Query 040426
Match_columns 120
No_of_seqs 139 out of 790
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 08:19:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040426.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040426hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2906 RNA polymerase III sub 100.0 2.4E-41 5.2E-46 218.1 4.7 101 9-119 1-105 (105)
2 COG1594 RPB9 DNA-directed RNA 100.0 3.2E-39 7E-44 217.1 7.1 108 8-120 1-113 (113)
3 KOG2691 RNA polymerase II subu 100.0 3.5E-38 7.6E-43 206.4 5.1 105 7-119 2-113 (113)
4 TIGR01384 TFS_arch transcripti 100.0 1.8E-37 3.8E-42 205.8 8.5 103 10-120 1-103 (104)
5 KOG2907 RNA polymerase I trans 100.0 1.9E-36 4.1E-41 199.9 4.1 110 6-120 4-115 (116)
6 smart00440 ZnF_C2C2 C2C2 Zinc 99.9 7.8E-27 1.7E-31 130.2 4.7 40 80-119 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 99.9 1.6E-25 3.5E-30 124.2 4.5 39 80-118 1-39 (39)
8 PHA02998 RNA polymerase subuni 99.8 7.4E-22 1.6E-26 140.2 4.6 45 74-118 137-182 (195)
9 TIGR01385 TFSII transcription 99.7 3.6E-18 7.8E-23 131.5 4.4 42 77-118 256-297 (299)
10 PF02150 RNA_POL_M_15KD: RNA p 99.4 1.1E-13 2.4E-18 74.9 1.3 31 9-39 1-34 (35)
11 KOG1105 Transcription elongati 99.0 1.5E-10 3.2E-15 88.9 3.5 41 78-118 254-294 (296)
12 smart00661 RPOL9 RNA polymeras 98.8 7.3E-09 1.6E-13 60.0 3.8 37 10-50 1-41 (52)
13 PRK00432 30S ribosomal protein 98.2 8.9E-07 1.9E-11 51.4 2.2 29 8-36 19-48 (50)
14 COG1998 RPS31 Ribosomal protei 97.2 0.0002 4.4E-09 41.1 1.9 30 8-37 18-49 (51)
15 PF14803 Nudix_N_2: Nudix N-te 97.2 0.00017 3.7E-09 38.5 1.5 26 10-35 1-32 (34)
16 PF04216 FdhE: Protein involve 97.2 0.00058 1.3E-08 52.5 4.7 68 10-118 173-249 (290)
17 PF04606 Ogr_Delta: Ogr/Delta- 97.0 0.00076 1.6E-08 38.4 2.6 37 81-119 1-39 (47)
18 PRK03564 formate dehydrogenase 97.0 0.0021 4.5E-08 50.2 5.9 67 9-118 187-263 (309)
19 PF08274 PhnA_Zn_Ribbon: PhnA 96.9 0.00035 7.5E-09 36.3 0.6 27 81-118 4-30 (30)
20 PHA00626 hypothetical protein 96.9 0.00078 1.7E-08 39.7 2.0 34 81-119 2-35 (59)
21 PF09297 zf-NADH-PPase: NADH p 96.8 0.0011 2.4E-08 34.7 2.1 27 9-35 3-31 (32)
22 PRK09678 DNA-binding transcrip 96.7 0.0015 3.2E-08 40.6 2.8 36 81-119 3-41 (72)
23 PF09855 DUF2082: Nucleic-acid 96.6 0.0038 8.1E-08 37.9 3.8 36 81-116 2-45 (64)
24 TIGR01562 FdhE formate dehydro 96.5 0.0064 1.4E-07 47.4 5.7 69 9-118 184-263 (305)
25 smart00661 RPOL9 RNA polymeras 96.4 0.0038 8.2E-08 35.7 2.9 32 81-120 2-33 (52)
26 PHA00626 hypothetical protein 96.4 0.0024 5.3E-08 37.6 1.9 32 10-41 1-39 (59)
27 PF13717 zinc_ribbon_4: zinc-r 96.1 0.0051 1.1E-07 33.1 2.2 32 79-118 2-36 (36)
28 PF12773 DZR: Double zinc ribb 96.1 0.0033 7.1E-08 35.8 1.4 32 5-36 8-40 (50)
29 PF12760 Zn_Tnp_IS1595: Transp 95.9 0.0065 1.4E-07 34.3 2.2 28 80-116 19-46 (46)
30 PRK00464 nrdR transcriptional 95.9 0.0094 2E-07 42.2 3.3 38 81-118 2-39 (154)
31 COG3478 Predicted nucleic-acid 95.9 0.0063 1.4E-07 36.9 2.0 35 80-116 5-49 (68)
32 PF08271 TF_Zn_Ribbon: TFIIB z 95.7 0.013 2.9E-07 32.4 2.9 30 81-119 2-31 (43)
33 PF14353 CpXC: CpXC protein 95.6 0.021 4.7E-07 38.6 4.1 40 80-119 2-50 (128)
34 PF09538 FYDLN_acid: Protein o 95.6 0.0099 2.2E-07 39.7 2.3 39 1-39 1-40 (108)
35 PF05876 Terminase_GpA: Phage 95.5 0.011 2.4E-07 49.5 2.9 42 78-119 199-241 (557)
36 COG4332 Uncharacterized protei 95.5 0.014 3E-07 42.3 2.9 46 73-118 11-60 (203)
37 PRK14973 DNA topoisomerase I; 95.4 0.021 4.5E-07 50.6 4.4 32 79-116 635-666 (936)
38 PF13248 zf-ribbon_3: zinc-rib 95.2 0.0087 1.9E-07 29.8 0.9 24 9-34 2-25 (26)
39 TIGR02098 MJ0042_CXXC MJ0042 f 95.2 0.023 5E-07 30.4 2.7 35 79-119 2-37 (38)
40 PF13240 zinc_ribbon_2: zinc-r 95.2 0.009 2E-07 29.0 0.9 22 11-34 1-22 (23)
41 PF11781 RRN7: RNA polymerase 95.2 0.012 2.6E-07 31.7 1.4 26 10-35 9-35 (36)
42 COG2888 Predicted Zn-ribbon RN 95.1 0.011 2.3E-07 35.3 1.2 26 9-34 9-36 (61)
43 PF07754 DUF1610: Domain of un 94.9 0.021 4.5E-07 28.1 1.7 22 12-33 1-24 (24)
44 PF13453 zf-TFIIB: Transcripti 94.9 0.048 1E-06 29.9 3.4 30 81-118 1-30 (41)
45 PF10571 UPF0547: Uncharacteri 94.9 0.016 3.4E-07 29.0 1.2 24 11-36 2-25 (26)
46 PF01396 zf-C4_Topoisom: Topoi 94.8 0.023 5E-07 31.0 1.9 29 10-38 2-37 (39)
47 PRK14890 putative Zn-ribbon RN 94.6 0.02 4.4E-07 34.1 1.4 24 10-33 8-33 (59)
48 PF08271 TF_Zn_Ribbon: TFIIB z 94.6 0.036 7.9E-07 30.6 2.4 28 10-37 1-31 (43)
49 TIGR03655 anti_R_Lar restricti 94.5 0.073 1.6E-06 30.8 3.7 34 80-116 2-35 (53)
50 PF08274 PhnA_Zn_Ribbon: PhnA 94.5 0.023 4.9E-07 29.4 1.3 26 10-35 3-29 (30)
51 cd00729 rubredoxin_SM Rubredox 94.5 0.029 6.3E-07 29.7 1.7 14 80-93 19-32 (34)
52 PRK04023 DNA polymerase II lar 94.4 0.025 5.4E-07 50.2 2.2 26 5-34 622-647 (1121)
53 PF01396 zf-C4_Topoisom: Topoi 94.4 0.059 1.3E-06 29.4 2.9 31 80-118 2-35 (39)
54 PRK00398 rpoP DNA-directed RNA 94.3 0.047 1E-06 30.6 2.5 30 10-39 4-35 (46)
55 PRK07220 DNA topoisomerase I; 94.3 0.11 2.4E-06 45.0 5.7 32 78-115 634-665 (740)
56 PF03811 Zn_Tnp_IS1: InsA N-te 94.2 0.076 1.7E-06 28.5 3.0 35 76-114 2-36 (36)
57 COG3478 Predicted nucleic-acid 94.2 0.034 7.4E-07 33.7 1.7 26 12-37 7-52 (68)
58 COG1779 C4-type Zn-finger prot 94.1 0.091 2E-06 38.6 4.1 42 77-119 12-55 (201)
59 PF13719 zinc_ribbon_5: zinc-r 94.0 0.034 7.4E-07 29.9 1.4 26 11-36 4-36 (37)
60 smart00709 Zpr1 Duplicated dom 93.8 0.11 2.3E-06 37.0 4.0 38 81-119 2-41 (160)
61 TIGR02098 MJ0042_CXXC MJ0042 f 93.7 0.038 8.2E-07 29.6 1.2 27 11-37 4-37 (38)
62 cd00730 rubredoxin Rubredoxin; 93.4 0.048 1E-06 31.5 1.4 15 79-93 34-48 (50)
63 COG1645 Uncharacterized Zn-fin 93.4 0.061 1.3E-06 37.1 2.1 29 11-39 30-58 (131)
64 TIGR02300 FYDLN_acid conserved 93.4 0.059 1.3E-06 36.9 2.0 39 1-39 1-40 (129)
65 PF00301 Rubredoxin: Rubredoxi 93.4 0.075 1.6E-06 30.3 2.2 14 26-39 2-15 (47)
66 PRK14714 DNA polymerase II lar 93.3 0.06 1.3E-06 48.8 2.5 14 79-92 709-722 (1337)
67 TIGR00244 transcriptional regu 93.1 0.093 2E-06 36.8 2.7 38 81-119 2-40 (147)
68 PRK00241 nudC NADH pyrophospha 93.0 0.075 1.6E-06 40.3 2.3 31 7-37 97-129 (256)
69 PF07282 OrfB_Zn_ribbon: Putat 92.9 0.1 2.2E-06 31.4 2.4 31 78-118 27-57 (69)
70 PF09855 DUF2082: Nucleic-acid 92.9 0.084 1.8E-06 32.0 2.0 26 12-37 3-48 (64)
71 PF10058 DUF2296: Predicted in 92.8 0.13 2.7E-06 30.2 2.6 37 72-115 13-52 (54)
72 PF09526 DUF2387: Probable met 92.7 0.17 3.8E-06 31.2 3.3 35 78-119 7-42 (71)
73 PF03367 zf-ZPR1: ZPR1 zinc-fi 92.5 0.15 3.2E-06 36.2 3.1 40 80-119 2-42 (161)
74 cd00350 rubredoxin_like Rubred 92.4 0.08 1.7E-06 27.7 1.3 25 11-35 3-27 (33)
75 PF03119 DNA_ligase_ZBD: NAD-d 92.4 0.09 2E-06 26.6 1.4 20 11-30 1-22 (28)
76 COG2816 NPY1 NTP pyrophosphohy 92.3 0.091 2E-06 40.5 2.0 30 7-36 109-140 (279)
77 COG2051 RPS27A Ribosomal prote 92.3 0.12 2.6E-06 31.5 2.1 35 73-116 13-47 (67)
78 PRK14559 putative protein seri 92.3 0.082 1.8E-06 45.2 1.9 12 79-90 41-52 (645)
79 TIGR02443 conserved hypothetic 92.3 0.27 5.9E-06 29.3 3.6 35 78-119 8-43 (59)
80 PF14354 Lar_restr_allev: Rest 92.2 0.23 4.9E-06 29.2 3.2 34 80-115 4-37 (61)
81 PF07282 OrfB_Zn_ribbon: Putat 92.1 0.11 2.4E-06 31.2 1.9 36 4-39 23-60 (69)
82 COG1773 Rubredoxin [Energy pro 92.0 0.1 2.2E-06 30.7 1.5 18 78-95 35-52 (55)
83 COG1198 PriA Primosomal protei 92.0 0.051 1.1E-06 47.0 0.3 21 80-100 476-496 (730)
84 PRK07219 DNA topoisomerase I; 91.9 0.4 8.6E-06 42.1 5.7 32 78-117 732-766 (822)
85 PF03604 DNA_RNApol_7kD: DNA d 91.8 0.07 1.5E-06 28.0 0.6 24 12-35 3-27 (32)
86 TIGR00595 priA primosomal prot 91.8 0.18 3.9E-06 41.8 3.3 27 12-38 225-253 (505)
87 PF09723 Zn-ribbon_8: Zinc rib 91.8 0.26 5.7E-06 27.1 3.0 12 26-37 6-17 (42)
88 TIGR00310 ZPR1_znf ZPR1 zinc f 91.8 0.25 5.5E-06 36.1 3.7 39 81-119 2-42 (192)
89 KOG3507 DNA-directed RNA polym 91.7 0.093 2E-06 31.2 1.1 27 9-35 20-47 (62)
90 PF04032 Rpr2: RNAse P Rpr2/Rp 91.5 0.18 3.9E-06 31.4 2.4 22 3-24 40-61 (85)
91 TIGR01053 LSD1 zinc finger dom 91.3 0.2 4.4E-06 26.0 2.0 25 11-35 3-29 (31)
92 smart00659 RPOLCX RNA polymera 91.2 0.43 9.4E-06 26.7 3.5 27 11-37 4-31 (44)
93 TIGR01206 lysW lysine biosynth 91.1 0.23 5E-06 29.1 2.3 29 11-39 4-36 (54)
94 PF06677 Auto_anti-p27: Sjogre 91.1 0.17 3.7E-06 28.0 1.7 23 10-32 18-41 (41)
95 COG2023 RPR2 RNase P subunit R 90.7 0.18 3.9E-06 33.5 1.9 28 10-37 57-94 (105)
96 COG1592 Rubrerythrin [Energy p 90.6 0.11 2.5E-06 37.1 0.9 14 79-92 149-162 (166)
97 PRK00420 hypothetical protein; 90.6 0.23 5.1E-06 33.3 2.4 30 10-39 24-54 (112)
98 PF08772 NOB1_Zn_bind: Nin one 90.5 0.11 2.3E-06 32.4 0.6 13 6-18 21-33 (73)
99 PF13717 zinc_ribbon_4: zinc-r 90.5 0.17 3.6E-06 27.1 1.3 25 11-35 4-35 (36)
100 TIGR00686 phnA alkylphosphonat 90.3 0.19 4.2E-06 33.5 1.7 31 9-39 2-33 (109)
101 PRK10220 hypothetical protein; 90.3 0.27 5.8E-06 32.9 2.4 32 8-39 2-34 (111)
102 PF14353 CpXC: CpXC protein 90.2 0.43 9.4E-06 32.1 3.5 14 26-39 2-15 (128)
103 PF11792 Baculo_LEF5_C: Baculo 90.0 0.011 2.5E-07 33.0 -3.6 30 85-115 13-42 (43)
104 PF01873 eIF-5_eIF-2B: Domain 90.0 0.54 1.2E-05 32.1 3.8 30 80-116 94-123 (125)
105 COG1096 Predicted RNA-binding 89.9 0.24 5.3E-06 36.1 2.2 28 10-37 150-177 (188)
106 COG1997 RPL43A Ribosomal prote 89.8 0.39 8.5E-06 30.8 2.8 31 78-118 34-64 (89)
107 COG0551 TopA Zn-finger domain 89.6 1.2 2.6E-05 30.5 5.4 35 77-117 58-95 (140)
108 PF09082 DUF1922: Domain of un 89.5 0.23 5E-06 30.4 1.5 27 11-39 5-33 (68)
109 PF14311 DUF4379: Domain of un 89.5 0.41 8.9E-06 27.7 2.6 16 103-118 24-39 (55)
110 COG1327 Predicted transcriptio 89.4 0.22 4.7E-06 35.2 1.5 38 81-118 2-39 (156)
111 COG1997 RPL43A Ribosomal prote 89.2 0.28 6.2E-06 31.5 1.8 31 8-39 34-67 (89)
112 PHA02942 putative transposase; 89.1 0.35 7.5E-06 38.8 2.7 34 6-39 322-356 (383)
113 COG1326 Uncharacterized archae 89.1 0.17 3.7E-06 37.1 0.8 37 78-118 5-41 (201)
114 PRK05580 primosome assembly pr 89.1 0.42 9E-06 41.0 3.3 12 26-37 409-420 (679)
115 TIGR00311 aIF-2beta translatio 88.7 0.59 1.3E-05 32.2 3.3 31 80-117 98-128 (133)
116 PF06044 DRP: Dam-replacing fa 88.4 0.26 5.6E-06 37.4 1.4 31 9-39 31-67 (254)
117 PRK11827 hypothetical protein; 88.3 0.38 8.3E-06 28.8 1.9 33 7-39 6-40 (60)
118 PRK11032 hypothetical protein; 88.0 0.48 1E-05 33.7 2.6 12 26-37 125-136 (160)
119 PF07295 DUF1451: Protein of u 88.0 0.47 1E-05 33.2 2.5 12 26-37 113-124 (146)
120 PRK14873 primosome assembly pr 87.8 0.54 1.2E-05 40.4 3.2 9 26-34 411-419 (665)
121 PRK03988 translation initiatio 87.8 0.75 1.6E-05 31.9 3.4 31 80-117 103-133 (138)
122 PRK12286 rpmF 50S ribosomal pr 87.8 0.46 9.9E-06 28.1 2.0 27 7-36 25-51 (57)
123 PRK06319 DNA topoisomerase I/S 87.7 0.9 1.9E-05 40.2 4.5 31 8-38 591-629 (860)
124 PF13408 Zn_ribbon_recom: Reco 87.6 0.37 8E-06 27.6 1.5 30 6-35 2-36 (58)
125 PRK09678 DNA-binding transcrip 87.6 0.44 9.6E-06 29.5 1.9 31 9-39 1-43 (72)
126 PF08792 A2L_zn_ribbon: A2L zi 87.4 0.71 1.5E-05 24.2 2.3 28 9-36 3-32 (33)
127 PF14446 Prok-RING_1: Prokaryo 87.1 0.44 9.6E-06 27.9 1.6 27 11-37 7-33 (54)
128 COG2888 Predicted Zn-ribbon RN 86.9 0.76 1.6E-05 27.5 2.5 24 11-34 29-59 (61)
129 PF14205 Cys_rich_KTR: Cystein 86.9 0.46 1E-05 27.9 1.6 31 8-38 3-41 (55)
130 COG0777 AccD Acetyl-CoA carbox 86.8 0.22 4.7E-06 38.5 0.2 32 8-39 27-61 (294)
131 PRK00415 rps27e 30S ribosomal 86.8 0.93 2E-05 27.0 2.9 36 73-117 5-40 (59)
132 smart00531 TFIIE Transcription 86.8 0.2 4.4E-06 34.8 0.0 31 78-117 98-133 (147)
133 smart00647 IBR In Between Ring 86.8 0.7 1.5E-05 26.8 2.4 29 7-35 16-50 (64)
134 COG2835 Uncharacterized conser 86.7 0.63 1.4E-05 27.8 2.1 35 5-39 4-40 (60)
135 TIGR00515 accD acetyl-CoA carb 86.7 0.16 3.5E-06 39.3 -0.5 31 9-39 26-59 (285)
136 PRK03824 hypA hydrogenase nick 86.5 0.81 1.8E-05 31.5 2.9 13 26-38 71-83 (135)
137 PRK14892 putative transcriptio 86.4 0.46 1E-05 31.2 1.6 30 8-37 20-54 (99)
138 PF10122 Mu-like_Com: Mu-like 86.4 0.37 8E-06 27.9 1.0 30 10-39 5-38 (51)
139 PF06943 zf-LSD1: LSD1 zinc fi 86.3 0.69 1.5E-05 22.9 1.8 23 12-34 1-25 (25)
140 PF09526 DUF2387: Probable met 86.2 0.71 1.5E-05 28.5 2.3 30 11-40 10-45 (71)
141 CHL00174 accD acetyl-CoA carbo 86.2 0.17 3.7E-06 39.4 -0.6 31 9-39 38-71 (296)
142 PF04216 FdhE: Protein involve 86.0 0.82 1.8E-05 35.1 3.0 35 79-118 172-208 (290)
143 COG4640 Predicted membrane pro 85.9 0.41 8.8E-06 38.8 1.3 27 9-37 1-27 (465)
144 PF05129 Elf1: Transcription e 85.8 1.6 3.5E-05 27.5 3.8 37 78-118 21-57 (81)
145 PF09151 DUF1936: Domain of un 85.5 0.88 1.9E-05 23.7 2.0 29 80-115 2-34 (36)
146 PF01780 Ribosomal_L37ae: Ribo 85.2 0.38 8.2E-06 31.1 0.7 31 9-39 35-67 (90)
147 KOG3084 NADH pyrophosphatase I 85.2 0.52 1.1E-05 37.1 1.6 32 8-39 149-187 (345)
148 PRK05654 acetyl-CoA carboxylas 84.8 0.24 5.2E-06 38.4 -0.4 30 9-38 27-59 (292)
149 PF02591 DUF164: Putative zinc 84.6 0.42 9E-06 27.8 0.7 14 6-19 43-56 (56)
150 smart00653 eIF2B_5 domain pres 84.6 1.5 3.1E-05 29.3 3.3 30 80-116 81-110 (110)
151 PF01485 IBR: IBR domain; Int 84.5 0.55 1.2E-05 27.2 1.2 30 6-35 15-50 (64)
152 PRK09710 lar restriction allev 84.5 1.8 3.8E-05 26.2 3.3 32 79-117 6-37 (64)
153 COG1571 Predicted DNA-binding 84.4 0.52 1.1E-05 38.4 1.3 30 10-39 351-381 (421)
154 PRK12336 translation initiatio 83.9 1.4 3.1E-05 32.3 3.4 31 80-117 99-129 (201)
155 PHA02942 putative transposase; 83.7 0.86 1.9E-05 36.6 2.3 29 78-117 324-352 (383)
156 TIGR03826 YvyF flagellar opero 83.7 0.1 2.3E-06 36.2 -2.6 28 7-35 1-28 (137)
157 COG1779 C4-type Zn-finger prot 83.5 0.54 1.2E-05 34.6 1.0 27 9-35 14-53 (201)
158 PF07191 zinc-ribbons_6: zinc- 83.4 1 2.3E-05 27.7 2.1 26 11-36 3-28 (70)
159 PF03966 Trm112p: Trm112p-like 83.4 1.3 2.9E-05 26.6 2.6 34 6-39 4-67 (68)
160 COG1571 Predicted DNA-binding 83.4 0.55 1.2E-05 38.3 1.1 31 78-119 349-379 (421)
161 KOG2767 Translation initiation 83.3 0.42 9E-06 38.1 0.4 32 80-117 97-128 (400)
162 PF01921 tRNA-synt_1f: tRNA sy 82.8 0.76 1.6E-05 36.8 1.6 35 78-117 173-209 (360)
163 PRK09521 exosome complex RNA-b 82.4 1.2 2.5E-05 32.2 2.3 29 9-37 149-178 (189)
164 PRK05452 anaerobic nitric oxid 82.3 1.2 2.7E-05 36.6 2.8 17 79-95 458-474 (479)
165 TIGR01031 rpmF_bact ribosomal 82.3 0.91 2E-05 26.6 1.5 26 7-35 24-49 (55)
166 PF01783 Ribosomal_L32p: Ribos 82.0 0.6 1.3E-05 27.3 0.6 26 8-36 25-50 (56)
167 KOG0696 Serine/threonine prote 82.0 0.28 6.1E-06 40.5 -1.1 29 6-34 118-147 (683)
168 cd00674 LysRS_core_class_I cat 81.7 1.4 3.1E-05 35.1 2.8 35 78-117 168-202 (353)
169 PRK14890 putative Zn-ribbon RN 81.6 1.9 4E-05 25.7 2.6 27 9-35 25-58 (59)
170 COG0675 Transposase and inacti 81.5 1.3 2.7E-05 33.6 2.4 26 77-117 307-332 (364)
171 PF01599 Ribosomal_S27: Riboso 81.1 1.3 2.9E-05 25.2 1.8 26 9-34 18-47 (47)
172 PF01927 Mut7-C: Mut7-C RNAse 80.9 1.5 3.3E-05 30.3 2.5 38 79-116 91-133 (147)
173 PRK00423 tfb transcription ini 80.6 1.3 2.8E-05 34.5 2.2 31 6-36 8-41 (310)
174 KOG0006 E3 ubiquitin-protein l 80.6 4.4 9.5E-05 32.3 5.1 27 8-34 314-345 (446)
175 COG4530 Uncharacterized protei 80.1 1.2 2.5E-05 30.0 1.6 42 1-42 1-43 (129)
176 PF13005 zf-IS66: zinc-finger 79.8 1.7 3.8E-05 23.9 2.0 14 9-22 2-15 (47)
177 TIGR00373 conserved hypothetic 79.8 0.43 9.4E-06 33.7 -0.6 30 78-116 108-137 (158)
178 PTZ00083 40S ribosomal protein 79.4 2.6 5.6E-05 26.9 2.9 35 73-116 29-63 (85)
179 COG1996 RPC10 DNA-directed RNA 79.3 1.5 3.2E-05 25.2 1.6 30 10-39 7-38 (49)
180 PRK06266 transcription initiat 79.3 0.42 9.1E-06 34.5 -0.8 30 78-116 116-145 (178)
181 PF06044 DRP: Dam-replacing fa 79.1 1.4 3E-05 33.5 1.8 34 78-117 30-63 (254)
182 PLN00209 ribosomal protein S27 78.4 2.7 5.9E-05 26.9 2.8 36 73-117 30-65 (86)
183 TIGR00280 L37a ribosomal prote 78.0 1.6 3.4E-05 28.3 1.6 32 8-39 34-67 (91)
184 PRK07219 DNA topoisomerase I; 77.9 6.4 0.00014 34.7 5.9 30 10-39 603-640 (822)
185 smart00834 CxxC_CXXC_SSSS Puta 77.9 1.5 3.2E-05 23.3 1.3 12 107-118 5-16 (41)
186 PRK12495 hypothetical protein; 77.8 1.3 2.9E-05 33.1 1.4 33 4-36 37-69 (226)
187 TIGR00467 lysS_arch lysyl-tRNA 77.4 2.5 5.5E-05 35.3 3.1 34 78-117 167-200 (515)
188 PF00130 C1_1: Phorbol esters/ 77.3 3.2 7E-05 23.3 2.7 31 7-37 9-40 (53)
189 KOG1842 FYVE finger-containing 76.7 0.63 1.4E-05 38.2 -0.6 28 7-34 178-205 (505)
190 PF06827 zf-FPG_IleRS: Zinc fi 76.7 1.1 2.3E-05 22.6 0.5 23 11-33 3-29 (30)
191 COG2176 PolC DNA polymerase II 76.5 2 4.3E-05 39.5 2.3 14 26-39 915-928 (1444)
192 COG0675 Transposase and inacti 76.3 2.5 5.3E-05 31.9 2.6 31 5-39 305-336 (364)
193 COG0333 RpmF Ribosomal protein 76.3 1.9 4.2E-05 25.5 1.5 26 8-36 26-51 (57)
194 PRK00564 hypA hydrogenase nick 76.2 1.2 2.6E-05 29.9 0.7 27 8-34 70-97 (117)
195 TIGR00340 zpr1_rel ZPR1-relate 76.1 1.9 4.2E-05 30.7 1.8 11 26-36 29-39 (163)
196 PRK12380 hydrogenase nickel in 75.9 1.4 3E-05 29.4 1.0 26 9-34 70-95 (113)
197 PTZ00255 60S ribosomal protein 75.7 2.2 4.8E-05 27.6 1.8 31 8-39 35-68 (90)
198 PF01667 Ribosomal_S27e: Ribos 75.5 0.71 1.5E-05 27.1 -0.4 31 77-116 5-35 (55)
199 TIGR00100 hypA hydrogenase nic 75.2 1.5 3.3E-05 29.3 1.0 26 9-34 70-95 (115)
200 TIGR03831 YgiT_finger YgiT-typ 75.1 4.5 9.6E-05 21.8 2.8 9 109-117 34-42 (46)
201 smart00531 TFIIE Transcription 74.8 1.4 3E-05 30.6 0.8 21 98-118 90-110 (147)
202 PF09862 DUF2089: Protein of u 74.1 2.6 5.7E-05 28.3 2.0 23 12-36 1-23 (113)
203 PF11672 DUF3268: Protein of u 73.7 3.9 8.5E-05 27.0 2.7 34 80-114 3-38 (102)
204 PRK05582 DNA topoisomerase I; 73.2 5.2 0.00011 34.3 4.0 30 79-115 611-643 (650)
205 PRK03954 ribonuclease P protei 73.1 2.6 5.7E-05 28.6 1.8 29 9-37 64-105 (121)
206 PHA02998 RNA polymerase subuni 72.6 3 6.4E-05 30.4 2.0 31 10-40 144-186 (195)
207 TIGR01562 FdhE formate dehydro 72.5 2.4 5.3E-05 33.1 1.8 38 79-118 184-221 (305)
208 PF08063 PADR1: PADR1 (NUC008) 72.2 1.7 3.7E-05 25.4 0.6 22 8-29 13-35 (55)
209 PF12172 DUF35_N: Rubredoxin-l 72.2 2 4.4E-05 22.6 0.9 23 9-33 11-33 (37)
210 cd00029 C1 Protein kinase C co 71.9 3.1 6.8E-05 22.7 1.7 29 8-36 10-39 (50)
211 PRK03976 rpl37ae 50S ribosomal 71.8 2.7 5.9E-05 27.1 1.6 32 8-39 35-68 (90)
212 PF00096 zf-C2H2: Zinc finger, 71.8 2.8 6E-05 19.3 1.3 11 108-118 1-11 (23)
213 PRK04136 rpl40e 50S ribosomal 71.3 2.8 6.1E-05 23.9 1.4 25 8-34 13-37 (48)
214 KOG3799 Rab3 effector RIM1 and 70.8 1.4 2.9E-05 30.8 0.0 32 8-39 88-121 (169)
215 PF08882 Acetone_carb_G: Aceto 70.8 1.8 3.9E-05 29.0 0.6 13 11-23 76-88 (112)
216 PRK05978 hypothetical protein; 70.7 2 4.3E-05 30.2 0.8 32 78-118 32-63 (148)
217 PF06750 DiS_P_DiS: Bacterial 70.7 3.3 7.1E-05 26.6 1.8 34 4-37 28-70 (92)
218 smart00109 C1 Protein kinase C 70.5 2.9 6.2E-05 22.6 1.3 30 7-36 9-38 (49)
219 PF13894 zf-C2H2_4: C2H2-type 70.4 3.5 7.6E-05 18.6 1.4 11 108-118 1-11 (24)
220 PRK03681 hypA hydrogenase nick 70.4 2.3 4.9E-05 28.4 1.0 26 9-34 70-96 (114)
221 COG1592 Rubrerythrin [Energy p 70.1 2.6 5.7E-05 30.2 1.3 23 11-34 136-158 (166)
222 TIGR00373 conserved hypothetic 69.1 3.2 7E-05 29.2 1.6 19 100-118 102-120 (158)
223 COG1499 NMD3 NMD protein affec 68.9 3.5 7.6E-05 33.0 1.9 23 79-101 129-153 (355)
224 PF12677 DUF3797: Domain of un 68.0 2 4.2E-05 24.6 0.2 14 6-19 10-23 (49)
225 COG3677 Transposase and inacti 67.7 4.2 9.1E-05 27.8 1.9 39 76-119 27-65 (129)
226 PF05180 zf-DNL: DNL zinc fing 67.6 2.9 6.4E-05 25.4 1.0 35 79-116 4-38 (66)
227 PF05502 Dynactin_p62: Dynacti 67.6 14 0.0003 30.7 5.2 31 7-37 3-38 (483)
228 COG3791 Uncharacterized conser 67.2 3.5 7.6E-05 28.1 1.4 18 6-23 66-83 (133)
229 COG1326 Uncharacterized archae 66.4 3.8 8.1E-05 30.2 1.5 28 10-37 7-42 (201)
230 COG1656 Uncharacterized conser 66.2 3.7 8E-05 29.4 1.4 28 9-36 97-141 (165)
231 PRK06266 transcription initiat 65.6 4.2 9E-05 29.3 1.6 19 100-118 110-128 (178)
232 PF13824 zf-Mss51: Zinc-finger 65.3 4.2 9.1E-05 23.9 1.3 27 11-38 1-27 (55)
233 PF04828 GFA: Glutathione-depe 65.3 2.1 4.5E-05 26.3 -0.0 15 7-21 46-60 (92)
234 TIGR02605 CxxC_CxxC_SSSS putat 65.2 4.2 9E-05 22.9 1.3 11 107-117 5-15 (52)
235 PF13878 zf-C2H2_3: zinc-finge 65.0 3.6 7.8E-05 22.5 0.9 14 9-23 13-26 (41)
236 COG3809 Uncharacterized protei 64.3 4.2 9.1E-05 25.7 1.3 28 9-36 1-32 (88)
237 cd04476 RPA1_DBD_C RPA1_DBD_C: 64.0 4.7 0.0001 28.1 1.6 26 10-35 35-61 (166)
238 PF05191 ADK_lid: Adenylate ki 63.7 2.1 4.4E-05 22.9 -0.2 23 11-33 3-29 (36)
239 COG4647 AcxC Acetone carboxyla 63.4 3.1 6.6E-05 28.9 0.6 15 10-24 121-135 (165)
240 PRK03564 formate dehydrogenase 63.3 7 0.00015 30.7 2.6 37 78-118 186-223 (309)
241 COG4888 Uncharacterized Zn rib 63.2 6.3 0.00014 26.0 2.0 29 11-39 24-60 (104)
242 PF08646 Rep_fac-A_C: Replicat 62.7 5.4 0.00012 27.2 1.7 25 11-35 20-47 (146)
243 PF02132 RecR: RecR protein; 62.7 2.7 5.8E-05 22.9 0.2 13 8-20 16-28 (41)
244 PRK00750 lysK lysyl-tRNA synth 62.2 11 0.00024 31.5 3.7 37 78-118 174-210 (510)
245 PRK01110 rpmF 50S ribosomal pr 61.5 5.5 0.00012 23.7 1.4 24 9-36 27-50 (60)
246 PRK14810 formamidopyrimidine-D 61.3 9.2 0.0002 29.2 2.9 29 78-114 243-271 (272)
247 PF07295 DUF1451: Protein of u 61.2 4.7 0.0001 28.2 1.2 32 5-36 108-141 (146)
248 PF01921 tRNA-synt_1f: tRNA sy 61.1 2.3 5E-05 34.0 -0.4 40 9-48 174-223 (360)
249 TIGR00155 pqiA_fam integral me 61.0 6.2 0.00013 32.0 2.0 27 9-35 13-43 (403)
250 PF06839 zf-GRF: GRF zinc fing 60.9 19 0.0004 19.7 3.4 29 81-112 2-30 (45)
251 PF09986 DUF2225: Uncharacteri 60.9 8.3 0.00018 28.4 2.5 15 26-40 6-20 (214)
252 COG2023 RPR2 RNase P subunit R 60.0 8.2 0.00018 25.6 2.1 44 73-118 48-93 (105)
253 COG1384 LysS Lysyl-tRNA synthe 59.6 8 0.00017 32.5 2.5 33 78-116 170-203 (521)
254 TIGR00319 desulf_FeS4 desulfof 59.2 6.6 0.00014 20.3 1.3 13 105-117 5-17 (34)
255 PF00628 PHD: PHD-finger; Int 59.1 13 0.00027 20.5 2.6 25 11-37 1-26 (51)
256 PF13465 zf-H2C2_2: Zinc-finge 58.9 6.8 0.00015 18.9 1.2 11 108-118 15-25 (26)
257 smart00401 ZnF_GATA zinc finge 58.8 4.1 8.9E-05 23.4 0.5 35 79-119 3-37 (52)
258 cd00974 DSRD Desulforedoxin (D 58.7 6.7 0.00014 20.3 1.3 12 106-117 3-14 (34)
259 PLN03086 PRLI-interacting fact 58.5 5.9 0.00013 33.6 1.5 21 15-35 441-463 (567)
260 PF04810 zf-Sec23_Sec24: Sec23 58.3 9.6 0.00021 20.5 1.9 30 9-38 2-37 (40)
261 KOG4537 Zn-ribbon-containing p 58.1 2.9 6.4E-05 29.7 -0.3 27 10-36 41-68 (178)
262 PF01155 HypA: Hydrogenase exp 58.1 1.8 3.9E-05 28.8 -1.3 26 10-35 71-96 (113)
263 PRK14811 formamidopyrimidine-D 58.0 11 0.00025 28.7 2.9 31 78-116 234-264 (269)
264 COG3364 Zn-ribbon containing p 58.0 5.4 0.00012 26.5 1.0 20 81-100 22-41 (112)
265 PRK12366 replication factor A; 57.8 6.2 0.00014 33.8 1.6 26 10-35 533-558 (637)
266 COG2824 PhnA Uncharacterized Z 57.4 8.4 0.00018 25.7 1.8 29 8-36 2-31 (112)
267 PRK14559 putative protein seri 56.6 6.6 0.00014 33.8 1.5 28 5-36 11-38 (645)
268 smart00532 LIGANc Ligase N fam 56.4 7.7 0.00017 31.9 1.8 28 8-35 398-429 (441)
269 PRK06393 rpoE DNA-directed RNA 56.3 15 0.00033 22.2 2.7 35 8-46 4-38 (64)
270 PF10005 DUF2248: Uncharacteri 56.0 6.7 0.00014 31.3 1.4 26 12-39 2-27 (343)
271 TIGR02820 formald_GSH S-(hydro 56.0 5.3 0.00012 29.0 0.8 14 9-22 89-102 (182)
272 KOG2703 C4-type Zn-finger prot 55.7 10 0.00022 31.0 2.4 40 77-116 37-77 (460)
273 PRK15103 paraquat-inducible me 55.6 8.5 0.00018 31.4 2.0 24 11-34 12-39 (419)
274 PF06397 Desulfoferrod_N: Desu 55.5 7.4 0.00016 20.8 1.1 13 104-116 3-15 (36)
275 PF11331 DUF3133: Protein of u 55.5 7.5 0.00016 22.0 1.2 30 7-36 4-42 (46)
276 PRK13945 formamidopyrimidine-D 55.2 14 0.0003 28.3 3.0 29 78-114 253-281 (282)
277 PRK05417 glutathione-dependent 55.1 6 0.00013 28.9 0.9 16 9-24 93-108 (191)
278 PRK11032 hypothetical protein; 54.2 6.5 0.00014 28.0 1.0 32 5-36 120-153 (160)
279 COG1405 SUA7 Transcription ini 53.5 8.8 0.00019 29.7 1.7 28 10-37 2-32 (285)
280 PRK01103 formamidopyrimidine/5 53.0 16 0.00034 27.9 3.0 30 78-115 244-273 (274)
281 COG1885 Uncharacterized protei 51.9 12 0.00025 25.0 1.8 15 80-94 50-65 (115)
282 COG5415 Predicted integral mem 51.8 9.4 0.0002 28.6 1.5 36 75-116 188-223 (251)
283 smart00778 Prim_Zn_Ribbon Zinc 51.5 13 0.00029 19.9 1.7 31 79-115 3-33 (37)
284 PF10083 DUF2321: Uncharacteri 51.3 3.6 7.9E-05 29.2 -0.7 44 76-119 36-82 (158)
285 PF14690 zf-ISL3: zinc-finger 51.3 7.3 0.00016 21.2 0.7 24 80-103 3-29 (47)
286 TIGR03829 YokU_near_AblA uncha 51.0 12 0.00026 24.1 1.7 11 108-118 36-46 (89)
287 PRK11088 rrmA 23S rRNA methylt 51.0 11 0.00024 28.3 1.8 28 10-38 3-30 (272)
288 PRK07218 replication factor A; 50.7 7.8 0.00017 31.7 1.0 27 9-39 297-323 (423)
289 COG4416 Com Mu-like prophage p 50.0 4.6 0.0001 23.7 -0.3 30 10-39 5-38 (60)
290 PF10080 DUF2318: Predicted me 49.3 8.4 0.00018 25.4 0.8 35 6-40 32-67 (102)
291 PF15135 UPF0515: Uncharacteri 49.2 8.5 0.00018 29.5 1.0 14 106-119 154-167 (278)
292 PRK10445 endonuclease VIII; Pr 48.8 20 0.00042 27.3 2.9 29 78-114 234-262 (263)
293 KOG3362 Predicted BBOX Zn-fing 48.2 5.8 0.00013 27.9 -0.0 23 9-36 118-140 (156)
294 COG4049 Uncharacterized protei 46.3 7.7 0.00017 23.0 0.3 13 106-118 16-28 (65)
295 smart00064 FYVE Protein presen 46.3 15 0.00033 21.5 1.6 28 9-36 10-37 (68)
296 PRK08351 DNA-directed RNA poly 46.2 33 0.00072 20.5 3.0 29 10-42 4-32 (61)
297 KOG1812 Predicted E3 ubiquitin 46.1 12 0.00026 30.2 1.4 28 7-35 304-333 (384)
298 TIGR00577 fpg formamidopyrimid 45.5 24 0.00052 26.9 3.0 28 79-114 245-272 (272)
299 TIGR00354 polC DNA polymerase, 45.4 11 0.00023 34.2 1.1 22 79-116 625-646 (1095)
300 KOG4236 Serine/threonine prote 45.1 3.7 8E-05 35.2 -1.7 30 5-34 152-182 (888)
301 COG2093 DNA-directed RNA polym 44.9 31 0.00067 20.8 2.7 37 8-46 3-39 (64)
302 TIGR00357 methionine-R-sulfoxi 44.6 26 0.00057 24.2 2.7 18 75-92 85-103 (134)
303 COG1545 Predicted nucleic-acid 44.5 18 0.0004 24.9 2.0 30 79-108 43-73 (140)
304 KOG2463 Predicted RNA-binding 43.8 10 0.00022 30.3 0.6 13 6-18 254-266 (376)
305 PF01363 FYVE: FYVE zinc finge 43.7 19 0.00042 21.1 1.8 30 8-37 8-37 (69)
306 PRK05508 methionine sulfoxide 43.2 25 0.00053 23.9 2.4 19 75-93 75-93 (119)
307 PRK04023 DNA polymerase II lar 42.7 12 0.00027 33.9 1.1 8 108-115 664-671 (1121)
308 PF13912 zf-C2H2_6: C2H2-type 42.3 18 0.00039 17.1 1.3 11 108-118 2-12 (27)
309 PRK13130 H/ACA RNA-protein com 42.2 16 0.00034 21.5 1.2 27 7-37 3-29 (56)
310 PF14122 YokU: YokU-like prote 42.1 25 0.00055 22.5 2.2 38 81-118 1-46 (87)
311 TIGR00155 pqiA_fam integral me 42.0 15 0.00032 29.8 1.4 27 9-36 215-241 (403)
312 PF04438 zf-HIT: HIT zinc fing 41.2 19 0.00041 18.3 1.2 20 10-34 3-22 (30)
313 PRK08402 replication factor A; 41.2 17 0.00037 29.1 1.6 28 9-36 212-241 (355)
314 PF08273 Prim_Zn_Ribbon: Zinc- 41.2 18 0.00039 19.7 1.2 23 11-33 5-34 (40)
315 PF00684 DnaJ_CXXCXGXG: DnaJ c 41.0 76 0.0016 18.7 4.3 35 78-114 14-48 (66)
316 PF14952 zf-tcix: Putative tre 40.4 12 0.00026 20.9 0.4 32 3-37 5-39 (44)
317 PRK00222 methionine sulfoxide 40.2 20 0.00044 25.0 1.7 20 74-93 87-106 (142)
318 TIGR01051 topA_bact DNA topois 40.2 24 0.00052 30.1 2.4 29 80-116 575-606 (610)
319 PF14255 Cys_rich_CPXG: Cystei 40.2 45 0.00097 19.2 2.9 31 81-115 2-32 (52)
320 cd00065 FYVE FYVE domain; Zinc 40.1 21 0.00047 20.0 1.5 28 9-36 2-29 (57)
321 PF01641 SelR: SelR domain; I 39.8 33 0.00071 23.4 2.6 19 75-93 82-100 (124)
322 PF07503 zf-HYPF: HypF finger; 39.3 6.4 0.00014 20.8 -0.7 24 12-35 2-31 (35)
323 PF00320 GATA: GATA zinc finge 39.3 2.5 5.5E-05 22.3 -2.4 31 82-118 1-31 (36)
324 PRK06319 DNA topoisomerase I/S 39.2 26 0.00056 31.2 2.5 14 78-91 591-604 (860)
325 PF14319 Zn_Tnp_IS91: Transpos 39.2 17 0.00037 24.1 1.1 34 73-116 36-69 (111)
326 TIGR01405 polC_Gram_pos DNA po 38.5 20 0.00044 33.2 1.8 14 26-39 684-697 (1213)
327 PF09845 DUF2072: Zn-ribbon co 38.2 19 0.00042 24.8 1.3 20 81-100 21-40 (131)
328 PF03107 C1_2: C1 domain; Int 38.0 35 0.00075 17.0 2.0 23 12-35 3-25 (30)
329 PF12647 RNHCP: RNHCP domain; 37.9 1.1E+02 0.0024 19.8 5.6 30 10-39 5-38 (92)
330 PF02012 BNR: BNR/Asp-box repe 37.3 16 0.00035 14.8 0.5 8 98-105 2-9 (12)
331 COG1552 RPL40A Ribosomal prote 37.3 7.2 0.00016 22.4 -0.8 24 10-35 15-38 (50)
332 PRK00448 polC DNA polymerase I 37.2 22 0.00047 33.6 1.8 14 26-39 909-922 (1437)
333 COG0272 Lig NAD-dependent DNA 36.8 23 0.00049 30.8 1.7 28 8-35 403-435 (667)
334 PRK08579 anaerobic ribonucleos 36.7 18 0.00038 31.2 1.1 26 6-33 565-590 (625)
335 PF13909 zf-H2C2_5: C2H2-type 36.4 22 0.00048 16.3 1.0 11 26-36 1-11 (24)
336 smart00355 ZnF_C2H2 zinc finge 35.9 12 0.00026 16.8 -0.0 11 108-118 1-11 (26)
337 COG2995 PqiA Uncharacterized p 35.8 27 0.00059 28.5 2.0 33 5-37 14-50 (418)
338 PF06061 Baculo_ME53: Baculovi 35.5 23 0.0005 28.1 1.5 28 9-37 260-289 (327)
339 COG1107 Archaea-specific RecJ- 35.1 1.3E+02 0.0027 26.3 5.8 88 9-116 2-89 (715)
340 PF07649 C1_3: C1-like domain; 35.1 27 0.00058 17.3 1.2 24 11-35 2-25 (30)
341 COG0375 HybF Zn finger protein 35.1 21 0.00046 24.1 1.1 24 11-34 72-95 (115)
342 PRK07220 DNA topoisomerase I; 35.0 36 0.00077 29.8 2.7 10 79-88 589-598 (740)
343 PF05715 zf-piccolo: Piccolo Z 34.8 19 0.00042 21.5 0.8 26 10-35 3-40 (61)
344 PF13913 zf-C2HC_2: zinc-finge 34.5 18 0.00039 17.4 0.5 9 80-88 3-11 (25)
345 KOG0954 PHD finger protein [Ge 34.3 20 0.00044 31.6 1.1 29 6-34 285-321 (893)
346 PF14149 YhfH: YhfH-like prote 34.2 2.2 4.8E-05 23.0 -3.0 18 4-21 8-25 (37)
347 PF15499 Peptidase_C98: Ubiqui 34.0 34 0.00073 26.5 2.1 16 73-88 164-179 (275)
348 PF09332 Mcm10: Mcm10 replicat 33.2 26 0.00057 28.0 1.5 14 103-116 281-294 (344)
349 PF06524 NOA36: NOA36 protein; 33.1 23 0.0005 27.5 1.1 34 3-36 135-182 (314)
350 PRK14973 DNA topoisomerase I; 32.5 22 0.00048 32.0 1.1 30 10-39 636-671 (936)
351 PRK08173 DNA topoisomerase III 32.5 30 0.00064 30.9 1.8 25 10-35 625-650 (862)
352 PF10825 DUF2752: Protein of u 32.3 11 0.00025 21.5 -0.5 19 77-95 7-25 (52)
353 PF00935 Ribosomal_L44: Riboso 32.2 41 0.0009 21.0 2.0 14 104-117 50-63 (77)
354 TIGR03830 CxxCG_CxxCG_HTH puta 31.9 30 0.00066 22.6 1.5 14 26-39 32-45 (127)
355 KOG0694 Serine/threonine prote 31.7 17 0.00036 31.6 0.2 28 6-33 238-266 (694)
356 COG3024 Uncharacterized protei 31.6 23 0.00051 21.4 0.8 14 77-90 5-18 (65)
357 PF12855 Ecl1: Life-span regul 31.6 15 0.00033 20.3 -0.0 21 9-29 6-27 (43)
358 PRK00762 hypA hydrogenase nick 31.3 23 0.0005 23.8 0.8 25 8-33 69-100 (124)
359 PRK07726 DNA topoisomerase III 31.1 37 0.0008 29.3 2.1 26 79-112 610-635 (658)
360 PF06107 DUF951: Bacterial pro 31.0 96 0.0021 18.3 3.3 13 103-115 27-39 (57)
361 PRK14704 anaerobic ribonucleos 30.7 23 0.00049 30.5 0.8 20 81-115 561-580 (618)
362 PF11062 DUF2863: Protein of u 30.7 31 0.00066 28.1 1.5 19 7-25 362-380 (398)
363 PHA02325 hypothetical protein 30.6 42 0.00092 20.4 1.7 23 80-102 4-29 (72)
364 PF14369 zf-RING_3: zinc-finge 30.5 32 0.0007 18.0 1.1 24 10-33 3-29 (35)
365 COG3877 Uncharacterized protei 30.4 35 0.00075 22.9 1.5 25 9-35 6-30 (122)
366 PF11023 DUF2614: Protein of u 30.4 21 0.00045 24.0 0.5 12 78-89 68-79 (114)
367 PRK07111 anaerobic ribonucleos 30.3 26 0.00056 30.7 1.1 26 5-33 676-701 (735)
368 TIGR02159 PA_CoA_Oxy4 phenylac 30.2 16 0.00034 25.5 -0.2 26 10-35 106-140 (146)
369 PF14400 Transglut_i_TM: Inact 30.0 59 0.0013 23.2 2.7 22 86-110 68-89 (165)
370 COG2260 Predicted Zn-ribbon RN 29.5 26 0.00057 20.8 0.7 14 77-90 15-28 (59)
371 PF05495 zf-CHY: CHY zinc fing 29.5 39 0.00084 20.4 1.5 24 9-32 41-68 (71)
372 PRK07956 ligA NAD-dependent DN 28.7 35 0.00077 29.5 1.6 28 8-35 403-435 (665)
373 KOG2879 Predicted E3 ubiquitin 28.2 32 0.0007 26.8 1.2 39 76-115 236-284 (298)
374 PRK06260 threonine synthase; V 28.2 33 0.00071 27.4 1.3 26 9-34 3-28 (397)
375 KOG3092 Casein kinase II, beta 27.5 26 0.00056 26.0 0.6 15 9-23 134-148 (216)
376 TIGR00375 conserved hypothetic 27.2 24 0.00052 28.4 0.4 25 9-34 240-267 (374)
377 PF10263 SprT-like: SprT-like 27.0 54 0.0012 22.2 2.1 35 76-118 120-154 (157)
378 KOG4317 Predicted Zn-finger pr 26.8 37 0.00079 27.1 1.3 27 5-35 3-29 (383)
379 COG2956 Predicted N-acetylgluc 26.8 26 0.00057 28.2 0.5 12 105-116 352-363 (389)
380 PRK14714 DNA polymerase II lar 26.7 35 0.00076 31.9 1.3 26 10-38 680-705 (1337)
381 TIGR01057 topA_arch DNA topois 26.5 52 0.0011 28.1 2.2 26 79-112 589-614 (618)
382 PRK07225 DNA-directed RNA poly 26.2 42 0.0009 28.8 1.6 31 6-36 541-573 (605)
383 PF08209 Sgf11: Sgf11 (transcr 26.2 45 0.00099 17.3 1.2 12 105-116 2-13 (33)
384 smart00731 SprT SprT homologue 26.1 81 0.0017 21.5 2.8 33 78-117 111-143 (146)
385 KOG0909 Peptide:N-glycanase [P 25.8 41 0.00089 27.9 1.5 38 79-116 161-203 (500)
386 COG0266 Nei Formamidopyrimidin 25.8 70 0.0015 24.8 2.6 31 77-115 243-273 (273)
387 PRK08329 threonine synthase; V 25.4 50 0.0011 25.9 1.8 24 9-34 1-24 (347)
388 KOG1701 Focal adhesion adaptor 25.3 46 0.001 27.5 1.6 19 5-23 423-441 (468)
389 PF08790 zf-LYAR: LYAR-type C2 25.0 47 0.001 16.7 1.1 11 108-118 1-11 (28)
390 COG1675 TFA1 Transcription ini 24.4 19 0.00041 26.0 -0.6 29 8-36 112-143 (176)
391 PF08421 Methyltransf_13: Puta 24.3 65 0.0014 18.8 1.8 26 13-38 19-53 (62)
392 KOG0402 60S ribosomal protein 24.2 38 0.00082 21.7 0.8 31 9-39 36-68 (92)
393 KOG3352 Cytochrome c oxidase, 24.2 99 0.0022 21.9 2.9 31 80-118 112-144 (153)
394 PF10601 zf-LITAF-like: LITAF- 24.2 43 0.00094 20.1 1.0 16 77-92 56-71 (73)
395 PF02701 zf-Dof: Dof domain, z 23.9 54 0.0012 19.7 1.4 39 78-119 4-42 (63)
396 TIGR00575 dnlj DNA ligase, NAD 23.7 56 0.0012 28.3 2.0 27 8-34 391-421 (652)
397 COG4469 CoiA Competence protei 23.7 36 0.00079 27.1 0.8 15 10-24 26-40 (342)
398 PF04194 PDCD2_C: Programmed c 23.6 61 0.0013 22.8 1.8 34 80-113 98-145 (164)
399 PRK03922 hypothetical protein; 23.6 43 0.00092 22.5 1.0 15 7-21 47-61 (113)
400 smart00714 LITAF Possible memb 23.5 49 0.0011 19.5 1.2 16 77-92 50-65 (67)
401 KOG1315 Predicted DHHC-type Zn 23.4 35 0.00076 26.8 0.6 24 6-31 106-129 (307)
402 TIGR00320 dfx_rbo desulfoferro 23.4 40 0.00087 22.8 0.9 22 7-28 5-29 (125)
403 PF14787 zf-CCHC_5: GAG-polypr 23.1 42 0.00091 17.9 0.7 10 80-89 3-12 (36)
404 PF15616 TerY-C: TerY-C metal 23.1 65 0.0014 22.2 1.8 28 10-37 78-117 (131)
405 PRK12496 hypothetical protein; 23.0 51 0.0011 23.3 1.4 24 12-35 130-153 (164)
406 PRK08116 hypothetical protein; 23.0 65 0.0014 24.4 2.0 31 79-115 16-47 (268)
407 COG1601 GCD7 Translation initi 23.0 21 0.00046 25.2 -0.6 30 10-39 106-140 (151)
408 PHA02611 51 baseplate hub asse 22.9 63 0.0014 24.7 1.9 17 79-95 82-98 (249)
409 PRK07561 DNA topoisomerase I s 22.7 69 0.0015 28.6 2.4 20 10-29 588-611 (859)
410 PRK11788 tetratricopeptide rep 22.7 62 0.0013 24.8 1.9 24 78-115 353-376 (389)
411 PRK04179 rpl37e 50S ribosomal 22.5 43 0.00093 20.1 0.7 25 8-33 16-40 (62)
412 cd02674 Peptidase_C19R A subfa 22.3 1E+02 0.0022 21.9 2.9 23 78-100 103-125 (230)
413 smart00154 ZnF_AN1 AN1-like Zi 22.3 76 0.0016 16.9 1.7 23 12-36 1-23 (39)
414 PRK14018 trifunctional thiored 22.2 1E+02 0.0023 26.0 3.2 18 75-92 463-481 (521)
415 COG4481 Uncharacterized protei 22.1 74 0.0016 18.7 1.7 14 103-116 30-43 (60)
