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 4689999999643221111111235779999999876543
No 59
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=86.26 E-value=0.31 Score=28.81 Aligned_cols=32 Identities=25% Similarity=0.837 Sum_probs=19.4
Q ss_pred cccCCCCCCCCeEEEE-e------ecCCceEEEEcCccCCe
Q 034528 22 VFSCPFCNHGTSVECR-I------DMKNLIGEAICNICQES 55 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vk-i------dk~~~~g~l~C~~Cg~~ 55 (92)
.|.||||+.. ++.. + .-......+.|.+|...
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 00122336899999864
No 60
>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=86.24 E-value=0.73 Score=32.23 Aligned_cols=32 Identities=19% Similarity=0.327 Sum_probs=25.0
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
+.--||.|+.+.+.-++- .++-.+.|..||.+
T Consensus 92 ~yVlC~~C~spdT~l~k~---~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 92 EYVLCPECGSPDTELIKE---GRLIFLKCKACGAS 123 (125)
T ss_dssp HHSSCTSTSSSSEEEEEE---TTCCEEEETTTSCE
T ss_pred HEEEcCCCCCCccEEEEc---CCEEEEEecccCCc
Confidence 445799999988654443 77789999999985
No 61
>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=86.14 E-value=0.38 Score=27.92 Aligned_cols=30 Identities=23% Similarity=0.438 Sum_probs=21.5
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQE 54 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~ 54 (92)
.|.|+.||+.-.+...++. ...+.|-.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~---~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSD---DPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecCC---CCCCCCCCCCC
Confidence 5899999986545444432 35678999997
No 62
>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=86.12 E-value=1.8 Score=27.75 Aligned_cols=36 Identities=17% Similarity=0.217 Sum_probs=27.8
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecC
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTIT 61 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~ 61 (92)
.||-|+.-+++.. -+.+++-.+.|-.||-+.+.+..
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 6999999875554 44667999999999987665444
No 63
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=86.09 E-value=1.7 Score=23.91 Aligned_cols=12 Identities=25% Similarity=0.775 Sum_probs=9.2
Q ss_pred EEcCccCCeeEe
Q 034528 47 AICNICQESFST 58 (92)
Q Consensus 47 l~C~~Cg~~~~~ 58 (92)
..|..||+.|-+
T Consensus 33 ~~C~~CGE~~~~ 44 (46)
T TIGR03831 33 LVCPQCGEEYLD 44 (46)
T ss_pred cccccCCCEeeC
Confidence 469999997743
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=85.86 E-value=0.35 Score=25.50 Aligned_cols=24 Identities=25% Similarity=0.652 Sum_probs=15.1
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFS 57 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~ 57 (92)
+||.|+++- ..+...|..||-.|+
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 234456778877664
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=85.70 E-value=1.4 Score=34.86 Aligned_cols=40 Identities=13% Similarity=0.463 Sum_probs=29.2
Q ss_pred CCCccccCCCCCCCCeEEEEeecC----CceEEEEcCccCCeeE
Q 034528 18 KLDTVFSCPFCNHGTSVECRIDMK----NLIGEAICNICQESFS 57 (92)
Q Consensus 18 kl~~~F~CPfC~~~~sV~vkidk~----~~~g~l~C~~Cg~~~~ 57 (92)
.....|.||.|+|.+++-..+.-. -+.-...|..||.++.
T Consensus 254 ~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 254 AVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred CCcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 344579999999988776655221 3456789999998765
No 66
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=85.45 E-value=0.45 Score=37.44 Aligned_cols=41 Identities=32% Similarity=0.538 Sum_probs=29.7
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHH
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWID 75 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD 75 (92)
.||.||.. .+..+..-|.+.|..||+--+ +..||-..+|--
T Consensus 3 ~CpeCg~~-----~~~~d~~~ge~VC~~CG~Vi~------~~~id~gpewr~ 43 (285)
T COG1405 3 SCPECGST-----NIITDYERGEIVCADCGLVLE------DSLIDPGPEWRA 43 (285)
T ss_pred CCCCCCCc-----cceeeccCCeEEeccCCEEec------cccccCCCCccc
Confidence 69999974 333344479999999998543 357788888873
No 67
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=85.28 E-value=1.6 Score=27.40 Aligned_cols=33 Identities=21% Similarity=0.368 Sum_probs=26.6
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
.||-|+.-+++. +-+.+++-.+.|-.||-+-+-
T Consensus 11 ~CP~C~~~Dtl~--~~~e~~~e~vECv~Cg~~~~~ 43 (59)
T TIGR02443 11 VCPACSAQDTLA--MWKENNIELVECVECGYQEQQ 43 (59)
T ss_pred cCCCCcCccEEE--EEEeCCceEEEeccCCCcccc
Confidence 699999988774 446788899999999976543
No 68
>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]
Probab=85.14 E-value=0.41 Score=42.57 Aligned_cols=37 Identities=22% Similarity=0.569 Sum_probs=28.6
Q ss_pred CccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
...|.|..|||+ +.+.+++..----..|..|+.++++
T Consensus 262 ~afFrC~vC~~~--~~ve~drg~i~eP~~C~~C~~~~~~ 298 (804)
T KOG0478|consen 262 EAFFRCSVCGHE--IAVESDRGRIKEPMLCKECGTTNSF 298 (804)
T ss_pred hHhhhhhhcCce--EEEEeecCccCCCcccccccCcccc
Confidence 368999999995 7777776554455789999988665
No 69
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=85.10 E-value=0.74 Score=32.91 Aligned_cols=27 Identities=26% Similarity=0.517 Sum_probs=20.0
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESF 56 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~ 56 (92)
--+||-||.+ +.+ ..|.+.|-+||.++
T Consensus 28 ~~hCp~Cg~P------LF~--KdG~v~CPvC~~~~ 54 (131)
T COG1645 28 AKHCPKCGTP------LFR--KDGEVFCPVCGYRE 54 (131)
T ss_pred HhhCcccCCc------cee--eCCeEECCCCCceE
Confidence 3579999975 222 55999999999543
No 70
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=84.96 E-value=1.1 Score=31.23 Aligned_cols=44 Identities=18% Similarity=0.403 Sum_probs=27.6
Q ss_pred CCCCCCCCeEEEEeecCCceEEEEcCccCCeeE----e-ecCCCCcchhhhhhHHHHHHhhc
Q 034528 25 CPFCNHGTSVECRIDMKNLIGEAICNICQESFS----T-TITALTEPIDIYSEWIDECERVN 81 (92)
Q Consensus 25 CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~----~-~i~~L~epVDVYs~WiD~~~~~n 81 (92)
||.||++ ..+-.+.|..|+...+ . ++..|+.. | -+||-.+....
T Consensus 1 CPvCg~~----------l~vt~l~C~~C~t~i~G~F~l~~~~~L~~E-~--~~Fi~~Fi~~r 49 (113)
T PF09862_consen 1 CPVCGGE----------LVVTRLKCPSCGTEIEGEFELPWFARLSPE-Q--LEFIKLFIKNR 49 (113)
T ss_pred CCCCCCc----------eEEEEEEcCCCCCEEEeeeccchhhcCCHH-H--HHHHHHHHHhc
Confidence 9999984 3456789999998643 3 34445433 2 34555555444
No 71
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=84.74 E-value=0.51 Score=29.64 Aligned_cols=34 Identities=24% Similarity=0.429 Sum_probs=19.1
Q ss_pred CccccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528 20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQE 54 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~ 54 (92)
-+.|.||.||.+.-..+.-=++.+ ..-.|..||.
T Consensus 23 ~~~F~CPnCG~~~I~RC~~CRk~~-~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEVIIYRCEKCRKQS-NPYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCeeEeechhHHhcC-CceECCCCCC
Confidence 378999999973222222222222 3456777775
No 72
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=84.49 E-value=0.45 Score=24.62 Aligned_cols=22 Identities=23% Similarity=0.537 Sum_probs=15.3
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
.||.||++. ..+...|..||..
T Consensus 4 ~Cp~Cg~~~----------~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 4 FCPNCGAEI----------DPDAKFCPNCGAK 25 (26)
T ss_pred CCcccCCcC----------CcccccChhhCCC
Confidence 599999842 2345678888864
No 73
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=84.43 E-value=0.79 Score=35.80 Aligned_cols=32 Identities=25% Similarity=0.508 Sum_probs=22.7
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
.-.||.||.. .+..| ..-|.+.|..||.-.+.
T Consensus 11 ~~~Cp~Cg~~---~iv~d--~~~Ge~vC~~CG~Vl~e 42 (310)
T PRK00423 11 KLVCPECGSD---KLIYD--YERGEIVCADCGLVIEE 42 (310)
T ss_pred CCcCcCCCCC---CeeEE--CCCCeEeecccCCcccc
Confidence 3469999963 34344 35699999999986543
No 74
>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=84.29 E-value=0.55 Score=24.57 Aligned_cols=12 Identities=33% Similarity=0.911 Sum_probs=10.0
Q ss_pred CCCccccCCCCC
Q 034528 18 KLDTVFSCPFCN 29 (92)
Q Consensus 18 kl~~~F~CPfC~ 29 (92)
..-..|.||.||
T Consensus 12 ~~~v~f~CPnCG 23 (24)
T PF07754_consen 12 EQAVPFPCPNCG 23 (24)
T ss_pred ccCceEeCCCCC
Confidence 346799999998
No 75
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=84.07 E-value=0.9 Score=36.32 Aligned_cols=38 Identities=18% Similarity=0.468 Sum_probs=25.9
Q ss_pred CccccCCCCCCCCeEEE-EeecCCceEEEEcCccCCeeE
Q 034528 20 DTVFSCPFCNHGTSVEC-RIDMKNLIGEAICNICQESFS 57 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~v-kidk~~~~g~l~C~~Cg~~~~ 57 (92)
+..=.||.||..-.+++ .+.-..|.-.+.|..|+....
T Consensus 185 ~~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~ 223 (309)
T PRK03564 185 EQRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWH 223 (309)
T ss_pred cCCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCccc
Confidence 45678999998765553 343456777888888887543
No 76
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=83.82 E-value=1.3 Score=33.77 Aligned_cols=38 Identities=21% Similarity=0.640 Sum_probs=26.1
Q ss_pred CCCccccCCCCCCCCeEEEEeec-------CCceEEEEcCccCCeeE
Q 034528 18 KLDTVFSCPFCNHGTSVECRIDM-------KNLIGEAICNICQESFS 57 (92)
Q Consensus 18 kl~~~F~CPfC~~~~sV~vkidk-------~~~~g~l~C~~Cg~~~~ 57 (92)
-..+.-+||.||+ .+...+.. .-.+-+..|..||-++.
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 3456779999998 34433322 23567899999998764
No 77
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=83.82 E-value=1.5 Score=32.60 Aligned_cols=35 Identities=11% Similarity=0.226 Sum_probs=26.6
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
..=.||.|+++.+--+ ++..+-.+.|..||.....
T Consensus 97 ~yV~C~~C~~pdT~l~---k~~~~~~l~C~aCGa~~~v 131 (201)
T PRK12336 97 EYVICSECGLPDTRLV---KEDRVLMLRCDACGAHRPV 131 (201)
T ss_pred heEECCCCCCCCcEEE---EcCCeEEEEcccCCCCccc
Confidence 3457999999876544 3467889999999987543
No 78
>PRK05978 hypothetical protein; Provisional
Probab=83.42 E-value=0.52 Score=34.11 Aligned_cols=31 Identities=29% Similarity=0.566 Sum_probs=21.5
Q ss_pred ccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
=.||.||..+ |-+.--.-.-+|.+||+.|+.
T Consensus 34 grCP~CG~G~-----LF~g~Lkv~~~C~~CG~~~~~ 64 (148)
T PRK05978 34 GRCPACGEGK-----LFRAFLKPVDHCAACGEDFTH 64 (148)
T ss_pred CcCCCCCCCc-----ccccccccCCCccccCCcccc
Confidence 3699999754 223333345689999998875
No 79
>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=83.42 E-value=1.4 Score=28.12 Aligned_cols=35 Identities=14% Similarity=0.333 Sum_probs=23.1
Q ss_pred cccCCCCCCCCeEEEEeecC---CceEEEEcCccCCeeEe
Q 034528 22 VFSCPFCNHGTSVECRIDMK---NLIGEAICNICQESFST 58 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~---~~~g~l~C~~Cg~~~~~ 58 (92)
.|+|..|++..+ =.|.+. .|+-.+.|..|+..+-.
T Consensus 4 ~FTC~~C~~Rs~--~~~sk~aY~~GvViv~C~gC~~~HlI 41 (66)
T PF05180_consen 4 TFTCNKCGTRSA--KMFSKQAYHKGVVIVQCPGCKNRHLI 41 (66)
T ss_dssp EEEETTTTEEEE--EEEEHHHHHTSEEEEE-TTS--EEES
T ss_pred EEEcCCCCCccc--eeeCHHHHhCCeEEEECCCCcceeee
Confidence 699999997322 233333 79999999999987654
No 80
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=83.39 E-value=3.6 Score=32.93 Aligned_cols=60 Identities=15% Similarity=0.293 Sum_probs=39.2
Q ss_pred cccCCCCCCCCeEEEE-eecC-CceEEEEcCccCCeeEe---ecCCCCcch--hhhhhHHHHHHhhc
Q 034528 22 VFSCPFCNHGTSVECR-IDMK-NLIGEAICNICQESFST---TITALTEPI--DIYSEWIDECERVN 81 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vk-idk~-~~~g~l~C~~Cg~~~~~---~i~~L~epV--DVYs~WiD~~~~~n 81 (92)
.-.||+||+.+.+..- ++-. ..+-.-+|..|+.+.-+ ..++..+|+ |+-+--+|..-+..
T Consensus 226 R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~~~~~~d~~~~p~adDlatL~LDl~a~e~ 292 (309)
T PRK03564 226 RVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYLKILYQEKDPKVEAVADDLASLVLDARMEQE 292 (309)
T ss_pred CccCCCCCCCCceeeeeecCCCcceEeeecccccccceecccccCCCCCcchhHHhhhHhHHHHHhc
Confidence 3479999987766643 4433 34556799999987554 233444455 77888888776543
No 81
>PHA02540 61 DNA primase; Provisional
Probab=83.08 E-value=1.4 Score=35.53 Aligned_cols=50 Identities=24% Similarity=0.347 Sum_probs=34.5
Q ss_pred ccccCCCCCCCC------eEEEEeecCCceEEEEcCccCCe-----eEeecCCCCcchhhhhhHHHHH
Q 034528 21 TVFSCPFCNHGT------SVECRIDMKNLIGEAICNICQES-----FSTTITALTEPIDIYSEWIDEC 77 (92)
Q Consensus 21 ~~F~CPfC~~~~------sV~vkidk~~~~g~l~C~~Cg~~-----~~~~i~~L~epVDVYs~WiD~~ 77 (92)
=.|.|||||..+ |..|.-++. ...-+|-.||.+ |-+.+..|+ |.+|+-..
T Consensus 26 ~~~~CPf~~ds~~~~~kpsF~V~p~k~--~~~yhCFgCGa~Gd~i~Flme~e~ls-----f~Eav~~l 86 (337)
T PHA02540 26 YNFRCPICGDSQKDKNKARGWIYEKKD--GGVFKCHNCGYHRPFGNFLKDYEPDL-----YREYIMER 86 (337)
T ss_pred EEecCCCCCCccccCcCCcEEEeccCC--ceEEEecCCCCCCCHHHHHHHhcCCC-----hHHHHHHH
Confidence 478999999743 566655444 578899999986 556666664 55676633
No 82
>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=83.05 E-value=0.61 Score=28.34 Aligned_cols=36 Identities=19% Similarity=0.356 Sum_probs=24.8
Q ss_pred CCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeec
Q 034528 19 LDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60 (92)
Q Consensus 19 l~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i 60 (92)
--|.=.||.||+...- ........|..||..+.--+
T Consensus 25 ~~TSq~C~~CG~~~~~------~~~~r~~~C~~Cg~~~~rD~ 60 (69)
T PF07282_consen 25 AYTSQTCPRCGHRNKK------RRSGRVFTCPNCGFEMDRDV 60 (69)
T ss_pred CCCccCccCccccccc------ccccceEEcCCCCCEECcHH
Confidence 3366789999984311 34556899999998765433
No 83
>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=82.22 E-value=1.8 Score=24.39 Aligned_cols=30 Identities=20% Similarity=0.403 Sum_probs=17.9
Q ss_pred ccCCCCCCCCeEEEEeec-CCceEEEEcCccC
Q 034528 23 FSCPFCNHGTSVECRIDM-KNLIGEAICNICQ 53 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk-~~~~g~l~C~~Cg 53 (92)
-.||+|+...+| ++--+ ..|.-.-.|..|.
T Consensus 6 v~CP~C~s~~~v-~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 6 VHCPRCQSTEGV-KKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeCCCCCCCCcc-eeCCCCCCCCEeEecCcCC
Confidence 479999986533 22222 2455567777773
No 84
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=82.05 E-value=0.6 Score=31.53 Aligned_cols=31 Identities=19% Similarity=0.722 Sum_probs=23.5
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFS 57 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~ 57 (92)
..++|+|||.. + | +..-+|+-.|+.|...+.
T Consensus 35 aky~CsfCGK~-~----v-KR~AvGiW~C~~C~kv~a 65 (92)
T KOG0402|consen 35 AKYTCSFCGKK-T----V-KRKAVGIWKCGSCKKVVA 65 (92)
T ss_pred hhhhhhhcchh-h----h-hhhceeEEecCCccceec
Confidence 56899999973 2 2 235789999999997654
No 85
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.01 E-value=0.94 Score=38.04 Aligned_cols=55 Identities=18% Similarity=0.342 Sum_probs=45.5
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhhc
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERVN 81 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~n 81 (92)
..=+||-|. |.|.+.+|--.-+|..||+.|-.--..+..|.|.|.-|-|...+-.
T Consensus 367 N~krCP~C~------v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~~nPYkHF~e~~s~c~ 421 (445)
T KOG1814|consen 367 NSKRCPKCK------VVIERSEGCNKMHCTKCGTYFCWICAELLYPENPYKHFSEPGSECY 421 (445)
T ss_pred cCCCCCccc------ceeecCCCccceeeccccccceeehhhhcCCCChhhhhcCCcCccc
Confidence 345799998 3567788889999999999999999999999999999887654443
No 86
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=81.93 E-value=0.59 Score=35.60 Aligned_cols=34 Identities=18% Similarity=0.362 Sum_probs=23.1
Q ss_pred cccCCCCCCCCeEEEEeecC-CceEEEEcCccCCee
Q 034528 22 VFSCPFCNHGTSVECRIDMK-NLIGEAICNICQESF 56 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~-~~~g~l~C~~Cg~~~ 56 (92)
...||.|+.+. +.=.+-+. ..-..+.|..||.-+
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 42233333 344789999999988
No 87
>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=81.72 E-value=2.2 Score=30.78 Aligned_cols=34 Identities=18% Similarity=0.383 Sum_probs=18.6
Q ss_pred cCCCCCCCCeEEEEee-----cCCceEEEEcCccCCeeE
Q 034528 24 SCPFCNHGTSVECRID-----MKNLIGEAICNICQESFS 57 (92)
Q Consensus 24 ~CPfC~~~~sV~vkid-----k~~~~g~l~C~~Cg~~~~ 57 (92)
.||.|++.....+.+. +.--+-...|..||-++.
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 5999998654433332 234556789999997754
No 88
>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=81.58 E-value=0.38 Score=29.77 Aligned_cols=24 Identities=21% Similarity=0.552 Sum_probs=16.4
Q ss_pred EEEeecCCceEEEEcCccCCeeEe
Q 034528 35 ECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 35 ~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
.+-++-.-.-|.+.|..||..|-.
T Consensus 42 ~~l~~~~i~eg~L~Cp~c~r~YPI 65 (68)
T PF03966_consen 42 HVLLEVEIVEGELICPECGREYPI 65 (68)
T ss_dssp EHHCTEETTTTEEEETTTTEEEEE
T ss_pred hhhhcccccCCEEEcCCCCCEEeC
Confidence 333333444589999999998854
No 89
>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=81.55 E-value=0.58 Score=24.00 Aligned_cols=11 Identities=27% Similarity=1.298 Sum_probs=8.8
Q ss_pred CccccCCCCCC
Q 034528 20 DTVFSCPFCNH 30 (92)
Q Consensus 20 ~~~F~CPfC~~ 30 (92)
++.|.||.|+.
T Consensus 12 ~k~~~C~~C~k 22 (26)
T PF13465_consen 12 EKPYKCPYCGK 22 (26)
T ss_dssp SSSEEESSSSE
T ss_pred CCCCCCCCCcC
Confidence 46799999984
No 90
>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=81.54 E-value=1.4 Score=37.26 Aligned_cols=33 Identities=21% Similarity=0.519 Sum_probs=25.8
Q ss_pred ccCCCCCCCCeEE---EEeec--CCceEEEEcCccCCe
Q 034528 23 FSCPFCNHGTSVE---CRIDM--KNLIGEAICNICQES 55 (92)
Q Consensus 23 F~CPfC~~~~sV~---vkidk--~~~~g~l~C~~Cg~~ 55 (92)
..||.|||.+.+. ++.+. ....+...|..||..
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~ 238 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCE 238 (557)
T ss_pred ccCCCCCCCccccccceeecCCCCccceEEECCCCcCC
Confidence 4799999998876 55543 356789999999975
No 91
>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=81.51 E-value=1.5 Score=36.66 Aligned_cols=48 Identities=21% Similarity=0.406 Sum_probs=32.0
Q ss_pred ccccCCCCCCCCeEEEEeecC------------CceEEEEcCccCCeeEeecCC-CCcchhhhh
Q 034528 21 TVFSCPFCNHGTSVECRIDMK------------NLIGEAICNICQESFSTTITA-LTEPIDIYS 71 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~------------~~~g~l~C~~Cg~~~~~~i~~-L~epVDVYs 71 (92)
.-|+||.|.+. +++..... .+...+.|.-|.=+.. .|+- .+.|=+++.
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 57999999984 55554432 4677899999986532 3333 355656665
No 92
>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=80.98 E-value=0.27 Score=36.18 Aligned_cols=60 Identities=25% Similarity=0.406 Sum_probs=39.7
Q ss_pred ccccCCCCCCCCeEEEEeecCCceE--------EEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhhcCccccc
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIG--------EAICNICQESFSTTITALTEPIDIYSEWIDECERVNNLEDDG 87 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g--------~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~n~~~~~~ 87 (92)
+.-.||.|++. +.=.- .-.++. --.|.+||..|-...+.| +.+.+-+++.++....+++.
T Consensus 38 tI~~Cp~C~~~--IrG~y-~v~gv~~~g~~~~~PsYC~~CGkpyPWt~~~L----~aa~el~ee~eeLs~deke~ 105 (158)
T PF10083_consen 38 TITSCPNCSTP--IRGDY-HVEGVFGLGGHYEAPSYCHNCGKPYPWTENAL----EAANELIEEDEELSPDEKEQ 105 (158)
T ss_pred HHHHCcCCCCC--CCCce-ecCCeeeeCCCCCCChhHHhCCCCCchHHHHH----HHHHHHHHHhhcCCHHHHHH
Confidence 45689999984 21110 012333 348999999997766555 77888899888887665554
No 93
>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=80.59 E-value=2.5 Score=33.69 Aligned_cols=59 Identities=15% Similarity=0.345 Sum_probs=34.8
Q ss_pred cccCCCCCCCCeEE-EEeec---CCceEEEEcCccCCeeEe---ecCCCCcch--hhhhhHHHHHHhh
Q 034528 22 VFSCPFCNHGTSVE-CRIDM---KNLIGEAICNICQESFST---TITALTEPI--DIYSEWIDECERV 80 (92)
Q Consensus 22 ~F~CPfC~~~~sV~-vkidk---~~~~g~l~C~~Cg~~~~~---~i~~L~epV--DVYs~WiD~~~~~ 80 (92)
.-.||+||+.+.+. ..++- ..++-.-+|..|+.+.-+ ...+..+|+ |+=|--+|...+.
T Consensus 224 R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~~~~~~d~~~~~~adDlaSL~LD~~a~e 291 (305)
T TIGR01562 224 RVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYLKILYQEKDPHADAVADDLASLALDMRMAE 291 (305)
T ss_pred CccCCCCCCCCceeeEeecCCCCCcceEEeeccccccchhhhccccCCccCchHHHHhhhHhhHHHHh
Confidence 34699999877664 33433 123445589999976433 233444555 6666666665543
No 94
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=80.21 E-value=0.72 Score=29.19 Aligned_cols=34 Identities=24% Similarity=0.372 Sum_probs=19.5
Q ss_pred CccccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528 20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQE 54 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~ 54 (92)
-..|.||.||.+.-..+..=++. -..-.|..||.
T Consensus 25 ~v~F~CPnCGe~~I~Rc~~CRk~-g~~Y~Cp~CGF 58 (61)
T COG2888 25 AVKFPCPNCGEVEIYRCAKCRKL-GNPYRCPKCGF 58 (61)
T ss_pred eeEeeCCCCCceeeehhhhHHHc-CCceECCCcCc
Confidence 36899999996322222222222 23457888885
No 95
>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=80.21 E-value=1 Score=35.91 Aligned_cols=36 Identities=14% Similarity=0.349 Sum_probs=24.0
Q ss_pred cccCCCCCCCCeEEEEee--cCCceEEEEcCccCCeeE
Q 034528 22 VFSCPFCNHGTSVECRID--MKNLIGEAICNICQESFS 57 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkid--k~~~~g~l~C~~Cg~~~~ 57 (92)
.=.||.||..-.+++-.. .+.|.-.++|..|+..+.
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~ 221 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWH 221 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCccc
Confidence 448999998765554333 246677888888876543
No 96
>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=79.59 E-value=2.5 Score=25.71 Aligned_cols=27 Identities=22% Similarity=0.512 Sum_probs=20.8
Q ss_pred CCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528 17 DKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQE 54 (92)
Q Consensus 17 ~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~ 54 (92)
.++|.+..||.||. -...+-.|..||.
T Consensus 21 l~~p~l~~C~~cG~-----------~~~~H~vc~~cG~ 47 (55)
T TIGR01031 21 LTAPTLVVCPNCGE-----------FKLPHRVCPSCGY 47 (55)
T ss_pred ccCCcceECCCCCC-----------cccCeeECCccCe
Confidence 35688889999996 3357788999994
No 97
>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=79.21 E-value=1.6 Score=28.61 Aligned_cols=33 Identities=15% Similarity=0.268 Sum_probs=19.7
Q ss_pred ccCCCCCCCCeEEEEeecC-----------CceEEEEcCccCCe
Q 034528 23 FSCPFCNHGTSVECRIDMK-----------NLIGEAICNICQES 55 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~-----------~~~g~l~C~~Cg~~ 55 (92)
-+|+-|..=+|=-|+|.-- ..-+.|+|..||..
