Query 035423
Match_columns 35
No_of_seqs 100 out of 153
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 02:53:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035423.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035423hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00659 RPOLCX RNA polymera 99.8 3.6E-20 7.8E-25 90.9 4.1 34 2-35 11-44 (44)
2 KOG3507 DNA-directed RNA polym 99.8 1.1E-20 2.4E-25 99.0 -1.5 35 1-35 28-62 (62)
3 COG1996 RPC10 DNA-directed RNA 99.6 6.5E-16 1.4E-20 77.9 3.4 31 5-35 19-49 (49)
4 PF03604 DNA_RNApol_7kD: DNA d 99.6 3.6E-16 7.8E-21 72.9 1.5 25 1-25 8-32 (32)
5 PRK00398 rpoP DNA-directed RNA 98.9 1.7E-09 3.7E-14 52.1 3.5 26 10-35 21-46 (46)
6 COG1579 Zn-ribbon protein, pos 96.1 0.0013 2.8E-08 41.3 -0.2 18 6-24 217-234 (239)
7 PF14255 Cys_rich_CPXG: Cystei 93.4 0.037 8.1E-07 27.8 0.9 12 11-22 1-12 (52)
8 PF13408 Zn_ribbon_recom: Reco 92.2 0.29 6.3E-06 23.0 3.0 21 8-28 3-23 (58)
9 TIGR02098 MJ0042_CXXC MJ0042 f 91.9 0.19 4.1E-06 22.6 2.0 14 8-21 23-36 (38)
10 PF10571 UPF0547: Uncharacteri 91.7 0.071 1.5E-06 23.4 0.5 12 8-19 12-23 (26)
11 PF09538 FYDLN_acid: Protein o 90.9 0.13 2.9E-06 28.8 1.1 14 5-19 22-35 (108)
12 PF12760 Zn_Tnp_IS1595: Transp 90.4 0.48 1E-05 22.4 2.8 22 5-26 13-34 (46)
13 PF01215 COX5B: Cytochrome c o 90.4 0.13 2.9E-06 30.1 0.9 15 5-19 107-121 (136)
14 PF13719 zinc_ribbon_5: zinc-r 90.3 0.26 5.7E-06 22.6 1.7 15 6-20 21-35 (37)
15 cd00924 Cyt_c_Oxidase_Vb Cytoc 90.0 0.18 3.9E-06 27.9 1.2 19 5-23 74-92 (97)
16 PF11672 DUF3268: Protein of u 89.6 0.23 5.1E-06 27.8 1.4 13 10-22 2-14 (102)
17 PF10276 zf-CHCC: Zinc-finger 89.4 0.24 5.3E-06 23.7 1.2 11 9-19 28-38 (40)
18 PF13248 zf-ribbon_3: zinc-rib 89.3 0.15 3.3E-06 21.9 0.4 10 10-19 2-11 (26)
19 PF13717 zinc_ribbon_4: zinc-r 89.0 0.35 7.6E-06 22.2 1.6 14 7-20 22-35 (36)
20 PF09855 DUF2082: Nucleic-acid 88.9 0.34 7.3E-06 25.1 1.6 27 2-28 28-54 (64)
21 COG4391 Uncharacterized protei 88.6 0.46 1E-05 24.9 2.1 16 4-19 42-57 (62)
22 PF13240 zinc_ribbon_2: zinc-r 88.2 0.17 3.6E-06 21.5 0.2 12 9-20 12-23 (23)
23 smart00834 CxxC_CXXC_SSSS Puta 88.2 0.26 5.6E-06 22.1 0.8 12 8-19 24-35 (41)
24 PF04606 Ogr_Delta: Ogr/Delta- 87.9 0.47 1E-05 22.7 1.7 13 12-24 1-13 (47)
25 PF09723 Zn-ribbon_8: Zinc rib 87.7 0.39 8.4E-06 22.5 1.3 12 7-18 23-34 (42)
26 PF08274 PhnA_Zn_Ribbon: PhnA 87.2 0.36 7.7E-06 21.9 1.0 17 4-20 13-29 (30)
27 COG4311 SoxD Sarcosine oxidase 87.1 0.28 6.1E-06 27.7 0.7 11 9-19 2-12 (97)
28 PF02591 DUF164: Putative zinc 87.0 0.26 5.6E-06 24.1 0.5 13 5-17 40-53 (56)
29 PF03884 DUF329: Domain of unk 86.9 0.43 9.3E-06 24.4 1.3 13 10-22 2-14 (57)
30 KOG3352 Cytochrome c oxidase, 86.7 0.3 6.4E-06 29.4 0.7 18 5-24 128-145 (153)
31 PF01396 zf-C4_Topoisom: Topoi 86.6 0.61 1.3E-05 21.7 1.6 14 11-24 2-15 (39)
32 PRK00464 nrdR transcriptional 86.0 0.32 6.9E-06 28.7 0.6 8 11-18 1-8 (154)
33 PF01096 TFIIS_C: Transcriptio 85.9 0.48 1E-05 22.0 1.1 12 11-22 1-12 (39)
34 PF14690 zf-ISL3: zinc-finger 85.6 0.47 1E-05 21.8 1.0 14 10-23 2-15 (47)
35 PF14205 Cys_rich_KTR: Cystein 85.5 0.87 1.9E-05 23.4 2.0 20 10-29 4-23 (55)
36 PF08792 A2L_zn_ribbon: A2L zi 85.4 0.92 2E-05 20.7 1.9 18 9-26 2-20 (33)
37 COG2888 Predicted Zn-ribbon RN 85.1 0.53 1.1E-05 24.7 1.1 13 7-19 47-59 (61)
38 TIGR00244 transcriptional regu 85.0 0.37 8.1E-06 28.6 0.6 8 11-18 1-8 (147)
39 TIGR02605 CxxC_CxxC_SSSS putat 84.8 0.82 1.8E-05 21.6 1.6 11 8-18 24-34 (52)
40 PF07754 DUF1610: Domain of un 84.7 0.68 1.5E-05 20.2 1.2 12 7-18 13-24 (24)
41 PF06107 DUF951: Bacterial pro 84.7 0.84 1.8E-05 23.5 1.7 15 9-23 30-44 (57)
42 PLN02294 cytochrome c oxidase 84.1 1.2 2.6E-05 27.3 2.5 19 5-23 136-154 (174)
43 smart00531 TFIIE Transcription 83.4 0.57 1.2E-05 26.7 0.8 20 9-28 122-141 (147)
44 cd00246 RabGEF Nucleotide exch 83.2 0.85 1.8E-05 25.8 1.5 13 10-22 2-14 (103)
45 PRK14890 putative Zn-ribbon RN 83.2 0.75 1.6E-05 23.9 1.2 12 7-18 45-56 (59)
46 COG4481 Uncharacterized protei 83.0 0.98 2.1E-05 23.6 1.6 13 10-22 34-46 (60)
47 PF14353 CpXC: CpXC protein 82.5 0.86 1.9E-05 25.0 1.3 11 10-20 38-48 (128)
48 COG1439 Predicted nucleic acid 82.3 0.97 2.1E-05 27.6 1.6 17 8-24 151-167 (177)
49 PF09986 DUF2225: Uncharacteri 81.9 0.66 1.4E-05 28.0 0.8 15 7-21 45-59 (214)
50 PF06054 CoiA: Competence prot 81.9 2 4.3E-05 27.9 3.0 25 8-32 28-52 (375)
51 PF03119 DNA_ligase_ZBD: NAD-d 81.9 1 2.2E-05 19.8 1.2 11 12-22 1-11 (28)
52 PRK09710 lar restriction allev 81.8 2.5 5.4E-05 22.2 2.8 21 12-32 8-28 (64)
53 TIGR03831 YgiT_finger YgiT-typ 80.9 1.1 2.4E-05 20.2 1.2 17 5-21 27-43 (46)
54 TIGR01374 soxD sarcosine oxida 80.7 0.73 1.6E-05 25.2 0.6 9 11-19 2-10 (84)
55 smart00709 Zpr1 Duplicated dom 80.6 0.89 1.9E-05 26.8 1.0 10 10-19 29-38 (160)
56 smart00238 BIR Baculoviral inh 80.2 1.1 2.4E-05 22.1 1.1 13 8-20 34-46 (71)
57 KOG2691 RNA polymerase II subu 80.1 0.99 2.1E-05 26.1 1.0 26 2-27 65-92 (113)
58 PF05605 zf-Di19: Drought indu 80.0 0.84 1.8E-05 22.0 0.6 9 10-18 2-10 (54)
59 TIGR00340 zpr1_rel ZPR1-relate 79.8 0.99 2.1E-05 26.8 1.0 10 10-19 28-37 (163)
60 PF00653 BIR: Inhibitor of Apo 79.2 1.3 2.9E-05 22.1 1.2 13 8-20 34-46 (70)
61 smart00440 ZnF_C2C2 C2C2 Zinc 79.1 0.94 2E-05 21.2 0.6 11 12-22 2-12 (40)
62 COG2051 RPS27A Ribosomal prote 79.1 1.1 2.4E-05 23.8 1.0 12 10-21 19-30 (67)
63 PF03367 zf-ZPR1: ZPR1 zinc-fi 78.9 1 2.2E-05 26.4 0.9 10 10-19 30-39 (161)
64 PF08271 TF_Zn_Ribbon: TFIIB z 78.3 1.8 3.8E-05 20.1 1.5 10 11-20 1-10 (43)
65 PF14446 Prok-RING_1: Prokaryo 78.0 1.6 3.5E-05 22.2 1.3 12 7-18 18-29 (54)
66 PRK15103 paraquat-inducible me 78.0 1.4 3.1E-05 29.1 1.5 23 4-27 24-46 (419)
67 TIGR02300 FYDLN_acid conserved 77.8 1.2 2.5E-05 26.2 0.9 12 9-20 25-36 (129)
68 TIGR00310 ZPR1_znf ZPR1 zinc f 77.8 1.2 2.6E-05 27.0 1.0 10 10-19 30-39 (192)
69 PRK09678 DNA-binding transcrip 77.6 1.1 2.5E-05 23.6 0.7 15 11-27 2-16 (72)
70 PF11023 DUF2614: Protein of u 77.6 1.3 2.7E-05 25.6 1.0 14 9-22 68-81 (114)
71 PF04267 SoxD: Sarcosine oxida 77.3 0.89 1.9E-05 24.8 0.3 9 11-19 2-10 (84)
72 PF11781 RRN7: RNA polymerase 77.2 2.3 5.1E-05 19.6 1.7 17 7-24 5-21 (36)
73 PF04828 GFA: Glutathione-depe 77.1 4 8.8E-05 20.1 2.7 24 9-32 47-71 (92)
74 KOG4080 Mitochondrial ribosoma 76.9 1.1 2.5E-05 27.5 0.7 14 5-18 87-101 (176)
75 TIGR00155 pqiA_fam integral me 76.5 1.6 3.6E-05 28.7 1.4 22 4-26 27-48 (403)
76 PF10609 ParA: ParA/MinD ATPas 76.4 1.6 3.4E-05 23.5 1.1 15 6-20 61-75 (81)
77 PF01194 RNA_pol_N: RNA polyme 75.6 0.91 2E-05 23.5 0.0 11 10-20 4-14 (60)
78 PTZ00043 cytochrome c oxidase 75.5 1.6 3.4E-05 28.3 1.1 15 5-19 176-190 (268)
79 COG3478 Predicted nucleic-acid 74.7 0.93 2E-05 24.2 -0.1 26 2-27 32-57 (68)
80 COG1327 Predicted transcriptio 74.0 1.4 3E-05 26.6 0.6 7 12-18 2-8 (156)
81 PF13878 zf-C2H2_3: zinc-finge 73.7 2 4.3E-05 20.2 1.0 10 9-18 12-21 (41)
82 cd00022 BIR Baculoviral inhibi 73.3 2.3 4.9E-05 20.8 1.2 13 8-20 32-44 (69)
83 smart00714 LITAF Possible memb 73.3 2.9 6.3E-05 20.8 1.6 16 10-25 3-18 (67)
84 PRK00418 DNA gyrase inhibitor; 72.8 2.3 4.9E-05 22.1 1.1 15 9-23 5-19 (62)
85 PF14803 Nudix_N_2: Nudix N-te 72.6 2.5 5.5E-05 19.4 1.1 12 13-24 3-14 (34)
86 PF04810 zf-Sec23_Sec24: Sec23 72.5 1.6 3.5E-05 20.2 0.5 10 9-18 1-10 (40)
87 PHA00626 hypothetical protein 71.9 2.8 6.1E-05 21.8 1.3 12 12-23 2-13 (59)