416 COG1631 RPL42A Ribosomal prote 21.9 52 0.0011 21.4 1.1 13 104-116 65-77 (94)
417 PF09463 Opy2: Opy2 protein; 21.8 91 0.002 16.5 1.8 16 81-96 10-25 (35)
418 PRK07591 threonine synthase; V 21.7 48 0.001 26.8 1.1 24 9-33 18-41 (421)
419 KOG3993 Transcription factor ( 21.7 33 0.00071 28.4 0.2 22 97-118 346-367 (500)
420 COG5349 Uncharacterized protei 21.6 35 0.00077 23.3 0.3 14 78-91 20-33 (126)
421 PF00412 LIM: LIM domain; Int 21.4 52 0.0011 18.2 1.0 25 12-36 1-37 (58)
422 PF12387 Peptidase_C74: Pestiv 21.4 45 0.00098 24.3 0.8 12 79-90 175-186 (200)
423 PF05207 zf-CSL: CSL zinc fing 21.2 1.1E+02 0.0024 17.6 2.3 13 104-117 15-27 (55)
424 PRK02935 hypothetical protein; 21.1 41 0.0009 22.4 0.5 11 78-88 69-79 (110)
425 smart00132 LIM Zinc-binding do 21.1 43 0.00093 16.6 0.5 11 12-22 2-12 (39)
426 PF00641 zf-RanBP: Zn-finger i 21.0 89 0.0019 15.3 1.7 12 26-37 5-16 (30)
427 PF07975 C1_4: TFIIH C1-like d 21.0 65 0.0014 18.5 1.3 12 105-116 19-30 (51)
428 TIGR03670 rpoB_arch DNA-direct 21.0 54 0.0012 28.1 1.3 30 7-36 536-567 (599)
429 cd01675 RNR_III Class III ribo 20.8 63 0.0014 27.3 1.7 15 79-93 532-546 (555)
430 PF10071 DUF2310: Zn-ribbon-co 20.8 51 0.0011 25.3 1.0 28 78-114 219-248 (258)
431 KOG4080 Mitochondrial ribosoma 20.7 41 0.00089 24.2 0.5 10 80-89 94-103 (176)
432 COG5525 Bacteriophage tail ass 20.6 45 0.00098 28.6 0.8 39 79-117 227-269 (611)
433 PRK14715 DNA polymerase II lar 20.6 49 0.0011 31.3 1.0 22 79-116 674-695 (1627)
434 PLN03165 chaperone protein dna 20.4 1.8E+02 0.0039 19.4 3.5 30 80-114 53-82 (111)
435 COG1328 NrdD Oxygen-sensitive 20.3 62 0.0014 28.4 1.6 15 82-96 658-672 (700)
436 PF13597 NRDD: Anaerobic ribon 20.3 52 0.0011 27.8 1.1 16 79-94 504-519 (546)
437 PF06573 Churchill: Churchill 20.2 1.5E+02 0.0032 19.9 3.0 36 77-116 56-94 (112)
438 TIGR02827 RNR_anaer_Bdell anae 20.1 67 0.0015 27.5 1.7 12 80-91 547-558 (586)
439 PF06170 DUF983: Protein of un 20.1 64 0.0014 20.4 1.2 14 77-90 6-19 (86)
No 1
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=100.00 E-value=2.4e-41 Score=218.15 Aligned_cols=101 Identities=34% Similarity=0.633 Sum_probs=83.6
Q ss_pred cccCccCCCcccccCCc----EEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCccccccccccccccc
Q 040426 9 FLFCKFCGTMLRMESNH----VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKRACEK 84 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~----~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~~~~Cpk 84 (120)
|.|||.|||||.++++. |.|++|+|..+++. +|..++. +..+.+++ ++.+...+++...+++.||+
T Consensus 1 m~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~~----ei~~r~~----~~~Kevd~--vlgg~~a~~nv~~t~~~Cp~ 70 (105)
T KOG2906|consen 1 MLFCPTCGNMLIVESGESCNRFSCRTCPYVFPISR----EISSRKY----PKLKEVDD--VLGGDEAWENVDQTEATCPT 70 (105)
T ss_pred CcccCCCCCEEEEecCCeEeeEEcCCCCceeeEee----eeecccc----Cchhhhhh--hcCCcccccchhhccCcCCC
Confidence 68999999999999764 99999999999975 3332221 22222233 56666678888999999999
Q ss_pred cCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426 85 CQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119 (120)
Q Consensus 85 Cg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~ 119 (120)
|||++|+|+|+|+||||||||+||+|.+|+|+||+
T Consensus 71 Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wre 105 (105)
T KOG2906|consen 71 CGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWRE 105 (105)
T ss_pred CCCCceEEEEeeeccCCCcHhHhhhhhcccccccC
Confidence 99999999999999999999999999999999996
No 2
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=100.00 E-value=3.2e-39 Score=217.08 Aligned_cols=108 Identities=33% Similarity=0.699 Sum_probs=80.3
Q ss_pred CcccCccCCCcccccCC---c-EEeCCCCCeeeccccccceEEEeeeh-hHHhhhhccccccccCCCccccccccccccc
Q 040426 8 DFLFCKFCGTMLRMESN---H-VVCSSCKFKKNVQDVADREISYAVTA-EEIKRELGISLFEQPQGDKGETQLSKVKRAC 82 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~---~-~~C~~C~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~i~~~~~~~~t~~~~~~~C 82 (120)
.|.|||+|||||+|+.+ . ++|++|||..++... .+++... ..++........++ .+....+++++..+.|
T Consensus 1 ~m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~~~----~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~C 75 (113)
T COG1594 1 SMRFCPKCGSLLYPKKDDEGGKLVCRKCGYEEEASNK----KVYRYSVKEAVEKKKEVVLVVE-DETQGAKTLPTAKEKC 75 (113)
T ss_pred CccccCCccCeeEEeEcCCCcEEECCCCCcchhcccc----ceeEEEEeeccCCcceeeeeec-ccccCccccccccccC
Confidence 48999999999999764 2 999999999998863 1221111 11222112111111 1334446777778899
Q ss_pred cccCCCceEEEEeecccCCCCceEEEEcCCCCceeccC
Q 040426 83 EKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES 120 (120)
Q Consensus 83 pkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~n 120 (120)
|+|||++|+|||+|+||||||||+||+|++|||+||++
T Consensus 76 pkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wre~ 113 (113)
T COG1594 76 PKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWREY 113 (113)
T ss_pred CCCCCceeEEEeeehhccCCCceEEEEecccCCEeecC
Confidence 99999999999999999999999999999999999986
No 3
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=100.00 E-value=3.5e-38 Score=206.42 Aligned_cols=105 Identities=26% Similarity=0.543 Sum_probs=90.7
Q ss_pred CCcccCccCCCcccccCCc------EEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCcccccccc-cc
Q 040426 7 RDFLFCKFCGTMLRMESNH------VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSK-VK 79 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~~~~~------~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~-~~ 79 (120)
++++||++|||||||++|+ |.||+|.|++.+++ ..+|+.... +...+. ..++.+...|||+|+ .+
T Consensus 2 ~~~rfC~eCNNmLYPkEDked~~L~laCrnCd~ve~A~s----~~vY~~~~~---~e~dE~-t~ii~Dl~~DPTLPrts~ 73 (113)
T KOG2691|consen 2 VGIRFCRECNNMLYPKEDKEDRILLLACRNCDYVEEADS----SRVYVNELS---HEHDEL-TQIIMDLASDPTLPRTSD 73 (113)
T ss_pred CccchhhhhhccccccccccccEEEEEecCCcceEecCC----cceEcCCcc---cchhhH-HHHHHhhccCCCcCcccc
Confidence 5799999999999999984 99999999999988 577776532 222322 337788899999995 78
Q ss_pred ccccccCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426 80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119 (120)
Q Consensus 80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~ 119 (120)
+.||+|||++|+|||.|+|.|||+|++||+|+.|||+|++
T Consensus 74 ~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~C~h~wte 113 (113)
T KOG2691|consen 74 KHCPKCGHREAVFFQAQTRRADEAMRLFYVCCSCGHRWTE 113 (113)
T ss_pred ccCCccCCcceEEEecccccccceEEEEEEeccccccccC
Confidence 9999999999999999999999999999999999999986
No 4
>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=100.00 E-value=1.8e-37 Score=205.76 Aligned_cols=103 Identities=27% Similarity=0.577 Sum_probs=79.1
Q ss_pred ccCccCCCcccccCCcEEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCccccccccccccccccCCCc
Q 040426 10 LFCKFCGTMLRMESNHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKRACEKCQNPE 89 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~~~~CpkCg~~e 89 (120)
.|||.||+||++.++.+.|+.|+|...+... ...+++.... .... +++ ++.+ +..+++|++++.||+|||++
T Consensus 1 ~fC~~Cg~~l~~~~~~~~C~~C~~~~~~~~~--~~~v~~~~~~---~~~~-~~~-~~~~-~~~~~~~~~~~~Cp~Cg~~~ 72 (104)
T TIGR01384 1 KFCPKCGSLMTPKNGVYVCPSCGYEKEKKPE--DDYKVTEKVK---HKIK-ETI-IIRE-EDSETLPTTRVECPKCGHKE 72 (104)
T ss_pred CCCcccCcccccCCCeEECcCCCCccccccc--cccEEEEEec---cccc-cce-eecc-ccccCCCcccCCCCCCCCCe
Confidence 4999999999998777999999999876421 1234443321 1111 112 1222 22388998899999999999
Q ss_pred eEEEEeecccCCCCceEEEEcCCCCceeccC
Q 040426 90 MYYSTRQTRSADEGQTTYYICPRCGHRCQES 120 (120)
Q Consensus 90 a~y~~~Q~RSADE~~T~fY~C~~C~~~w~~n 120 (120)
|+|||+|+||||||||+||+|++|||+|+++
T Consensus 73 a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~ 103 (104)
T TIGR01384 73 AYYWLLQTRRADEPETRFYKCTKCGYVWREY 103 (104)
T ss_pred eEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence 9999999999999999999999999999985
No 5
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=100.00 E-value=1.9e-36 Score=199.93 Aligned_cols=110 Identities=33% Similarity=0.615 Sum_probs=89.3
Q ss_pred CCCcccCccCCCcccccCCc--EEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCcccccccccccccc
Q 040426 6 GRDFLFCKFCGTMLRMESNH--VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKRACE 83 (120)
Q Consensus 6 ~~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~~~~Cp 83 (120)
..++.||+.||+||+.+... ..|..|+..++.+.+....+...+....++.++..+ + +...+..+|+++++||
T Consensus 4 ~~~~~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~~~~~~~v~~~~~~~~~~~A~~~~---v--e~~~~~~ga~I~~kCp 78 (116)
T KOG2907|consen 4 NGDLDFCSDCGSLLEEPSAQSTVLCIRCKIEYPVSQFSGLVVETKSLFDEFTSALAEK---V--ENESSADGAVIKHKCP 78 (116)
T ss_pred ccCcchhhhhhhhcccccccCceEeccccccCCHHHhCCeeEEEEEeecccchhhhhh---h--cccccccccchhccCc
Confidence 44899999999999998765 889999999999888776666655555444433322 1 1222346789999999
Q ss_pred ccCCCceEEEEeecccCCCCceEEEEcCCCCceeccC
Q 040426 84 KCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES 120 (120)
Q Consensus 84 kCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~n 120 (120)
||||++|.|.++||||||||||+||.|++|+|++++|
T Consensus 79 kCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~e~ 115 (116)
T KOG2907|consen 79 KCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFTEN 115 (116)
T ss_pred ccCCchhhhhhhhcccccCCceEEEEcCccceeeecc
Confidence 9999999999999999999999999999999999986
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=99.93 E-value=7.8e-27 Score=130.20 Aligned_cols=40 Identities=50% Similarity=0.952 Sum_probs=38.4
Q ss_pred ccccccCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426 80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119 (120)
Q Consensus 80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~ 119 (120)
.+||+|||++|+|||+|+||||||||+||+|++|||+|++
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~~ 40 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWRE 40 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeCC
Confidence 3699999999999999999999999999999999999986
No 7
>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=99.92 E-value=1.6e-25 Score=124.24 Aligned_cols=39 Identities=46% Similarity=0.848 Sum_probs=35.0
Q ss_pred ccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
.+||+|||++|+|+|+|+||||||||+||+|.+|||+||
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 369999999999999999999999999999999999997
No 8
>PHA02998 RNA polymerase subunit; Provisional
Probab=99.85 E-value=7.4e-22 Score=140.17 Aligned_cols=45 Identities=24% Similarity=0.419 Sum_probs=42.6
Q ss_pred cccc-ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 74 QLSK-VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 74 t~~~-~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
-+|+ ++.+||+|||++|+|+|+|+||||||||+||+|++|||+|+
T Consensus 137 vlpkkt~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 137 VLDEKYNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred ccCcccCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccC
Confidence 4665 88999999999999999999999999999999999999997
No 9
>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=99.72 E-value=3.6e-18 Score=131.49 Aligned_cols=42 Identities=40% Similarity=0.683 Sum_probs=40.0
Q ss_pred cccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 77 KVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 77 ~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
+....||+||+++++|||+|+||||||||+||+|++|||+|+
T Consensus 256 t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 256 TDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 456799999999999999999999999999999999999997
No 10
>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=99.39 E-value=1.1e-13 Score=74.86 Aligned_cols=31 Identities=26% Similarity=0.820 Sum_probs=24.5
Q ss_pred cccCccCCCcccccCCc---EEeCCCCCeeeccc
Q 040426 9 FLFCKFCGTMLRMESNH---VVCSSCKFKKNVQD 39 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~---~~C~~C~~~~~~~~ 39 (120)
|.|||+|||||+|+++. ..|++|||+++++.
T Consensus 1 m~FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~~~~ 34 (35)
T PF02150_consen 1 MRFCPECGNLLYPKEDKEKRVACRTCGYEEPISQ 34 (35)
T ss_dssp --BETTTTSBEEEEEETTTTEEESSSS-EEE-SS
T ss_pred CeeCCCCCccceEcCCCccCcCCCCCCCccCCCC
Confidence 68999999999999875 68999999999875
No 11
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=99.04 E-value=1.5e-10 Score=88.86 Aligned_cols=41 Identities=41% Similarity=0.714 Sum_probs=39.0
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
....|.+|+.....|+|+|+||||||||.|-.|.+||.+|+
T Consensus 254 d~fkcgkckk~~cty~q~Qtrs~DePmtTfv~C~ecgnrWk 294 (296)
T KOG1105|consen 254 DLFKCGKCKKKNCTYTQLQTRSADEPMTTFVTCNECGNRWK 294 (296)
T ss_pred cceeeccccccceeEEeeccCCCCCCcceeeeecccCCccc
Confidence 35789999999999999999999999999999999999996
No 12
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=98.79 E-value=7.3e-09 Score=60.05 Aligned_cols=37 Identities=27% Similarity=0.718 Sum_probs=30.0
Q ss_pred ccCccCCCcccccCC----cEEeCCCCCeeeccccccceEEEeee
Q 040426 10 LFCKFCGTMLRMESN----HVVCSSCKFKKNVQDVADREISYAVT 50 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~----~~~C~~C~~~~~~~~~~~~~~~~~~~ 50 (120)
.|||+||+||+++++ .++|+.|||...+.. .++|...
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~~----~~~~~~~ 41 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEEPIEQ----KYVYKEK 41 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeEECCC----cEEEEEE
Confidence 599999999999864 299999999998866 4566543
No 13
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=98.21 E-value=8.9e-07 Score=51.36 Aligned_cols=29 Identities=21% Similarity=0.617 Sum_probs=25.5
Q ss_pred CcccCccCCC-cccccCCcEEeCCCCCeee
Q 040426 8 DFLFCKFCGT-MLRMESNHVVCSSCKFKKN 36 (120)
Q Consensus 8 ~~~FCp~Cgn-lL~~~~~~~~C~~C~~~~~ 36 (120)
...|||.||+ +|.+..+.+.|..|||++-
T Consensus 19 ~~~fCP~Cg~~~m~~~~~r~~C~~Cgyt~~ 48 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHLDRWHCGKCGYTEF 48 (50)
T ss_pred ccCcCcCCCcchheccCCcEECCCcCCEEe
Confidence 4569999999 9999888899999999863
No 14
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=97.24 E-value=0.0002 Score=41.10 Aligned_cols=30 Identities=20% Similarity=0.596 Sum_probs=23.9
Q ss_pred CcccCccCC--CcccccCCcEEeCCCCCeeec
Q 040426 8 DFLFCKFCG--TMLRMESNHVVCSSCKFKKNV 37 (120)
Q Consensus 8 ~~~FCp~Cg--nlL~~~~~~~~C~~C~~~~~~ 37 (120)
.-.|||.|| .+|---.++++|-.|||++-.
T Consensus 18 k~~~CPrCG~gvfmA~H~dR~~CGkCgyTe~~ 49 (51)
T COG1998 18 KNRFCPRCGPGVFMADHKDRWACGKCGYTEFK 49 (51)
T ss_pred ccccCCCCCCcchhhhcCceeEeccccceEee
Confidence 457999999 666655667999999998753
No 15
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=97.24 E-value=0.00017 Score=38.49 Aligned_cols=26 Identities=35% Similarity=0.871 Sum_probs=16.2
Q ss_pred ccCccCCCccccc---CCc---EEeCCCCCee
Q 040426 10 LFCKFCGTMLRME---SNH---VVCSSCKFKK 35 (120)
Q Consensus 10 ~FCp~CgnlL~~~---~~~---~~C~~C~~~~ 35 (120)
+|||.||..|... .+. ++|..||++.
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTEEE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCCEE
Confidence 5999999999754 232 9999999864
No 16
>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=97.20 E-value=0.00058 Score=52.48 Aligned_cols=68 Identities=24% Similarity=0.462 Sum_probs=32.9
Q ss_pred ccCccCCCc-----ccccC--C-c-EEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCccccccccccc
Q 040426 10 LFCKFCGTM-----LRMES--N-H-VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKR 80 (120)
Q Consensus 10 ~FCp~Cgnl-----L~~~~--~-~-~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~~~ 80 (120)
.+||.||+. |...+ + + +.|..|++.... ...
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~----------------------------------------~R~ 212 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRF----------------------------------------VRI 212 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE------------------------------------------TT
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeee----------------------------------------cCC
Confidence 699999986 33333 2 2 999999998753 134
Q ss_pred cccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
.||.||+.+..=+.. +...+++.-..++|.+|+..++
T Consensus 213 ~Cp~Cg~~~~~~l~~-~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 213 KCPYCGNTDHEKLEY-FTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp S-TTT---SS-EEE---------SEEEEEETTTTEEEE
T ss_pred CCcCCCCCCCcceee-EecCCCCcEEEEECCcccchHH
Confidence 599999976642111 2246777889999999998775
No 17
>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=96.98 E-value=0.00076 Score=38.37 Aligned_cols=37 Identities=24% Similarity=0.561 Sum_probs=26.5
Q ss_pred cccccCCCceEEEEeecccCCCCceEEEEcCC--CCceecc
Q 040426 81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPR--CGHRCQE 119 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~--C~~~w~~ 119 (120)
.||.||+.-......++ .++--.++|.|.+ |||+|..
T Consensus 1 ~CP~Cg~~a~ir~S~~~--s~~~~~~Y~qC~N~~Cg~tfv~ 39 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQL--SPLTRELYCQCTNPECGHTFVA 39 (47)
T ss_pred CcCCCCCeeEEEEchhh--CcceEEEEEEECCCcCCCEEEE
Confidence 49999998665544332 3444558999997 9999963
No 18
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=96.98 E-value=0.0021 Score=50.17 Aligned_cols=67 Identities=22% Similarity=0.622 Sum_probs=45.5
Q ss_pred cccCccCCCcc-----cccC-C--c-EEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCcccccccccc
Q 040426 9 FLFCKFCGTML-----RMES-N--H-VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVK 79 (120)
Q Consensus 9 ~~FCp~CgnlL-----~~~~-~--~-~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~~ 79 (120)
-.+||.||+.= .... + + +.|..|+..... .+
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~----------------------------------------~R 226 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHV----------------------------------------VR 226 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccc----------------------------------------cC
Confidence 57999999872 1211 2 2 999999987742 24
Q ss_pred ccccccCCC-ceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 80 RACEKCQNP-EMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 80 ~~CpkCg~~-ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
..||.||+. +..||.+- .+++.-..+.|..|+..++
T Consensus 227 ~~C~~Cg~~~~l~y~~~~---~~~~~~r~e~C~~C~~YlK 263 (309)
T PRK03564 227 VKCSNCEQSGKLHYWSLD---SEQAAVKAESCGDCGTYLK 263 (309)
T ss_pred ccCCCCCCCCceeeeeec---CCCcceEeeecccccccce
Confidence 569999986 44576552 2234567899999987665
No 19
>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=96.88 E-value=0.00035 Score=36.28 Aligned_cols=27 Identities=30% Similarity=0.869 Sum_probs=14.7
Q ss_pred cccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
+||+||....+ . -...|+|..|+|.|.
T Consensus 4 ~Cp~C~se~~y--------~---D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 4 KCPLCGSEYTY--------E---DGELLVCPECGHEWN 30 (30)
T ss_dssp --TTT-----E--------E----SSSEEETTTTEEE-
T ss_pred CCCCCCCccee--------c---cCCEEeCCcccccCC
Confidence 69999999887 2 223499999999994
No 20
>PHA00626 hypothetical protein
Probab=96.87 E-value=0.00078 Score=39.74 Aligned_cols=34 Identities=26% Similarity=0.656 Sum_probs=23.1
Q ss_pred cccccCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426 81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~ 119 (120)
.||+||+.+.+- -...| .+..-|+|.+|||.++.
T Consensus 2 ~CP~CGS~~Ivr-cg~cr----~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 2 SCPKCGSGNIAK-EKTMR----GWSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCceeee-eceec----ccCcceEcCCCCCeech
Confidence 599999987652 11111 23455999999999863
No 21
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=96.78 E-value=0.0011 Score=34.65 Aligned_cols=27 Identities=26% Similarity=0.603 Sum_probs=18.9
Q ss_pred cccCccCCCcccccCCc--EEeCCCCCee
Q 040426 9 FLFCKFCGTMLRMESNH--VVCSSCKFKK 35 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~--~~C~~C~~~~ 35 (120)
-+||+.||.-+.+.... ..|..|+...
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-EE
T ss_pred CcccCcCCccccCCCCcCEeECCCCcCEe
Confidence 57999999999998775 9999999764
No 22
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=96.75 E-value=0.0015 Score=40.62 Aligned_cols=36 Identities=22% Similarity=0.495 Sum_probs=26.6
Q ss_pred cccccCCCceEEEEeecccCCCCce-EEEEcC--CCCceecc
Q 040426 81 ACEKCQNPEMYYSTRQTRSADEGQT-TYYICP--RCGHRCQE 119 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q~RSADE~~T-~fY~C~--~C~~~w~~ 119 (120)
.||.||+.-.+ .-.|..+++.. ++|.|+ +|||+|..
T Consensus 3 ~CP~Cg~~a~i---rtSr~~s~~~~~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 3 HCPLCQHAAHA---RTSRYITDTTKERYHQCQNVNCSATFIT 41 (72)
T ss_pred cCCCCCCccEE---EEChhcChhhheeeeecCCCCCCCEEEE
Confidence 69999998733 33455565544 889999 89999974
No 23
>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=96.61 E-value=0.0038 Score=37.94 Aligned_cols=36 Identities=28% Similarity=0.525 Sum_probs=21.3
Q ss_pred cccccCCCceEEEEeecccC------C--CCceEEEEcCCCCce
Q 040426 81 ACEKCQNPEMYYSTRQTRSA------D--EGQTTYYICPRCGHR 116 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q~RSA------D--E~~T~fY~C~~C~~~ 116 (120)
.|||||+.+...-++|+--. | +..-+...|++|||+
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYT 45 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCE
Confidence 69999998765443332110 1 112245679999997
No 24
>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=96.54 E-value=0.0064 Score=47.41 Aligned_cols=69 Identities=20% Similarity=0.484 Sum_probs=46.1
Q ss_pred cccCccCCCcc-----ccc--CC--c-EEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCccccccccc
Q 040426 9 FLFCKFCGTML-----RME--SN--H-VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKV 78 (120)
Q Consensus 9 ~~FCp~CgnlL-----~~~--~~--~-~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~ 78 (120)
-.+||.||+.= ... .+ + +.|..|+..... .
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~----------------------------------------~ 223 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHY----------------------------------------V 223 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccc----------------------------------------c
Confidence 45999999873 221 12 2 999999987742 2
Q ss_pred cccccccCCCc-eEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 79 KRACEKCQNPE-MYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 79 ~~~CpkCg~~e-a~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
+..||.||+.+ ..||.+-. ..+++-.....|..|+...+
T Consensus 224 R~~C~~Cg~~~~l~y~~~e~-~~~~~~~r~e~C~~C~~YlK 263 (305)
T TIGR01562 224 RVKCSHCEESKHLAYLSLEH-DAEKAVLKAETCDSCQGYLK 263 (305)
T ss_pred CccCCCCCCCCceeeEeecC-CCCCcceEEeeccccccchh
Confidence 45699999974 45776522 11245678889999987654
No 25
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=96.42 E-value=0.0038 Score=35.67 Aligned_cols=32 Identities=25% Similarity=0.686 Sum_probs=19.9
Q ss_pred cccccCCCceEEEEeecccCCCCceEEEEcCCCCceeccC
Q 040426 81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES 120 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~n 120 (120)
-||+||+ +.| .+ .++ ....|.|..|||.++.+
T Consensus 2 FCp~Cg~--~l~----~~-~~~-~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGN--MLI----PK-EGK-EKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCC--ccc----cc-cCC-CCCEEECCcCCCeEECC
Confidence 4999988 222 12 122 12378999999987653
No 26
>PHA00626 hypothetical protein
Probab=96.37 E-value=0.0024 Score=37.65 Aligned_cols=32 Identities=19% Similarity=0.555 Sum_probs=23.7
Q ss_pred ccCccCCCcccccC-------CcEEeCCCCCeeeccccc
Q 040426 10 LFCKFCGTMLRMES-------NHVVCSSCKFKKNVQDVA 41 (120)
Q Consensus 10 ~FCp~CgnlL~~~~-------~~~~C~~C~~~~~~~~~~ 41 (120)
+.||.||+--..+. +.|.|..|||....+.+.
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~~~ 39 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDAFG 39 (59)
T ss_pred CCCCCCCCceeeeeceecccCcceEcCCCCCeechhhhh
Confidence 47999999544442 239999999998776653
No 27
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=96.12 E-value=0.0051 Score=33.09 Aligned_cols=32 Identities=31% Similarity=0.645 Sum_probs=21.4
Q ss_pred cccccccCCCceEEEEeecccCCC---CceEEEEcCCCCceec
Q 040426 79 KRACEKCQNPEMYYSTRQTRSADE---GQTTYYICPRCGHRCQ 118 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~Q~RSADE---~~T~fY~C~~C~~~w~ 118 (120)
...||+|+.. | +-+|| +..+-.+|.+|||.|+
T Consensus 2 ~i~Cp~C~~~---y-----~i~d~~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 2 IITCPNCQAK---Y-----EIDDEKIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred EEECCCCCCE---E-----eCCHHHCCCCCcEEECCCCCCEeC
Confidence 3568888753 2 22444 4556789999999995
No 28
>PF12773 DZR: Double zinc ribbon
Probab=96.08 E-value=0.0033 Score=35.77 Aligned_cols=32 Identities=28% Similarity=0.592 Sum_probs=24.6
Q ss_pred CCCCcccCccCCCcccccCC-cEEeCCCCCeee
Q 040426 5 LGRDFLFCKFCGTMLRMESN-HVVCSSCKFKKN 36 (120)
Q Consensus 5 ~~~~~~FCp~CgnlL~~~~~-~~~C~~C~~~~~ 36 (120)
+..+..|||.||..|..... .+.|..|++...
T Consensus 8 ~~~~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 8 NPDDAKFCPHCGTPLPPPDQSKKICPNCGAENP 40 (50)
T ss_pred CCccccCChhhcCChhhccCCCCCCcCCcCCCc
Confidence 44568899999999994333 399999999643
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=95.95 E-value=0.0065 Score=34.25 Aligned_cols=28 Identities=21% Similarity=0.582 Sum_probs=21.1
Q ss_pred ccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426 80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
..||+||+.+++.... ...|+|..|+++
T Consensus 19 ~~CP~Cg~~~~~~~~~---------~~~~~C~~C~~q 46 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKT---------RGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCeeeEEeCC---------CCeEECCCCCCc
Confidence 5599999995554432 567999999874
No 30
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=95.90 E-value=0.0094 Score=42.17 Aligned_cols=38 Identities=18% Similarity=0.427 Sum_probs=22.5
Q ss_pred cccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
+||-||++...-...-.=|--.--+.+|.|.+||.+|.
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~ 39 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFT 39 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcce
Confidence 69999998742111000000001556899999999885
No 31
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=95.89 E-value=0.0063 Score=36.90 Aligned_cols=35 Identities=23% Similarity=0.586 Sum_probs=23.7
Q ss_pred ccccccCCCceEEEEeecccCCCCceEE--------E--EcCCCCce
Q 040426 80 RACEKCQNPEMYYSTRQTRSADEGQTTY--------Y--ICPRCGHR 116 (120)
Q Consensus 80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~f--------Y--~C~~C~~~ 116 (120)
.+|||||+++. .+-+++...++..-+ + .|.+|||+
T Consensus 5 ~kCpKCgn~~~--~ekei~~tg~~lskifdvq~n~f~~itCk~CgYt 49 (68)
T COG3478 5 FKCPKCGNTNY--EEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYT 49 (68)
T ss_pred ccCCCcCCcch--hhceeeccCCCcceeEEecccEEEEEEeccCCch
Confidence 35999999875 455556665665433 3 48899986
No 32
>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=95.74 E-value=0.013 Score=32.42 Aligned_cols=30 Identities=27% Similarity=0.642 Sum_probs=20.7
Q ss_pred cccccCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426 81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~ 119 (120)
.||.||+.. ..+- ..+-.++|..||....+
T Consensus 2 ~Cp~Cg~~~-~~~D--------~~~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKE-IVFD--------PERGELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSSE-EEEE--------TTTTEEEETTT-BBEE-
T ss_pred CCcCCcCCc-eEEc--------CCCCeEECCCCCCEeec
Confidence 699999988 3332 45566899999986544
No 33
>PF14353 CpXC: CpXC protein
Probab=95.61 E-value=0.021 Score=38.59 Aligned_cols=40 Identities=28% Similarity=0.640 Sum_probs=26.1
Q ss_pred ccccccCCC-ceEEEEeecccCC--------CCceEEEEcCCCCceecc
Q 040426 80 RACEKCQNP-EMYYSTRQTRSAD--------EGQTTYYICPRCGHRCQE 119 (120)
Q Consensus 80 ~~CpkCg~~-ea~y~~~Q~RSAD--------E~~T~fY~C~~C~~~w~~ 119 (120)
..||+||+. ++..|+.=.-+.| +|.--.|+|..||+..+.
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRL 50 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceec
Confidence 469999997 5556654332333 234457899999988653
No 34
>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=95.59 E-value=0.0099 Score=39.67 Aligned_cols=39 Identities=23% Similarity=0.374 Sum_probs=33.5
Q ss_pred CCCCCCCCcccCccCCCcccccC-CcEEeCCCCCeeeccc
Q 040426 1 MADPLGRDFLFCKFCGTMLRMES-NHVVCSSCKFKKNVQD 39 (120)
Q Consensus 1 ~~~~~~~~~~FCp~CgnlL~~~~-~~~~C~~C~~~~~~~~ 39 (120)
|+++--+.-+.||.||.-.|=-. +.++|+.||..+++..
T Consensus 1 MakpelGtKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~~ 40 (108)
T PF09538_consen 1 MAKPELGTKRTCPSCGAKFYDLNKDPIVCPKCGTEFPPEP 40 (108)
T ss_pred CCccccCCcccCCCCcchhccCCCCCccCCCCCCccCccc
Confidence 89999999999999999887543 3399999999998873
No 35
>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=95.54 E-value=0.011 Score=49.50 Aligned_cols=42 Identities=21% Similarity=0.607 Sum_probs=30.6
Q ss_pred ccccccccCCCc-eEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426 78 VKRACEKCQNPE-MYYSTRQTRSADEGQTTYYICPRCGHRCQE 119 (120)
Q Consensus 78 ~~~~CpkCg~~e-a~y~~~Q~RSADE~~T~fY~C~~C~~~w~~ 119 (120)
-.++||.||+.. ..|-.++--.-..+.+..|+|..||+.|.+
T Consensus 199 ~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 199 YYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred EEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCH
Confidence 357999999974 455555541111589999999999999875
No 36
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=95.47 E-value=0.014 Score=42.32 Aligned_cols=46 Identities=15% Similarity=0.438 Sum_probs=33.0
Q ss_pred cccccccccccccCCCceEEEEeecccCCCCce----EEEEcCCCCceec
Q 040426 73 TQLSKVKRACEKCQNPEMYYSTRQTRSADEGQT----TYYICPRCGHRCQ 118 (120)
Q Consensus 73 ~t~~~~~~~CpkCg~~ea~y~~~Q~RSADE~~T----~fY~C~~C~~~w~ 118 (120)
.++|..-..|++||..+++--.--.|---.|-- ++|+|+.|.++|.
T Consensus 11 ~~~pq~~k~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWlIYkC~~Cd~tWN 60 (203)
T COG4332 11 VGAPQPAKRCNSCGVKRAFTCSGKFRVNAQGKVLDVWLIYKCTHCDYTWN 60 (203)
T ss_pred ccCChhhhhCcccCCcceeeecCcEEEcCCCcEEEEEEEEEeeccCCccc
Confidence 355667788999999988744333444444432 6899999999995
No 37
>PRK14973 DNA topoisomerase I; Provisional
Probab=95.43 E-value=0.021 Score=50.60 Aligned_cols=32 Identities=22% Similarity=0.359 Sum_probs=23.4
Q ss_pred cccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426 79 KRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
+..||+||.+. .+.+|...-|+ |.-|++|.|.
T Consensus 635 ~~~Cp~CG~p~----~~~~r~Gr~g~--fl~CP~C~~~ 666 (936)
T PRK14973 635 DEVCPIHHLNH----VRLIRKGARPW--DIGCPLCSHI 666 (936)
T ss_pred CCCCCCCCCCc----eEEeecCCCcc--cccCccccch
Confidence 55899999972 23346666666 7789999885
No 38
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=95.24 E-value=0.0087 Score=29.77 Aligned_cols=24 Identities=29% Similarity=0.836 Sum_probs=16.9
Q ss_pred cccCccCCCcccccCCcEEeCCCCCe
Q 040426 9 FLFCKFCGTMLRMESNHVVCSSCKFK 34 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~~~C~~C~~~ 34 (120)
..+||.||..+ +.+.-.|+.||..
T Consensus 2 ~~~Cp~Cg~~~--~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 2 EMFCPNCGAEI--DPDAKFCPNCGAK 25 (26)
T ss_pred cCCCcccCCcC--CcccccChhhCCC
Confidence 46899999843 3334688888864
No 39
>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=95.24 E-value=0.023 Score=30.45 Aligned_cols=35 Identities=20% Similarity=0.478 Sum_probs=21.5
Q ss_pred cccccccCCCceEEEEeecc-cCCCCceEEEEcCCCCceecc
Q 040426 79 KRACEKCQNPEMYYSTRQTR-SADEGQTTYYICPRCGHRCQE 119 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~Q~R-SADE~~T~fY~C~~C~~~w~~ 119 (120)
...||.||.. |.++.. -.+++. -.+|.+||+.|..
T Consensus 2 ~~~CP~C~~~----~~v~~~~~~~~~~--~v~C~~C~~~~~~ 37 (38)
T TIGR02098 2 RIQCPNCKTS----FRVVDSQLGANGG--KVRCGKCGHVWYA 37 (38)
T ss_pred EEECCCCCCE----EEeCHHHcCCCCC--EEECCCCCCEEEe
Confidence 3579999875 222221 223333 6789999999863
No 40
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=95.23 E-value=0.009 Score=28.99 Aligned_cols=22 Identities=23% Similarity=0.757 Sum_probs=15.2
Q ss_pred cCccCCCcccccCCcEEeCCCCCe
Q 040426 11 FCKFCGTMLRMESNHVVCSSCKFK 34 (120)
Q Consensus 11 FCp~CgnlL~~~~~~~~C~~C~~~ 34 (120)
|||.||+-|.. +.-.|..||+.
T Consensus 1 ~Cp~CG~~~~~--~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIED--DAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCC--cCcchhhhCCc
Confidence 78888887743 23458888863
No 41
>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=95.19 E-value=0.012 Score=31.70 Aligned_cols=26 Identities=19% Similarity=0.529 Sum_probs=22.3
Q ss_pred ccCccCCCcccccCCc-EEeCCCCCee
Q 040426 10 LFCKFCGTMLRMESNH-VVCSSCKFKK 35 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~-~~C~~C~~~~ 35 (120)
.=|+.|++.+....+. +.|..||++.
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGHQS 35 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCceEc
Confidence 3499999998888777 9999999864
No 42
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=95.12 E-value=0.011 Score=35.32 Aligned_cols=26 Identities=19% Similarity=0.430 Sum_probs=15.8
Q ss_pred cccCccCCCcccccCCc--EEeCCCCCe
Q 040426 9 FLFCKFCGTMLRMESNH--VVCSSCKFK 34 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~--~~C~~C~~~ 34 (120)
..-|..||-.|.|.+.. |.|++||.+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~ 36 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEV 36 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCce
Confidence 44666677666555543 666666643
No 43
>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=94.94 E-value=0.021 Score=28.07 Aligned_cols=22 Identities=27% Similarity=0.786 Sum_probs=18.4
Q ss_pred CccCCCcccccCC-c-EEeCCCCC
Q 040426 12 CKFCGTMLRMESN-H-VVCSSCKF 33 (120)
Q Consensus 12 Cp~CgnlL~~~~~-~-~~C~~C~~ 33 (120)
|..||-.|.+.+. . |.|++||+
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 6789999998873 3 99999985
No 44
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=94.93 E-value=0.048 Score=29.86 Aligned_cols=30 Identities=23% Similarity=0.600 Sum_probs=21.0
Q ss_pred cccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
.||+|++. +.=..+ +-...+.|.+|+-.|=
T Consensus 1 ~CP~C~~~-l~~~~~-------~~~~id~C~~C~G~W~ 30 (41)
T PF13453_consen 1 KCPRCGTE-LEPVRL-------GDVEIDVCPSCGGIWF 30 (41)
T ss_pred CcCCCCcc-cceEEE-------CCEEEEECCCCCeEEc
Confidence 49999984 432221 3367799999998884
No 45
>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=94.87 E-value=0.016 Score=28.99 Aligned_cols=24 Identities=21% Similarity=0.605 Sum_probs=18.0
Q ss_pred cCccCCCcccccCCcEEeCCCCCeee
Q 040426 11 FCKFCGTMLRMESNHVVCSSCKFKKN 36 (120)
Q Consensus 11 FCp~CgnlL~~~~~~~~C~~C~~~~~ 36 (120)
=||+|+..+... .-.|+.|||...