T Consensus 23 d~c~tCSsC~SkLV~~Sdvtk~sl~~~~~~g~~~tLsCsACGS~ 66 (74)
T PF05077_consen 23 DDCTTCSSCQSKLVKFSDVTKVSLDEYKVAGKGNTLSCSACGSE 66 (74)
T ss_pred CCccchhhhhhheeeeecccceehhhhcccCCCCeEeehhcccc
Confidence 5666665544444544221 13368999999964
No 98
>PHA02998 RNA polymerase subunit; Provisional
Probab=79.08 E-value=3.6 Score=31.21 Aligned_cols=38 Identities=18% Similarity=0.451 Sum_probs=28.7
Q ss_pred ccccCCCCCCCCeEEEEeecC----CceEEEEcCccCCeeEe
Q 034528 21 TVFSCPFCNHGTSVECRIDMK----NLIGEAICNICQESFST 58 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~----~~~g~l~C~~Cg~~~~~ 58 (92)
+.-.||.|+|.++.-..+.-. -+.-...|..||-+|.-
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 567899999998886655332 25677899999987753
No 99
>PRK00420 hypothetical protein; Validated
Probab=78.48 E-value=1.6 Score=30.28 Aligned_cols=29 Identities=21% Similarity=0.411 Sum_probs=21.3
Q ss_pred ccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
-.||.||.+- .+ ...|.+.|-+||..+..
T Consensus 24 ~~CP~Cg~pL------f~-lk~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 24 KHCPVCGLPL------FE-LKDGEVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCCCcc------ee-cCCCceECCCCCCeeee
Confidence 6899999742 11 14579999999996654
No 100
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=78.07 E-value=1.3 Score=32.49 Aligned_cols=34 Identities=24% Similarity=0.341 Sum_probs=25.1
Q ss_pred CCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCC
Q 034528 18 KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITA 62 (92)
Q Consensus 18 kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~ 62 (92)
+-.|.=.||.||+ .......|..||..+.--+|+
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 4456678999998 335788999999876655443
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=77.67 E-value=2.7 Score=30.65 Aligned_cols=31 Identities=23% Similarity=0.511 Sum_probs=16.9
Q ss_pred CCCCCCCCeEEEEe-------ecCCceEEEEcCccCCee
Q 034528 25 CPFCNHGTSVECRI-------DMKNLIGEAICNICQESF 56 (92)
Q Consensus 25 CPfC~~~~sV~vki-------dk~~~~g~l~C~~Cg~~~ 56 (92)
||.||++ ++...+ .++--+-+..|..||.++
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 7777764 333322 112344566777777654
No 102
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=76.82 E-value=4.1 Score=30.39 Aligned_cols=33 Identities=21% Similarity=0.399 Sum_probs=18.8
Q ss_pred cCCCCCCCCeEEEEeec------CCceEEEEcCccCCee
Q 034528 24 SCPFCNHGTSVECRIDM------KNLIGEAICNICQESF 56 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk------~~~~g~l~C~~Cg~~~ 56 (92)
+||.||........+-. .--+-+..|..||-++
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~ 40 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRS 40 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCcc
Confidence 58888765433333222 2234567788888764
No 103
>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=76.54 E-value=0.72 Score=26.07 Aligned_cols=14 Identities=21% Similarity=0.778 Sum_probs=9.0
Q ss_pred ccccCCCCCCCCeE
Q 034528 21 TVFSCPFCNHGTSV 34 (92)
Q Consensus 21 ~~F~CPfC~~~~sV 34 (92)
+.+.|+||++.+.|
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 58999999986644
No 104
>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=76.51 E-value=0.64 Score=33.23 Aligned_cols=36 Identities=22% Similarity=0.420 Sum_probs=25.2
Q ss_pred cccCCCCCCCCeEEEEeecC-CceEEEEcCccCCeeE
Q 034528 22 VFSCPFCNHGTSVECRIDMK-NLIGEAICNICQESFS 57 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~-~~~g~l~C~~Cg~~~~ 57 (92)
.-.||+||+.++..+...-. .=.+...|..|.+-|+
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 46999999988766654332 2346678889987664
No 105
>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=76.11 E-value=1.3 Score=26.58 Aligned_cols=18 Identities=28% Similarity=0.811 Sum_probs=14.8
Q ss_pred CCCCCccccCCCCCCCCe
Q 034528 16 VDKLDTVFSCPFCNHGTS 33 (92)
Q Consensus 16 ~~kl~~~F~CPfC~~~~s 33 (92)
-..||-.|.||.|+..++
T Consensus 28 f~~Lp~~w~CP~C~a~K~ 45 (50)
T cd00730 28 FEDLPDDWVCPVCGAGKD 45 (50)
T ss_pred HhHCCCCCCCCCCCCcHH
Confidence 456899999999998754
No 106
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=76.09 E-value=1.2 Score=26.38 Aligned_cols=18 Identities=28% Similarity=0.691 Sum_probs=12.0
Q ss_pred CCCCCccccCCCCCCCCe
Q 034528 16 VDKLDTVFSCPFCNHGTS 33 (92)
Q Consensus 16 ~~kl~~~F~CPfC~~~~s 33 (92)
-..||..|.||.|++.++
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 457899999999998653
No 107
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=75.18 E-value=4.3 Score=25.40 Aligned_cols=28 Identities=18% Similarity=0.583 Sum_probs=20.7
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESF 56 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~ 56 (92)
.||-|+++ .+.+++.. -.+.|.+||..-
T Consensus 13 kCp~C~n~---q~vFsha~--t~V~C~~Cg~~L 40 (59)
T PRK00415 13 KCPDCGNE---QVVFSHAS--TVVRCLVCGKTL 40 (59)
T ss_pred ECCCCCCe---EEEEecCC--cEEECcccCCCc
Confidence 69999984 45565543 678999999753
No 108
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=74.46 E-value=4 Score=25.67 Aligned_cols=41 Identities=27% Similarity=0.597 Sum_probs=29.1
Q ss_pred CCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe--ecCCCC
Q 034528 18 KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST--TITALT 64 (92)
Q Consensus 18 kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~--~i~~L~ 64 (92)
+|--..-||.|.+. ...+... ..+.|..|++.|-. .|+-|-
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 45556789999986 3333333 49999999999975 466653
No 109
>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=74.44 E-value=1.3 Score=20.70 Aligned_cols=8 Identities=50% Similarity=1.655 Sum_probs=3.4
Q ss_pred ccCCCCCC
Q 034528 23 FSCPFCNH 30 (92)
Q Consensus 23 F~CPfC~~ 30 (92)
|.||.|+.
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 110
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=74.43 E-value=4 Score=26.86 Aligned_cols=34 Identities=29% Similarity=0.557 Sum_probs=18.5
Q ss_pred CCCCCCCCeEEEEee----cCC-----ceEEEEcCccCCeeEe
Q 034528 25 CPFCNHGTSVECRID----MKN-----LIGEAICNICQESFST 58 (92)
Q Consensus 25 CPfC~~~~sV~vkid----k~~-----~~g~l~C~~Cg~~~~~ 58 (92)
||+|+...-+....+ -+. .+....|..||..|-+
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~~~ 43 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEELLD 43 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEEEc
Confidence 999996433322111 111 2234679999987654
No 111
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=74.37 E-value=5.2 Score=28.95 Aligned_cols=10 Identities=20% Similarity=0.434 Sum_probs=5.0
Q ss_pred EEEcCccCCe
Q 034528 46 EAICNICQES 55 (92)
Q Consensus 46 ~l~C~~Cg~~ 55 (92)
...|..||-+
T Consensus 29 sf~C~~CGyk 38 (160)
T smart00709 29 SFECEHCGYR 38 (160)
T ss_pred EEECCCCCCc
Confidence 4455555543
No 112
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=73.98 E-value=2.1 Score=26.19 Aligned_cols=26 Identities=23% Similarity=0.478 Sum_probs=16.4
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
.||.||. .++--. .+ -...|+.||-+
T Consensus 21 ~CPrCG~-gvfmA~--H~---dR~~CGkCgyT 46 (51)
T COG1998 21 FCPRCGP-GVFMAD--HK---DRWACGKCGYT 46 (51)
T ss_pred cCCCCCC-cchhhh--cC---ceeEeccccce
Confidence 4999995 222211 12 27899999964
No 113
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=72.33 E-value=2.6 Score=26.17 Aligned_cols=29 Identities=24% Similarity=0.450 Sum_probs=22.3
Q ss_pred CCCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 16 VDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 16 ~~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
.-++++.=.||.||+ ..+.+-.|..||..
T Consensus 21 ~l~~~~~~~c~~cG~-----------~~l~Hrvc~~cg~Y 49 (57)
T COG0333 21 ALKAPTLSVCPNCGE-----------YKLPHRVCLKCGYY 49 (57)
T ss_pred hhhCccceeccCCCC-----------cccCceEcCCCCCc
Confidence 446678889999996 44577789999953
No 114
>PRK11827 hypothetical protein; Provisional
Probab=72.08 E-value=2.9 Score=26.11 Aligned_cols=39 Identities=28% Similarity=0.545 Sum_probs=26.4
Q ss_pred CCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe--ecCCC
Q 034528 19 LDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST--TITAL 63 (92)
Q Consensus 19 l~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~--~i~~L 63 (92)
|-...-||.|..+ +. .+.. ...+.|..|++.|.. .|+-|
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 4456789999873 33 3332 246889999999975 36554
No 115
>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=71.69 E-value=5.1 Score=26.25 Aligned_cols=32 Identities=19% Similarity=0.353 Sum_probs=16.2
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESF 56 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~ 56 (92)
...||||+. ++=+..|+.+. +.-.|-.||...
T Consensus 33 ~~~CPfH~d-~~pS~~i~~~k--~~~~Cf~Cg~~G 64 (97)
T PF01807_consen 33 RCLCPFHDD-KTPSFSINPDK--NRFKCFGCGKGG 64 (97)
T ss_dssp EE--SSS---SS--EEEETTT--TEEEETTT--EE
T ss_pred EEECcCCCC-CCCceEEECCC--CeEEECCCCCCC
Confidence 477999995 33455555444 368999999764
No 116
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=71.16 E-value=9.4 Score=32.02 Aligned_cols=38 Identities=18% Similarity=0.328 Sum_probs=29.3
Q ss_pred cCCCCCCCCeEEE-EeecCCceEEEEcCccCCeeEeecCC
Q 034528 24 SCPFCNHGTSVEC-RIDMKNLIGEAICNICQESFSTTITA 62 (92)
Q Consensus 24 ~CPfC~~~~sV~v-kidk~~~~g~l~C~~Cg~~~~~~i~~ 62 (92)
-||.||...++.+ .+|-..+.-.-.|. ||-..++.|..
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 67777665555776 99988887764
No 117
>smart00400 ZnF_CHCC zinc finger.
Probab=70.66 E-value=5.4 Score=23.40 Aligned_cols=38 Identities=16% Similarity=0.236 Sum_probs=25.0
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhh
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSE 72 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~ 72 (92)
.|||++- ++=+..|+.. .....|..||... ..||.|.+
T Consensus 4 ~cPfh~d-~~pSf~v~~~--kn~~~Cf~cg~gG--------d~i~fv~~ 41 (55)
T smart00400 4 LCPFHGE-KTPSFSVSPD--KQFFHCFGCGAGG--------NVISFLMK 41 (55)
T ss_pred cCcCCCC-CCCCEEEECC--CCEEEEeCCCCCC--------CHHHHHHH
Confidence 4999984 5556666544 3568999998643 45665553
No 118
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=70.42 E-value=4.2 Score=35.78 Aligned_cols=47 Identities=26% Similarity=0.423 Sum_probs=30.7
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCcc---CCeeEeecCCCCcchhh
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNIC---QESFSTTITALTEPIDI 69 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~C---g~~~~~~i~~L~epVDV 69 (92)
-.|.|+.|||. +.+.++.....-...|..| +......++..++.+|.
T Consensus 128 ~~~~C~~Cg~~--~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~s~f~d~ 177 (682)
T COG1241 128 AVFECPKCGRE--VEVEQSEFRVEPPRECENCGKFGKGPLKLVPRKSEFIDF 177 (682)
T ss_pred EEEEcCCCCCE--EEEEeccccccCCccCCCccccCCCceEEecCcceeeec
Confidence 58999999994 6666655554455779999 22223445666666653
No 119
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=70.41 E-value=1.2 Score=37.30 Aligned_cols=38 Identities=26% Similarity=0.476 Sum_probs=24.0
Q ss_pred CccccCCCCCCCC-eEEEEeecCCceEEEEcCccCCeeE
Q 034528 20 DTVFSCPFCNHGT-SVECRIDMKNLIGEAICNICQESFS 57 (92)
Q Consensus 20 ~~~F~CPfC~~~~-sV~vkidk~~~~g~l~C~~Cg~~~~ 57 (92)
..-|-||+|+..= ++.+---.....|...|.+||..-.
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelv 164 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELV 164 (436)
T ss_pred cccccCCccccchhhhHHHHhhcccCceEEEecCCCchh
Confidence 4579999999741 1211111123468999999997643
No 120
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=69.47 E-value=1.5 Score=23.90 Aligned_cols=25 Identities=20% Similarity=0.538 Sum_probs=11.1
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
.||.|+.+.+. ..-..+.|..|+-.
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 12245678888743
No 121
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=69.18 E-value=4.1 Score=25.17 Aligned_cols=28 Identities=4% Similarity=-0.269 Sum_probs=18.4
Q ss_pred CCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528 17 DKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESF 56 (92)
Q Consensus 17 ~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~ 56 (92)
-+++..=.||.||. -...+-.|. ||...
T Consensus 22 ~~~~~~~~c~~cg~-----------~~~pH~vc~-cG~Y~ 49 (60)
T PRK01110 22 LTAPTLSVDKTTGE-----------YHLPHHVSP-KGYYK 49 (60)
T ss_pred ccCCceeEcCCCCc-----------eeccceecC-CcccC
Confidence 34566778999996 223455688 98543
No 122
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.30 E-value=5.4 Score=26.74 Aligned_cols=27 Identities=26% Similarity=0.694 Sum_probs=21.6
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQE 54 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~ 54 (92)
-||.|| |+..+....++-+-.|..|+-
T Consensus 3 lCP~C~----v~l~~~~rs~vEiD~CPrCrG 29 (88)
T COG3809 3 LCPICG----VELVMSVRSGVEIDYCPRCRG 29 (88)
T ss_pred ccCcCC----ceeeeeeecCceeeeCCcccc
Confidence 499999 455666678899999999974
No 123
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=68.13 E-value=7 Score=26.75 Aligned_cols=30 Identities=20% Similarity=0.427 Sum_probs=18.9
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFS 57 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~ 57 (92)
-||-||+ -+..+- +...+.+.|+.||-.++
T Consensus 4 FCp~Cgs--ll~p~~--~~~~~~l~C~kCgye~~ 33 (113)
T COG1594 4 FCPKCGS--LLYPKK--DDEGGKLVCRKCGYEEE 33 (113)
T ss_pred ccCCccC--eeEEeE--cCCCcEEECCCCCcchh
Confidence 3899986 233332 22334999999996554
No 124
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.93 E-value=3.5 Score=33.54 Aligned_cols=30 Identities=23% Similarity=0.573 Sum_probs=23.7
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
--+||-|+|. |.+..|-.+++|+ ||..|-+
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 4589999982 4677889999999 9976543
No 125
>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=67.87 E-value=8.8 Score=22.08 Aligned_cols=25 Identities=20% Similarity=0.433 Sum_probs=18.1
Q ss_pred CCCCeEEEEeecCCceEEEEcCccCCee
Q 034528 29 NHGTSVECRIDMKNLIGEAICNICQESF 56 (92)
Q Consensus 29 ~~~~sV~vkidk~~~~g~l~C~~Cg~~~ 56 (92)
+|+. |-+.|+...+ .+.|.=||..|
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 4654 7788877544 88999999887
No 126
>PF14122 YokU: YokU-like protein
Probab=67.87 E-value=4.6 Score=27.17 Aligned_cols=35 Identities=17% Similarity=0.477 Sum_probs=22.4
Q ss_pred cCCCCCCCCeEEEEee----cC--------CceEEEEcCccCCeeEe
Q 034528 24 SCPFCNHGTSVECRID----MK--------NLIGEAICNICQESFST 58 (92)
Q Consensus 24 ~CPfC~~~~sV~vkid----k~--------~~~g~l~C~~Cg~~~~~ 58 (92)
.|-.|+..+++...-. .- ...-.+.|..||..|+.
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~ 47 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQD 47 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEeh
Confidence 4788887655443221 11 23356899999999985
No 127
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=67.63 E-value=2.1 Score=31.76 Aligned_cols=32 Identities=19% Similarity=0.408 Sum_probs=21.3
Q ss_pred cccCCCCCCCCeEEEEeecCCceE------------EEEcCccCCee
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIG------------EAICNICQESF 56 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g------------~l~C~~Cg~~~ 56 (92)
.=.||.||. .-+++.+..-.+ ...|-+||.-|
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 346999996 455665554332 34599999876
No 128
>PF15616 TerY-C: TerY-C metal binding domain
Probab=66.34 E-value=6.4 Score=28.04 Aligned_cols=35 Identities=23% Similarity=0.421 Sum_probs=22.5
Q ss_pred cCCCCCCCCeEEEE-eec---CCceEEEEcCccCCeeEe
Q 034528 24 SCPFCNHGTSVECR-IDM---KNLIGEAICNICQESFST 58 (92)
Q Consensus 24 ~CPfC~~~~sV~vk-idk---~~~~g~l~C~~Cg~~~~~ 58 (92)
.||.||+.-.+.+- =.+ =.+-+.+.|.-||..-.+
T Consensus 79 gCP~CGn~~~fa~C~CGkl~Ci~g~~~~~CPwCg~~g~~ 117 (131)
T PF15616_consen 79 GCPHCGNQYAFAVCGCGKLFCIDGEGEVTCPWCGNEGSF 117 (131)
T ss_pred CCCCCcChhcEEEecCCCEEEeCCCCCEECCCCCCeeee
Confidence 69999997444433 111 134567899999986554
No 129
>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=66.24 E-value=2.5 Score=22.83 Aligned_cols=13 Identities=23% Similarity=0.787 Sum_probs=10.3
Q ss_pred ccccCCCCCCCCe
Q 034528 21 TVFSCPFCNHGTS 33 (92)
Q Consensus 21 ~~F~CPfC~~~~s 33 (92)
..+.||.||+.++
T Consensus 16 ~~~~CP~Cg~~~~ 28 (33)
T cd00350 16 APWVCPVCGAPKD 28 (33)
T ss_pred CCCcCcCCCCcHH
Confidence 5789999998653
No 130
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=65.55 E-value=4.9 Score=32.45 Aligned_cols=44 Identities=27% Similarity=0.532 Sum_probs=30.7
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHH
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDE 76 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~ 76 (92)
.||-|....- .+.-| ..-|...|..||+.++.. .||+-|+|--.
T Consensus 2 ~c~~C~~~~~-~~V~d--~~~gdtvC~~CGlVl~~r------~Id~~sEwrtf 45 (308)
T KOG1597|consen 2 TCPDCKRHPE-NLVED--HSAGDTVCSECGLVLEDR------IIDEGSEWRTF 45 (308)
T ss_pred CCCCCCCCCC-Ceeee--ccCCceecccCCeeeccc------ccccccccccc
Confidence 4788876654 33333 345788999999988754 57888888643
No 131
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=65.18 E-value=6.1 Score=25.80 Aligned_cols=28 Identities=21% Similarity=0.560 Sum_probs=18.3
Q ss_pred ccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
|.||-||+. +|+.......-.|.+|+=.
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 3333332236789999843
No 132
>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=64.33 E-value=8.3 Score=26.93 Aligned_cols=32 Identities=19% Similarity=0.333 Sum_probs=20.8
Q ss_pred cccCCCCCCCCeEEEEeecCCc------------eEEEEcCccCCee
Q 034528 22 VFSCPFCNHGTSVECRIDMKNL------------IGEAICNICQESF 56 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~------------~g~l~C~~Cg~~~ 56 (92)
.=.||.||. .-..+++..- --.-.|..||.-|
T Consensus 91 ~sRC~~CN~---~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 91 FSRCPKCNG---PLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CCccCCCCc---EeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 346999997 3344444321 1257899999877
No 133
>KOG1296 consensus Uncharacterized conserved protein [Function unknown]
Probab=64.25 E-value=6.5 Score=29.04 Aligned_cols=60 Identities=23% Similarity=0.345 Sum_probs=37.9
Q ss_pred cccCCCCCCCCeEEEEeecC-----------CceEEEEcCccCC-eeEe---------ecCCCCcchhhhh-hHHHHHHh
Q 034528 22 VFSCPFCNHGTSVECRIDMK-----------NLIGEAICNICQE-SFST---------TITALTEPIDIYS-EWIDECER 79 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~-----------~~~g~l~C~~Cg~-~~~~---------~i~~L~epVDVYs-~WiD~~~~ 79 (92)
+-.|-||+.++||++--+.. .-+...-||-|.. .|.. .-..-.+.||.=+ +|.|-=+.
T Consensus 64 v~KCK~C~Rensv~iv~~~~~pyt~ed~e~~~~i~vfdCRG~EpidF~p~~~w~a~s~esG~~f~eidlse~ew~dYDdk 143 (161)
T KOG1296|consen 64 VMKCKFCSRENSVTIVAFEDKPYTAEDSEKFKTIVVFDCRGLEPIDFYPRTGWFAVSAESGTAFSEIDLSEKEWTDYDDK 143 (161)
T ss_pred hhhhhhhcccCcEEEecCCCCcccccccccccceEEEeccCCcceeecCCceEEEEecccCceeeeeecccccceehhhc
Confidence 45799999999999865432 2466788999874 2221 1122345666666 78875444
Q ss_pred hc
Q 034528 80 VN 81 (92)
Q Consensus 80 ~n 81 (92)
++
T Consensus 144 ~~ 145 (161)
T KOG1296|consen 144 AG 145 (161)
T ss_pred CC
Confidence 43
No 134
>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=62.87 E-value=8.7 Score=26.21 Aligned_cols=33 Identities=18% Similarity=0.473 Sum_probs=22.9
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFS 57 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~ 57 (92)
-.+.|+-|+.+ + ...++.......|+.|+..+.
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 47899999973 3 333333566789999997653
No 135
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=62.15 E-value=3.4 Score=34.85 Aligned_cols=18 Identities=33% Similarity=0.713 Sum_probs=12.8
Q ss_pred CCCccccCCCCCCCCeEEE
Q 034528 18 KLDTVFSCPFCNHGTSVEC 36 (92)
Q Consensus 18 kl~~~F~CPfC~~~~sV~v 36 (92)
-+--.|.||+|||.+ +++
T Consensus 64 vVimSF~CpHCG~kN-~ei 81 (460)
T KOG2703|consen 64 VVIMSFECPHCGHKN-NEI 81 (460)
T ss_pred eeeEEeecCccCCcc-ccc
Confidence 344679999999943 444
No 136
>PRK12495 hypothetical protein; Provisional
Probab=62.03 E-value=5 Score=31.14 Aligned_cols=34 Identities=21% Similarity=0.385 Sum_probs=25.9
Q ss_pred CCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 17 DKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 17 ~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
..-...|.|+.||.+-- ...|.+.|-+|+..+.-
T Consensus 37 gatmsa~hC~~CG~PIp--------a~pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 37 GATMTNAHCDECGDPIF--------RHDGQEFCPTCQQPVTE 70 (226)
T ss_pred hcccchhhcccccCccc--------CCCCeeECCCCCCcccc
Confidence 34567899999998632 33699999999987653
No 137
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=61.67 E-value=18 Score=25.01 Aligned_cols=31 Identities=19% Similarity=0.457 Sum_probs=22.1
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
=||-||+ -+.|+- ....-.++|+.|+-.|..
T Consensus 3 FCP~Cgn--~Live~--g~~~~rf~C~tCpY~~~I 33 (105)
T KOG2906|consen 3 FCPTCGN--MLIVES--GESCNRFSCRTCPYVFPI 33 (105)
T ss_pred ccCCCCC--EEEEec--CCeEeeEEcCCCCceeeE
Confidence 4999997 355544 334788999999976643
No 138
>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=61.43 E-value=6.5 Score=25.35 Aligned_cols=28 Identities=25% Similarity=0.816 Sum_probs=15.5
Q ss_pred ccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
..||-|+++ |+... +...|..|+..|..
T Consensus 2 ~~CP~C~~~------L~~~~--~~~~C~~C~~~~~~ 29 (70)
T PF07191_consen 2 NTCPKCQQE------LEWQG--GHYHCEACQKDYKK 29 (70)
T ss_dssp -B-SSS-SB------EEEET--TEEEETTT--EEEE
T ss_pred CcCCCCCCc------cEEeC--CEEECcccccccee
Confidence 368999874 33333 67788888888765
No 139
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=61.14 E-value=5.5 Score=25.02 Aligned_cols=31 Identities=19% Similarity=0.382 Sum_probs=27.1
Q ss_pred EcCccCCeeEeecCCCCcchhhhhhHHHHHH
Q 034528 48 ICNICQESFSTTITALTEPIDIYSEWIDECE 78 (92)
Q Consensus 48 ~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~ 78 (92)
.|.+||..-...+++-+.|.|=|++.--++.
T Consensus 19 ~Cp~CG~~t~~~~PprFSPeD~y~kYR~~lk 49 (59)
T COG2260 19 KCPVCGGDTKVPHPPRFSPEDKYGKYRRELK 49 (59)
T ss_pred cCCCCCCccccCCCCCCCccchHHHHHHHHH
Confidence 6999999999999999999999999865544
No 140
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=61.12 E-value=2.8 Score=23.91 Aligned_cols=16 Identities=25% Similarity=0.632 Sum_probs=12.9
Q ss_pred eEEEEcCccCCeeEee
Q 034528 44 IGEAICNICQESFSTT 59 (92)
Q Consensus 44 ~g~l~C~~Cg~~~~~~ 59 (92)
.|...|..||..|...