88 PF08772 NOB1_Zn_bind: Nin one 71.4 2.3 5E-05 22.5 1.0 18 7-24 21-38 (73)
89 TIGR02159 PA_CoA_Oxy4 phenylac 70.8 1.9 4.2E-05 25.0 0.7 10 10-19 105-114 (146)
90 cd00729 rubredoxin_SM Rubredox 70.6 2.4 5.2E-05 19.2 0.8 11 11-21 3-13 (34)
91 PRK00423 tfb transcription ini 70.6 3 6.4E-05 26.3 1.5 18 5-22 6-24 (310)
92 PF13894 zf-C2H2_4: C2H2-type 70.4 3 6.5E-05 15.8 1.0 9 12-20 2-10 (24)
93 TIGR01206 lysW lysine biosynth 69.3 2.9 6.3E-05 21.0 1.0 9 12-20 4-12 (54)
94 PRK12496 hypothetical protein; 69.2 1.6 3.4E-05 25.6 0.1 10 11-20 144-153 (164)
95 PF07967 zf-C3HC: C3HC zinc fi 69.1 5.2 0.00011 22.2 2.1 16 8-23 41-56 (133)
96 PF13913 zf-C2HC_2: zinc-finge 69.1 2.5 5.4E-05 17.9 0.6 10 10-19 2-11 (25)
97 COG2956 Predicted N-acetylgluc 69.0 2.1 4.6E-05 29.0 0.6 17 4-20 348-364 (389)
98 PF10058 DUF2296: Predicted in 68.9 2.6 5.5E-05 21.0 0.8 9 10-18 44-52 (54)
99 PRK00564 hypA hydrogenase nick 68.1 3 6.6E-05 23.2 1.0 10 10-19 88-97 (117)
100 PF14354 Lar_restr_allev: Rest 68.0 4.1 8.8E-05 19.6 1.4 15 12-26 5-19 (61)
101 TIGR01384 TFS_arch transcripti 67.7 4 8.7E-05 21.6 1.4 13 9-21 61-73 (104)
102 cd00350 rubredoxin_like Rubred 67.5 3.1 6.7E-05 18.5 0.8 8 12-19 3-10 (33)
103 PF06750 DiS_P_DiS: Bacterial 67.1 2.3 4.9E-05 22.9 0.4 10 10-19 33-42 (92)
104 PF14311 DUF4379: Domain of un 67.1 3.1 6.6E-05 20.0 0.8 14 11-26 29-42 (55)
105 PF13465 zf-H2C2_2: Zinc-finge 67.0 3.2 7E-05 17.4 0.8 11 9-19 13-23 (26)
106 COG1545 Predicted nucleic-acid 66.9 2.9 6.3E-05 23.9 0.8 12 8-19 27-38 (140)
107 COG3024 Uncharacterized protei 66.8 3.3 7.2E-05 21.9 1.0 16 7-22 4-19 (65)
108 TIGR00686 phnA alkylphosphonat 66.4 3.5 7.6E-05 23.6 1.1 14 6-19 15-28 (109)
109 PF04502 DUF572: Family of unk 66.3 4.7 0.0001 25.7 1.7 17 11-27 78-94 (324)
110 smart00661 RPOL9 RNA polymeras 66.3 5.3 0.00012 18.5 1.6 10 10-19 20-29 (52)
111 PF08209 Sgf11: Sgf11 (transcr 66.1 5.5 0.00012 18.3 1.5 13 8-20 2-14 (33)
112 PF12677 DUF3797: Domain of un 66.1 3.6 7.7E-05 20.7 1.0 12 10-21 13-24 (49)
113 KOG2907 RNA polymerase I trans 66.1 2.7 5.8E-05 24.4 0.6 8 12-19 76-83 (116)
114 PF09237 GAGA: GAGA factor; I 66.0 5.7 0.00012 20.4 1.7 18 3-20 17-34 (54)
115 PF10122 Mu-like_Com: Mu-like 65.7 3.4 7.4E-05 20.9 0.9 10 10-19 24-33 (51)
116 PF09297 zf-NADH-PPase: NADH p 65.5 6.3 0.00014 17.2 1.6 15 6-20 17-31 (32)
117 PF14952 zf-tcix: Putative tre 65.0 2.9 6.2E-05 20.7 0.5 9 10-18 11-19 (44)
118 PF13909 zf-H2C2_5: C2H2-type 64.9 3.9 8.4E-05 16.4 0.8 10 11-20 1-10 (24)
119 PRK12286 rpmF 50S ribosomal pr 64.9 4.5 9.8E-05 20.3 1.2 16 5-20 22-37 (57)
120 PRK00415 rps27e 30S ribosomal 64.8 3.9 8.5E-05 21.1 1.0 12 9-20 10-21 (59)
121 PF13395 HNH_4: HNH endonuclea 64.7 2.9 6.4E-05 20.2 0.5 9 13-21 1-9 (54)
122 PRK03824 hypA hydrogenase nick 64.5 2.8 6.1E-05 23.8 0.5 10 10-19 107-116 (135)
123 PF00096 zf-C2H2: Zinc finger, 64.4 3.4 7.5E-05 16.2 0.6 8 12-19 2-9 (23)
124 COG1096 Predicted RNA-binding 63.7 4 8.7E-05 25.2 1.1 17 6-22 161-177 (188)
125 COG3357 Predicted transcriptio 63.7 2.7 5.8E-05 23.8 0.3 11 9-19 57-67 (97)
126 PF09158 MotCF: Bacteriophage 63.4 8.4 0.00018 21.9 2.3 17 18-34 32-48 (103)
127 PF07503 zf-HYPF: HypF finger; 63.0 4.1 8.8E-05 18.8 0.8 14 7-20 18-31 (35)
128 PF14369 zf-RING_3: zinc-finge 62.4 6.7 0.00014 17.9 1.5 14 8-21 19-32 (35)
129 PRK00432 30S ribosomal protein 62.1 5.4 0.00012 19.5 1.2 8 12-19 22-29 (50)
130 PF01783 Ribosomal_L32p: Ribos 62.0 5.5 0.00012 19.6 1.2 15 5-19 21-35 (56)
131 PF10825 DUF2752: Protein of u 61.5 3.3 7.2E-05 20.2 0.3 13 6-18 5-17 (52)
132 COG1326 Uncharacterized archae 61.5 4.2 9.1E-05 25.4 0.9 11 9-19 29-39 (201)
133 COG1645 Uncharacterized Zn-fin 61.2 9 0.00019 22.4 2.2 15 7-21 41-55 (131)
134 KOG3404 G10 protein/predicted 61.0 3.5 7.6E-05 24.6 0.4 16 4-19 125-140 (145)
135 PF01485 IBR: IBR domain; Int 60.7 5.6 0.00012 18.6 1.1 10 11-20 41-50 (64)
136 PF04161 Arv1: Arv1-like famil 60.7 5.3 0.00011 23.9 1.2 17 12-28 2-20 (208)
137 PF12773 DZR: Double zinc ribb 60.7 4.5 9.7E-05 18.8 0.7 11 9-19 28-38 (50)
138 PF10601 zf-LITAF-like: LITAF- 60.5 9.5 0.00021 19.1 2.0 17 9-25 57-73 (73)
139 TIGR03829 YokU_near_AblA uncha 60.4 4.2 9.1E-05 22.4 0.6 17 4-20 29-45 (89)
140 TIGR03655 anti_R_Lar restricti 60.3 4.3 9.4E-05 19.5 0.6 10 12-21 3-12 (53)
141 TIGR00375 conserved hypothetic 60.2 3.8 8.1E-05 27.1 0.5 10 10-20 259-268 (374)
142 PRK10220 hypothetical protein; 60.1 6.4 0.00014 22.6 1.4 14 6-19 16-29 (111)
143 PRK00807 50S ribosomal protein 59.8 5.3 0.00012 19.7 0.9 10 12-21 3-12 (52)
144 PF09082 DUF1922: Domain of un 59.8 5.3 0.00012 21.2 1.0 16 10-26 20-35 (68)
145 COG1571 Predicted DNA-binding 59.7 4.3 9.2E-05 27.6 0.7 17 10-26 367-383 (421)
146 PF05876 Terminase_GpA: Phage 59.4 4.1 8.9E-05 27.7 0.6 14 10-23 200-213 (557)
147 smart00647 IBR In Between Ring 59.3 9.2 0.0002 17.9 1.7 16 7-22 37-52 (64)
148 PF14447 Prok-RING_4: Prokaryo 59.1 4.5 9.8E-05 20.6 0.6 10 11-20 40-49 (55)
149 PF07282 OrfB_Zn_ribbon: Putat 58.7 8.1 0.00017 18.9 1.5 11 9-19 45-55 (69)
150 PRK14892 putative transcriptio 58.5 9.9 0.00022 21.1 2.0 16 6-21 17-32 (99)
151 PF01667 Ribosomal_S27e: Ribos 58.0 5.7 0.00012 20.1 0.9 10 10-19 7-16 (55)
152 COG3364 Zn-ribbon containing p 57.9 3.9 8.5E-05 23.6 0.3 9 12-20 22-30 (112)
153 PF02176 zf-TRAF: TRAF-type zi 57.7 10 0.00022 17.8 1.7 14 8-21 7-21 (60)
154 PF12172 DUF35_N: Rubredoxin-l 57.7 5 0.00011 17.9 0.6 13 10-22 11-23 (37)
155 PF14206 Cys_rich_CPCC: Cystei 57.5 6.6 0.00014 21.0 1.1 13 11-23 2-14 (78)
156 PF10263 SprT-like: SprT-like 57.4 11 0.00024 20.7 2.0 20 7-26 120-139 (157)
157 TIGR01031 rpmF_bact ribosomal 57.3 8 0.00017 19.2 1.3 15 5-19 21-35 (55)
158 PF13005 zf-IS66: zinc-finger 57.2 6.9 0.00015 17.9 1.0 12 10-21 2-13 (47)
159 COG1779 C4-type Zn-finger prot 56.8 5.5 0.00012 24.8 0.8 10 10-19 43-52 (201)
160 smart00746 TRASH metallochaper 56.8 5.7 0.00012 15.5 0.6 9 13-21 1-9 (39)
161 COG1592 Rubrerythrin [Energy p 56.5 6.2 0.00014 23.7 1.0 12 8-19 132-143 (166)
162 PF02892 zf-BED: BED zinc fing 56.3 7.5 0.00016 17.5 1.1 17 7-23 13-29 (45)
163 COG4640 Predicted membrane pro 56.1 5 0.00011 27.7 0.6 15 6-20 11-25 (465)
164 COG0551 TopA Zn-finger domain 56.0 11 0.00024 20.9 1.9 17 8-24 15-31 (140)
165 PF02748 PyrI_C: Aspartate car 55.9 10 0.00022 18.7 1.5 15 6-20 31-45 (52)
166 COG1379 PHP family phosphoeste 55.8 4.5 9.9E-05 27.5 0.3 11 10-20 265-275 (403)
167 PF01246 Ribosomal_L24e: Ribos 55.7 6.5 0.00014 20.7 0.9 11 10-20 3-13 (71)
168 PF10955 DUF2757: Protein of u 55.4 6.7 0.00014 21.1 0.9 10 11-20 5-14 (76)
169 PF04423 Rad50_zn_hook: Rad50 54.8 6.3 0.00014 18.9 0.7 14 5-19 16-29 (54)
170 PF00471 Ribosomal_L33: Riboso 54.6 12 0.00025 18.3 1.6 13 12-24 34-46 (48)
171 TIGR03830 CxxCG_CxxCG_HTH puta 54.5 14 0.00029 19.6 2.0 19 13-31 1-19 (127)
172 PF09889 DUF2116: Uncharacteri 54.5 5.5 0.00012 20.3 0.5 9 12-20 5-13 (59)
173 COG0333 RpmF Ribosomal protein 54.3 7.8 0.00017 19.8 1.0 16 5-20 22-37 (57)
174 cd00472 Ribosomal_L24e_L24 Rib 54.3 6.5 0.00014 19.7 0.7 11 10-20 3-13 (54)
175 PHA02998 RNA polymerase subuni 54.2 7.2 0.00016 24.3 1.0 13 9-21 142-154 (195)
176 COG5132 BUD31 Cell cycle contr 54.0 3.7 8E-05 24.5 -0.3 15 5-19 126-140 (146)
177 COG1997 RPL43A Ribosomal prote 53.4 3.5 7.5E-05 23.0 -0.4 17 4-20 29-45 (89)