T Consensus 2 ~CP~C~~~V~~~--~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPES--AKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhh--cCcCCCCCCCCc
Confidence 399999876333 378999999764
No 46
>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=94.80 E-value=0.023 Score=31.00 Aligned_cols=29 Identities=28% Similarity=0.655 Sum_probs=24.1
Q ss_pred ccCccCCCcccccCCc----EEeCC---CCCeeecc
Q 040426 10 LFCKFCGTMLRMESNH----VVCSS---CKFKKNVQ 38 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~----~~C~~---C~~~~~~~ 38 (120)
..||.||..|..+..+ +.|.. |.|+..+.
T Consensus 2 ~~CP~Cg~~lv~r~~k~g~F~~Cs~yP~C~~~~~~~ 37 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKGKFLGCSNYPECKYTEPLP 37 (39)
T ss_pred cCCCCCCceeEEEECCCCCEEECCCCCCcCCeEeCC
Confidence 4699999999988764 89987 99988764
No 47
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=94.61 E-value=0.02 Score=34.10 Aligned_cols=24 Identities=21% Similarity=0.560 Sum_probs=10.6
Q ss_pred ccCccCCCcccccCCc--EEeCCCCC
Q 040426 10 LFCKFCGTMLRMESNH--VVCSSCKF 33 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~--~~C~~C~~ 33 (120)
..|.-||-.|.+.+.. |.|.+||.
T Consensus 8 ~~CtSCg~~i~~~~~~~~F~CPnCG~ 33 (59)
T PRK14890 8 PKCTSCGIEIAPREKAVKFLCPNCGE 33 (59)
T ss_pred ccccCCCCcccCCCccCEeeCCCCCC
Confidence 3444455444444311 44444444
No 48
>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=94.60 E-value=0.036 Score=30.63 Aligned_cols=28 Identities=21% Similarity=0.617 Sum_probs=18.1
Q ss_pred ccCccCCCcc-cccC--CcEEeCCCCCeeec
Q 040426 10 LFCKFCGTML-RMES--NHVVCSSCKFKKNV 37 (120)
Q Consensus 10 ~FCp~CgnlL-~~~~--~~~~C~~C~~~~~~ 37 (120)
..||.||+-. .... ..++|..||.+.+-
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVLEE 31 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBEE-
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEeec
Confidence 3699999854 2222 22999999998653
No 49
>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=94.54 E-value=0.073 Score=30.77 Aligned_cols=34 Identities=21% Similarity=0.635 Sum_probs=22.9
Q ss_pred ccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426 80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
.+||.||.....+. -+..|-+-.-+|.|.+||+.
T Consensus 2 kPCPfCGg~~~~~~---~~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLR---RGFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCcceeeE---eccCCCCCEEEEECCCCCCC
Confidence 47999999655342 12345556666799999975
No 50
>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=94.53 E-value=0.023 Score=29.43 Aligned_cols=26 Identities=27% Similarity=0.701 Sum_probs=14.3
Q ss_pred ccCccCCCcccccCCc-EEeCCCCCee
Q 040426 10 LFCKFCGTMLRMESNH-VVCSSCKFKK 35 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~-~~C~~C~~~~ 35 (120)
.=||.||+-.....+. ++|..|+++.
T Consensus 3 p~Cp~C~se~~y~D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGELLVCPECGHEW 29 (30)
T ss_dssp ---TTT-----EE-SSSEEETTTTEEE
T ss_pred CCCCCCCCcceeccCCEEeCCcccccC
Confidence 3599999887775554 9999999975
No 51
>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=94.49 E-value=0.029 Score=29.71 Aligned_cols=14 Identities=21% Similarity=0.693 Sum_probs=10.9
Q ss_pred ccccccCCCceEEE
Q 040426 80 RACEKCQNPEMYYS 93 (120)
Q Consensus 80 ~~CpkCg~~ea~y~ 93 (120)
..||.||++...|.
T Consensus 19 ~~CP~Cg~~~~~F~ 32 (34)
T cd00729 19 EKCPICGAPKEKFE 32 (34)
T ss_pred CcCcCCCCchHHcE
Confidence 36999999877664
No 52
>PRK04023 DNA polymerase II large subunit; Validated
Probab=94.43 E-value=0.025 Score=50.18 Aligned_cols=26 Identities=19% Similarity=0.278 Sum_probs=20.4
Q ss_pred CCCCcccCccCCCcccccCCcEEeCCCCCe
Q 040426 5 LGRDFLFCKFCGTMLRMESNHVVCSSCKFK 34 (120)
Q Consensus 5 ~~~~~~FCp~CgnlL~~~~~~~~C~~C~~~ 34 (120)
...+.+|||.||..+ ..+.|+.||..
T Consensus 622 VEVg~RfCpsCG~~t----~~frCP~CG~~ 647 (1121)
T PRK04023 622 VEIGRRKCPSCGKET----FYRRCPFCGTH 647 (1121)
T ss_pred ecccCccCCCCCCcC----CcccCCCCCCC
Confidence 345678999999884 23899999986
No 53
>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=94.38 E-value=0.059 Score=29.36 Aligned_cols=31 Identities=23% Similarity=0.577 Sum_probs=22.1
Q ss_pred ccccccCCCceEEEEeecccCCCCceEEEEcCC---CCceec
Q 040426 80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPR---CGHRCQ 118 (120)
Q Consensus 80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~---C~~~w~ 118 (120)
+.||+|| ..+ .+|.+--| .|+-|.+ |.++-.
T Consensus 2 ~~CP~Cg-~~l-----v~r~~k~g--~F~~Cs~yP~C~~~~~ 35 (39)
T PF01396_consen 2 EKCPKCG-GPL-----VLRRGKKG--KFLGCSNYPECKYTEP 35 (39)
T ss_pred cCCCCCC-cee-----EEEECCCC--CEEECCCCCCcCCeEe
Confidence 5799999 333 34555556 9999985 988643
No 54
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=94.31 E-value=0.047 Score=30.60 Aligned_cols=30 Identities=20% Similarity=0.605 Sum_probs=23.9
Q ss_pred ccCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426 10 LFCKFCGTMLRMESNH--VVCSSCKFKKNVQD 39 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~ 39 (120)
.=|+.||..+...... +.|+.||......+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILFKE 35 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEEcc
Confidence 3599999999887654 99999998766544
No 55
>PRK07220 DNA topoisomerase I; Validated
Probab=94.29 E-value=0.11 Score=45.03 Aligned_cols=32 Identities=16% Similarity=0.340 Sum_probs=19.5
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCc
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGH 115 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~ 115 (120)
++..||+||.+..... +....+ -||.|.+|.|
T Consensus 634 ~~~~Cp~Cg~~~~k~~----~~g~~~--~~~~Cp~C~~ 665 (740)
T PRK07220 634 TDKVCEAHGLNHIRII----NGGKRP--WDLGCPQCNF 665 (740)
T ss_pred CCCCCCCCCCceEEEE----ecCCcc--ceeeCCCCCC
Confidence 3567999997643111 222112 2889999987
No 56
>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=94.21 E-value=0.076 Score=28.55 Aligned_cols=35 Identities=26% Similarity=0.607 Sum_probs=24.2
Q ss_pred ccccccccccCCCceEEEEeecccCCCCceEEEEcCCCC
Q 040426 76 SKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCG 114 (120)
Q Consensus 76 ~~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~ 114 (120)
+++++.||.|+..+.++--- ....|- .-|.|..|.
T Consensus 2 a~i~v~CP~C~s~~~v~k~G---~~~~G~-qryrC~~C~ 36 (36)
T PF03811_consen 2 AKIDVHCPRCQSTEGVKKNG---KSPSGH-QRYRCKDCR 36 (36)
T ss_pred CcEeeeCCCCCCCCcceeCC---CCCCCC-EeEecCcCC
Confidence 46889999999999776542 233343 348888873
No 57
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=94.17 E-value=0.034 Score=33.73 Aligned_cols=26 Identities=23% Similarity=0.669 Sum_probs=19.7
Q ss_pred CccCCCcccccCC-----------------c---EEeCCCCCeeec
Q 040426 12 CKFCGTMLRMESN-----------------H---VVCSSCKFKKNV 37 (120)
Q Consensus 12 Cp~CgnlL~~~~~-----------------~---~~C~~C~~~~~~ 37 (120)
||.|||--+.+.. . ..|.+|||++--
T Consensus 7 CpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYtEfY 52 (68)
T COG3478 7 CPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYTEFY 52 (68)
T ss_pred CCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCchhhe
Confidence 9999997665421 1 899999998753
No 58
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=94.06 E-value=0.091 Score=38.60 Aligned_cols=42 Identities=19% Similarity=0.377 Sum_probs=31.0
Q ss_pred cccccccccCCCceEEEEeecccCCCC--ceEEEEcCCCCceecc
Q 040426 77 KVKRACEKCQNPEMYYSTRQTRSADEG--QTTYYICPRCGHRCQE 119 (120)
Q Consensus 77 ~~~~~CpkCg~~ea~y~~~Q~RSADE~--~T~fY~C~~C~~~w~~ 119 (120)
..+..||-||+ .....+....--=.| +-..+.|.+|||+.++
T Consensus 12 ~~~~~CPvCg~-~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~D 55 (201)
T COG1779 12 ETRIDCPVCGG-TLKAHMYLYDIPYFGEVLISTGVCERCGYRSTD 55 (201)
T ss_pred eeeecCCcccc-eeeEEEeeecCCccceEEEEEEEccccCCcccc
Confidence 45788999999 666666665555555 4466789999999764
No 59
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.99 E-value=0.034 Score=29.93 Aligned_cols=26 Identities=27% Similarity=0.603 Sum_probs=21.0
Q ss_pred cCccCCCcccccCCc-------EEeCCCCCeee
Q 040426 11 FCKFCGTMLRMESNH-------VVCSSCKFKKN 36 (120)
Q Consensus 11 FCp~CgnlL~~~~~~-------~~C~~C~~~~~ 36 (120)
=||.|+..+.++.+. +.|..|++.+.
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 499999998877541 99999998764
No 60
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=93.79 E-value=0.11 Score=37.01 Aligned_cols=38 Identities=21% Similarity=0.337 Sum_probs=25.1
Q ss_pred cccccCCCceEEEEeecccCCCCce--EEEEcCCCCceecc
Q 040426 81 ACEKCQNPEMYYSTRQTRSADEGQT--TYYICPRCGHRCQE 119 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q~RSADE~~T--~fY~C~~C~~~w~~ 119 (120)
.||.||++ .......+.--.-+.. .-|.|..|||+..+
T Consensus 2 ~Cp~C~~~-~~~~~~~~~IP~F~evii~sf~C~~CGyk~~e 41 (160)
T smart00709 2 DCPSCGGN-GTTRMLLTSIPYFREVIIMSFECEHCGYRNNE 41 (160)
T ss_pred cCCCCCCC-CEEEEEEecCCCcceEEEEEEECCCCCCccce
Confidence 59999986 3444445544444433 35889999998764
No 61
>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=93.70 E-value=0.038 Score=29.57 Aligned_cols=27 Identities=26% Similarity=0.498 Sum_probs=20.8
Q ss_pred cCccCCCcccccCC-----c--EEeCCCCCeeec
Q 040426 11 FCKFCGTMLRMESN-----H--VVCSSCKFKKNV 37 (120)
Q Consensus 11 FCp~CgnlL~~~~~-----~--~~C~~C~~~~~~ 37 (120)
=||.||....+..+ . +.|.+|+....+
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWYA 37 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEEe
Confidence 49999998777643 2 999999987653
No 62
>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=93.40 E-value=0.048 Score=31.46 Aligned_cols=15 Identities=13% Similarity=0.392 Sum_probs=12.6
Q ss_pred cccccccCCCceEEE
Q 040426 79 KRACEKCQNPEMYYS 93 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~ 93 (120)
++.||.||..+..|.
T Consensus 34 ~w~CP~C~a~K~~F~ 48 (50)
T cd00730 34 DWVCPVCGAGKDDFE 48 (50)
T ss_pred CCCCCCCCCcHHHcE
Confidence 789999999887664
No 63
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=93.39 E-value=0.061 Score=37.06 Aligned_cols=29 Identities=31% Similarity=0.730 Sum_probs=23.3
Q ss_pred cCccCCCcccccCCcEEeCCCCCeeeccc
Q 040426 11 FCKFCGTMLRMESNHVVCSSCKFKKNVQD 39 (120)
Q Consensus 11 FCp~CgnlL~~~~~~~~C~~C~~~~~~~~ 39 (120)
-||.||.=|.-+.+.+.|+.|+|......
T Consensus 30 hCp~Cg~PLF~KdG~v~CPvC~~~~~~v~ 58 (131)
T COG1645 30 HCPKCGTPLFRKDGEVFCPVCGYREVVVE 58 (131)
T ss_pred hCcccCCcceeeCCeEECCCCCceEEEee
Confidence 79999999888555599999998765443
No 64
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=93.38 E-value=0.059 Score=36.93 Aligned_cols=39 Identities=15% Similarity=0.067 Sum_probs=33.0
Q ss_pred CCCCCCCCcccCccCCCcccccCCc-EEeCCCCCeeeccc
Q 040426 1 MADPLGRDFLFCKFCGTMLRMESNH-VVCSSCKFKKNVQD 39 (120)
Q Consensus 1 ~~~~~~~~~~FCp~CgnlL~~~~~~-~~C~~C~~~~~~~~ 39 (120)
|+++-.+.-+-||.||.-.|--... ++|+.||..++...
T Consensus 1 m~k~elGtKr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~~ 40 (129)
T TIGR02300 1 MAKPDLGTKRICPNTGSKFYDLNRRPAVSPYTGEQFPPEE 40 (129)
T ss_pred CCchhhCccccCCCcCccccccCCCCccCCCcCCccCcch
Confidence 7888889999999999998865434 99999999987763
No 65
>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=93.37 E-value=0.075 Score=30.27 Aligned_cols=14 Identities=14% Similarity=0.539 Sum_probs=11.2
Q ss_pred EEeCCCCCeeeccc
Q 040426 26 VVCSSCKFKKNVQD 39 (120)
Q Consensus 26 ~~C~~C~~~~~~~~ 39 (120)
+.|+.|+|+..-..
T Consensus 2 y~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 2 YQCPVCGYVYDPEK 15 (47)
T ss_dssp EEETTTSBEEETTT
T ss_pred cCCCCCCEEEcCCc
Confidence 78999999986543
No 66
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=93.34 E-value=0.06 Score=48.84 Aligned_cols=14 Identities=21% Similarity=0.605 Sum_probs=9.9
Q ss_pred cccccccCCCceEE
Q 040426 79 KRACEKCQNPEMYY 92 (120)
Q Consensus 79 ~~~CpkCg~~ea~y 92 (120)
...||+||.+-..+
T Consensus 709 a~~CP~CGtplv~~ 722 (1337)
T PRK14714 709 RVECPRCDVELTPY 722 (1337)
T ss_pred cccCCCCCCccccc
Confidence 44699999875543
No 67
>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=93.09 E-value=0.093 Score=36.84 Aligned_cols=38 Identities=18% Similarity=0.301 Sum_probs=21.3
Q ss_pred cccccCCCceEEEEeecccCCC-CceEEEEcCCCCceecc
Q 040426 81 ACEKCQNPEMYYSTRQTRSADE-GQTTYYICPRCGHRCQE 119 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q~RSADE-~~T~fY~C~~C~~~w~~ 119 (120)
.||.|||++-.-.-.-.- .|- ..-+=-+|..||++|+.
T Consensus 2 ~CP~C~~~dtkViDSR~~-~dg~~IRRRReC~~C~~RFTT 40 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLV-EDGQSIRRRRECLECHERFTT 40 (147)
T ss_pred CCCCCCCCCCEeeecccc-CCCCeeeecccCCccCCccce
Confidence 699999987754321000 000 00012469999999873
No 68
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=92.98 E-value=0.075 Score=40.35 Aligned_cols=31 Identities=23% Similarity=0.707 Sum_probs=25.3
Q ss_pred CCcccCccCCCcccccCCc--EEeCCCCCeeec
Q 040426 7 RDFLFCKFCGTMLRMESNH--VVCSSCKFKKNV 37 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~ 37 (120)
...+|||.||.-|....+. ..|..|+...-.
T Consensus 97 ~~~~fC~~CG~~~~~~~~~~~~~C~~c~~~~yp 129 (256)
T PRK00241 97 RSHRFCGYCGHPMHPSKTEWAMLCPHCRERYYP 129 (256)
T ss_pred hcCccccccCCCCeecCCceeEECCCCCCEECC
Confidence 4578999999999877654 999999987643
No 69
>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=92.94 E-value=0.1 Score=31.42 Aligned_cols=31 Identities=19% Similarity=0.684 Sum_probs=24.1
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
+...||.||+.... ......|.|..||+.+-
T Consensus 27 TSq~C~~CG~~~~~----------~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK----------RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CccCccCccccccc----------ccccceEEcCCCCCEEC
Confidence 56679999998664 24556799999999863
No 70
>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=92.89 E-value=0.084 Score=32.02 Aligned_cols=26 Identities=23% Similarity=0.622 Sum_probs=18.8
Q ss_pred CccCCCcccccC-----------------Cc---EEeCCCCCeeec
Q 040426 12 CKFCGTMLRMES-----------------NH---VVCSSCKFKKNV 37 (120)
Q Consensus 12 Cp~CgnlL~~~~-----------------~~---~~C~~C~~~~~~ 37 (120)
||+||+--+-.. .+ ++|.+|||++--
T Consensus 3 C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYTE~Y 48 (64)
T PF09855_consen 3 CPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYTEFY 48 (64)
T ss_pred CCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCEEEE
Confidence 899998655332 11 899999998743
No 71
>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=92.83 E-value=0.13 Score=30.16 Aligned_cols=37 Identities=24% Similarity=0.538 Sum_probs=25.8
Q ss_pred ccccc--cccccccccCCC-ceEEEEeecccCCCCceEEEEcCCCCc
Q 040426 72 ETQLS--KVKRACEKCQNP-EMYYSTRQTRSADEGQTTYYICPRCGH 115 (120)
Q Consensus 72 ~~t~~--~~~~~CpkCg~~-ea~y~~~Q~RSADE~~T~fY~C~~C~~ 115 (120)
||+++ +....|++|..+ .++. ..|...+-|+|..||+
T Consensus 13 d~~~~~~r~aLIC~~C~~hNGla~-------~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 13 DPTSPSNRYALICSKCFSHNGLAP-------KEEFEEIQYRCPYCGA 52 (54)
T ss_pred CCccccCceeEECcccchhhcccc-------cccCCceEEEcCCCCC
Confidence 34555 345679999665 4432 4567777999999986
No 72
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=92.71 E-value=0.17 Score=31.23 Aligned_cols=35 Identities=26% Similarity=0.612 Sum_probs=23.4
Q ss_pred ccccccccCCCc-eEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426 78 VKRACEKCQNPE-MYYSTRQTRSADEGQTTYYICPRCGHRCQE 119 (120)
Q Consensus 78 ~~~~CpkCg~~e-a~y~~~Q~RSADE~~T~fY~C~~C~~~w~~ 119 (120)
....||+|+... ..+|. -+ + .-.-+|++|||+-+.
T Consensus 7 AGa~CP~C~~~D~i~~~~-----e~-~-ve~vECV~CGy~e~~ 42 (71)
T PF09526_consen 7 AGAVCPKCQAMDTIMMWR-----EN-G-VEYVECVECGYTERQ 42 (71)
T ss_pred cCccCCCCcCccEEEEEE-----eC-C-ceEEEecCCCCeecc
Confidence 457899999864 34443 12 2 455679999998653
No 73
>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=92.49 E-value=0.15 Score=36.24 Aligned_cols=40 Identities=18% Similarity=0.330 Sum_probs=20.1
Q ss_pred ccccccCCCceE-EEEeecccCCCCceEEEEcCCCCceecc
Q 040426 80 RACEKCQNPEMY-YSTRQTRSADEGQTTYYICPRCGHRCQE 119 (120)
Q Consensus 80 ~~CpkCg~~ea~-y~~~Q~RSADE~~T~fY~C~~C~~~w~~ 119 (120)
..||.||++... .....+=--.|=.-.-|.|..|||+.++
T Consensus 2 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~e 42 (161)
T PF03367_consen 2 SLCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNNE 42 (161)
T ss_dssp EE-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEEE
T ss_pred CcCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEeee
Confidence 469999997543 2222221122223455889999999764
No 74
>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=92.39 E-value=0.08 Score=27.68 Aligned_cols=25 Identities=32% Similarity=0.677 Sum_probs=19.2
Q ss_pred cCccCCCcccccCCcEEeCCCCCee
Q 040426 11 FCKFCGTMLRMESNHVVCSSCKFKK 35 (120)
Q Consensus 11 FCp~CgnlL~~~~~~~~C~~C~~~~ 35 (120)
-|+.||.+..+....+.|+.||...
T Consensus 3 ~C~~CGy~y~~~~~~~~CP~Cg~~~ 27 (33)
T cd00350 3 VCPVCGYIYDGEEAPWVCPVCGAPK 27 (33)
T ss_pred ECCCCCCEECCCcCCCcCcCCCCcH
Confidence 3888998877666668999998744
No 75
>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=92.37 E-value=0.09 Score=26.63 Aligned_cols=20 Identities=30% Similarity=0.763 Sum_probs=10.7
Q ss_pred cCccCCCcccccCCc--EEeCC
Q 040426 11 FCKFCGTMLRMESNH--VVCSS 30 (120)
Q Consensus 11 FCp~CgnlL~~~~~~--~~C~~ 30 (120)
+||.||+-|.-.++. +.|.+
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~N 22 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCPN 22 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE--
T ss_pred CcCCCCCEeEcCCCCEeEECCC
Confidence 699999999855553 77753
No 76
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=92.35 E-value=0.091 Score=40.53 Aligned_cols=30 Identities=30% Similarity=0.587 Sum_probs=26.1
Q ss_pred CCcccCccCCCcccccCCc--EEeCCCCCeee
Q 040426 7 RDFLFCKFCGTMLRMESNH--VVCSSCKFKKN 36 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~ 36 (120)
..-+||+.||.-+++.... ..|..|++..-
T Consensus 109 ~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~f 140 (279)
T COG2816 109 RSHRFCGRCGTKTYPREGGWARVCPKCGHEHF 140 (279)
T ss_pred hhCcCCCCCCCcCccccCceeeeCCCCCCccC
Confidence 4568999999999999876 99999999753
No 77
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=92.34 E-value=0.12 Score=31.50 Aligned_cols=35 Identities=23% Similarity=0.537 Sum_probs=25.7
Q ss_pred cccccccccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426 73 TQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 73 ~t~~~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
|..--.+++||.|||...+|--.| | --.|..||..
T Consensus 13 p~s~Fl~VkCpdC~N~q~vFshas--------t-~V~C~~CG~~ 47 (67)
T COG2051 13 PRSRFLRVKCPDCGNEQVVFSHAS--------T-VVTCLICGTT 47 (67)
T ss_pred CCceEEEEECCCCCCEEEEeccCc--------e-EEEecccccE
Confidence 333357889999999999996533 3 3678888864
No 78
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=92.29 E-value=0.082 Score=45.18 Aligned_cols=12 Identities=17% Similarity=0.492 Sum_probs=7.4
Q ss_pred cccccccCCCce
Q 040426 79 KRACEKCQNPEM 90 (120)
Q Consensus 79 ~~~CpkCg~~ea 90 (120)
...||+||+.-.
T Consensus 41 ~~fC~~CG~~~~ 52 (645)
T PRK14559 41 EAHCPNCGAETG 52 (645)
T ss_pred cccccccCCccc
Confidence 345777777644
No 79
>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=92.29 E-value=0.27 Score=29.29 Aligned_cols=35 Identities=20% Similarity=0.438 Sum_probs=23.9
Q ss_pred ccccccccCCCce-EEEEeecccCCCCceEEEEcCCCCceecc
Q 040426 78 VKRACEKCQNPEM-YYSTRQTRSADEGQTTYYICPRCGHRCQE 119 (120)
Q Consensus 78 ~~~~CpkCg~~ea-~y~~~Q~RSADE~~T~fY~C~~C~~~w~~ 119 (120)
....||+|+.... ..|. |.-.-.-+|+.|||+-+.
T Consensus 8 AGA~CP~C~~~Dtl~~~~-------e~~~e~vECv~Cg~~~~~ 43 (59)
T TIGR02443 8 AGAVCPACSAQDTLAMWK-------ENNIELVECVECGYQEQQ 43 (59)
T ss_pred ccccCCCCcCccEEEEEE-------eCCceEEEeccCCCcccc
Confidence 4578999998644 4443 223355789999998653
No 80
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=92.18 E-value=0.23 Score=29.15 Aligned_cols=34 Identities=24% Similarity=0.595 Sum_probs=22.1
Q ss_pred ccccccCCCceEEEEeecccCCCCceEEEEcCCCCc
Q 040426 80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGH 115 (120)
Q Consensus 80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~ 115 (120)
.+||-||.......+ ...-+.++..+-.|..||.
T Consensus 4 kPCPFCG~~~~~~~~--~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQ--DEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred cCCCCCCCcceEeec--ccCCCCCCEEEEEcCCCCC
Confidence 579999877766554 2333344445555999986
No 81
>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=92.12 E-value=0.11 Score=31.22 Aligned_cols=36 Identities=17% Similarity=0.373 Sum_probs=27.2
Q ss_pred CCCCCcccCccCCCcccccC-Cc-EEeCCCCCeeeccc
Q 040426 4 PLGRDFLFCKFCGTMLRMES-NH-VVCSSCKFKKNVQD 39 (120)
Q Consensus 4 ~~~~~~~FCp~CgnlL~~~~-~~-~~C~~C~~~~~~~~ 39 (120)
....+..=||.||..+.-.. .. +.|..||+..+.+.
T Consensus 23 ~~~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~~rD~ 60 (69)
T PF07282_consen 23 DEAYTSQTCPRCGHRNKKRRSGRVFTCPNCGFEMDRDV 60 (69)
T ss_pred CCCCCccCccCcccccccccccceEEcCCCCCEECcHH
Confidence 34446778999999988732 33 99999999977654
No 82
>COG1773 Rubredoxin [Energy production and conversion]
Probab=92.03 E-value=0.1 Score=30.75 Aligned_cols=18 Identities=11% Similarity=0.266 Sum_probs=14.3
Q ss_pred ccccccccCCCceEEEEe
Q 040426 78 VKRACEKCQNPEMYYSTR 95 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~ 95 (120)
.+..||-||..+..|-.+
T Consensus 35 d~w~CP~Cg~~K~~F~~~ 52 (55)
T COG1773 35 DDWVCPECGVGKKDFEMI 52 (55)
T ss_pred CccCCCCCCCCHhHeeec
Confidence 478899999988877554
No 83
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=91.97 E-value=0.051 Score=47.00 Aligned_cols=21 Identities=14% Similarity=0.363 Sum_probs=12.4
Q ss_pred ccccccCCCceEEEEeecccC
Q 040426 80 RACEKCQNPEMYYSTRQTRSA 100 (120)
Q Consensus 80 ~~CpkCg~~ea~y~~~Q~RSA 100 (120)
..||+||.....++-.-|...
T Consensus 476 ~~Cp~Cgs~~L~~~G~Gteri 496 (730)
T COG1198 476 QSCPECGSEHLRAVGPGTERI 496 (730)
T ss_pred CCCCCCCCCeeEEecccHHHH
Confidence 347777777666655444433
No 84
>PRK07219 DNA topoisomerase I; Validated
Probab=91.93 E-value=0.4 Score=42.07 Aligned_cols=32 Identities=22% Similarity=0.492 Sum_probs=19.3
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEc---CCCCcee
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYIC---PRCGHRC 117 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C---~~C~~~w 117 (120)
+...||+||.+-.. ...| .| .|+.| ..|++..
T Consensus 732 ~~~~CpkCg~~l~~---~k~~---~g--~~~~Cs~~p~C~~~~ 766 (822)
T PRK07219 732 TDEKCPECGLPLLR---VKGG---FG--DELGCCNNPKCNYTE 766 (822)
T ss_pred ccCCCCCCCCeEEE---EecC---CC--ceeeeCCCCCCCccc
Confidence 56789999985322 2222 12 37888 5688643
No 85
>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=91.79 E-value=0.07 Score=27.96 Aligned_cols=24 Identities=21% Similarity=0.760 Sum_probs=18.0
Q ss_pred CccCCCcccccCCc-EEeCCCCCee
Q 040426 12 CKFCGTMLRMESNH-VVCSSCKFKK 35 (120)
Q Consensus 12 Cp~CgnlL~~~~~~-~~C~~C~~~~ 35 (120)
|.+||....++... +.|+.|||..
T Consensus 3 C~~Cg~~~~~~~~~~irC~~CG~RI 27 (32)
T PF03604_consen 3 CGECGAEVELKPGDPIRCPECGHRI 27 (32)
T ss_dssp ESSSSSSE-BSTSSTSSBSSSS-SE
T ss_pred CCcCCCeeEcCCCCcEECCcCCCeE
Confidence 88999888877554 9999999964
No 86
>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=91.78 E-value=0.18 Score=41.78 Aligned_cols=27 Identities=19% Similarity=0.630 Sum_probs=14.2
Q ss_pred CccCCCcccccC-Cc-EEeCCCCCeeecc
Q 040426 12 CKFCGTMLRMES-NH-VVCSSCKFKKNVQ 38 (120)
Q Consensus 12 Cp~CgnlL~~~~-~~-~~C~~C~~~~~~~ 38 (120)
||.|+.-|..-. .+ +.|..|||..++.
T Consensus 225 C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~ 253 (505)
T TIGR00595 225 CPNCDVSLTYHKKEGKLRCHYCGYQEPIP 253 (505)
T ss_pred CCCCCCceEEecCCCeEEcCCCcCcCCCC
Confidence 444444443322 22 7777777766543
No 87
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=91.77 E-value=0.26 Score=27.11 Aligned_cols=12 Identities=25% Similarity=0.592 Sum_probs=10.0
Q ss_pred EEeCCCCCeeec
Q 040426 26 VVCSSCKFKKNV 37 (120)
Q Consensus 26 ~~C~~C~~~~~~ 37 (120)
|.|..||+..++
T Consensus 6 y~C~~Cg~~fe~ 17 (42)
T PF09723_consen 6 YRCEECGHEFEV 17 (42)
T ss_pred EEeCCCCCEEEE
Confidence 899999987754
No 88
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=91.76 E-value=0.25 Score=36.12 Aligned_cols=39 Identities=28% Similarity=0.476 Sum_probs=22.8
Q ss_pred cccccCCC-ceEEEEee-cccCCCCceEEEEcCCCCceecc
Q 040426 81 ACEKCQNP-EMYYSTRQ-TRSADEGQTTYYICPRCGHRCQE 119 (120)
Q Consensus 81 ~CpkCg~~-ea~y~~~Q-~RSADE~~T~fY~C~~C~~~w~~ 119 (120)
.||.||.+ .....+.+ +=--.|=.-.-|.|..|||+.++
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~e 42 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSND 42 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccce
Confidence 59999976 22233322 11122223456899999998764
No 89
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=91.69 E-value=0.093 Score=31.25 Aligned_cols=27 Identities=19% Similarity=0.668 Sum_probs=22.9
Q ss_pred cccCccCCCcccccCCc-EEeCCCCCee
Q 040426 9 FLFCKFCGTMLRMESNH-VVCSSCKFKK 35 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~-~~C~~C~~~~ 35 (120)
+--|.+||.-+.++... +.||-|||..
T Consensus 20 iYiCgdC~~en~lk~~D~irCReCG~RI 47 (62)
T KOG3507|consen 20 IYICGDCGQENTLKRGDVIRCRECGYRI 47 (62)
T ss_pred EEEeccccccccccCCCcEehhhcchHH
Confidence 44799999999888765 9999999964
No 90
>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=91.50 E-value=0.18 Score=31.39 Aligned_cols=22 Identities=32% Similarity=0.457 Sum_probs=11.5
Q ss_pred CCCCCCcccCccCCCcccccCC
Q 040426 3 DPLGRDFLFCKFCGTMLRMESN 24 (120)
Q Consensus 3 ~~~~~~~~FCp~CgnlL~~~~~ 24 (120)
.+....-.||..||++|.|-.+
T Consensus 40 l~~~~kr~~Ck~C~~~liPG~~ 61 (85)
T PF04032_consen 40 LPPEIKRTICKKCGSLLIPGVN 61 (85)
T ss_dssp -STTCCCTB-TTT--B--CTTT
T ss_pred CChHHhcccccCCCCEEeCCCc
Confidence 3445566799999999998753
No 91
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=91.28 E-value=0.2 Score=25.99 Aligned_cols=25 Identities=28% Similarity=0.586 Sum_probs=20.0
Q ss_pred cCccCCCcccccCCc--EEeCCCCCee
Q 040426 11 FCKFCGTMLRMESNH--VVCSSCKFKK 35 (120)
Q Consensus 11 FCp~CgnlL~~~~~~--~~C~~C~~~~ 35 (120)
-|..|+++|..+.+. +.|..|....
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs~C~~vt 29 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCALCQTVN 29 (31)
T ss_pred CcCCCCcEeecCCCCCeEECCCCCeEe
Confidence 489999999776553 9999998754
No 92
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=91.15 E-value=0.43 Score=26.67 Aligned_cols=27 Identities=26% Similarity=0.652 Sum_probs=21.4
Q ss_pred cCccCCCcccccCCc-EEeCCCCCeeec
Q 040426 11 FCKFCGTMLRMESNH-VVCSSCKFKKNV 37 (120)
Q Consensus 11 FCp~CgnlL~~~~~~-~~C~~C~~~~~~ 37 (120)
-|.+||.-..++... +.|+.||+..-.
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG~rIly 31 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECGYRILY 31 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCCceEEE
Confidence 489999988877544 999999996543
No 93
>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=91.07 E-value=0.23 Score=29.10 Aligned_cols=29 Identities=28% Similarity=0.671 Sum_probs=24.1
Q ss_pred cCccCCCcccccCCc----EEeCCCCCeeeccc
Q 040426 11 FCKFCGTMLRMESNH----VVCSSCKFKKNVQD 39 (120)
Q Consensus 11 FCp~CgnlL~~~~~~----~~C~~C~~~~~~~~ 39 (120)
=||.||.-+.+..+. +.|..||....+.+
T Consensus 4 ~CP~CG~~iev~~~~~GeiV~Cp~CGaeleVv~ 36 (54)
T TIGR01206 4 ECPDCGAEIELENPELGELVICDECGAELEVVS 36 (54)
T ss_pred CCCCCCCEEecCCCccCCEEeCCCCCCEEEEEe
Confidence 599999999887642 99999999887644
No 94
>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=91.07 E-value=0.17 Score=27.97 Aligned_cols=23 Identities=35% Similarity=0.739 Sum_probs=18.4
Q ss_pred ccCccCCCcccccCCc-EEeCCCC
Q 040426 10 LFCKFCGTMLRMESNH-VVCSSCK 32 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~-~~C~~C~ 32 (120)
.-||.||..|.-..++ ..|..|+
T Consensus 18 ~~Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEEecCCCEECCCCC
Confidence 4799999998874444 9999985
No 95
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=90.74 E-value=0.18 Score=33.45 Aligned_cols=28 Identities=32% Similarity=0.496 Sum_probs=23.3
Q ss_pred ccCccCCCcccccCCc----------EEeCCCCCeeec
Q 040426 10 LFCKFCGTMLRMESNH----------VVCSSCKFKKNV 37 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~----------~~C~~C~~~~~~ 37 (120)
.||+.|+++|.|..+- +.|..||+..-.
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~ 94 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRY 94 (105)
T ss_pred HhccccCcccccCcceEEEEcCCeEEEEecCCCcEEEe
Confidence 5999999999987641 999999998643
No 96
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=90.62 E-value=0.11 Score=37.12 Aligned_cols=14 Identities=21% Similarity=0.686 Sum_probs=11.3
Q ss_pred cccccccCCCceEE
Q 040426 79 KRACEKCQNPEMYY 92 (120)
Q Consensus 79 ~~~CpkCg~~ea~y 92 (120)
...||-||+++..|
T Consensus 149 P~~CPiCga~k~~F 162 (166)
T COG1592 149 PEVCPICGAPKEKF 162 (166)
T ss_pred CCcCCCCCChHHHh
Confidence 35699999998766
No 97
>PRK00420 hypothetical protein; Validated
Probab=90.59 E-value=0.23 Score=33.33 Aligned_cols=30 Identities=27% Similarity=0.393 Sum_probs=23.9
Q ss_pred ccCccCCCcccc-cCCcEEeCCCCCeeeccc
Q 040426 10 LFCKFCGTMLRM-ESNHVVCSSCKFKKNVQD 39 (120)
Q Consensus 10 ~FCp~CgnlL~~-~~~~~~C~~C~~~~~~~~ 39 (120)
.-||.||.-|.- +.+...|++||....+++
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVYIVKS 54 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCeeeecc
Confidence 479999988876 444499999999876655
No 98
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=90.52 E-value=0.11 Score=32.39 Aligned_cols=13 Identities=31% Similarity=0.667 Sum_probs=5.8
Q ss_pred CCCcccCccCCCc
Q 040426 6 GRDFLFCKFCGTM 18 (120)
Q Consensus 6 ~~~~~FCp~Cgnl 18 (120)
.++-.|||.|||-
T Consensus 21 ~~~k~FCp~CGn~ 33 (73)
T PF08772_consen 21 DMTKQFCPKCGNA 33 (73)
T ss_dssp -SS--S-SSS--S
T ss_pred CCCceeCcccCCC
Confidence 4567899999986
No 99
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=90.48 E-value=0.17 Score=27.06 Aligned_cols=25 Identities=24% Similarity=0.579 Sum_probs=17.9
Q ss_pred cCccCCCcccccCCc-------EEeCCCCCee
Q 040426 11 FCKFCGTMLRMESNH-------VVCSSCKFKK 35 (120)
Q Consensus 11 FCp~CgnlL~~~~~~-------~~C~~C~~~~ 35 (120)
=||.|+.-..++++. +.|..|+++.
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 488888877665431 8888888764
No 100
>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=90.30 E-value=0.19 Score=33.48 Aligned_cols=31 Identities=19% Similarity=0.560 Sum_probs=24.7
Q ss_pred cccCccCCCcccccCCc-EEeCCCCCeeeccc
Q 040426 9 FLFCKFCGTMLRMESNH-VVCSSCKFKKNVQD 39 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~-~~C~~C~~~~~~~~ 39 (120)
+.=||.|++-...+... |.|+-|+|.+...+
T Consensus 2 lp~CP~C~seytY~dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 2 LPPCPKCNSEYTYHDGTQLICPSCLYEWNENE 33 (109)
T ss_pred CCcCCcCCCcceEecCCeeECccccccccccc
Confidence 34699999887776555 99999999986554
No 101
>PRK10220 hypothetical protein; Provisional
Probab=90.26 E-value=0.27 Score=32.87 Aligned_cols=32 Identities=22% Similarity=0.536 Sum_probs=25.8
Q ss_pred CcccCccCCCcccccCCc-EEeCCCCCeeeccc
Q 040426 8 DFLFCKFCGTMLRMESNH-VVCSSCKFKKNVQD 39 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~~-~~C~~C~~~~~~~~ 39 (120)
.+.=||.|++-...+.+. |.|+-|+|.+...+
T Consensus 2 ~lP~CP~C~seytY~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 2 SLPHCPKCNSEYTYEDNGMYICPECAHEWNDAE 34 (111)
T ss_pred CCCcCCCCCCcceEcCCCeEECCcccCcCCccc
Confidence 456799999887666555 99999999987655
No 102
>PF14353 CpXC: CpXC protein
Probab=90.21 E-value=0.43 Score=32.13 Aligned_cols=14 Identities=14% Similarity=0.543 Sum_probs=11.3
Q ss_pred EEeCCCCCeeeccc
Q 040426 26 VVCSSCKFKKNVQD 39 (120)
Q Consensus 26 ~~C~~C~~~~~~~~ 39 (120)
+.|+.|++...++-
T Consensus 2 itCP~C~~~~~~~v 15 (128)
T PF14353_consen 2 ITCPHCGHEFEFEV 15 (128)
T ss_pred cCCCCCCCeeEEEE
Confidence 57999999987654
No 103
>PF11792 Baculo_LEF5_C: Baculoviridae late expression factor 5 C-terminal domain; InterPro: IPR021758 This C-terminal domain is likely to be a zinc-binding domain.
Probab=90.03 E-value=0.011 Score=32.97 Aligned_cols=30 Identities=27% Similarity=0.604 Sum_probs=23.2
Q ss_pred cCCCceEEEEeecccCCCCceEEEEcCCCCc
Q 040426 85 CQNPEMYYSTRQTRSADEGQTTYYICPRCGH 115 (120)
Q Consensus 85 Cg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~ 115 (120)
|.|.-. -...|+|+.||.-+.+-.|.+|+.
T Consensus 13 C~H~f~-~~E~Q~RAGDE~VSfI~~C~~C~~ 42 (43)
T PF11792_consen 13 CKHKFV-TIEKQLRAGDEAVSFIKYCQKCGQ 42 (43)
T ss_pred ceeeee-ehhhhhcccchHHHHHHHHHHhCC
Confidence 655544 456799999999888778988875
No 104
>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=89.97 E-value=0.54 Score=32.07 Aligned_cols=30 Identities=23% Similarity=0.697 Sum_probs=25.1
Q ss_pred ccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426 80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
+.||.|++++-.+.-- +-+.|-+|..||.+
T Consensus 94 VlC~~C~spdT~l~k~-------~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 94 VLCPECGSPDTELIKE-------GRLIFLKCKACGAS 123 (125)
T ss_dssp SSCTSTSSSSEEEEEE-------TTCCEEEETTTSCE
T ss_pred EEcCCCCCCccEEEEc-------CCEEEEEecccCCc
Confidence 6899999999877542 67799999999975
No 105
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=89.93 E-value=0.24 Score=36.06 Aligned_cols=28 Identities=21% Similarity=0.450 Sum_probs=24.1
Q ss_pred ccCccCCCcccccCCcEEeCCCCCeeec
Q 040426 10 LFCKFCGTMLRMESNHVVCSSCKFKKNV 37 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~~~C~~C~~~~~~ 37 (120)
--|+.|+..|..+...+.|++||+++..
T Consensus 150 A~CsrC~~~L~~~~~~l~Cp~Cg~tEkR 177 (188)
T COG1096 150 ARCSRCRAPLVKKGNMLKCPNCGNTEKR 177 (188)
T ss_pred EEccCCCcceEEcCcEEECCCCCCEEee
Confidence 3699999999996666999999998864
No 106
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=89.77 E-value=0.39 Score=30.84 Aligned_cols=31 Identities=26% Similarity=0.613 Sum_probs=23.4
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
....||.||.+... | -.|=+..|.+||++|.
T Consensus 34 ~~~~Cp~C~~~~Vk------R----~a~GIW~C~kCg~~fA 64 (89)
T COG1997 34 AKHVCPFCGRTTVK------R----IATGIWKCRKCGAKFA 64 (89)
T ss_pred cCCcCCCCCCccee------e----eccCeEEcCCCCCeec
Confidence 36789999998332 1 2466799999999985
No 107
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=89.59 E-value=1.2 Score=30.45 Aligned_cols=35 Identities=20% Similarity=0.488 Sum_probs=21.0
Q ss_pred cccccccccCCCceEEEEeecccCCCCceEEEEcC---CCCcee
Q 040426 77 KVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICP---RCGHRC 117 (120)
Q Consensus 77 ~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~---~C~~~w 117 (120)
.+.+.||+||...... |.+.-| ..||.|. +|.+.+
T Consensus 58 ~~~~~Cp~C~~~~~~~-----k~~~~~-~~f~~~~~~Pkc~~~~ 95 (140)
T COG0551 58 KTGVKCPKCGKGLLVL-----KKGRFG-KNFLGCSNYPKCRFTE 95 (140)
T ss_pred cCceeCCCCCCCceEE-----EeccCC-ceEEeecCCCcCceee
Confidence 3567899999744432 333222 6788765 566654
No 108
>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=89.53 E-value=0.23 Score=30.44 Aligned_cols=27 Identities=26% Similarity=0.551 Sum_probs=19.7
Q ss_pred cCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426 11 FCKFCGTMLRMESNH--VVCSSCKFKKNVQD 39 (120)
Q Consensus 11 FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~ 39 (120)
=| .||+.||.+++. =.| .||+...++.
T Consensus 5 rC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~ 33 (68)
T PF09082_consen 5 RC-DCGRYLYAKEGAKTKKC-VCGKTLKVKE 33 (68)
T ss_dssp EE-TTS--EEEETT-SEEEE-TTTEEEE--S
T ss_pred Ee-cCCCEEEecCCcceeEe-cCCCeeeeee
Confidence 37 899999999876 899 9999998877
No 109
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=89.52 E-value=0.41 Score=27.65 Aligned_cols=16 Identities=31% Similarity=1.142 Sum_probs=9.2
Q ss_pred CceEEEEcCCCCceec
Q 040426 103 GQTTYYICPRCGHRCQ 118 (120)
Q Consensus 103 ~~T~fY~C~~C~~~w~ 118 (120)
...+..+|.+|||.|+
T Consensus 24 ~~~v~W~C~~Cgh~w~ 39 (55)
T PF14311_consen 24 NKKVWWKCPKCGHEWK 39 (55)
T ss_pred CCEEEEECCCCCCeeE
Confidence 3445566666666665
No 110
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=89.44 E-value=0.22 Score=35.20 Aligned_cols=38 Identities=16% Similarity=0.365 Sum_probs=20.8
Q ss_pred cccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
.||.|+|++..-.-.-.=..-...-+=-+|.+||++|+
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFT 39 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFT 39 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccc
Confidence 69999999875442100000000002345999999986
No 111
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=89.18 E-value=0.28 Score=31.48 Aligned_cols=31 Identities=23% Similarity=0.450 Sum_probs=23.1
Q ss_pred CcccCccCCCcccccC-Cc--EEeCCCCCeeeccc
Q 040426 8 DFLFCKFCGTMLRMES-NH--VVCSSCKFKKNVQD 39 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~-~~--~~C~~C~~~~~~~~ 39 (120)
...-||.||.- ..+. .. |.|+.||+..---.