T Consensus 11 ~~~~~C~~CgM~Y~~~ 26 (41)
T PF13878_consen 11 FGATTCPTCGMLYSPG 26 (41)
T ss_pred cCCcCCCCCCCEECCC
Confidence 4678999999998754
No 141
>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=61.10 E-value=4.9 Score=27.50 Aligned_cols=36 Identities=22% Similarity=0.455 Sum_probs=25.8
Q ss_pred CCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee
Q 034528 17 DKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT 59 (92)
Q Consensus 17 ~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~ 59 (92)
+-|=|-..||.||.. +- ..+.--|.|-.||..|...
T Consensus 4 pelGtKR~Cp~CG~k------FY-DLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 4 PELGTKRTCPSCGAK------FY-DLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCcccCCCCcch------hc-cCCCCCccCCCCCCccCcc
Confidence 466677899999972 32 2233568899999998765
No 142
>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=60.92 E-value=6.6 Score=29.09 Aligned_cols=42 Identities=24% Similarity=0.375 Sum_probs=31.6
Q ss_pred ccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCC
Q 034528 23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALT 64 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~ 64 (92)
-+|-|||.-=.|+|=-..--.+-++.||-|.-=.+.++.++.
T Consensus 13 VhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~~~ 54 (170)
T PF04690_consen 13 VHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRALL 54 (170)
T ss_pred EEcCCcCeEEEEecchhhhhhhhceeccCccceeeeeccccc
Confidence 479999987666666666678889999999976665555444
No 143
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=60.76 E-value=3.7 Score=32.09 Aligned_cols=19 Identities=47% Similarity=0.878 Sum_probs=13.1
Q ss_pred cccCCCCCCCC-eEEEEeec
Q 034528 22 VFSCPFCNHGT-SVECRIDM 40 (92)
Q Consensus 22 ~F~CPfC~~~~-sV~vkidk 40 (92)
.|-||||||-+ .+.-.+|.
T Consensus 214 efiC~~Cn~~n~~~~~~~ds 233 (251)
T COG5415 214 EFICPHCNHKNDEVKEREDS 233 (251)
T ss_pred heecccchhhcCcccccccc
Confidence 79999999976 44444443
No 144
>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=60.49 E-value=4.6 Score=22.16 Aligned_cols=25 Identities=20% Similarity=0.468 Sum_probs=14.0
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
.|..||++. + |.... .+.|..||-+
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 577788753 2 43333 3578888754
No 145
>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=60.37 E-value=15 Score=27.62 Aligned_cols=62 Identities=18% Similarity=0.206 Sum_probs=37.1
Q ss_pred CCCCccccCCCCCCCCeEEEEeecCCc---eEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHh
Q 034528 17 DKLDTVFSCPFCNHGTSVECRIDMKNL---IGEAICNICQESFSTTITALTEPIDIYSEWIDECER 79 (92)
Q Consensus 17 ~kl~~~F~CPfC~~~~sV~vkidk~~~---~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~ 79 (92)
.+++-.|.||-||++..+.+.+++..- ...+. -.=|..-.++.|.|++--|++.-..+-++.
T Consensus 73 ~~v~~~~~C~~cg~~~~~~i~l~~~~l~~~~~~~~-~~~~i~i~~ryP~~~~~~~~~~mi~~cI~~ 137 (205)
T PF12322_consen 73 TKVPVNYTCPDCGEEVKVPINLDQIKLTDGKNEIK-LSDGIKIKMRYPSLFEFDDVFEMIASCIDY 137 (205)
T ss_pred ccceEEEECCCCCcEEEEEecchhcccCCCCcceE-ecCCEEEEEeCCcccccCCHHHHHHHHHHe
Confidence 357889999999997666666655322 22222 222344566777777666666655444443
No 146
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=60.09 E-value=3.9 Score=28.61 Aligned_cols=15 Identities=20% Similarity=0.523 Sum_probs=11.6
Q ss_pred CCCccccCCCCCCCC
Q 034528 18 KLDTVFSCPFCNHGT 32 (92)
Q Consensus 18 kl~~~F~CPfC~~~~ 32 (92)
..|-.+.|+.||+.-
T Consensus 66 ~~p~~~~C~~CG~~~ 80 (135)
T PRK03824 66 EEEAVLKCRNCGNEW 80 (135)
T ss_pred ecceEEECCCCCCEE
Confidence 556789999999753
No 147
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=59.89 E-value=13 Score=21.45 Aligned_cols=35 Identities=20% Similarity=0.380 Sum_probs=22.2
Q ss_pred ccccCC--CCCCCCeEEEEeecCCceEEEEcCccCCeeEee
Q 034528 21 TVFSCP--FCNHGTSVECRIDMKNLIGEAICNICQESFSTT 59 (92)
Q Consensus 21 ~~F~CP--fC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~ 59 (92)
+.--|| .|+. .+.. +...+...+.|..||..|-..
T Consensus 17 ~~~~CP~~~C~~--~~~~--~~~~~~~~v~C~~C~~~fC~~ 53 (64)
T smart00647 17 DLKWCPAPDCSA--AIIV--TEEEGCNRVTCPKCGFSFCFR 53 (64)
T ss_pred CccCCCCCCCcc--eEEe--cCCCCCCeeECCCCCCeECCC
Confidence 444699 9976 2222 213355688998899887653
No 148
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=59.87 E-value=7.3 Score=34.57 Aligned_cols=29 Identities=21% Similarity=0.622 Sum_probs=18.4
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
.+|.||+|+.. + ++-+. .+.+.|.-||-.
T Consensus 443 ~v~~Cp~Cd~~--l--t~H~~--~~~L~CH~Cg~~ 471 (730)
T COG1198 443 YIAECPNCDSP--L--TLHKA--TGQLRCHYCGYQ 471 (730)
T ss_pred CcccCCCCCcc--e--EEecC--CCeeEeCCCCCC
Confidence 57889999863 3 33222 267777777754
No 149
>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=59.76 E-value=3.9 Score=29.83 Aligned_cols=38 Identities=16% Similarity=0.343 Sum_probs=16.4
Q ss_pred CccccCCCCCCCCeEEEEeecCC---ceEEEEcCccCCeeE
Q 034528 20 DTVFSCPFCNHGTSVECRIDMKN---LIGEAICNICQESFS 57 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~~---~~g~l~C~~Cg~~~~ 57 (92)
|=.|.||.|+++..+.=.+.... ....+.|..|+..+.
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 44799999998643322222111 123689999998443
No 150
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=59.73 E-value=3.8 Score=19.96 Aligned_cols=8 Identities=38% Similarity=1.431 Sum_probs=4.3
Q ss_pred ccCCCCCC
Q 034528 23 FSCPFCNH 30 (92)
Q Consensus 23 F~CPfC~~ 30 (92)
|.|++|+-
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 151
>PLN00209 ribosomal protein S27; Provisional
Probab=59.62 E-value=14 Score=24.78 Aligned_cols=38 Identities=18% Similarity=0.467 Sum_probs=26.3
Q ss_pred CCCCCccc---cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 16 VDKLDTVF---SCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 16 ~~kl~~~F---~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
.+...+.| .||-|++ +.+.+... .-.+.|.+||.....
T Consensus 27 v~~PnS~Fm~VkCp~C~n---~q~VFShA--~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 27 VQSPNSFFMDVKCQGCFN---ITTVFSHS--QTVVVCGSCQTVLCQ 67 (86)
T ss_pred ecCCCCEEEEEECCCCCC---eeEEEecC--ceEEEccccCCEeec
Confidence 44445666 7999998 45556544 367899999976543
No 152
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=58.98 E-value=3 Score=34.64 Aligned_cols=38 Identities=21% Similarity=0.384 Sum_probs=27.5
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeec
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i 60 (92)
+.-.||+|+++.+ .+.|.++. .-...|..||.+..+..
T Consensus 95 KFVlC~~C~NPET-el~itk~q-~i~~~CkACG~r~~~d~ 132 (400)
T KOG2767|consen 95 KFVLCPSCENPET-ELIITKKQ-TISLKCKACGFRSDMDL 132 (400)
T ss_pred HheeCcCCCCCce-eEEecccc-hhhhHHHHcCCcccccc
Confidence 4567999999864 45555533 34579999999887765
No 153
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=58.76 E-value=6.4 Score=27.73 Aligned_cols=36 Identities=19% Similarity=0.458 Sum_probs=23.7
Q ss_pred ccCCCCCCCCeEEEEeec----CCceEEEEcCccCCeeEe
Q 034528 23 FSCPFCNHGTSVECRIDM----KNLIGEAICNICQESFST 58 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk----~~~~g~l~C~~Cg~~~~~ 58 (92)
-.||-|||+.-.-=++.. ....-.-+|-.|+-.|..
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 359999998644333322 123456799999988764
No 154
>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=58.57 E-value=4.4 Score=32.93 Aligned_cols=32 Identities=19% Similarity=0.552 Sum_probs=15.1
Q ss_pred CCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 18 KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 18 kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
.+-..|.|+.||. . ++.+++ +-.-.|..||..
T Consensus 281 a~KRFFkC~~C~~-R--t~sl~r---~P~~~C~~Cg~~ 312 (344)
T PF09332_consen 281 AVKRFFKCKDCGN-R--TISLER---LPKKHCSNCGSS 312 (344)
T ss_dssp EE-EEEE-T-TS--E--EEESSS---S--S--TTT-S-
T ss_pred eeeeeEECCCCCC-e--eeeccc---CCCCCCCcCCcC
Confidence 3446899999998 3 445543 345699999974
No 155
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=57.62 E-value=9.1 Score=24.55 Aligned_cols=34 Identities=26% Similarity=0.523 Sum_probs=23.1
Q ss_pred CCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcc
Q 034528 25 CPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEP 66 (92)
Q Consensus 25 CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~ep 66 (92)
||.|...+ +.. ..+.|.| .||+++.+.-..++..
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 99999743 433 4467999 5668888875555543
No 156
>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=57.58 E-value=3.9 Score=19.50 Aligned_cols=10 Identities=60% Similarity=1.185 Sum_probs=5.3
Q ss_pred EcCccCCeeE
Q 034528 48 ICNICQESFS 57 (92)
Q Consensus 48 ~C~~Cg~~~~ 57 (92)
.|..|+..|.
T Consensus 2 ~C~~C~~~f~ 11 (23)
T PF00096_consen 2 KCPICGKSFS 11 (23)
T ss_dssp EETTTTEEES
T ss_pred CCCCCCCccC
Confidence 3555555554
No 157
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=57.38 E-value=11 Score=28.90 Aligned_cols=27 Identities=26% Similarity=0.671 Sum_probs=17.0
Q ss_pred CCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528 25 CPFCNHGTSVECRIDMKNLIGEAICNICQESFS 57 (92)
Q Consensus 25 CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~ 57 (92)
||.||+...+ ...+ -...|..||..+-
T Consensus 102 C~~CG~~~~~-----~~~~-~~~~C~~c~~~~y 128 (256)
T PRK00241 102 CGYCGHPMHP-----SKTE-WAMLCPHCRERYY 128 (256)
T ss_pred ccccCCCCee-----cCCc-eeEECCCCCCEEC
Confidence 9999985322 1233 3467999997543
No 158
>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=57.34 E-value=12 Score=30.61 Aligned_cols=39 Identities=21% Similarity=0.232 Sum_probs=24.6
Q ss_pred cCCCCCCC-CeEEEEeecCCceEEEEcCccCCeeEeecCC
Q 034528 24 SCPFCNHG-TSVECRIDMKNLIGEAICNICQESFSTTITA 62 (92)
Q Consensus 24 ~CPfC~~~-~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~ 62 (92)
-|+.||.- .+-.+..|...+.-.-.|..||..-+..+..
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 49999984 4444577777889999999999988887765
No 159
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=57.20 E-value=16 Score=24.42 Aligned_cols=38 Identities=18% Similarity=0.509 Sum_probs=26.4
Q ss_pred CCCCCccc---cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 16 VDKLDTVF---SCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 16 ~~kl~~~F---~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
.+...+.| .||-|++ +.+.+... .-.+.|.+||.....
T Consensus 26 v~~PnS~Fm~VkCp~C~n---~q~VFShA--~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 26 VQGPNSYFMDVKCPGCSQ---ITTVFSHA--QTVVLCGGCSSQLCQ 66 (85)
T ss_pred ecCCCCeEEEEECCCCCC---eeEEEecC--ceEEEccccCCEeec
Confidence 44445666 7999998 45556554 367899999976543
No 160
>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=57.14 E-value=5.5 Score=23.42 Aligned_cols=13 Identities=38% Similarity=1.020 Sum_probs=9.5
Q ss_pred cchhhhhhHHHHH
Q 034528 65 EPIDIYSEWIDEC 77 (92)
Q Consensus 65 epVDVYs~WiD~~ 77 (92)
.|==||.+|+|+-
T Consensus 17 t~RLvYADWL~e~ 29 (42)
T TIGR02996 17 TPRLVYADWLDEH 29 (42)
T ss_pred chHHHHHHHHHHc
Confidence 3445999999863
No 161
>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=56.80 E-value=6.9 Score=23.67 Aligned_cols=15 Identities=20% Similarity=0.733 Sum_probs=11.4
Q ss_pred CCCCccccCCCCCCC
Q 034528 17 DKLDTVFSCPFCNHG 31 (92)
Q Consensus 17 ~kl~~~F~CPfC~~~ 31 (92)
..-+..|.||+||+-
T Consensus 39 ~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 39 EFEEIQYRCPYCGAL 53 (54)
T ss_pred cCCceEEEcCCCCCc
Confidence 344569999999973
No 162
>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=56.43 E-value=18 Score=22.20 Aligned_cols=31 Identities=16% Similarity=0.518 Sum_probs=18.5
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT 59 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~ 59 (92)
.||-|++ +.+.+++.. -.+.|.+||..-..+
T Consensus 9 kCp~C~~---~q~vFSha~--t~V~C~~Cg~~L~~P 39 (55)
T PF01667_consen 9 KCPGCYN---IQTVFSHAQ--TVVKCVVCGTVLAQP 39 (55)
T ss_dssp E-TTT-S---EEEEETT-S--S-EE-SSSTSEEEEE
T ss_pred ECCCCCC---eeEEEecCC--eEEEcccCCCEecCC
Confidence 6999998 455575554 578999999876543
No 163
>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=56.40 E-value=12 Score=20.86 Aligned_cols=27 Identities=22% Similarity=0.434 Sum_probs=18.0
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
.|.|+.|+. + ... ..-|...|..||-.
T Consensus 8 ~~~C~~C~~---~--~~~--~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 8 NEPCPVCGS---R--WFY--SDDGFYYCDRCGHQ 34 (36)
T ss_pred CCcCCCCCC---e--EeE--ccCCEEEhhhCceE
Confidence 366999996 2 222 23478889888853
No 164
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=56.27 E-value=8.2 Score=23.49 Aligned_cols=20 Identities=25% Similarity=0.645 Sum_probs=13.4
Q ss_pred CccccCCCCCCCCeEEEEeecC
Q 034528 20 DTVFSCPFCNHGTSVECRIDMK 41 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~ 41 (92)
|..+.||+||+. +.-.++..
T Consensus 1 p~~i~Cp~C~~~--~~T~v~~~ 20 (67)
T smart00714 1 PYQLFCPRCQNN--VTTRVETE 20 (67)
T ss_pred CcceECCCCCCE--EEEEEEEE
Confidence 457899999974 44445444
No 165
>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=55.93 E-value=9.3 Score=23.35 Aligned_cols=42 Identities=19% Similarity=0.326 Sum_probs=25.7
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee-cCCCCcc
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT-ITALTEP 66 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~-i~~L~ep 66 (92)
+.+.|+.||.- -.+.. .-....|.|..|+.-.... ..+..+|
T Consensus 3 ~eiRC~~Cnkl---La~~g-~~~~leIKCpRC~tiN~~~a~~~~~~p 45 (51)
T PF10122_consen 3 KEIRCGHCNKL---LAKAG-EVIELEIKCPRCKTINHVRATSPEPEP 45 (51)
T ss_pred cceeccchhHH---Hhhhc-CccEEEEECCCCCccceEeccCCCCCc
Confidence 46889999972 11110 1224689999999876654 4444444
No 166
>MTH00038 COX2 cytochrome c oxidase subunit II; Provisional
Probab=55.85 E-value=11 Score=28.37 Aligned_cols=50 Identities=14% Similarity=0.270 Sum_probs=34.4
Q ss_pred CCCCeEEEEeecCCceEEEEcCc-cCCeeE-eecCCCCcchhhhhhHHHHHHh
Q 034528 29 NHGTSVECRIDMKNLIGEAICNI-CQESFS-TTITALTEPIDIYSEWIDECER 79 (92)
Q Consensus 29 ~~~~sV~vkidk~~~~g~l~C~~-Cg~~~~-~~i~~L~epVDVYs~WiD~~~~ 79 (92)
|..+.+....++ .|+....|.. ||..+. |++.--..+-|.|.+|+++..|
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 444556655543 5777899998 999775 4655544567889999976543
No 167
>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=55.52 E-value=5.5 Score=28.46 Aligned_cols=11 Identities=36% Similarity=1.050 Sum_probs=9.1
Q ss_pred CccccCCCCCC
Q 034528 20 DTVFSCPFCNH 30 (92)
Q Consensus 20 ~~~F~CPfC~~ 30 (92)
+.-|.||.||.
T Consensus 126 ~~~F~Cp~Cg~ 136 (158)
T TIGR00373 126 ELNFTCPRCGA 136 (158)
T ss_pred HcCCcCCCCCC
Confidence 45799999997
No 168
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.07 E-value=3.2 Score=30.25 Aligned_cols=46 Identities=20% Similarity=0.443 Sum_probs=27.0
Q ss_pred CccccCCCCCCCCeEEEEee--cCCceE-----EEEcCccCCeeEeecCCCCcch
Q 034528 20 DTVFSCPFCNHGTSVECRID--MKNLIG-----EAICNICQESFSTTITALTEPI 67 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkid--k~~~~g-----~l~C~~Cg~~~~~~i~~L~epV 67 (92)
.|+-+||.|+.. +.=..- --.+.| --.|.+||.+|-..-..|..++
T Consensus 37 ati~qcp~csas--irgd~~vegvlglg~dye~psfchncgs~fpwterkiaga~ 89 (160)
T COG4306 37 ATITQCPICSAS--IRGDYYVEGVLGLGGDYEPPSFCHNCGSRFPWTERKIAGAV 89 (160)
T ss_pred HHHhcCCccCCc--ccccceeeeeeccCCCCCCcchhhcCCCCCCcHHHHHhHHH
Confidence 467899999973 211110 011112 2479999999987655555443
No 169
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=54.91 E-value=11 Score=30.65 Aligned_cols=30 Identities=27% Similarity=0.315 Sum_probs=20.6
Q ss_pred cccCCCCCCCC-eEEEEeecCCceEEEEcCccCCe
Q 034528 22 VFSCPFCNHGT-SVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 22 ~F~CPfC~~~~-sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
..-||||+... |..|.. . .+.-.|-.||..
T Consensus 34 ~~~CPfh~ek~pSf~v~~--~--k~~~~Cf~Cg~~ 64 (415)
T TIGR01391 34 VGLCPFHHEKTPSFSVSP--E--KQFYHCFGCGAG 64 (415)
T ss_pred EeeCCCCCCCCCeEEEEc--C--CCcEEECCCCCC
Confidence 45799998643 455543 3 356899999985
No 170
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=54.76 E-value=21 Score=24.72 Aligned_cols=41 Identities=12% Similarity=0.155 Sum_probs=28.3
Q ss_pred ccccCCCCCCC--CeEEEEeecCCceEEEEcCccCCeeEeecC
Q 034528 21 TVFSCPFCNHG--TSVECRIDMKNLIGEAICNICQESFSTTIT 61 (92)
Q Consensus 21 ~~F~CPfC~~~--~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~ 61 (92)
+.+-|+.|+.. --+.+.+-...+.-.++|..||...-+++.
T Consensus 55 KR~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~p~~ 97 (105)
T COG2023 55 KRTICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRYPYG 97 (105)
T ss_pred HHHhccccCcccccCcceEEEEcCCeEEEEecCCCcEEEeccc
Confidence 56789999982 223444444555689999999987666554
No 171
>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=54.68 E-value=8.5 Score=23.76 Aligned_cols=22 Identities=27% Similarity=0.723 Sum_probs=14.5
Q ss_pred CCCccccCCCCCCCCeEEEEeecC
Q 034528 18 KLDTVFSCPFCNHGTSVECRIDMK 41 (92)
Q Consensus 18 kl~~~F~CPfC~~~~sV~vkidk~ 41 (92)
+-|....||+||+. +.=.+..+
T Consensus 3 ~~p~~~~CP~C~~~--~~T~v~~~ 24 (73)
T PF10601_consen 3 PEPVRIYCPYCQQQ--VQTRVEYK 24 (73)
T ss_pred CCceeeECCCCCCE--EEEEEEEE
Confidence 34678899999973 44444443
No 172
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=54.34 E-value=5.3 Score=32.48 Aligned_cols=13 Identities=38% Similarity=0.846 Sum_probs=11.0
Q ss_pred CccccCCCCCCCC
Q 034528 20 DTVFSCPFCNHGT 32 (92)
Q Consensus 20 ~~~F~CPfC~~~~ 32 (92)
...|-||||||-+
T Consensus 240 yi~F~C~~Cn~LN 252 (328)
T KOG2846|consen 240 YITFRCPHCNALN 252 (328)
T ss_pred ceEEECccccccC
Confidence 5789999999854
No 173
>PRK04023 DNA polymerase II large subunit; Validated
Probab=54.31 E-value=11 Score=35.13 Aligned_cols=23 Identities=13% Similarity=0.102 Sum_probs=17.1
Q ss_pred CCCcchhhhhhHHHHHHhhcCcc
Q 034528 62 ALTEPIDIYSEWIDECERVNNLE 84 (92)
Q Consensus 62 ~L~epVDVYs~WiD~~~~~n~~~ 84 (92)
.-..-||+=..|-++.+......
T Consensus 676 ~s~~~i~l~~~~~~A~~~lg~~~ 698 (1121)
T PRK04023 676 YSKRKIDLKELYDRALENLGERK 698 (1121)
T ss_pred cceEEecHHHHHHHHHHHhCCcC
Confidence 34467899999999998877433
No 174
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=53.98 E-value=8.1 Score=30.91 Aligned_cols=57 Identities=16% Similarity=0.485 Sum_probs=40.3
Q ss_pred CccccCCCCCCCCeEE----------EEeecC--CceEEEEcCccCCeeEe----ecCCCCcchhhhhh-HHHH
Q 034528 20 DTVFSCPFCNHGTSVE----------CRIDMK--NLIGEAICNICQESFST----TITALTEPIDIYSE-WIDE 76 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~----------vkidk~--~~~g~l~C~~Cg~~~~~----~i~~L~epVDVYs~-WiD~ 76 (92)
...|.||.=|++.+=. |.+.-. ..+..-+|-+||+-|+. -||+-.|-+|+|.. |-+.
T Consensus 109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeikas~C~~C~a~y~~~dvIvlNg~~E~~dllk~rme~~ 182 (293)
T KOG3113|consen 109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIKASVCHVCGAAYQEDDVIVLNGTEEDVDLLKTRMEER 182 (293)
T ss_pred cceeecccccceecceEEEEEEeccceeccHHHHHHhhhccccccCCcccccCeEeeCCCHHHHHHHHHHHHHH
Confidence 4689999988765422 222211 34567789999999985 58999999999985 4443
No 175
>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=53.85 E-value=30 Score=27.93 Aligned_cols=37 Identities=22% Similarity=0.319 Sum_probs=27.0
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecC
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTIT 61 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~ 61 (92)
-||.||--.+..+.+|-..+.-.-.|. ||-.-++.|.
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 499999654444467777776777895 9988888774
No 176
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=53.80 E-value=19 Score=26.70 Aligned_cols=66 Identities=12% Similarity=0.206 Sum_probs=45.6
Q ss_pred CCCCCCCCccccCCCCCCCCeEEEEeec---CCceEEEEcCccCCeeEee-cCCCCcchhhhhhHHHHHHhhc
Q 034528 13 KKRVDKLDTVFSCPFCNHGTSVECRIDM---KNLIGEAICNICQESFSTT-ITALTEPIDIYSEWIDECERVN 81 (92)
Q Consensus 13 kk~~~kl~~~F~CPfC~~~~sV~vkidk---~~~~g~l~C~~Cg~~~~~~-i~~L~epVDVYs~WiD~~~~~n 81 (92)
+..++.+.-.|+|-.||.-.+ =.|.+ ..|+-++.|.-|....-.- =-.|+..+|+|. =|+.+..++
T Consensus 70 ~~~kp~m~l~yTCkvCntRs~--ktisk~AY~~GvVivqC~gC~~~HliaDnL~~F~d~~~~~-nied~l~~k 139 (165)
T KOG3277|consen 70 KVPKPRMQLAYTCKVCNTRST--KTISKQAYEKGVVIVQCPGCKNHHLIADNLGWFHDLKGKR-NIEDILAAK 139 (165)
T ss_pred cCCCcceEEEEEeeccCCccc--cccChhhhhCceEEEECCCCccceeehhhhcccccccccc-cHHHHHHhc
Confidence 344677888999999998665 33444 3789999999999877652 123556678886 355555544
No 177
>PHA02611 51 baseplate hub assembly protein; Provisional
Probab=53.64 E-value=9.9 Score=29.85 Aligned_cols=25 Identities=24% Similarity=0.626 Sum_probs=20.3
Q ss_pred CCCCccccCCCCCCCCeEEEEeecC
Q 034528 17 DKLDTVFSCPFCNHGTSVECRIDMK 41 (92)
Q Consensus 17 ~kl~~~F~CPfC~~~~sV~vkidk~ 41 (92)
.+.|..|.||-||+++.|...+++.
T Consensus 77 ~~v~~~~tCp~Cg~e~~v~~~l~~~ 101 (249)
T PHA02611 77 TKIPVTFTCPKCKKEKTVLFNLKQE 101 (249)
T ss_pred ceeeEEEECCCCCCceeEEEEeehh
Confidence 4568899999999998788777554
No 178
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=53.57 E-value=3.7 Score=21.71 Aligned_cols=7 Identities=43% Similarity=1.540 Sum_probs=3.4
Q ss_pred cCCCCCC
Q 034528 24 SCPFCNH 30 (92)
Q Consensus 24 ~CPfC~~ 30 (92)
.||.||+
T Consensus 1 ~CP~C~s 7 (28)
T PF03119_consen 1 TCPVCGS 7 (28)
T ss_dssp B-TTT--
T ss_pred CcCCCCC
Confidence 5999997
No 179
>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=53.50 E-value=11 Score=31.56 Aligned_cols=30 Identities=23% Similarity=0.568 Sum_probs=17.7
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFS 57 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~ 57 (92)
.+.||+|+.. .+.-+. .+.+.|.-||.+..