178 COG3091 SprT Zn-dependent meta 53.4 12 0.00026 22.6 1.9 20 5-24 135-154 (156)
179 PRK11866 2-oxoacid ferredoxin 53.3 2.3 5E-05 26.9 -1.3 15 8-22 5-19 (279)
180 PRK03681 hypA hydrogenase nick 53.2 7.2 0.00016 21.6 0.8 9 11-19 88-96 (114)
181 PHA00616 hypothetical protein 52.9 4.7 0.0001 19.6 0.1 11 11-21 2-12 (44)
182 PRK04860 hypothetical protein; 52.9 14 0.0003 21.8 2.0 17 8-24 141-157 (160)
183 PF02150 RNA_POL_M_15KD: RNA p 52.8 15 0.00032 16.6 1.8 12 12-23 3-14 (35)
184 smart00614 ZnF_BED BED zinc fi 52.6 10 0.00022 17.8 1.2 16 9-24 17-32 (50)
185 PRK00595 rpmG 50S ribosomal pr 52.5 14 0.00029 18.3 1.7 12 13-24 40-51 (53)
186 PRK04136 rpl40e 50S ribosomal 52.1 8 0.00017 19.4 0.8 13 7-19 25-37 (48)
187 PF14122 YokU: YokU-like prote 52.1 8.8 0.00019 21.3 1.1 15 4-18 29-43 (87)
188 COG4049 Uncharacterized protei 52.0 6.4 0.00014 20.7 0.5 9 10-18 17-25 (65)
189 PF06677 Auto_anti-p27: Sjogre 51.8 20 0.00043 17.0 2.2 16 11-27 18-33 (41)
190 PF09845 DUF2072: Zn-ribbon co 51.7 6.2 0.00013 23.1 0.4 10 12-21 21-30 (131)
191 PF07295 DUF1451: Protein of u 51.6 12 0.00026 21.9 1.6 16 9-24 111-126 (146)
192 PRK09521 exosome complex RNA-b 51.4 9.9 0.00022 22.2 1.3 12 9-20 165-176 (189)
193 PF10533 Plant_zn_clust: Plant 51.3 13 0.00029 18.5 1.5 25 7-34 16-40 (47)
194 PTZ00255 60S ribosomal protein 51.3 3.9 8.5E-05 22.6 -0.4 17 3-19 29-45 (90)
195 smart00731 SprT SprT homologue 51.2 15 0.00032 20.6 1.9 24 8-31 110-133 (146)
196 cd02772 MopB_NDH-1_NuoG2 MopB_ 50.7 26 0.00057 22.0 3.1 23 12-34 3-27 (414)
197 PF03811 Zn_Tnp_IS1: InsA N-te 50.5 11 0.00024 17.4 1.2 14 10-23 5-19 (36)
198 PRK08351 DNA-directed RNA poly 50.5 7.6 0.00016 20.0 0.6 9 12-20 17-25 (61)
199 COG1644 RPB10 DNA-directed RNA 50.4 6.5 0.00014 20.7 0.4 12 9-20 3-14 (63)
200 COG1631 RPL42A Ribosomal prote 50.4 12 0.00026 21.0 1.4 13 10-22 68-80 (94)
201 PRK01343 zinc-binding protein; 50.2 7.2 0.00016 20.0 0.5 18 8-25 7-24 (57)
202 PF04475 DUF555: Protein of un 50.1 7.7 0.00017 22.1 0.7 16 4-20 42-57 (102)
203 TIGR00100 hypA hydrogenase nic 50.0 7 0.00015 21.6 0.5 10 10-19 86-95 (115)
204 TIGR01385 TFSII transcription 49.6 9.3 0.0002 24.5 1.0 15 6-20 254-268 (299)
205 PF05129 Elf1: Transcription e 49.6 6.8 0.00015 20.7 0.4 11 9-19 21-31 (81)
206 TIGR01023 rpmG_bact ribosomal 49.4 16 0.00035 18.2 1.7 12 13-24 41-52 (54)
207 COG1743 Adenine-specific DNA m 49.0 8.6 0.00019 28.5 0.9 10 10-19 178-187 (875)
208 PF09151 DUF1936: Domain of un 48.8 9.2 0.0002 18.0 0.7 11 12-22 3-13 (36)
209 PF15494 SRCR_2: Scavenger rec 48.7 9.4 0.0002 20.0 0.8 10 10-19 88-97 (98)
210 PRK00420 hypothetical protein; 48.6 17 0.00036 20.6 1.9 16 8-23 38-53 (112)
211 PRK02935 hypothetical protein; 48.3 10 0.00022 21.8 1.0 11 9-19 69-79 (110)
212 COG1594 RPB9 DNA-directed RNA 48.2 11 0.00023 21.0 1.0 11 10-20 72-82 (113)
213 PRK00762 hypA hydrogenase nick 48.2 7.5 0.00016 21.8 0.4 8 11-18 93-100 (124)
214 PF03330 DPBB_1: Rare lipoprot 48.1 13 0.00027 18.7 1.2 11 11-21 46-56 (78)
215 PF04216 FdhE: Protein involve 48.0 6.2 0.00013 24.4 0.0 10 10-19 211-220 (290)
216 PF15288 zf-CCHC_6: Zinc knuck 47.8 6.9 0.00015 18.8 0.2 8 11-18 2-9 (40)
217 PRK11788 tetratricopeptide rep 47.4 12 0.00026 22.5 1.2 16 4-19 348-363 (389)
218 TIGR00319 desulf_FeS4 desulfof 47.4 22 0.00048 15.5 1.9 16 8-23 5-20 (34)
219 PF10080 DUF2318: Predicted me 47.3 11 0.00024 20.9 1.0 15 6-20 48-62 (102)
220 cd00974 DSRD Desulforedoxin (D 47.2 23 0.00049 15.5 1.9 16 9-24 3-18 (34)
221 cd02768 MopB_NADH-Q-OR-NuoG2 M 46.8 32 0.0007 21.2 3.1 23 12-34 3-27 (386)
222 COG5349 Uncharacterized protei 46.8 5.4 0.00012 23.4 -0.3 18 5-22 16-33 (126)
223 PRK11032 hypothetical protein; 46.3 17 0.00037 21.7 1.7 16 9-24 123-138 (160)
224 COG1656 Uncharacterized conser 46.2 6 0.00013 24.0 -0.2 18 10-27 97-114 (165)
225 PF06676 DUF1178: Protein of u 46.2 11 0.00023 22.3 0.9 19 6-24 28-46 (148)
226 PRK04173 glycyl-tRNA synthetas 45.8 10 0.00022 25.3 0.8 15 10-24 125-148 (456)
227 PF09706 Cas_CXXC_CXXC: CRISPR 45.7 14 0.0003 18.9 1.2 20 7-26 2-21 (69)
228 PF00301 Rubredoxin: Rubredoxi 45.4 11 0.00023 18.4 0.6 8 11-18 2-9 (47)
229 cd02753 MopB_Formate-Dh-H Form 45.3 34 0.00073 22.2 3.1 23 12-34 3-27 (512)
230 PF00935 Ribosomal_L44: Riboso 45.2 16 0.00034 19.6 1.4 14 10-23 53-66 (77)
231 KOG1088 Uncharacterized conser 45.2 12 0.00026 21.9 1.0 11 9-19 97-107 (124)
232 KOG2463 Predicted RNA-binding 45.1 14 0.00031 25.0 1.4 17 7-23 254-270 (376)
233 PF14577 SEO_C: Sieve element 45.0 12 0.00027 23.6 1.1 13 7-19 211-223 (235)
234 cd02008 TPP_IOR_alpha Thiamine 44.9 4.4 9.6E-05 23.0 -0.9 17 8-24 2-18 (178)
235 TIGR00373 conserved hypothetic 44.8 16 0.00034 21.2 1.4 13 10-22 128-140 (158)
236 PF05265 DUF723: Protein of un 44.7 10 0.00022 19.7 0.5 6 12-17 55-60 (60)
237 PF08996 zf-DNA_Pol: DNA Polym 44.7 17 0.00037 21.4 1.6 15 10-24 18-32 (188)
238 PRK01103 formamidopyrimidine/5 44.7 26 0.00056 21.6 2.4 15 10-24 245-259 (274)
239 COG0846 SIR2 NAD-dependent pro 44.7 15 0.00032 23.1 1.3 14 6-19 142-155 (250)
240 PRK05978 hypothetical protein; 44.7 10 0.00022 22.4 0.6 15 9-23 32-46 (148)
241 cd04482 RPA2_OBF_like RPA2_OBF 44.6 10 0.00022 20.0 0.5 8 10-17 84-91 (91)
242 PRK11823 DNA repair protein Ra 44.6 15 0.00032 24.3 1.4 14 6-19 3-16 (446)
243 cd00368 Molybdopterin-Binding 44.4 39 0.00085 20.5 3.1 23 12-34 3-27 (374)
244 COG2093 DNA-directed RNA polym 44.2 14 0.00031 19.4 1.1 13 7-19 15-27 (64)
245 PRK10445 endonuclease VIII; Pr 43.7 27 0.00059 21.6 2.4 19 10-28 235-253 (263)
246 PRK14891 50S ribosomal protein 43.7 11 0.00024 22.2 0.6 10 11-20 5-14 (131)
247 PF14996 RMP: Retinal Maintena 43.5 16 0.00034 21.8 1.3 16 7-22 65-80 (146)
248 cd02771 MopB_NDH-1_NuoG2-N7 Mo 43.1 35 0.00076 21.9 2.9 23 12-34 3-27 (472)
249 TIGR00416 sms DNA repair prote 43.1 16 0.00035 24.3 1.4 13 7-19 4-16 (454)
250 smart00355 ZnF_C2H2 zinc finge 42.9 12 0.00026 14.0 0.5 8 12-19 2-9 (26)
251 PRK06386 replication factor A; 42.6 11 0.00024 24.9 0.6 11 11-21 237-247 (358)
252 PF09332 Mcm10: Mcm10 replicat 42.4 16 0.00035 24.1 1.3 12 11-22 286-297 (344)
253 PF06957 COPI_C: Coatomer (COP 42.4 15 0.00032 24.9 1.2 13 8-20 378-390 (422)
254 PF06524 NOA36: NOA36 protein; 42.3 14 0.00031 24.4 1.1 15 6-20 205-219 (314)
255 PRK01110 rpmF 50S ribosomal pr 42.2 22 0.00048 17.9 1.6 16 5-20 22-37 (60)
256 PF06906 DUF1272: Protein of u 42.1 11 0.00025 19.4 0.5 11 10-20 41-51 (57)
257 PF08063 PADR1: PADR1 (NUC008) 41.9 17 0.00037 18.0 1.1 17 8-24 12-29 (55)
258 PRK12380 hydrogenase nickel in 41.9 14 0.0003 20.4 0.8 11 9-19 69-79 (113)
259 PRK04016 DNA-directed RNA poly 41.8 13 0.00029 19.3 0.7 12 9-20 3-14 (62)
260 cd03375 TPP_OGFOR Thiamine pyr 41.7 3.4 7.4E-05 24.1 -1.7 11 13-23 2-12 (193)
261 PF01155 HypA: Hydrogenase exp 41.6 13 0.00029 20.3 0.8 9 11-19 71-79 (113)
262 PF08882 Acetone_carb_G: Aceto 41.2 14 0.00029 21.3 0.7 9 10-19 24-32 (112)
263 COG4530 Uncharacterized protei 41.2 13 0.00029 21.8 0.7 12 8-19 24-35 (129)
264 PRK06393 rpoE DNA-directed RNA 41.1 13 0.00028 19.4 0.6 9 11-19 18-26 (64)
265 KOG2703 C4-type Zn-finger prot 41.0 12 0.00025 26.0 0.5 10 10-19 68-77 (460)
266 TIGR00280 L37a ribosomal prote 40.9 6.6 0.00014 21.7 -0.5 17 3-19 28-44 (91)
267 PHA02768 hypothetical protein; 40.8 12 0.00025 19.0 0.4 9 11-19 6-14 (55)