T Consensus 34 ~~~~Cp~C~~~-~VkR~a~GIW~C~kCg~~fAGga 67 (89)
T COG1997 34 AKHVCPFCGRT-TVKRIATGIWKCRKCGAKFAGGA 67 (89)
T ss_pred cCCcCCCCCCc-ceeeeccCeEEcCCCCCeecccc
Confidence 45679999988 4443 32 99999999986544
No 112
>PHA02942 putative transposase; Provisional
Probab=89.09 E-value=0.35 Score=38.83 Aligned_cols=34 Identities=18% Similarity=0.454 Sum_probs=26.0
Q ss_pred CCCcccCccCCCcccccCCc-EEeCCCCCeeeccc
Q 040426 6 GRDFLFCKFCGTMLRMESNH-VVCSSCKFKKNVQD 39 (120)
Q Consensus 6 ~~~~~FCp~CgnlL~~~~~~-~~C~~C~~~~~~~~ 39 (120)
..+..-||.||.......++ |.|..|||..+.+-
T Consensus 322 ~yTSq~Cs~CG~~~~~l~~r~f~C~~CG~~~drD~ 356 (383)
T PHA02942 322 SYSSVSCPKCGHKMVEIAHRYFHCPSCGYENDRDV 356 (383)
T ss_pred CCCCccCCCCCCccCcCCCCEEECCCCCCEeCcHH
Confidence 34678999999876533344 99999999987655
No 113
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=89.09 E-value=0.17 Score=37.10 Aligned_cols=37 Identities=19% Similarity=0.497 Sum_probs=24.4
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
+...||.||..+. -+. =++. .|...-++|.+||+.|+
T Consensus 5 iy~~Cp~Cg~eev-~hE-Vik~--~g~~~lvrC~eCG~V~~ 41 (201)
T COG1326 5 IYIECPSCGSEEV-SHE-VIKE--RGREPLVRCEECGTVHP 41 (201)
T ss_pred EEEECCCCCcchh-hHH-HHHh--cCCceEEEccCCCcEee
Confidence 4678999994443 111 1222 35558899999999995
No 114
>PRK05580 primosome assembly protein PriA; Validated
Probab=89.06 E-value=0.42 Score=41.04 Aligned_cols=12 Identities=17% Similarity=0.869 Sum_probs=8.3
Q ss_pred EEeCCCCCeeec
Q 040426 26 VVCSSCKFKKNV 37 (120)
Q Consensus 26 ~~C~~C~~~~~~ 37 (120)
+.|..|||..+.
T Consensus 409 l~Ch~Cg~~~~~ 420 (679)
T PRK05580 409 LRCHHCGYQEPI 420 (679)
T ss_pred EECCCCcCCCCC
Confidence 777777776544
No 115
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=88.67 E-value=0.59 Score=32.25 Aligned_cols=31 Identities=26% Similarity=0.756 Sum_probs=24.2
Q ss_pred ccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426 80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC 117 (120)
Q Consensus 80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w 117 (120)
+.||.||+++-.+.- ++-..|-.|..||++-
T Consensus 98 VlC~~C~sPdT~l~k-------~~r~~~l~C~ACGa~~ 128 (133)
T TIGR00311 98 VICRECNRPDTRIIK-------EGRVSLLKCEACGAKA 128 (133)
T ss_pred EECCCCCCCCcEEEE-------eCCeEEEecccCCCCC
Confidence 689999999987642 2556677999999864
No 116
>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=88.40 E-value=0.26 Score=37.37 Aligned_cols=31 Identities=23% Similarity=0.629 Sum_probs=14.8
Q ss_pred cccCccCCCc-ccccCCc-----EEeCCCCCeeeccc
Q 040426 9 FLFCKFCGTM-LRMESNH-----VVCSSCKFKKNVQD 39 (120)
Q Consensus 9 ~~FCp~Cgnl-L~~~~~~-----~~C~~C~~~~~~~~ 39 (120)
-.+||.||+. |.--+++ |.|..|+..++.++
T Consensus 31 n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyELKS 67 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKFENNRPVADFYCPNCNEEYELKS 67 (254)
T ss_dssp H---TTT--SS-EE--------EEE-TTT--EEEEEE
T ss_pred CCcCCCCCChhHhhccCCCccceeECCCCchHHhhhh
Confidence 3599999998 5433332 99999999988776
No 117
>PRK11827 hypothetical protein; Provisional
Probab=88.33 E-value=0.38 Score=28.78 Aligned_cols=33 Identities=15% Similarity=0.451 Sum_probs=27.9
Q ss_pred CCcccCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426 7 RDFLFCKFCGTMLRMESNH--VVCSSCKFKKNVQD 39 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~ 39 (120)
..+.-||.|+.-|....+. +.|..|+-.+++.+
T Consensus 6 LeILaCP~ckg~L~~~~~~~~Lic~~~~laYPI~d 40 (60)
T PRK11827 6 LEIIACPVCNGKLWYNQEKQELICKLDNLAFPLRD 40 (60)
T ss_pred HhheECCCCCCcCeEcCCCCeEECCccCeeccccC
Confidence 4577899999988876554 99999999999877
No 118
>PRK11032 hypothetical protein; Provisional
Probab=88.02 E-value=0.48 Score=33.73 Aligned_cols=12 Identities=25% Similarity=0.758 Sum_probs=9.8
Q ss_pred EEeCCCCCeeec
Q 040426 26 VVCSSCKFKKNV 37 (120)
Q Consensus 26 ~~C~~C~~~~~~ 37 (120)
++|..||+...+
T Consensus 125 LvC~~Cg~~~~~ 136 (160)
T PRK11032 125 LVCEKCHHHLAF 136 (160)
T ss_pred EEecCCCCEEEe
Confidence 999999997643
No 119
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=87.96 E-value=0.47 Score=33.25 Aligned_cols=12 Identities=25% Similarity=0.841 Sum_probs=10.0
Q ss_pred EEeCCCCCeeec
Q 040426 26 VVCSSCKFKKNV 37 (120)
Q Consensus 26 ~~C~~C~~~~~~ 37 (120)
|+|..||+...+
T Consensus 113 l~C~~Cg~~~~~ 124 (146)
T PF07295_consen 113 LVCENCGHEVEL 124 (146)
T ss_pred EecccCCCEEEe
Confidence 999999997643
No 120
>PRK14873 primosome assembly protein PriA; Provisional
Probab=87.83 E-value=0.54 Score=40.42 Aligned_cols=9 Identities=22% Similarity=0.408 Sum_probs=5.2
Q ss_pred EEeCCCCCe
Q 040426 26 VVCSSCKFK 34 (120)
Q Consensus 26 ~~C~~C~~~ 34 (120)
+.|..|||.
T Consensus 411 l~Ch~CG~~ 419 (665)
T PRK14873 411 PRCRWCGRA 419 (665)
T ss_pred eECCCCcCC
Confidence 556666653
No 121
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=87.83 E-value=0.75 Score=31.93 Aligned_cols=31 Identities=26% Similarity=0.632 Sum_probs=25.3
Q ss_pred ccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426 80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC 117 (120)
Q Consensus 80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w 117 (120)
+.||.||+++-.+.- ++-+.|-.|..||++-
T Consensus 103 VlC~~C~spdT~l~k-------~~r~~~l~C~ACGa~~ 133 (138)
T PRK03988 103 VICPECGSPDTKLIK-------EGRIWVLKCEACGAET 133 (138)
T ss_pred EECCCCCCCCcEEEE-------cCCeEEEEcccCCCCC
Confidence 689999999987642 3668899999999863
No 122
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=87.76 E-value=0.46 Score=28.08 Aligned_cols=27 Identities=33% Similarity=0.670 Sum_probs=20.8
Q ss_pred CCcccCccCCCcccccCCcEEeCCCCCeee
Q 040426 7 RDFLFCKFCGTMLRMESNHVVCSSCKFKKN 36 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~~~~~~~C~~C~~~~~ 36 (120)
..+..||.||++..+ ..+|..|||-..
T Consensus 25 ~~l~~C~~CG~~~~~---H~vC~~CG~Y~g 51 (57)
T PRK12286 25 PGLVECPNCGEPKLP---HRVCPSCGYYKG 51 (57)
T ss_pred CcceECCCCCCccCC---eEECCCCCcCCC
Confidence 446789999988554 389999998654
No 123
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=87.73 E-value=0.9 Score=40.15 Aligned_cols=31 Identities=23% Similarity=0.391 Sum_probs=20.8
Q ss_pred CcccCccCCC-cccccCCc----EEeCC---CCCeeecc
Q 040426 8 DFLFCKFCGT-MLRMESNH----VVCSS---CKFKKNVQ 38 (120)
Q Consensus 8 ~~~FCp~Cgn-lL~~~~~~----~~C~~---C~~~~~~~ 38 (120)
...=||.||. .|..+..+ +.|.. |.|..++.
T Consensus 591 ~~~~CP~Cg~~~L~~k~gr~G~Fl~Cs~yP~C~~t~~~~ 629 (860)
T PRK06319 591 TEIDCPKCHKGKLVKIWAKNRYFYGCSEYPECDYKTSEE 629 (860)
T ss_pred cCcccCCCCCcceeEEecCCCceeeccCCccccccCCcc
Confidence 3456999964 66554332 89976 88876654
No 124
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=87.58 E-value=0.37 Score=27.57 Aligned_cols=30 Identities=23% Similarity=0.445 Sum_probs=22.5
Q ss_pred CCCcccCccCCCcccccCCc-----EEeCCCCCee
Q 040426 6 GRDFLFCKFCGTMLRMESNH-----VVCSSCKFKK 35 (120)
Q Consensus 6 ~~~~~FCp~CgnlL~~~~~~-----~~C~~C~~~~ 35 (120)
-.++.||+.||.-|...... |.|.+.....
T Consensus 2 l~g~l~C~~CG~~m~~~~~~~~~~yy~C~~~~~~~ 36 (58)
T PF13408_consen 2 LSGLLRCGHCGSKMTRRKRKGKYRYYRCSNRRRKG 36 (58)
T ss_pred CCCcEEcccCCcEeEEEECCCCceEEEcCCCcCCC
Confidence 35789999999999876431 8888776444
No 125
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=87.58 E-value=0.44 Score=29.52 Aligned_cols=31 Identities=13% Similarity=0.446 Sum_probs=23.9
Q ss_pred cccCccCCCcccccCCc----------EEeC--CCCCeeeccc
Q 040426 9 FLFCKFCGTMLRMESNH----------VVCS--SCKFKKNVQD 39 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~----------~~C~--~C~~~~~~~~ 39 (120)
|+.||.||.-......+ ..|. .||+.+..-.
T Consensus 1 mm~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 1 MFHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFITYE 43 (72)
T ss_pred CccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEEEE
Confidence 67999999988665431 8999 8999986543
No 126
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=87.36 E-value=0.71 Score=24.24 Aligned_cols=28 Identities=21% Similarity=0.363 Sum_probs=21.7
Q ss_pred cccCccCCCcccc-cCCc-EEeCCCCCeee
Q 040426 9 FLFCKFCGTMLRM-ESNH-VVCSSCKFKKN 36 (120)
Q Consensus 9 ~~FCp~CgnlL~~-~~~~-~~C~~C~~~~~ 36 (120)
+.-|+.||.-+.. +++. +.|..||.+.+
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSSFP 32 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcEee
Confidence 4568889877766 6555 99999998765
No 127
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=87.14 E-value=0.44 Score=27.92 Aligned_cols=27 Identities=26% Similarity=0.610 Sum_probs=23.7
Q ss_pred cCccCCCcccccCCcEEeCCCCCeeec
Q 040426 11 FCKFCGTMLRMESNHVVCSSCKFKKNV 37 (120)
Q Consensus 11 FCp~CgnlL~~~~~~~~C~~C~~~~~~ 37 (120)
-|+.||.-|.+..|.++|..|+.....
T Consensus 7 ~C~~Cg~~~~~~dDiVvCp~CgapyHR 33 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIVVCPECGAPYHR 33 (54)
T ss_pred cChhhCCcccCCCCEEECCCCCCcccH
Confidence 599999999888888999999998764
No 128
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=86.92 E-value=0.76 Score=27.46 Aligned_cols=24 Identities=25% Similarity=0.646 Sum_probs=15.6
Q ss_pred cCccCCCcccccCCc-------EEeCCCCCe
Q 040426 11 FCKFCGTMLRMESNH-------VVCSSCKFK 34 (120)
Q Consensus 11 FCp~CgnlL~~~~~~-------~~C~~C~~~ 34 (120)
-||.||+.+..+-.+ |.|.+||+.
T Consensus 29 ~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF~ 59 (61)
T COG2888 29 PCPNCGEVEIYRCAKCRKLGNPYRCPKCGFE 59 (61)
T ss_pred eCCCCCceeeehhhhHHHcCCceECCCcCcc
Confidence 477777666655321 777777775
No 129
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=86.88 E-value=0.46 Score=27.86 Aligned_cols=31 Identities=23% Similarity=0.849 Sum_probs=23.0
Q ss_pred CcccCccCCCc--ccccCCc------EEeCCCCCeeecc
Q 040426 8 DFLFCKFCGTM--LRMESNH------VVCSSCKFKKNVQ 38 (120)
Q Consensus 8 ~~~FCp~Cgnl--L~~~~~~------~~C~~C~~~~~~~ 38 (120)
.+..||.|||- +..++|. +.|+.|..+.-+.
T Consensus 3 ~Wi~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI~ 41 (55)
T PF14205_consen 3 EWILCPICGNKTRLKIREDTVLKNFPLYCPKCKQETLID 41 (55)
T ss_pred eEEECCCCCCccceeeecCceeccccccCCCCCceEEEE
Confidence 46789999975 4555553 9999999876553
No 130
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=86.84 E-value=0.22 Score=38.51 Aligned_cols=32 Identities=25% Similarity=0.542 Sum_probs=26.0
Q ss_pred CcccCccCCCcccccCC--c-EEeCCCCCeeeccc
Q 040426 8 DFLFCKFCGTMLRMESN--H-VVCSSCKFKKNVQD 39 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~--~-~~C~~C~~~~~~~~ 39 (120)
-+.=||.|+.|||-++- + .+|..|+|-..+..
T Consensus 27 lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri~A 61 (294)
T COG0777 27 LWTKCPSCGEMLYRKELESNLKVCPKCGHHMRISA 61 (294)
T ss_pred ceeECCCccceeeHHHHHhhhhcccccCcccccCH
Confidence 36679999999998863 2 99999999876554
No 131
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=86.84 E-value=0.93 Score=27.03 Aligned_cols=36 Identities=25% Similarity=0.508 Sum_probs=26.4
Q ss_pred cccccccccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426 73 TQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC 117 (120)
Q Consensus 73 ~t~~~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w 117 (120)
|+.--.+++||.|++...+|--.| .--.|..||..-
T Consensus 5 p~S~F~~VkCp~C~n~q~vFsha~---------t~V~C~~Cg~~L 40 (59)
T PRK00415 5 PRSRFLKVKCPDCGNEQVVFSHAS---------TVVRCLVCGKTL 40 (59)
T ss_pred CCCeEEEEECCCCCCeEEEEecCC---------cEEECcccCCCc
Confidence 333357889999999999996543 236798898753
No 132
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=86.78 E-value=0.2 Score=34.81 Aligned_cols=31 Identities=32% Similarity=0.762 Sum_probs=20.1
Q ss_pred ccccccccCCCceEEEEeecccCCCCceE-----EEEcCCCCcee
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTT-----YYICPRCGHRC 117 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~-----fY~C~~C~~~w 117 (120)
..-.||+||. .|. ++|.+.. -|.|+.||..-
T Consensus 98 ~~Y~Cp~C~~---~y~------~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 98 AYYKCPNCQS---KYT------FLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred cEEECcCCCC---Eee------HHHHHHhcCCCCcEECCCCCCEE
Confidence 4568999983 222 2333433 49999999764
No 133
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=86.77 E-value=0.7 Score=26.77 Aligned_cols=29 Identities=24% Similarity=0.676 Sum_probs=22.9
Q ss_pred CCcccCc--cCCCcccccC--C-c-EEeCCCCCee
Q 040426 7 RDFLFCK--FCGTMLRMES--N-H-VVCSSCKFKK 35 (120)
Q Consensus 7 ~~~~FCp--~CgnlL~~~~--~-~-~~C~~C~~~~ 35 (120)
..+.+|| .|+.++.... . . +.|..|++..
T Consensus 16 ~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~f 50 (64)
T smart00647 16 PDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSF 50 (64)
T ss_pred CCccCCCCCCCcceEEecCCCCCCeeECCCCCCeE
Confidence 4678999 9999998873 2 2 9999898865
No 134
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=86.71 E-value=0.63 Score=27.82 Aligned_cols=35 Identities=23% Similarity=0.571 Sum_probs=29.9
Q ss_pred CCCCcccCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426 5 LGRDFLFCKFCGTMLRMESNH--VVCSSCKFKKNVQD 39 (120)
Q Consensus 5 ~~~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~ 39 (120)
....+.-||.|..-|...+.+ +.|+.|+--+++.+
T Consensus 4 ~LLeiLaCP~~kg~L~~~~~~~~L~c~~~~~aYpI~d 40 (60)
T COG2835 4 RLLEILACPVCKGPLVYDEEKQELICPRCKLAYPIRD 40 (60)
T ss_pred hhheeeeccCcCCcceEeccCCEEEecccCceeeccc
Confidence 446788999999999887665 99999999999877
No 135
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=86.65 E-value=0.16 Score=39.27 Aligned_cols=31 Identities=23% Similarity=0.588 Sum_probs=25.0
Q ss_pred cccCccCCCcccccCC--c-EEeCCCCCeeeccc
Q 040426 9 FLFCKFCGTMLRMESN--H-VVCSSCKFKKNVQD 39 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~--~-~~C~~C~~~~~~~~ 39 (120)
+.=||.|+.+|+.++- + ++|+.|||-..+..
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~a 59 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHMRMDA 59 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcCcCCH
Confidence 6679999999998742 3 99999999876533
No 136
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=86.48 E-value=0.81 Score=31.50 Aligned_cols=13 Identities=15% Similarity=0.552 Sum_probs=11.6
Q ss_pred EEeCCCCCeeecc
Q 040426 26 VVCSSCKFKKNVQ 38 (120)
Q Consensus 26 ~~C~~C~~~~~~~ 38 (120)
+.|+.||+.....
T Consensus 71 ~~C~~CG~~~~~~ 83 (135)
T PRK03824 71 LKCRNCGNEWSLK 83 (135)
T ss_pred EECCCCCCEEecc
Confidence 9999999988775
No 137
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=86.43 E-value=0.46 Score=31.20 Aligned_cols=30 Identities=17% Similarity=0.551 Sum_probs=20.4
Q ss_pred CcccCccCCCccc-ccCC--c--EEeCCCCCeeec
Q 040426 8 DFLFCKFCGTMLR-MESN--H--VVCSSCKFKKNV 37 (120)
Q Consensus 8 ~~~FCp~CgnlL~-~~~~--~--~~C~~C~~~~~~ 37 (120)
.+.-||.||+... .+-+ . .+|++||+....
T Consensus 20 t~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred cEeECCCCCCeEeeeecCCCcceEECCCCCCccCE
Confidence 4567999995322 2222 2 999999998754
No 138
>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=86.37 E-value=0.37 Score=27.89 Aligned_cols=30 Identities=23% Similarity=0.621 Sum_probs=23.4
Q ss_pred ccCccCCCcccccCC-c---EEeCCCCCeeeccc
Q 040426 10 LFCKFCGTMLRMESN-H---VVCSSCKFKKNVQD 39 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~-~---~~C~~C~~~~~~~~ 39 (120)
.=|+.||.+|---.+ . +.|..|+....+..
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a 38 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA 38 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCccceEec
Confidence 359999999977422 2 99999999887655
No 139
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=86.33 E-value=0.69 Score=22.86 Aligned_cols=23 Identities=30% Similarity=0.638 Sum_probs=17.4
Q ss_pred CccCCCcccccCC-c-EEeCCCCCe
Q 040426 12 CKFCGTMLRMESN-H-VVCSSCKFK 34 (120)
Q Consensus 12 Cp~CgnlL~~~~~-~-~~C~~C~~~ 34 (120)
|..|..+|..+.+ . ..|..|.++
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~V 25 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHTV 25 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCcC
Confidence 6778888866654 3 999999863
No 140
>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=86.23 E-value=0.71 Score=28.49 Aligned_cols=30 Identities=27% Similarity=0.587 Sum_probs=21.8
Q ss_pred cCccCCCccccc---CCc---EEeCCCCCeeecccc
Q 040426 11 FCKFCGTMLRME---SNH---VVCSSCKFKKNVQDV 40 (120)
Q Consensus 11 FCp~CgnlL~~~---~~~---~~C~~C~~~~~~~~~ 40 (120)
-||.|+.|=.+. ++. ..|-.|||.......
T Consensus 10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWRENGVEYVECVECGYTERQPDQ 45 (71)
T ss_pred cCCCCcCccEEEEEEeCCceEEEecCCCCeeccCCc
Confidence 599999864332 232 999999999876653
No 141
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=86.17 E-value=0.17 Score=39.39 Aligned_cols=31 Identities=13% Similarity=0.445 Sum_probs=25.0
Q ss_pred cccCccCCCcccccCC--c-EEeCCCCCeeeccc
Q 040426 9 FLFCKFCGTMLRMESN--H-VVCSSCKFKKNVQD 39 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~--~-~~C~~C~~~~~~~~ 39 (120)
+.=||.|+.+|+.+.- + ++|+.|+|-.....
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rltA 71 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGYHLKMSS 71 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCCCcCCCH
Confidence 6679999999998853 2 89999999765543
No 142
>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=85.97 E-value=0.82 Score=35.11 Aligned_cols=35 Identities=26% Similarity=0.691 Sum_probs=17.9
Q ss_pred cccccccCCC-ceEEEEeecccCC-CCceEEEEcCCCCceec
Q 040426 79 KRACEKCQNP-EMYYSTRQTRSAD-EGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 79 ~~~CpkCg~~-ea~y~~~Q~RSAD-E~~T~fY~C~~C~~~w~ 118 (120)
...||-||.. .+.... ..+ +|. +|..|.-|++.|+
T Consensus 172 ~g~CPvCGs~P~~s~l~----~~~~~G~-R~L~Cs~C~t~W~ 208 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLR----GGEREGK-RYLHCSLCGTEWR 208 (290)
T ss_dssp -SS-TTT---EEEEEEE----------E-EEEEETTT--EEE
T ss_pred CCcCCCCCCcCceEEEe----cCCCCcc-EEEEcCCCCCeee
Confidence 4689999987 444433 322 376 9999999999996
No 143
>COG4640 Predicted membrane protein [Function unknown]
Probab=85.86 E-value=0.41 Score=38.78 Aligned_cols=27 Identities=30% Similarity=0.727 Sum_probs=19.2
Q ss_pred cccCccCCCcccccCCcEEeCCCCCeeec
Q 040426 9 FLFCKFCGTMLRMESNHVVCSSCKFKKNV 37 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~~~C~~C~~~~~~ 37 (120)
|+|||.||.- -.++.+.|..||+....
T Consensus 1 M~fC~kcG~q--k~Ed~~qC~qCG~~~t~ 27 (465)
T COG4640 1 MKFCPKCGSQ--KAEDDVQCTQCGHKFTS 27 (465)
T ss_pred CCcccccccc--cccccccccccCCcCCc
Confidence 7999999942 12334669999997543
No 144
>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=85.78 E-value=1.6 Score=27.52 Aligned_cols=37 Identities=16% Similarity=0.305 Sum_probs=19.9
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
+.-.||-|||..++--.+.-. -.+-.-.|..||..|.
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk----~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKK----EGIGILSCRVCGESFQ 57 (81)
T ss_dssp S----TTT--SS-EEEEEETT----TTEEEEEESSS--EEE
T ss_pred ceEcCCcCCCCCeEEEEEEcc----CCEEEEEecCCCCeEE
Confidence 456799999999987776321 3455578999998775
No 145
>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=85.50 E-value=0.88 Score=23.70 Aligned_cols=29 Identities=24% Similarity=0.701 Sum_probs=15.6
Q ss_pred ccccccCCCce--EEEEeecccCCCCceEEEEcCC--CCc
Q 040426 80 RACEKCQNPEM--YYSTRQTRSADEGQTTYYICPR--CGH 115 (120)
Q Consensus 80 ~~CpkCg~~ea--~y~~~Q~RSADE~~T~fY~C~~--C~~ 115 (120)
..|||||-.-. +|-+ .|....|+|.+ |.+
T Consensus 2 hlcpkcgvgvl~pvy~~-------kgeikvfrcsnpacdy 34 (36)
T PF09151_consen 2 HLCPKCGVGVLEPVYNQ-------KGEIKVFRCSNPACDY 34 (36)
T ss_dssp -B-TTTSSSBEEEEE-T-------TS-EEEEEES-TT---
T ss_pred ccCCccCceEEEEeecC-------CCcEEEEEcCCCcccc
Confidence 57999998744 4533 37788899974 765
No 146
>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=85.19 E-value=0.38 Score=31.10 Aligned_cols=31 Identities=23% Similarity=0.354 Sum_probs=22.0
Q ss_pred cccCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426 9 FLFCKFCGTMLRMESNH--VVCSSCKFKKNVQD 39 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~ 39 (120)
-.+||.||..-.-+... |.|+.|++..---.
T Consensus 35 ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AGGA 67 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRVATGIWKCKKCGKKFAGGA 67 (90)
T ss_dssp -BEESSSSSSEEEEEETTEEEETTTTEEEE-BS
T ss_pred CCcCCCCCCceeEEeeeEEeecCCCCCEEeCCC
Confidence 45899999886444332 99999999875444
No 147
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=85.18 E-value=0.52 Score=37.12 Aligned_cols=32 Identities=28% Similarity=0.611 Sum_probs=23.3
Q ss_pred CcccCccCCCcccccCCc--EEeC--CCC---Ceeeccc
Q 040426 8 DFLFCKFCGTMLRMESNH--VVCS--SCK---FKKNVQD 39 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~~--~~C~--~C~---~~~~~~~ 39 (120)
..+|||-||+-+.+++.+ ..|+ +|. +.++..+
T Consensus 149 kykFCp~CG~~tkp~e~g~k~~Cs~~~C~~~n~~yPr~d 187 (345)
T KOG3084|consen 149 KYKFCPGCGSPTKPEEAGTKLQCSDETCPSCNVIYPRTD 187 (345)
T ss_pred HhccCcccCCCcccccCCccceeecccCCcCCeeccCCC
Confidence 467999999999999875 6666 555 4554444
No 148
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=84.83 E-value=0.24 Score=38.44 Aligned_cols=30 Identities=23% Similarity=0.591 Sum_probs=24.9
Q ss_pred cccCccCCCcccccCC--c-EEeCCCCCeeecc
Q 040426 9 FLFCKFCGTMLRMESN--H-VVCSSCKFKKNVQ 38 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~--~-~~C~~C~~~~~~~ 38 (120)
+.=||.|+.+||-++- + .+|+.|+|-....
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHHMRIS 59 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCCeeCC
Confidence 6789999999998753 2 8999999987654
No 149
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=84.61 E-value=0.42 Score=27.77 Aligned_cols=14 Identities=43% Similarity=1.213 Sum_probs=11.6
Q ss_pred CCCcccCccCCCcc
Q 040426 6 GRDFLFCKFCGTML 19 (120)
Q Consensus 6 ~~~~~FCp~CgnlL 19 (120)
...+.|||.||-||
T Consensus 43 ~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 43 GDEIVFCPNCGRIL 56 (56)
T ss_pred CCCeEECcCCCccC
Confidence 34688999999887
No 150
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=84.57 E-value=1.5 Score=29.33 Aligned_cols=30 Identities=27% Similarity=0.701 Sum_probs=23.9
Q ss_pred ccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426 80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
+.||.||+++..+.- |+-+.|-+|..||.+
T Consensus 81 VlC~~C~spdT~l~k-------~~r~~~l~C~aCGa~ 110 (110)
T smart00653 81 VLCPECGSPDTELIK-------ENRLFFLKCEACGAR 110 (110)
T ss_pred EECCCCCCCCcEEEE-------eCCeEEEEccccCCC
Confidence 689999999986643 256788899999964
No 151
>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=84.54 E-value=0.55 Score=27.19 Aligned_cols=30 Identities=20% Similarity=0.563 Sum_probs=16.2
Q ss_pred CCCcccCcc--CCCcccccCCc----EEeCCCCCee
Q 040426 6 GRDFLFCKF--CGTMLRMESNH----VVCSSCKFKK 35 (120)
Q Consensus 6 ~~~~~FCp~--CgnlL~~~~~~----~~C~~C~~~~ 35 (120)
...+++||. |+.++...... +.|..|++..
T Consensus 15 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 15 DPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp ---CC--TTSST---ECS-SSTTS--CCTTSCCSEE
T ss_pred CCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcC
Confidence 345679977 99999887653 7899888864
No 152
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=84.48 E-value=1.8 Score=26.24 Aligned_cols=32 Identities=19% Similarity=0.364 Sum_probs=23.3
Q ss_pred cccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426 79 KRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC 117 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w 117 (120)
-++||-||.+.+..-+ + +-.-++.|.+|+-.+
T Consensus 6 lKPCPFCG~~~~~v~~------~-~g~~~v~C~~CgA~~ 37 (64)
T PRK09710 6 VKPCPFCGCPSVTVKA------I-SGYYRAKCNGCESRT 37 (64)
T ss_pred ccCCCCCCCceeEEEe------c-CceEEEEcCCCCcCc
Confidence 4679999999887653 1 335568899998654
No 153
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=84.40 E-value=0.52 Score=38.39 Aligned_cols=30 Identities=17% Similarity=0.462 Sum_probs=25.3
Q ss_pred ccCccCCCcccccCCc-EEeCCCCCeeeccc
Q 040426 10 LFCKFCGTMLRMESNH-VVCSSCKFKKNVQD 39 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~-~~C~~C~~~~~~~~ 39 (120)
.-||.||.-|.....+ |.|+.||+..+-..
T Consensus 351 p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 351 PVCPRCGGRMKSAGRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCCccCCchhhcCCCCcccccccccCCccc
Confidence 3699999999988764 99999999887555
No 154
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=83.90 E-value=1.4 Score=32.30 Aligned_cols=31 Identities=23% Similarity=0.558 Sum_probs=25.0
Q ss_pred ccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426 80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC 117 (120)
Q Consensus 80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w 117 (120)
+.||.||+++-.+.- ++.+.|-.|..||..-
T Consensus 99 V~C~~C~~pdT~l~k-------~~~~~~l~C~aCGa~~ 129 (201)
T PRK12336 99 VICSECGLPDTRLVK-------EDRVLMLRCDACGAHR 129 (201)
T ss_pred EECCCCCCCCcEEEE-------cCCeEEEEcccCCCCc
Confidence 689999999987642 2578888999999753
No 155
>PHA02942 putative transposase; Provisional
Probab=83.70 E-value=0.86 Score=36.60 Aligned_cols=29 Identities=28% Similarity=0.712 Sum_probs=20.8
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC 117 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w 117 (120)
+...||.|||... . .....|.|.+||+..
T Consensus 324 TSq~Cs~CG~~~~---~--------l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 324 SSVSCPKCGHKMV---E--------IAHRYFHCPSCGYEN 352 (383)
T ss_pred CCccCCCCCCccC---c--------CCCCEEECCCCCCEe
Confidence 4577999999642 1 012479999999975
No 156
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=83.65 E-value=0.1 Score=36.20 Aligned_cols=28 Identities=25% Similarity=0.603 Sum_probs=21.1
Q ss_pred CCcccCccCCCcccccCCcEEeCCCCCee
Q 040426 7 RDFLFCKFCGTMLRMESNHVVCSSCKFKK 35 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~~~~~~~C~~C~~~~ 35 (120)
+.+.-||.||.+... ...-.|..|....
T Consensus 1 m~l~nC~~CgklF~~-~~~~iCp~C~~~~ 28 (137)
T TIGR03826 1 MELANCPKCGRLFVK-TGRDVCPSCYEEE 28 (137)
T ss_pred CCCccccccchhhhh-cCCccCHHHhHHH
Confidence 467789999997665 3446799998753
No 157
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=83.49 E-value=0.54 Score=34.61 Aligned_cols=27 Identities=26% Similarity=0.696 Sum_probs=20.4
Q ss_pred cccCccCCCcccccCC--------c-----EEeCCCCCee
Q 040426 9 FLFCKFCGTMLRMESN--------H-----VVCSSCKFKK 35 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~--------~-----~~C~~C~~~~ 35 (120)
..=||.||.-|..-.- . +.|.+|||..
T Consensus 14 ~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~ 53 (201)
T COG1779 14 RIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRS 53 (201)
T ss_pred eecCCcccceeeEEEeeecCCccceEEEEEEEccccCCcc
Confidence 4469999998765421 1 9999999985
No 158
>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=83.42 E-value=1 Score=27.72 Aligned_cols=26 Identities=23% Similarity=0.570 Sum_probs=18.9
Q ss_pred cCccCCCcccccCCcEEeCCCCCeee
Q 040426 11 FCKFCGTMLRMESNHVVCSSCKFKKN 36 (120)
Q Consensus 11 FCp~CgnlL~~~~~~~~C~~C~~~~~ 36 (120)
-||.|.+-|.+..+.+.|..|+....
T Consensus 3 ~CP~C~~~L~~~~~~~~C~~C~~~~~ 28 (70)
T PF07191_consen 3 TCPKCQQELEWQGGHYHCEACQKDYK 28 (70)
T ss_dssp B-SSS-SBEEEETTEEEETTT--EEE
T ss_pred cCCCCCCccEEeCCEEECccccccce
Confidence 49999999999987799999988543
No 159
>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=83.41 E-value=1.3 Score=26.63 Aligned_cols=34 Identities=21% Similarity=0.529 Sum_probs=24.2
Q ss_pred CCCcccCccCCCcc------------------------------cccCCcEEeCCCCCeeeccc
Q 040426 6 GRDFLFCKFCGTML------------------------------RMESNHVVCSSCKFKKNVQD 39 (120)
Q Consensus 6 ~~~~~FCp~CgnlL------------------------------~~~~~~~~C~~C~~~~~~~~ 39 (120)
-..++-||.|.+=| .+.++.+.|+.|+..+++.+
T Consensus 4 llniL~Cp~ck~pL~~~~l~~~~~~~~~~lp~~~~~~~~~l~~~~i~eg~L~Cp~c~r~YPI~d 67 (68)
T PF03966_consen 4 LLNILACPVCKGPLDWEALVETAQLGLSELPKELPEDYHVLLEVEIVEGELICPECGREYPIRD 67 (68)
T ss_dssp GCGTBB-TTTSSBEHHHHHHHHHHCCCCHCHHCHHCHCEHHCTEETTTTEEEETTTTEEEEEET
T ss_pred HHhhhcCCCCCCcchHHHHHHHHHhCcccCCCCCccchhhhhcccccCCEEEcCCCCCEEeCCC
Confidence 45678899999866 12233399999999998764
No 160
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=83.38 E-value=0.55 Score=38.26 Aligned_cols=31 Identities=35% Similarity=0.890 Sum_probs=23.5
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~ 119 (120)
.+-.||.||.. +.|| |.+ -|+|.+||++.++
T Consensus 349 ~~p~Cp~Cg~~--------m~S~--G~~-g~rC~kCg~~~~~ 379 (421)
T COG1571 349 VNPVCPRCGGR--------MKSA--GRN-GFRCKKCGTRARE 379 (421)
T ss_pred cCCCCCccCCc--------hhhc--CCC-CcccccccccCCc
Confidence 34479999974 3456 666 8999999998764
No 161
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=83.32 E-value=0.42 Score=38.14 Aligned_cols=32 Identities=34% Similarity=0.650 Sum_probs=26.7
Q ss_pred ccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426 80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC 117 (120)
Q Consensus 80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w 117 (120)
+.||.|+|+|-.++-. + -||+-+.|..||++-
T Consensus 97 VlC~~C~NPETel~it----k--~q~i~~~CkACG~r~ 128 (400)
T KOG2767|consen 97 VLCPSCENPETELIIT----K--KQTISLKCKACGFRS 128 (400)
T ss_pred eeCcCCCCCceeEEec----c--cchhhhHHHHcCCcc
Confidence 5899999999987652 2 589999999999864
No 162
>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=82.79 E-value=0.76 Score=36.76 Aligned_cols=35 Identities=37% Similarity=0.700 Sum_probs=20.7
Q ss_pred ccccccccCC-CceEEEEeecccCC-CCceEEEEcCCCCcee
Q 040426 78 VKRACEKCQN-PEMYYSTRQTRSAD-EGQTTYYICPRCGHRC 117 (120)
Q Consensus 78 ~~~~CpkCg~-~ea~y~~~Q~RSAD-E~~T~fY~C~~C~~~w 117 (120)
....|++||. ....-. +-| ++-|+.|+|..|||+-
T Consensus 173 f~piC~~cGri~tt~v~-----~~d~~~~~v~Y~c~~cG~~g 209 (360)
T PF01921_consen 173 FLPICEKCGRIDTTEVT-----EYDPEGGTVTYRCEECGHEG 209 (360)
T ss_dssp EEEEETTTEE--EEEEE-----EE--SSSEEEEE--TTS---
T ss_pred eeeeccccCCcccceee-----EeecCCCEEEEEecCCCCEE
Confidence 3567999998 544322 334 7899999999999974
No 163
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=82.36 E-value=1.2 Score=32.19 Aligned_cols=29 Identities=24% Similarity=0.560 Sum_probs=24.3
Q ss_pred cccCccCCCcccccC-CcEEeCCCCCeeec
Q 040426 9 FLFCKFCGTMLRMES-NHVVCSSCKFKKNV 37 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~-~~~~C~~C~~~~~~ 37 (120)
..+|+.||..|.|.. +.+.|..|++.+..
T Consensus 149 ~a~~~~~g~~~~~~~~~~~~c~~~~~~e~r 178 (189)
T PRK09521 149 YAMCSRCRTPLVKKGENELKCPNCGNIETR 178 (189)
T ss_pred EEEccccCCceEECCCCEEECCCCCCEEee
Confidence 348999999998877 55999999988763
No 164
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=82.32 E-value=1.2 Score=36.64 Aligned_cols=17 Identities=12% Similarity=0.317 Sum_probs=14.1
Q ss_pred cccccccCCCceEEEEe
Q 040426 79 KRACEKCQNPEMYYSTR 95 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~ 95 (120)
++.||-||..+..|..+
T Consensus 458 ~~~cp~c~~~k~~f~~~ 474 (479)
T PRK05452 458 NFLCPECSLGKDVFDEL 474 (479)
T ss_pred CCcCcCCCCcHHHhEec
Confidence 78999999998877543
No 165
>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=82.28 E-value=0.91 Score=26.58 Aligned_cols=26 Identities=35% Similarity=0.792 Sum_probs=19.5
Q ss_pred CCcccCccCCCcccccCCcEEeCCCCCee
Q 040426 7 RDFLFCKFCGTMLRMESNHVVCSSCKFKK 35 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~~~~~~~C~~C~~~~ 35 (120)
..+..||.||.+-.+ ..+|..|||-.
T Consensus 24 p~l~~C~~cG~~~~~---H~vc~~cG~Y~ 49 (55)
T TIGR01031 24 PTLVVCPNCGEFKLP---HRVCPSCGYYK 49 (55)
T ss_pred CcceECCCCCCcccC---eeECCccCeEC
Confidence 346689999986443 38999999865
No 166
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=82.03 E-value=0.6 Score=27.32 Aligned_cols=26 Identities=31% Similarity=0.671 Sum_probs=19.7
Q ss_pred CcccCccCCCcccccCCcEEeCCCCCeee
Q 040426 8 DFLFCKFCGTMLRMESNHVVCSSCKFKKN 36 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~~~~C~~C~~~~~ 36 (120)
.+..||.||.+-.+- ..|..|||...
T Consensus 25 ~l~~c~~cg~~~~~H---~vc~~cG~y~~ 50 (56)
T PF01783_consen 25 NLVKCPNCGEPKLPH---RVCPSCGYYKG 50 (56)
T ss_dssp SEEESSSSSSEESTT---SBCTTTBBSSS
T ss_pred ceeeeccCCCEeccc---EeeCCCCeECC
Confidence 577899999765443 78999997654
No 167
>KOG0696 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=82.01 E-value=0.28 Score=40.53 Aligned_cols=29 Identities=24% Similarity=0.653 Sum_probs=23.3
Q ss_pred CCCcccCccCCCcccccCCc-EEeCCCCCe
Q 040426 6 GRDFLFCKFCGTMLRMESNH-VVCSSCKFK 34 (120)
Q Consensus 6 ~~~~~FCp~CgnlL~~~~~~-~~C~~C~~~ 34 (120)
++++-||.+||+|||--... +.|.+|.-.
T Consensus 118 YssPTFCDhCGsLLyGl~HQGmKC~~C~mN 147 (683)
T KOG0696|consen 118 YSSPTFCDHCGSLLYGLIHQGMKCDTCDMN 147 (683)
T ss_pred cCCCchhhhHHHHHHHHHhcccccccccch
Confidence 56789999999999976544 888888753
No 168
>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=81.73 E-value=1.4 Score=35.06 Aligned_cols=35 Identities=31% Similarity=0.606 Sum_probs=22.2
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC 117 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w 117 (120)
..-.||+||.-. ..+ +--..+.-|+.|+| .|||.-
T Consensus 168 ~~p~c~~cg~~~---~~v-~~~d~~~~~v~y~c-~cG~~g 202 (353)
T cd00674 168 FMPYCEKCGKDT---TTV-EAYDAKAGTVTYKC-ECGHEE 202 (353)
T ss_pred eeeecCCcCcce---eEE-EEEeCCCCeEEEEc-CCCCEE
Confidence 455799999322 111 22233466999999 699964
No 169
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=81.59 E-value=1.9 Score=25.73 Aligned_cols=27 Identities=22% Similarity=0.704 Sum_probs=18.7
Q ss_pred cccCccCCCcccccCC-------cEEeCCCCCee
Q 040426 9 FLFCKFCGTMLRMESN-------HVVCSSCKFKK 35 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~-------~~~C~~C~~~~ 35 (120)
.-.||.||..+..+-. .|.|..||+.-
T Consensus 25 ~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CGF~G 58 (59)
T PRK14890 25 KFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGFEG 58 (59)
T ss_pred EeeCCCCCCeeEeechhHHhcCCceECCCCCCcC
Confidence 4478888887665532 18888888753
No 170
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=81.45 E-value=1.3 Score=33.55 Aligned_cols=26 Identities=27% Similarity=0.733 Sum_probs=20.7
Q ss_pred cccccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426 77 KVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC 117 (120)
Q Consensus 77 ~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w 117 (120)
.+...||.||+ -...-|.|..||+.+
T Consensus 307 ~tS~~C~~cg~---------------~~~r~~~C~~cg~~~ 332 (364)
T COG0675 307 YTSKTCPCCGH---------------LSGRLFKCPRCGFVH 332 (364)
T ss_pred CCcccccccCC---------------ccceeEECCCCCCee
Confidence 45678999999 125679999999976
No 171
>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=81.11 E-value=1.3 Score=25.16 Aligned_cols=26 Identities=19% Similarity=0.535 Sum_probs=17.6
Q ss_pred cccCc--cCCCc--ccccCCcEEeCCCCCe
Q 040426 9 FLFCK--FCGTM--LRMESNHVVCSSCKFK 34 (120)
Q Consensus 9 ~~FCp--~Cgnl--L~~~~~~~~C~~C~~~ 34 (120)
-..|| +||.- |---.+++.|-.|+++
T Consensus 18 rk~CP~~~CG~GvFMA~H~dR~~CGKCg~T 47 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEHKDRHYCGKCGYT 47 (47)
T ss_dssp SEE-TSTTTTSSSEEEE-SSEEEETTTSS-
T ss_pred hhcCCCcccCCceEeeecCCCccCCCcccC
Confidence 46899 99983 3334566999999984
No 172
>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=80.88 E-value=1.5 Score=30.32 Aligned_cols=38 Identities=26% Similarity=0.579 Sum_probs=20.7
Q ss_pred cccccccCCCceEEEEeecc-----cCCCCceEEEEcCCCCce
Q 040426 79 KRACEKCQNPEMYYSTRQTR-----SADEGQTTYYICPRCGHR 116 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~Q~R-----SADE~~T~fY~C~~C~~~ 116 (120)
--.|+.|+..-..---.+.+ ..-+....||.|+.||..
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~ki 133 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKI 133 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCE
Confidence 45899999832111000000 011224469999999875
No 173
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=80.64 E-value=1.3 Score=34.48 Aligned_cols=31 Identities=26% Similarity=0.553 Sum_probs=20.5
Q ss_pred CCCcccCccCCCc-c-cccCCc-EEeCCCCCeee
Q 040426 6 GRDFLFCKFCGTM-L-RMESNH-VVCSSCKFKKN 36 (120)
Q Consensus 6 ~~~~~FCp~Cgnl-L-~~~~~~-~~C~~C~~~~~ 36 (120)
......||+||.- + +-.+.+ ++|..||++-.
T Consensus 8 ~~~~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 8 EEEKLVCPECGSDKLIYDYERGEIVCADCGLVIE 41 (310)
T ss_pred cccCCcCcCCCCCCeeEECCCCeEeecccCCccc
Confidence 3446789999972 2 111222 99999999754
No 174
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=80.56 E-value=4.4 Score=32.26 Aligned_cols=27 Identities=33% Similarity=0.727 Sum_probs=19.1
Q ss_pred CcccC--ccCCCcccccCCc--EEeCC-CCCe
Q 040426 8 DFLFC--KFCGTMLRMESNH--VVCSS-CKFK 34 (120)
Q Consensus 8 ~~~FC--p~CgnlL~~~~~~--~~C~~-C~~~ 34 (120)
+-.-| |-||.=|.++.|. ..|.. |||.
T Consensus 314 gGVlCP~pgCG~gll~EPD~rkvtC~~gCgf~ 345 (446)
T KOG0006|consen 314 GGVLCPRPGCGAGLLPEPDQRKVTCEGGCGFA 345 (446)
T ss_pred CCEecCCCCCCcccccCCCCCcccCCCCchhH
Confidence 34457 4699888887764 77776 7775
No 175
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=80.12 E-value=1.2 Score=30.02 Aligned_cols=42 Identities=12% Similarity=-0.083 Sum_probs=34.5
Q ss_pred CCCCCCCCcccCccCCCcccccCC-cEEeCCCCCeeecccccc
Q 040426 1 MADPLGRDFLFCKFCGTMLRMESN-HVVCSSCKFKKNVQDVAD 42 (120)
Q Consensus 1 ~~~~~~~~~~FCp~CgnlL~~~~~-~~~C~~C~~~~~~~~~~~ 42 (120)
||++-.+.-+-||+||.-.|--.- .++|+.||.+++.+-+..