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 4567777742 233233 34788888886543
No 180
>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=53.40 E-value=6.9 Score=22.53 Aligned_cols=34 Identities=21% Similarity=0.291 Sum_probs=15.7
Q ss_pred ccccCCC--CCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 21 TVFSCPF--CNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 21 ~~F~CPf--C~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
..-.||. |+.. +.++.......+.|..|+..|-+
T Consensus 17 ~~~~Cp~~~C~~~----~~~~~~~~~~~~~C~~C~~~fC~ 52 (64)
T PF01485_consen 17 NIRWCPNPDCEYI----IEKDDGCNSPIVTCPSCGTEFCF 52 (64)
T ss_dssp -CC--TTSST-------ECS-SSTTS--CCTTSCCSEECS
T ss_pred CccCCCCCCCccc----EEecCCCCCCeeECCCCCCcCcc
Confidence 4458988 8862 23333333336889888887754
No 181
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=53.02 E-value=5.5 Score=33.23 Aligned_cols=31 Identities=19% Similarity=0.349 Sum_probs=20.5
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQE 54 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~ 54 (92)
-.|.||.||.+...+.+= ...... .|.-||.
T Consensus 326 ~~~~c~~~~~e~~~t~~~--~~~~~~-~~~~~~~ 356 (411)
T COG1503 326 VTYKCPTCGYENLKSKRE--FEQKRF-RCPECGS 356 (411)
T ss_pred eeecCCCcchhhhhcccc--cccccc-cCccccc
Confidence 379999999975433322 222234 9999998
No 182
>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=52.07 E-value=14 Score=20.76 Aligned_cols=30 Identities=17% Similarity=0.485 Sum_probs=22.0
Q ss_pred CCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCC
Q 034528 25 CPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITAL 63 (92)
Q Consensus 25 CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L 63 (92)
|++|+. .......|.|..|+..|-..--.+
T Consensus 2 C~vC~~---------~~~~~~~i~C~~C~~~~H~~C~~~ 31 (51)
T PF00628_consen 2 CPVCGQ---------SDDDGDMIQCDSCNRWYHQECVGP 31 (51)
T ss_dssp BTTTTS---------SCTTSSEEEBSTTSCEEETTTSTS
T ss_pred CcCCCC---------cCCCCCeEEcCCCChhhCcccCCC
Confidence 788886 234557899999999998754333
No 183
>PHA02942 putative transposase; Provisional
Probab=52.02 E-value=13 Score=30.14 Aligned_cols=51 Identities=14% Similarity=0.180 Sum_probs=33.3
Q ss_pred CccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhh
Q 034528 20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERV 80 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~ 80 (92)
-|.=.||.|||... ......-.|..||....--+| .++.++..+++.+.-+
T Consensus 323 yTSq~Cs~CG~~~~-------~l~~r~f~C~~CG~~~drD~n---AA~NI~~rg~~~~~~~ 373 (383)
T PHA02942 323 YSSVSCPKCGHKMV-------EIAHRYFHCPSCGYENDRDVI---AIMNLNGRGSLTLSTA 373 (383)
T ss_pred CCCccCCCCCCccC-------cCCCCEEECCCCCCEeCcHHH---HHHHHHHHHHHHhccC
Confidence 36667999999531 122347899999987655444 4567777776655443
No 184
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=51.95 E-value=14 Score=35.58 Aligned_cols=49 Identities=18% Similarity=0.367 Sum_probs=35.9
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhhcC
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERVNN 82 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~n~ 82 (92)
-.|.||.||+.. -...|..||..-+. -++-...||+=..|-+|.+....
T Consensus 673 ~~~~Cp~Cg~~~------------~~~~Cp~CG~~~~~-~~~~~~~i~~~~~~~~A~~~v~~ 721 (1627)
T PRK14715 673 AFFKCPKCGKVG------------LYHVCPFCGTRVEL-KPYARREIPPKDYWYAALENLKI 721 (1627)
T ss_pred EeeeCCCCCCcc------------ccccCcccCCcccC-CCccceecCHHHHHHHHHHHhCC
Confidence 358899999842 35689999987332 23344689999999999988763
No 185
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=51.63 E-value=5.7 Score=26.98 Aligned_cols=30 Identities=17% Similarity=0.276 Sum_probs=18.4
Q ss_pred CCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528 17 DKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQE 54 (92)
Q Consensus 17 ~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~ 54 (92)
..+|-.+.|+.||++-.+ . . ....|..||.
T Consensus 65 ~~vp~~~~C~~Cg~~~~~--~----~--~~~~CP~Cgs 94 (113)
T PRK12380 65 VYKPAQAWCWDCSQVVEI--H----Q--HDAQCPHCHG 94 (113)
T ss_pred EeeCcEEEcccCCCEEec--C----C--cCccCcCCCC
Confidence 456778889999864221 1 1 2234888884
No 186
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=51.39 E-value=7.3 Score=31.07 Aligned_cols=35 Identities=29% Similarity=0.636 Sum_probs=22.5
Q ss_pred CccccCCCCCCCCeEEEEeecC-----CceEEEEcCccCCeeE
Q 034528 20 DTVFSCPFCNHGTSVECRIDMK-----NLIGEAICNICQESFS 57 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~-----~~~g~l~C~~Cg~~~~ 57 (92)
.+.|.|+.|+. +-|.|--. ...---.|.+||..|.
T Consensus 159 ~ka~~C~~C~K---~YvSmpALkMHirTH~l~c~C~iCGKaFS 198 (279)
T KOG2462|consen 159 KKAFSCKYCGK---VYVSMPALKMHIRTHTLPCECGICGKAFS 198 (279)
T ss_pred cccccCCCCCc---eeeehHHHhhHhhccCCCccccccccccc
Confidence 46788888886 55555221 2223467888988876
No 187
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=51.05 E-value=7.2 Score=28.54 Aligned_cols=9 Identities=44% Similarity=1.198 Sum_probs=4.8
Q ss_pred ccccCCCCC
Q 034528 21 TVFSCPFCN 29 (92)
Q Consensus 21 ~~F~CPfC~ 29 (92)
..|.||.|+
T Consensus 116 ~~Y~Cp~C~ 124 (178)
T PRK06266 116 MFFFCPNCH 124 (178)
T ss_pred CEEECCCCC
Confidence 355555554
No 188
>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=50.57 E-value=5 Score=22.36 Aligned_cols=26 Identities=15% Similarity=0.565 Sum_probs=18.5
Q ss_pred EcCccCCeeEeecCCCCcchhhhhhH
Q 034528 48 ICNICQESFSTTITALTEPIDIYSEW 73 (92)
Q Consensus 48 ~C~~Cg~~~~~~i~~L~epVDVYs~W 73 (92)
.|+.|.-+..+-...=-+|||||.+|
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 46677776655555557899999876
No 189
>PHA00616 hypothetical protein
Probab=50.51 E-value=5.6 Score=23.46 Aligned_cols=9 Identities=22% Similarity=0.866 Sum_probs=6.5
Q ss_pred cccCCCCCC
Q 034528 22 VFSCPFCNH 30 (92)
Q Consensus 22 ~F~CPfC~~ 30 (92)
.|+||.||.
T Consensus 1 pYqC~~CG~ 9 (44)
T PHA00616 1 MYQCLRCGG 9 (44)
T ss_pred CCccchhhH
Confidence 377888874
No 190
>PRK04011 peptide chain release factor 1; Provisional
Probab=50.06 E-value=19 Score=29.53 Aligned_cols=53 Identities=21% Similarity=0.434 Sum_probs=35.8
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhhc
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERVN 81 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~n 81 (92)
.|.||.||+.....++- ....-.-.|..||...+. .+..|.+-.+++.+++.+
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 68899999875444443 333444689999975332 355678888888887755
No 191
>PRK05667 dnaG DNA primase; Validated
Probab=49.95 E-value=15 Score=31.50 Aligned_cols=30 Identities=23% Similarity=0.258 Sum_probs=20.9
Q ss_pred cccCCCCCCCC-eEEEEeecCCceEEEEcCccCCe
Q 034528 22 VFSCPFCNHGT-SVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 22 ~F~CPfC~~~~-sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
..-||||+... |.+|.. . .+.-.|-.||..
T Consensus 36 ~~~CPfH~ektpSf~V~~--~--k~~~~CF~Cg~~ 66 (580)
T PRK05667 36 KGLCPFHDEKTPSFTVSP--D--KQFYHCFGCGAG 66 (580)
T ss_pred eecCCCCCCCCCceEEEC--C--CCeEEECCCCCC
Confidence 45799999543 555543 3 357899999984
No 192
>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=49.85 E-value=7.1 Score=21.34 Aligned_cols=11 Identities=27% Similarity=0.791 Sum_probs=8.5
Q ss_pred ccCCCCCCCCe
Q 034528 23 FSCPFCNHGTS 33 (92)
Q Consensus 23 F~CPfC~~~~s 33 (92)
-.||.||+.++
T Consensus 19 ~~CP~Cg~~~~ 29 (34)
T cd00729 19 EKCPICGAPKE 29 (34)
T ss_pred CcCcCCCCchH
Confidence 38999998653
No 193
>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=49.27 E-value=7.2 Score=21.61 Aligned_cols=10 Identities=30% Similarity=0.926 Sum_probs=6.8
Q ss_pred ccccCCCCCC
Q 034528 21 TVFSCPFCNH 30 (92)
Q Consensus 21 ~~F~CPfC~~ 30 (92)
..|.||.|+.
T Consensus 3 ~~~~C~nC~R 12 (33)
T PF08209_consen 3 PYVECPNCGR 12 (33)
T ss_dssp -EEE-TTTSS
T ss_pred CeEECCCCcC
Confidence 4689999986
No 194
>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=49.10 E-value=11 Score=20.02 Aligned_cols=26 Identities=19% Similarity=0.241 Sum_probs=11.3
Q ss_pred CCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528 25 CPFCNHGTSVECRIDMKNLIGEAICNICQESF 56 (92)
Q Consensus 25 CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~ 56 (92)
||.||.+. + . ..+--...|..||..+
T Consensus 6 C~~CG~~t-~--~---~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 6 CGRCGAPT-K--P---APGGWARRCPSCGHEH 31 (32)
T ss_dssp -TTT--BE-E--E----SSSS-EEESSSS-EE
T ss_pred cCcCCccc-c--C---CCCcCEeECCCCcCEe
Confidence 88888742 1 1 1222346788888653
No 195
>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 COG5216 Uncharacterized conserved protein [Function unknown]
Probab=48.60 E-value=19 Score=23.02 Aligned_cols=31 Identities=26% Similarity=0.557 Sum_probs=22.4
Q ss_pred cccCCCCCCCCeEEEEeec-CCceEEEEcCccCCe
Q 034528 22 VFSCPFCNHGTSVECRIDM-KNLIGEAICNICQES 55 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk-~~~~g~l~C~~Cg~~ 55 (92)
+|.|| ||. -.++.++. .+|--.+.|..|.+-
T Consensus 22 tyPCP-CGD--RFeIsLeDl~~GE~VArCPSCSLi 53 (67)
T COG5216 22 TYPCP-CGD--RFEISLEDLRNGEVVARCPSCSLI 53 (67)
T ss_pred EecCC-CCC--EeEEEHHHhhCCceEEEcCCceEE
Confidence 46787 774 47777743 567778899999874
No 197
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=48.18 E-value=6.9 Score=22.97 Aligned_cols=8 Identities=50% Similarity=1.555 Sum_probs=4.5
Q ss_pred ccCCCCCC
Q 034528 23 FSCPFCNH 30 (92)
Q Consensus 23 F~CPfC~~ 30 (92)
+.||.|||
T Consensus 29 W~C~~Cgh 36 (55)
T PF14311_consen 29 WKCPKCGH 36 (55)
T ss_pred EECCCCCC
Confidence 55555555
No 198
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=48.05 E-value=22 Score=24.58 Aligned_cols=33 Identities=18% Similarity=0.445 Sum_probs=25.2
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFS 57 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~ 57 (92)
.+.|.-|+... ....+...+....|+.||..+.
T Consensus 112 ~y~C~~C~~~~---~~~rr~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 112 PYRCTGCGQRY---LRVRRSNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEECCCCCCCC---ceEccccCcceEEcCCCCCEEE
Confidence 78999999743 2455556679999999998764
No 199
>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=47.52 E-value=12 Score=30.12 Aligned_cols=39 Identities=13% Similarity=0.233 Sum_probs=27.0
Q ss_pred eEEEEcCccCCeeEee-cCCCCcchhhhhhHHHHHHhhcC
Q 034528 44 IGEAICNICQESFSTT-ITALTEPIDIYSEWIDECERVNN 82 (92)
Q Consensus 44 ~g~l~C~~Cg~~~~~~-i~~L~epVDVYs~WiD~~~~~n~ 82 (92)
+-...|..||..-+.+ ...+.=++.-|.+|+.+..+.+.
T Consensus 164 l~~p~~~~~g~~~~~r~e~~~ff~L~~~~~~L~~~l~~~~ 203 (391)
T PF09334_consen 164 LINPVCKICGSPPEVREEENYFFKLSKFRDQLREWLESNP 203 (391)
T ss_dssp SECEEETTTS-B-EEEEEEEEEE-GGGGHHHHHHHHHHST
T ss_pred ccCCccccccccCccccceEEEEehHHhHHHHHHHHhcCC
Confidence 3456888888776664 66777778889999988887774
No 200
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.27 E-value=19 Score=25.43 Aligned_cols=24 Identities=25% Similarity=0.787 Sum_probs=18.4
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
.-.||.||.+ --+-.+.|.+|+.+
T Consensus 6 ~~~cPvcg~~----------~iVTeL~c~~~etT 29 (122)
T COG3877 6 INRCPVCGRK----------LIVTELKCSNCETT 29 (122)
T ss_pred CCCCCccccc----------ceeEEEecCCCCce
Confidence 3469999974 33567999999986
No 201
>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=45.99 E-value=6.7 Score=19.38 Aligned_cols=12 Identities=33% Similarity=0.830 Sum_probs=8.4
Q ss_pred EEcCccCCeeEe
Q 034528 47 AICNICQESFST 58 (92)
Q Consensus 47 l~C~~Cg~~~~~ 58 (92)
..|..|+..|.+
T Consensus 2 ~~C~~C~~~F~~ 13 (27)
T PF13912_consen 2 FECDECGKTFSS 13 (27)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCccCCccCC
Confidence 367888887754
No 202
>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=45.91 E-value=16 Score=22.24 Aligned_cols=28 Identities=25% Similarity=0.331 Sum_probs=23.4
Q ss_pred EcCccCCeeEeecCCCCcchhhhhhHHH
Q 034528 48 ICNICQESFSTTITALTEPIDIYSEWID 75 (92)
Q Consensus 48 ~C~~Cg~~~~~~i~~L~epVDVYs~WiD 75 (92)
.|..||..-...-++-+.|-|-|++.-=
T Consensus 19 ~cp~cG~~T~~ahPaRFSPdDky~~yRi 46 (53)
T PF04135_consen 19 KCPPCGGPTESAHPARFSPDDKYSKYRI 46 (53)
T ss_dssp BBTTTSSBSEESSSSSS-TTTTTCHHHH
T ss_pred ccCCCCCCCcCCcCCCCCCCCccHHHHH
Confidence 4999999888899999999999998643
No 203
>PHA00732 hypothetical protein
Probab=45.25 E-value=2.6 Score=27.21 Aligned_cols=48 Identities=21% Similarity=0.465 Sum_probs=25.3
Q ss_pred cccCCCCCCCCeEEEEeecCCc--eEEEEcCccCCeeEeecCCCCcchhh
Q 034528 22 VFSCPFCNHGTSVECRIDMKNL--IGEAICNICQESFSTTITALTEPIDI 69 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~--~g~l~C~~Cg~~~~~~i~~L~epVDV 69 (92)
.|.|+.|+..-+-.-.+..-.. -..-.|..||.+|.........--|+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~~l~~H~~~~~~~ 50 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYRRLNQHFYSQYDI 50 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeCChhhhhcccCCc
Confidence 3789999864221111110000 00127999999998655555444443
No 204
>KOG3456 consensus NADH:ubiquinone oxidoreductase, NDUFS6/13 kDa subunit [Energy production and conversion]
Probab=44.90 E-value=13 Score=26.18 Aligned_cols=26 Identities=27% Similarity=0.447 Sum_probs=19.6
Q ss_pred CCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528 28 CNHGTSVECRIDMKNLIGEAICNICQESFS 57 (92)
Q Consensus 28 C~~~~sV~vkidk~~~~g~l~C~~Cg~~~~ 57 (92)
=||++ |-|.+|+... ..|+-||++|-
T Consensus 90 LGHPk-vyInLDk~~~---~~CgYCGlrf~ 115 (120)
T KOG3456|consen 90 LGHPK-VYINLDKPGP---HICGYCGLRFV 115 (120)
T ss_pred CCCCe-EEEEcCCCCC---cccccchhhhh
Confidence 36765 7788877643 78999999884
No 205
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=44.83 E-value=8.8 Score=24.32 Aligned_cols=13 Identities=23% Similarity=0.695 Sum_probs=10.5
Q ss_pred CCCccccCCCCCC
Q 034528 18 KLDTVFSCPFCNH 30 (92)
Q Consensus 18 kl~~~F~CPfC~~ 30 (92)
-=+..|.||.|+.
T Consensus 13 DGE~~lrCPRC~~ 25 (65)
T COG4049 13 DGEEFLRCPRCGM 25 (65)
T ss_pred CCceeeeCCchhH
Confidence 4468899999985
No 206
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=44.79 E-value=23 Score=24.87 Aligned_cols=48 Identities=21% Similarity=0.307 Sum_probs=36.8
Q ss_pred CCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe-----ecCCCCcchhhhhhHH
Q 034528 25 CPFCNHGTSVECRIDMKNLIGEAICNICQESFST-----TITALTEPIDIYSEWI 74 (92)
Q Consensus 25 CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~-----~i~~L~epVDVYs~Wi 74 (92)
|+-||+ -+--+=|+.+.+=.++|++|.-.++- .+|+|+-.+|=..--|
T Consensus 7 C~eCNN--mLYPkEDked~~L~laCrnCd~ve~A~s~~vY~~~~~~e~dE~t~ii 59 (113)
T KOG2691|consen 7 CRECNN--MLYPKEDKEDRILLLACRNCDYVEEADSSRVYVNELSHEHDELTQII 59 (113)
T ss_pred hhhhhc--cccccccccccEEEEEecCCcceEecCCcceEcCCcccchhhHHHHH
Confidence 888986 46666688889999999999976653 5888888887655544
No 207
>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=44.69 E-value=20 Score=27.13 Aligned_cols=47 Identities=13% Similarity=0.230 Sum_probs=32.9
Q ss_pred CCCCeEEEEeecCCceEEEEcCc-cCCeeE-eecCCCCcchhhhhhHHHH
Q 034528 29 NHGTSVECRIDMKNLIGEAICNI-CQESFS-TTITALTEPIDIYSEWIDE 76 (92)
Q Consensus 29 ~~~~sV~vkidk~~~~g~l~C~~-Cg~~~~-~~i~~L~epVDVYs~WiD~ 76 (92)
|+.+.+..+.++ .|.....|.. ||..+. |.+.-.-.+-|-|.+|+++
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 455566666654 5678899998 999764 4544444456899999975
No 208
>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=43.77 E-value=8.5 Score=26.14 Aligned_cols=29 Identities=17% Similarity=0.319 Sum_probs=17.6
Q ss_pred CCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528 18 KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQE 54 (92)
Q Consensus 18 kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~ 54 (92)
.+|-.+.|+.||+.- .+.- ....|..||.
T Consensus 66 ~~p~~~~C~~Cg~~~--~~~~------~~~~CP~Cgs 94 (115)
T TIGR00100 66 DEPVECECEDCSEEV--SPEI------DLYRCPKCHG 94 (115)
T ss_pred eeCcEEEcccCCCEE--ecCC------cCccCcCCcC
Confidence 456678888888642 2211 1356888885
No 209
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=43.77 E-value=10 Score=31.78 Aligned_cols=29 Identities=24% Similarity=0.478 Sum_probs=20.7
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT 59 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~ 59 (92)
-||+||. .|..+... -..|..||.++.+.
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 5999996 34444333 68999999987653
No 210
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.42 E-value=7.9 Score=27.63 Aligned_cols=31 Identities=23% Similarity=0.441 Sum_probs=20.0
Q ss_pred ccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
=.||.||.-+ +.+---.-.-.|..||+.|..
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 3699999643 333222334579999998753
No 211
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=43.32 E-value=14 Score=22.84 Aligned_cols=15 Identities=27% Similarity=0.496 Sum_probs=12.0
Q ss_pred CCCCccccCCCCCCC
Q 034528 17 DKLDTVFSCPFCNHG 31 (92)
Q Consensus 17 ~kl~~~F~CPfC~~~ 31 (92)
.+..-.|+||.||-.
T Consensus 9 ~~~~v~~~Cp~cGip 23 (55)
T PF13824_consen 9 LPAHVNFECPDCGIP 23 (55)
T ss_pred cccccCCcCCCCCCc
Confidence 366788999999964
No 212
>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=43.30 E-value=46 Score=28.27 Aligned_cols=36 Identities=25% Similarity=0.350 Sum_probs=26.1
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecC
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTIT 61 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~ 61 (92)
-||.||...+-.+..|-.. .-.-.|. ||-..++.|.
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 4999999877556666555 3445785 9998888774
No 213
>MTH00129 COX2 cytochrome c oxidase subunit II; Provisional
Probab=43.22 E-value=23 Score=26.77 Aligned_cols=49 Identities=12% Similarity=0.184 Sum_probs=33.5
Q ss_pred CCCCeEEEEeecCCceEEEEcCc-cCCeeE-eecCCCCcchhhhhhHHHHHH
Q 034528 29 NHGTSVECRIDMKNLIGEAICNI-CQESFS-TTITALTEPIDIYSEWIDECE 78 (92)
Q Consensus 29 ~~~~sV~vkidk~~~~g~l~C~~-Cg~~~~-~~i~~L~epVDVYs~WiD~~~ 78 (92)
|..+.+....++ .|+....|.. ||..+. |++.-...+.+.|.+|+..-.
T Consensus 177 G~~~~~~~~~~~-~G~~~g~C~e~CG~~H~~M~~~v~vv~~~~f~~Wl~~~~ 227 (230)
T MTH00129 177 GRLNQTAFIASR-PGVFYGQCSEICGANHSFMPIVVEAVPLEHFENWSSLML 227 (230)
T ss_pred CceEEEEEEeCC-ceEEEEEChhhccccccCCcEEEEEECHHHHHHHHHHhh
Confidence 444555555543 4667788988 998765 466655567799999986543
No 214
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=42.97 E-value=19 Score=21.60 Aligned_cols=16 Identities=25% Similarity=0.453 Sum_probs=13.1
Q ss_pred EEEcCccCCeeEeecC
Q 034528 46 EAICNICQESFSTTIT 61 (92)
Q Consensus 46 ~l~C~~Cg~~~~~~i~ 61 (92)
.|.|..||..|.+...
T Consensus 4 ~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 4 TLTCKDCGAEFVFTAG 19 (49)
T ss_pred eEEcccCCCeEEEehh
Confidence 5899999999887654
No 215
>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=42.54 E-value=12 Score=26.74 Aligned_cols=36 Identities=19% Similarity=0.182 Sum_probs=24.6
Q ss_pred CCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee
Q 034528 17 DKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT 59 (92)
Q Consensus 17 ~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~ 59 (92)
+-|=|-..||.||.. + -..+.--+.|-.||..|...
T Consensus 4 ~elGtKr~Cp~cg~k------F-YDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 4 PDLGTKRICPNTGSK------F-YDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred hhhCccccCCCcCcc------c-cccCCCCccCCCcCCccCcc
Confidence 456677889999962 2 12334668899999887543
No 216
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.38 E-value=10 Score=29.98 Aligned_cols=11 Identities=36% Similarity=1.090 Sum_probs=9.5
Q ss_pred CccccCCCCCC
Q 034528 20 DTVFSCPFCNH 30 (92)
Q Consensus 20 ~~~F~CPfC~~ 30 (92)
.+.|+||+||.
T Consensus 17 kk~ieCPvC~t 27 (267)
T COG1655 17 KKTIECPVCNT 27 (267)
T ss_pred hceeccCcccc
Confidence 57899999995
No 217
>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=42.11 E-value=62 Score=18.20 Aligned_cols=27 Identities=26% Similarity=0.359 Sum_probs=17.5
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCc
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNI 51 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~ 51 (92)
-||-||- ..+.-..+.+..|-...|.+
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 5999996 55666667787788888876
No 218
>MTH00080 COX2 cytochrome c oxidase subunit II; Provisional
Probab=41.80 E-value=26 Score=26.69 Aligned_cols=48 Identities=17% Similarity=0.231 Sum_probs=34.8
Q ss_pred CCCCeEEEEeecCCceEEEEcCc-cCCeeE-eecCCCCcchhhhhhHHHHH
Q 034528 29 NHGTSVECRIDMKNLIGEAICNI-CQESFS-TTITALTEPIDIYSEWIDEC 77 (92)
Q Consensus 29 ~~~~sV~vkidk~~~~g~l~C~~-Cg~~~~-~~i~~L~epVDVYs~WiD~~ 77 (92)
|.-+.+....++ .|+-...|.. ||..+. |++.--..+-+-|.+|+..+
T Consensus 180 Gr~n~~~~~~~~-~G~y~g~CsE~CG~~Hs~M~~~v~vv~~~~f~~Wl~~~ 229 (231)
T MTH00080 180 GILSTLCYSFPM-PGVFYGQCSEICGANHSFMPIAVEVTLLDNFKEWCKLL 229 (231)
T ss_pred CceEEEEEEEcC-ceEEEEEehhhcCcCccCCEEEEEEECHHHHHHHHHHh
Confidence 455566666554 5778899987 999775 46665556778999999765
No 219
>PHA00733 hypothetical protein
Probab=40.56 E-value=4.5 Score=28.07 Aligned_cols=40 Identities=20% Similarity=0.490 Sum_probs=22.5
Q ss_pred CccccCCCCCCCCeEEEEeecCCc--eEEEEcCccCCeeEee
Q 034528 20 DTVFSCPFCNHGTSVECRIDMKNL--IGEAICNICQESFSTT 59 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~~~--~g~l~C~~Cg~~~~~~ 59 (92)
.+.|.|+.|+..-+-...+..-.. .....|.+|+..|...