268 COG2260 Predicted Zn-ribbon RN 40.8 13 0.00027 19.4 0.5 9 11-19 18-26 (59)
269 cd00730 rubredoxin Rubredoxin; 40.8 12 0.00027 18.3 0.5 8 11-18 2-9 (50)
270 COG2995 PqiA Uncharacterized p 40.6 17 0.00036 25.0 1.2 16 5-20 33-48 (418)
271 CHL00104 rpl33 ribosomal prote 40.5 24 0.00052 18.4 1.6 12 13-24 52-63 (66)
272 PRK08116 hypothetical protein; 40.3 18 0.00038 22.3 1.2 18 6-23 12-29 (268)
273 PRK03976 rpl37ae 50S ribosomal 40.2 7.3 0.00016 21.5 -0.4 17 3-19 29-45 (90)
274 PRK07218 replication factor A; 39.8 12 0.00026 25.2 0.4 10 11-20 298-307 (423)
275 TIGR00354 polC DNA polymerase, 39.8 16 0.00035 27.8 1.1 13 11-23 1029-1041(1095)
276 PF11682 DUF3279: Protein of u 39.7 27 0.00059 20.2 1.9 18 6-23 24-41 (128)
277 PF09526 DUF2387: Probable met 39.5 17 0.00036 19.0 0.9 12 8-19 28-39 (71)
278 PRK11869 2-oxoacid ferredoxin 39.4 5 0.00011 25.4 -1.3 18 6-23 4-21 (280)
279 TIGR00577 fpg formamidopyrimid 39.3 33 0.00071 21.2 2.3 15 10-24 245-259 (272)
280 COG1998 RPS31 Ribosomal protei 39.3 14 0.0003 18.7 0.5 10 11-20 20-29 (51)
281 COG0267 RpmG Ribosomal protein 39.2 25 0.00055 17.5 1.5 12 13-24 37-48 (50)
282 cd00085 HNHc HNH nucleases; HN 39.2 14 0.0003 16.3 0.5 10 11-20 12-21 (57)
283 PLN00209 ribosomal protein S27 39.2 18 0.00038 20.0 1.0 10 10-19 36-45 (86)
284 PF12013 DUF3505: Protein of u 39.1 22 0.00047 18.9 1.3 15 5-19 75-93 (109)
285 PF02318 FYVE_2: FYVE-type zin 39.1 21 0.00046 19.5 1.3 13 8-20 69-81 (118)
286 PF09696 Ctf8: Ctf8; InterPro 39.1 14 0.0003 20.7 0.6 12 16-27 109-120 (122)
287 PLN00032 DNA-directed RNA poly 38.9 17 0.00036 19.4 0.8 11 10-20 4-14 (71)
288 KOG2906 RNA polymerase III sub 38.9 51 0.0011 18.8 2.8 16 12-27 3-18 (105)
289 COG0675 Transposase and inacti 38.7 22 0.00048 20.8 1.4 8 10-17 309-316 (364)
290 PF13824 zf-Mss51: Zinc-finger 38.7 15 0.00032 18.7 0.6 12 8-19 12-23 (55)
291 TIGR02820 formald_GSH S-(hydro 38.5 14 0.00031 22.3 0.6 13 12-24 91-103 (182)
292 KOG3497 DNA-directed RNA polym 38.5 14 0.0003 19.7 0.5 11 10-20 4-14 (69)
293 PRK05767 rpl44e 50S ribosomal 38.4 23 0.00051 19.6 1.4 14 10-23 67-80 (92)
294 PF01428 zf-AN1: AN1-like Zinc 38.4 18 0.00039 16.7 0.8 12 9-20 12-23 (43)
295 TIGR02443 conserved hypothetic 38.4 17 0.00036 18.8 0.8 11 9-19 30-40 (59)
296 PRK06266 transcription initiat 38.3 16 0.00035 21.6 0.8 13 10-22 136-148 (178)
297 PRK09335 30S ribosomal protein 38.2 17 0.00037 20.4 0.8 13 8-20 18-30 (95)
298 PRK14810 formamidopyrimidine-D 38.1 18 0.00038 22.5 1.0 13 10-22 244-256 (272)
299 cd02759 MopB_Acetylene-hydrata 38.0 52 0.0011 21.4 3.1 23 12-34 3-27 (477)
300 PF06170 DUF983: Protein of un 38.0 13 0.00027 20.0 0.3 10 10-19 8-17 (86)
301 PF05180 zf-DNL: DNL zinc fing 37.8 25 0.00054 18.3 1.4 12 10-21 29-40 (66)
302 COG2126 RPL37A Ribosomal prote 37.7 11 0.00025 19.7 0.1 17 8-25 14-30 (61)
303 CHL00174 accD acetyl-CoA carbo 37.7 15 0.00033 23.8 0.6 7 12-18 59-65 (296)
304 PRK14714 DNA polymerase II lar 37.6 18 0.00039 28.0 1.1 13 11-23 1270-1282(1337)
305 TIGR02177 PorB_KorB 2-oxoacid: 37.6 4.8 0.0001 25.6 -1.6 12 11-22 2-13 (287)
306 PF11793 FANCL_C: FANCL C-term 37.5 21 0.00045 18.1 1.1 12 11-22 56-67 (70)
307 COG1552 RPL40A Ribosomal prote 37.4 9.9 0.00021 19.2 -0.2 16 6-21 24-39 (50)
308 PF01283 Ribosomal_S26e: Ribos 37.2 20 0.00042 20.6 1.0 13 8-20 18-30 (113)
309 PF00130 C1_1: Phorbol esters/ 37.1 31 0.00067 15.8 1.6 14 7-20 25-38 (53)
310 COG4888 Uncharacterized Zn rib 37.0 15 0.00034 20.9 0.6 13 10-22 22-34 (104)
311 COG4896 Uncharacterized protei 36.8 11 0.00023 20.1 -0.1 15 9-23 30-44 (68)
312 PRK14811 formamidopyrimidine-D 36.8 18 0.00039 22.5 0.9 15 10-24 235-249 (269)
313 PF12230 PRP21_like_P: Pre-mRN 36.6 12 0.00025 22.4 0.0 12 9-20 167-178 (229)
314 PF13575 DUF4135: Domain of un 36.6 23 0.00049 22.5 1.3 12 16-27 69-80 (370)
315 COG1885 Uncharacterized protei 36.5 16 0.00034 21.2 0.5 9 11-19 50-58 (115)
316 PRK05320 rhodanese superfamily 36.4 23 0.00049 21.9 1.2 18 3-20 237-254 (257)
317 PF01125 G10: G10 protein; In 36.1 17 0.00037 21.6 0.7 16 4-19 126-141 (145)
318 PF10005 DUF2248: Uncharacteri 36.0 19 0.00041 24.0 0.9 11 12-22 1-11 (343)
319 PRK04023 DNA polymerase II lar 36.0 23 0.00049 27.1 1.4 13 11-23 1054-1066(1121)
320 PRK13130 H/ACA RNA-protein com 35.6 17 0.00036 18.4 0.5 10 10-19 17-26 (56)
321 COG5525 Bacteriophage tail ass 35.5 19 0.00041 25.8 0.9 9 11-19 228-236 (611)
322 PF06397 Desulfoferrod_N: Desu 35.4 43 0.00093 15.6 1.9 17 7-23 3-19 (36)
323 COG1468 CRISPR-associated prot 35.2 31 0.00067 20.7 1.7 19 5-23 169-187 (190)
324 PLN03166 60S ribosomal protein 35.2 23 0.00049 19.7 1.0 15 6-20 37-51 (96)
325 cd00029 C1 Protein kinase C co 34.8 24 0.00053 15.6 1.0 12 8-19 26-37 (50)
326 PTZ00172 40S ribosomal protein 34.5 21 0.00045 20.4 0.8 13 8-20 18-30 (108)
327 PTZ00083 40S ribosomal protein 34.4 23 0.00051 19.5 1.0 10 10-19 35-44 (85)
328 smart00778 Prim_Zn_Ribbon Zinc 34.4 20 0.00043 16.7 0.6 9 10-18 3-11 (37)
329 PF06827 zf-FPG_IleRS: Zinc fi 34.4 44 0.00096 14.0 2.5 11 12-22 3-13 (30)
330 PF03691 UPF0167: Uncharacteri 34.2 30 0.00065 20.9 1.5 13 10-22 160-172 (176)
331 TIGR01562 FdhE formate dehydro 34.0 19 0.00041 23.3 0.7 10 10-19 224-233 (305)
332 COG1773 Rubredoxin [Energy pro 33.9 18 0.0004 18.3 0.5 8 11-18 4-11 (55)
333 PF11648 RIG-I_C-RD: C-termina 33.9 16 0.00034 20.5 0.2 15 5-19 55-69 (123)
334 PF10367 Vps39_2: Vacuolar sor 33.8 16 0.00035 18.6 0.3 16 7-22 75-90 (109)
335 PF14319 Zn_Tnp_IS91: Transpos 33.5 24 0.00053 19.4 1.0 15 7-21 39-53 (111)
336 TIGR02652 conserved hypothetic 33.5 14 0.00031 22.4 0.1 14 7-20 6-19 (163)
337 PF08295 Sin3_corepress: Sin3 33.5 13 0.00027 20.6 -0.2 14 12-25 1-16 (101)
338 PF08273 Prim_Zn_Ribbon: Zinc- 33.4 19 0.00042 17.0 0.5 8 11-18 4-11 (40)
339 PLN00186 ribosomal protein S26 33.2 23 0.00049 20.3 0.8 13 8-20 18-30 (109)
340 smart00734 ZnF_Rad18 Rad18-lik 33.2 21 0.00046 15.1 0.6 10 11-20 2-11 (26)
341 PF10083 DUF2321: Uncharacteri 33.0 18 0.00039 21.9 0.4 10 11-20 40-49 (158)
342 PRK04059 rpl34e 50S ribosomal 33.0 26 0.00056 19.2 1.0 15 6-20 30-44 (88)
343 PF09862 DUF2089: Protein of u 32.9 36 0.00078 19.3 1.6 9 13-21 1-9 (113)
344 PRK14715 DNA polymerase II lar 32.7 27 0.00058 27.7 1.3 13 11-23 1558-1570(1627)
345 COG3791 Uncharacterized conser 32.5 31 0.00066 19.3 1.3 16 11-26 70-85 (133)
346 PF02146 SIR2: Sir2 family; I 32.4 26 0.00057 19.9 1.0 12 8-19 127-138 (178)
347 PRK00504 rpmG 50S ribosomal pr 32.3 41 0.00089 16.5 1.6 12 13-24 37-48 (50)
348 PF08394 Arc_trans_TRASH: Arch 32.2 21 0.00046 16.7 0.5 8 13-20 1-8 (37)
349 PF01780 Ribosomal_L37ae: Ribo 32.2 6.9 0.00015 21.6 -1.3 17 4-20 29-45 (90)
350 COG4830 RPS26B Ribosomal prote 32.2 22 0.00047 20.4 0.6 12 9-20 19-30 (108)
351 cd00162 RING RING-finger (Real 32.0 22 0.00047 14.8 0.5 10 10-19 35-44 (45)
352 PF14149 YhfH: YhfH-like prote 31.7 6.1 0.00013 18.8 -1.4 15 6-20 9-23 (37)
353 PF11290 DUF3090: Protein of u 31.7 21 0.00045 21.8 0.5 9 12-20 156-164 (171)
354 PHA02942 putative transposase; 31.6 28 0.0006 22.8 1.1 10 10-19 342-351 (383)
355 PF12322 T4_baseplate: T4 bact 31.5 23 0.0005 21.5 0.7 12 7-19 181-192 (205)
356 TIGR00269 conserved hypothetic 31.5 23 0.00049 19.0 0.6 11 9-19 79-89 (104)
357 PRK03954 ribonuclease P protei 31.5 26 0.00057 20.0 0.9 11 9-19 92-102 (121)