T Consensus 1 mAk~eLGtKridPetg~KFYDLNrdPiVsPytG~s~P~s~fe~ 43 (129)
T COG4530 1 MAKPELGTKRIDPETGKKFYDLNRDPIVSPYTGKSYPRSYFEE 43 (129)
T ss_pred CCcccccccccCccccchhhccCCCccccCcccccchHHHHHh
Confidence 788888999999999998876543 399999999997666544
No 176
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=79.84 E-value=1.7 Score=23.92 Aligned_cols=14 Identities=29% Similarity=0.361 Sum_probs=10.4
Q ss_pred cccCccCCCccccc
Q 040426 9 FLFCKFCGTMLRME 22 (120)
Q Consensus 9 ~~FCp~CgnlL~~~ 22 (120)
...||.||.-|..-
T Consensus 2 ~~~C~~Cg~~l~~i 15 (47)
T PF13005_consen 2 PRACPDCGGELKEI 15 (47)
T ss_pred CCcCCCCCceeeEC
Confidence 45789999888743
No 177
>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=79.83 E-value=0.43 Score=33.67 Aligned_cols=30 Identities=23% Similarity=0.593 Sum_probs=23.0
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
.--.||+|| ..| |.||.+..-|.|+.||..
T Consensus 108 ~~Y~Cp~c~---~r~------tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 108 MFFICPNMC---VRF------TFNEAMELNFTCPRCGAM 137 (158)
T ss_pred CeEECCCCC---cEe------eHHHHHHcCCcCCCCCCE
Confidence 456799999 333 457778889999999975
No 178
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=79.44 E-value=2.6 Score=26.93 Aligned_cols=35 Identities=20% Similarity=0.433 Sum_probs=27.0
Q ss_pred cccccccccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426 73 TQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 73 ~t~~~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
|+.--.+++||.|++...+|--.| | --.|..||..
T Consensus 29 PnS~Fm~VkCp~C~n~q~VFShA~--------t-~V~C~~Cg~~ 63 (85)
T PTZ00083 29 PNSYFMDVKCPGCSQITTVFSHAQ--------T-VVLCGGCSSQ 63 (85)
T ss_pred CCCeEEEEECCCCCCeeEEEecCc--------e-EEEccccCCE
Confidence 444468999999999999997754 3 3678888865
No 179
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=79.35 E-value=1.5 Score=25.19 Aligned_cols=30 Identities=20% Similarity=0.594 Sum_probs=22.2
Q ss_pred ccCccCCCccccc-CCc-EEeCCCCCeeeccc
Q 040426 10 LFCKFCGTMLRME-SNH-VVCSSCKFKKNVQD 39 (120)
Q Consensus 10 ~FCp~CgnlL~~~-~~~-~~C~~C~~~~~~~~ 39 (120)
--|..||..+... ... +.|+.||+..-.+.
T Consensus 7 Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~K~ 38 (49)
T COG1996 7 YKCARCGREVELDQETRGIRCPYCGSRILVKE 38 (49)
T ss_pred EEhhhcCCeeehhhccCceeCCCCCcEEEEec
Confidence 3589999998633 333 99999999776544
No 180
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=79.34 E-value=0.42 Score=34.46 Aligned_cols=30 Identities=27% Similarity=0.713 Sum_probs=22.8
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
.--.||.|| ..| +.+|++..-|.|..||..
T Consensus 116 ~~Y~Cp~C~---~ry------tf~eA~~~~F~Cp~Cg~~ 145 (178)
T PRK06266 116 MFFFCPNCH---IRF------TFDEAMEYGFRCPQCGEM 145 (178)
T ss_pred CEEECCCCC---cEE------eHHHHhhcCCcCCCCCCC
Confidence 456799999 333 356778889999999964
No 181
>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=79.07 E-value=1.4 Score=33.53 Aligned_cols=34 Identities=21% Similarity=0.540 Sum_probs=13.0
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC 117 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w 117 (120)
.+.-||.||+....=|.-=..+|| |-|..|+..+
T Consensus 30 ~n~yCP~Cg~~~L~~f~NN~PVaD------F~C~~C~eey 63 (254)
T PF06044_consen 30 ENMYCPNCGSKPLSKFENNRPVAD------FYCPNCNEEY 63 (254)
T ss_dssp HH---TTT--SS-EE--------E------EE-TTT--EE
T ss_pred HCCcCCCCCChhHhhccCCCccce------eECCCCchHH
Confidence 456899999996655544444444 8899998876
No 182
>PLN00209 ribosomal protein S27; Provisional
Probab=78.41 E-value=2.7 Score=26.87 Aligned_cols=36 Identities=22% Similarity=0.390 Sum_probs=27.3
Q ss_pred cccccccccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426 73 TQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC 117 (120)
Q Consensus 73 ~t~~~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w 117 (120)
|+.--.+++||.|++...+|--.| .--.|..||..-
T Consensus 30 PnS~Fm~VkCp~C~n~q~VFShA~---------t~V~C~~Cg~~L 65 (86)
T PLN00209 30 PNSFFMDVKCQGCFNITTVFSHSQ---------TVVVCGSCQTVL 65 (86)
T ss_pred CCCEEEEEECCCCCCeeEEEecCc---------eEEEccccCCEe
Confidence 444468999999999999997644 236788888653
No 183
>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=77.96 E-value=1.6 Score=28.28 Aligned_cols=32 Identities=22% Similarity=0.404 Sum_probs=21.9
Q ss_pred CcccCccCCCcccccCC-c-EEeCCCCCeeeccc
Q 040426 8 DFLFCKFCGTMLRMESN-H-VVCSSCKFKKNVQD 39 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~-~-~~C~~C~~~~~~~~ 39 (120)
....||.||..=.-+.. . |.|+.|+++.---.
T Consensus 34 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGA 67 (91)
T TIGR00280 34 AKYVCPFCGKKTVKRGSTGIWTCRKCGAKFAGGA 67 (91)
T ss_pred cCccCCCCCCCceEEEeeEEEEcCCCCCEEeCCc
Confidence 35689999864322222 2 99999999976544
No 184
>PRK07219 DNA topoisomerase I; Validated
Probab=77.92 E-value=6.4 Score=34.71 Aligned_cols=30 Identities=27% Similarity=0.435 Sum_probs=20.6
Q ss_pred ccCccCCCccccc---CC-c-EEeCC---CCCeeeccc
Q 040426 10 LFCKFCGTMLRME---SN-H-VVCSS---CKFKKNVQD 39 (120)
Q Consensus 10 ~FCp~CgnlL~~~---~~-~-~~C~~---C~~~~~~~~ 39 (120)
.=||.||.-|..+ .. . +.|.. |++..++..
T Consensus 603 ~~CP~Cg~~l~~r~~~~g~~F~gCs~yp~C~~t~~lp~ 640 (822)
T PRK07219 603 GKCPECGGDLIIIRTDKGSRFVGCSGYPDCRNTFPLPS 640 (822)
T ss_pred CcCCCCCCcceeeeccCCceeeecCCCcCCCCeeecCC
Confidence 4599999755432 22 3 89987 999877654
No 185
>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=77.87 E-value=1.5 Score=23.29 Aligned_cols=12 Identities=42% Similarity=1.060 Sum_probs=9.5
Q ss_pred EEEcCCCCceec
Q 040426 107 YYICPRCGHRCQ 118 (120)
Q Consensus 107 fY~C~~C~~~w~ 118 (120)
-|+|.+||+.|.
T Consensus 5 ~y~C~~Cg~~fe 16 (41)
T smart00834 5 EYRCEDCGHTFE 16 (41)
T ss_pred EEEcCCCCCEEE
Confidence 478999998774
No 186
>PRK12495 hypothetical protein; Provisional
Probab=77.76 E-value=1.3 Score=33.08 Aligned_cols=33 Identities=15% Similarity=0.349 Sum_probs=24.8
Q ss_pred CCCCCcccCccCCCcccccCCcEEeCCCCCeee
Q 040426 4 PLGRDFLFCKFCGTMLRMESNHVVCSSCKFKKN 36 (120)
Q Consensus 4 ~~~~~~~FCp~CgnlL~~~~~~~~C~~C~~~~~ 36 (120)
...+...+|+.||.-|.-..+...|..|+....
T Consensus 37 gatmsa~hC~~CG~PIpa~pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 37 GATMTNAHCDECGDPIFRHDGQEFCPTCQQPVT 69 (226)
T ss_pred hcccchhhcccccCcccCCCCeeECCCCCCccc
Confidence 345667899999998884333399999998743
No 187
>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=77.45 E-value=2.5 Score=35.33 Aligned_cols=34 Identities=24% Similarity=0.572 Sum_probs=22.2
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC 117 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w 117 (120)
..-.||+||.-... .. +-|..-|+.|+| +|||.-
T Consensus 167 ~~pic~~cGrv~~~--~~---~~~~~~~v~Y~c-~cG~~g 200 (515)
T TIGR00467 167 ISVFCENCGRDTTT--VN---NYDNEYSIEYSC-ECGNQE 200 (515)
T ss_pred eeeecCCcCccCce--EE---EecCCceEEEEc-CCCCEE
Confidence 45679999997331 11 223233899999 699863
No 188
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=77.34 E-value=3.2 Score=23.27 Aligned_cols=31 Identities=19% Similarity=0.448 Sum_probs=22.0
Q ss_pred CCcccCccCCCcccccCC-cEEeCCCCCeeec
Q 040426 7 RDFLFCKFCGTMLRMESN-HVVCSSCKFKKNV 37 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~~~~-~~~C~~C~~~~~~ 37 (120)
..+.+|..|+.+|..... .+.|..|++....
T Consensus 9 ~~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~ 40 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGKQGYRCSWCGLVCHK 40 (53)
T ss_dssp SSTEB-TTSSSBECSSSSCEEEETTTT-EEET
T ss_pred CCCCCCcccCcccCCCCCCeEEECCCCChHhh
Confidence 567899999999954322 3999999997653
No 189
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=76.66 E-value=0.63 Score=38.22 Aligned_cols=28 Identities=18% Similarity=0.465 Sum_probs=22.2
Q ss_pred CCcccCccCCCcccccCCcEEeCCCCCe
Q 040426 7 RDFLFCKFCGTMLRMESNHVVCSSCKFK 34 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~~~~~~~C~~C~~~ 34 (120)
.+..|||.|+|-.-+..-+-.||.||-+
T Consensus 178 s~V~~CP~Ca~~F~l~rRrHHCRLCG~V 205 (505)
T KOG1842|consen 178 SSVQFCPECANSFGLTRRRHHCRLCGRV 205 (505)
T ss_pred CcccccccccchhhhHHHhhhhhhcchH
Confidence 4578999999987776555888888876
No 190
>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=76.65 E-value=1.1 Score=22.63 Aligned_cols=23 Identities=17% Similarity=0.436 Sum_probs=12.8
Q ss_pred cCccCCCcccccCC--c--EEeCCCCC
Q 040426 11 FCKFCGTMLRMESN--H--VVCSSCKF 33 (120)
Q Consensus 11 FCp~CgnlL~~~~~--~--~~C~~C~~ 33 (120)
=||.|++.+..... + +.|..|..
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred cCccCCCcceEeEecCCCCeECcCCcC
Confidence 38999998765432 2 88988864
No 191
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=76.47 E-value=2 Score=39.48 Aligned_cols=14 Identities=29% Similarity=0.940 Sum_probs=12.0
Q ss_pred EEeCCCCCeeeccc
Q 040426 26 VVCSSCKFKKNVQD 39 (120)
Q Consensus 26 ~~C~~C~~~~~~~~ 39 (120)
|.|+.|.|.+-+++
T Consensus 915 Y~Cp~Cky~Ef~~d 928 (1444)
T COG2176 915 YLCPECKYSEFIDD 928 (1444)
T ss_pred ccCCCCceeeeecC
Confidence 99999999887654
No 192
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=76.35 E-value=2.5 Score=31.93 Aligned_cols=31 Identities=23% Similarity=0.406 Sum_probs=24.4
Q ss_pred CCCCcccCccCCCcccccCCc-EEeCCCCCeeeccc
Q 040426 5 LGRDFLFCKFCGTMLRMESNH-VVCSSCKFKKNVQD 39 (120)
Q Consensus 5 ~~~~~~FCp~CgnlL~~~~~~-~~C~~C~~~~~~~~ 39 (120)
...+..=||.||. ...+ +.|..||+..+++.
T Consensus 305 ~~~tS~~C~~cg~----~~~r~~~C~~cg~~~~rD~ 336 (364)
T COG0675 305 PYYTSKTCPCCGH----LSGRLFKCPRCGFVHDRDV 336 (364)
T ss_pred CCCCcccccccCC----ccceeEECCCCCCeehhhH
Confidence 3556678999999 3334 99999999988766
No 193
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=76.26 E-value=1.9 Score=25.50 Aligned_cols=26 Identities=27% Similarity=0.605 Sum_probs=20.4
Q ss_pred CcccCccCCCcccccCCcEEeCCCCCeee
Q 040426 8 DFLFCKFCGTMLRMESNHVVCSSCKFKKN 36 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~~~~C~~C~~~~~ 36 (120)
.+..||.||.+..+- -+|..|||-..
T Consensus 26 ~~~~c~~cG~~~l~H---rvc~~cg~Y~g 51 (57)
T COG0333 26 TLSVCPNCGEYKLPH---RVCLKCGYYKG 51 (57)
T ss_pred cceeccCCCCcccCc---eEcCCCCCccC
Confidence 378999999886554 78999998654
No 194
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=76.19 E-value=1.2 Score=29.90 Aligned_cols=27 Identities=30% Similarity=0.529 Sum_probs=19.9
Q ss_pred CcccCccCCCcccccCCc-EEeCCCCCe
Q 040426 8 DFLFCKFCGTMLRMESNH-VVCSSCKFK 34 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~~-~~C~~C~~~ 34 (120)
...+|..||+.-.+.... +.|+.||-.
T Consensus 70 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 70 VELECKDCSHVFKPNALDYGVCEKCHSK 97 (117)
T ss_pred CEEEhhhCCCccccCCccCCcCcCCCCC
Confidence 356899999776666544 459999964
No 195
>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=76.11 E-value=1.9 Score=30.69 Aligned_cols=11 Identities=18% Similarity=0.987 Sum_probs=9.7
Q ss_pred EEeCCCCCeee
Q 040426 26 VVCSSCKFKKN 36 (120)
Q Consensus 26 ~~C~~C~~~~~ 36 (120)
+.|..|||...
T Consensus 29 f~C~~CGyr~~ 39 (163)
T TIGR00340 29 YICEKCGYRST 39 (163)
T ss_pred EECCCCCCchh
Confidence 99999999853
No 196
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=75.93 E-value=1.4 Score=29.43 Aligned_cols=26 Identities=15% Similarity=0.540 Sum_probs=18.4
Q ss_pred cccCccCCCcccccCCcEEeCCCCCe
Q 040426 9 FLFCKFCGTMLRMESNHVVCSSCKFK 34 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~~~C~~C~~~ 34 (120)
..+|+.||..-.+....+.|+.||-.
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 70 QAWCWDCSQVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred EEEcccCCCEEecCCcCccCcCCCCC
Confidence 45899999666655444779999843
No 197
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=75.71 E-value=2.2 Score=27.56 Aligned_cols=31 Identities=26% Similarity=0.558 Sum_probs=21.6
Q ss_pred CcccCccCCCcccccCC--c-EEeCCCCCeeeccc
Q 040426 8 DFLFCKFCGTMLRMESN--H-VVCSSCKFKKNVQD 39 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~--~-~~C~~C~~~~~~~~ 39 (120)
....||.||.. .++.. . |.|+.|++..---.
T Consensus 35 a~y~CpfCgk~-~vkR~a~GIW~C~~C~~~~AGGA 68 (90)
T PTZ00255 35 AKYFCPFCGKH-AVKRQAVGIWRCKGCKKTVAGGA 68 (90)
T ss_pred CCccCCCCCCC-ceeeeeeEEEEcCCCCCEEeCCc
Confidence 45689999854 33322 3 99999999876544
No 198
>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=75.47 E-value=0.71 Score=27.15 Aligned_cols=31 Identities=29% Similarity=0.530 Sum_probs=19.7
Q ss_pred cccccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426 77 KVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 77 ~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
-.+++||.|++...+|-..| |+ -.|..||..
T Consensus 5 Fm~VkCp~C~~~q~vFSha~--------t~-V~C~~Cg~~ 35 (55)
T PF01667_consen 5 FMDVKCPGCYNIQTVFSHAQ--------TV-VKCVVCGTV 35 (55)
T ss_dssp EEEEE-TTT-SEEEEETT-S--------S--EE-SSSTSE
T ss_pred EEEEECCCCCCeeEEEecCC--------eE-EEcccCCCE
Confidence 35789999999999986543 33 578888764
No 199
>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=75.15 E-value=1.5 Score=29.29 Aligned_cols=26 Identities=19% Similarity=0.305 Sum_probs=18.7
Q ss_pred cccCccCCCcccccCCcEEeCCCCCe
Q 040426 9 FLFCKFCGTMLRMESNHVVCSSCKFK 34 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~~~C~~C~~~ 34 (120)
..+|+.||..-.+....+.|+.||-.
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (115)
T TIGR00100 70 ECECEDCSEEVSPEIDLYRCPKCHGI 95 (115)
T ss_pred EEEcccCCCEEecCCcCccCcCCcCC
Confidence 45899999666555445889999854
No 200
>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=75.12 E-value=4.5 Score=21.77 Aligned_cols=9 Identities=44% Similarity=1.556 Sum_probs=4.8
Q ss_pred EcCCCCcee
Q 040426 109 ICPRCGHRC 117 (120)
Q Consensus 109 ~C~~C~~~w 117 (120)
.|..||..+
T Consensus 34 ~C~~CGE~~ 42 (46)
T TIGR03831 34 VCPQCGEEY 42 (46)
T ss_pred ccccCCCEe
Confidence 466666543
No 201
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=74.80 E-value=1.4 Score=30.59 Aligned_cols=21 Identities=33% Similarity=0.872 Sum_probs=16.8
Q ss_pred ccCCCCceEEEEcCCCCceec
Q 040426 98 RSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 98 RSADE~~T~fY~C~~C~~~w~ 118 (120)
|-..|....||.|++||.+|.
T Consensus 90 ~l~~e~~~~~Y~Cp~C~~~y~ 110 (147)
T smart00531 90 KLEDETNNAYYKCPNCQSKYT 110 (147)
T ss_pred HHhcccCCcEEECcCCCCEee
Confidence 444566678999999999986
No 202
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=74.07 E-value=2.6 Score=28.31 Aligned_cols=23 Identities=30% Similarity=0.761 Sum_probs=18.9
Q ss_pred CccCCCcccccCCcEEeCCCCCeee
Q 040426 12 CKFCGTMLRMESNHVVCSSCKFKKN 36 (120)
Q Consensus 12 Cp~CgnlL~~~~~~~~C~~C~~~~~ 36 (120)
||.||.-|... .+.|..|+....
T Consensus 1 CPvCg~~l~vt--~l~C~~C~t~i~ 23 (113)
T PF09862_consen 1 CPVCGGELVVT--RLKCPSCGTEIE 23 (113)
T ss_pred CCCCCCceEEE--EEEcCCCCCEEE
Confidence 99999887764 499999998754
No 203
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=73.74 E-value=3.9 Score=26.98 Aligned_cols=34 Identities=24% Similarity=0.585 Sum_probs=19.7
Q ss_pred ccccccCCCceEEE--EeecccCCCCceEEEEcCCCC
Q 040426 80 RACEKCQNPEMYYS--TRQTRSADEGQTTYYICPRCG 114 (120)
Q Consensus 80 ~~CpkCg~~ea~y~--~~Q~RSADE~~T~fY~C~~C~ 114 (120)
..||-||.+-..-- .+--++.|++. .+|.|+.|+
T Consensus 3 ~~CpYCg~~~~l~~~~~iYg~~~~~~~-~~y~C~~C~ 38 (102)
T PF11672_consen 3 IICPYCGGPAELVDGSEIYGHRYDDGP-YLYVCTPCD 38 (102)
T ss_pred cccCCCCCeeEEcccchhcCccCCCCc-eeEECCCCC
Confidence 46999998422100 00014555554 459999996
No 204
>PRK05582 DNA topoisomerase I; Validated
Probab=73.24 E-value=5.2 Score=34.27 Aligned_cols=30 Identities=30% Similarity=0.814 Sum_probs=17.6
Q ss_pred cccccccCCCceEEEEeecccCCCCceEEEEcCC---CCc
Q 040426 79 KRACEKCQNPEMYYSTRQTRSADEGQTTYYICPR---CGH 115 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~---C~~ 115 (120)
...||+||.. +. +|....| ..|+.|.+ |++
T Consensus 611 ~~~CP~C~~~-l~-----l~k~k~g-k~f~~Cs~~p~C~~ 643 (650)
T PRK05582 611 GVKCPKCGGQ-IV-----ERKSKKG-RKFYGCSRYPECDF 643 (650)
T ss_pred CCCCCCCCCc-eE-----EEcCCCC-ceeeccCCCCCCCc
Confidence 4679999864 21 2333223 25888954 864
No 205
>PRK03954 ribonuclease P protein component 4; Validated
Probab=73.12 E-value=2.6 Score=28.64 Aligned_cols=29 Identities=28% Similarity=0.583 Sum_probs=22.7
Q ss_pred cccCccCCCcccccCC-----------c--EEeCCCCCeeec
Q 040426 9 FLFCKFCGTMLRMESN-----------H--VVCSSCKFKKNV 37 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~-----------~--~~C~~C~~~~~~ 37 (120)
-.||..|+++|.|-.+ . +.|..||++.-.
T Consensus 64 R~~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~kR~ 105 (121)
T PRK03954 64 RRYCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHIMRY 105 (121)
T ss_pred HHHhhcCCCeeecCCceEEEEecCCcceEEEECccCCCEEee
Confidence 4599999999998532 1 789999998643
No 206
>PHA02998 RNA polymerase subunit; Provisional
Probab=72.63 E-value=3 Score=30.39 Aligned_cols=31 Identities=16% Similarity=0.394 Sum_probs=21.9
Q ss_pred ccCccCCCc------ccccCCc------EEeCCCCCeeecccc
Q 040426 10 LFCKFCGTM------LRMESNH------VVCSSCKFKKNVQDV 40 (120)
Q Consensus 10 ~FCp~Cgnl------L~~~~~~------~~C~~C~~~~~~~~~ 40 (120)
.=||.||+- |..++.. +.|..||+......+
T Consensus 144 v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkppkf 186 (195)
T PHA02998 144 TPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKPPKF 186 (195)
T ss_pred CCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCCccc
Confidence 569999973 3344321 999999999876553
No 207
>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=72.52 E-value=2.4 Score=33.15 Aligned_cols=38 Identities=21% Similarity=0.576 Sum_probs=25.9
Q ss_pred cccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 79 KRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
...||-||..-.. -.++....++| -+|..|.-|++.|+
T Consensus 184 ~~~CPvCGs~P~~-s~~~~~~~~~G-~RyL~CslC~teW~ 221 (305)
T TIGR01562 184 RTLCPACGSPPVA-SMVRQGGKETG-LRYLSCSLCATEWH 221 (305)
T ss_pred CCcCCCCCChhhh-hhhcccCCCCC-ceEEEcCCCCCccc
Confidence 4489999987421 11222233566 78899999999996
No 208
>PF08063 PADR1: PADR1 (NUC008) domain; InterPro: IPR012982 This domain is found in poly(ADP-ribose)-synthetases []. The function of this domain is unknown.; GO: 0003950 NAD+ ADP-ribosyltransferase activity, 0005634 nucleus; PDB: 2JVN_A 4DQY_E 2RIQ_A.
Probab=72.23 E-value=1.7 Score=25.42 Aligned_cols=22 Identities=18% Similarity=0.419 Sum_probs=14.6
Q ss_pred CcccCccCCC-cccccCCcEEeC
Q 040426 8 DFLFCKFCGT-MLRMESNHVVCS 29 (120)
Q Consensus 8 ~~~FCp~Cgn-lL~~~~~~~~C~ 29 (120)
.+.=||+|++ .|+.....|.|.
T Consensus 13 al~~Cp~C~~~~l~~~~~~Y~C~ 35 (55)
T PF08063_consen 13 ALEPCPKCKGGQLYFDGSGYKCT 35 (55)
T ss_dssp EE---SSSSE-EEEEETTEEEEE
T ss_pred CCCCCCCCCCCeEEecCCccEeC
Confidence 4556999999 677766678886
No 209
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=72.18 E-value=2 Score=22.60 Aligned_cols=23 Identities=26% Similarity=0.467 Sum_probs=13.6
Q ss_pred cccCccCCCcccccCCcEEeCCCCC
Q 040426 9 FLFCKFCGTMLRMESNHVVCSSCKF 33 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~~~C~~C~~ 33 (120)
..-|+.||.+..|+. ..|+.|+-
T Consensus 11 ~~rC~~Cg~~~~pPr--~~Cp~C~s 33 (37)
T PF12172_consen 11 GQRCRDCGRVQFPPR--PVCPHCGS 33 (37)
T ss_dssp EEE-TTT--EEES----SEETTTT-
T ss_pred EEEcCCCCCEecCCC--cCCCCcCc
Confidence 457999999987774 68888874
No 210
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=71.90 E-value=3.1 Score=22.71 Aligned_cols=29 Identities=28% Similarity=0.480 Sum_probs=22.8
Q ss_pred CcccCccCCCcccccC-CcEEeCCCCCeee
Q 040426 8 DFLFCKFCGTMLRMES-NHVVCSSCKFKKN 36 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~-~~~~C~~C~~~~~ 36 (120)
...||..|+..|.... ..+.|+.|++...
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~~C~~C~~~~H 39 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQGLRCSWCKVKCH 39 (50)
T ss_pred CCCChhhcchhhhccccceeEcCCCCCchh
Confidence 5779999999987542 3399999998654
No 211
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=71.84 E-value=2.7 Score=27.14 Aligned_cols=32 Identities=19% Similarity=0.252 Sum_probs=21.5
Q ss_pred CcccCccCCCcccccCC-c-EEeCCCCCeeeccc
Q 040426 8 DFLFCKFCGTMLRMESN-H-VVCSSCKFKKNVQD 39 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~-~-~~C~~C~~~~~~~~ 39 (120)
.-..||.||..=.-+.. . |.|+.|++..---.
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGA 68 (90)
T PRK03976 35 AKHVCPVCGRPKVKRVGTGIWECRKCGAKFAGGA 68 (90)
T ss_pred cCccCCCCCCCceEEEEEEEEEcCCCCCEEeCCc
Confidence 34689999754222222 2 99999999876544
No 212
>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=71.78 E-value=2.8 Score=19.26 Aligned_cols=11 Identities=45% Similarity=1.219 Sum_probs=8.8
Q ss_pred EEcCCCCceec
Q 040426 108 YICPRCGHRCQ 118 (120)
Q Consensus 108 Y~C~~C~~~w~ 118 (120)
|+|..|+..++
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 78888888765
No 213
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=71.31 E-value=2.8 Score=23.91 Aligned_cols=25 Identities=20% Similarity=0.547 Sum_probs=20.2
Q ss_pred CcccCccCCCcccccCCcEEeCCCCCe
Q 040426 8 DFLFCKFCGTMLRMESNHVVCSSCKFK 34 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~~~~C~~C~~~ 34 (120)
....|-.|+-.|.+... .||.|||.
T Consensus 13 ~k~ICrkC~ARnp~~A~--~CRKCg~~ 37 (48)
T PRK04136 13 NKKICMRCNARNPWRAT--KCRKCGYK 37 (48)
T ss_pred cccchhcccCCCCcccc--ccccCCCC
Confidence 45689999999888754 79999984
No 214
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=70.82 E-value=1.4 Score=30.81 Aligned_cols=32 Identities=28% Similarity=0.682 Sum_probs=27.2
Q ss_pred CcccCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426 8 DFLFCKFCGTMLRMESNH--VVCSSCKFKKNVQD 39 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~ 39 (120)
-++||..||.-..++++. ++|..|.....+-.
T Consensus 88 q~r~CARCGGrv~lrsNKv~wvcnlc~k~q~il~ 121 (169)
T KOG3799|consen 88 QTRFCARCGGRVSLRSNKVMWVCNLCRKQQEILT 121 (169)
T ss_pred hhhHHHhcCCeeeeccCceEEeccCCcHHHHHHH
Confidence 478999999999999886 99999999876543
No 215
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=70.79 E-value=1.8 Score=29.01 Aligned_cols=13 Identities=46% Similarity=1.053 Sum_probs=11.2
Q ss_pred cCccCCCcccccC
Q 040426 11 FCKFCGTMLRMES 23 (120)
Q Consensus 11 FCp~CgnlL~~~~ 23 (120)
+||.||.||..+.
T Consensus 76 yCP~Cgt~levE~ 88 (112)
T PF08882_consen 76 YCPGCGTQLEVEA 88 (112)
T ss_pred ECCCCcceeEEcc
Confidence 8999999998764
No 216
>PRK05978 hypothetical protein; Provisional
Probab=70.74 E-value=2 Score=30.25 Aligned_cols=32 Identities=16% Similarity=0.479 Sum_probs=22.1
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
...+||+||..+++-- -.++-=.|..||..+.
T Consensus 32 l~grCP~CG~G~LF~g---------~Lkv~~~C~~CG~~~~ 63 (148)
T PRK05978 32 FRGRCPACGEGKLFRA---------FLKPVDHCAACGEDFT 63 (148)
T ss_pred HcCcCCCCCCCccccc---------ccccCCCccccCCccc
Confidence 4568999999988621 1334456888987664
No 217
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=70.71 E-value=3.3 Score=26.63 Aligned_cols=34 Identities=18% Similarity=0.161 Sum_probs=26.6
Q ss_pred CCCCCcccCccCCCcccccCCc---------EEeCCCCCeeec
Q 040426 4 PLGRDFLFCKFCGTMLRMESNH---------VVCSSCKFKKNV 37 (120)
Q Consensus 4 ~~~~~~~FCp~CgnlL~~~~~~---------~~C~~C~~~~~~ 37 (120)
+.....-+|+.|+..|...+.- -.|+.|+...+.
T Consensus 28 ~i~~~rS~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 28 SIIFPRSHCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAPIPP 70 (92)
T ss_pred CccCCCCcCcCCCCcCcccccchHHHHHHhCCCCcccCCCCCh
Confidence 4455667999999999988752 789999976654
No 218
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=70.47 E-value=2.9 Score=22.61 Aligned_cols=30 Identities=23% Similarity=0.377 Sum_probs=23.3
Q ss_pred CCcccCccCCCcccccCCcEEeCCCCCeee
Q 040426 7 RDFLFCKFCGTMLRMESNHVVCSSCKFKKN 36 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~~~~~~~C~~C~~~~~ 36 (120)
..+.||-.|+..|......+.|+.|++...
T Consensus 9 ~~~~~C~~C~~~i~~~~~~~~C~~C~~~~H 38 (49)
T smart00109 9 KKPTKCCVCRKSIWGSFQGLRCSWCKVKCH 38 (49)
T ss_pred CCCCCccccccccCcCCCCcCCCCCCchHH
Confidence 457799999999876443499999988653
No 219
>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=70.37 E-value=3.5 Score=18.56 Aligned_cols=11 Identities=36% Similarity=1.183 Sum_probs=6.9
Q ss_pred EEcCCCCceec
Q 040426 108 YICPRCGHRCQ 118 (120)
Q Consensus 108 Y~C~~C~~~w~ 118 (120)
|.|..|+..++
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 67888888765
No 220
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=70.36 E-value=2.3 Score=28.41 Aligned_cols=26 Identities=15% Similarity=0.499 Sum_probs=18.1
Q ss_pred cccCccCCCcccccCCc-EEeCCCCCe
Q 040426 9 FLFCKFCGTMLRMESNH-VVCSSCKFK 34 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~-~~C~~C~~~ 34 (120)
..+|+.||..-...... +.|+.||-.
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 70 ECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred EEEcccCCCeeecCCccCCcCcCcCCC
Confidence 45899999765554444 779999853
No 221
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=70.12 E-value=2.6 Score=30.19 Aligned_cols=23 Identities=26% Similarity=0.574 Sum_probs=12.0
Q ss_pred cCccCCCcccccCCcEEeCCCCCe
Q 040426 11 FCKFCGTMLRMESNHVVCSSCKFK 34 (120)
Q Consensus 11 FCp~CgnlL~~~~~~~~C~~C~~~ 34 (120)
-||.||.+..- +..-+|+.||..
T Consensus 136 vC~vCGy~~~g-e~P~~CPiCga~ 158 (166)
T COG1592 136 VCPVCGYTHEG-EAPEVCPICGAP 158 (166)
T ss_pred EcCCCCCcccC-CCCCcCCCCCCh
Confidence 45666655444 333556666543
No 222
>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=69.09 E-value=3.2 Score=29.23 Aligned_cols=19 Identities=26% Similarity=0.548 Sum_probs=15.9
Q ss_pred CCCCceEEEEcCCCCceec
Q 040426 100 ADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 100 ADE~~T~fY~C~~C~~~w~ 118 (120)
..|.-..||.|++|+.+|+
T Consensus 102 ~~e~~~~~Y~Cp~c~~r~t 120 (158)
T TIGR00373 102 EFETNNMFFICPNMCVRFT 120 (158)
T ss_pred hhccCCCeEECCCCCcEee
Confidence 3566779999999999986
No 223
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=68.87 E-value=3.5 Score=32.97 Aligned_cols=23 Identities=22% Similarity=0.394 Sum_probs=17.1
Q ss_pred cccccccCCCceEEE--EeecccCC
Q 040426 79 KRACEKCQNPEMYYS--TRQTRSAD 101 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~--~~Q~RSAD 101 (120)
...||.|+.--..|| .+|+|+.-
T Consensus 129 ~~~Cp~C~r~~~~y~eAivQvR~~~ 153 (355)
T COG1499 129 RTLCPRCSRFTGGYYEAIVQVRAKG 153 (355)
T ss_pred EeEChhhhccccceeEEEEEEEecc
Confidence 458999999655554 67999864
No 224
>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=67.95 E-value=2 Score=24.63 Aligned_cols=14 Identities=21% Similarity=0.539 Sum_probs=8.8
Q ss_pred CCCcccCccCCCcc
Q 040426 6 GRDFLFCKFCGTML 19 (120)
Q Consensus 6 ~~~~~FCp~CgnlL 19 (120)
...-.+||.|||=-
T Consensus 10 ~~kY~~Cp~CGN~~ 23 (49)
T PF12677_consen 10 SNKYCKCPKCGNDK 23 (49)
T ss_pred hhhhccCcccCCcE
Confidence 33445788888753
No 225
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=67.74 E-value=4.2 Score=27.80 Aligned_cols=39 Identities=18% Similarity=0.439 Sum_probs=26.4
Q ss_pred ccccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426 76 SKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119 (120)
Q Consensus 76 ~~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~ 119 (120)
......||.|+..- +.---.. ++. -.=|+|..|+..|..
T Consensus 27 ~~~~~~cP~C~s~~-~~k~g~~-~~~---~qRyrC~~C~~tf~~ 65 (129)
T COG3677 27 QITKVNCPRCKSSN-VVKIGGI-RRG---HQRYKCKSCGSTFTV 65 (129)
T ss_pred hcccCcCCCCCccc-eeeECCc-ccc---ccccccCCcCcceee
Confidence 35678899999887 4433332 222 345999999998863
No 226
>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=67.64 E-value=2.9 Score=25.44 Aligned_cols=35 Identities=23% Similarity=0.483 Sum_probs=24.0
Q ss_pred cccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426 79 KRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
.-.|..||++.+.-+.. .|=+-=+|+-+|..|+.+
T Consensus 4 ~FTC~~C~~Rs~~~~sk---~aY~~GvViv~C~gC~~~ 38 (66)
T PF05180_consen 4 TFTCNKCGTRSAKMFSK---QAYHKGVVIVQCPGCKNR 38 (66)
T ss_dssp EEEETTTTEEEEEEEEH---HHHHTSEEEEE-TTS--E
T ss_pred EEEcCCCCCccceeeCH---HHHhCCeEEEECCCCcce
Confidence 34699999988877763 455566799999999754
No 227
>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=67.63 E-value=14 Score=30.75 Aligned_cols=31 Identities=19% Similarity=0.573 Sum_probs=22.7
Q ss_pred CCcccCccCCCcccccCC-----cEEeCCCCCeeec
Q 040426 7 RDFLFCKFCGTMLRMESN-----HVVCSSCKFKKNV 37 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~~~~-----~~~C~~C~~~~~~ 37 (120)
..+.||..|..+--+.-. .++|++|-...+.
T Consensus 3 ~~L~fC~~C~~irc~~c~~~Ei~~~yCp~CL~~~p~ 38 (483)
T PF05502_consen 3 EELYFCEHCHKIRCPRCVSEEIDSYYCPNCLFEVPS 38 (483)
T ss_pred ccceecccccccCChhhcccccceeECccccccCCh
Confidence 457899999988665532 2999999876654
No 228
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=67.20 E-value=3.5 Score=28.12 Aligned_cols=18 Identities=28% Similarity=0.479 Sum_probs=13.9
Q ss_pred CCCcccCccCCCcccccC
Q 040426 6 GRDFLFCKFCGTMLRMES 23 (120)
Q Consensus 6 ~~~~~FCp~CgnlL~~~~ 23 (120)
.....||+.||.-|+-+.
T Consensus 66 ~~~r~FC~~CGs~l~~~~ 83 (133)
T COG3791 66 SAGRGFCPTCGSPLFWRG 83 (133)
T ss_pred CCCCeecccCCCceEEec
Confidence 344569999999998774
No 229
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=66.40 E-value=3.8 Score=30.17 Aligned_cols=28 Identities=21% Similarity=0.586 Sum_probs=18.9
Q ss_pred ccCccCCCc------ccccCCc--EEeCCCCCeeec
Q 040426 10 LFCKFCGTM------LRMESNH--VVCSSCKFKKNV 37 (120)
Q Consensus 10 ~FCp~Cgnl------L~~~~~~--~~C~~C~~~~~~ 37 (120)
.-||.||.. |.-+... +.|..||+.+++
T Consensus 7 ~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 7 IECPSCGSEEVSHEVIKERGREPLVRCEECGTVHPA 42 (201)
T ss_pred EECCCCCcchhhHHHHHhcCCceEEEccCCCcEeec
Confidence 369999922 2222222 999999999955
No 230
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=66.18 E-value=3.7 Score=29.42 Aligned_cols=28 Identities=25% Similarity=0.355 Sum_probs=20.5
Q ss_pred cccCccCCCcccccCC----------------c-EEeCCCCCeee
Q 040426 9 FLFCKFCGTMLRMESN----------------H-VVCSSCKFKKN 36 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~----------------~-~~C~~C~~~~~ 36 (120)
..=||+||.-|..-.. . +.|..||..+=
T Consensus 97 ~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW 141 (165)
T COG1656 97 FSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYW 141 (165)
T ss_pred cccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccccc
Confidence 4459999999865321 1 77999999864
No 231
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=65.56 E-value=4.2 Score=29.29 Aligned_cols=19 Identities=26% Similarity=0.850 Sum_probs=15.7
Q ss_pred CCCCceEEEEcCCCCceec
Q 040426 100 ADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 100 ADE~~T~fY~C~~C~~~w~ 118 (120)
..|....||.|++|+.+|+
T Consensus 110 ~~e~~~~~Y~Cp~C~~ryt 128 (178)
T PRK06266 110 EEEENNMFFFCPNCHIRFT 128 (178)
T ss_pred hhccCCCEEECCCCCcEEe
Confidence 3555678999999999986
No 232
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=65.33 E-value=4.2 Score=23.88 Aligned_cols=27 Identities=19% Similarity=0.541 Sum_probs=19.8
Q ss_pred cCccCCCcccccCCcEEeCCCCCeeecc
Q 040426 11 FCKFCGTMLRMESNHVVCSSCKFKKNVQ 38 (120)
Q Consensus 11 FCp~CgnlL~~~~~~~~C~~C~~~~~~~ 38 (120)
+||.|+.-+ +....|.|+.||....-+
T Consensus 1 ~Cpv~~~~~-~~~v~~~Cp~cGipthcS 27 (55)
T PF13824_consen 1 LCPVCKKDL-PAHVNFECPDCGIPTHCS 27 (55)
T ss_pred CCCCCcccc-ccccCCcCCCCCCcCccC
Confidence 699999876 333449999999876443
No 233
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=65.26 E-value=2.1 Score=26.32 Aligned_cols=15 Identities=33% Similarity=0.662 Sum_probs=10.0
Q ss_pred CCcccCccCCCcccc
Q 040426 7 RDFLFCKFCGTMLRM 21 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~ 21 (120)
..-.||+.||+-|..
T Consensus 46 ~~r~FC~~CGs~l~~ 60 (92)
T PF04828_consen 46 VERYFCPTCGSPLFS 60 (92)
T ss_dssp CEEEEETTT--EEEE
T ss_pred CcCcccCCCCCeeec
Confidence 345699999999885
No 234
>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=65.21 E-value=4.2 Score=22.85 Aligned_cols=11 Identities=55% Similarity=1.262 Sum_probs=8.4
Q ss_pred EEEcCCCCcee
Q 040426 107 YYICPRCGHRC 117 (120)
Q Consensus 107 fY~C~~C~~~w 117 (120)
=|+|.+||+.+
T Consensus 5 ey~C~~Cg~~f 15 (52)
T TIGR02605 5 EYRCTACGHRF 15 (52)
T ss_pred EEEeCCCCCEe
Confidence 47888888855
No 235
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=64.98 E-value=3.6 Score=22.46 Aligned_cols=14 Identities=36% Similarity=0.619 Sum_probs=10.0
Q ss_pred cccCccCCCcccccC
Q 040426 9 FLFCKFCGTMLRMES 23 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~ 23 (120)
..=|+.|| |+|...
T Consensus 13 ~~~C~~Cg-M~Y~~~ 26 (41)
T PF13878_consen 13 ATTCPTCG-MLYSPG 26 (41)
T ss_pred CcCCCCCC-CEECCC
Confidence 56899999 556553
No 236
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.25 E-value=4.2 Score=25.73 Aligned_cols=28 Identities=29% Similarity=0.592 Sum_probs=21.9
Q ss_pred cccCccCCCcccccCCc----EEeCCCCCeee
Q 040426 9 FLFCKFCGTMLRMESNH----VVCSSCKFKKN 36 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~----~~C~~C~~~~~ 36 (120)
|+.||.||--|.+..-. -.|+.|.=+.-
T Consensus 1 ~llCP~C~v~l~~~~rs~vEiD~CPrCrGVWL 32 (88)
T COG3809 1 MLLCPICGVELVMSVRSGVEIDYCPRCRGVWL 32 (88)
T ss_pred CcccCcCCceeeeeeecCceeeeCCccccEee
Confidence 46799999998877532 78999988764
No 237
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=64.01 E-value=4.7 Score=28.13 Aligned_cols=26 Identities=19% Similarity=0.382 Sum_probs=21.4
Q ss_pred ccCccCCCcccccC-CcEEeCCCCCee
Q 040426 10 LFCKFCGTMLRMES-NHVVCSSCKFKK 35 (120)
Q Consensus 10 ~FCp~CgnlL~~~~-~~~~C~~C~~~~ 35 (120)
.-||.|+.-+.... +.|.|..|+...
T Consensus 35 ~aC~~C~kkv~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 35 PACPGCNKKVVEEGNGTYRCEKCNKSV 61 (166)
T ss_pred ccccccCcccEeCCCCcEECCCCCCcC
Confidence 36999999988776 349999999874
No 238
>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=63.70 E-value=2.1 Score=22.86 Aligned_cols=23 Identities=35% Similarity=0.801 Sum_probs=10.7
Q ss_pred cCccCCCcccccCC----cEEeCCCCC
Q 040426 11 FCKFCGTMLRMESN----HVVCSSCKF 33 (120)
Q Consensus 11 FCp~CgnlL~~~~~----~~~C~~C~~ 33 (120)
.||.||.+....-+ .-.|..||-
T Consensus 3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp EETTTTEEEETTTB--SSTTBCTTTTE
T ss_pred CcCCCCCccccccCCCCCCCccCCCCC
Confidence 45556555433222 155555553
No 239
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=63.43 E-value=3.1 Score=28.89 Aligned_cols=15 Identities=27% Similarity=0.773 Sum_probs=12.6
Q ss_pred ccCccCCCcccccCC
Q 040426 10 LFCKFCGTMLRMESN 24 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~ 24 (120)
-|||+||.|+..+..
T Consensus 121 ficpecg~l~eveaa 135 (165)
T COG4647 121 FICPECGILHEVEAA 135 (165)
T ss_pred hhCccccceeeeccC
Confidence 499999999988754
No 240
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=63.27 E-value=7 Score=30.72 Aligned_cols=37 Identities=19% Similarity=0.429 Sum_probs=26.0
Q ss_pred ccccccccCCCc-eEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 78 VKRACEKCQNPE-MYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 78 ~~~~CpkCg~~e-a~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
....||-||..- +... .+ ..++|. +|..|.-|++.|+
T Consensus 186 ~~~~CPvCGs~P~~s~v--~~-~~~~G~-RyL~CslC~teW~ 223 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVV--QI-GTTQGL-RYLHCNLCESEWH 223 (309)
T ss_pred CCCCCCCCCCcchhhee--ec-cCCCCc-eEEEcCCCCCccc
Confidence 356899999874 3322 22 234554 8999999999996
No 241
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=63.15 E-value=6.3 Score=26.03 Aligned_cols=29 Identities=21% Similarity=0.464 Sum_probs=21.9
Q ss_pred cCccCCCcccccC-----Cc---EEeCCCCCeeeccc
Q 040426 11 FCKFCGTMLRMES-----NH---VVCSSCKFKKNVQD 39 (120)
Q Consensus 11 FCp~CgnlL~~~~-----~~---~~C~~C~~~~~~~~ 39 (120)
=||.||......- ++ +.|.+||-....+.
T Consensus 24 tCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev 60 (104)
T COG4888 24 TCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEV 60 (104)
T ss_pred ecCccCCeeeeEEEEEecCceeEEEcccCcceEEEec
Confidence 5999999876631 22 99999999876554
No 242
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=62.73 E-value=5.4 Score=27.24 Aligned_cols=25 Identities=16% Similarity=0.450 Sum_probs=18.1
Q ss_pred cCc--cCCCcccccCCc-EEeCCCCCee
Q 040426 11 FCK--FCGTMLRMESNH-VVCSSCKFKK 35 (120)
Q Consensus 11 FCp--~CgnlL~~~~~~-~~C~~C~~~~ 35 (120)
=|| .|+.-+....++ |.|..|+...
T Consensus 20 aC~~~~C~kKv~~~~~~~y~C~~C~~~~ 47 (146)
T PF08646_consen 20 ACPNEKCNKKVTENGDGSYRCEKCNKTV 47 (146)
T ss_dssp E-TSTTTS-B-EEETTTEEEETTTTEEE
T ss_pred CCCCccCCCEeecCCCcEEECCCCCCcC
Confidence 499 999988877554 9999999874
No 243
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=62.69 E-value=2.7 Score=22.87 Aligned_cols=13 Identities=31% Similarity=1.035 Sum_probs=6.5
Q ss_pred CcccCccCCCccc
Q 040426 8 DFLFCKFCGTMLR 20 (120)
Q Consensus 8 ~~~FCp~CgnlL~ 20 (120)
.+.||+.|||+=.
T Consensus 16 ~i~~C~~C~nlse 28 (41)
T PF02132_consen 16 NIKFCSICGNLSE 28 (41)
T ss_dssp H-EE-SSS--EES
T ss_pred cCCccCCCCCcCC
Confidence 4679999998743
No 244
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=62.22 E-value=11 Score=31.45 Aligned_cols=37 Identities=27% Similarity=0.461 Sum_probs=23.5
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
..-.||+||.---+-.. .--.+.-||.|.| +|||...