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 467999999963211111111000 1246999999988653
No 220
>PF12773 DZR: Double zinc ribbon
Probab=40.14 E-value=9.5 Score=21.61 Aligned_cols=11 Identities=27% Similarity=0.718 Sum_probs=6.8
Q ss_pred EEEEcCccCCe
Q 034528 45 GEAICNICQES 55 (92)
Q Consensus 45 g~l~C~~Cg~~ 55 (92)
..+.|..||..
T Consensus 28 ~~~~C~~Cg~~ 38 (50)
T PF12773_consen 28 SKKICPNCGAE 38 (50)
T ss_pred CCCCCcCCcCC
Confidence 44567777763
No 221
>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=40.00 E-value=84 Score=19.25 Aligned_cols=33 Identities=24% Similarity=0.377 Sum_probs=20.7
Q ss_pred ccccCCCCCC----CCeEEEEeec---CCceEEEEcCccC
Q 034528 21 TVFSCPFCNH----GTSVECRIDM---KNLIGEAICNICQ 53 (92)
Q Consensus 21 ~~F~CPfC~~----~~sV~vkidk---~~~~g~l~C~~Cg 53 (92)
+..-|..|+. ..++++.|.+ ..+.-.+.|..||
T Consensus 45 kr~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~ 84 (85)
T PF04032_consen 45 KRTICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCG 84 (85)
T ss_dssp CCTB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTT
T ss_pred hcccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccC
Confidence 5667999997 2356777763 3567789999998
No 222
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=39.82 E-value=20 Score=19.85 Aligned_cols=11 Identities=27% Similarity=0.751 Sum_probs=8.7
Q ss_pred cccCCCCCCCC
Q 034528 22 VFSCPFCNHGT 32 (92)
Q Consensus 22 ~F~CPfC~~~~ 32 (92)
...||.||...
T Consensus 2 ~~~Cp~Cg~~~ 12 (47)
T PF14690_consen 2 PPRCPHCGSPS 12 (47)
T ss_pred CccCCCcCCCc
Confidence 46799999754
No 223
>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=39.67 E-value=62 Score=17.98 Aligned_cols=28 Identities=25% Similarity=0.483 Sum_probs=18.5
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCc---cCCe
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNI---CQES 55 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~---Cg~~ 55 (92)
.||-||+ .+..+..+.. -.+.|.. |.-.
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 3555554444 5688887 6643
No 224
>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=39.43 E-value=1e+02 Score=19.71 Aligned_cols=47 Identities=13% Similarity=0.169 Sum_probs=34.9
Q ss_pred ecCCceEEEEcCccCCeeEe-ecCCCCcchhhhhhHHHHHHhhcCcccc
Q 034528 39 DMKNLIGEAICNICQESFST-TITALTEPIDIYSEWIDECERVNNLEDD 86 (92)
Q Consensus 39 dk~~~~g~l~C~~Cg~~~~~-~i~~L~epVDVYs~WiD~~~~~n~~~~~ 86 (92)
|.......+.|.. |..|.. -.++.++|=+++..|+....-.+.+.+.
T Consensus 23 ~~~~~~l~lk~~t-~r~~yl~L~~~~~~~~~~F~~w~~lv~lL~~p~s~ 70 (77)
T PF12480_consen 23 DLEKQQLKLKLVT-GRPFYLQLCAPADKPETLFGEWIRLVSLLRPPLSA 70 (77)
T ss_pred cCcccEEEEEEcc-CCEEEEEEeCcccCcchhHHHHHHHHHHcCCCccc
Confidence 5556777888877 445555 4888999999999999988766655443
No 225
>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=39.37 E-value=27 Score=32.56 Aligned_cols=49 Identities=14% Similarity=0.304 Sum_probs=34.8
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhhcC
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERVNN 82 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~n~ 82 (92)
-.|.||-||+. .-...|..||..- ..+.+-..-||+=..|-+|.+....
T Consensus 624 ~~RKCPkCG~y------------Tlk~rCP~CG~~T-e~~~pc~~~i~l~~~~~~A~~~lg~ 672 (1095)
T TIGR00354 624 AIRKCPQCGKE------------SFWLKCPVCGELT-EQLYYGKRKVDLRELYEEAIANLGE 672 (1095)
T ss_pred EEEECCCCCcc------------cccccCCCCCCcc-ccccceeEEecHHHHHHHHHHHhCC
Confidence 35778888863 2345899999863 2334446789999999999988764
No 226
>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=39.36 E-value=12 Score=24.54 Aligned_cols=11 Identities=36% Similarity=1.111 Sum_probs=5.9
Q ss_pred ccccCCCCCCC
Q 034528 21 TVFSCPFCNHG 31 (92)
Q Consensus 21 ~~F~CPfC~~~ 31 (92)
..|.||.||+.
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 57999999973
No 227
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=39.34 E-value=23 Score=28.66 Aligned_cols=32 Identities=13% Similarity=0.218 Sum_probs=22.3
Q ss_pred CccccCCCCCCCCeEEEEeecC--CceEEEEcCc
Q 034528 20 DTVFSCPFCNHGTSVECRIDMK--NLIGEAICNI 51 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~--~~~g~l~C~~ 51 (92)
+..--||.||..-++++.++-. +|.-.++|..
T Consensus 183 e~~~~CPvCGS~PvaSmV~~g~~~~GlRYL~Csl 216 (308)
T COG3058 183 ESRQYCPVCGSMPVASMVQIGETEQGLRYLHCSL 216 (308)
T ss_pred cccccCCCcCCCCcceeeeecCccccchhhhhhh
Confidence 7788899999988888877652 3444444443
No 228
>MTH00117 COX2 cytochrome c oxidase subunit II; Provisional
Probab=39.24 E-value=28 Score=26.27 Aligned_cols=48 Identities=13% Similarity=0.194 Sum_probs=31.8
Q ss_pred CCCCeEEEEeecCCceEEEEcCc-cCCeeE-eecCCCCcchhhhhhHHHHH
Q 034528 29 NHGTSVECRIDMKNLIGEAICNI-CQESFS-TTITALTEPIDIYSEWIDEC 77 (92)
Q Consensus 29 ~~~~sV~vkidk~~~~g~l~C~~-Cg~~~~-~~i~~L~epVDVYs~WiD~~ 77 (92)
|.-+.+....++ .|+....|.. ||..+. |++.--..+.+-|..|++++
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 334455555544 4677788988 999765 45554445568899999763
No 229
>PRK14873 primosome assembly protein PriA; Provisional
Probab=38.97 E-value=23 Score=30.90 Aligned_cols=29 Identities=21% Similarity=0.413 Sum_probs=17.4
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
..+.||+|+.. ++. -+ ..+.+.|.-||..
T Consensus 391 ~~~~C~~C~~~--L~~--h~--~~~~l~Ch~CG~~ 419 (665)
T PRK14873 391 TPARCRHCTGP--LGL--PS--AGGTPRCRWCGRA 419 (665)
T ss_pred CeeECCCCCCc--eeE--ec--CCCeeECCCCcCC
Confidence 45778888753 322 22 2357888888864
No 230
>MTH00154 COX2 cytochrome c oxidase subunit II; Provisional
Probab=38.88 E-value=29 Score=26.19 Aligned_cols=47 Identities=15% Similarity=0.270 Sum_probs=33.5
Q ss_pred CCCCeEEEEeecCCceEEEEcCc-cCCeeE-eecCCCCcchhhhhhHHHH
Q 034528 29 NHGTSVECRIDMKNLIGEAICNI-CQESFS-TTITALTEPIDIYSEWIDE 76 (92)
Q Consensus 29 ~~~~sV~vkidk~~~~g~l~C~~-Cg~~~~-~~i~~L~epVDVYs~WiD~ 76 (92)
|..+.+....++ .|+....|.. ||..+. |++.-.-.+.+-|.+|+..
T Consensus 177 G~~~~~~~~~~~-~G~y~g~Cse~CG~~H~~M~~~v~vv~~~~f~~Wl~~ 225 (227)
T MTH00154 177 GRLNQLNFLINR-PGLFFGQCSEICGANHSFMPIVIESVSVNNFINWIKN 225 (227)
T ss_pred CceEEEEEEEcC-ceEEEEEeechhCcCccCCeEEEEEeCHHHHHHHHHh
Confidence 555566666654 5778899988 999765 4655555567889999854
No 231
>MTH00185 COX2 cytochrome c oxidase subunit II; Provisional
Probab=38.81 E-value=32 Score=26.10 Aligned_cols=47 Identities=15% Similarity=0.290 Sum_probs=32.0
Q ss_pred CeEEEEeecCCceEEEEcCc-cCCeeE-eecCCCCcchhhhhhHHHHHHh
Q 034528 32 TSVECRIDMKNLIGEAICNI-CQESFS-TTITALTEPIDIYSEWIDECER 79 (92)
Q Consensus 32 ~sV~vkidk~~~~g~l~C~~-Cg~~~~-~~i~~L~epVDVYs~WiD~~~~ 79 (92)
+.+....+ ..|+....|.. ||..+. |++.-...+-|.|..|+....|
T Consensus 180 ~~~~~~~~-~~G~~~g~Cse~CG~~Hs~M~~~v~vv~~~~f~~W~~~~~~ 228 (230)
T MTH00185 180 NQATFIIS-RPGLYYGQCSEICGANHSFMPIVVEAVPLEHFENWSSLMLE 228 (230)
T ss_pred EEEEEEeC-CcEEEEEEchhhcCcCcCCCeEEEEEECHHHHHHHHHHHHh
Confidence 34444433 24566788987 998765 4665555577899999987765
No 232
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=37.77 E-value=36 Score=32.53 Aligned_cols=25 Identities=20% Similarity=0.238 Sum_probs=18.6
Q ss_pred cCCCCcchhhhhhHHHHHHhhcCcc
Q 034528 60 ITALTEPIDIYSEWIDECERVNNLE 84 (92)
Q Consensus 60 i~~L~epVDVYs~WiD~~~~~n~~~ 84 (92)
+.+-..-||+=..|-+|.+......
T Consensus 720 v~~~~~~i~~~~~~~~A~~~~g~~~ 744 (1337)
T PRK14714 720 TPYQRRTINVKEEYRSALENVGERE 744 (1337)
T ss_pred cccceEEecHHHHHHHHHHHhCccc
Confidence 3444557899999999999887543
No 233
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=37.65 E-value=20 Score=20.33 Aligned_cols=15 Identities=20% Similarity=0.485 Sum_probs=11.4
Q ss_pred eEEEEcCccCCeeEe
Q 034528 44 IGEAICNICQESFST 58 (92)
Q Consensus 44 ~g~l~C~~Cg~~~~~ 58 (92)
.|.|.|+.||..+..
T Consensus 3 ~g~l~C~~CG~~m~~ 17 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTR 17 (58)
T ss_pred CCcEEcccCCcEeEE
Confidence 367889999977654
No 234
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=37.13 E-value=22 Score=24.44 Aligned_cols=9 Identities=33% Similarity=1.198 Sum_probs=7.2
Q ss_pred ccCCCCCCC
Q 034528 23 FSCPFCNHG 31 (92)
Q Consensus 23 F~CPfC~~~ 31 (92)
|.||.||..
T Consensus 93 ~~CP~Cgs~ 101 (124)
T PRK00762 93 IECPVCGNK 101 (124)
T ss_pred CcCcCCCCC
Confidence 689999963
No 235
>MTH00139 COX2 cytochrome c oxidase subunit II; Provisional
Probab=36.91 E-value=27 Score=26.20 Aligned_cols=47 Identities=21% Similarity=0.246 Sum_probs=32.2
Q ss_pred CCCCeEEEEeecCCceEEEEcCc-cCCeeE-eecCCCCcchhhhhhHHHH
Q 034528 29 NHGTSVECRIDMKNLIGEAICNI-CQESFS-TTITALTEPIDIYSEWIDE 76 (92)
Q Consensus 29 ~~~~sV~vkidk~~~~g~l~C~~-Cg~~~~-~~i~~L~epVDVYs~WiD~ 76 (92)
|+.+.+....++ .|+....|.. ||..+. |++.--..+-+.|..|+++
T Consensus 177 G~~n~~~~~~~~-~G~y~g~CsE~CG~~Hs~M~~~v~vv~~~~f~~Wl~~ 225 (226)
T MTH00139 177 GRLNQVGFFINR-PGVFYGQCSEICGANHSFMPIVVEAISPKFFLEWILE 225 (226)
T ss_pred CcEEEEEEEcCC-CEEEEEEChhhcCcCcCCCeEEEEEeCHHHHHHHHhh
Confidence 455555665543 5678899998 999765 4555444566899999864
No 236
>KOG3022 consensus Predicted ATPase, nucleotide-binding [Cell cycle control, cell division, chromosome partitioning]
Probab=36.50 E-value=19 Score=29.03 Aligned_cols=12 Identities=50% Similarity=1.132 Sum_probs=10.3
Q ss_pred ccccCCCCCCCC
Q 034528 21 TVFSCPFCNHGT 32 (92)
Q Consensus 21 ~~F~CPfC~~~~ 32 (92)
+.|.||.|+|..
T Consensus 221 s~f~Cp~C~~~~ 232 (300)
T KOG3022|consen 221 SGFVCPKCGHST 232 (300)
T ss_pred ccccCCCCCCcc
Confidence 579999999954
No 237
>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=36.40 E-value=35 Score=28.45 Aligned_cols=33 Identities=21% Similarity=0.279 Sum_probs=29.9
Q ss_pred CCCeEEEEeecCCceEEEEcCccCCeeEe-ecCC
Q 034528 30 HGTSVECRIDMKNLIGEAICNICQESFST-TITA 62 (92)
Q Consensus 30 ~~~sV~vkidk~~~~g~l~C~~Cg~~~~~-~i~~ 62 (92)
|...|.|.+|...|.+...-..|.++|++ +||.
T Consensus 367 ~~~ei~I~vdLg~G~~~~~~w~cDLt~eYV~INa 400 (404)
T TIGR00120 367 ESDEIEIVVDLGTGDGAGTAWGCDLSYDYVRINA 400 (404)
T ss_pred CCCEEEEEEEeCCCCceEEEEcccCCccceeECC
Confidence 56789999999999999999999999998 7886
No 238
>MTH00051 COX2 cytochrome c oxidase subunit II; Provisional
Probab=36.33 E-value=39 Score=25.64 Aligned_cols=46 Identities=17% Similarity=0.249 Sum_probs=32.1
Q ss_pred CCCeEEEEeecCCceEEEEcCc-cCCeeE-eecCCCCcchhhhhhHHHH
Q 034528 30 HGTSVECRIDMKNLIGEAICNI-CQESFS-TTITALTEPIDIYSEWIDE 76 (92)
Q Consensus 30 ~~~sV~vkidk~~~~g~l~C~~-Cg~~~~-~~i~~L~epVDVYs~WiD~ 76 (92)
..+.+....++ .|+....|.. ||..+. |++.--..+.+-|.+|+.+
T Consensus 182 ~~~~~~~~~~~-~G~y~g~Cse~CG~~Hs~M~i~v~vv~~~~f~~Wl~~ 229 (234)
T MTH00051 182 RLNQTSFFIKR-PGVFYGQCSEICGANHSFMPIVIEGVSLDKYINWVAT 229 (234)
T ss_pred ceEeEEEEeCC-CEEEEEEChhhcCcccccCeeEEEEECHHHHHHHHHH
Confidence 33445555543 4667788987 999775 4666555677999999965
No 239
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=36.06 E-value=18 Score=27.14 Aligned_cols=25 Identities=28% Similarity=0.766 Sum_probs=16.7
Q ss_pred CCCccccCCCCCCCCeEEEEeecCCceEEEEcCccC
Q 034528 18 KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQ 53 (92)
Q Consensus 18 kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg 53 (92)
.....=.||-|||-+ .++.-|.-|=
T Consensus 89 ~k~nl~~CP~CGh~k-----------~a~~LC~~Cy 113 (176)
T KOG4080|consen 89 PKDNLNTCPACGHIK-----------PAHTLCDYCY 113 (176)
T ss_pred chhccccCcccCccc-----------cccccHHHHH
Confidence 344577899999942 3556676663
No 240
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=35.71 E-value=18 Score=18.38 Aligned_cols=11 Identities=36% Similarity=0.939 Sum_probs=7.0
Q ss_pred EEcCccCCeeE
Q 034528 47 AICNICQESFS 57 (92)
Q Consensus 47 l~C~~Cg~~~~ 57 (92)
+.|..||.+|.
T Consensus 3 ~~C~~CgR~F~ 13 (25)
T PF13913_consen 3 VPCPICGRKFN 13 (25)
T ss_pred CcCCCCCCEEC
Confidence 35677777663
No 241
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=35.68 E-value=31 Score=26.52 Aligned_cols=26 Identities=23% Similarity=0.436 Sum_probs=18.3
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccC
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQ 53 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg 53 (92)
.||.||+. | ...+-.+.++-.|..|.
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 22223567889999996
No 242
>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=35.49 E-value=24 Score=19.94 Aligned_cols=26 Identities=23% Similarity=0.526 Sum_probs=12.7
Q ss_pred CCccccCCCCCCCCeEEEEeecCCceEEEEc
Q 034528 19 LDTVFSCPFCNHGTSVECRIDMKNLIGEAIC 49 (92)
Q Consensus 19 l~~~F~CPfC~~~~sV~vkidk~~~~g~l~C 49 (92)
.-.+|.|..||+ -|+|.- .+-|.+.|
T Consensus 3 ~~~~YkC~~CGn--iVev~~---~g~g~lvC 28 (36)
T PF06397_consen 3 KGEFYKCEHCGN--IVEVVH---DGGGPLVC 28 (36)
T ss_dssp TTEEEE-TTT----EEEEEE-----SS-EEE
T ss_pred cccEEEccCCCC--EEEEEE---CCCCCEEe
Confidence 346899999997 354443 34456766
No 243
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=35.47 E-value=29 Score=26.67 Aligned_cols=28 Identities=25% Similarity=0.479 Sum_probs=20.0
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
.||.||+. |....-.+.++-.|..|...
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 69999973 22233356788999999864
No 244
>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=35.47 E-value=25 Score=25.94 Aligned_cols=33 Identities=21% Similarity=0.300 Sum_probs=22.5
Q ss_pred ccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
|-|-.||++-.---+.-..+++-.-.|..||.-
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~v 33 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKV 33 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCCc
Confidence 568999996221123334567888999999974
No 245
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=35.34 E-value=24 Score=30.48 Aligned_cols=27 Identities=19% Similarity=0.566 Sum_probs=21.4
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
.|++||.. .++++.-.|.+.|.-||.-
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 3566667899999999974
No 246
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=35.14 E-value=43 Score=17.77 Aligned_cols=26 Identities=19% Similarity=0.552 Sum_probs=15.8
Q ss_pred CccccCCCCCCCCeEEEEeecCCceEEEEcC
Q 034528 20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICN 50 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~ 50 (92)
-++|.|..|++ +...+. .+-+.+.|-
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 35899999997 333332 333456663
No 247
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=34.99 E-value=17 Score=26.97 Aligned_cols=10 Identities=40% Similarity=1.065 Sum_probs=8.3
Q ss_pred ccccCCCCCC
Q 034528 21 TVFSCPFCNH 30 (92)
Q Consensus 21 ~~F~CPfC~~ 30 (92)
..|.||-||.
T Consensus 131 ~~F~Cp~Cg~ 140 (176)
T COG1675 131 LGFTCPKCGE 140 (176)
T ss_pred hCCCCCCCCc
Confidence 4599999996
No 248
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=34.64 E-value=16 Score=25.03 Aligned_cols=29 Identities=31% Similarity=0.524 Sum_probs=19.5
Q ss_pred EEcCccCCeeEe-ecCCCCcchhhhhhHHH
Q 034528 47 AICNICQESFST-TITALTEPIDIYSEWID 75 (92)
Q Consensus 47 l~C~~Cg~~~~~-~i~~L~epVDVYs~WiD 75 (92)
..|+.||..|.. +|+.-|--=--=|+||.
T Consensus 59 a~CkkCGfef~~~~ik~pSRCP~CKSE~Ie 88 (97)
T COG3357 59 ARCKKCGFEFRDDKIKKPSRCPKCKSEWIE 88 (97)
T ss_pred hhhcccCccccccccCCcccCCcchhhccc
Confidence 579999988865 66654444455667764
No 249
>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=34.40 E-value=16 Score=26.84 Aligned_cols=12 Identities=42% Similarity=1.090 Sum_probs=3.2
Q ss_pred CCccccCCCCCC
Q 034528 19 LDTVFSCPFCNH 30 (92)
Q Consensus 19 l~~~F~CPfC~~ 30 (92)
+-.-|.||||+-
T Consensus 151 ~~~~~~Cp~C~~ 162 (175)
T PF05280_consen 151 PRHSFVCPFCQP 162 (175)
T ss_dssp -SS----TT---
T ss_pred CCcCcCCCCCCC
Confidence 456899999994
No 250
>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=34.34 E-value=36 Score=19.55 Aligned_cols=24 Identities=33% Similarity=0.629 Sum_probs=14.8
Q ss_pred ccCCCCCCCCeEEEEeecCCceEEEEcCccC
Q 034528 23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQ 53 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg 53 (92)
-.||.|+.+ -.+ ++ -|.+.|-+|+
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 3567898885
No 251
>PHA02893 hypothetical protein; Provisional
Probab=34.25 E-value=34 Score=23.05 Aligned_cols=11 Identities=27% Similarity=0.582 Sum_probs=8.9
Q ss_pred EEEEcCccCCe
Q 034528 45 GEAICNICQES 55 (92)
Q Consensus 45 g~l~C~~Cg~~ 55 (92)
..|+|..||..
T Consensus 68 ~tL~CaACGS~ 78 (88)
T PHA02893 68 SNIKCIACGSS 78 (88)
T ss_pred Cceeehhhchh
Confidence 57999999964
No 252
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=33.76 E-value=19 Score=25.02 Aligned_cols=23 Identities=30% Similarity=0.898 Sum_probs=12.7
Q ss_pred ccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
|.||.|+.. .++|- +.|.+||+.
T Consensus 2 Y~CPrC~sk---vC~LP-------~~CpiCgLt 24 (112)
T TIGR00622 2 YFCPQCRAK---VCELP-------VECPICGLT 24 (112)
T ss_pred ccCCCCCCC---ccCCC-------CcCCcCCCE
Confidence 567777752 22221 466777764
No 253
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=33.52 E-value=20 Score=26.41 Aligned_cols=11 Identities=27% Similarity=0.712 Sum_probs=5.5
Q ss_pred ccccCCCCCCC
Q 034528 21 TVFSCPFCNHG 31 (92)
Q Consensus 21 ~~F~CPfC~~~ 31 (92)
.+-.||.||+.
T Consensus 148 ~P~~CPiCga~ 158 (166)
T COG1592 148 APEVCPICGAP 158 (166)
T ss_pred CCCcCCCCCCh
Confidence 34455555553
No 254
>PF14913 DPCD: DPCD protein family
Probab=33.45 E-value=21 Score=27.09 Aligned_cols=24 Identities=42% Similarity=0.574 Sum_probs=20.1
Q ss_pred CCeeEeecCCCCcchhhhhhHHHH
Q 034528 53 QESFSTTITALTEPIDIYSEWIDE 76 (92)
Q Consensus 53 g~~~~~~i~~L~epVDVYs~WiD~ 76 (92)
...|+..|..|.=|.|||+-=+|.
T Consensus 95 k~~fqWRIRNLPYP~dvYsVtvd~ 118 (194)
T PF14913_consen 95 KTSFQWRIRNLPYPKDVYSVTVDE 118 (194)
T ss_pred ccceEEEEccCCCCccceEEEEcC
Confidence 456999999999999999966553
No 255
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=33.41 E-value=19 Score=24.66 Aligned_cols=9 Identities=33% Similarity=1.468 Sum_probs=6.8
Q ss_pred cccCCCCCC
Q 034528 22 VFSCPFCNH 30 (92)
Q Consensus 22 ~F~CPfC~~ 30 (92)
.+.||+||-
T Consensus 3 LI~CP~Cg~ 11 (97)
T COG4311 3 LIPCPYCGE 11 (97)
T ss_pred eecCCCCCC
Confidence 467888885
No 256
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=33.34 E-value=7.7 Score=24.80 Aligned_cols=30 Identities=20% Similarity=0.461 Sum_probs=23.3
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
.||-|+..+++ -|=+.+++-++.|-.||-.
T Consensus 12 ~CP~C~~~Dtl--~mW~En~ve~vECV~CG~~ 41 (66)
T COG3529 12 VCPACQAQDTL--AMWRENNVEIVECVKCGHH 41 (66)
T ss_pred CCcccchhhHH--HHHHhcCCceEehhhcchH
Confidence 69999986543 3455788999999999953
No 257
>smart00350 MCM minichromosome maintenance proteins.
Probab=32.52 E-value=25 Score=29.19 Aligned_cols=34 Identities=24% Similarity=0.500 Sum_probs=21.2
Q ss_pred CccccCCCCCCCCeEEEEeecCCceEEEEcCc--cCCe
Q 034528 20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNI--CQES 55 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~--Cg~~ 55 (92)
.-.|.|..||+...+. ++...-.--..|.. |+..
T Consensus 35 ~~~f~C~~C~~~~~~~--~~~~~~~~p~~C~~~~C~~~ 70 (509)
T smart00350 35 RASFTCEKCGATLGPE--IQSGRETEPTVCPPRECQSP 70 (509)
T ss_pred EEEEEecCCCCEEeEE--ecCCcccCCCcCCCCcCCCC
Confidence 3589999999965444 33222122347877 8864
No 258
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=32.42 E-value=19 Score=21.09 Aligned_cols=8 Identities=50% Similarity=1.651 Sum_probs=3.8
Q ss_pred ccCCCCCC
Q 034528 23 FSCPFCNH 30 (92)
Q Consensus 23 F~CPfC~~ 30 (92)
+.||.|+.