358 PRK08665 ribonucleotide-diphos 31.2 25 0.00054 25.1 0.9 13 11-23 725-737 (752)
359 TIGR01054 rgy reverse gyrase. 31.2 21 0.00045 26.7 0.6 12 9-20 6-17 (1171)
360 PTZ00157 60S ribosomal protein 31.1 34 0.00073 18.7 1.3 13 10-22 69-81 (84)
361 PF09814 HECT_2: HECT-like Ubi 31.0 30 0.00064 21.5 1.2 17 5-21 100-117 (354)
362 PF06769 Plasmid_Txe: Plasmid 30.9 74 0.0016 16.8 2.5 19 17-35 59-77 (80)
363 TIGR00598 rad14 DNA repair pro 30.9 37 0.0008 20.7 1.5 12 11-22 158-169 (172)
364 PRK11867 2-oxoglutarate ferred 30.9 6.8 0.00015 24.7 -1.7 15 8-22 15-29 (286)
365 cd02750 MopB_Nitrate-R-NarG-li 30.6 82 0.0018 20.4 3.2 24 11-34 7-32 (461)
366 PF13453 zf-TFIIB: Transcripti 30.6 23 0.00051 16.0 0.5 8 12-19 1-8 (41)
367 COG1060 ThiH Thiamine biosynth 30.6 20 0.00043 23.6 0.4 11 10-20 70-80 (370)
368 PF09654 DUF2396: Protein of u 30.6 17 0.00038 22.0 0.1 13 8-20 4-16 (161)
369 COG1198 PriA Primosomal protei 30.5 31 0.00067 24.9 1.3 10 10-19 475-484 (730)
370 TIGR03847 conserved hypothetic 30.5 22 0.00048 21.9 0.5 9 12-20 158-166 (177)
371 PF12653 DUF3785: Protein of u 30.5 43 0.00094 19.9 1.7 13 10-22 120-132 (138)
372 PF03243 MerB: Alkylmercury ly 30.5 1E+02 0.0022 17.1 3.2 21 11-31 40-60 (127)
373 COG0635 HemN Coproporphyrinoge 30.5 29 0.00063 22.9 1.1 17 10-26 45-61 (416)
374 TIGR00595 priA primosomal prot 30.5 50 0.0011 22.2 2.2 8 12-19 224-231 (505)
375 PF09963 DUF2197: Uncharacteri 30.2 13 0.00029 18.9 -0.4 16 6-21 27-42 (56)
376 COG5415 Predicted integral mem 30.0 22 0.00047 23.0 0.4 15 4-18 186-200 (251)
377 PF06044 DRP: Dam-replacing fa 29.8 21 0.00045 23.1 0.3 14 10-23 31-44 (254)
378 smart00109 C1 Protein kinase C 29.8 18 0.0004 15.8 0.1 11 9-19 26-36 (49)
379 smart00507 HNHc HNH nucleases. 29.7 22 0.00047 15.3 0.3 11 11-21 11-21 (52)
380 cd02018 TPP_PFOR Thiamine pyro 29.5 7.1 0.00015 23.6 -1.7 14 11-24 6-19 (237)
381 PF01844 HNH: HNH endonuclease 29.5 24 0.00052 15.6 0.5 10 13-22 1-10 (47)
382 COG4647 AcxC Acetone carboxyla 29.4 23 0.00049 21.5 0.4 8 11-18 121-128 (165)
383 PF15616 TerY-C: TerY-C metal 29.4 57 0.0012 19.0 2.1 16 8-23 103-118 (131)
384 TIGR02646 conserved hypothetic 29.4 22 0.00048 20.0 0.4 12 9-20 23-34 (144)
385 PRK14873 primosome assembly pr 29.4 60 0.0013 23.0 2.5 10 10-19 410-419 (665)
386 TIGR01053 LSD1 zinc finger dom 29.2 39 0.00084 15.1 1.1 13 11-23 2-14 (31)
387 PF06467 zf-FCS: MYM-type Zinc 29.2 40 0.00087 14.8 1.2 15 7-21 3-17 (43)
388 TIGR03129 one_C_dehyd_B formyl 29.1 83 0.0018 19.5 2.9 22 11-32 2-26 (421)
389 cd02754 MopB_Nitrate-R-NapA-li 29.1 88 0.0019 20.6 3.1 23 12-34 3-27 (565)
390 COG2331 Uncharacterized protei 29.1 27 0.00057 19.2 0.6 12 8-19 31-42 (82)
391 PF04032 Rpr2: RNAse P Rpr2/Rp 29.0 27 0.00058 17.4 0.6 9 10-18 77-85 (85)
392 PF02701 zf-Dof: Dof domain, z 29.0 32 0.00069 18.1 0.9 13 6-18 1-13 (63)
393 PRK03988 translation initiatio 28.9 32 0.0007 19.9 1.0 10 10-19 102-111 (138)
394 cd04511 Nudix_Hydrolase_4 Memb 28.8 27 0.00058 18.5 0.6 7 13-19 1-7 (130)
395 PF14599 zinc_ribbon_6: Zinc-r 28.8 25 0.00054 17.9 0.5 8 11-18 49-56 (61)
396 PRK13945 formamidopyrimidine-D 28.7 29 0.00064 21.6 0.9 14 10-23 254-267 (282)
397 PF03966 Trm112p: Trm112p-like 28.4 30 0.00066 17.2 0.7 11 9-19 52-62 (68)
398 PRK03922 hypothetical protein; 28.4 27 0.00058 20.2 0.6 10 10-19 49-58 (113)
399 PF01199 Ribosomal_L34e: Ribos 28.2 28 0.00061 19.2 0.6 15 6-20 37-51 (94)
400 COG2023 RPR2 RNase P subunit R 28.1 48 0.001 18.8 1.6 14 9-22 81-94 (105)
401 cd02752 MopB_Formate-Dh-Na-lik 27.8 91 0.002 21.9 3.2 22 12-33 3-26 (649)
402 PRK07726 DNA topoisomerase III 27.8 32 0.00069 23.9 1.0 14 10-23 610-623 (658)
403 PF14634 zf-RING_5: zinc-RING 27.7 31 0.00067 15.6 0.7 10 8-17 34-43 (44)
404 TIGR00320 dfx_rbo desulfoferro 27.7 44 0.00096 18.9 1.4 15 8-22 5-19 (125)
405 TIGR03336 IOR_alpha indolepyru 27.5 14 0.00031 25.0 -0.7 18 5-22 351-368 (595)
406 TIGR01591 Fdh-alpha formate de 27.5 95 0.0021 20.9 3.1 22 13-34 3-26 (671)
407 PF10891 DUF2719: Protein of u 27.5 37 0.00081 18.6 1.0 12 7-18 19-30 (81)
408 PF06221 zf-C2HC5: Putative zi 27.4 28 0.0006 17.6 0.5 12 10-21 35-46 (57)
409 PRK03564 formate dehydrogenase 27.4 29 0.00062 22.6 0.7 9 10-18 226-234 (309)
410 cd02762 MopB_1 The MopB_1 CD i 27.4 90 0.002 20.6 3.0 23 12-34 3-27 (539)
411 PRK09401 reverse gyrase; Revie 27.3 27 0.00058 26.2 0.6 11 10-20 7-17 (1176)
412 PRK11865 pyruvate ferredoxin o 27.1 8.4 0.00018 24.7 -1.8 14 10-23 18-31 (299)
413 PRK05654 acetyl-CoA carboxylas 27.0 21 0.00046 22.8 0.0 17 7-24 24-40 (292)
414 TIGR02116 toxin_Txe_YoeB toxin 26.9 95 0.0021 15.5 2.8 24 11-34 52-76 (80)
415 cd02755 MopB_Thiosulfate-R-lik 26.7 90 0.002 20.2 2.8 22 12-33 4-27 (454)
416 PRK05417 glutathione-dependent 26.7 29 0.00063 21.1 0.6 12 12-23 95-106 (191)
417 TIGR02174 CXXU_selWTH selT/sel 26.6 30 0.00064 17.5 0.5 9 11-19 4-12 (72)
418 PF01907 Ribosomal_L37e: Ribos 26.6 57 0.0012 16.6 1.6 13 9-21 14-26 (55)
419 PF01930 Cas_Cas4: Domain of u 26.6 40 0.00088 18.6 1.1 12 8-19 146-157 (162)
420 PF00098 zf-CCHC: Zinc knuckle 26.5 32 0.00069 13.5 0.5 7 12-18 2-8 (18)
421 smart00653 eIF2B_5 domain pres 26.4 39 0.00084 18.8 1.0 10 10-19 80-89 (110)
422 cd04792 LanM-like LanM-like pr 26.3 36 0.00078 23.6 1.0 12 17-28 113-124 (825)
423 PF04438 zf-HIT: HIT zinc fing 25.9 50 0.0011 14.5 1.2 11 9-19 12-22 (30)
424 PF13912 zf-C2H2_6: C2H2-type 25.8 42 0.00091 13.3 0.8 9 11-19 2-10 (27)
425 PF10164 DUF2367: Uncharacteri 25.8 32 0.00068 19.4 0.6 10 10-19 88-97 (98)
426 COG3813 Uncharacterized protei 25.5 32 0.00068 18.9 0.5 13 12-24 43-55 (84)
427 cd01412 SIRT5_Af1_CobB SIRT5_A 25.3 33 0.00072 20.2 0.6 11 9-19 129-139 (224)
428 COG1856 Uncharacterized homolo 25.3 8.1 0.00018 25.2 -2.1 13 10-22 22-34 (275)
429 cd01675 RNR_III Class III ribo 25.1 31 0.00067 23.6 0.5 12 8-19 530-541 (555)
430 COG5216 Uncharacterized conser 25.0 34 0.00074 18.1 0.6 10 9-18 43-52 (67)
431 TIGR00515 accD acetyl-CoA carb 25.0 27 0.00058 22.3 0.2 12 9-20 25-36 (285)
432 smart00154 ZnF_AN1 AN1-like Zi 24.7 46 0.001 15.2 0.9 11 10-20 12-22 (39)
433 PF05191 ADK_lid: Adenylate ki 24.6 33 0.00072 15.6 0.4 7 12-18 3-9 (36)
434 PF01873 eIF-5_eIF-2B: Domain 24.5 33 0.00071 19.4 0.5 9 11-19 94-102 (125)
435 KOG3456 NADH:ubiquinone oxidor 24.3 35 0.00076 19.9 0.6 13 7-19 101-113 (120)
436 PF01258 zf-dskA_traR: Prokary 24.2 56 0.0012 14.3 1.2 10 13-22 6-15 (36)
437 PRK00893 aspartate carbamoyltr 24.1 57 0.0012 19.4 1.5 14 7-20 131-144 (152)
438 PRK02048 4-hydroxy-3-methylbut 24.0 46 0.001 23.9 1.2 18 4-22 512-529 (611)
439 COG4307 Uncharacterized protei 23.8 48 0.0011 22.2 1.2 15 11-25 4-18 (349)
440 PF11789 zf-Nse: Zinc-finger o 23.8 43 0.00093 16.5 0.8 12 7-18 21-32 (57)
441 COG1405 SUA7 Transcription ini 23.5 35 0.00075 21.8 0.5 10 11-20 2-11 (285)
442 COG5319 Uncharacterized protei 23.5 42 0.00091 20.1 0.8 12 8-19 30-41 (142)
443 cd01411 SIR2H SIR2H: Uncharact 23.4 43 0.00093 20.1 0.9 10 10-19 136-145 (225)
444 COG5533 UBP5 Ubiquitin C-termi 23.4 31 0.00067 23.6 0.3 17 3-19 277-293 (415)
445 PTZ00033 60S ribosomal protein 23.4 36 0.00078 19.9 0.5 11 10-20 3-13 (125)
446 COG0375 HybF Zn finger protein 23.3 1.1E+02 0.0023 17.5 2.5 9 11-19 87-95 (115)