T Consensus 174 ~~pic~~cg~~~~~~~~---~~d~~~~~v~y~~-~cG~~~~ 210 (510)
T PRK00750 174 FLPICPKCGKVLTTPVI---SYDAEAGTVTYDC-ECGHEGE 210 (510)
T ss_pred eeeeCCCCCccceEEEE---EEeCCCCEEEEEc-CCCCEEE
Confidence 45679999997432221 1123445899998 5999753
No 245
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=61.46 E-value=5.5 Score=23.67 Aligned_cols=24 Identities=17% Similarity=0.031 Sum_probs=19.0
Q ss_pred cccCccCCCcccccCCcEEeCCCCCeee
Q 040426 9 FLFCKFCGTMLRMESNHVVCSSCKFKKN 36 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~~~C~~C~~~~~ 36 (120)
+..||.||.+..|- -+|. |||...
T Consensus 27 ~~~c~~cg~~~~pH---~vc~-cG~Y~g 50 (60)
T PRK01110 27 LSVDKTTGEYHLPH---HVSP-KGYYKG 50 (60)
T ss_pred eeEcCCCCceeccc---eecC-CcccCC
Confidence 66899999887765 6699 997654
No 246
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=61.30 E-value=9.2 Score=29.21 Aligned_cols=29 Identities=21% Similarity=0.553 Sum_probs=19.0
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCC
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCG 114 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~ 114 (120)
...+||+||..-..-.+ +.-.-|-|..|.
T Consensus 243 ~g~pCprCG~~I~~~~~--------~gR~t~~CP~CQ 271 (272)
T PRK14810 243 TGEPCLNCKTPIRRVVV--------AGRSSHYCPHCQ 271 (272)
T ss_pred CCCcCCCCCCeeEEEEE--------CCCccEECcCCc
Confidence 35799999976543332 224448899996
No 247
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=61.21 E-value=4.7 Score=28.24 Aligned_cols=32 Identities=22% Similarity=0.584 Sum_probs=26.3
Q ss_pred CCCCcccCccCCCcccccCCc--EEeCCCCCeee
Q 040426 5 LGRDFLFCKFCGTMLRMESNH--VVCSSCKFKKN 36 (120)
Q Consensus 5 ~~~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~ 36 (120)
.+.|...|-.||..+.+.... -.|+.||...-
T Consensus 108 ~g~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F 141 (146)
T PF07295_consen 108 VGPGTLVCENCGHEVELTHPERLPPCPKCGHTEF 141 (146)
T ss_pred ecCceEecccCCCEEEecCCCcCCCCCCCCCCee
Confidence 456788999999999887544 89999998764
No 248
>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=61.12 E-value=2.3 Score=34.04 Aligned_cols=40 Identities=18% Similarity=0.472 Sum_probs=21.1
Q ss_pred cccCccCCCcccccC-------Cc--EEeCCCCCeeecccccc-ceEEEe
Q 040426 9 FLFCKFCGTMLRMES-------NH--VVCSSCKFKKNVQDVAD-REISYA 48 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~-------~~--~~C~~C~~~~~~~~~~~-~~~~~~ 48 (120)
+.+|++||.++...- .. |+|..||+...++-... .++..+
T Consensus 174 ~piC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~~~i~~g~gKL~Wk 223 (360)
T PF01921_consen 174 LPICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGEVDITGGNGKLQWK 223 (360)
T ss_dssp EEEETTTEE--EEEEEEE--SSSEEEEE--TTS---EEETTTT-EEE-HH
T ss_pred eeeccccCCcccceeeEeecCCCEEEEEecCCCCEEEEecCCCcccccCC
Confidence 458999999876542 12 99999999987766432 344444
No 249
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=61.01 E-value=6.2 Score=31.98 Aligned_cols=27 Identities=15% Similarity=0.616 Sum_probs=16.5
Q ss_pred cccCccCCCcccccC---C-cEEeCCCCCee
Q 040426 9 FLFCKFCGTMLRMES---N-HVVCSSCKFKK 35 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~---~-~~~C~~C~~~~ 35 (120)
..=||+|+-+...+. + ...|++||+.-
T Consensus 13 ~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 13 HILCSQCDMLVALPRIESGQKAACPRCGTTL 43 (403)
T ss_pred eeeCCCCCCcccccCCCCCCeeECCCCCCCC
Confidence 345888886664332 1 27788887764
No 250
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 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 presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=60.90 E-value=19 Score=19.75 Aligned_cols=29 Identities=21% Similarity=0.600 Sum_probs=17.8
Q ss_pred cccccCCCceEEEEeecccCCCCceEEEEcCC
Q 040426 81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPR 112 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~ 112 (120)
.|+ || ..++-+++. +..+.+=-+||.|..
T Consensus 2 ~C~-Cg-~~~~~~~s~-k~~~N~GR~Fy~C~~ 30 (45)
T PF06839_consen 2 KCP-CG-EPAVRRTSK-KTGPNPGRRFYKCPN 30 (45)
T ss_pred CCC-CC-CEeEEEEEe-CCCCCCCCcceECCC
Confidence 366 66 444444432 256677779999984
No 251
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=60.87 E-value=8.3 Score=28.45 Aligned_cols=15 Identities=20% Similarity=0.561 Sum_probs=12.5
Q ss_pred EEeCCCCCeeecccc
Q 040426 26 VVCSSCKFKKNVQDV 40 (120)
Q Consensus 26 ~~C~~C~~~~~~~~~ 40 (120)
+.|+.|+.....+..
T Consensus 6 ~~CPvC~~~F~~~~v 20 (214)
T PF09986_consen 6 ITCPVCGKEFKTKKV 20 (214)
T ss_pred eECCCCCCeeeeeEE
Confidence 899999999887653
No 252
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=59.99 E-value=8.2 Score=25.63 Aligned_cols=44 Identities=20% Similarity=0.428 Sum_probs=28.3
Q ss_pred cccc-c-ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 73 TQLS-K-VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 73 ~t~~-~-~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
-++| . ....|++|...-.-....-.|...+- +..+|..||+.-+
T Consensus 48 v~lp~~iKR~~CkkC~t~Lvpg~n~rvR~~~~~--v~vtC~~CG~~~R 93 (105)
T COG2023 48 VRLPREIKRTICKKCYTPLVPGKNARVRLRKGR--VVVTCLECGTIRR 93 (105)
T ss_pred cccCHHHHHHhccccCcccccCcceEEEEcCCe--EEEEecCCCcEEE
Confidence 4555 2 34579999995444434444544444 8899999998643
No 253
>COG1384 LysS Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]
Probab=59.63 E-value=8 Score=32.45 Aligned_cols=33 Identities=33% Similarity=0.580 Sum_probs=22.3
Q ss_pred ccccccccCC-CceEEEEeecccCCCCceEEEEcCCCCce
Q 040426 78 VKRACEKCQN-PEMYYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 78 ~~~~CpkCg~-~ea~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
....||+||. ....-. +-|.+-|+-|+| .|||.
T Consensus 170 ~~piC~kcGri~~t~v~-----~~d~~~~v~Y~C-e~Gh~ 203 (521)
T COG1384 170 FMPICEKCGRILTTPVI-----EWDGEGTVEYRC-ECGHE 203 (521)
T ss_pred ccccccccCCcceeEEE-----EecCCceEEEEe-cCCcc
Confidence 4567999999 544221 234447999999 58874
No 254
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=59.24 E-value=6.6 Score=20.25 Aligned_cols=13 Identities=31% Similarity=0.754 Sum_probs=10.3
Q ss_pred eEEEEcCCCCcee
Q 040426 105 TTYYICPRCGHRC 117 (120)
Q Consensus 105 T~fY~C~~C~~~w 117 (120)
--||+|..||+.-
T Consensus 5 ~~~ykC~~Cgniv 17 (34)
T TIGR00319 5 GQVYKCEVCGNIV 17 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 3499999999753
No 255
>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=59.14 E-value=13 Score=20.51 Aligned_cols=25 Identities=24% Similarity=0.720 Sum_probs=17.7
Q ss_pred cCccCCCcccccCCc-EEeCCCCCeeec
Q 040426 11 FCKFCGTMLRMESNH-VVCSSCKFKKNV 37 (120)
Q Consensus 11 FCp~CgnlL~~~~~~-~~C~~C~~~~~~ 37 (120)
||+.||. ....+. +.|..|+.....
T Consensus 1 ~C~vC~~--~~~~~~~i~C~~C~~~~H~ 26 (51)
T PF00628_consen 1 YCPVCGQ--SDDDGDMIQCDSCNRWYHQ 26 (51)
T ss_dssp EBTTTTS--SCTTSSEEEBSTTSCEEET
T ss_pred eCcCCCC--cCCCCCeEEcCCCChhhCc
Confidence 6899998 222222 999999977664
No 256
>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=58.95 E-value=6.8 Score=18.94 Aligned_cols=11 Identities=45% Similarity=1.237 Sum_probs=7.5
Q ss_pred EEcCCCCceec
Q 040426 108 YICPRCGHRCQ 118 (120)
Q Consensus 108 Y~C~~C~~~w~ 118 (120)
|.|..|+.++.
T Consensus 15 ~~C~~C~k~F~ 25 (26)
T PF13465_consen 15 YKCPYCGKSFS 25 (26)
T ss_dssp EEESSSSEEES
T ss_pred CCCCCCcCeeC
Confidence 77777776654
No 257
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=58.81 E-value=4.1 Score=23.36 Aligned_cols=35 Identities=26% Similarity=0.592 Sum_probs=24.3
Q ss_pred cccccccCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426 79 KRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~ 119 (120)
...|..||-.+.-.| |....|. -..|-.||-.|+.
T Consensus 3 ~~~C~~C~~~~T~~W----R~g~~g~--~~LCnaCgl~~~k 37 (52)
T smart00401 3 GRSCSNCGTTETPLW----RRGPSGN--KTLCNACGLYYKK 37 (52)
T ss_pred CCCcCCCCCCCCCcc----ccCCCCC--CcEeecccHHHHH
Confidence 456999998777544 7777776 2557788877753
No 258
>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=58.73 E-value=6.7 Score=20.25 Aligned_cols=12 Identities=33% Similarity=0.833 Sum_probs=9.8
Q ss_pred EEEEcCCCCcee
Q 040426 106 TYYICPRCGHRC 117 (120)
Q Consensus 106 ~fY~C~~C~~~w 117 (120)
-||+|..||+.-
T Consensus 3 ~~ykC~~CGniv 14 (34)
T cd00974 3 EVYKCEICGNIV 14 (34)
T ss_pred cEEEcCCCCcEE
Confidence 489999999753
No 259
>PLN03086 PRLI-interacting factor K; Provisional
Probab=58.50 E-value=5.9 Score=33.63 Aligned_cols=21 Identities=38% Similarity=0.806 Sum_probs=10.7
Q ss_pred CCCcccccCCc--EEeCCCCCee
Q 040426 15 CGTMLRMESNH--VVCSSCKFKK 35 (120)
Q Consensus 15 CgnlL~~~~~~--~~C~~C~~~~ 35 (120)
||.++...+-. +.|..|+...
T Consensus 441 Cg~v~~r~el~~H~~C~~Cgk~f 463 (567)
T PLN03086 441 CGIVLRVEEAKNHVHCEKCGQAF 463 (567)
T ss_pred ccceeeccccccCccCCCCCCcc
Confidence 66555333221 6666666544
No 260
>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=58.25 E-value=9.6 Score=20.50 Aligned_cols=30 Identities=20% Similarity=0.432 Sum_probs=16.1
Q ss_pred cccCccCCCcccccC----C-c-EEeCCCCCeeecc
Q 040426 9 FLFCKFCGTMLRMES----N-H-VVCSSCKFKKNVQ 38 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~----~-~-~~C~~C~~~~~~~ 38 (120)
+.-|..|+..|-|-. + + +.|.-|+...++.
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~lp 37 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGTKNPLP 37 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--EEE--
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCCcCCCC
Confidence 557999999997653 2 2 9999999987654
No 261
>KOG4537 consensus Zn-ribbon-containing protein implicated in mitosis [Cell cycle control, cell division, chromosome partitioning; Defense mechanisms]
Probab=58.12 E-value=2.9 Score=29.74 Aligned_cols=27 Identities=22% Similarity=0.580 Sum_probs=22.0
Q ss_pred ccCccCCCcccccCCc-EEeCCCCCeee
Q 040426 10 LFCKFCGTMLRMESNH-VVCSSCKFKKN 36 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~-~~C~~C~~~~~ 36 (120)
..||.|+.+|.-..++ ..|-.|.-..+
T Consensus 41 e~Cp~C~~Ilm~dr~~~~~CVsC~~~~d 68 (178)
T KOG4537|consen 41 EICPKCEKILMRDRDNPMFCVSCINDLD 68 (178)
T ss_pred hhcchHHHHHHhhccCceEEEeeecccc
Confidence 3899999998877766 99999977653
No 262
>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=58.08 E-value=1.8 Score=28.76 Aligned_cols=26 Identities=19% Similarity=0.508 Sum_probs=15.0
Q ss_pred ccCccCCCcccccCCcEEeCCCCCee
Q 040426 10 LFCKFCGTMLRMESNHVVCSSCKFKK 35 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~~~C~~C~~~~ 35 (120)
.+|..||.--.+....+.|+.||...
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEFDFSCPRCGSPD 96 (113)
T ss_dssp EEETTTS-EEECHHCCHH-SSSSSS-
T ss_pred EECCCCCCEEecCCCCCCCcCCcCCC
Confidence 46777776666655556677777653
No 263
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=58.02 E-value=11 Score=28.65 Aligned_cols=31 Identities=23% Similarity=0.543 Sum_probs=20.8
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
...+||.||..-..-...+ |+ -|-|..|...
T Consensus 234 ~g~pC~~Cg~~I~~~~~~g-R~-------ty~Cp~CQ~~ 264 (269)
T PRK14811 234 EGQPCPRCGTPIEKIVVGG-RG-------THFCPQCQPL 264 (269)
T ss_pred CcCCCCcCCCeeEEEEECC-CC-------cEECCCCcCC
Confidence 3568999998855444322 33 3889999754
No 264
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=57.97 E-value=5.4 Score=26.46 Aligned_cols=20 Identities=30% Similarity=0.698 Sum_probs=15.8
Q ss_pred cccccCCCceEEEEeecccC
Q 040426 81 ACEKCQNPEMYYSTRQTRSA 100 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q~RSA 100 (120)
-||+||.+.-.|.-.-.|.|
T Consensus 22 GCp~CG~nkF~yv~~e~rpa 41 (112)
T COG3364 22 GCPKCGCNKFLYVPEEKRPA 41 (112)
T ss_pred cCccccchheEecccccccc
Confidence 49999999988876666555
No 265
>PRK12366 replication factor A; Reviewed
Probab=57.80 E-value=6.2 Score=33.81 Aligned_cols=26 Identities=15% Similarity=0.452 Sum_probs=20.5
Q ss_pred ccCccCCCcccccCCcEEeCCCCCee
Q 040426 10 LFCKFCGTMLRMESNHVVCSSCKFKK 35 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~~~C~~C~~~~ 35 (120)
.=||.|+.-|.-..+.|.|..|+...
T Consensus 533 ~aCp~CnkKv~~~~g~~~C~~c~~~~ 558 (637)
T PRK12366 533 YLCPNCRKRVEEVDGEYICEFCGEVE 558 (637)
T ss_pred ecccccCeEeEcCCCcEECCCCCCCC
Confidence 46999999986533349999999873
No 266
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=57.35 E-value=8.4 Score=25.72 Aligned_cols=29 Identities=21% Similarity=0.548 Sum_probs=23.7
Q ss_pred CcccCccCCCcccccCCc-EEeCCCCCeee
Q 040426 8 DFLFCKFCGTMLRMESNH-VVCSSCKFKKN 36 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~~-~~C~~C~~~~~ 36 (120)
.+.-||.|++-...+... |.|+-|.|...
T Consensus 2 ~lp~cp~c~sEytYed~~~~~cpec~~ew~ 31 (112)
T COG2824 2 SLPPCPKCNSEYTYEDGGQLICPECAHEWN 31 (112)
T ss_pred CCCCCCccCCceEEecCceEeCchhccccc
Confidence 356799999987776655 99999999875
No 267
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=56.59 E-value=6.6 Score=33.84 Aligned_cols=28 Identities=29% Similarity=0.587 Sum_probs=17.5
Q ss_pred CCCCcccCccCCCcccccCCcEEeCCCCCeee
Q 040426 5 LGRDFLFCKFCGTMLRMESNHVVCSSCKFKKN 36 (120)
Q Consensus 5 ~~~~~~FCp~CgnlL~~~~~~~~C~~C~~~~~ 36 (120)
+..+.+||+.||.-|..+ .|..||+..+
T Consensus 11 n~~~akFC~~CG~~l~~~----~Cp~CG~~~~ 38 (645)
T PRK14559 11 NPNNNRFCQKCGTSLTHK----PCPQCGTEVP 38 (645)
T ss_pred CCCCCccccccCCCCCCC----cCCCCCCCCC
Confidence 345677999999887532 3555555433
No 268
>smart00532 LIGANc Ligase N family.
Probab=56.35 E-value=7.7 Score=31.88 Aligned_cols=28 Identities=25% Similarity=0.528 Sum_probs=21.0
Q ss_pred CcccCccCCCcccccCCc--EEeCC--CCCee
Q 040426 8 DFLFCKFCGTMLRMESNH--VVCSS--CKFKK 35 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~~--~~C~~--C~~~~ 35 (120)
-+.+||.||+.|...++. +.|.+ |+.+.
T Consensus 398 ~P~~CP~C~s~l~~~~~~~~~~C~n~~C~aq~ 429 (441)
T smart00532 398 MPTHCPSCGSELVREEGEVDIRCPNPLCPAQL 429 (441)
T ss_pred CCCCCCCCCCEeEecCCceEEEeCCCCCHHHH
Confidence 468999999999776554 88974 66543
No 269
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=56.26 E-value=15 Score=22.20 Aligned_cols=35 Identities=17% Similarity=0.221 Sum_probs=22.9
Q ss_pred CcccCccCCCcccccCCcEEeCCCCCeeeccccccceEE
Q 040426 8 DFLFCKFCGTMLRMESNHVVCSSCKFKKNVQDVADREIS 46 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~~~~C~~C~~~~~~~~~~~~~~~ 46 (120)
..+-|.+|+.+... -.|+.||...-.+++....++
T Consensus 4 ~~~AC~~C~~i~~~----~~Cp~Cgs~~~S~~w~G~v~i 38 (64)
T PRK06393 4 QYRACKKCKRLTPE----KTCPVHGDEKTTTEWFGFLII 38 (64)
T ss_pred hhhhHhhCCcccCC----CcCCCCCCCcCCcCcceEEEE
Confidence 34568999988732 289999997545555443333
No 270
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=55.97 E-value=6.7 Score=31.26 Aligned_cols=26 Identities=27% Similarity=0.560 Sum_probs=21.1
Q ss_pred CccCCCcccccCCcEEeCCCCCeeeccc
Q 040426 12 CKFCGTMLRMESNHVVCSSCKFKKNVQD 39 (120)
Q Consensus 12 Cp~CgnlL~~~~~~~~C~~C~~~~~~~~ 39 (120)
|+.||+.|+.++ -.|-+||..-.-..
T Consensus 2 C~~Cg~~v~FeN--t~C~~Cg~~LGf~p 27 (343)
T PF10005_consen 2 CPNCGQPVFFEN--TRCLSCGSALGFDP 27 (343)
T ss_pred CCCCCCcceeCC--CccccCCccccCCC
Confidence 999999999985 48999998765433
No 271
>TIGR02820 formald_GSH S-(hydroxymethyl)glutathione synthase. The formation of S-(hydroxymethyl)glutathione synthase from glutathione and formaldehyde occurs naturally, but this enzyme speeds its formation in some species as part of a pathway of formaldehyde detoxification.
Probab=55.96 E-value=5.3 Score=29.01 Aligned_cols=14 Identities=36% Similarity=0.460 Sum_probs=11.6
Q ss_pred cccCccCCCccccc
Q 040426 9 FLFCKFCGTMLRME 22 (120)
Q Consensus 9 ~~FCp~CgnlL~~~ 22 (120)
-.||+.||+-|+..
T Consensus 89 R~FC~~CGS~L~~~ 102 (182)
T TIGR02820 89 RHACKGCGTHMYGR 102 (182)
T ss_pred eecCCCCCCccccc
Confidence 34999999999765
No 272
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=55.71 E-value=10 Score=30.98 Aligned_cols=40 Identities=23% Similarity=0.478 Sum_probs=22.6
Q ss_pred cccccccccCCCce-EEEEeecccCCCCceEEEEcCCCCce
Q 040426 77 KVKRACEKCQNPEM-YYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 77 ~~~~~CpkCg~~ea-~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
.++-.|+.||.+.. .+.-.-+----|-----|+|.+|||+
T Consensus 37 EvES~Cm~Cg~nG~TRlllT~IP~fREvVimSF~CpHCG~k 77 (460)
T KOG2703|consen 37 EVESLCMNCGENGTTRLLLTSIPYFREVVIMSFECPHCGHK 77 (460)
T ss_pred HHHHhhhhcccCCceeEEEeecchhheeeeEEeecCccCCc
Confidence 46678999998854 22211111111223344889999986
No 273
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=55.59 E-value=8.5 Score=31.37 Aligned_cols=24 Identities=17% Similarity=0.675 Sum_probs=11.1
Q ss_pred cCccCCCcccccC---C-cEEeCCCCCe
Q 040426 11 FCKFCGTMLRMES---N-HVVCSSCKFK 34 (120)
Q Consensus 11 FCp~CgnlL~~~~---~-~~~C~~C~~~ 34 (120)
=||+|+.+...+. + ...|++||+.
T Consensus 12 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~ 39 (419)
T PRK15103 12 LCPQCDMLVALPRLEHGQKAACPRCGTT 39 (419)
T ss_pred cCCCCCceeecCCCCCCCeeECCCCCCC
Confidence 3555554443221 1 1555555554
No 274
>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=55.52 E-value=7.4 Score=20.83 Aligned_cols=13 Identities=31% Similarity=1.014 Sum_probs=7.7
Q ss_pred ceEEEEcCCCCce
Q 040426 104 QTTYYICPRCGHR 116 (120)
Q Consensus 104 ~T~fY~C~~C~~~ 116 (120)
+.-||+|..||..
T Consensus 3 ~~~~YkC~~CGni 15 (36)
T PF06397_consen 3 KGEFYKCEHCGNI 15 (36)
T ss_dssp TTEEEE-TTT--E
T ss_pred cccEEEccCCCCE
Confidence 3468999999975
No 275
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=55.48 E-value=7.5 Score=21.97 Aligned_cols=30 Identities=20% Similarity=0.585 Sum_probs=23.0
Q ss_pred CCcccCccCCCcccccCCc---------EEeCCCCCeee
Q 040426 7 RDFLFCKFCGTMLRMESNH---------VVCSSCKFKKN 36 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~~~~~---------~~C~~C~~~~~ 36 (120)
.....|..|.++|.++.+. +.|-.|.....
T Consensus 4 APFv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~ 42 (46)
T PF11331_consen 4 APFVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLS 42 (46)
T ss_pred CCEeECccHHHHHcCCCccCCCccceeEEeCCCCceeEE
Confidence 4466899999999987641 89999976543
No 276
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=55.17 E-value=14 Score=28.33 Aligned_cols=29 Identities=24% Similarity=0.586 Sum_probs=19.3
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCC
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCG 114 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~ 114 (120)
...+||.||..-..-.+. .-.-|-|..|.
T Consensus 253 ~g~pC~~Cg~~I~~~~~~--------gR~t~~CP~CQ 281 (282)
T PRK13945 253 TGKPCRKCGTPIERIKLA--------GRSTHWCPNCQ 281 (282)
T ss_pred CcCCCCcCCCeeEEEEEC--------CCccEECCCCc
Confidence 357999999875543332 23348899986
No 277
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=55.05 E-value=6 Score=28.94 Aligned_cols=16 Identities=25% Similarity=0.359 Sum_probs=12.9
Q ss_pred cccCccCCCcccccCC
Q 040426 9 FLFCKFCGTMLRMESN 24 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~ 24 (120)
-.||+.||+-|+....
T Consensus 93 R~FC~~CGS~L~~~~e 108 (191)
T PRK05417 93 RHACKECGVHMYGRIE 108 (191)
T ss_pred eeeCCCCCCccccccc
Confidence 4599999999987643
No 278
>PRK11032 hypothetical protein; Provisional
Probab=54.17 E-value=6.5 Score=27.98 Aligned_cols=32 Identities=22% Similarity=0.518 Sum_probs=26.1
Q ss_pred CCCCcccCccCCCcccccCCc--EEeCCCCCeee
Q 040426 5 LGRDFLFCKFCGTMLRMESNH--VVCSSCKFKKN 36 (120)
Q Consensus 5 ~~~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~ 36 (120)
.+-|.+-|-.||..+.+.... -.|..||..+-
T Consensus 120 vg~G~LvC~~Cg~~~~~~~p~~i~pCp~C~~~~F 153 (160)
T PRK11032 120 VGLGNLVCEKCHHHLAFYTPEVLPLCPKCGHDQF 153 (160)
T ss_pred eecceEEecCCCCEEEecCCCcCCCCCCCCCCee
Confidence 456788999999999887544 89999998764
No 279
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=53.53 E-value=8.8 Score=29.74 Aligned_cols=28 Identities=21% Similarity=0.602 Sum_probs=20.3
Q ss_pred ccCccCCCcccccC---CcEEeCCCCCeeec
Q 040426 10 LFCKFCGTMLRMES---NHVVCSSCKFKKNV 37 (120)
Q Consensus 10 ~FCp~CgnlL~~~~---~~~~C~~C~~~~~~ 37 (120)
.=||+||..-...+ +.++|..||-.-..
T Consensus 2 ~~CpeCg~~~~~~d~~~ge~VC~~CG~Vi~~ 32 (285)
T COG1405 2 MSCPECGSTNIITDYERGEIVCADCGLVLED 32 (285)
T ss_pred CCCCCCCCccceeeccCCeEEeccCCEEecc
Confidence 35999999843332 22999999998654
No 280
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=53.05 E-value=16 Score=27.90 Aligned_cols=30 Identities=27% Similarity=0.741 Sum_probs=19.5
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCc
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGH 115 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~ 115 (120)
...+||.||..-..-... -| .-|-|+.|..
T Consensus 244 ~g~pC~~Cg~~I~~~~~~-gR-------~t~~CP~CQ~ 273 (274)
T PRK01103 244 EGEPCRRCGTPIEKIKQG-GR-------STFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCCeeEEEEEC-CC-------CcEECcCCCC
Confidence 356899999875543332 13 3388999975
No 281
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=51.87 E-value=12 Score=24.96 Aligned_cols=15 Identities=33% Similarity=0.849 Sum_probs=11.8
Q ss_pred ccccccCCC-ceEEEE
Q 040426 80 RACEKCQNP-EMYYST 94 (120)
Q Consensus 80 ~~CpkCg~~-ea~y~~ 94 (120)
..||+||.+ ++.|..
T Consensus 50 t~CP~Cg~~~e~~fvv 65 (115)
T COG1885 50 TSCPKCGEPFESAFVV 65 (115)
T ss_pred ccCCCCCCccceeEEE
Confidence 479999998 777754
No 282
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=51.79 E-value=9.4 Score=28.60 Aligned_cols=36 Identities=28% Similarity=0.666 Sum_probs=24.9
Q ss_pred cccccccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426 75 LSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 75 ~~~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
.|.....||+|.|+..-| |-|.-+.. =|.|..|+|.
T Consensus 188 ~~~~alIC~~C~hhngl~-----~~~ek~~~-efiC~~Cn~~ 223 (251)
T COG5415 188 SPFKALICPQCHHHNGLY-----RLAEKPII-EFICPHCNHK 223 (251)
T ss_pred Cchhhhcccccccccccc-----ccccccch-heecccchhh
Confidence 445667899998876544 33444444 6999999875
No 283
>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=51.50 E-value=13 Score=19.88 Aligned_cols=31 Identities=19% Similarity=0.631 Sum_probs=18.2
Q ss_pred cccccccCCCceEEEEeecccCCCCceEEEEcCCCCc
Q 040426 79 KRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGH 115 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~ 115 (120)
..+||.||....+-|. |-..+=-+.|..|+.
T Consensus 3 ~~pCP~CGG~DrFr~~------d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFRFD------DKDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCccccccc------cCCCCcCEEeCCCCC
Confidence 4689999987765442 212223356666653
No 284
>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=51.28 E-value=3.6 Score=29.18 Aligned_cols=44 Identities=20% Similarity=0.409 Sum_probs=21.9
Q ss_pred ccccccccccCCC-ceEEEEeecccCCCCceEEEEcCCCCce--ecc
Q 040426 76 SKVKRACEKCQNP-EMYYSTRQTRSADEGQTTYYICPRCGHR--CQE 119 (120)
Q Consensus 76 ~~~~~~CpkCg~~-ea~y~~~Q~RSADE~~T~fY~C~~C~~~--w~~ 119 (120)
..+-..||+|+++ +-.|+---.=+-.-...+=.-|-+||+. |++
T Consensus 36 ~~tI~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyPWt~ 82 (158)
T PF10083_consen 36 AKTITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYPWTE 82 (158)
T ss_pred HHHHHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCchHH
Confidence 3344569999986 3333320000000112233558899975 654
No 285
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=51.26 E-value=7.3 Score=21.19 Aligned_cols=24 Identities=33% Similarity=0.711 Sum_probs=15.7
Q ss_pred ccccccCCCceE---EEEeecccCCCC
Q 040426 80 RACEKCQNPEMY---YSTRQTRSADEG 103 (120)
Q Consensus 80 ~~CpkCg~~ea~---y~~~Q~RSADE~ 103 (120)
..||.||..... +.+..+|..+=+
T Consensus 3 ~~Cp~Cg~~~~~~~g~~~r~i~~l~~~ 29 (47)
T PF14690_consen 3 PRCPHCGSPSVHRHGYKTRRIRHLPIG 29 (47)
T ss_pred ccCCCcCCCceECCceEEEEEeecccC
Confidence 469999988644 455555555544
No 286
>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=51.00 E-value=12 Score=24.12 Aligned_cols=11 Identities=36% Similarity=0.890 Sum_probs=6.5
Q ss_pred EEcCCCCceec
Q 040426 108 YICPRCGHRCQ 118 (120)
Q Consensus 108 Y~C~~C~~~w~ 118 (120)
..|..||-.|-
T Consensus 36 ~~C~~CGe~y~ 46 (89)
T TIGR03829 36 ISCSHCGMEYQ 46 (89)
T ss_pred ccccCCCcEee
Confidence 45666666653
No 287
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=50.96 E-value=11 Score=28.31 Aligned_cols=28 Identities=21% Similarity=0.542 Sum_probs=21.4
Q ss_pred ccCccCCCcccccCCcEEeCCCCCeeecc
Q 040426 10 LFCKFCGTMLRMESNHVVCSSCKFKKNVQ 38 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~~~C~~C~~~~~~~ 38 (120)
.=||.|+.-|......+.|.+ ++..++.
T Consensus 3 ~~CP~C~~~l~~~~~~~~C~~-~h~fd~a 30 (272)
T PRK11088 3 YQCPLCHQPLTLEENSWICPQ-NHQFDCA 30 (272)
T ss_pred ccCCCCCcchhcCCCEEEcCC-CCCCccc
Confidence 459999999977555599999 7776443
No 288
>PRK07218 replication factor A; Provisional
Probab=50.68 E-value=7.8 Score=31.71 Aligned_cols=27 Identities=22% Similarity=0.421 Sum_probs=21.9
Q ss_pred cccCccCCCcccccCCcEEeCCCCCeeeccc
Q 040426 9 FLFCKFCGTMLRMESNHVVCSSCKFKKNVQD 39 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~~~C~~C~~~~~~~~ 39 (120)
+.=||+|+..|. +..|+.||...+..+
T Consensus 297 i~rCP~C~r~v~----~~~C~~hG~ve~~~d 323 (423)
T PRK07218 297 IERCPECGRVIQ----KGQCRSHGAVEGEDD 323 (423)
T ss_pred eecCcCcccccc----CCcCCCCCCcCCeee
Confidence 457999999982 389999999877655
No 289
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=50.02 E-value=4.6 Score=23.69 Aligned_cols=30 Identities=20% Similarity=0.435 Sum_probs=22.3
Q ss_pred ccCccCCCcccccCCc----EEeCCCCCeeeccc
Q 040426 10 LFCKFCGTMLRMESNH----VVCSSCKFKKNVQD 39 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~----~~C~~C~~~~~~~~ 39 (120)
.-|..||.+|---+.. ..|+.|.-......
T Consensus 5 iRC~~CnKlLa~a~~~~yle~KCPrCK~vN~~~~ 38 (60)
T COG4416 5 IRCAKCNKLLAEAEGQAYLEKKCPRCKEVNEFYI 38 (60)
T ss_pred eehHHHhHHHHhcccceeeeecCCccceeeeeec
Confidence 3588999998765543 89999988776544
No 290
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=49.28 E-value=8.4 Score=25.36 Aligned_cols=35 Identities=23% Similarity=0.575 Sum_probs=28.4
Q ss_pred CCCcccCccCCCcccccCCc-EEeCCCCCeeecccc
Q 040426 6 GRDFLFCKFCGTMLRMESNH-VVCSSCKFKKNVQDV 40 (120)
Q Consensus 6 ~~~~~FCp~CgnlL~~~~~~-~~C~~C~~~~~~~~~ 40 (120)
......|.-|+..=|..++. +.|.+|+-...+...
T Consensus 32 ~va~daCeiC~~~GY~q~g~~lvC~~C~~~~~~~~i 67 (102)
T PF10080_consen 32 RVAFDACEICGPKGYYQEGDQLVCKNCGVRFNLPTI 67 (102)
T ss_pred EEEEEeccccCCCceEEECCEEEEecCCCEEehhhc
Confidence 44567899999888887665 999999999887664
No 291
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=49.20 E-value=8.5 Score=29.49 Aligned_cols=14 Identities=29% Similarity=0.935 Sum_probs=11.2
Q ss_pred EEEEcCCCCceecc
Q 040426 106 TYYICPRCGHRCQE 119 (120)
Q Consensus 106 ~fY~C~~C~~~w~~ 119 (120)
-+|.|.+|+|.|+.
T Consensus 154 aef~C~~C~h~F~G 167 (278)
T PF15135_consen 154 AEFHCPKCRHNFRG 167 (278)
T ss_pred eeeecccccccchh
Confidence 36899999998873
No 292
>PRK10445 endonuclease VIII; Provisional
Probab=48.82 E-value=20 Score=27.26 Aligned_cols=29 Identities=28% Similarity=0.651 Sum_probs=18.6
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCC
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCG 114 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~ 114 (120)
...+||.||..-..-.. +.-.-|-|.+|.
T Consensus 234 ~g~~Cp~Cg~~I~~~~~--------~gR~t~~CP~CQ 262 (263)
T PRK10445 234 DGEACERCGGIIEKTTL--------SSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCCEeEEEEE--------CCCCcEECCCCc
Confidence 35789999977443333 223338899986
No 293
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=48.21 E-value=5.8 Score=27.89 Aligned_cols=23 Identities=30% Similarity=0.644 Sum_probs=17.0
Q ss_pred cccCccCCCcccccCCcEEeCCCCCeee
Q 040426 9 FLFCKFCGTMLRMESNHVVCSSCKFKKN 36 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~~~C~~C~~~~~ 36 (120)
..||..||.. ..|.|-+||..+-
T Consensus 118 r~fCaVCG~~-----S~ysC~~CG~kyC 140 (156)
T KOG3362|consen 118 RKFCAVCGYD-----SKYSCVNCGTKYC 140 (156)
T ss_pred chhhhhcCCC-----chhHHHhcCCcee
Confidence 3599999932 2388999998754
No 294
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=46.27 E-value=7.7 Score=23.01 Aligned_cols=13 Identities=38% Similarity=1.073 Sum_probs=7.3
Q ss_pred EEEEcCCCCceec
Q 040426 106 TYYICPRCGHRCQ 118 (120)
Q Consensus 106 ~fY~C~~C~~~w~ 118 (120)
+|++|+.||..||
T Consensus 16 ~~lrCPRC~~~FR 28 (65)
T COG4049 16 EFLRCPRCGMVFR 28 (65)
T ss_pred eeeeCCchhHHHH
Confidence 4566666665443
No 295
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=46.17 E-value=33 Score=20.48 Aligned_cols=29 Identities=17% Similarity=0.446 Sum_probs=20.0
Q ss_pred ccCccCCCcccccCCcEEeCCCCCeeecccccc
Q 040426 10 LFCKFCGTMLRMESNHVVCSSCKFKKNVQDVAD 42 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~~~C~~C~~~~~~~~~~~ 42 (120)
+-|.+|+-++..+ .|+.||...-.++-..
T Consensus 4 kAC~~C~~i~~~~----~CP~Cgs~~~T~~W~G 32 (61)
T PRK08351 4 KACRHCHYITTED----RCPVCGSRDLSDEWFD 32 (61)
T ss_pred hhhhhCCcccCCC----cCCCCcCCcccccccc
Confidence 4699999887322 6999999775444333
No 297
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.13 E-value=12 Score=30.17 Aligned_cols=28 Identities=18% Similarity=0.574 Sum_probs=22.0
Q ss_pred CCcccCccCCCcccccCCc--EEeCCCCCee
Q 040426 7 RDFLFCKFCGTMLRMESNH--VVCSSCKFKK 35 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~ 35 (120)
..++=||.|+.++....+= +.|| ||+..
T Consensus 304 ~~wr~CpkC~~~ie~~~GCnhm~Cr-C~~~f 333 (384)
T KOG1812|consen 304 KRWRQCPKCKFMIELSEGCNHMTCR-CGHQF 333 (384)
T ss_pred HhcCcCcccceeeeecCCcceEEee-ccccc
Confidence 4477899999998776652 9999 99753
No 298
>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=45.51 E-value=24 Score=26.88 Aligned_cols=28 Identities=25% Similarity=0.701 Sum_probs=17.9
Q ss_pred cccccccCCCceEEEEeecccCCCCceEEEEcCCCC
Q 040426 79 KRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCG 114 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~ 114 (120)
..+||+||..-..-... -|++ |-|+.|.
T Consensus 245 g~pC~~Cg~~I~~~~~~-gR~t-------~~CP~CQ 272 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVG-GRGT-------HFCPQCQ 272 (272)
T ss_pred CCCCCCCCCeeEEEEEC-CCCC-------EECCCCC
Confidence 56899999875543332 2333 7788884
No 299
>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=45.37 E-value=11 Score=34.20 Aligned_cols=22 Identities=32% Similarity=0.945 Sum_probs=17.4
Q ss_pred cccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426 79 KRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
..+||+||+ .|.+.+|.+||-+
T Consensus 625 ~RKCPkCG~----------------yTlk~rCP~CG~~ 646 (1095)
T TIGR00354 625 IRKCPQCGK----------------ESFWLKCPVCGEL 646 (1095)
T ss_pred EEECCCCCc----------------ccccccCCCCCCc
Confidence 468999996 5777899999854
No 300
>KOG4236 consensus Serine/threonine protein kinase PKC mu/PKD and related proteins [Signal transduction mechanisms]
Probab=45.07 E-value=3.7 Score=35.20 Aligned_cols=30 Identities=30% Similarity=0.641 Sum_probs=22.9
Q ss_pred CCCCcccCccCCCcccccC-CcEEeCCCCCe
Q 040426 5 LGRDFLFCKFCGTMLRMES-NHVVCSSCKFK 34 (120)
Q Consensus 5 ~~~~~~FCp~CgnlL~~~~-~~~~C~~C~~~ 34 (120)
-++.+-||..||-||.--- .++.|..||--
T Consensus 152 SY~~PtFCD~CGEmL~GLvrQGlKC~gCglN 182 (888)
T KOG4236|consen 152 SYKAPTFCDFCGEMLFGLVRQGLKCEGCGLN 182 (888)
T ss_pred cccCchHHHHHHHHHHHHHHccccccCCCCc
Confidence 3567889999999997442 34999998864
No 301
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=44.95 E-value=31 Score=20.82 Aligned_cols=37 Identities=16% Similarity=0.259 Sum_probs=23.6
Q ss_pred CcccCccCCCcccccCCcEEeCCCCCeeeccccccceEE
Q 040426 8 DFLFCKFCGTMLRMESNHVVCSSCKFKKNVQDVADREIS 46 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~~~~C~~C~~~~~~~~~~~~~~~ 46 (120)
..+-|..|+.++... .-.|+.||-..-.++-....++
T Consensus 3 ~~kAC~~Ck~l~~~d--~e~CP~Cgs~~~te~W~G~~iI 39 (64)
T COG2093 3 TEKACKNCKRLTPED--TEICPVCGSTDLTEEWFGLLII 39 (64)
T ss_pred hhHHHhhccccCCCC--CccCCCCCCcccchhhccEEEE
Confidence 455688888776544 3579999988665553333343
No 302
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=44.60 E-value=26 Score=24.23 Aligned_cols=18 Identities=11% Similarity=0.440 Sum_probs=13.6
Q ss_pred cccccccccccCCCce-EE
Q 040426 75 LSKVKRACEKCQNPEM-YY 92 (120)
Q Consensus 75 ~~~~~~~CpkCg~~ea-~y 92 (120)
+.++++.|.+||.+-- +|
T Consensus 85 m~RtEv~C~~Cg~HLGHVF 103 (134)
T TIGR00357 85 MIRTEVRCRNCDAHLGHVF 103 (134)
T ss_pred cEEEEEEecCCCCccCccc
Confidence 4578999999987744 45
No 303
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=44.45 E-value=18 Score=24.88 Aligned_cols=30 Identities=23% Similarity=0.402 Sum_probs=18.8
Q ss_pred cccccccCCC-ceEEEEeecccCCCCceEEE
Q 040426 79 KRACEKCQNP-EMYYSTRQTRSADEGQTTYY 108 (120)
Q Consensus 79 ~~~CpkCg~~-ea~y~~~Q~RSADE~~T~fY 108 (120)
...||+||.. ++.+..+-.|-.=+..|+.|
T Consensus 43 r~~Cp~C~~~~~~E~vels~~G~V~t~Tv~~ 73 (140)
T COG1545 43 RAYCPKCGSETELEWVELSGEGKVETYTVVY 73 (140)
T ss_pred cccCCCCCCCCceEEEEeCCCeEEEEEEEEe
Confidence 4558999888 66777655444444455554
No 304
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=43.79 E-value=10 Score=30.28 Aligned_cols=13 Identities=31% Similarity=0.539 Sum_probs=10.3
Q ss_pred CCCcccCccCCCc
Q 040426 6 GRDFLFCKFCGTM 18 (120)
Q Consensus 6 ~~~~~FCp~Cgnl 18 (120)
.++-.|||.||+-
T Consensus 254 ~m~k~FCp~CG~~ 266 (376)
T KOG2463|consen 254 EMPKDFCPSCGHK 266 (376)
T ss_pred ccchhcccccCCC
Confidence 3456799999986
No 305
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=43.68 E-value=19 Score=21.13 Aligned_cols=30 Identities=17% Similarity=0.376 Sum_probs=15.2
Q ss_pred CcccCccCCCcccccCCcEEeCCCCCeeec
Q 040426 8 DFLFCKFCGTMLRMESNHVVCSSCKFKKNV 37 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~~~~C~~C~~~~~~ 37 (120)
....|..|+.-..+-.-+..|+.||...=.
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~ 37 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCS 37 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEEC
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECC
Confidence 456899999887655445999999987643
No 306
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=43.23 E-value=25 Score=23.89 Aligned_cols=19 Identities=11% Similarity=0.120 Sum_probs=14.0
Q ss_pred cccccccccccCCCceEEE
Q 040426 75 LSKVKRACEKCQNPEMYYS 93 (120)
Q Consensus 75 ~~~~~~~CpkCg~~ea~y~ 93 (120)
..++++.|.+||.+--.-|
T Consensus 75 ~~RtEv~C~~C~~HLGHVF 93 (119)
T PRK05508 75 GRRTEIVCANCGGHLGHVF 93 (119)
T ss_pred CcEEEEEeCCCCCccCccc
Confidence 4578999999987744433
No 307
>PRK04023 DNA polymerase II large subunit; Validated
Probab=42.74 E-value=12 Score=33.92 Aligned_cols=8 Identities=38% Similarity=1.119 Sum_probs=4.1
Q ss_pred EEcCCCCc
Q 040426 108 YICPRCGH 115 (120)
Q Consensus 108 Y~C~~C~~ 115 (120)
|.|.+||.
T Consensus 664 y~CPKCG~ 671 (1121)
T PRK04023 664 DECEKCGR 671 (1121)
T ss_pred CcCCCCCC
Confidence 44555554
No 308
>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=42.27 E-value=18 Score=17.06 Aligned_cols=11 Identities=27% Similarity=0.954 Sum_probs=8.8
Q ss_pred EEcCCCCceec
Q 040426 108 YICPRCGHRCQ 118 (120)
Q Consensus 108 Y~C~~C~~~w~ 118 (120)
|+|..|+..+.
T Consensus 2 ~~C~~C~~~F~ 12 (27)
T PF13912_consen 2 FECDECGKTFS 12 (27)
T ss_dssp EEETTTTEEES
T ss_pred CCCCccCCccC
Confidence 78888987764
No 309
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=42.25 E-value=16 Score=21.47 Aligned_cols=27 Identities=22% Similarity=0.540 Sum_probs=19.8
Q ss_pred CCcccCccCCCcccccCCcEEeCCCCCeeec
Q 040426 7 RDFLFCKFCGTMLRMESNHVVCSSCKFKKNV 37 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~~~~~~~C~~C~~~~~~ 37 (120)
+.|+.|+.||.. .+ .-.|..||-....
T Consensus 3 s~mr~C~~CgvY-TL---k~~CP~CG~~t~~ 29 (56)
T PRK13130 3 SKIRKCPKCGVY-TL---KEICPVCGGKTKN 29 (56)
T ss_pred ccceECCCCCCE-Ec---cccCcCCCCCCCC
Confidence 458899999965 33 3689999987543
No 310
>PF14122 YokU: YokU-like protein
Probab=42.06 E-value=25 Score=22.50 Aligned_cols=38 Identities=29% Similarity=0.512 Sum_probs=21.2
Q ss_pred cccccCCCce------EEEEeeccc--CCCCceEEEEcCCCCceec
Q 040426 81 ACEKCQNPEM------YYSTRQTRS--ADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 81 ~CpkCg~~ea------~y~~~Q~RS--ADE~~T~fY~C~~C~~~w~ 118 (120)
+|.-||..+| +||.+...+ -.=..|--..|.+||-.+.
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq 46 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQ 46 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEe
Confidence 3666776543 477554322 1223455577888877654
No 311
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=42.00 E-value=15 Score=29.79 Aligned_cols=27 Identities=22% Similarity=0.461 Sum_probs=19.8
Q ss_pred cccCccCCCcccccCCcEEeCCCCCeee
Q 040426 9 FLFCKFCGTMLRMESNHVVCSSCKFKKN 36 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~~~C~~C~~~~~ 36 (120)
..=||+|+-.+.+ .....|++||+.-.