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 259
>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=32.28 E-value=30 Score=21.97 Aligned_cols=37 Identities=16% Similarity=0.461 Sum_probs=21.8
Q ss_pred CccccCCCCCCCCeEEEEeecC-CceEEEEcCccCCee
Q 034528 20 DTVFSCPFCNHGTSVECRIDMK-NLIGEAICNICQESF 56 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~-~~~g~l~C~~Cg~~~ 56 (92)
+....||.|+..++==+=.... ...-.-.|..|...+
T Consensus 3 ~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~ryw 40 (63)
T PF02701_consen 3 EQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYW 40 (63)
T ss_pred ccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHH
Confidence 4567899999876544443322 223345677776544
No 260
>MTH00008 COX2 cytochrome c oxidase subunit II; Validated
Probab=32.22 E-value=33 Score=25.91 Aligned_cols=47 Identities=13% Similarity=0.222 Sum_probs=32.2
Q ss_pred CCCCeEEEEeecCCceEEEEcCc-cCCeeE-eecCCCCcchhhhhhHHHH
Q 034528 29 NHGTSVECRIDMKNLIGEAICNI-CQESFS-TTITALTEPIDIYSEWIDE 76 (92)
Q Consensus 29 ~~~~sV~vkidk~~~~g~l~C~~-Cg~~~~-~~i~~L~epVDVYs~WiD~ 76 (92)
|.-+.+....++ .|+....|.. ||..+. |++.-...+.+.|.+|+.+
T Consensus 177 G~~~~~~~~~~~-~G~~~g~Cse~CG~~Hs~M~~~v~vv~~~~f~~Wl~~ 225 (228)
T MTH00008 177 GRLNQIGFTITR-PGVFYGQCSEICGANHSFMPIVLEAVDTKSFMKWVSS 225 (228)
T ss_pred CceEEEEEEeCC-CEEEEEEChhhcCcCccCceeEEEEECHHHHHHHHHh
Confidence 333455555543 4677899987 999775 4666555677899999854
No 261
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=31.96 E-value=24 Score=20.74 Aligned_cols=11 Identities=36% Similarity=1.014 Sum_probs=9.3
Q ss_pred CccccCCCCCC
Q 034528 20 DTVFSCPFCNH 30 (92)
Q Consensus 20 ~~~F~CPfC~~ 30 (92)
+....||.||.
T Consensus 44 ~~i~~Cp~CgR 54 (56)
T PF02591_consen 44 DEIVFCPNCGR 54 (56)
T ss_pred CCeEECcCCCc
Confidence 67899999985
No 262
>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=31.88 E-value=54 Score=17.42 Aligned_cols=25 Identities=28% Similarity=0.678 Sum_probs=15.4
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcC
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICN 50 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~ 50 (92)
+.|.|..||+ -|.+ +. .+-+.+.|-
T Consensus 3 ~~ykC~~CGn--iv~v-~~--~~~~~l~Cc 27 (34)
T cd00974 3 EVYKCEICGN--IVEV-LN--VGGGTLVCC 27 (34)
T ss_pred cEEEcCCCCc--EEEE-EE--CCCcceeec
Confidence 4799999997 2333 32 344556664
No 263
>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=31.77 E-value=11 Score=23.59 Aligned_cols=36 Identities=19% Similarity=0.563 Sum_probs=15.7
Q ss_pred CccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528 20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFS 57 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~ 57 (92)
.+.|.|.+|..+.+ .=.|++.. +..+.|+.|+....
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 45667777754432 22233322 23677777776443
No 264
>PTZ00047 cytochrome c oxidase subunit II; Provisional
Probab=31.71 E-value=50 Score=24.34 Aligned_cols=46 Identities=11% Similarity=0.121 Sum_probs=31.1
Q ss_pred CeEEEEeecCCceEEEEcCc-cCCeeE-eecCCCCcchhhhhhHHHHHH
Q 034528 32 TSVECRIDMKNLIGEAICNI-CQESFS-TTITALTEPIDIYSEWIDECE 78 (92)
Q Consensus 32 ~sV~vkidk~~~~g~l~C~~-Cg~~~~-~~i~~L~epVDVYs~WiD~~~ 78 (92)
+.+...++ ..|+-...|.. ||..+. |.+.-...+-+.|..|+....
T Consensus 113 n~l~~~~~-~~G~y~gqCsElCG~gHs~M~~~V~vvs~~~F~~w~~~~~ 160 (162)
T PTZ00047 113 HKINTFIL-REGVFYGQCSEMCGTLHGFMPIVVEAVSPEAYAAHAKKYY 160 (162)
T ss_pred EEEEEecC-CCeEEEEEcchhcCcCccCceEEEEEeCHHHHHHHHHHHh
Confidence 34444443 36777899987 998775 455544456788999997653
No 265
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.50 E-value=19 Score=24.53 Aligned_cols=30 Identities=17% Similarity=0.476 Sum_probs=17.4
Q ss_pred CCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528 18 KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQE 54 (92)
Q Consensus 18 kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~ 54 (92)
..|-.|.|+.||+.-++. ......|..||.
T Consensus 67 ~vp~~~~C~~Cg~~~~~~-------~~~~~~CP~Cgs 96 (117)
T PRK00564 67 DEKVELECKDCSHVFKPN-------ALDYGVCEKCHS 96 (117)
T ss_pred ecCCEEEhhhCCCccccC-------CccCCcCcCCCC
Confidence 456678888888642221 113345888885
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=31.27 E-value=18 Score=24.39 Aligned_cols=11 Identities=27% Similarity=0.830 Sum_probs=8.6
Q ss_pred ccccCCCCCCC
Q 034528 21 TVFSCPFCNHG 31 (92)
Q Consensus 21 ~~F~CPfC~~~ 31 (92)
.-|.||+|-+-
T Consensus 23 ~D~~Cp~C~~~ 33 (178)
T cd03019 23 FSYGCPHCYNF 33 (178)
T ss_pred ECCCCcchhhh
Confidence 45899999863
No 267
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=31.25 E-value=41 Score=25.73 Aligned_cols=27 Identities=19% Similarity=0.392 Sum_probs=18.7
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQE 54 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~ 54 (92)
.||.||.. | ....-.+.++-.|..|..
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 222335678899999974
No 268
>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=30.99 E-value=82 Score=16.10 Aligned_cols=26 Identities=31% Similarity=0.543 Sum_probs=14.3
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccC
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQ 53 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg 53 (92)
.||.|++. ...+.+ .+...-.|..|.
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 269
>smart00355 ZnF_C2H2 zinc finger.
Probab=30.92 E-value=24 Score=16.02 Aligned_cols=8 Identities=38% Similarity=1.065 Sum_probs=4.0
Q ss_pred cCccCCee
Q 034528 49 CNICQESF 56 (92)
Q Consensus 49 C~~Cg~~~ 56 (92)
|..|+..|
T Consensus 3 C~~C~~~f 10 (26)
T smart00355 3 CPECGKVF 10 (26)
T ss_pred CCCCcchh
Confidence 45555444
No 270
>PRK04351 hypothetical protein; Provisional
Probab=30.83 E-value=50 Score=23.56 Aligned_cols=34 Identities=15% Similarity=0.358 Sum_probs=22.6
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
=.+.|.-||+. .... +.-+...-.|+.|+..+..
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 35889999973 2233 3445577889999976643
No 271
>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=30.78 E-value=35 Score=24.89 Aligned_cols=45 Identities=11% Similarity=0.154 Sum_probs=30.0
Q ss_pred CCCCeEEEEeecCCceEEEEcCc-cCCeeE-eecCCCCcchhhhhhHH
Q 034528 29 NHGTSVECRIDMKNLIGEAICNI-CQESFS-TTITALTEPIDIYSEWI 74 (92)
Q Consensus 29 ~~~~sV~vkidk~~~~g~l~C~~-Cg~~~~-~~i~~L~epVDVYs~Wi 74 (92)
|..+++..+.++ .|.....|.. ||..+. |.+.-.-.+-+-|.+|+
T Consensus 154 G~~~~~~~~~~~-~G~y~~~c~e~cG~~h~~M~~~v~v~~~~~f~~Wl 200 (201)
T TIGR02866 154 GQYNALWFNADE-PGVYYGYCAELCGAGHSLMLFKVVVVEREEFDAYI 200 (201)
T ss_pred CcEEEEEEEeCC-CEEEEEEehhhCCcCccCCeEEEEEECHHHHHHHh
Confidence 344455565543 5677899998 999875 45444444557899997
No 272
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=30.68 E-value=24 Score=31.18 Aligned_cols=21 Identities=29% Similarity=0.654 Sum_probs=14.0
Q ss_pred ccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528 23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQE 54 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~ 54 (92)
=.|+.||+.... .-.|..||.
T Consensus 681 ~~C~~CG~~~~~-----------~~~CP~CG~ 701 (735)
T PRK07111 681 DRCPVCGYLGVI-----------EDKCPKCGS 701 (735)
T ss_pred eecCCCCCCCCc-----------CccCcCCCC
Confidence 358888874321 158999984
No 273
>PRK15338 type III secretion system regulator InvE; Provisional
Probab=30.59 E-value=25 Score=29.07 Aligned_cols=22 Identities=23% Similarity=0.588 Sum_probs=16.3
Q ss_pred cCCCCcchhhhhhHHHHHHhhc
Q 034528 60 ITALTEPIDIYSEWIDECERVN 81 (92)
Q Consensus 60 i~~L~epVDVYs~WiD~~~~~n 81 (92)
|..=..++++|.+||+.+...+
T Consensus 194 l~~d~~~~~iY~~Wieeyg~~~ 215 (372)
T PRK15338 194 LQSESHEVEIYSDWIASYGYQR 215 (372)
T ss_pred HhccCcHHHHHHHHHHHhCccH
Confidence 3344578999999999985443
No 274
>COG1364 ArgJ N-acetylglutamate synthase (N-acetylornithine aminotransferase) [Amino acid transport and metabolism]
Probab=30.59 E-value=32 Score=28.80 Aligned_cols=32 Identities=22% Similarity=0.254 Sum_probs=27.9
Q ss_pred CeEEEEeecCCceEEEEcCccCCeeEe-ecCCC
Q 034528 32 TSVECRIDMKNLIGEAICNICQESFST-TITAL 63 (92)
Q Consensus 32 ~sV~vkidk~~~~g~l~C~~Cg~~~~~-~i~~L 63 (92)
.-|.|.+|...|.+...+..|.++|++ +||.-
T Consensus 369 ~ei~I~VdLg~G~~~at~wgCDLt~dYV~INa~ 401 (404)
T COG1364 369 DEITIRVDLGVGDGAATAWGCDLTYDYVRINAD 401 (404)
T ss_pred CcEEEEEEeccCCcceEEEeccCchhhEEeece
Confidence 348888888999999999999999998 78864
No 275
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=30.42 E-value=37 Score=20.82 Aligned_cols=25 Identities=24% Similarity=0.712 Sum_probs=17.6
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESF 56 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~ 56 (92)
.|+.||-. | +.+-.++.|..||.-|
T Consensus 7 ~C~~Cg~~------~--~~~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 7 KCPVCGKK------F--KDGDDIVVCPECGAPY 31 (54)
T ss_pred cChhhCCc------c--cCCCCEEECCCCCCcc
Confidence 58888852 1 3455688999999865
No 276
>COG1773 Rubredoxin [Energy production and conversion]
Probab=30.38 E-value=30 Score=21.31 Aligned_cols=23 Identities=22% Similarity=0.375 Sum_probs=17.0
Q ss_pred CCCCCCccccCCCCCCCCeEEEE
Q 034528 15 RVDKLDTVFSCPFCNHGTSVECR 37 (92)
Q Consensus 15 ~~~kl~~~F~CPfC~~~~sV~vk 37 (92)
+-.-||-.+.||.|+..++.-..
T Consensus 29 ~fedlPd~w~CP~Cg~~K~~F~~ 51 (55)
T COG1773 29 PFEDLPDDWVCPECGVGKKDFEM 51 (55)
T ss_pred chhhCCCccCCCCCCCCHhHeee
Confidence 34678999999999976554333
No 277
>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=58 Score=20.97 Aligned_cols=37 Identities=35% Similarity=0.736 Sum_probs=24.5
Q ss_pred CCCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhh
Q 034528 16 VDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSE 72 (92)
Q Consensus 16 ~~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~ 72 (92)
..+.++.-.|..|..+..+ ++.|..|+. +-|+|-||+
T Consensus 31 ~~~~~~~i~C~~ct~~q~~-----------El~C~~C~~---------~k~ld~FSK 67 (84)
T PF12898_consen 31 VDPANSGIRCRECTGGQVV-----------ELTCSPCGK---------TKPLDEFSK 67 (84)
T ss_pred CccCCCCCCCccCCCCCcC-----------cCEeccCCC---------CcCHHHHhH
Confidence 3455667788888875544 448999986 356666653
No 278
>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=30.17 E-value=59 Score=26.65 Aligned_cols=53 Identities=21% Similarity=0.382 Sum_probs=30.4
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhhc
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERVN 81 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~n 81 (92)
.|.||.||++..+.++ .......-.|..||... .+.+..|++-.+++.+++.+
T Consensus 320 ~~rc~~c~~~~~~~~~--~~~~~~~~~~~~~~~~~-----~~~~~~~~ve~L~e~a~~~G 372 (403)
T TIGR03676 320 TFKCPNCGYEEEKTVK--PEEGDKSEACPKCGSEL-----EIVEEEDIIEELSELAEESG 372 (403)
T ss_pred EEEcCCCCcceeeecc--cccccccccCcccCccc-----ccchhhhHHHHHHHHHHHcC
Confidence 5999999986544442 22221224588888742 22234566666666666654
No 279
>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=30.09 E-value=31 Score=24.85 Aligned_cols=34 Identities=21% Similarity=0.321 Sum_probs=20.6
Q ss_pred CccccCCCCCCCCeEEEEeecC-----------CceEEEEcCccC
Q 034528 20 DTVFSCPFCNHGTSVECRIDMK-----------NLIGEAICNICQ 53 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~-----------~~~g~l~C~~Cg 53 (92)
.=++.|.+|+++.|+++.-... ..+..+.||-|.
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 4468999999999998764321 246778999985
No 280
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.84 E-value=43 Score=25.84 Aligned_cols=26 Identities=19% Similarity=0.341 Sum_probs=18.4
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccC
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQ 53 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg 53 (92)
.||.||.. -...+ -.+.++-.|..|.
T Consensus 256 pC~~Cg~~-I~~~~---~~gR~t~~CP~CQ 281 (282)
T PRK13945 256 PCRKCGTP-IERIK---LAGRSTHWCPNCQ 281 (282)
T ss_pred CCCcCCCe-eEEEE---ECCCccEECCCCc
Confidence 79999973 12222 3567889999996
No 281
>MTH00023 COX2 cytochrome c oxidase subunit II; Validated
Probab=29.72 E-value=49 Score=25.17 Aligned_cols=46 Identities=17% Similarity=0.227 Sum_probs=30.6
Q ss_pred CCCeEEEEeecCCceEEEEcCc-cCCeeE-eecCCCCcchhhhhhHHHH
Q 034528 30 HGTSVECRIDMKNLIGEAICNI-CQESFS-TTITALTEPIDIYSEWIDE 76 (92)
Q Consensus 30 ~~~sV~vkidk~~~~g~l~C~~-Cg~~~~-~~i~~L~epVDVYs~WiD~ 76 (92)
+.+.+....++ .|+-...|.. ||..+. |++.--..+.+.|.+|+.+
T Consensus 189 ~~n~~~~~~~~-~G~y~g~C~e~CG~~Hs~M~~~v~vv~~~~f~~Wl~~ 236 (240)
T MTH00023 189 RLNQTGFFIKR-PGVFYGQCSEICGANHSFMPIVIEAVSLDKYINWLLS 236 (240)
T ss_pred cceeEEEEcCC-CEEEEEEchhhcCcCccCCeEEEEEECHHHHHHHHHH
Confidence 33445555443 4677889987 999775 4555444566899999844
No 282
>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=29.65 E-value=28 Score=26.05 Aligned_cols=17 Identities=24% Similarity=0.340 Sum_probs=12.9
Q ss_pred CceEEEEcCccCCeeEe
Q 034528 42 NLIGEAICNICQESFST 58 (92)
Q Consensus 42 ~~~g~l~C~~Cg~~~~~ 58 (92)
..+-...|..||..+.-
T Consensus 31 ~~i~v~~C~~Cg~~~~~ 47 (236)
T PF04981_consen 31 DRIEVTICPKCGRYRIG 47 (236)
T ss_pred CccCceECCCCCCEECC
Confidence 44567899999987753
No 283
>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=29.63 E-value=38 Score=22.76 Aligned_cols=11 Identities=27% Similarity=0.588 Sum_probs=4.6
Q ss_pred CccccCCCCCC
Q 034528 20 DTVFSCPFCNH 30 (92)
Q Consensus 20 ~~~F~CPfC~~ 30 (92)
|-.|.|+.||+
T Consensus 68 p~~~~C~~Cg~ 78 (113)
T PF01155_consen 68 PARARCRDCGH 78 (113)
T ss_dssp --EEEETTTS-
T ss_pred CCcEECCCCCC
Confidence 44555555555
No 284
>PRK10445 endonuclease VIII; Provisional
Probab=29.62 E-value=45 Score=25.53 Aligned_cols=26 Identities=19% Similarity=0.280 Sum_probs=18.0
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccC
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQ 53 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg 53 (92)
.||.||.. -..+++ .+.++-.|..|.
T Consensus 237 ~Cp~Cg~~-I~~~~~---~gR~t~~CP~CQ 262 (263)
T PRK10445 237 ACERCGGI-IEKTTL---SSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCE-eEEEEE---CCCCcEECCCCc
Confidence 59999973 222333 567888999996
No 285
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=29.40 E-value=71 Score=26.07 Aligned_cols=56 Identities=14% Similarity=0.245 Sum_probs=30.7
Q ss_pred cCCCCCCCCe-E------------EEEeecCCceEEEEcCccCCeeEe-ecCCCCcchhhhhhHHHHHHh
Q 034528 24 SCPFCNHGTS-V------------ECRIDMKNLIGEAICNICQESFST-TITALTEPIDIYSEWIDECER 79 (92)
Q Consensus 24 ~CPfC~~~~s-V------------~vkidk~~~~g~l~C~~Cg~~~~~-~i~~L~epVDVYs~WiD~~~~ 79 (92)
-||+||.+.. + ...+.....+....|+.||+.+-- ...-++..-+.+....|....
T Consensus 8 ~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cga~~~~~~W~~~~~~~~~l~~~~~~~~~ 77 (355)
T COG1499 8 LCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCGAYRIRGRWVDEEGANRLLEALEDEVLR 77 (355)
T ss_pred EeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCCCccCCCcceeccccchHHHHHHHHHhh
Confidence 4899997541 0 112222457778999999943321 222244455566655555443
No 286
>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=29.24 E-value=44 Score=25.62 Aligned_cols=26 Identities=23% Similarity=0.456 Sum_probs=17.6
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccC
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQ 53 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg 53 (92)
.||.||++ | ....-.+.++-.|..|.
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 69999973 2 22223467788898885
No 287
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=29.09 E-value=15 Score=22.91 Aligned_cols=17 Identities=18% Similarity=0.622 Sum_probs=8.4
Q ss_pred CccccCCCCCCCCeEEEEe
Q 034528 20 DTVFSCPFCNHGTSVECRI 38 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vki 38 (92)
+..=+||+|..+ |++++
T Consensus 53 ~~~G~CP~C~~~--i~~~~ 69 (70)
T PF11793_consen 53 PIFGECPYCSSP--ISWSF 69 (70)
T ss_dssp --EEE-TTT-SE--EEGGG
T ss_pred ccccCCcCCCCe--eeEec
Confidence 444579999974 55544
No 288
>PF14369 zf-RING_3: zinc-finger
Probab=29.07 E-value=81 Score=17.26 Aligned_cols=32 Identities=22% Similarity=0.432 Sum_probs=17.7
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
.|=|-.|+. .|.+....... +.|..|+-.|-.
T Consensus 2 ~ywCh~C~~--~V~~~~~~~~~---~~CP~C~~gFvE 33 (35)
T PF14369_consen 2 RYWCHQCNR--FVRIAPSPDSD---VACPRCHGGFVE 33 (35)
T ss_pred CEeCccCCC--EeEeCcCCCCC---cCCcCCCCcEeE
Confidence 344667774 45554432222 368888776643
No 289
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.87 E-value=33 Score=22.04 Aligned_cols=33 Identities=21% Similarity=0.578 Sum_probs=22.1
Q ss_pred cccCCCCCCCCeEEEEee-cCCceEEEEcCccCCeeE
Q 034528 22 VFSCPFCNHGTSVECRID-MKNLIGEAICNICQESFS 57 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkid-k~~~~g~l~C~~Cg~~~~ 57 (92)
.|.|| ||- -..|..+ ..+|-..+.|-.|.+.-+
T Consensus 22 ~yPCp-CGD--rf~It~edL~~ge~Va~CpsCSL~I~ 55 (67)
T KOG2923|consen 22 YYPCP-CGD--RFQITLEDLENGEDVARCPSCSLIIR 55 (67)
T ss_pred EcCCC-CCC--eeeecHHHHhCCCeeecCCCceEEEE
Confidence 35566 774 3666663 357888899999987543
No 290
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=28.84 E-value=27 Score=25.79 Aligned_cols=34 Identities=21% Similarity=0.521 Sum_probs=22.9
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
+-|-|.+|++. .|.--++. .....|..|+.-|-.
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 45889999875 33333333 378899999987743
No 291
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.78 E-value=20 Score=28.17 Aligned_cols=29 Identities=31% Similarity=0.833 Sum_probs=20.5
Q ss_pred CCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528 18 KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESF 56 (92)
Q Consensus 18 kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~ 56 (92)
..+.-|-||.|.. +-|++- ..|.+||..|
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 3456689998885 555552 3899999865
No 292
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=28.78 E-value=79 Score=26.28 Aligned_cols=43 Identities=21% Similarity=0.337 Sum_probs=27.9
Q ss_pred CCCCccccCCCCCCCCe--EEEEeecCCceEEEEcCc------cCCeeEeecC
Q 034528 17 DKLDTVFSCPFCNHGTS--VECRIDMKNLIGEAICNI------CQESFSTTIT 61 (92)
Q Consensus 17 ~kl~~~F~CPfC~~~~s--V~vkidk~~~~g~l~C~~------Cg~~~~~~i~ 61 (92)
.-+++.| ||.|||..- |+|.++.+ |-+++.|.- =|..|+-.-|
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 3456777 999999632 45666655 667777763 3777755443
No 293
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=28.53 E-value=69 Score=28.65 Aligned_cols=42 Identities=24% Similarity=0.424 Sum_probs=30.8
Q ss_pred CCCCccc--cCCCCCCCCeEEEEeecC--CceE-EEEcCccCCeeEe
Q 034528 17 DKLDTVF--SCPFCNHGTSVECRIDMK--NLIG-EAICNICQESFST 58 (92)
Q Consensus 17 ~kl~~~F--~CPfC~~~~sV~vkidk~--~~~g-~l~C~~Cg~~~~~ 58 (92)
..+.-.| .||+|.-..+|.|-.... .|.| .+.|.+||..+--
T Consensus 46 ~D~~~~~~~pc~~c~gkG~V~v~~~c~~c~G~gkv~~c~~cG~~~~~ 92 (715)
T COG1107 46 VDLFASFEIPCPKCRGKGTVTVYDTCPECGGTGKVLTCDICGDIIVP 92 (715)
T ss_pred ccccccCCCCCCeeccceeEEEEeecccCCCceeEEeeccccceecC
Confidence 4455555 799999999999877554 4555 5889999976543
No 294
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=28.47 E-value=16 Score=29.13 Aligned_cols=35 Identities=17% Similarity=0.455 Sum_probs=21.6
Q ss_pred cccCCCCCCCCeEEEEeec----CCceEEEEcCccCCeeEe
Q 034528 22 VFSCPFCNHGTSVECRIDM----KNLIGEAICNICQESFST 58 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk----~~~~g~l~C~~Cg~~~~~ 58 (92)
.|+|..||- ..=-..+++ -.+ +..+|--||..|+-
T Consensus 3 ~FtCnvCgE-svKKp~vekH~srCrn-~~fSCIDC~k~F~~ 41 (276)
T KOG2186|consen 3 FFTCNVCGE-SVKKPQVEKHMSRCRN-AYFSCIDCGKTFER 41 (276)
T ss_pred EEehhhhhh-hccccchHHHHHhccC-CeeEEeeccccccc
Confidence 589999994 111111111 234 78999999988753
No 295
>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=28.45 E-value=49 Score=22.99 Aligned_cols=30 Identities=23% Similarity=0.743 Sum_probs=18.8
Q ss_pred CccccCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528 20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESF 56 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~ 56 (92)
-+.|.|+.||+ |...+. .+-+.++| ||+..
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 45899999997 333332 34466777 46543
No 296
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=28.31 E-value=21 Score=23.44 Aligned_cols=11 Identities=27% Similarity=0.643 Sum_probs=8.8
Q ss_pred EcCccCCeeEe
Q 034528 48 ICNICQESFST 58 (92)
Q Consensus 48 ~C~~Cg~~~~~ 58 (92)
+|..||+.|+.
T Consensus 10 ~C~~CG~d~~~ 20 (86)
T PF06170_consen 10 RCPHCGLDYSH 20 (86)
T ss_pred cccccCCcccc
Confidence 69999988764
No 297
>PRK12722 transcriptional activator FlhC; Provisional
Probab=28.26 E-value=26 Score=26.33 Aligned_cols=13 Identities=23% Similarity=0.516 Sum_probs=10.4
Q ss_pred CCccccCCCCCCC
Q 034528 19 LDTVFSCPFCNHG 31 (92)
Q Consensus 19 l~~~F~CPfC~~~ 31 (92)
+-..|.||+|+-+
T Consensus 151 ~~~~f~CplC~~p 163 (187)
T PRK12722 151 PVGSFVCGLCQPP 163 (187)
T ss_pred cCCCCcCCCCCCc
Confidence 4568999999963
No 298
>MTH00168 COX2 cytochrome c oxidase subunit II; Provisional
Probab=28.22 E-value=43 Score=25.16 Aligned_cols=43 Identities=16% Similarity=0.315 Sum_probs=29.3
Q ss_pred CeEEEEeecCCceEEEEcCc-cCCeeE-eecCCCCcchhhhhhHHH
Q 034528 32 TSVECRIDMKNLIGEAICNI-CQESFS-TTITALTEPIDIYSEWID 75 (92)
Q Consensus 32 ~sV~vkidk~~~~g~l~C~~-Cg~~~~-~~i~~L~epVDVYs~WiD 75 (92)
+.+....+ +.|+-...|.. ||..+. |++.-...+-+.|.+|++
T Consensus 180 n~~~~~~~-~~G~~~g~CsE~CG~~Hs~M~~~v~vv~~~~f~~W~~ 224 (225)
T MTH00168 180 NQLAFLSS-RPGSFYGQCSEICGANHSFMPIVVEFVPWETFENWVD 224 (225)
T ss_pred EEEEEEcC-CCEEEEEEcccccCcCcCCCeEEEEEeCHHHHHHHHh
Confidence 34455544 35677889987 999775 465554456688999984
No 299
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=28.14 E-value=28 Score=17.94 Aligned_cols=8 Identities=38% Similarity=1.186 Sum_probs=5.0
Q ss_pred ccCCCCCC
Q 034528 23 FSCPFCNH 30 (92)
Q Consensus 23 F~CPfC~~ 30 (92)
+.||.|+.