447 PF01927 Mut7-C: Mut7-C RNAse 23.3 66 0.0014 18.1 1.6 15 10-25 91-105 (147)
448 KOG2817 Predicted E3 ubiquitin 23.2 32 0.00068 23.5 0.3 14 5-18 367-382 (394)
449 cd01121 Sms Sms (bacterial rad 23.2 37 0.0008 22.1 0.6 8 11-18 15-22 (372)
450 PF00645 zf-PARP: Poly(ADP-rib 23.2 62 0.0013 16.2 1.4 15 7-21 4-18 (82)
451 PRK05776 DNA topoisomerase I; 23.1 58 0.0013 22.9 1.5 11 10-20 596-606 (670)
452 PRK00241 nudC NADH pyrophospha 23.1 34 0.00073 21.1 0.4 11 12-22 101-111 (256)
453 PTZ00074 60S ribosomal protein 23.1 48 0.001 19.5 1.0 15 6-20 37-51 (135)
454 PHA02325 hypothetical protein 23.0 63 0.0014 17.3 1.4 13 9-21 2-14 (72)
455 PF11331 DUF3133: Protein of u 22.9 84 0.0018 15.3 1.7 18 8-25 29-46 (46)
456 PRK07219 DNA topoisomerase I; 22.9 52 0.0011 23.6 1.3 16 10-25 602-617 (822)
457 cd01407 SIR2-fam SIR2 family o 22.8 47 0.001 19.6 1.0 11 9-19 132-142 (218)
458 KOG0320 Predicted E3 ubiquitin 22.8 36 0.00079 21.1 0.5 12 10-21 167-178 (187)
459 TIGR00433 bioB biotin syntheta 22.7 31 0.00066 20.7 0.1 16 8-23 38-53 (296)
460 PF10238 Eapp_C: E2F-associate 22.6 54 0.0012 19.1 1.2 20 6-25 105-124 (136)
461 TIGR01051 topA_bact DNA topois 22.5 64 0.0014 22.3 1.7 14 11-24 575-588 (610)
462 PRK07220 DNA topoisomerase I; 22.5 62 0.0013 23.0 1.6 15 10-24 589-603 (740)
463 PF10235 Cript: Microtubule-as 22.4 42 0.0009 18.5 0.6 11 11-21 70-80 (90)
464 TIGR00311 aIF-2beta translatio 22.4 51 0.0011 18.9 1.0 10 10-19 97-106 (133)
465 COG0777 AccD Acetyl-CoA carbox 22.3 35 0.00077 22.5 0.4 16 7-23 25-40 (294)
466 PF13451 zf-trcl: Probable zin 22.3 78 0.0017 15.6 1.5 13 10-22 4-16 (49)
467 PF01430 HSP33: Hsp33 protein; 22.2 63 0.0014 20.0 1.5 14 9-22 265-278 (280)
468 PF04135 Nop10p: Nucleolar RNA 22.1 44 0.00095 16.7 0.6 8 12-19 19-26 (53)
469 PF04060 FeS: Putative Fe-S cl 22.0 42 0.0009 15.1 0.5 11 9-19 3-13 (35)
470 PRK12495 hypothetical protein; 21.9 34 0.00074 21.8 0.2 12 10-21 42-53 (226)
471 KOG3125 Thymidine kinase [Nucl 21.8 56 0.0012 20.9 1.2 24 10-33 165-188 (234)
472 COG4469 CoiA Competence protei 21.8 52 0.0011 22.1 1.1 20 10-29 25-44 (342)
473 cd00296 SIR2 SIR2 superfamily 21.7 41 0.0009 19.4 0.6 11 9-19 133-143 (222)
474 PRK04351 hypothetical protein; 21.7 1.1E+02 0.0024 17.7 2.4 15 9-23 111-125 (149)
475 smart00132 LIM Zinc-binding do 21.6 42 0.00091 13.7 0.5 10 12-21 1-10 (39)
476 TIGR02487 NrdD anaerobic ribon 21.4 42 0.0009 23.2 0.6 9 11-19 539-547 (579)
477 TIGR00143 hypF [NiFe] hydrogen 21.2 68 0.0015 22.9 1.6 17 8-24 138-154 (711)
478 COG1601 GCD7 Translation initi 21.0 47 0.001 19.6 0.7 9 10-18 105-113 (151)
479 cd01413 SIR2_Af2 SIR2_Af2: Arc 21.0 46 0.00099 19.9 0.6 11 9-19 135-145 (222)
480 PF03470 zf-XS: XS zinc finger 20.9 43 0.00093 16.2 0.4 7 13-19 1-7 (43)
481 PF05502 Dynactin_p62: Dynacti 20.9 44 0.00096 22.7 0.6 19 5-24 293-311 (483)
482 PRK08780 DNA topoisomerase I; 20.7 77 0.0017 22.7 1.8 14 11-24 592-605 (780)
483 PF08421 Methyltransf_13: Puta 20.6 83 0.0018 15.4 1.5 10 13-22 1-10 (62)
484 cd02757 MopB_Arsenate-R This C 20.6 1.5E+02 0.0033 19.7 3.1 23 12-34 5-29 (523)
485 PRK14704 anaerobic ribonucleos 20.6 43 0.00094 23.5 0.5 9 11-19 573-581 (618)
486 COG1655 Uncharacterized protei 20.6 34 0.00073 22.3 0.0 14 6-19 58-71 (267)
487 KOG3940 Uncharacterized conser 20.5 58 0.0013 22.0 1.1 11 9-19 321-331 (351)
488 PRK12336 translation initiatio 20.4 57 0.0012 19.6 1.0 10 10-19 98-107 (201)
489 PRK09129 NADH dehydrogenase su 20.3 1.5E+02 0.0032 20.7 3.1 24 11-34 220-245 (776)
490 COG4357 Zinc finger domain con 20.2 45 0.00097 19.1 0.5 12 8-19 78-89 (105)
491 PF13597 NRDD: Anaerobic ribon 20.2 74 0.0016 21.8 1.6 13 10-22 504-517 (546)
492 cd02763 MopB_2 The MopB_2 CD i 20.0 1.4E+02 0.0031 21.1 3.0 23 12-34 3-27 (679)
493 smart00532 LIGANc Ligase N fam 20.0 61 0.0013 21.9 1.1 14 9-22 398-411 (441)
No 1
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=99.81 E-value=3.6e-20 Score=90.92 Aligned_cols=34 Identities=68% Similarity=1.249 Sum_probs=32.5
Q ss_pred ccccCCCCceecCCCCCeEEEeecCCceEEEEeC
Q 035423 2 ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35 (35)
Q Consensus 2 ~~~lk~~~~irC~~CG~RIlyK~R~~~~~~~~Ar 35 (35)
+++++.+++|+||+||||||||+||+++++|+||
T Consensus 11 ~~~~~~~~~irC~~CG~rIlyK~R~~~~~~~~Ar 44 (44)
T smart00659 11 ENEIKSKDVVRCRECGYRILYKKRTKRLVEVKAR 44 (44)
T ss_pred EeecCCCCceECCCCCceEEEEeCCCceEEEEcC
Confidence 6788999999999999999999999999999997
No 2
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=99.77 E-value=1.1e-20 Score=99.03 Aligned_cols=35 Identities=83% Similarity=1.401 Sum_probs=33.7
Q ss_pred CccccCCCCceecCCCCCeEEEeecCCceEEEEeC
Q 035423 1 MENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35 (35)
Q Consensus 1 ~~~~lk~~~~irC~~CG~RIlyK~R~~~~~~~~Ar 35 (35)
.+|+|+.+|+|||++||||||||+|+++++||+||
T Consensus 28 ~en~lk~~D~irCReCG~RIlyKkRtkrlvqfear 62 (62)
T KOG3507|consen 28 QENTLKRGDVIRCRECGYRILYKKRTKRLVQFEAR 62 (62)
T ss_pred ccccccCCCcEehhhcchHHHHHHHHhhhheeecC
Confidence 47999999999999999999999999999999997
No 3
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=99.61 E-value=6.5e-16 Score=77.89 Aligned_cols=31 Identities=35% Similarity=0.515 Sum_probs=29.7
Q ss_pred cCCCCceecCCCCCeEEEeecCCceEEEEeC
Q 035423 5 LKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35 (35)
Q Consensus 5 lk~~~~irC~~CG~RIlyK~R~~~~~~~~Ar 35 (35)
++.++.||||+||||||||.||+.+++|+|+
T Consensus 19 ~~~~~~irCp~Cg~rIl~K~R~~~~krvkA~ 49 (49)
T COG1996 19 DQETRGIRCPYCGSRILVKERPKVPKRVKAR 49 (49)
T ss_pred hhccCceeCCCCCcEEEEeccCCccEEEecC
Confidence 6789999999999999999999999999997
No 4
>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=99.59 E-value=3.6e-16 Score=72.93 Aligned_cols=25 Identities=72% Similarity=1.226 Sum_probs=19.8
Q ss_pred CccccCCCCceecCCCCCeEEEeec
Q 035423 1 MENTLKPGDVIQCRECGYRILYKKR 25 (35)
Q Consensus 1 ~~~~lk~~~~irC~~CG~RIlyK~R 25 (35)
++|+|+.+|+|||++||||||||+|
T Consensus 8 ~~~~~~~~~~irC~~CG~RIlyK~R 32 (32)
T PF03604_consen 8 AEVELKPGDPIRCPECGHRILYKKR 32 (32)
T ss_dssp SSE-BSTSSTSSBSSSS-SEEBE--
T ss_pred CeeEcCCCCcEECCcCCCeEEEecC
Confidence 3688999999999999999999998
No 5
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=98.92 E-value=1.7e-09 Score=52.15 Aligned_cols=26 Identities=42% Similarity=0.888 Sum_probs=25.0
Q ss_pred ceecCCCCCeEEEeecCCceEEEEeC
Q 035423 10 VIQCRECGYRILYKKRTRRIVQYEAR 35 (35)
Q Consensus 10 ~irC~~CG~RIlyK~R~~~~~~~~Ar 35 (35)
.++||+||++++||.|++.++.++|+
T Consensus 21 ~~~Cp~CG~~~~~~~~~~~v~~~~~~ 46 (46)
T PRK00398 21 GVRCPYCGYRILFKERPPVVKRVKAR 46 (46)
T ss_pred ceECCCCCCeEEEccCCCcceEeecC
Confidence 89999999999999999999999986
No 6
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=96.13 E-value=0.0013 Score=41.26 Aligned_cols=18 Identities=44% Similarity=0.997 Sum_probs=14.5
Q ss_pred CCCCceecCCCCCeEEEee
Q 035423 6 KPGDVIQCRECGYRILYKK 24 (35)
Q Consensus 6 k~~~~irC~~CG~RIlyK~ 24 (35)
+..+.|.||+|| ||||..
T Consensus 217 ~~d~iv~CP~Cg-RILy~~ 234 (239)
T COG1579 217 KKDEIVFCPYCG-RILYYD 234 (239)
T ss_pred cCCCCccCCccc-hHHHhh
Confidence 467889999999 678754
No 7
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=93.44 E-value=0.037 Score=27.77 Aligned_cols=12 Identities=50% Similarity=0.822 Sum_probs=9.8
Q ss_pred eecCCCCCeEEE
Q 035423 11 IQCRECGYRILY 22 (35)
Q Consensus 11 irC~~CG~RIly 22 (35)
|.||+||+.|-.