T Consensus 215 ~~~C~~Cd~~~~~-~~~a~CpRC~~~L~ 241 (403)
T TIGR00155 215 LRSCSACHTTILP-AQEPVCPRCSTPLY 241 (403)
T ss_pred CCcCCCCCCccCC-CCCcCCcCCCCccc
Confidence 4569999986533 33489999999754
No 312
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=41.24 E-value=19 Score=18.28 Aligned_cols=20 Identities=25% Similarity=0.816 Sum_probs=11.7
Q ss_pred ccCccCCCcccccCCcEEeCCCCCe
Q 040426 10 LFCKFCGTMLRMESNHVVCSSCKFK 34 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~~~C~~C~~~ 34 (120)
.+|..||+ . ..|.|+.|+..
T Consensus 3 ~~C~vC~~--~---~kY~Cp~C~~~ 22 (30)
T PF04438_consen 3 KLCSVCGN--P---AKYRCPRCGAR 22 (30)
T ss_dssp EEETSSSS--E---ESEE-TTT--E
T ss_pred CCCccCcC--C---CEEECCCcCCc
Confidence 47888887 2 23888888764
No 313
>PRK08402 replication factor A; Reviewed
Probab=41.23 E-value=17 Score=29.06 Aligned_cols=28 Identities=11% Similarity=0.290 Sum_probs=20.8
Q ss_pred cccCccCCCcccccC-C-cEEeCCCCCeee
Q 040426 9 FLFCKFCGTMLRMES-N-HVVCSSCKFKKN 36 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~-~-~~~C~~C~~~~~ 36 (120)
..=||.|+.-+..+. + .+.|..||...+
T Consensus 212 y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p 241 (355)
T PRK08402 212 YDACPECRRKVDYDPATDTWICPEHGEVEP 241 (355)
T ss_pred EecCCCCCeEEEEecCCCCEeCCCCCCcCc
Confidence 456999999887443 3 399999996544
No 314
>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=41.15 E-value=18 Score=19.72 Aligned_cols=23 Identities=26% Similarity=0.661 Sum_probs=12.1
Q ss_pred cCccCCCccccc----CC---cEEeCCCCC
Q 040426 11 FCKFCGTMLRME----SN---HVVCSSCKF 33 (120)
Q Consensus 11 FCp~CgnlL~~~----~~---~~~C~~C~~ 33 (120)
=||.||.---.. .+ .+.|+.|+.
T Consensus 5 pCP~CGG~DrFri~~d~~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 5 PCPICGGKDRFRIFDDKDGRGTWICRQCGG 34 (40)
T ss_dssp --TTTT-TTTEEEETT----S-EEETTTTB
T ss_pred CCCCCcCccccccCcCcccCCCEECCCCCC
Confidence 388898743332 11 299999943
No 315
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=41.04 E-value=76 Score=18.66 Aligned_cols=35 Identities=20% Similarity=0.534 Sum_probs=20.2
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCC
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCG 114 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~ 114 (120)
....||.|+-...+....| ...=.+..--.|..|+
T Consensus 14 ~~~~C~~C~G~G~~~~~~~--~~~~~~~~~~~C~~C~ 48 (66)
T PF00684_consen 14 KPKTCPQCNGSGQVTRRQQ--TPGGVFQMQQTCPKCG 48 (66)
T ss_dssp T-EE-TTSSSSSEEEEEEE--SSSTTEEEEEE-TTTS
T ss_pred CCcCCcCCCCeeEEEEEEe--CCCeEEEEEEECCCCc
Confidence 3457999999888777655 2222334445588884
No 316
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=40.35 E-value=12 Score=20.92 Aligned_cols=32 Identities=31% Similarity=0.553 Sum_probs=22.1
Q ss_pred CCCCCCcccCccCCCcccccCCc-EEeCC--CCCeeec
Q 040426 3 DPLGRDFLFCKFCGTMLRMESNH-VVCSS--CKFKKNV 37 (120)
Q Consensus 3 ~~~~~~~~FCp~CgnlL~~~~~~-~~C~~--C~~~~~~ 37 (120)
.|-..+++=||.||.+- ..+ +.|.+ |++....
T Consensus 5 k~TlRGirkCp~CGt~N---G~R~~~CKN~~C~~~~~~ 39 (44)
T PF14952_consen 5 KPTLRGIRKCPKCGTYN---GTRGLSCKNKSCPQVFNV 39 (44)
T ss_pred hhhHhccccCCcCcCcc---CcccccccCCccchhhhc
Confidence 34557888999999764 222 88875 8876543
No 317
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=40.22 E-value=20 Score=25.01 Aligned_cols=20 Identities=10% Similarity=0.238 Sum_probs=14.1
Q ss_pred ccccccccccccCCCceEEE
Q 040426 74 QLSKVKRACEKCQNPEMYYS 93 (120)
Q Consensus 74 t~~~~~~~CpkCg~~ea~y~ 93 (120)
...++++.|.+||.+--.-|
T Consensus 87 gm~RtEv~C~~Cg~HLGHVF 106 (142)
T PRK00222 87 GMVRTEVRCANCDSHLGHVF 106 (142)
T ss_pred CceEEEEEeCCCCCccCccc
Confidence 34478999999988744433
No 318
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=40.19 E-value=24 Score=30.11 Aligned_cols=29 Identities=21% Similarity=0.637 Sum_probs=18.8
Q ss_pred ccccccCCCceEEEEeecccCCCCceEEEEcCC---CCce
Q 040426 80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPR---CGHR 116 (120)
Q Consensus 80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~---C~~~ 116 (120)
..||+||++ +..|+..-| .||.|.+ |++.
T Consensus 575 ~~CP~Cg~~------~~~~~~~~g--kf~gCs~y~~C~~~ 606 (610)
T TIGR01051 575 QDCPLCGRP------MVVKLGKYG--PFLACSNFPECKYT 606 (610)
T ss_pred CCCCCCCCe------eEEEecCCC--ceeeCCCCCCCCCC
Confidence 579999974 223444334 4899987 7654
No 319
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=40.16 E-value=45 Score=19.19 Aligned_cols=31 Identities=19% Similarity=0.376 Sum_probs=15.9
Q ss_pred cccccCCCceEEEEeecccCCCCceEEEEcCCCCc
Q 040426 81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGH 115 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~ 115 (120)
.||-||+.-... +-...++|...--|.-|-.
T Consensus 2 ~CPyCge~~~~~----iD~s~~~Q~yiEDC~vCC~ 32 (52)
T PF14255_consen 2 QCPYCGEPIEIL----IDPSAGDQEYIEDCQVCCR 32 (52)
T ss_pred CCCCCCCeeEEE----EecCCCCeeEEeehhhcCC
Confidence 477777654432 2233335555555665543
No 320
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=40.05 E-value=21 Score=19.99 Aligned_cols=28 Identities=18% Similarity=0.321 Sum_probs=20.7
Q ss_pred cccCccCCCcccccCCcEEeCCCCCeee
Q 040426 9 FLFCKFCGTMLRMESNHVVCSSCKFKKN 36 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~~~C~~C~~~~~ 36 (120)
...|+.|+.-+..-.-+..|+.||...=
T Consensus 2 ~~~C~~C~~~F~~~~rk~~Cr~Cg~~~C 29 (57)
T cd00065 2 ASSCMGCGKPFTLTRRRHHCRNCGRIFC 29 (57)
T ss_pred cCcCcccCccccCCccccccCcCcCCcC
Confidence 3578899987776544589999998753
No 321
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=39.82 E-value=33 Score=23.39 Aligned_cols=19 Identities=11% Similarity=0.268 Sum_probs=14.7
Q ss_pred cccccccccccCCCceEEE
Q 040426 75 LSKVKRACEKCQNPEMYYS 93 (120)
Q Consensus 75 ~~~~~~~CpkCg~~ea~y~ 93 (120)
...+++.|.+||.+--.-|
T Consensus 82 ~~R~Ev~C~~Cg~HLGHVF 100 (124)
T PF01641_consen 82 MVRTEVRCARCGSHLGHVF 100 (124)
T ss_dssp SEEEEEEETTTCCEEEEEE
T ss_pred ceEEEEEecCCCCccccEe
Confidence 5578999999988755444
No 322
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=39.35 E-value=6.4 Score=20.84 Aligned_cols=24 Identities=25% Similarity=0.498 Sum_probs=12.2
Q ss_pred CccCCCcccccCCc------EEeCCCCCee
Q 040426 12 CKFCGTMLRMESNH------VVCSSCKFKK 35 (120)
Q Consensus 12 Cp~CgnlL~~~~~~------~~C~~C~~~~ 35 (120)
|++|-.-+.-+.++ ..|..||=..
T Consensus 2 C~~C~~Ey~~p~~RR~~~~~isC~~CGPr~ 31 (35)
T PF07503_consen 2 CDDCLKEYFDPSNRRFHYQFISCTNCGPRY 31 (35)
T ss_dssp -HHHHHHHCSTTSTTTT-TT--BTTCC-SC
T ss_pred CHHHHHHHcCCCCCcccCcCccCCCCCCCE
Confidence 66676655444443 8888888543
No 323
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=39.27 E-value=2.5 Score=22.33 Aligned_cols=31 Identities=32% Similarity=0.707 Sum_probs=12.9
Q ss_pred ccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 82 CEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 82 CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
|..|+-.+.. |-|.+..|..+ .|..||-.|+
T Consensus 1 C~~C~tt~t~----~WR~~~~g~~~--LCn~Cg~~~k 31 (36)
T PF00320_consen 1 CSNCGTTETP----QWRRGPNGNRT--LCNACGLYYK 31 (36)
T ss_dssp -TTT--ST-S----SEEEETTSEE---EEHHHHHHHH
T ss_pred CcCCcCCCCc----hhhcCCCCCCH--HHHHHHHHHH
Confidence 4455555532 23444444333 5666665554
No 324
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=39.23 E-value=26 Score=31.25 Aligned_cols=14 Identities=21% Similarity=0.655 Sum_probs=10.4
Q ss_pred ccccccccCCCceE
Q 040426 78 VKRACEKCQNPEMY 91 (120)
Q Consensus 78 ~~~~CpkCg~~ea~ 91 (120)
.+..||+||...+.
T Consensus 591 ~~~~CP~Cg~~~L~ 604 (860)
T PRK06319 591 TEIDCPKCHKGKLV 604 (860)
T ss_pred cCcccCCCCCccee
Confidence 45789999876554
No 325
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=39.16 E-value=17 Score=24.06 Aligned_cols=34 Identities=26% Similarity=0.709 Sum_probs=23.2
Q ss_pred cccccccccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426 73 TQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 73 ~t~~~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
..+......|+.|||..-+|+.=--| -|+.||++
T Consensus 36 ~~~G~~~~~C~~Cg~~~~~~~SCk~R----------~CP~C~~~ 69 (111)
T PF14319_consen 36 EALGFHRYRCEDCGHEKIVYNSCKNR----------HCPSCQAK 69 (111)
T ss_pred ccCCcceeecCCCCceEEecCcccCc----------CCCCCCCh
Confidence 44456778899999998777643222 47778775
No 326
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=38.51 E-value=20 Score=33.22 Aligned_cols=14 Identities=29% Similarity=0.935 Sum_probs=11.2
Q ss_pred EEeCCCCCeeeccc
Q 040426 26 VVCSSCKFKKNVQD 39 (120)
Q Consensus 26 ~~C~~C~~~~~~~~ 39 (120)
|.|..|.|.+-.++
T Consensus 684 y~c~~c~~~ef~~~ 697 (1213)
T TIGR01405 684 YLCPNCKYSEFITD 697 (1213)
T ss_pred ccCccccccccccc
Confidence 89999999876544
No 327
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=38.19 E-value=19 Score=24.79 Aligned_cols=20 Identities=15% Similarity=0.562 Sum_probs=14.5
Q ss_pred cccccCCCceEEEEeecccC
Q 040426 81 ACEKCQNPEMYYSTRQTRSA 100 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q~RSA 100 (120)
-||.||.+.-.|..-..+..
T Consensus 21 GCP~CGg~kF~yv~~~~~~~ 40 (131)
T PF09845_consen 21 GCPECGGNKFQYVPEEKDAE 40 (131)
T ss_pred cCcccCCcceEEcCCCcccc
Confidence 39999999988865444333
No 328
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=38.02 E-value=35 Score=16.99 Aligned_cols=23 Identities=26% Similarity=0.560 Sum_probs=16.5
Q ss_pred CccCCCcccccCCcEEeCCCCCee
Q 040426 12 CKFCGTMLRMESNHVVCSSCKFKK 35 (120)
Q Consensus 12 Cp~CgnlL~~~~~~~~C~~C~~~~ 35 (120)
|..|+..+.... .|.|..|++..
T Consensus 3 C~~C~~~~~~~~-~Y~C~~c~f~l 25 (30)
T PF03107_consen 3 CDVCRRKIDGFY-FYHCSECCFTL 25 (30)
T ss_pred CCCCCCCcCCCE-eEEeCCCCCeE
Confidence 667777766665 68888888654
No 329
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=37.93 E-value=1.1e+02 Score=19.76 Aligned_cols=30 Identities=23% Similarity=0.420 Sum_probs=20.5
Q ss_pred ccCccCCCcccccCCc----EEeCCCCCeeeccc
Q 040426 10 LFCKFCGTMLRMESNH----VVCSSCKFKKNVQD 39 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~----~~C~~C~~~~~~~~ 39 (120)
.-|..||....|.... -.|+.|=++...+.
T Consensus 5 F~C~~CG~~V~p~~~g~~~RNHCP~CL~S~Hvd~ 38 (92)
T PF12647_consen 5 FTCVHCGLTVSPLAAGSAHRNHCPSCLSSLHVDI 38 (92)
T ss_pred cCccccCCCcccCCCCCCccCcCcccccccccCC
Confidence 3588888877664332 78888888776553
No 330
>PF02012 BNR: BNR/Asp-box repeat; InterPro: IPR002860 Members of this entry contain multiple BNR (bacterial neuraminidase repeat) repeats or Asp-boxes. The repeats are short, however the repeats are never found closer than 40 residues together suggesting that the repeat is structurally longer. These repeats are found in a variety of non-homologous proteins, including bacterial ribonucleases, sulphite oxidases, reelin, netrins, sialidases, neuraminidases, some lipoprotein receptors, and a variety of glycosyl hydrolases [].; PDB: 2JKB_A 2VW0_A 2VW2_A 2VW1_A 2CN2_D 2CN3_B 2VK7_B 2VK5_A 2VK6_A 2BF6_A ....
Probab=37.34 E-value=16 Score=14.83 Aligned_cols=8 Identities=50% Similarity=0.646 Sum_probs=5.8
Q ss_pred ccCCCCce
Q 040426 98 RSADEGQT 105 (120)
Q Consensus 98 RSADE~~T 105 (120)
+|.|.|+|
T Consensus 2 ~S~D~G~T 9 (12)
T PF02012_consen 2 YSTDGGKT 9 (12)
T ss_dssp EESSTTSS
T ss_pred EeCCCccc
Confidence 57777776
No 331
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=37.29 E-value=7.2 Score=22.37 Aligned_cols=24 Identities=21% Similarity=0.566 Sum_probs=16.3
Q ss_pred ccCccCCCcccccCCcEEeCCCCCee
Q 040426 10 LFCKFCGTMLRMESNHVVCSSCKFKK 35 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~~~C~~C~~~~ 35 (120)
.-|-.||-...+.. -.||.|+|..
T Consensus 15 kIC~rC~Arnp~~A--~kCRkC~~k~ 38 (50)
T COG1552 15 KICRRCYARNPPRA--TKCRKCGYKN 38 (50)
T ss_pred HHHHHhcCCCCcch--hHHhhccCCC
Confidence 35777876665553 4788888864
No 332
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=37.18 E-value=22 Score=33.61 Aligned_cols=14 Identities=36% Similarity=0.902 Sum_probs=11.3
Q ss_pred EEeCCCCCeeeccc
Q 040426 26 VVCSSCKFKKNVQD 39 (120)
Q Consensus 26 ~~C~~C~~~~~~~~ 39 (120)
|.|..|.|.+-.++
T Consensus 909 y~C~~C~~~ef~~~ 922 (1437)
T PRK00448 909 YVCPNCKYSEFFTD 922 (1437)
T ss_pred ccCccccccccccc
Confidence 89999999876544
No 333
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=36.80 E-value=23 Score=30.79 Aligned_cols=28 Identities=25% Similarity=0.558 Sum_probs=22.1
Q ss_pred CcccCccCCCcccccCCc--EEeCC---CCCee
Q 040426 8 DFLFCKFCGTMLRMESNH--VVCSS---CKFKK 35 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~~--~~C~~---C~~~~ 35 (120)
-+.+||.||+-|...++. +.|.+ |+.+.
T Consensus 403 ~P~~CP~C~s~l~r~~~e~~~rC~n~~~C~aq~ 435 (667)
T COG0272 403 FPTHCPVCGSELVREEGEVVIRCTNGLNCPAQL 435 (667)
T ss_pred CCCCCCCCCCeeEeccCceeEecCCCCCChHHH
Confidence 467999999999875443 99987 88764
No 334
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=36.71 E-value=18 Score=31.18 Aligned_cols=26 Identities=19% Similarity=0.438 Sum_probs=18.8
Q ss_pred CCCcccCccCCCcccccCCcEEeCCCCC
Q 040426 6 GRDFLFCKFCGTMLRMESNHVVCSSCKF 33 (120)
Q Consensus 6 ~~~~~FCp~CgnlL~~~~~~~~C~~C~~ 33 (120)
..+..+|++||..+ ......|+.||-
T Consensus 565 np~~~~C~~CG~~~--~g~~~~CP~CGs 590 (625)
T PRK08579 565 TPAITVCNKCGRST--TGLYTRCPRCGS 590 (625)
T ss_pred CCCCccCCCCCCcc--CCCCCcCcCCCC
Confidence 34577999999844 222389999986
No 335
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=36.41 E-value=22 Score=16.33 Aligned_cols=11 Identities=18% Similarity=0.809 Sum_probs=7.1
Q ss_pred EEeCCCCCeee
Q 040426 26 VVCSSCKFKKN 36 (120)
Q Consensus 26 ~~C~~C~~~~~ 36 (120)
|.|+.|+|...
T Consensus 1 y~C~~C~y~t~ 11 (24)
T PF13909_consen 1 YKCPHCSYSTS 11 (24)
T ss_dssp EE-SSSS-EES
T ss_pred CCCCCCCCcCC
Confidence 57999998764
No 336
>smart00355 ZnF_C2H2 zinc finger.
Probab=35.95 E-value=12 Score=16.76 Aligned_cols=11 Identities=45% Similarity=1.280 Sum_probs=6.2
Q ss_pred EEcCCCCceec
Q 040426 108 YICPRCGHRCQ 118 (120)
Q Consensus 108 Y~C~~C~~~w~ 118 (120)
|.|..|+..++
T Consensus 1 ~~C~~C~~~f~ 11 (26)
T smart00355 1 YRCPECGKVFK 11 (26)
T ss_pred CCCCCCcchhC
Confidence 45666665543
No 337
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=35.81 E-value=27 Score=28.52 Aligned_cols=33 Identities=12% Similarity=0.430 Sum_probs=24.2
Q ss_pred CCCCcccCccCCCcccccCC---c-EEeCCCCCeeec
Q 040426 5 LGRDFLFCKFCGTMLRMESN---H-VVCSSCKFKKNV 37 (120)
Q Consensus 5 ~~~~~~FCp~CgnlL~~~~~---~-~~C~~C~~~~~~ 37 (120)
+.....-||+|+-+...+.- . -.|++||+.--.
T Consensus 14 ~~~~~~~C~eCd~~~~~P~l~~~q~A~CPRC~~~l~~ 50 (418)
T COG2995 14 PPGHLILCPECDMLVSLPRLDSGQSAYCPRCGHTLTR 50 (418)
T ss_pred CccceecCCCCCceeccccCCCCCcccCCCCCCcccc
Confidence 44557789999987765532 2 999999997543
No 338
>PF06061 Baculo_ME53: Baculoviridae ME53; InterPro: IPR010336 ME53 is one of the major early-transcribed genes. The ME53 protein is reported to contain a putative zinc finger motif [].; GO: 0003677 DNA binding, 0008270 zinc ion binding
Probab=35.52 E-value=23 Score=28.05 Aligned_cols=28 Identities=32% Similarity=0.670 Sum_probs=22.7
Q ss_pred cccCccCC-CcccccCCc-EEeCCCCCeeec
Q 040426 9 FLFCKFCG-TMLRMESNH-VVCSSCKFKKNV 37 (120)
Q Consensus 9 ~~FCp~Cg-nlL~~~~~~-~~C~~C~~~~~~ 37 (120)
..+|-.|- +-|+ .... +.|+.||++.+.
T Consensus 260 ~~~C~~Ck~~K~y-k~nPVLyCS~CGFTd~~ 289 (327)
T PF06061_consen 260 KRECKYCKKNKLY-KNNPVLYCSKCGFTDPN 289 (327)
T ss_pred chhhhhcccccee-cCCceEEEcccCCCChh
Confidence 45699999 9999 5455 999999998754
No 339
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=35.14 E-value=1.3e+02 Score=26.27 Aligned_cols=88 Identities=16% Similarity=0.285 Sum_probs=45.3
Q ss_pred cccCccCCCcccccCCcEEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCccccccccccccccccCCC
Q 040426 9 FLFCKFCGTMLRMESNHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKRACEKCQNP 88 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~~~~CpkCg~~ 88 (120)
+.-||+|+.-=+.....-.|..|+..-..+++..+ .+ .++ ..+.+ ..-..-+.+||+|...
T Consensus 2 ~~~C~~C~g~G~i~v~~e~c~vc~gtG~~~~~d~k-~~-----~~~----~~~~~---------D~~~~~~~pc~~c~gk 62 (715)
T COG1107 2 IKKCPECGGKGKIVVGEEECPVCHGTGFSDDFDPK-GV-----ANL----SRETV---------DLFASFEIPCPKCRGK 62 (715)
T ss_pred CccccccCCCceEeeeeeecccccccccccccChh-hh-----hhh----hhccc---------cccccCCCCCCeeccc
Confidence 45699999833332222669999988776553210 00 000 00000 0001235678888655
Q ss_pred ceEEEEeecccCCCCceEEEEcCCCCce
Q 040426 89 EMYYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 89 ea~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
..+=.. -+++.=.|.--.++|..||-.
T Consensus 63 G~V~v~-~~c~~c~G~gkv~~c~~cG~~ 89 (715)
T COG1107 63 GTVTVY-DTCPECGGTGKVLTCDICGDI 89 (715)
T ss_pred eeEEEE-eecccCCCceeEEeeccccce
Confidence 443221 346666666666777777643
No 340
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=35.08 E-value=27 Score=17.30 Aligned_cols=24 Identities=29% Similarity=0.642 Sum_probs=8.2
Q ss_pred cCccCCCcccccCCcEEeCCCCCee
Q 040426 11 FCKFCGTMLRMESNHVVCSSCKFKK 35 (120)
Q Consensus 11 FCp~CgnlL~~~~~~~~C~~C~~~~ 35 (120)
.|..|+.-+.. ...|.|..|+|..
T Consensus 2 ~C~~C~~~~~~-~~~Y~C~~Cdf~l 25 (30)
T PF07649_consen 2 RCDACGKPIDG-GWFYRCSECDFDL 25 (30)
T ss_dssp --TTTS----S---EEE-TTT----
T ss_pred cCCcCCCcCCC-CceEECccCCCcc
Confidence 46677765554 2239999998864
No 341
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=35.07 E-value=21 Score=24.06 Aligned_cols=24 Identities=25% Similarity=0.628 Sum_probs=15.7
Q ss_pred cCccCCCcccccCCcEEeCCCCCe
Q 040426 11 FCKFCGTMLRMESNHVVCSSCKFK 34 (120)
Q Consensus 11 FCp~CgnlL~~~~~~~~C~~C~~~ 34 (120)
-|..|+.-+.+....+.|+.||-.
T Consensus 72 ~C~~C~~~~~~e~~~~~CP~C~s~ 95 (115)
T COG0375 72 WCLDCGQEVELEELDYRCPKCGSI 95 (115)
T ss_pred EeccCCCeecchhheeECCCCCCC
Confidence 477776666665555668888743
No 342
>PRK07220 DNA topoisomerase I; Validated
Probab=35.01 E-value=36 Score=29.81 Aligned_cols=10 Identities=20% Similarity=0.537 Sum_probs=7.7
Q ss_pred cccccccCCC
Q 040426 79 KRACEKCQNP 88 (120)
Q Consensus 79 ~~~CpkCg~~ 88 (120)
...||+||++
T Consensus 589 ~~~CP~Cg~~ 598 (740)
T PRK07220 589 IGKCPLCGSD 598 (740)
T ss_pred ccccccCCCe
Confidence 3579999964
No 343
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=34.76 E-value=19 Score=21.45 Aligned_cols=26 Identities=35% Similarity=0.823 Sum_probs=18.2
Q ss_pred ccCccCCCcccccCC-----c-------EEeCCCCCee
Q 040426 10 LFCKFCGTMLRMESN-----H-------VVCSSCKFKK 35 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~-----~-------~~C~~C~~~~ 35 (120)
..||.|...|..-.. + -+|..|||.-
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFNP 40 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFNP 40 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHhhhhhcccCCCC
Confidence 469999988854321 0 7888899853
No 344
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=34.47 E-value=18 Score=17.39 Aligned_cols=9 Identities=22% Similarity=0.645 Sum_probs=5.8
Q ss_pred ccccccCCC
Q 040426 80 RACEKCQNP 88 (120)
Q Consensus 80 ~~CpkCg~~ 88 (120)
++||.||..
T Consensus 3 ~~C~~CgR~ 11 (25)
T PF13913_consen 3 VPCPICGRK 11 (25)
T ss_pred CcCCCCCCE
Confidence 457777753
No 345
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=34.35 E-value=20 Score=31.60 Aligned_cols=29 Identities=21% Similarity=0.752 Sum_probs=22.2
Q ss_pred CCCcccCccCCC--------cccccCCcEEeCCCCCe
Q 040426 6 GRDFLFCKFCGT--------MLRMESNHVVCSSCKFK 34 (120)
Q Consensus 6 ~~~~~FCp~Cgn--------lL~~~~~~~~C~~C~~~ 34 (120)
+..|.||..|+. ||..++..|.|++|..-
T Consensus 285 ~neMVfCd~Cn~cVHqaCyGIle~p~gpWlCr~Calg 321 (893)
T KOG0954|consen 285 ANEMVFCDKCNICVHQACYGILEVPEGPWLCRTCALG 321 (893)
T ss_pred cceeEEeccchhHHHHhhhceeecCCCCeeehhcccc
Confidence 457999999874 56666656999998765
No 346
>PF14149 YhfH: YhfH-like protein
Probab=34.15 E-value=2.2 Score=23.02 Aligned_cols=18 Identities=17% Similarity=0.139 Sum_probs=12.0
Q ss_pred CCCCCcccCccCCCcccc
Q 040426 4 PLGRDFLFCKFCGTMLRM 21 (120)
Q Consensus 4 ~~~~~~~FCp~CgnlL~~ 21 (120)
.+--+..-|++||..+.-
T Consensus 8 frnLp~K~C~~CG~~i~E 25 (37)
T PF14149_consen 8 FRNLPPKKCTECGKEIEE 25 (37)
T ss_pred HHhCCCcccHHHHHHHHH
Confidence 344556778999887643
No 347
>PF15499 Peptidase_C98: Ubiquitin-specific peptidase-like, SUMO isopeptidase
Probab=33.99 E-value=34 Score=26.46 Aligned_cols=16 Identities=13% Similarity=0.291 Sum_probs=11.8
Q ss_pred cccccccccccccCCC
Q 040426 73 TQLSKVKRACEKCQNP 88 (120)
Q Consensus 73 ~t~~~~~~~CpkCg~~ 88 (120)
|--+.--.+|++|+++
T Consensus 164 PLnA~h~~pCn~C~~k 179 (275)
T PF15499_consen 164 PLNAVHFGPCNSCNSK 179 (275)
T ss_pred cccccccCCCcccCCh
Confidence 4445667899999985
No 348
>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=33.24 E-value=26 Score=27.97 Aligned_cols=14 Identities=29% Similarity=0.990 Sum_probs=8.8
Q ss_pred CceEEEEcCCCCce
Q 040426 103 GQTTYYICPRCGHR 116 (120)
Q Consensus 103 ~~T~fY~C~~C~~~ 116 (120)
+.-+||+|.+||++
T Consensus 281 a~KRFFkC~~C~~R 294 (344)
T PF09332_consen 281 AVKRFFKCKDCGNR 294 (344)
T ss_dssp EE-EEEE-T-TS-E
T ss_pred eeeeeEECCCCCCe
Confidence 57799999999986
No 349
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=33.14 E-value=23 Score=27.46 Aligned_cols=34 Identities=21% Similarity=0.396 Sum_probs=22.6
Q ss_pred CCCCCC-cccCccCCCcccccC-------------CcEEeCCCCCeee
Q 040426 3 DPLGRD-FLFCKFCGTMLRMES-------------NHVVCSSCKFKKN 36 (120)
Q Consensus 3 ~~~~~~-~~FCp~CgnlL~~~~-------------~~~~C~~C~~~~~ 36 (120)
+|-.++ +.-|..|+|.|--.. .+|.|..|+..-.
T Consensus 135 vw~hGGrif~CsfC~~flCEDDQFEHQAsCQvLe~E~~KC~SCNrlGq 182 (314)
T PF06524_consen 135 VWDHGGRIFKCSFCDNFLCEDDQFEHQASCQVLESETFKCQSCNRLGQ 182 (314)
T ss_pred cccCCCeEEEeecCCCeeeccchhhhhhhhhhhhcccccccccccccc
Confidence 455555 445999999995432 1288888887543
No 350
>PRK14973 DNA topoisomerase I; Provisional
Probab=32.54 E-value=22 Score=32.04 Aligned_cols=30 Identities=10% Similarity=0.297 Sum_probs=22.1
Q ss_pred ccCccCCC--cccccCCc----EEeCCCCCeeeccc
Q 040426 10 LFCKFCGT--MLRMESNH----VVCSSCKFKKNVQD 39 (120)
Q Consensus 10 ~FCp~Cgn--lL~~~~~~----~~C~~C~~~~~~~~ 39 (120)
.-||+||. ++..+.++ +.|+.|.|......
T Consensus 636 ~~Cp~CG~p~~~~~r~Gr~g~fl~CP~C~~~~~~~~ 671 (936)
T PRK14973 636 EVCPIHHLNHVRLIRKGARPWDIGCPLCSHIESNTE 671 (936)
T ss_pred CCCCCCCCCceEEeecCCCcccccCccccchhhccc
Confidence 36999997 55555554 78999999877544
No 351
>PRK08173 DNA topoisomerase III; Validated
Probab=32.46 E-value=30 Score=30.92 Aligned_cols=25 Identities=28% Similarity=0.743 Sum_probs=18.4
Q ss_pred ccCccCCCcccccCCc-EEeCCCCCee
Q 040426 10 LFCKFCGTMLRMESNH-VVCSSCKFKK 35 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~-~~C~~C~~~~ 35 (120)
.-||.||.-| ..... |.|..|++..
T Consensus 625 ~~CP~Cg~~~-~~~~~~~~Cs~C~f~~ 650 (862)
T PRK08173 625 TPCPNCGGVV-KENYRRFACTKCDFSI 650 (862)
T ss_pred ccCCcccccc-cccCceeEcCCCCccc
Confidence 4599999865 22233 9999999764
No 352
>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=32.32 E-value=11 Score=21.48 Aligned_cols=19 Identities=11% Similarity=0.259 Sum_probs=14.0
Q ss_pred cccccccccCCCceEEEEe
Q 040426 77 KVKRACEKCQNPEMYYSTR 95 (120)
Q Consensus 77 ~~~~~CpkCg~~ea~y~~~ 95 (120)
.+...||.||-.+|....+
T Consensus 7 ltG~~CPgCG~tRa~~~ll 25 (52)
T PF10825_consen 7 LTGIPCPGCGMTRAFIALL 25 (52)
T ss_pred hhCCCCCCCcHHHHHHHHH
Confidence 3577899999888765443
No 353
>PF00935 Ribosomal_L44: Ribosomal protein L44; InterPro: IPR000552 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 consists of mammalian [], Trypanosoma brucei, Caenorhabditis elegans and fungal L44, and Haloarcula marismortui LA [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_r 1S1I_Z 3O5H_f 3O58_f 3IZR_r 1M1K_4 3CCQ_3 3CCL_3 3CME_3 1K73_4 ....
Probab=32.15 E-value=41 Score=21.02 Aligned_cols=14 Identities=21% Similarity=0.503 Sum_probs=10.1
Q ss_pred ceEEEEcCCCCcee
Q 040426 104 QTTYYICPRCGHRC 117 (120)
Q Consensus 104 ~T~fY~C~~C~~~w 117 (120)
..+-|+|+.|++.+
T Consensus 50 i~Lrl~C~~C~~~~ 63 (77)
T PF00935_consen 50 IVLRLECTECGKAH 63 (77)
T ss_dssp BEEEEEETTTS-EE
T ss_pred EEEEEEeCCCCccc
Confidence 55778888888765
No 354
>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=31.95 E-value=30 Score=22.55 Aligned_cols=14 Identities=14% Similarity=0.275 Sum_probs=10.3
Q ss_pred EEeCCCCCeeeccc
Q 040426 26 VVCSSCKFKKNVQD 39 (120)
Q Consensus 26 ~~C~~C~~~~~~~~ 39 (120)
++|..||-..-..+
T Consensus 32 ~~C~~CGe~~~~~e 45 (127)
T TIGR03830 32 WYCPACGEELLDPE 45 (127)
T ss_pred eECCCCCCEEEcHH
Confidence 89999998754433
No 355
>KOG0694 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=31.68 E-value=17 Score=31.63 Aligned_cols=28 Identities=29% Similarity=0.680 Sum_probs=23.2
Q ss_pred CCCcccCccCCCcccccCCc-EEeCCCCC
Q 040426 6 GRDFLFCKFCGTMLRMESNH-VVCSSCKF 33 (120)
Q Consensus 6 ~~~~~FCp~CgnlL~~~~~~-~~C~~C~~ 33 (120)
.....||-.||++|+..... +.|..|+-
T Consensus 238 ~q~ptFc~hCGs~L~r~~qqGlkCs~Cg~ 266 (694)
T KOG0694|consen 238 RQRPTFCDHCGSVLYRLRQQGLKCSTCGR 266 (694)
T ss_pred ccCccHHHhcchhhhhhcccCeeehhhhc
Confidence 45678999999999988665 88888887
No 356
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.64 E-value=23 Score=21.40 Aligned_cols=14 Identities=21% Similarity=0.807 Sum_probs=10.9
Q ss_pred cccccccccCCCce
Q 040426 77 KVKRACEKCQNPEM 90 (120)
Q Consensus 77 ~~~~~CpkCg~~ea 90 (120)
...++||.||.+-.
T Consensus 5 ~~~v~CP~Cgkpv~ 18 (65)
T COG3024 5 RITVPCPTCGKPVV 18 (65)
T ss_pred cccccCCCCCCccc
Confidence 35678999998755
No 357
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=31.61 E-value=15 Score=20.32 Aligned_cols=21 Identities=19% Similarity=0.532 Sum_probs=16.6
Q ss_pred cccCccCCCcccccCCc-EEeC
Q 040426 9 FLFCKFCGTMLRMESNH-VVCS 29 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~-~~C~ 29 (120)
..||-.|+.+..+..+. ++|.
T Consensus 6 ~~yC~~Cdk~~~~~~~~~lYCS 27 (43)
T PF12855_consen 6 NDYCIVCDKQIDPPDDGSLYCS 27 (43)
T ss_pred hhHHHHhhccccCCCCCccccC
Confidence 57999999998776665 7776
No 358
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.25 E-value=23 Score=23.85 Aligned_cols=25 Identities=20% Similarity=0.438 Sum_probs=15.7
Q ss_pred CcccCccCCCcccccCC-----c--EEeCCCCC
Q 040426 8 DFLFCKFCGTMLRMESN-----H--VVCSSCKF 33 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~-----~--~~C~~C~~ 33 (120)
...+| .||..-.+... . +.|+.||-
T Consensus 69 ~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs 100 (124)
T PRK00762 69 VEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGN 100 (124)
T ss_pred eeEEe-eCcCcccccccchhccccCCcCcCCCC
Confidence 34589 99966444311 1 57999983
No 359
>PRK07726 DNA topoisomerase III; Provisional
Probab=31.07 E-value=37 Score=29.26 Aligned_cols=26 Identities=19% Similarity=0.551 Sum_probs=15.5
Q ss_pred cccccccCCCceEEEEeecccCCCCceEEEEcCC
Q 040426 79 KRACEKCQNPEMYYSTRQTRSADEGQTTYYICPR 112 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~ 112 (120)
...||+||++ ... |... -..||-|.+
T Consensus 610 ~~~CP~C~~~-~~~-----~~~~--~~~f~~Cs~ 635 (658)
T PRK07726 610 GPKCPDCGKP-MLK-----VKGK--NGKMLVCQD 635 (658)
T ss_pred cccccccCcc-cee-----eccc--CCeeEecCC
Confidence 3679999976 211 1111 135899987
No 360
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=31.00 E-value=96 Score=18.28 Aligned_cols=13 Identities=31% Similarity=0.713 Sum_probs=6.3
Q ss_pred CceEEEEcCCCCc
Q 040426 103 GQTTYYICPRCGH 115 (120)
Q Consensus 103 ~~T~fY~C~~C~~ 115 (120)
|+-+=.+|..|||
T Consensus 27 GaDikikC~gCg~ 39 (57)
T PF06107_consen 27 GADIKIKCLGCGR 39 (57)
T ss_pred cCcEEEEECCCCC
Confidence 4444444555554
No 361
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=30.72 E-value=23 Score=30.47 Aligned_cols=20 Identities=30% Similarity=0.811 Sum_probs=14.1
Q ss_pred cccccCCCceEEEEeecccCCCCceEEEEcCCCCc
Q 040426 81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGH 115 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~ 115 (120)
.|++||+.... .+.|+.||.
T Consensus 561 ~C~~CGy~g~~---------------~~~CP~CG~ 580 (618)
T PRK14704 561 RCKCCSYHGVI---------------GNECPSCGN 580 (618)
T ss_pred ecCCCCCCCCc---------------CccCcCCCC
Confidence 59999974321 188999984
No 362
>PF11062 DUF2863: Protein of unknown function (DUF2863); InterPro: IPR021292 This bacterial family of proteins have no known function.
Probab=30.67 E-value=31 Score=28.12 Aligned_cols=19 Identities=26% Similarity=0.399 Sum_probs=15.7
Q ss_pred CCcccCccCCCcccccCCc
Q 040426 7 RDFLFCKFCGTMLRMESNH 25 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~~~~~ 25 (120)
-.|.||.+||.=|||...+
T Consensus 362 f~~E~CdDCGaPlypd~~G 380 (398)
T PF11062_consen 362 FPPEFCDDCGAPLYPDPEG 380 (398)
T ss_pred CCchhcccCCCCCCCCCCc
Confidence 4588999999999998653
No 363
>PHA02325 hypothetical protein
Probab=30.56 E-value=42 Score=20.39 Aligned_cols=23 Identities=17% Similarity=0.440 Sum_probs=14.3
Q ss_pred ccccccCCC---ceEEEEeecccCCC
Q 040426 80 RACEKCQNP---EMYYSTRQTRSADE 102 (120)
Q Consensus 80 ~~CpkCg~~---ea~y~~~Q~RSADE 102 (120)
..||+||.. .-.||.---|-+++
T Consensus 4 k~CPkC~A~WldgqhYWsgTgk~g~~ 29 (72)
T PHA02325 4 KICPKCGARWLDGQHYWSGTGKKGNP 29 (72)
T ss_pred cccCccCCEeEcceeeeccCCCcCCc
Confidence 569999984 55677644444443
No 364
>PF14369 zf-RING_3: zinc-finger
Probab=30.52 E-value=32 Score=17.99 Aligned_cols=24 Identities=25% Similarity=0.832 Sum_probs=14.9
Q ss_pred ccCccCCCcccccC--Cc-EEeCCCCC
Q 040426 10 LFCKFCGTMLRMES--NH-VVCSSCKF 33 (120)
Q Consensus 10 ~FCp~CgnlL~~~~--~~-~~C~~C~~ 33 (120)
-||-.|+....+.. +. ..|+.|+-
T Consensus 3 ywCh~C~~~V~~~~~~~~~~~CP~C~~ 29 (35)
T PF14369_consen 3 YWCHQCNRFVRIAPSPDSDVACPRCHG 29 (35)
T ss_pred EeCccCCCEeEeCcCCCCCcCCcCCCC
Confidence 47778887766542 22 44877763
No 365
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.43 E-value=35 Score=22.89 Aligned_cols=25 Identities=28% Similarity=0.659 Sum_probs=19.3
Q ss_pred cccCccCCCcccccCCcEEeCCCCCee
Q 040426 9 FLFCKFCGTMLRMESNHVVCSSCKFKK 35 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~~~C~~C~~~~ 35 (120)
+.=||.||.-|..- .+.|++|+.+-
T Consensus 6 ~~~cPvcg~~~iVT--eL~c~~~etTV 30 (122)
T COG3877 6 INRCPVCGRKLIVT--ELKCSNCETTV 30 (122)
T ss_pred CCCCCcccccceeE--EEecCCCCceE
Confidence 55799999876653 39999999864
No 366
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=30.42 E-value=21 Score=24.02 Aligned_cols=12 Identities=25% Similarity=0.714 Sum_probs=9.8
Q ss_pred ccccccccCCCc
Q 040426 78 VKRACEKCQNPE 89 (120)
Q Consensus 78 ~~~~CpkCg~~e 89 (120)
+.+.||.||+.-
T Consensus 68 v~V~CP~C~K~T 79 (114)
T PF11023_consen 68 VQVECPNCGKQT 79 (114)
T ss_pred eeeECCCCCChH
Confidence 567899999974
No 367
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=30.29 E-value=26 Score=30.73 Aligned_cols=26 Identities=19% Similarity=0.473 Sum_probs=17.8
Q ss_pred CCCCcccCccCCCcccccCCcEEeCCCCC
Q 040426 5 LGRDFLFCKFCGTMLRMESNHVVCSSCKF 33 (120)
Q Consensus 5 ~~~~~~FCp~CgnlL~~~~~~~~C~~C~~ 33 (120)
....+..|++||.+ ..-.+.|+.||-
T Consensus 676 in~~~~~C~~CG~~---~~~~~~CP~CG~ 701 (735)
T PRK07111 676 INHPVDRCPVCGYL---GVIEDKCPKCGS 701 (735)
T ss_pred eCCCCeecCCCCCC---CCcCccCcCCCC
Confidence 34457789999932 222389999986
No 368
>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=30.25 E-value=16 Score=25.52 Aligned_cols=26 Identities=23% Similarity=0.446 Sum_probs=16.4
Q ss_pred ccCccCCCcccccCCc---------EEeCCCCCee
Q 040426 10 LFCKFCGTMLRMESNH---------VVCSSCKFKK 35 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~---------~~C~~C~~~~ 35 (120)
.=||.||+.-.-..+. |.|+.|.--+
T Consensus 106 ~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 106 VQCPRCGSADTTITSIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCcH
Confidence 5688888765433321 8888886543
No 369
>PF14400 Transglut_i_TM: Inactive transglutaminase fused to 7 transmembrane helices
Probab=29.96 E-value=59 Score=23.24 Aligned_cols=22 Identities=36% Similarity=0.406 Sum_probs=17.8
Q ss_pred CCCceEEEEeecccCCCCceEEEEc
Q 040426 86 QNPEMYYSTRQTRSADEGQTTYYIC 110 (120)
Q Consensus 86 g~~ea~y~~~Q~RSADE~~T~fY~C 110 (120)
++++|.|- +|+|.-.||+||+=
T Consensus 68 ~~RrA~WS---~R~A~G~QtLYYr~ 89 (165)
T PF14400_consen 68 GNRRAEWS---IRRASGPQTLYYRV 89 (165)
T ss_pred CCcEEEEe---cccCCCceEEEEEE
Confidence 56778773 68999999999974
No 370
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=29.53 E-value=26 Score=20.81 Aligned_cols=14 Identities=21% Similarity=0.551 Sum_probs=10.2
Q ss_pred cccccccccCCCce
Q 040426 77 KVKRACEKCQNPEM 90 (120)
Q Consensus 77 ~~~~~CpkCg~~ea 90 (120)
|-.+.||.||..-.
T Consensus 15 TLke~Cp~CG~~t~ 28 (59)
T COG2260 15 TLKEKCPVCGGDTK 28 (59)
T ss_pred eecccCCCCCCccc
Confidence 44578999998643
No 371
>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=29.47 E-value=39 Score=20.44 Aligned_cols=24 Identities=21% Similarity=0.544 Sum_probs=10.5
Q ss_pred cccCccCCCcccccCC----cEEeCCCC
Q 040426 9 FLFCKFCGTMLRMESN----HVVCSSCK 32 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~----~~~C~~C~ 32 (120)
...|..|++.+.+.+. .+.|+.|+
T Consensus 41 ~v~Cg~C~~~~~~~~~~c~~~~~C~~C~ 68 (71)
T PF05495_consen 41 RVICGKCRTEQPIDEYSCGADYFCPICG 68 (71)
T ss_dssp EEEETTT--EEES-SBTT--SEEETTTT
T ss_pred CeECCCCCCccChhhhhcCCCccCcCcC
Confidence 3455555555555442 25555554
No 372
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=28.72 E-value=35 Score=29.54 Aligned_cols=28 Identities=21% Similarity=0.495 Sum_probs=20.7
Q ss_pred CcccCccCCCcccccCCc--EEeCC---CCCee
Q 040426 8 DFLFCKFCGTMLRMESNH--VVCSS---CKFKK 35 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~~--~~C~~---C~~~~ 35 (120)
-+.+||.||+-|...++. +.|.+ |+.+.
T Consensus 403 ~P~~CP~Cgs~l~~~~~~~~~~C~n~~~C~aq~ 435 (665)
T PRK07956 403 MPTHCPVCGSELVRVEGEAVLRCTNGLSCPAQL 435 (665)
T ss_pred CCCCCCCCCCEeEecCCCeEEECCCCCCCHHHH
Confidence 367999999999765543 88973 86653
No 373
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.23 E-value=32 Score=26.76 Aligned_cols=39 Identities=18% Similarity=0.461 Sum_probs=23.1
Q ss_pred ccccccccccCCCceEEEEee----------cccCCCCceEEEEcCCCCc
Q 040426 76 SKVKRACEKCQNPEMYYSTRQ----------TRSADEGQTTYYICPRCGH 115 (120)
Q Consensus 76 ~~~~~~CpkCg~~ea~y~~~Q----------~RSADE~~T~fY~C~~C~~ 115 (120)
.+.+..||-||..-+.=+++| ++++=+ ....|.|.+||.