T Consensus 2 v~CPiC~~ 9 (26)
T smart00734 2 VQCPVCFR 9 (26)
T ss_pred CcCCCCcC
Confidence 45777764
No 300
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=28.13 E-value=27 Score=29.54 Aligned_cols=32 Identities=34% Similarity=0.653 Sum_probs=20.4
Q ss_pred CccccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
++...||.|+-++-- +.-...+.++|..|...
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 678899999753211 11123345899999985
No 301
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=28.08 E-value=49 Score=26.36 Aligned_cols=27 Identities=15% Similarity=0.264 Sum_probs=17.6
Q ss_pred CCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528 25 CPFCNHGTSVECRIDMKNLIGEAICNICQESFS 57 (92)
Q Consensus 25 CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~ 57 (92)
|+.||++ +....+--...|..||..+-
T Consensus 114 Cg~CG~~------~~~~~~g~~~~C~~cg~~~f 140 (279)
T COG2816 114 CGRCGTK------TYPREGGWARVCPKCGHEHF 140 (279)
T ss_pred CCCCCCc------CccccCceeeeCCCCCCccC
Confidence 7777774 34445555677888887643
No 302
>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=27.93 E-value=66 Score=18.96 Aligned_cols=31 Identities=13% Similarity=0.492 Sum_probs=20.2
Q ss_pred cCCCCCCCCeEEE-Eeec----CCceEEEEcCccCC
Q 034528 24 SCPFCNHGTSVEC-RIDM----KNLIGEAICNICQE 54 (92)
Q Consensus 24 ~CPfC~~~~sV~v-kidk----~~~~g~l~C~~Cg~ 54 (92)
.|.+|+++..+++ .+-. ...-+.+.|..|..
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 303
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=27.90 E-value=30 Score=20.57 Aligned_cols=30 Identities=23% Similarity=0.514 Sum_probs=19.6
Q ss_pred CCCccccCCCCCCCCeEEEEeecCCceEEEEcCc--cCCeeE
Q 034528 18 KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNI--CQESFS 57 (92)
Q Consensus 18 kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~--Cg~~~~ 57 (92)
.|--+-.||.||.-+ +.-.+.|.+ |++.|.
T Consensus 7 TlRGirkCp~CGt~N----------G~R~~~CKN~~C~~~~~ 38 (44)
T PF14952_consen 7 TLRGIRKCPKCGTYN----------GTRGLSCKNKSCPQVFN 38 (44)
T ss_pred hHhccccCCcCcCcc----------CcccccccCCccchhhh
Confidence 344456799999743 344477876 777654
No 304
>TIGR01432 QOXA cytochrome aa3 quinol oxidase, subunit II. This enzyme catalyzes the oxidation of quinol with the concomitant reduction of molecular oxygen to water. This acts as the terminal electron acceptor in the respiratory chain. This subunit contains two transmembrane helices and a large external domain responsible for the binding and oxidation of quinol. QuoX is (presently) only found in gram positive bacteria of the Bacillus/Staphylococcus group. Like CyoA, the ubiquinol oxidase found in proteobacteria, the residues responsible for the ligation of Cu(a) and cytochrome c (found in the related cyt. c oxidases) are absent. Unlike CyoA, QoxA is in complex with a subunit I which contains cytochromes a similar to the cyt. c oxidases (as opposed to cytochromes b).
Probab=27.84 E-value=57 Score=24.17 Aligned_cols=47 Identities=13% Similarity=0.070 Sum_probs=31.4
Q ss_pred CCCCeEEEEeecCCceEEEEcCc-cCCeeE-eecCCCCcchhhhhhHHHH
Q 034528 29 NHGTSVECRIDMKNLIGEAICNI-CQESFS-TTITALTEPIDIYSEWIDE 76 (92)
Q Consensus 29 ~~~~sV~vkidk~~~~g~l~C~~-Cg~~~~-~~i~~L~epVDVYs~WiD~ 76 (92)
|..+.+..+.++ .|.....|.. ||..+. |.+.-.-.+-+-|.+|+++
T Consensus 167 G~~~~~~~~~~~-~G~y~g~Cae~CG~~Hs~M~~~v~v~~~~~f~~W~~~ 215 (217)
T TIGR01432 167 GMTMNWYLQADQ-VGTYRGRNANFNGEGFADQTFDVNAVSEKDFDKWVKE 215 (217)
T ss_pred CceEEEEEEeCC-CEEEEEEehhhcCccccCCeEEEEEeCHHHHHHHHHh
Confidence 444556666543 5788899998 999775 4444333345779999965
No 305
>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=27.66 E-value=75 Score=25.75 Aligned_cols=54 Identities=20% Similarity=0.454 Sum_probs=33.1
Q ss_pred CCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe----ecCCCCcchhhhhhHHHHHHhh
Q 034528 17 DKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST----TITALTEPIDIYSEWIDECERV 80 (92)
Q Consensus 17 ~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~----~i~~L~epVDVYs~WiD~~~~~ 80 (92)
.++--++.|+.|++.+.+.-. . ...-.|..||..+.. ++.+|.++ +|++.+.+.
T Consensus 228 ~~~g~v~~C~~c~~~~~~~~~-~----~~~~~C~~c~~~~~~~GPlW~G~l~d~-----~fl~~m~~~ 285 (374)
T TIGR00308 228 ESTGYTYHCSRCLHNKPVNGI-S----QRKGRCKECGGEYHLAGPLYAGPLHDK-----EFIEEVLRI 285 (374)
T ss_pred HhceeEEECCCcccccccccc-c----CCCCCCCCCCCcceeecCcccCccCCH-----HHHHHHHHh
Confidence 456678999999986543210 0 112369999987643 46666653 566665543
No 306
>KOG2805 consensus tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=27.66 E-value=37 Score=28.15 Aligned_cols=22 Identities=23% Similarity=0.339 Sum_probs=19.7
Q ss_pred hhhhhhHHHHHHhhcCccccch
Q 034528 67 IDIYSEWIDECERVNNLEDDGA 88 (92)
Q Consensus 67 VDVYs~WiD~~~~~n~~~~~~~ 88 (92)
.||++.++|.++.|..++-|+.
T Consensus 81 ~~Vfs~~L~~Y~~G~TPNPDI~ 102 (377)
T KOG2805|consen 81 NDVFSPFLEEYENGRTPNPDIL 102 (377)
T ss_pred HHHHHHHHHHHhcCCCCCCCcc
Confidence 5999999999999999988764
No 307
>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=27.65 E-value=37 Score=25.38 Aligned_cols=19 Identities=26% Similarity=0.719 Sum_probs=16.5
Q ss_pred CcchhhhhhHHHHHHhhcC
Q 034528 64 TEPIDIYSEWIDECERVNN 82 (92)
Q Consensus 64 ~epVDVYs~WiD~~~~~n~ 82 (92)
.+|+|++..|+++..+.+-
T Consensus 28 ~~P~~~f~~W~~~a~~~~~ 46 (217)
T TIGR00558 28 DDPIDLFEIWFNEAIEARL 46 (217)
T ss_pred CCHHHHHHHHHHHHHhcCC
Confidence 5999999999999887663
No 308
>PRK05580 primosome assembly protein PriA; Validated
Probab=27.50 E-value=48 Score=28.70 Aligned_cols=30 Identities=20% Similarity=0.491 Sum_probs=16.9
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFS 57 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~ 57 (92)
.+.||.|+- .....+ ....+.|.-||.+..
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 222222 235688888886543
No 309
>PF10932 DUF2783: Protein of unknown function (DUF2783); InterPro: IPR021233 This is a bacterial family of uncharacterised protein.
Probab=27.49 E-value=30 Score=21.73 Aligned_cols=26 Identities=19% Similarity=0.420 Sum_probs=21.1
Q ss_pred CCCCcchhhhhhHHHHHHhhcCcccc
Q 034528 61 TALTEPIDIYSEWIDECERVNNLEDD 86 (92)
Q Consensus 61 ~~L~epVDVYs~WiD~~~~~n~~~~~ 86 (92)
+.|..|=|.|..+|++-+.....+++
T Consensus 5 pnl~~pD~fY~~Li~aH~gLs~e~S~ 30 (60)
T PF10932_consen 5 PNLADPDDFYEALIEAHRGLSDEQSA 30 (60)
T ss_pred CCCCChhHHHHHHHHHHhCCCHHHHH
Confidence 56889999999999998877765544
No 310
>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=27.26 E-value=21 Score=20.85 Aligned_cols=7 Identities=43% Similarity=1.602 Sum_probs=3.4
Q ss_pred cCCCCCC
Q 034528 24 SCPFCNH 30 (92)
Q Consensus 24 ~CPfC~~ 30 (92)
.||.|+.
T Consensus 22 ~CPlC~r 28 (54)
T PF04423_consen 22 CCPLCGR 28 (54)
T ss_dssp E-TTT--
T ss_pred cCCCCCC
Confidence 7899986
No 311
>CHL00136 rpl31 ribosomal protein L31; Validated
Probab=27.16 E-value=63 Score=20.43 Aligned_cols=34 Identities=12% Similarity=0.037 Sum_probs=17.6
Q ss_pred CccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528 20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFS 57 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~ 57 (92)
...+.| -|+.. ..+.-. ...+..-.|..|+--|.
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 345667 46652 222222 23366667777775554
No 312
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.16 E-value=14 Score=31.72 Aligned_cols=33 Identities=30% Similarity=0.690 Sum_probs=27.2
Q ss_pred CccccCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528 20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESF 56 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~ 56 (92)
+|...||+|=++.+|.+.+. -|++.|..|-+.|
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 34689999999999988774 6999999988754
No 313
>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=27.11 E-value=26 Score=24.45 Aligned_cols=15 Identities=27% Similarity=0.368 Sum_probs=11.5
Q ss_pred CCccccCCCCCCCCe
Q 034528 19 LDTVFSCPFCNHGTS 33 (92)
Q Consensus 19 l~~~F~CPfC~~~~s 33 (92)
-...|-||-|+||=+
T Consensus 16 dg~~~iCpeC~~EW~ 30 (109)
T TIGR00686 16 DGTQLICPSCLYEWN 30 (109)
T ss_pred cCCeeECcccccccc
Confidence 345799999999753
No 314
>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=26.86 E-value=36 Score=20.04 Aligned_cols=7 Identities=57% Similarity=1.625 Sum_probs=5.2
Q ss_pred CCCCCCC
Q 034528 25 CPFCNHG 31 (92)
Q Consensus 25 CPfC~~~ 31 (92)
||||...
T Consensus 1 CP~C~~k 7 (43)
T PF03470_consen 1 CPFCPGK 7 (43)
T ss_pred CCCCCCC
Confidence 8888763
No 315
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=26.70 E-value=42 Score=25.11 Aligned_cols=7 Identities=43% Similarity=1.436 Sum_probs=6.5
Q ss_pred CCCCCCC
Q 034528 25 CPFCNHG 31 (92)
Q Consensus 25 CPfC~~~ 31 (92)
||.|||.
T Consensus 156 Cp~CG~~ 162 (177)
T COG1439 156 CPICGSP 162 (177)
T ss_pred CCCCCCc
Confidence 9999996
No 316
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=26.49 E-value=34 Score=21.66 Aligned_cols=31 Identities=13% Similarity=0.384 Sum_probs=22.8
Q ss_pred CCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 18 KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 18 kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
+-+-.+-|--|+.++++ .+. -.+.|+-||-+
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 222 46899999964
No 317
>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=26.28 E-value=21 Score=23.09 Aligned_cols=11 Identities=18% Similarity=0.739 Sum_probs=8.0
Q ss_pred ccccCCCCCCC
Q 034528 21 TVFSCPFCNHG 31 (92)
Q Consensus 21 ~~F~CPfC~~~ 31 (92)
.-|.||+|..-
T Consensus 13 ~D~~Cp~C~~~ 23 (154)
T cd03023 13 FDYNCGYCKKL 23 (154)
T ss_pred ECCCChhHHHh
Confidence 35789999863
No 318
>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=26.25 E-value=30 Score=22.94 Aligned_cols=8 Identities=38% Similarity=1.514 Sum_probs=5.8
Q ss_pred ccCCCCCC
Q 034528 23 FSCPFCNH 30 (92)
Q Consensus 23 F~CPfC~~ 30 (92)
-+||+||-
T Consensus 2 I~CP~CG~ 9 (84)
T TIGR01374 2 IPCPYCGP 9 (84)
T ss_pred ccCCCCCC
Confidence 36888884
No 319
>KOG3309 consensus Ferredoxin [Energy production and conversion]
Probab=26.12 E-value=32 Score=25.45 Aligned_cols=38 Identities=21% Similarity=0.361 Sum_probs=31.3
Q ss_pred EEEEcCccCCeeEe-ecCCCCcchhhhhhHHHHHHhhcC
Q 034528 45 GEAICNICQESFST-TITALTEPIDIYSEWIDECERVNN 82 (92)
Q Consensus 45 g~l~C~~Cg~~~~~-~i~~L~epVDVYs~WiD~~~~~n~ 82 (92)
|++.|..|++.++. ....|.+|-|==.+-+|.....++
T Consensus 83 gslACSTCHViv~~~~yekl~ep~DeE~DmLDlA~gLt~ 121 (159)
T KOG3309|consen 83 GSLACSTCHVIVDEEYYEKLPEPEDEENDMLDLAFGLTE 121 (159)
T ss_pred ccccccceEEEEcHHHHhcCCCCcchHHHHHHhhhcccc
Confidence 78999999999876 456899999988888888776553
No 320
>MTH00027 COX2 cytochrome c oxidase subunit II; Provisional
Probab=25.98 E-value=52 Score=25.62 Aligned_cols=46 Identities=20% Similarity=0.275 Sum_probs=31.6
Q ss_pred CCCCeEEEEeecCCceEEEEcCc-cCCeeE-eecCCCCcchhhhhhHHH
Q 034528 29 NHGTSVECRIDMKNLIGEAICNI-CQESFS-TTITALTEPIDIYSEWID 75 (92)
Q Consensus 29 ~~~~sV~vkidk~~~~g~l~C~~-Cg~~~~-~~i~~L~epVDVYs~WiD 75 (92)
|+-+.+....++ .|+-...|.. ||..+. |++.-...+-+.|.+|++
T Consensus 211 Gr~n~~~~~~~~-~G~y~g~CsE~CG~~Hs~Mpi~v~vv~~~~f~~Wl~ 258 (262)
T MTH00027 211 GRINETGFLIKR-PGIFYGQCSEICGANHSFMPIVVESVSLSKYIDWIG 258 (262)
T ss_pred CceeeEEEEcCC-cEEEEEEcchhcCcCcCCCeEEEEEECHHHHHHHHc
Confidence 344555555544 4677889987 999875 466555556688999984
No 321
>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=25.92 E-value=36 Score=18.86 Aligned_cols=15 Identities=20% Similarity=0.594 Sum_probs=11.2
Q ss_pred EEcCccCCeeEeecC
Q 034528 47 AICNICQESFSTTIT 61 (92)
Q Consensus 47 l~C~~Cg~~~~~~i~ 61 (92)
..|..||..|....+
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 479999999876433
No 322
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=25.92 E-value=41 Score=16.02 Aligned_cols=12 Identities=50% Similarity=1.198 Sum_probs=8.5
Q ss_pred EcCccCCeeEee
Q 034528 48 ICNICQESFSTT 59 (92)
Q Consensus 48 ~C~~Cg~~~~~~ 59 (92)
.|.+|+..|...
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 588888877543
No 323
>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=25.85 E-value=34 Score=21.01 Aligned_cols=15 Identities=20% Similarity=0.631 Sum_probs=6.1
Q ss_pred CCCccccCCCCCCCC
Q 034528 18 KLDTVFSCPFCNHGT 32 (92)
Q Consensus 18 kl~~~F~CPfC~~~~ 32 (92)
|+-..+.||.||+..
T Consensus 29 PvLr~y~Cp~CgAtG 43 (55)
T PF05741_consen 29 PVLRKYVCPICGATG 43 (55)
T ss_dssp TTGGG---TTT---G
T ss_pred HHHhcCcCCCCcCcC
Confidence 444678999999743
No 324
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=25.77 E-value=20 Score=28.79 Aligned_cols=31 Identities=23% Similarity=0.458 Sum_probs=14.1
Q ss_pred CCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 25 CPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 25 CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
|=+||.+--=+=-+..-.+--+..|-+|+..
T Consensus 13 cwycnrefddekiliqhqkakhfkchichkk 43 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAKHFKCHICHKK 43 (341)
T ss_pred eeecccccchhhhhhhhhhhccceeeeehhh
Confidence 6677764211111111123345677777654
No 325
>PRK12860 transcriptional activator FlhC; Provisional
Probab=25.73 E-value=34 Score=25.72 Aligned_cols=13 Identities=31% Similarity=0.787 Sum_probs=10.3
Q ss_pred CCCccccCCCCCC
Q 034528 18 KLDTVFSCPFCNH 30 (92)
Q Consensus 18 kl~~~F~CPfC~~ 30 (92)
-+-..|.||+|+-
T Consensus 150 e~~~~f~CplC~~ 162 (189)
T PRK12860 150 DLRHNFVCGLCQP 162 (189)
T ss_pred ccCCCCcCCCCCC
Confidence 3456899999994
No 326
>COG1622 CyoA Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]
Probab=25.32 E-value=45 Score=25.75 Aligned_cols=38 Identities=21% Similarity=0.490 Sum_probs=28.0
Q ss_pred CCceEEEEcCc-cCCeeEe---ecCCCCcchhhhhhHHHHHHhh
Q 034528 41 KNLIGEAICNI-CQESFST---TITALTEPIDIYSEWIDECERV 80 (92)
Q Consensus 41 ~~~~g~l~C~~-Cg~~~~~---~i~~L~epVDVYs~WiD~~~~~ 80 (92)
+.|.....|.. ||..|.. .|.-.++. | |..|+..-.+.
T Consensus 185 ~~G~Y~g~Cae~CG~gH~~M~~~v~vvs~~-~-f~~W~~~~~~~ 226 (247)
T COG1622 185 KPGTYRGICAEYCGPGHSFMRFKVIVVSQE-D-FDAWVAEVKAA 226 (247)
T ss_pred CCeEEEEEcHhhcCCCcccceEEEEEEcHH-H-HHHHHHhhhhc
Confidence 45788999998 9998863 56666554 5 99999755444
No 327
>PF13397 DUF4109: Domain of unknown function (DUF4109)
Probab=25.23 E-value=39 Score=23.33 Aligned_cols=15 Identities=20% Similarity=0.682 Sum_probs=11.9
Q ss_pred CCCCccccCCCCCCC
Q 034528 17 DKLDTVFSCPFCNHG 31 (92)
Q Consensus 17 ~kl~~~F~CPfC~~~ 31 (92)
.-+|-+.+||+||.+
T Consensus 45 AevP~~WeC~~cG~~ 59 (105)
T PF13397_consen 45 AEVPATWECPRCGLP 59 (105)
T ss_pred CCCCCceeCCCCCCc
Confidence 357888999999975
No 328
>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=25.02 E-value=69 Score=19.06 Aligned_cols=27 Identities=22% Similarity=0.523 Sum_probs=14.7
Q ss_pred ccCC--CCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 23 FSCP--FCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 23 F~CP--fC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
=.|| .||.. ..--.. .....|+.||.+
T Consensus 19 k~CP~~~CG~G-vFMA~H-----~dR~~CGKCg~T 47 (47)
T PF01599_consen 19 KECPSPRCGAG-VFMAEH-----KDRHYCGKCGYT 47 (47)
T ss_dssp EE-TSTTTTSS-SEEEE------SSEEEETTTSS-
T ss_pred hcCCCcccCCc-eEeeec-----CCCccCCCcccC
Confidence 3689 99963 211111 126799999863
No 329
>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=24.94 E-value=34 Score=20.72 Aligned_cols=13 Identities=23% Similarity=0.759 Sum_probs=10.3
Q ss_pred CccccCCCCCCCC
Q 034528 20 DTVFSCPFCNHGT 32 (92)
Q Consensus 20 ~~~F~CPfC~~~~ 32 (92)
.++=.||.||++.
T Consensus 11 ~kY~~Cp~CGN~~ 23 (49)
T PF12677_consen 11 NKYCKCPKCGNDK 23 (49)
T ss_pred hhhccCcccCCcE
Confidence 4677999999853
No 330
>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=24.91 E-value=46 Score=24.08 Aligned_cols=11 Identities=36% Similarity=0.993 Sum_probs=8.8
Q ss_pred ccccCCCCCCC
Q 034528 21 TVFSCPFCNHG 31 (92)
Q Consensus 21 ~~F~CPfC~~~ 31 (92)
...+||+||..
T Consensus 31 glv~CP~Cgs~ 41 (148)
T PF06676_consen 31 GLVSCPVCGST 41 (148)
T ss_pred CCccCCCCCCC
Confidence 35789999974
No 331
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=24.73 E-value=51 Score=32.33 Aligned_cols=30 Identities=30% Similarity=0.659 Sum_probs=20.6
Q ss_pred cCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 24 SCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
.||.|+...---|++...+ |=+.|..||-+
T Consensus 1706 ~cp~c~~~~~~~~~~~~~~--gc~~c~~cg~s 1735 (1740)
T PRK08332 1706 YCPVCYEKEGKLVELRMES--GCATCPVCGWS 1735 (1740)
T ss_pred CCCCCCCCCCcceeeEecC--CceeCCCCCCc
Confidence 3999998643344454455 45699999965
No 332
>PF13132 DUF3950: Domain of unknown function (DUF3950)
Probab=24.55 E-value=50 Score=18.13 Aligned_cols=10 Identities=50% Similarity=1.527 Sum_probs=6.8
Q ss_pred hhhHH-HHHHh
Q 034528 70 YSEWI-DECER 79 (92)
Q Consensus 70 Ys~Wi-D~~~~ 79 (92)
||.|+ |+|.+
T Consensus 17 FSaWV~dACr~ 27 (30)
T PF13132_consen 17 FSAWVKDACRR 27 (30)
T ss_pred hHHHHHHHHHH
Confidence 68885 66654
No 333
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=24.53 E-value=35 Score=29.87 Aligned_cols=13 Identities=31% Similarity=0.529 Sum_probs=6.5
Q ss_pred EEEEcCccCCeeE
Q 034528 45 GEAICNICQESFS 57 (92)
Q Consensus 45 g~l~C~~Cg~~~~ 57 (92)
+.-.|..||....
T Consensus 40 ~~~fC~~CG~~~~ 52 (645)
T PRK14559 40 DEAHCPNCGAETG 52 (645)
T ss_pred ccccccccCCccc
Confidence 3445555555433
No 334
>PRK10220 hypothetical protein; Provisional
Probab=24.20 E-value=34 Score=23.91 Aligned_cols=17 Identities=24% Similarity=0.575 Sum_probs=12.4
Q ss_pred CCCccccCCCCCCCCeE
Q 034528 18 KLDTVFSCPFCNHGTSV 34 (92)
Q Consensus 18 kl~~~F~CPfC~~~~sV 34 (92)
.-...|-||-|+||=+-
T Consensus 16 ~d~~~~vCpeC~hEW~~ 32 (111)
T PRK10220 16 EDNGMYICPECAHEWND 32 (111)
T ss_pred cCCCeEECCcccCcCCc
Confidence 34467999999997543
No 335
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=24.17 E-value=34 Score=28.36 Aligned_cols=18 Identities=28% Similarity=0.663 Sum_probs=14.7
Q ss_pred CCCCCccccCCCCCCCCe
Q 034528 16 VDKLDTVFSCPFCNHGTS 33 (92)
Q Consensus 16 ~~kl~~~F~CPfC~~~~s 33 (92)
-..||-.|.||.|+..++
T Consensus 452 ~~~lp~~~~cp~c~~~k~ 469 (479)
T PRK05452 452 WSEVPDNFLCPECSLGKD 469 (479)
T ss_pred hhhCCCCCcCcCCCCcHH
Confidence 457888899999998765
No 336
>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=24.16 E-value=49 Score=22.71 Aligned_cols=15 Identities=20% Similarity=0.813 Sum_probs=12.5
Q ss_pred hhhhhHHHHHHhhcC
Q 034528 68 DIYSEWIDECERVNN 82 (92)
Q Consensus 68 DVYs~WiD~~~~~n~ 82 (92)
.-|.+|+.+|.-+.+
T Consensus 90 eqya~Wmaa~rlas~ 104 (106)
T cd01237 90 KQYAKWMAACRLASK 104 (106)
T ss_pred HHHHHHHHHHHHhhC
Confidence 579999999988764
No 337
>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]
Probab=24.11 E-value=38 Score=24.92 Aligned_cols=11 Identities=36% Similarity=0.918 Sum_probs=8.9
Q ss_pred CccccCCCCCC
Q 034528 20 DTVFSCPFCNH 30 (92)
Q Consensus 20 ~~~F~CPfC~~ 30 (92)
...|.||.|||
T Consensus 131 ge~~rc~eCG~ 141 (153)
T KOG3352|consen 131 GETQRCPECGH 141 (153)
T ss_pred CCcccCCcccc
Confidence 35788999998
No 338
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=24.11 E-value=42 Score=21.01 Aligned_cols=9 Identities=33% Similarity=1.099 Sum_probs=7.2
Q ss_pred cCCCCCCCC
Q 034528 24 SCPFCNHGT 32 (92)
Q Consensus 24 ~CPfC~~~~ 32 (92)
.||.||...
T Consensus 17 ~CP~Cgs~~ 25 (61)
T PRK08351 17 RCPVCGSRD 25 (61)
T ss_pred cCCCCcCCc
Confidence 699999853
No 339
>MTH00076 COX2 cytochrome c oxidase subunit II; Provisional
Probab=23.97 E-value=59 Score=24.55 Aligned_cols=46 Identities=13% Similarity=0.240 Sum_probs=29.7
Q ss_pred CCCeEEEEeecCCceEEEEcCc-cCCeeE-eecCCCCcchhhhhhHHHH
Q 034528 30 HGTSVECRIDMKNLIGEAICNI-CQESFS-TTITALTEPIDIYSEWIDE 76 (92)
Q Consensus 30 ~~~sV~vkidk~~~~g~l~C~~-Cg~~~~-~~i~~L~epVDVYs~WiD~ 76 (92)
..+.+....++ .|+....|.. ||..+. |++.--.-+-+.|.+|+++
T Consensus 178 ~~n~~~~~~~~-~G~~~g~C~e~CG~~Hs~M~~~v~vv~~~~f~~wl~~ 225 (228)
T MTH00076 178 RLNQTSFIASR-PGVYYGQCSEICGANHSFMPIVVEATPLNNFLNWSSS 225 (228)
T ss_pred cceeEEEEeCC-cEEEEEEChhhcCccccCCceEEEEeCHHHHHHHHHh
Confidence 33445555443 4666788987 998775 4554433455889999965
No 340
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=23.88 E-value=56 Score=26.36 Aligned_cols=60 Identities=17% Similarity=0.371 Sum_probs=35.3
Q ss_pred ccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee-----------------------cCCCCcc-hhhhhhHHHHHH
Q 034528 23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT-----------------------ITALTEP-IDIYSEWIDECE 78 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~-----------------------i~~L~ep-VDVYs~WiD~~~ 78 (92)
-.||-|++ + -..+....-.-.|-.|+-.+.+. .++|.-+ -+.|.+||.+..