T Consensus 1 i~CPyCge~~~~ 12 (52)
T PF14255_consen 1 IQCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCCeeEE
Confidence 579999998754
No 8
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=92.19 E-value=0.29 Score=23.04 Aligned_cols=21 Identities=24% Similarity=0.765 Sum_probs=16.4
Q ss_pred CCceecCCCCCeEEEeecCCc
Q 035423 8 GDVIQCRECGYRILYKKRTRR 28 (35)
Q Consensus 8 ~~~irC~~CG~RIlyK~R~~~ 28 (35)
...++|.+||++...+.++..
T Consensus 3 ~g~l~C~~CG~~m~~~~~~~~ 23 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTRRKRKGK 23 (58)
T ss_pred CCcEEcccCCcEeEEEECCCC
Confidence 356899999999888776643
No 9
>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=91.89 E-value=0.19 Score=22.65 Aligned_cols=14 Identities=29% Similarity=0.795 Sum_probs=10.9
Q ss_pred CCceecCCCCCeEE
Q 035423 8 GDVIQCRECGYRIL 21 (35)
Q Consensus 8 ~~~irC~~CG~RIl 21 (35)
+..++|++||+.+.
T Consensus 23 ~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 23 GGKVRCGKCGHVWY 36 (38)
T ss_pred CCEEECCCCCCEEE
Confidence 34699999999753
No 10
>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=91.70 E-value=0.071 Score=23.41 Aligned_cols=12 Identities=33% Similarity=0.880 Sum_probs=9.5
Q ss_pred CCceecCCCCCe
Q 035423 8 GDVIQCRECGYR 19 (35)
Q Consensus 8 ~~~irC~~CG~R 19 (35)
.....||+|||-
T Consensus 12 ~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 12 ESAKFCPHCGYD 23 (26)
T ss_pred hhcCcCCCCCCC
Confidence 456789999985
No 11
>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=90.89 E-value=0.13 Score=28.81 Aligned_cols=14 Identities=43% Similarity=0.904 Sum_probs=11.2
Q ss_pred cCCCCceecCCCCCe
Q 035423 5 LKPGDVIQCRECGYR 19 (35)
Q Consensus 5 lk~~~~irC~~CG~R 19 (35)
|+. ++|.||+||.-
T Consensus 22 Lnk-~PivCP~CG~~ 35 (108)
T PF09538_consen 22 LNK-DPIVCPKCGTE 35 (108)
T ss_pred CCC-CCccCCCCCCc
Confidence 455 78999999974
No 12
>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=90.45 E-value=0.48 Score=22.41 Aligned_cols=22 Identities=27% Similarity=0.552 Sum_probs=16.9
Q ss_pred cCCCCceecCCCCCeEEEeecC
Q 035423 5 LKPGDVIQCRECGYRILYKKRT 26 (35)
Q Consensus 5 lk~~~~irC~~CG~RIlyK~R~ 26 (35)
+.=.+++.||.||+.-.|..++
T Consensus 13 ~RW~~g~~CP~Cg~~~~~~~~~ 34 (46)
T PF12760_consen 13 IRWPDGFVCPHCGSTKHYRLKT 34 (46)
T ss_pred hcCCCCCCCCCCCCeeeEEeCC
Confidence 3445668899999987887776
No 13
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=90.37 E-value=0.13 Score=30.06 Aligned_cols=15 Identities=40% Similarity=0.833 Sum_probs=12.6
Q ss_pred cCCCCceecCCCCCe
Q 035423 5 LKPGDVIQCRECGYR 19 (35)
Q Consensus 5 lk~~~~irC~~CG~R 19 (35)
|..+.+-||++||+=
T Consensus 107 l~~g~~~RCpeCG~~ 121 (136)
T PF01215_consen 107 LHKGKPQRCPECGQV 121 (136)
T ss_dssp EETTSEEEETTTEEE
T ss_pred EeCCCccCCCCCCeE
Confidence 567889999999983
No 14
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=90.30 E-value=0.26 Score=22.64 Aligned_cols=15 Identities=27% Similarity=0.753 Sum_probs=11.8
Q ss_pred CCCCceecCCCCCeE
Q 035423 6 KPGDVIQCRECGYRI 20 (35)
Q Consensus 6 k~~~~irC~~CG~RI 20 (35)
..+..+||+.||+..
T Consensus 21 ~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 21 AGGRKVRCPKCGHVF 35 (37)
T ss_pred cCCcEEECCCCCcEe
Confidence 346689999999864
No 15
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=89.97 E-value=0.18 Score=27.91 Aligned_cols=19 Identities=32% Similarity=0.607 Sum_probs=14.6
Q ss_pred cCCCCceecCCCCCeEEEe
Q 035423 5 LKPGDVIQCRECGYRILYK 23 (35)
Q Consensus 5 lk~~~~irC~~CG~RIlyK 23 (35)
|..+.+-||++||+=...+
T Consensus 74 l~~g~~~rC~eCG~~fkL~ 92 (97)
T cd00924 74 LEKGKPKRCPECGHVFKLV 92 (97)
T ss_pred EeCCCceeCCCCCcEEEEE
Confidence 5677899999999954433
No 16
>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=89.59 E-value=0.23 Score=27.79 Aligned_cols=13 Identities=31% Similarity=0.457 Sum_probs=11.5
Q ss_pred ceecCCCCCeEEE
Q 035423 10 VIQCRECGYRILY 22 (35)
Q Consensus 10 ~irC~~CG~RIly 22 (35)
+++||+||-.+.+
T Consensus 2 p~~CpYCg~~~~l 14 (102)
T PF11672_consen 2 PIICPYCGGPAEL 14 (102)
T ss_pred CcccCCCCCeeEE
Confidence 6899999998876
No 17
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=89.37 E-value=0.24 Score=23.68 Aligned_cols=11 Identities=36% Similarity=0.869 Sum_probs=9.3
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
..+.|||||-+
T Consensus 28 ~~~~CpYCg~~ 38 (40)
T PF10276_consen 28 GPVVCPYCGTR 38 (40)
T ss_dssp CEEEETTTTEE
T ss_pred CeEECCCCCCE
Confidence 46999999976
No 18
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=89.27 E-value=0.15 Score=21.87 Aligned_cols=10 Identities=30% Similarity=0.860 Sum_probs=7.0
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
.+.||+||..
T Consensus 2 ~~~Cp~Cg~~ 11 (26)
T PF13248_consen 2 EMFCPNCGAE 11 (26)
T ss_pred cCCCcccCCc
Confidence 4678888874
No 19
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=89.02 E-value=0.35 Score=22.22 Aligned_cols=14 Identities=29% Similarity=0.857 Sum_probs=11.0
Q ss_pred CCCceecCCCCCeE
Q 035423 7 PGDVIQCRECGYRI 20 (35)
Q Consensus 7 ~~~~irC~~CG~RI 20 (35)
.+..++|+.||+.+
T Consensus 22 ~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 22 KGRKVRCSKCGHVF 35 (36)
T ss_pred CCcEEECCCCCCEe
Confidence 45679999999864
No 20
>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=88.86 E-value=0.34 Score=25.13 Aligned_cols=27 Identities=30% Similarity=0.634 Sum_probs=21.5
Q ss_pred ccccCCCCceecCCCCCeEEEeecCCc
Q 035423 2 ENTLKPGDVIQCRECGYRILYKKRTRR 28 (35)
Q Consensus 2 ~~~lk~~~~irC~~CG~RIlyK~R~~~ 28 (35)
+++.+....+-|++|||-=||+.-+..
T Consensus 28 dvq~~~f~~v~C~~CGYTE~Y~~~~~~ 54 (64)
T PF09855_consen 28 DVQNKKFTTVSCTNCGYTEFYKAKTSN 54 (64)
T ss_pred EecCcEEEEEECCCCCCEEEEeecCcc
Confidence 445566778999999999999976654
No 21
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=88.63 E-value=0.46 Score=24.95 Aligned_cols=16 Identities=19% Similarity=0.472 Sum_probs=13.1
Q ss_pred ccCCCCceecCCCCCe
Q 035423 4 TLKPGDVIQCRECGYR 19 (35)
Q Consensus 4 ~lk~~~~irC~~CG~R 19 (35)
++.....+.|||||-+
T Consensus 42 ~mg~~gev~CPYC~t~ 57 (62)
T COG4391 42 DMGDEGEVVCPYCSTR 57 (62)
T ss_pred EcCCCCcEecCccccE
Confidence 4567778999999986
No 22
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=88.24 E-value=0.17 Score=21.52 Aligned_cols=12 Identities=33% Similarity=0.825 Sum_probs=8.2
Q ss_pred CceecCCCCCeE
Q 035423 9 DVIQCRECGYRI 20 (35)
Q Consensus 9 ~~irC~~CG~RI 20 (35)
+..-|++||+.|
T Consensus 12 ~~~fC~~CG~~l 23 (23)
T PF13240_consen 12 DAKFCPNCGTPL 23 (23)
T ss_pred cCcchhhhCCcC
Confidence 455688888764
No 23
>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=88.16 E-value=0.26 Score=22.09 Aligned_cols=12 Identities=33% Similarity=0.789 Sum_probs=10.1
Q ss_pred CCceecCCCCCe
Q 035423 8 GDVIQCRECGYR 19 (35)
Q Consensus 8 ~~~irC~~CG~R 19 (35)
.+.+.||+||..
T Consensus 24 ~~~~~CP~Cg~~ 35 (41)
T smart00834 24 DPLATCPECGGD 35 (41)
T ss_pred CCCCCCCCCCCc
Confidence 678899999984
No 24
>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=87.87 E-value=0.47 Score=22.67 Aligned_cols=13 Identities=23% Similarity=0.782 Sum_probs=9.8
Q ss_pred ecCCCCCeEEEee
Q 035423 12 QCRECGYRILYKK 24 (35)
Q Consensus 12 rC~~CG~RIlyK~ 24 (35)
+||+||.+-....
T Consensus 1 ~CP~Cg~~a~ir~ 13 (47)
T PF04606_consen 1 RCPHCGSKARIRT 13 (47)
T ss_pred CcCCCCCeeEEEE
Confidence 5999999865544
No 25
>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=87.74 E-value=0.39 Score=22.53 Aligned_cols=12 Identities=42% Similarity=0.994 Sum_probs=9.6
Q ss_pred CCCceecCCCCC
Q 035423 7 PGDVIQCRECGY 18 (35)
Q Consensus 7 ~~~~irC~~CG~ 18 (35)
..+.+.||.||.
T Consensus 23 ~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 23 EDDPVPCPECGS 34 (42)
T ss_pred CCCCCcCCCCCC
Confidence 356888999998
No 26
>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=87.19 E-value=0.36 Score=21.89 Aligned_cols=17 Identities=35% Similarity=0.864 Sum_probs=11.7
Q ss_pred ccCCCCceecCCCCCeE
Q 035423 4 TLKPGDVIQCRECGYRI 20 (35)
Q Consensus 4 ~lk~~~~irC~~CG~RI 20 (35)
.+..+...-||+|||-|
T Consensus 13 ~y~D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 13 TYEDGELLVCPECGHEW 29 (30)
T ss_dssp -EE-SSSEEETTTTEEE
T ss_pred eeccCCEEeCCcccccC
Confidence 34567778899999864
No 27
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=87.14 E-value=0.28 Score=27.67 Aligned_cols=11 Identities=45% Similarity=0.896 Sum_probs=9.1
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
..|.||+||-|
T Consensus 2 lLI~CP~Cg~R 12 (97)
T COG4311 2 LLIPCPYCGER 12 (97)
T ss_pred ceecCCCCCCC
Confidence 35899999976
No 28
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=87.03 E-value=0.26 Score=24.06 Aligned_cols=13 Identities=31% Similarity=1.214 Sum_probs=9.8
Q ss_pred cCCC-CceecCCCC
Q 035423 5 LKPG-DVIQCRECG 17 (35)
Q Consensus 5 lk~~-~~irC~~CG 17 (35)
++.. ..+.||+||
T Consensus 40 i~~~~~i~~Cp~Cg 53 (56)
T PF02591_consen 40 IRKGDEIVFCPNCG 53 (56)
T ss_pred HHcCCCeEECcCCC
Confidence 4344 679999998
No 29
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=86.87 E-value=0.43 Score=24.39 Aligned_cols=13 Identities=23% Similarity=0.820 Sum_probs=8.1
Q ss_pred ceecCCCCCeEEE
Q 035423 10 VIQCRECGYRILY 22 (35)
Q Consensus 10 ~irC~~CG~RIly 22 (35)
.++||.||..+.+
T Consensus 2 ~v~CP~C~k~~~~ 14 (57)
T PF03884_consen 2 TVKCPICGKPVEW 14 (57)
T ss_dssp EEE-TTT--EEE-
T ss_pred cccCCCCCCeecc
Confidence 5899999999988
No 30
>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]
Probab=86.68 E-value=0.3 Score=29.39 Aligned_cols=18 Identities=39% Similarity=0.888 Sum_probs=14.3
Q ss_pred cCCCCceecCCCCCeEEEee
Q 035423 5 LKPGDVIQCRECGYRILYKK 24 (35)
Q Consensus 5 lk~~~~irC~~CG~RIlyK~ 24 (35)
|..++.-||++|||- ||.