T Consensus 236 ~t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~-~~asf~Cp~Cg~ 284 (298)
T KOG2879|consen 236 GTSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRL-WDASFTCPLCGE 284 (298)
T ss_pred ccCCceeeccCCCCCCCeeeccccceeehhhhhhhhc-chhhcccCccCC
Confidence 356778998888766655555 111111 223478888875
No 374
>PRK06260 threonine synthase; Validated
Probab=28.22 E-value=33 Score=27.42 Aligned_cols=26 Identities=23% Similarity=0.453 Sum_probs=19.2
Q ss_pred cccCccCCCcccccCCcEEeCCCCCe
Q 040426 9 FLFCKFCGTMLRMESNHVVCSSCKFK 34 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~~~C~~C~~~ 34 (120)
...|+.||..+.+..-.+.|+.||-.
T Consensus 3 ~~~C~~cg~~~~~~~~~~~Cp~cg~~ 28 (397)
T PRK06260 3 WLKCIECGKEYDPDEIIYTCPECGGL 28 (397)
T ss_pred EEEECCCCCCCCCCCccccCCCCCCe
Confidence 36799999886655444889999743
No 375
>KOG3092 consensus Casein kinase II, beta subunit [Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Transcription]
Probab=27.52 E-value=26 Score=25.97 Aligned_cols=15 Identities=27% Similarity=0.551 Sum_probs=8.8
Q ss_pred cccCccCCCcccccC
Q 040426 9 FLFCKFCGTMLRMES 23 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~ 23 (120)
..+||.|.++..|++
T Consensus 134 klYCP~C~dvY~P~s 148 (216)
T KOG3092|consen 134 KLYCPSCEDVYIPKS 148 (216)
T ss_pred EEeCCCccccccccc
Confidence 346666666665554
No 376
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=27.20 E-value=24 Score=28.45 Aligned_cols=25 Identities=24% Similarity=0.495 Sum_probs=21.4
Q ss_pred cccCccCCCcccccCCc---EEeCCCCCe
Q 040426 9 FLFCKFCGTMLRMESNH---VVCSSCKFK 34 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~---~~C~~C~~~ 34 (120)
..+|..|+..|.+.+.. ..|+ ||..
T Consensus 240 ~~~c~~C~~~~~~~~~~~~~~~Cp-CG~~ 267 (374)
T TIGR00375 240 QTACEACGEPAVSEDAETACANCP-CGGR 267 (374)
T ss_pred hhhhcccCCcCCchhhhhcCCCCC-CCCc
Confidence 45899999999988764 9999 9987
No 377
>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=27.00 E-value=54 Score=22.21 Aligned_cols=35 Identities=31% Similarity=0.576 Sum_probs=22.5
Q ss_pred ccccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 76 SKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 76 ~~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
++-...|+.||..-. ...|+ .+.-|.|..|+-.++
T Consensus 120 ~~~~~~C~~C~~~~~----r~~~~----~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 120 KKYVYRCPSCGREYK----RHRRS----KRKRYRCGRCGGPLV 154 (157)
T ss_pred cceEEEcCCCCCEee----eeccc----chhhEECCCCCCEEE
Confidence 345678999998742 22333 222399999987654
No 378
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=26.83 E-value=37 Score=27.07 Aligned_cols=27 Identities=26% Similarity=0.686 Sum_probs=19.1
Q ss_pred CCCCcccCccCCCcccccCCcEEeCCCCCee
Q 040426 5 LGRDFLFCKFCGTMLRMESNHVVCSSCKFKK 35 (120)
Q Consensus 5 ~~~~~~FCp~CgnlL~~~~~~~~C~~C~~~~ 35 (120)
..++..||+.||-- ...|.|++|+..+
T Consensus 3 pts~~~~C~ic~vq----~~~YtCPRCn~~Y 29 (383)
T KOG4317|consen 3 PTSSFLACGICGVQ----KREYTCPRCNLLY 29 (383)
T ss_pred CCCceeeccccccc----cccccCCCCCccc
Confidence 35667899999831 2229999998764
No 379
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=26.81 E-value=26 Score=28.15 Aligned_cols=12 Identities=33% Similarity=0.921 Sum_probs=9.5
Q ss_pred eEEEEcCCCCce
Q 040426 105 TTYYICPRCGHR 116 (120)
Q Consensus 105 T~fY~C~~C~~~ 116 (120)
+.-|+|++||++
T Consensus 352 ~~~YRC~~CGF~ 363 (389)
T COG2956 352 KPRYRCQNCGFT 363 (389)
T ss_pred cCCceecccCCc
Confidence 456999999975
No 380
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=26.69 E-value=35 Score=31.90 Aligned_cols=26 Identities=27% Similarity=0.447 Sum_probs=17.0
Q ss_pred ccCccCCCcccccCCcEEeCCCCCeeecc
Q 040426 10 LFCKFCGTMLRMESNHVVCSSCKFKKNVQ 38 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~~~C~~C~~~~~~~ 38 (120)
.|||+||.-+.+. +.|..||...+.+
T Consensus 680 ~fCP~CGs~te~v---y~CPsCGaev~~d 705 (1337)
T PRK14714 680 NRCPDCGTHTEPV---YVCPDCGAEVPPD 705 (1337)
T ss_pred ccCcccCCcCCCc---eeCccCCCccCCC
Confidence 3777777666432 7888888865444
No 381
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=26.50 E-value=52 Score=28.12 Aligned_cols=26 Identities=23% Similarity=0.542 Sum_probs=15.4
Q ss_pred cccccccCCCceEEEEeecccCCCCceEEEEcCC
Q 040426 79 KRACEKCQNPEMYYSTRQTRSADEGQTTYYICPR 112 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~ 112 (120)
...||+||++ +-.|...-| .||-|.+
T Consensus 589 ~~~CPkCg~~------l~~~~~k~g--~f~gCs~ 614 (618)
T TIGR01057 589 VGKCPKCGGK------LVSKYAKKG--RFVGCSN 614 (618)
T ss_pred cCCCCcCCCe------eeeeecCCc--cEEECCC
Confidence 3579999975 112222222 5899975
No 382
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=26.23 E-value=42 Score=28.84 Aligned_cols=31 Identities=16% Similarity=0.498 Sum_probs=22.2
Q ss_pred CCCcccCccCCCcccccCC--cEEeCCCCCeee
Q 040426 6 GRDFLFCKFCGTMLRMESN--HVVCSSCKFKKN 36 (120)
Q Consensus 6 ~~~~~FCp~CgnlL~~~~~--~~~C~~C~~~~~ 36 (120)
......|..||.++..... .+.|+.|+....
T Consensus 541 ~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~ 573 (605)
T PRK07225 541 KVEIYVCAKCGMIAIYDKKRNRKYCPICGEETD 573 (605)
T ss_pred ceeEEeecCcCcceehhcccCceeecccCCCCc
Confidence 3446789999999865432 388999986543
No 383
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=26.19 E-value=45 Score=17.35 Aligned_cols=12 Identities=42% Similarity=1.187 Sum_probs=6.8
Q ss_pred eEEEEcCCCCce
Q 040426 105 TTYYICPRCGHR 116 (120)
Q Consensus 105 T~fY~C~~C~~~ 116 (120)
+..+.|.+|+-.
T Consensus 2 ~~~~~C~nC~R~ 13 (33)
T PF08209_consen 2 SPYVECPNCGRP 13 (33)
T ss_dssp S-EEE-TTTSSE
T ss_pred CCeEECCCCcCC
Confidence 356788888754
No 384
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=26.12 E-value=81 Score=21.50 Aligned_cols=33 Identities=27% Similarity=0.647 Sum_probs=22.5
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC 117 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w 117 (120)
-...|.+||..-. .+.|+-+ +..|.|-+||-+.
T Consensus 111 ~~y~C~~C~~~~~----~~rr~~~---~~~y~C~~C~g~l 143 (146)
T smart00731 111 YPYRCTGCGQRYL----RVRRSNN---VSRYRCGKCGGKL 143 (146)
T ss_pred EEEECCCCCCCCc----eEccccC---cceEEcCCCCCEE
Confidence 3567988997643 3445554 2779999998764
No 385
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=25.85 E-value=41 Score=27.94 Aligned_cols=38 Identities=29% Similarity=0.628 Sum_probs=23.6
Q ss_pred cccccccCCCceEEEEeecccCCC---C--ceEEEEcCCCCce
Q 040426 79 KRACEKCQNPEMYYSTRQTRSADE---G--QTTYYICPRCGHR 116 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~Q~RSADE---~--~T~fY~C~~C~~~ 116 (120)
+-+|++||.+.-.=...|.=..+| | -.-.|.|..||+.
T Consensus 161 ~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~ 203 (500)
T KOG0909|consen 161 NPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTE 203 (500)
T ss_pred CCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCc
Confidence 457999999876211112123444 2 3457999999975
No 386
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=25.85 E-value=70 Score=24.76 Aligned_cols=31 Identities=23% Similarity=0.694 Sum_probs=21.5
Q ss_pred cccccccccCCCceEEEEeecccCCCCceEEEEcCCCCc
Q 040426 77 KVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGH 115 (120)
Q Consensus 77 ~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~ 115 (120)
...++|+.||..-..-.. +.--.|=|..|.+
T Consensus 243 R~GepC~~CGt~I~k~~~--------~gR~t~~CP~CQ~ 273 (273)
T COG0266 243 RAGEPCRRCGTPIEKIKL--------GGRSTFYCPVCQK 273 (273)
T ss_pred CCCCCCCccCCEeEEEEE--------cCCcCEeCCCCCC
Confidence 467899999997554433 3344588999863
No 387
>PRK08329 threonine synthase; Validated
Probab=25.39 E-value=50 Score=25.91 Aligned_cols=24 Identities=25% Similarity=0.587 Sum_probs=17.4
Q ss_pred cccCccCCCcccccCCcEEeCCCCCe
Q 040426 9 FLFCKFCGTMLRMESNHVVCSSCKFK 34 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~~~C~~C~~~ 34 (120)
|..|+.||..+.+. ..+.| .|+-.
T Consensus 1 ~l~C~~Cg~~~~~~-~~~~C-~c~~~ 24 (347)
T PRK08329 1 MLRCTKCGRTYEEK-FKLRC-DCGGT 24 (347)
T ss_pred CcCcCCCCCCcCCC-Cceec-CCCCc
Confidence 47899999887533 23899 69754
No 388
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=25.26 E-value=46 Score=27.52 Aligned_cols=19 Identities=26% Similarity=0.539 Sum_probs=9.5
Q ss_pred CCCCcccCccCCCcccccC
Q 040426 5 LGRDFLFCKFCGTMLRMES 23 (120)
Q Consensus 5 ~~~~~~FCp~CgnlL~~~~ 23 (120)
+...---|.+||-+|-.+.
T Consensus 423 fHv~CY~CEDCg~~LS~e~ 441 (468)
T KOG1701|consen 423 FHVNCYKCEDCGLLLSSEE 441 (468)
T ss_pred ccccceehhhcCccccccC
Confidence 3333344666665555443
No 389
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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 C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=25.00 E-value=47 Score=16.73 Aligned_cols=11 Identities=18% Similarity=0.733 Sum_probs=8.7
Q ss_pred EEcCCCCceec
Q 040426 108 YICPRCGHRCQ 118 (120)
Q Consensus 108 Y~C~~C~~~w~ 118 (120)
|.|..|+..|.
T Consensus 1 ~sCiDC~~~F~ 11 (28)
T PF08790_consen 1 FSCIDCSKDFD 11 (28)
T ss_dssp EEETTTTEEEE
T ss_pred CeeecCCCCcC
Confidence 67899988764
No 390
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=24.37 E-value=19 Score=26.04 Aligned_cols=29 Identities=14% Similarity=0.512 Sum_probs=21.4
Q ss_pred CcccCccCCCcccccCCc---EEeCCCCCeee
Q 040426 8 DFLFCKFCGTMLRMESNH---VVCSSCKFKKN 36 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~~---~~C~~C~~~~~ 36 (120)
..-.||.|+.-+...+.. |.|+.||-.-.
T Consensus 112 ~~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L~ 143 (176)
T COG1675 112 NYYVCPNCHVKYSFDEAMELGFTCPKCGEDLE 143 (176)
T ss_pred CceeCCCCCCcccHHHHHHhCCCCCCCCchhh
Confidence 345798888777666543 99999998644
No 391
>PF08421 Methyltransf_13: Putative zinc binding domain; InterPro: IPR013630 This domain is found at the N terminus of bacterial methyltransferases. ; PDB: 4E2X_A 3NDJ_A 3NDI_A 4E32_A 4E33_A 4E31_A 4E2Y_A 4E2W_A 4E2Z_A 4E30_A.
Probab=24.30 E-value=65 Score=18.84 Aligned_cols=26 Identities=19% Similarity=0.479 Sum_probs=12.3
Q ss_pred ccCCCcccccCCc---------EEeCCCCCeeecc
Q 040426 13 KFCGTMLRMESNH---------VVCSSCKFKKNVQ 38 (120)
Q Consensus 13 p~CgnlL~~~~~~---------~~C~~C~~~~~~~ 38 (120)
|-++.++.+..+. +.|..|+...-..
T Consensus 19 Pl~~~f~~~~~~~~e~~~pL~l~~C~~CglvQl~~ 53 (62)
T PF08421_consen 19 PLANSFLKPELDEPEPRYPLDLYVCEDCGLVQLEE 53 (62)
T ss_dssp E-TT--B-TTS-S---EEEEEEEEETTT--EEESS
T ss_pred CccccccChhhCCCceEECCEEEECCCCCchhcCC
Confidence 4566666662111 9999999987543
No 392
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=24.24 E-value=38 Score=21.68 Aligned_cols=31 Identities=26% Similarity=0.391 Sum_probs=22.1
Q ss_pred cccCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426 9 FLFCKFCGTMLRMESNH--VVCSSCKFKKNVQD 39 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~ 39 (120)
--+|+.||..-.-+... |.|..|.....--.
T Consensus 36 ky~CsfCGK~~vKR~AvGiW~C~~C~kv~agga 68 (92)
T KOG0402|consen 36 KYTCSFCGKKTVKRKAVGIWKCGSCKKVVAGGA 68 (92)
T ss_pred hhhhhhcchhhhhhhceeEEecCCccceeccce
Confidence 35899999775544432 99999998765433
No 393
>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]
Probab=24.17 E-value=99 Score=21.88 Aligned_cols=31 Identities=26% Similarity=0.668 Sum_probs=20.3
Q ss_pred ccccccCCC--ceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426 80 RACEKCQNP--EMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 80 ~~CpkCg~~--ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~ 118 (120)
+-| -|+.+ -..||.++ .+|+ .+|+.|||.|+
T Consensus 112 VGC-~c~eD~~~V~Wmwl~---Kge~----~rc~eCG~~fk 144 (153)
T KOG3352|consen 112 VGC-GCEEDSHAVVWMWLE---KGET----QRCPECGHYFK 144 (153)
T ss_pred Eee-cccCCCcceEEEEEE---cCCc----ccCCcccceEE
Confidence 347 66554 34577766 4454 45999999886
No 394
>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=24.16 E-value=43 Score=20.07 Aligned_cols=16 Identities=25% Similarity=0.376 Sum_probs=12.9
Q ss_pred cccccccccCCCceEE
Q 040426 77 KVKRACEKCQNPEMYY 92 (120)
Q Consensus 77 ~~~~~CpkCg~~ea~y 92 (120)
.+.+.||+||+.-+.|
T Consensus 56 d~~H~Cp~C~~~lg~~ 71 (73)
T PF10601_consen 56 DVYHYCPNCGAFLGTY 71 (73)
T ss_pred CceEECCCCCCEeEEE
Confidence 4678899999987765
No 395
>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=23.90 E-value=54 Score=19.71 Aligned_cols=39 Identities=15% Similarity=0.455 Sum_probs=22.6
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~ 119 (120)
...+||+|+.....|------+. .|-+ |.|..|.-.|+.
T Consensus 4 ~~~~CPRC~S~nTKFcYyNNy~~--~QPR-~~Ck~C~rywT~ 42 (63)
T PF02701_consen 4 QPLPCPRCDSTNTKFCYYNNYNL--SQPR-YFCKSCRRYWTH 42 (63)
T ss_pred cCCCCCCcCCCCCEEEeecCCCC--CCcc-hhhHHHHHHHHh
Confidence 35679999987665421111111 2223 678888888864
No 396
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=23.73 E-value=56 Score=28.27 Aligned_cols=27 Identities=22% Similarity=0.482 Sum_probs=19.8
Q ss_pred CcccCccCCCcccccCCc--EEeC--CCCCe
Q 040426 8 DFLFCKFCGTMLRMESNH--VVCS--SCKFK 34 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~~--~~C~--~C~~~ 34 (120)
-+..||.||+-|...++. +.|. .|+.+
T Consensus 391 ~P~~CP~C~s~l~~~~~~~~~~C~n~~C~aq 421 (652)
T TIGR00575 391 FPTHCPSCGSPLVKIEEEAVIRCPNLNCPAQ 421 (652)
T ss_pred CCCCCCCCCCEeEecCCcEEEEECCCCCHHH
Confidence 367999999999765443 8896 46554
No 397
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=23.72 E-value=36 Score=27.12 Aligned_cols=15 Identities=33% Similarity=0.941 Sum_probs=13.5
Q ss_pred ccCccCCCcccccCC
Q 040426 10 LFCKFCGTMLRMESN 24 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~ 24 (120)
.|||.||.=|.++.+
T Consensus 26 ffCPaC~~~l~lK~G 40 (342)
T COG4469 26 FFCPACGSQLILKQG 40 (342)
T ss_pred cccCCCCCeeeeecC
Confidence 599999999999876
No 398
>PF04194 PDCD2_C: Programmed cell death protein 2, C-terminal putative domain ; InterPro: IPR007320 PDCD2 is localized predominantly in the cytosol of cells situated at the opposite pole of the germinal centre from the centroblasts as well as in cells in the mantle zone. It has been shown to interact with BCL6, an evolutionarily conserved Kruppel-type zinc finger protein that functions as a strong transcriptional repressor and is required for germinal centre development. The rat homologue, Rp8, is associated with programmed cell death in thymocytes.; GO: 0005737 cytoplasm
Probab=23.62 E-value=61 Score=22.77 Aligned_cols=34 Identities=26% Similarity=0.632 Sum_probs=23.0
Q ss_pred ccccccCCCceEEEEee------cccC-------CCCceEEEEcCC-C
Q 040426 80 RACEKCQNPEMYYSTRQ------TRSA-------DEGQTTYYICPR-C 113 (120)
Q Consensus 80 ~~CpkCg~~ea~y~~~Q------~RSA-------DE~~T~fY~C~~-C 113 (120)
-.|+.||.++.+=||+. ++.. |=|--+.|+|.+ |
T Consensus 98 p~C~~Cg~~R~FEfQlmP~li~~L~~~~~~~~~~dwgtv~VyTCs~sC 145 (164)
T PF04194_consen 98 PKCENCGSPRVFEFQLMPQLIYYLEVDDEGSDSMDWGTVLVYTCSASC 145 (164)
T ss_pred CCCccCCCccEEEEEechHHHHHhhccccCCCCceeeEEEEEEehHHc
Confidence 36999999988755542 2333 334568899984 7
No 399
>PRK03922 hypothetical protein; Provisional
Probab=23.60 E-value=43 Score=22.47 Aligned_cols=15 Identities=20% Similarity=0.518 Sum_probs=10.5
Q ss_pred CCcccCccCCCcccc
Q 040426 7 RDFLFCKFCGTMLRM 21 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~ 21 (120)
.+...||.||.-|.+
T Consensus 47 vG~~~cP~cge~~~~ 61 (113)
T PRK03922 47 VGLTICPKCGEPFDS 61 (113)
T ss_pred cCcccCCCCCCcCCc
Confidence 456788888876654
No 400
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=23.52 E-value=49 Score=19.51 Aligned_cols=16 Identities=25% Similarity=0.436 Sum_probs=13.1
Q ss_pred cccccccccCCCceEE
Q 040426 77 KVKRACEKCQNPEMYY 92 (120)
Q Consensus 77 ~~~~~CpkCg~~ea~y 92 (120)
.+.+.||+||+.-+.|
T Consensus 50 d~~H~Cp~C~~~lg~~ 65 (67)
T smart00714 50 DVNHYCPNCGAFLGTY 65 (67)
T ss_pred CccEECCCCCCEeEEe
Confidence 4678899999987766
No 401
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=23.42 E-value=35 Score=26.80 Aligned_cols=24 Identities=21% Similarity=0.581 Sum_probs=17.1
Q ss_pred CCCcccCccCCCcccccCCcEEeCCC
Q 040426 6 GRDFLFCKFCGTMLRMESNHVVCSSC 31 (120)
Q Consensus 6 ~~~~~FCp~CgnlL~~~~~~~~C~~C 31 (120)
.+..+||.+|+.+.+++.. .|+.|
T Consensus 106 ~g~~R~C~kC~~iKPdRaH--HCsvC 129 (307)
T KOG1315|consen 106 DGAVRYCDKCKCIKPDRAH--HCSVC 129 (307)
T ss_pred CCCceeecccccccCCccc--cchhh
Confidence 4578999999988766644 45555
No 402
>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=23.37 E-value=40 Score=22.84 Aligned_cols=22 Identities=23% Similarity=0.664 Sum_probs=15.0
Q ss_pred CCcccCccCCCcccccC--Cc-EEe
Q 040426 7 RDFLFCKFCGTMLRMES--NH-VVC 28 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~~~--~~-~~C 28 (120)
+.+.-|+.|||++..-. +. ++|
T Consensus 5 ~~fYkC~~CGniv~v~~~g~~~l~C 29 (125)
T TIGR00320 5 LQVYKCEVCGNIVEVLNAGIGQLVC 29 (125)
T ss_pred CcEEECCCCCcEEEEEECCCcceee
Confidence 45678999999995332 22 666
No 403
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=23.13 E-value=42 Score=17.95 Aligned_cols=10 Identities=20% Similarity=0.577 Sum_probs=5.9
Q ss_pred ccccccCCCc
Q 040426 80 RACEKCQNPE 89 (120)
Q Consensus 80 ~~CpkCg~~e 89 (120)
..||+||...
T Consensus 3 ~~CprC~kg~ 12 (36)
T PF14787_consen 3 GLCPRCGKGF 12 (36)
T ss_dssp -C-TTTSSSC
T ss_pred ccCcccCCCc
Confidence 3699998754
No 404
>PF15616 TerY-C: TerY-C metal binding domain
Probab=23.12 E-value=65 Score=22.19 Aligned_cols=28 Identities=21% Similarity=0.527 Sum_probs=15.3
Q ss_pred ccCccCCCcc-----------cccCCc-EEeCCCCCeeec
Q 040426 10 LFCKFCGTML-----------RMESNH-VVCSSCKFKKNV 37 (120)
Q Consensus 10 ~FCp~CgnlL-----------~~~~~~-~~C~~C~~~~~~ 37 (120)
.=||.|||.. =..... ..|+-|+..-..
T Consensus 78 PgCP~CGn~~~fa~C~CGkl~Ci~g~~~~~CPwCg~~g~~ 117 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVCGCGKLFCIDGEGEVTCPWCGNEGSF 117 (131)
T ss_pred CCCCCCcChhcEEEecCCCEEEeCCCCCEECCCCCCeeee
Confidence 4577777663 222222 667777765443
No 405
>PRK12496 hypothetical protein; Provisional
Probab=23.00 E-value=51 Score=23.29 Aligned_cols=24 Identities=25% Similarity=0.441 Sum_probs=13.8
Q ss_pred CccCCCcccccCCcEEeCCCCCee
Q 040426 12 CKFCGTMLRMESNHVVCSSCKFKK 35 (120)
Q Consensus 12 Cp~CgnlL~~~~~~~~C~~C~~~~ 35 (120)
|+-||.........-.|+.||..-
T Consensus 130 C~gC~~~~~~~~~~~~C~~CG~~~ 153 (164)
T PRK12496 130 CKGCKKKYPEDYPDDVCEICGSPV 153 (164)
T ss_pred CCCCCccccCCCCCCcCCCCCChh
Confidence 777776643222224677777643
No 406
>PRK08116 hypothetical protein; Validated
Probab=22.98 E-value=65 Score=24.36 Aligned_cols=31 Identities=19% Similarity=0.253 Sum_probs=18.5
Q ss_pred cccccccCCCceEEEEeecccCCCCceEEE-EcCCCCc
Q 040426 79 KRACEKCQNPEMYYSTRQTRSADEGQTTYY-ICPRCGH 115 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY-~C~~C~~ 115 (120)
...||.||......+. .-|.+..+ .|+.|..
T Consensus 16 ~~~C~~Cg~~~~~~~~------~~~~~~~~~~~c~C~~ 47 (268)
T PRK08116 16 GEYCEVCGKRIEKVVE------LLGKNRIVPIMCECER 47 (268)
T ss_pred CccCcCCCCcceeeec------ccCcceecCCCCCChH
Confidence 4469999997654332 22444333 4778854
No 407
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=22.97 E-value=21 Score=25.17 Aligned_cols=30 Identities=23% Similarity=0.454 Sum_probs=21.7
Q ss_pred ccCccCCCccccc--CCc---EEeCCCCCeeeccc
Q 040426 10 LFCKFCGTMLRME--SNH---VVCSSCKFKKNVQD 39 (120)
Q Consensus 10 ~FCp~CgnlL~~~--~~~---~~C~~C~~~~~~~~ 39 (120)
.-|+.||.+=..- +.+ ++|..||...+...
T Consensus 106 v~C~~c~s~dt~l~~~~R~~~l~c~acGa~~pv~~ 140 (151)
T COG1601 106 VKCKECGSPDTELIKEERLLFLKCEACGAIRPVKL 140 (151)
T ss_pred eEeccCCCCchhhhhhhhhHhhHHHHhCCcccchh
Confidence 3599999875443 233 99999999888754
No 408
>PHA02611 51 baseplate hub assembly protein; Provisional
Probab=22.92 E-value=63 Score=24.71 Aligned_cols=17 Identities=18% Similarity=0.393 Sum_probs=12.4
Q ss_pred cccccccCCCceEEEEe
Q 040426 79 KRACEKCQNPEMYYSTR 95 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~ 95 (120)
.+.||+||+..-+++.+
T Consensus 82 ~~tCp~Cg~e~~v~~~l 98 (249)
T PHA02611 82 TFTCPKCKKEKTVLFNL 98 (249)
T ss_pred EEECCCCCCceeEEEEe
Confidence 46899999996555444
No 409
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=22.72 E-value=69 Score=28.57 Aligned_cols=20 Identities=25% Similarity=0.597 Sum_probs=14.3
Q ss_pred ccCccCCCcccccCCc----EEeC
Q 040426 10 LFCKFCGTMLRMESNH----VVCS 29 (120)
Q Consensus 10 ~FCp~CgnlL~~~~~~----~~C~ 29 (120)
.=||.||.-|..+..+ +.|.
T Consensus 588 ~~CP~Cg~~l~~r~gr~G~Fl~Cs 611 (859)
T PRK07561 588 RDCPTCGRGMGIRTGKTGVFLGCS 611 (859)
T ss_pred ccCcccCCcceEEecCCCCeeecc
Confidence 5799999876665432 7786
No 410
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=22.67 E-value=62 Score=24.77 Aligned_cols=24 Identities=25% Similarity=0.740 Sum_probs=17.6
Q ss_pred ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCc
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGH 115 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~ 115 (120)
-+..|.+||+.-..| ++.|++||-
T Consensus 353 p~~~c~~cg~~~~~~--------------~~~c~~c~~ 376 (389)
T PRK11788 353 PRYRCRNCGFTARTL--------------YWHCPSCKA 376 (389)
T ss_pred CCEECCCCCCCCccc--------------eeECcCCCC
Confidence 346799999876555 488999963
No 411
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=22.54 E-value=43 Score=20.12 Aligned_cols=25 Identities=24% Similarity=0.644 Sum_probs=18.1
Q ss_pred CcccCccCCCcccccCCcEEeCCCCC
Q 040426 8 DFLFCKFCGTMLRMESNHVVCSSCKF 33 (120)
Q Consensus 8 ~~~FCp~CgnlL~~~~~~~~C~~C~~ 33 (120)
.-.+|..||..-+-. ..-.|..|||
T Consensus 16 tHt~CrRCG~~syh~-qK~~CasCGy 40 (62)
T PRK04179 16 THIRCRRCGRHSYNV-RKKYCAACGF 40 (62)
T ss_pred ccchhcccCcccccc-cccchhhcCC
Confidence 456899999774432 1288999999
No 412
>cd02674 Peptidase_C19R A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=22.31 E-value=1e+02 Score=21.85 Aligned_cols=23 Identities=13% Similarity=0.198 Sum_probs=14.3
Q ss_pred ccccccccCCCceEEEEeecccC
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSA 100 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSA 100 (120)
....|++||...-...+..++++
T Consensus 103 ~~~~C~~C~~~~~~~~~~~i~~l 125 (230)
T cd02674 103 NAWKCPKCKKKRKATKKLTISRL 125 (230)
T ss_pred CceeCCCCCCccceEEEEEEecC
Confidence 35789999987654444444433
No 413
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=22.28 E-value=76 Score=16.90 Aligned_cols=23 Identities=22% Similarity=0.580 Sum_probs=15.0
Q ss_pred CccCCCcccccCCcEEeCCCCCeee
Q 040426 12 CKFCGTMLRMESNHVVCSSCKFKKN 36 (120)
Q Consensus 12 Cp~CgnlL~~~~~~~~C~~C~~~~~ 36 (120)
|..|+....+- .+.|+.|+...=
T Consensus 1 C~~C~~~~~l~--~f~C~~C~~~FC 23 (39)
T smart00154 1 CHFCRKKVGLT--GFKCRHCGNLFC 23 (39)
T ss_pred CcccCCccccc--CeECCccCCccc
Confidence 45577655442 388999987654
No 414
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=22.24 E-value=1e+02 Score=25.99 Aligned_cols=18 Identities=0% Similarity=0.133 Sum_probs=13.6
Q ss_pred cccccccccccCCC-ceEE
Q 040426 75 LSKVKRACEKCQNP-EMYY 92 (120)
Q Consensus 75 ~~~~~~~CpkCg~~-ea~y 92 (120)
+.++++.|.+||.+ .-+|
T Consensus 463 ~~R~Ev~c~~c~~HLGHvf 481 (521)
T PRK14018 463 MRRTEVRSRAADSHLGHVF 481 (521)
T ss_pred ceEEEEEECCCCCcCCccc
Confidence 45789999999866 4455
No 415
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.11 E-value=74 Score=18.73 Aligned_cols=14 Identities=36% Similarity=0.859 Sum_probs=8.8
Q ss_pred CceEEEEcCCCCce
Q 040426 103 GQTTYYICPRCGHR 116 (120)
Q Consensus 103 ~~T~fY~C~~C~~~ 116 (120)
|+-+--.|.+|||.
T Consensus 30 GaDIkikC~nC~h~ 43 (60)
T COG4481 30 GADIKIKCENCGHS 43 (60)
T ss_pred cCcEEEEecCCCcE
Confidence 55566666666664
No 416
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=21.94 E-value=52 Score=21.36 Aligned_cols=13 Identities=23% Similarity=0.593 Sum_probs=10.4
Q ss_pred ceEEEEcCCCCce
Q 040426 104 QTTYYICPRCGHR 116 (120)
Q Consensus 104 ~T~fY~C~~C~~~ 116 (120)
.++-|+|++||+.
T Consensus 65 v~Lr~~Ct~Cgka 77 (94)
T COG1631 65 VDLRLRCTECGKA 77 (94)
T ss_pred EEEEEEehhhccc
Confidence 5688999999864
No 417
>PF09463 Opy2: Opy2 protein; InterPro: IPR018571 Opy2p acts as a membrane anchor in the HOG signalling pathway []. This entry represents a conserved N-terminal domain.
Probab=21.84 E-value=91 Score=16.51 Aligned_cols=16 Identities=31% Similarity=0.536 Sum_probs=12.5
Q ss_pred cccccCCCceEEEEee
Q 040426 81 ACEKCQNPEMYYSTRQ 96 (120)
Q Consensus 81 ~CpkCg~~ea~y~~~Q 96 (120)
.||.|+.++.-.++.|
T Consensus 10 ~CP~C~~ge~C~~t~~ 25 (35)
T PF09463_consen 10 SCPSCPSGEECVLTSQ 25 (35)
T ss_pred CCCCCCCCCEEEecCC
Confidence 7999999987666544
No 418
>PRK07591 threonine synthase; Validated
Probab=21.69 E-value=48 Score=26.82 Aligned_cols=24 Identities=29% Similarity=0.562 Sum_probs=18.6
Q ss_pred cccCccCCCcccccCCcEEeCCCCC
Q 040426 9 FLFCKFCGTMLRMESNHVVCSSCKF 33 (120)
Q Consensus 9 ~~FCp~CgnlL~~~~~~~~C~~C~~ 33 (120)
-+.|..||..+.+... +.|..||-
T Consensus 18 ~l~C~~Cg~~~~~~~~-~~C~~cg~ 41 (421)
T PRK07591 18 ALKCRECGAEYPLGPI-HVCEECFG 41 (421)
T ss_pred EEEeCCCCCcCCCCCC-ccCCCCCC
Confidence 3689999988766544 99999974
No 419
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=21.66 E-value=33 Score=28.40 Aligned_cols=22 Identities=27% Similarity=0.767 Sum_probs=17.8
Q ss_pred cccCCCCceEEEEcCCCCceec
Q 040426 97 TRSADEGQTTYYICPRCGHRCQ 118 (120)
Q Consensus 97 ~RSADE~~T~fY~C~~C~~~w~ 118 (120)
.||.|+...-+|.|..|+++||
T Consensus 346 ~rsg~dss~gi~~C~~C~KkFr 367 (500)
T KOG3993|consen 346 ERSGDDSSSGIFSCHTCGKKFR 367 (500)
T ss_pred cccCCcccCceeecHHhhhhhH
Confidence 4577766666999999999986
No 420
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.64 E-value=35 Score=23.29 Aligned_cols=14 Identities=14% Similarity=0.826 Sum_probs=11.3
Q ss_pred ccccccccCCCceE
Q 040426 78 VKRACEKCQNPEMY 91 (120)
Q Consensus 78 ~~~~CpkCg~~ea~ 91 (120)
....||+||..+.+
T Consensus 20 l~grCP~CGeGrLF 33 (126)
T COG5349 20 LRGRCPRCGEGRLF 33 (126)
T ss_pred hcCCCCCCCCchhh
Confidence 45689999998774
No 421
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=21.42 E-value=52 Score=18.19 Aligned_cols=25 Identities=28% Similarity=0.527 Sum_probs=16.9
Q ss_pred CccCCCcccccCC------c------EEeCCCCCeee
Q 040426 12 CKFCGTMLRMESN------H------VVCSSCKFKKN 36 (120)
Q Consensus 12 Cp~CgnlL~~~~~------~------~~C~~C~~~~~ 36 (120)
|+.|+..+.+... . +.|..|+....
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 37 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLN 37 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccC
Confidence 6778877765431 1 89999997543
No 422
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=21.38 E-value=45 Score=24.26 Aligned_cols=12 Identities=25% Similarity=0.537 Sum_probs=8.8
Q ss_pred cccccccCCCce
Q 040426 79 KRACEKCQNPEM 90 (120)
Q Consensus 79 ~~~CpkCg~~ea 90 (120)
...|||||...-
T Consensus 175 g~~CPKCGr~G~ 186 (200)
T PF12387_consen 175 GGNCPKCGRHGK 186 (200)
T ss_pred CCCCCcccCCCC
Confidence 456999998653
No 423
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 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 probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=21.17 E-value=1.1e+02 Score=17.56 Aligned_cols=13 Identities=38% Similarity=0.843 Sum_probs=8.9
Q ss_pred ceEEEEcCCCCcee
Q 040426 104 QTTYYICPRCGHRC 117 (120)
Q Consensus 104 ~T~fY~C~~C~~~w 117 (120)
.+.+|.| .||-.+
T Consensus 15 ~~~~y~C-RCG~~f 27 (55)
T PF05207_consen 15 GVYSYPC-RCGGEF 27 (55)
T ss_dssp TEEEEEE-TTSSEE
T ss_pred CEEEEcC-CCCCEE
Confidence 3567778 788665
No 424
>PRK02935 hypothetical protein; Provisional
Probab=21.14 E-value=41 Score=22.40 Aligned_cols=11 Identities=36% Similarity=1.053 Sum_probs=9.3
Q ss_pred ccccccccCCC
Q 040426 78 VKRACEKCQNP 88 (120)
Q Consensus 78 ~~~~CpkCg~~ 88 (120)
+.+.||.|++.
T Consensus 69 vqV~CP~C~K~ 79 (110)
T PRK02935 69 VQVICPSCEKP 79 (110)
T ss_pred eeeECCCCCch
Confidence 56789999986
No 425
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=21.09 E-value=43 Score=16.57 Aligned_cols=11 Identities=36% Similarity=0.754 Sum_probs=6.9
Q ss_pred CccCCCccccc
Q 040426 12 CKFCGTMLRME 22 (120)
Q Consensus 12 Cp~CgnlL~~~ 22 (120)
|+.|+..+.+.
T Consensus 2 C~~C~~~i~~~ 12 (39)
T smart00132 2 CAGCGKPIRGG 12 (39)
T ss_pred ccccCCcccCC
Confidence 66777666553
No 426
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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 RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=21.04 E-value=89 Score=15.27 Aligned_cols=12 Identities=33% Similarity=0.750 Sum_probs=6.5
Q ss_pred EEeCCCCCeeec
Q 040426 26 VVCSSCKFKKNV 37 (120)
Q Consensus 26 ~~C~~C~~~~~~ 37 (120)
+.|..|.+....
T Consensus 5 W~C~~C~~~N~~ 16 (30)
T PF00641_consen 5 WKCPSCTFMNPA 16 (30)
T ss_dssp EEETTTTEEEES
T ss_pred ccCCCCcCCchH
Confidence 556666555443
No 427
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=20.99 E-value=65 Score=18.48 Aligned_cols=12 Identities=33% Similarity=1.126 Sum_probs=4.1
Q ss_pred eEEEEcCCCCce
Q 040426 105 TTYYICPRCGHR 116 (120)
Q Consensus 105 T~fY~C~~C~~~ 116 (120)
...|+|.+|++.
T Consensus 19 ~~~y~C~~C~~~ 30 (51)
T PF07975_consen 19 SSRYRCPKCKNH 30 (51)
T ss_dssp -EEE--TTTT--
T ss_pred CCeEECCCCCCc
Confidence 455666666543
No 428
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Probab=20.96 E-value=54 Score=28.12 Aligned_cols=30 Identities=17% Similarity=0.458 Sum_probs=21.5
Q ss_pred CCcccCccCCCcccccC--CcEEeCCCCCeee
Q 040426 7 RDFLFCKFCGTMLRMES--NHVVCSSCKFKKN 36 (120)
Q Consensus 7 ~~~~FCp~CgnlL~~~~--~~~~C~~C~~~~~ 36 (120)
.....|..||.++.... ..+.|+.|+....
T Consensus 536 ~~~~vC~~CG~~~~~~~~~~~~~C~~c~~~~~ 567 (599)
T TIGR03670 536 YVVYVCENCGHIAWEDKRKGTAYCPVCGETGD 567 (599)
T ss_pred eeEEeecccCceeehhcccCceeccccCCCCc
Confidence 34568999999986543 2388999987543
No 429
>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=20.78 E-value=63 Score=27.31 Aligned_cols=15 Identities=20% Similarity=0.425 Sum_probs=9.3
Q ss_pred cccccccCCCceEEE
Q 040426 79 KRACEKCQNPEMYYS 93 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~ 93 (120)
...||+||+.....+
T Consensus 532 ~~~CP~CGs~~~~~~ 546 (555)
T cd01675 532 GFKCPKCGSEDVEVI 546 (555)
T ss_pred CCCCcCCCCcCceEE
Confidence 356888887654443
No 430
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=20.75 E-value=51 Score=25.32 Aligned_cols=28 Identities=21% Similarity=0.420 Sum_probs=15.6
Q ss_pred ccccccccCCCceEEEEeecccCCCCc--eEEEEcCCCC
Q 040426 78 VKRACEKCQNPEMYYSTRQTRSADEGQ--TTYYICPRCG 114 (120)
Q Consensus 78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~--T~fY~C~~C~ 114 (120)
...+||.||.+=. -+||. ---|+|-.|.
T Consensus 219 ~~r~CP~Cg~~W~---------L~~plh~iFdFKCD~CR 248 (258)
T PF10071_consen 219 QARKCPSCGGDWR---------LKEPLHDIFDFKCDPCR 248 (258)
T ss_pred hCCCCCCCCCccc---------cCCchhhceeccCCcce
Confidence 4567888887421 24443 2336677774
No 431
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=20.73 E-value=41 Score=24.23 Aligned_cols=10 Identities=20% Similarity=0.727 Sum_probs=8.1
Q ss_pred ccccccCCCc
Q 040426 80 RACEKCQNPE 89 (120)
Q Consensus 80 ~~CpkCg~~e 89 (120)
..||.|||-.
T Consensus 94 ~~CP~CGh~k 103 (176)
T KOG4080|consen 94 NTCPACGHIK 103 (176)
T ss_pred ccCcccCccc
Confidence 5799999953
No 432
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=20.58 E-value=45 Score=28.63 Aligned_cols=39 Identities=15% Similarity=0.444 Sum_probs=22.9
Q ss_pred cccccccCCCce-EE-EEeec-ccCCCC-ceEEEEcCCCCcee
Q 040426 79 KRACEKCQNPEM-YY-STRQT-RSADEG-QTTYYICPRCGHRC 117 (120)
Q Consensus 79 ~~~CpkCg~~ea-~y-~~~Q~-RSADE~-~T~fY~C~~C~~~w 117 (120)
.++||.||+..- .| ...+. +-.|++ ...||.|..|++.=
T Consensus 227 yvpCPHCGe~q~l~~~e~~~~~g~~~~~~~~~~~~c~h~~~~i 269 (611)
T COG5525 227 YVPCPHCGEEQQLKFGEKSGPRGLKDTPAEAAFIQCEHCGCVI 269 (611)
T ss_pred EeeCCCCCchhhccccccCCCcCcccchhhhhhhhccccCcee
Confidence 468999998532 22 11111 222222 56899999998753
No 433
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=20.55 E-value=49 Score=31.33 Aligned_cols=22 Identities=41% Similarity=0.931 Sum_probs=15.7
Q ss_pred cccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426 79 KRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
...||+||+. |.+.+|..||-.
T Consensus 674 ~~~Cp~Cg~~----------------~~~~~Cp~CG~~ 695 (1627)
T PRK14715 674 FFKCPKCGKV----------------GLYHVCPFCGTR 695 (1627)
T ss_pred eeeCCCCCCc----------------cccccCcccCCc
Confidence 4579999874 445778888754
No 434
>PLN03165 chaperone protein dnaJ-related; Provisional
Probab=20.36 E-value=1.8e+02 Score=19.38 Aligned_cols=30 Identities=17% Similarity=0.378 Sum_probs=17.7
Q ss_pred ccccccCCCceEEEEeecccCCCCceEEEEcCCCC
Q 040426 80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCG 114 (120)
Q Consensus 80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~ 114 (120)
..|++|+.....-.+. . -.++..-.|..|+
T Consensus 53 ~~C~~C~G~G~v~~~~--~---g~~q~~~~C~~C~ 82 (111)
T PLN03165 53 QVCRFCVGSGNVTVEL--G---GGEKEVSKCINCD 82 (111)
T ss_pred cCCCCCcCcCeEEEEe--C---CcEEEEEECCCCC
Confidence 4799998887654332 1 1355555666663
No 435
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=20.34 E-value=62 Score=28.36 Aligned_cols=15 Identities=27% Similarity=0.603 Sum_probs=11.6
Q ss_pred ccccCCCceEEEEee
Q 040426 82 CEKCQNPEMYYSTRQ 96 (120)
Q Consensus 82 CpkCg~~ea~y~~~Q 96 (120)
||+||++.+..+...
T Consensus 658 Cp~CG~~dve~~~Ri 672 (700)
T COG1328 658 CPKCGSEDVEVFSRI 672 (700)
T ss_pred CCCCCCccceeeeee
Confidence 999999986666544
No 436
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=20.29 E-value=52 Score=27.76 Aligned_cols=16 Identities=19% Similarity=0.470 Sum_probs=6.8
Q ss_pred cccccccCCCceEEEE
Q 040426 79 KRACEKCQNPEMYYST 94 (120)
Q Consensus 79 ~~~CpkCg~~ea~y~~ 94 (120)
...||+||++.+..+.
T Consensus 504 ~~~CP~CGs~~~~~~~ 519 (546)
T PF13597_consen 504 GDKCPKCGSENIEVYS 519 (546)
T ss_dssp EEE-CCC----EEEEB
T ss_pred CCCCCCCCCcccceEE
Confidence 4568888888755443
No 437
>PF06573 Churchill: Churchill protein; InterPro: IPR009508 This family consists of several eukaryotic Churchill proteins. This protein contains a novel zinc binding region that mediates FGF signalling during neural development. The slow induction by FGF of a transcription factor (Churchill) in the neural plate in turn induces expression of Sip1 (Smad interacting protein-1), which inhibits mesodermal genes and sensitizes cells to later neural inducing factors [].; GO: 0008270 zinc ion binding, 0007275 multicellular organismal development, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2JOX_A.
Probab=20.24 E-value=1.5e+02 Score=19.89 Aligned_cols=36 Identities=22% Similarity=0.511 Sum_probs=19.8
Q ss_pred cccccccccCCCceE--E-EEeecccCCCCceEEEEcCCCCce
Q 040426 77 KVKRACEKCQNPEMY--Y-STRQTRSADEGQTTYYICPRCGHR 116 (120)
Q Consensus 77 ~~~~~CpkCg~~ea~--y-~~~Q~RSADE~~T~fY~C~~C~~~ 116 (120)
+-++.|++|+|--|. | |.+ .|+-|----.|.-||+-
T Consensus 56 TY~HvC~nC~HvIA~HEYtF~V----~~~yQeY~M~ClLCG~~ 94 (112)
T PF06573_consen 56 TYDHVCKNCHHVIARHEYTFSV----VDDYQEYTMLCLLCGKA 94 (112)
T ss_dssp EEEEEETTT--EEEEEEEEEEE----ETTEEEEEEEETTTEEE
T ss_pred EeeeccCccceEEEeeeEEEEE----eccchhhhHHHHHhCCc
Confidence 557788888886553 3 332 24444444457778763
No 438
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=20.10 E-value=67 Score=27.52 Aligned_cols=12 Identities=17% Similarity=0.600 Sum_probs=7.5
Q ss_pred ccccccCCCceE
Q 040426 80 RACEKCQNPEMY 91 (120)
Q Consensus 80 ~~CpkCg~~ea~ 91 (120)
..||+||+....
T Consensus 547 ~~CP~CGs~~~e 558 (586)
T TIGR02827 547 HRCPVCGSANID 558 (586)
T ss_pred CcCcCCCCccce
Confidence 567777765543
No 439
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=20.07 E-value=64 Score=20.43 Aligned_cols=14 Identities=29% Similarity=0.453 Sum_probs=10.5
Q ss_pred cccccccccCCCce
Q 040426 77 KVKRACEKCQNPEM 90 (120)
Q Consensus 77 ~~~~~CpkCg~~ea 90 (120)
+....|+.||.+=.
T Consensus 6 k~~~~C~~CG~d~~ 19 (86)
T PF06170_consen 6 KVAPRCPHCGLDYS 19 (86)
T ss_pred cCCCcccccCCccc
Confidence 35667999998754
Done!