T Consensus 29 ~KCp~c~~---~--~y~~eL~~n~~vcp~c~~h~ri~A~~Ri~~llD~gsf~el~~~l~~~dPL~F~d~k~Y~~rL~~a~ 103 (294)
T COG0777 29 TKCPSCGE---M--LYRKELESNLKVCPKCGHHMRISARERLEALLDEGSFEELDSPLEPKDPLKFPDSKKYKDRLEAAR 103 (294)
T ss_pred eECCCccc---e--eeHHHHHhhhhcccccCcccccCHHHHHHHhhCCCcceecccCCCcCCcccCCcchhhHHHHHHHH
Confidence 46999997 2 12222333456799998654321 1233222 137999998888
Q ss_pred hhcCccccc
Q 034528 79 RVNNLEDDG 87 (92)
Q Consensus 79 ~~n~~~~~~ 87 (92)
+.....+.+
T Consensus 104 ~~tg~~dav 112 (294)
T COG0777 104 KKTGLDDAV 112 (294)
T ss_pred hhcCCCcce
Confidence 777655554
No 341
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=23.86 E-value=40 Score=28.62 Aligned_cols=11 Identities=27% Similarity=0.591 Sum_probs=4.7
Q ss_pred cccCCCCCCCC
Q 034528 22 VFSCPFCNHGT 32 (92)
Q Consensus 22 ~F~CPfC~~~~ 32 (92)
.+.||.||.++
T Consensus 504 ~~~CP~CGs~~ 514 (546)
T PF13597_consen 504 GDKCPKCGSEN 514 (546)
T ss_dssp EEE-CCC----
T ss_pred CCCCCCCCCcc
Confidence 67788888765
No 342
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=23.86 E-value=56 Score=22.10 Aligned_cols=31 Identities=13% Similarity=0.315 Sum_probs=19.2
Q ss_pred CCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528 17 DKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQE 54 (92)
Q Consensus 17 ~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~ 54 (92)
..+|-.|.|+.||+ ...+. ......|..||.
T Consensus 65 ~~~p~~~~C~~Cg~----~~~~~---~~~~~~CP~Cgs 95 (114)
T PRK03681 65 EEQEAECWCETCQQ----YVTLL---TQRVRRCPQCHG 95 (114)
T ss_pred EeeCcEEEcccCCC----eeecC---CccCCcCcCcCC
Confidence 45677889999996 12221 112256999994
No 343
>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=23.84 E-value=23 Score=23.46 Aligned_cols=6 Identities=50% Similarity=1.735 Sum_probs=4.1
Q ss_pred cCCCCC
Q 034528 24 SCPFCN 29 (92)
Q Consensus 24 ~CPfC~ 29 (92)
.||+||
T Consensus 3 ~CP~CG 8 (84)
T PF04267_consen 3 PCPHCG 8 (84)
T ss_dssp EETTTE
T ss_pred cCCCCC
Confidence 577776
No 344
>PTZ00293 thymidine kinase; Provisional
Probab=23.74 E-value=69 Score=24.19 Aligned_cols=31 Identities=29% Similarity=0.441 Sum_probs=23.1
Q ss_pred cCCCCCCCCeEEEEeecCC--------ceEEEEcCccCC
Q 034528 24 SCPFCNHGTSVECRIDMKN--------LIGEAICNICQE 54 (92)
Q Consensus 24 ~CPfC~~~~sV~vkidk~~--------~~g~l~C~~Cg~ 54 (92)
-|.+||.+-+.+.++.... ......|+.|-.
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 4999999998888885432 124788999984
No 345
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=23.69 E-value=26 Score=32.05 Aligned_cols=61 Identities=18% Similarity=0.242 Sum_probs=0.0
Q ss_pred ccccCCCCCCCCeEEEEeecCC--ceEEEEcCccCCeeE---------eecCCCCcchhhhhhHHHHHHhhcC
Q 034528 21 TVFSCPFCNHGTSVECRIDMKN--LIGEAICNICQESFS---------TTITALTEPIDIYSEWIDECERVNN 82 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~--~~g~l~C~~Cg~~~~---------~~i~~L~epVDVYs~WiD~~~~~n~ 82 (92)
-.|.||-||++ |....=..-. -.-.-.|..|+.... ....+-..-||+=+.|-.|++....
T Consensus 654 ~~r~Cp~Cg~~-t~~~~Cp~CG~~T~~~~~Cp~C~~~~~~~~C~~C~~~~~~~~~~~i~l~~~~~~A~e~lg~ 725 (900)
T PF03833_consen 654 GRRRCPKCGKE-TFYNRCPECGSHTEPVYVCPDCGIEVEEDECPKCGRETTSYSKQKIDLKEEYDRALENLGE 725 (900)
T ss_dssp -------------------------------------------------------------------------
T ss_pred ecccCcccCCc-chhhcCcccCCccccceeccccccccCccccccccccCcccceeecCHHHHHHHHHHhhcc
Confidence 35678877763 2322221111 112345555555431 1334455678888888888877653
No 346
>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=23.42 E-value=48 Score=20.76 Aligned_cols=18 Identities=28% Similarity=0.527 Sum_probs=10.8
Q ss_pred eEEEEcCccCCeeEeecC
Q 034528 44 IGEAICNICQESFSTTIT 61 (92)
Q Consensus 44 ~g~l~C~~Cg~~~~~~i~ 61 (92)
...+.|..||..|.+.-+
T Consensus 11 ~v~v~c~s~g~~~~~~St 28 (69)
T PF01197_consen 11 EVKVTCSSCGNTFETRST 28 (69)
T ss_dssp EEEEEES-SSSCECECSS
T ss_pred EEEEEEcCCCCEEEEEEC
Confidence 356677777777766433
No 347
>PRK09502 iscA iron-sulfur cluster assembly protein; Provisional
Probab=22.94 E-value=29 Score=22.90 Aligned_cols=12 Identities=42% Similarity=0.830 Sum_probs=9.5
Q ss_pred EEEEcCccCCeeE
Q 034528 45 GEAICNICQESFS 57 (92)
Q Consensus 45 g~l~C~~Cg~~~~ 57 (92)
+.-+|+ ||.+|+
T Consensus 95 a~~~Cg-CG~Sf~ 106 (107)
T PRK09502 95 VKDECG-CGESFH 106 (107)
T ss_pred CCCccC-CCCCee
Confidence 456799 999986
No 348
>PF07450 HycH: Formate hydrogenlyase maturation protein HycH; InterPro: IPR010005 This family contains the bacterial formate hydrogenlyase maturation protein HycH, which is approximately 140 residues long. This may be required for the conversion of a precursor form of the large subunit of hydrogenlyase 3 into a mature form [].
Probab=22.85 E-value=35 Score=24.48 Aligned_cols=31 Identities=23% Similarity=0.419 Sum_probs=23.6
Q ss_pred CCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhh
Q 034528 41 KNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERV 80 (92)
Q Consensus 41 ~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~ 80 (92)
-..+|.|-|-.+ .|.=|.+.|.+||+.+.++
T Consensus 34 GHhvGvIDcle~---------~l~cp~~~y~~wi~~lp~~ 64 (131)
T PF07450_consen 34 GHHVGVIDCLEK---------VLECPLEEYERWIAQLPEG 64 (131)
T ss_pred ccccceEeechh---------hccCCHHHHHHHHHhCCcH
Confidence 346778877765 4567899999999998554
No 349
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=22.79 E-value=39 Score=19.96 Aligned_cols=13 Identities=31% Similarity=0.639 Sum_probs=9.3
Q ss_pred ccccCCCCCCCCe
Q 034528 21 TVFSCPFCNHGTS 33 (92)
Q Consensus 21 ~~F~CPfC~~~~s 33 (92)
|=+.||-||-..+
T Consensus 8 tG~~CPgCG~tRa 20 (52)
T PF10825_consen 8 TGIPCPGCGMTRA 20 (52)
T ss_pred hCCCCCCCcHHHH
Confidence 4578999986544
No 350
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=22.79 E-value=47 Score=18.38 Aligned_cols=11 Identities=27% Similarity=0.966 Sum_probs=8.3
Q ss_pred CccccCCCCCC
Q 034528 20 DTVFSCPFCNH 30 (92)
Q Consensus 20 ~~~F~CPfC~~ 30 (92)
...+.||+|+.
T Consensus 34 ~~~~~CP~C~k 44 (44)
T PF14634_consen 34 GKSVKCPICRK 44 (44)
T ss_pred CCCCCCcCCCC
Confidence 45778999973
No 351
>PRK06260 threonine synthase; Validated
Probab=22.71 E-value=65 Score=25.73 Aligned_cols=9 Identities=22% Similarity=0.696 Sum_probs=5.0
Q ss_pred ccCCCCCCC
Q 034528 23 FSCPFCNHG 31 (92)
Q Consensus 23 F~CPfC~~~ 31 (92)
|.|+.||++
T Consensus 4 ~~C~~cg~~ 12 (397)
T PRK06260 4 LKCIECGKE 12 (397)
T ss_pred EEECCCCCC
Confidence 556666653
No 352
>cd02152 OAT Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in the arginine biosynthetic pathway. Members of this family may experience feedback inhibition by L-arginine. The active enzyme is a heterotetramer of two alpha and two beta chains, where the alpha and beta chains are the result of autocatalytic cleavage. OATs found in the clavulanic acid biosynthesis gene cluster catalyze the fifth step only, and may utilize acetyl acceptors other than glutamate.
Probab=22.69 E-value=89 Score=25.96 Aligned_cols=32 Identities=19% Similarity=0.229 Sum_probs=28.5
Q ss_pred CeEEEEeecCCceEEEEcCccCCeeEe-ecCCC
Q 034528 32 TSVECRIDMKNLIGEAICNICQESFST-TITAL 63 (92)
Q Consensus 32 ~sV~vkidk~~~~g~l~C~~Cg~~~~~-~i~~L 63 (92)
..|.|.+|...|.+...-..|.++|++ +||.-
T Consensus 355 ~ei~I~vdL~~G~~~~t~w~cDLt~~YV~INa~ 387 (390)
T cd02152 355 DEITITVDLGRGDGSATVWGCDLTYDYVKINAD 387 (390)
T ss_pred CeEEEEEEeCCCCceEEEEcccCCccceeECCc
Confidence 468999999999999999999999998 78864
No 353
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=22.62 E-value=43 Score=20.63 Aligned_cols=9 Identities=44% Similarity=1.283 Sum_probs=7.7
Q ss_pred cccCCCCCC
Q 034528 22 VFSCPFCNH 30 (92)
Q Consensus 22 ~F~CPfC~~ 30 (92)
...|||||.
T Consensus 35 ~~pC~fCg~ 43 (57)
T PF06221_consen 35 LGPCPFCGT 43 (57)
T ss_pred cCcCCCCCC
Confidence 678999995
No 354
>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=22.43 E-value=69 Score=23.37 Aligned_cols=37 Identities=22% Similarity=0.426 Sum_probs=21.0
Q ss_pred CCC-CccccCCCCCCCCeEEEEe--ecCCceEEEEcCc-cC
Q 034528 17 DKL-DTVFSCPFCNHGTSVECRI--DMKNLIGEAICNI-CQ 53 (92)
Q Consensus 17 ~kl-~~~F~CPfC~~~~sV~vki--dk~~~~g~l~C~~-Cg 53 (92)
-+| ++++.|-.||..+....-+ -+.+.+-.|-||. |-
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 355 7999999999988655554 3456788999998 86
No 355
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=22.27 E-value=68 Score=26.43 Aligned_cols=33 Identities=18% Similarity=0.440 Sum_probs=20.1
Q ss_pred CccccCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528 20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESF 56 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~ 56 (92)
+..=.||.|+. + +.+..-..-....|..||..-
T Consensus 8 ~~~~~C~~Cd~---l-~~~~~l~~g~~a~CpRCg~~L 40 (419)
T PRK15103 8 AKHILCPQCDM---L-VALPRLEHGQKAACPRCGTTL 40 (419)
T ss_pred CCcccCCCCCc---e-eecCCCCCCCeeECCCCCCCC
Confidence 34456999996 2 222222223468899999754
No 356
>PRK12496 hypothetical protein; Provisional
Probab=22.24 E-value=43 Score=24.10 Aligned_cols=8 Identities=25% Similarity=0.596 Sum_probs=5.2
Q ss_pred ccCCCCCC
Q 034528 23 FSCPFCNH 30 (92)
Q Consensus 23 F~CPfC~~ 30 (92)
+.|+-|+.
T Consensus 128 ~~C~gC~~ 135 (164)
T PRK12496 128 KVCKGCKK 135 (164)
T ss_pred EECCCCCc
Confidence 56777775
No 357
>PHA02768 hypothetical protein; Provisional
Probab=21.79 E-value=35 Score=20.92 Aligned_cols=38 Identities=13% Similarity=0.137 Sum_probs=21.3
Q ss_pred cccCCCCCCCCeEEEEeecCCce--EEEEcCccCCeeEee
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLI--GEAICNICQESFSTT 59 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~--g~l~C~~Cg~~~~~~ 59 (92)
-|.||.||..=+..-.+..-..+ -...|..|+..|...
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 48999999642222222111111 134899999987743
No 358
>PF14940 TMEM219: Transmembrane 219
Probab=21.77 E-value=89 Score=24.02 Aligned_cols=28 Identities=18% Similarity=0.310 Sum_probs=23.1
Q ss_pred CeeEeecCCCCcchhhhhhHHHHHHhhcC
Q 034528 54 ESFSTTITALTEPIDIYSEWIDECERVNN 82 (92)
Q Consensus 54 ~~~~~~i~~L~epVDVYs~WiD~~~~~n~ 82 (92)
+.|....+.|-.| ||+.||-..+.+.++
T Consensus 28 Lg~yi~~~~l~nP-Di~~DWN~fL~~ls~ 55 (223)
T PF14940_consen 28 LGYYIKRNELKNP-DIPQDWNTFLLSLSQ 55 (223)
T ss_pred eeeEecccCCCcc-cchhhHHHHHHhhcC
Confidence 3455688999999 999999998887774
No 359
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=21.67 E-value=6.8 Score=27.68 Aligned_cols=57 Identities=16% Similarity=0.256 Sum_probs=30.5
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhh
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERV 80 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~ 80 (92)
.+.|..|++.-...--.+.-.....-.|..||..--..|--..|+++ .+|-.+.++.
T Consensus 105 ~~~C~~C~~~~~~~~~~~~~~~~~~~~C~~C~~~lrp~vv~fgE~~~--~~~~~~~~~~ 161 (178)
T PF02146_consen 105 RLRCSKCGKEYDREDIVDSIDEEEPPRCPKCGGLLRPDVVLFGESLP--EEIEEAIEDA 161 (178)
T ss_dssp EEEETTTSBEEEGHHHHHHHHTTSSCBCTTTSCBEEEEE--BTSB-S--HHHHHHHHHH
T ss_pred eeeecCCCccccchhhcccccccccccccccCccCCCCeeecCCCCH--HHHHHHHHHH
Confidence 46899998732111000000000112899999887777777888888 6666655543
No 360
>PRK10954 periplasmic protein disulfide isomerase I; Provisional
Probab=21.66 E-value=28 Score=25.10 Aligned_cols=13 Identities=31% Similarity=0.695 Sum_probs=9.8
Q ss_pred ccccCCCCCCCCe
Q 034528 21 TVFSCPFCNHGTS 33 (92)
Q Consensus 21 ~~F~CPfC~~~~s 33 (92)
--|.||+|.+-..
T Consensus 45 fdy~CphC~~~~~ 57 (207)
T PRK10954 45 FSFYCPHCYQFEE 57 (207)
T ss_pred eCCCCccHHHhcc
Confidence 4578999998544
No 361
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=21.62 E-value=67 Score=17.91 Aligned_cols=9 Identities=33% Similarity=1.014 Sum_probs=4.7
Q ss_pred cccCCCCCC
Q 034528 22 VFSCPFCNH 30 (92)
Q Consensus 22 ~F~CPfC~~ 30 (92)
.|.|.+|+.
T Consensus 12 ~f~C~~C~~ 20 (39)
T smart00154 12 GFKCRHCGN 20 (39)
T ss_pred CeECCccCC
Confidence 455555553
No 362
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.49 E-value=91 Score=19.74 Aligned_cols=35 Identities=26% Similarity=0.492 Sum_probs=23.3
Q ss_pred CccccCCCC----CCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 20 DTVFSCPFC----NHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 20 ~~~F~CPfC----~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
+..|.||== +|.. |-+.| ..-|++.|.=|+..|..
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 455666432 3443 66666 45589999999998864
No 363
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=21.44 E-value=50 Score=20.89 Aligned_cols=9 Identities=22% Similarity=0.722 Sum_probs=7.4
Q ss_pred cCCCCCCCC
Q 034528 24 SCPFCNHGT 32 (92)
Q Consensus 24 ~CPfC~~~~ 32 (92)
.||.||...
T Consensus 19 ~Cp~Cgs~~ 27 (64)
T PRK06393 19 TCPVHGDEK 27 (64)
T ss_pred cCCCCCCCc
Confidence 899999853
No 364
>PRK08402 replication factor A; Reviewed
Probab=21.44 E-value=58 Score=26.45 Aligned_cols=26 Identities=27% Similarity=0.538 Sum_probs=15.9
Q ss_pred ccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528 23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQE 54 (92)
Q Consensus 23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~ 54 (92)
=.||.||. ++..+.+-+.-.|..||.
T Consensus 213 ~aCp~CnK------kv~~~~~~~~~~Ce~~~~ 238 (355)
T PRK08402 213 DACPECRR------KVDYDPATDTWICPEHGE 238 (355)
T ss_pred ecCCCCCe------EEEEecCCCCEeCCCCCC
Confidence 46888886 233233345567888874
No 365
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=21.24 E-value=46 Score=21.36 Aligned_cols=29 Identities=21% Similarity=0.573 Sum_probs=17.7
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST 58 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~ 58 (92)
+|.| -||.. +--+++..+-.| +||-.-.-
T Consensus 3 ifrC-~Cgr~------lya~e~~kTkkC-~CG~~l~v 31 (68)
T PF09082_consen 3 IFRC-DCGRY------LYAKEGAKTKKC-VCGKTLKV 31 (68)
T ss_dssp EEEE-TTS--------EEEETT-SEEEE-TTTEEEE-
T ss_pred EEEe-cCCCE------EEecCCcceeEe-cCCCeeee
Confidence 5899 79972 122466678899 99965443
No 366
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=21.20 E-value=50 Score=28.04 Aligned_cols=11 Identities=36% Similarity=0.924 Sum_probs=7.9
Q ss_pred cccCCCCCCCC
Q 034528 22 VFSCPFCNHGT 32 (92)
Q Consensus 22 ~F~CPfC~~~~ 32 (92)
.+.||.||+++
T Consensus 532 ~~~CP~CGs~~ 542 (555)
T cd01675 532 GFKCPKCGSED 542 (555)
T ss_pred CCCCcCCCCcC
Confidence 57888888654
No 367
>MTH00098 COX2 cytochrome c oxidase subunit II; Validated
Probab=21.10 E-value=74 Score=24.03 Aligned_cols=46 Identities=13% Similarity=0.208 Sum_probs=30.7
Q ss_pred CCCCeEEEEeecCCceEEEEcCc-cCCeeE-eecCCCCcchhhhhhHHH
Q 034528 29 NHGTSVECRIDMKNLIGEAICNI-CQESFS-TTITALTEPIDIYSEWID 75 (92)
Q Consensus 29 ~~~~sV~vkidk~~~~g~l~C~~-Cg~~~~-~~i~~L~epVDVYs~WiD 75 (92)
|..+.+.+..++ .|+....|.. ||..+. +++.-...+.|.|.+|+-
T Consensus 177 G~~~~~~~~~~~-~G~~~g~Cse~CG~~H~~M~~~v~v~~~~~f~~W~~ 224 (227)
T MTH00098 177 GRLNQTTLMSTR-PGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSA 224 (227)
T ss_pred CceEEEEEecCC-cEEEEEECccccCcCcCCceEEEEEeCHHHHHHHHH
Confidence 444455555543 4566788987 999775 465554456689999984
No 368
>PRK15084 formate hydrogenlyase maturation protein HycH; Provisional
Probab=21.05 E-value=41 Score=24.21 Aligned_cols=31 Identities=35% Similarity=0.524 Sum_probs=23.5
Q ss_pred CCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhh
Q 034528 41 KNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERV 80 (92)
Q Consensus 41 ~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~ 80 (92)
-..+|.|-|-.+ .|+=|.+.|.+||+...++
T Consensus 36 GHhvGvIDcle~---------~L~~~~e~y~~wi~~l~~~ 66 (133)
T PRK15084 36 GHHVGVIDCLEA---------ALTCPLDEYLAWIATLEEG 66 (133)
T ss_pred ccccceEecchh---------hhcCCHHHHHHHHHhCChH
Confidence 346777877664 4677999999999998554
No 369
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=21.01 E-value=44 Score=24.95 Aligned_cols=25 Identities=20% Similarity=0.630 Sum_probs=17.0
Q ss_pred cccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528 22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQE 54 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~ 54 (92)
.|.||.|+.+ +.. . -..+.|.+.+.
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 14699998554
No 370
>PRK04860 hypothetical protein; Provisional
Probab=20.86 E-value=51 Score=23.82 Aligned_cols=34 Identities=15% Similarity=0.345 Sum_probs=22.8
Q ss_pred cccCCCCCCCCeEEEEeec----CCceEEEEcCccCCeeEee
Q 034528 22 VFSCPFCNHGTSVECRIDM----KNLIGEAICNICQESFSTT 59 (92)
Q Consensus 22 ~F~CPfC~~~~sV~vkidk----~~~~g~l~C~~Cg~~~~~~ 59 (92)
.|.|+ |+. ..+.+.+ ..+.....|+.|+..+...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 59999 986 3332222 2345678999999988653
No 371
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=20.81 E-value=94 Score=23.33 Aligned_cols=37 Identities=19% Similarity=0.277 Sum_probs=24.8
Q ss_pred CCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe-ecCCCC
Q 034528 18 KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST-TITALT 64 (92)
Q Consensus 18 kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~-~i~~L~ 64 (92)
+.+-.|.|..||+. ...-...|..||.--+. .|..|+
T Consensus 350 ~~~p~~~c~~cg~~----------~~~~~~~c~~c~~~~~~~~~~~~~ 387 (389)
T PRK11788 350 KRKPRYRCRNCGFT----------ARTLYWHCPSCKAWETIKPIRGLD 387 (389)
T ss_pred hCCCCEECCCCCCC----------CccceeECcCCCCccCcCCcccCC
Confidence 44455889999983 34467899999974332 455554
No 372
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=20.65 E-value=74 Score=21.44 Aligned_cols=31 Identities=26% Similarity=0.507 Sum_probs=19.0
Q ss_pred ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528 21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFS 57 (92)
Q Consensus 21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~ 57 (92)
..+.|+.|||..-+ - ..-..=.|..||..+.
T Consensus 41 ~~~~C~~Cg~~~~~---~---~SCk~R~CP~C~~~~~ 71 (111)
T PF14319_consen 41 HRYRCEDCGHEKIV---Y---NSCKNRHCPSCQAKAT 71 (111)
T ss_pred ceeecCCCCceEEe---c---CcccCcCCCCCCChHH
Confidence 47889999995321 1 1122337888887543
No 373
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=20.47 E-value=36 Score=27.06 Aligned_cols=35 Identities=20% Similarity=0.386 Sum_probs=24.7
Q ss_pred CCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 18 KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 18 kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
-+.-+|+||.|-+. +..-|- .-.-|+|.|..|-..
T Consensus 44 ~~~~lleCPvC~~~--l~~Pi~-QC~nGHlaCssC~~~ 78 (299)
T KOG3002|consen 44 LDLDLLDCPVCFNP--LSPPIF-QCDNGHLACSSCRTK 78 (299)
T ss_pred cchhhccCchhhcc--Ccccce-ecCCCcEehhhhhhh
Confidence 35678999999974 444443 334589999998843
No 374
>TIGR01908 cas_CXXC_CXXC CRISPR-associated CXXC_CXXC protein Cst1. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model describes a conserved region from an otherwise highly divergent protein found in the Tneap subtype of CRISPR/Cas regions. This Cys-rich region features two motifs of CXXC.
Probab=20.37 E-value=61 Score=25.71 Aligned_cols=22 Identities=14% Similarity=0.012 Sum_probs=15.3
Q ss_pred CCccccCCCCCCCCeEEEEeec
Q 034528 19 LDTVFSCPFCNHGTSVECRIDM 40 (92)
Q Consensus 19 l~~~F~CPfC~~~~sV~vkidk 40 (92)
.++.+.|+|||-..+....+.+
T Consensus 2 ~~~~~~C~~Cg~r~a~~~~~~~ 23 (309)
T TIGR01908 2 DKNSPLCINCGERHAKKDTIFD 23 (309)
T ss_pred CCCCCcCCCcCCcchhcccccc
Confidence 4678899999987764433433
No 375
>PRK11823 DNA repair protein RadA; Provisional
Probab=20.08 E-value=83 Score=25.88 Aligned_cols=26 Identities=19% Similarity=0.358 Sum_probs=19.0
Q ss_pred CccccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528 20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQES 55 (92)
Q Consensus 20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~ 55 (92)
.+.|.|..||+. ...=.-.|..|+..
T Consensus 5 ~~~y~C~~Cg~~----------~~~~~g~Cp~C~~w 30 (446)
T PRK11823 5 KTAYVCQECGAE----------SPKWLGRCPECGAW 30 (446)
T ss_pred CCeEECCcCCCC----------CcccCeeCcCCCCc
Confidence 357999999984 23345589999974
Done!