T Consensus 128 l~Kge~~rc~eCG~~--fkL 145 (153)
T KOG3352|consen 128 LEKGETQRCPECGHY--FKL 145 (153)
T ss_pred EEcCCcccCCcccce--EEe
Confidence 567888999999995 553
No 31
>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=86.60 E-value=0.61 Score=21.70 Aligned_cols=14 Identities=21% Similarity=0.804 Sum_probs=10.2
Q ss_pred eecCCCCCeEEEee
Q 035423 11 IQCRECGYRILYKK 24 (35)
Q Consensus 11 irC~~CG~RIlyK~ 24 (35)
..||.||..++.|.
T Consensus 2 ~~CP~Cg~~lv~r~ 15 (39)
T PF01396_consen 2 EKCPKCGGPLVLRR 15 (39)
T ss_pred cCCCCCCceeEEEE
Confidence 57999997755544
No 32
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=86.02 E-value=0.32 Score=28.68 Aligned_cols=8 Identities=38% Similarity=1.107 Sum_probs=6.1
Q ss_pred eecCCCCC
Q 035423 11 IQCRECGY 18 (35)
Q Consensus 11 irC~~CG~ 18 (35)
.+||+||+
T Consensus 1 m~cp~c~~ 8 (154)
T PRK00464 1 MRCPFCGH 8 (154)
T ss_pred CcCCCCCC
Confidence 37888886
No 33
>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=85.90 E-value=0.48 Score=22.01 Aligned_cols=12 Identities=33% Similarity=0.791 Sum_probs=6.4
Q ss_pred eecCCCCCeEEE
Q 035423 11 IQCRECGYRILY 22 (35)
Q Consensus 11 irC~~CG~RIly 22 (35)
|.||.||++-.+
T Consensus 1 ~~Cp~Cg~~~a~ 12 (39)
T PF01096_consen 1 IKCPKCGHNEAV 12 (39)
T ss_dssp S--SSS-SSEEE
T ss_pred CCCcCCCCCeEE
Confidence 579999987543
No 34
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=85.61 E-value=0.47 Score=21.85 Aligned_cols=14 Identities=21% Similarity=0.570 Sum_probs=11.1
Q ss_pred ceecCCCCCeEEEe
Q 035423 10 VIQCRECGYRILYK 23 (35)
Q Consensus 10 ~irC~~CG~RIlyK 23 (35)
+..||.||..-+++
T Consensus 2 ~~~Cp~Cg~~~~~~ 15 (47)
T PF14690_consen 2 PPRCPHCGSPSVHR 15 (47)
T ss_pred CccCCCcCCCceEC
Confidence 56899999887554
No 35
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=85.46 E-value=0.87 Score=23.41 Aligned_cols=20 Identities=30% Similarity=0.544 Sum_probs=16.6
Q ss_pred ceecCCCCCeEEEeecCCce
Q 035423 10 VIQCRECGYRILYKKRTRRI 29 (35)
Q Consensus 10 ~irC~~CG~RIlyK~R~~~~ 29 (35)
=+.||.||.+-..|.|.+.+
T Consensus 4 Wi~CP~CgnKTR~kir~DT~ 23 (55)
T PF14205_consen 4 WILCPICGNKTRLKIREDTV 23 (55)
T ss_pred EEECCCCCCccceeeecCce
Confidence 47899999998888888754
No 36
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=85.44 E-value=0.92 Score=20.71 Aligned_cols=18 Identities=22% Similarity=0.586 Sum_probs=13.8
Q ss_pred CceecCCCCCeEEE-eecC
Q 035423 9 DVIQCRECGYRILY-KKRT 26 (35)
Q Consensus 9 ~~irC~~CG~RIly-K~R~ 26 (35)
+..+|..||+..++ ++..
T Consensus 2 ~~~~C~~C~~~~i~~~~~~ 20 (33)
T PF08792_consen 2 NLKKCSKCGGNGIVNKEDD 20 (33)
T ss_pred CceEcCCCCCCeEEEecCC
Confidence 45789999999888 6544
No 37
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=85.07 E-value=0.53 Score=24.67 Aligned_cols=13 Identities=31% Similarity=1.048 Sum_probs=9.1
Q ss_pred CCCceecCCCCCe
Q 035423 7 PGDVIQCRECGYR 19 (35)
Q Consensus 7 ~~~~irC~~CG~R 19 (35)
.+.+.+||+||+.
T Consensus 47 ~g~~Y~Cp~CGF~ 59 (61)
T COG2888 47 LGNPYRCPKCGFE 59 (61)
T ss_pred cCCceECCCcCcc
Confidence 4566778888863
No 38
>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=84.96 E-value=0.37 Score=28.65 Aligned_cols=8 Identities=25% Similarity=0.779 Sum_probs=5.9
Q ss_pred eecCCCCC
Q 035423 11 IQCRECGY 18 (35)
Q Consensus 11 irC~~CG~ 18 (35)
++||+|||
T Consensus 1 M~CP~C~~ 8 (147)
T TIGR00244 1 MHCPFCQH 8 (147)
T ss_pred CCCCCCCC
Confidence 36888877
No 39
>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=84.77 E-value=0.82 Score=21.59 Aligned_cols=11 Identities=36% Similarity=0.869 Sum_probs=9.2
Q ss_pred CCceecCCCCC
Q 035423 8 GDVIQCRECGY 18 (35)
Q Consensus 8 ~~~irC~~CG~ 18 (35)
.+.+.||.||.
T Consensus 24 ~~~~~CP~Cg~ 34 (52)
T TIGR02605 24 DPLATCPECGG 34 (52)
T ss_pred CCCCCCCCCCC
Confidence 45788999998
No 40
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=84.72 E-value=0.68 Score=20.16 Aligned_cols=12 Identities=25% Similarity=0.863 Sum_probs=9.3
Q ss_pred CCCceecCCCCC
Q 035423 7 PGDVIQCRECGY 18 (35)
Q Consensus 7 ~~~~irC~~CG~ 18 (35)
.+-...||+||.
T Consensus 13 ~~v~f~CPnCG~ 24 (24)
T PF07754_consen 13 QAVPFPCPNCGF 24 (24)
T ss_pred cCceEeCCCCCC
Confidence 355788999995
No 41
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=84.68 E-value=0.84 Score=23.52 Aligned_cols=15 Identities=33% Similarity=0.722 Sum_probs=12.5
Q ss_pred CceecCCCCCeEEEe
Q 035423 9 DVIQCRECGYRILYK 23 (35)
Q Consensus 9 ~~irC~~CG~RIlyK 23 (35)
-.++|..||+.||.-
T Consensus 30 ikikC~gCg~~imlp 44 (57)
T PF06107_consen 30 IKIKCLGCGRQIMLP 44 (57)
T ss_pred EEEEECCCCCEEEEe
Confidence 358999999998864
No 42
>PLN02294 cytochrome c oxidase subunit Vb
Probab=84.09 E-value=1.2 Score=27.26 Aligned_cols=19 Identities=21% Similarity=0.499 Sum_probs=15.3
Q ss_pred cCCCCceecCCCCCeEEEe
Q 035423 5 LKPGDVIQCRECGYRILYK 23 (35)
Q Consensus 5 lk~~~~irC~~CG~RIlyK 23 (35)
|..+.+.||++||+-...|
T Consensus 136 L~kGkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 136 LEKGKSFECPVCTQYFELE 154 (174)
T ss_pred ecCCCceeCCCCCCEEEEE
Confidence 5678899999999965544
No 43
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=83.37 E-value=0.57 Score=26.65 Aligned_cols=20 Identities=15% Similarity=0.459 Sum_probs=15.4
Q ss_pred CceecCCCCCeEEEeecCCc
Q 035423 9 DVIQCRECGYRILYKKRTRR 28 (35)
Q Consensus 9 ~~irC~~CG~RIlyK~R~~~ 28 (35)
....||+||..+.+...+..
T Consensus 122 ~~f~Cp~Cg~~l~~~dn~~~ 141 (147)
T smart00531 122 GTFTCPRCGEELEEDDNSEP 141 (147)
T ss_pred CcEECCCCCCEEEEcCchhh
Confidence 34899999999888766554
No 44
>cd00246 RabGEF Nucleotide exchange factor for Rab-like small GTPases (RabGEF), Mss4 type; RabGEF positely regulates the function of Rab GTPase by promoting exchange of GDP for GTP; members of the Rab subfamily of Ras GTPases are important in vesicular transport;
Probab=83.22 E-value=0.85 Score=25.84 Aligned_cols=13 Identities=38% Similarity=1.053 Sum_probs=11.4
Q ss_pred ceecCCCCCeEEE
Q 035423 10 VIQCRECGYRILY 22 (35)
Q Consensus 10 ~irC~~CG~RIly 22 (35)
.|+|+.||..||=
T Consensus 2 ~v~C~~C~S~VL~ 14 (103)
T cd00246 2 AVLCQRCGSRVLT 14 (103)
T ss_pred ceECCCCCCEEEe
Confidence 4899999999983
No 45
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=83.21 E-value=0.75 Score=23.86 Aligned_cols=12 Identities=25% Similarity=0.969 Sum_probs=7.5
Q ss_pred CCCceecCCCCC
Q 035423 7 PGDVIQCRECGY 18 (35)
Q Consensus 7 ~~~~irC~~CG~ 18 (35)
.+.+.+||+||+
T Consensus 45 ~~~~Y~CP~CGF 56 (59)
T PRK14890 45 QSNPYTCPKCGF 56 (59)
T ss_pred cCCceECCCCCC
Confidence 345567777775
No 46
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=82.98 E-value=0.98 Score=23.58 Aligned_cols=13 Identities=31% Similarity=0.973 Sum_probs=11.4
Q ss_pred ceecCCCCCeEEE
Q 035423 10 VIQCRECGYRILY 22 (35)
Q Consensus 10 ~irC~~CG~RIly 22 (35)
.|+|.+|||-||.
T Consensus 34 kikC~nC~h~vm~ 46 (60)
T COG4481 34 KIKCENCGHSVMM 46 (60)
T ss_pred EEEecCCCcEEEe
Confidence 5789999999886
No 47
>PF14353 CpXC: CpXC protein
Probab=82.46 E-value=0.86 Score=24.97 Aligned_cols=11 Identities=27% Similarity=0.921 Sum_probs=8.8
Q ss_pred ceecCCCCCeE
Q 035423 10 VIQCRECGYRI 20 (35)
Q Consensus 10 ~irC~~CG~RI 20 (35)
...||+||+..
T Consensus 38 ~~~CP~Cg~~~ 48 (128)
T PF14353_consen 38 SFTCPSCGHKF 48 (128)
T ss_pred EEECCCCCCce
Confidence 57899999764
No 48
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=82.31 E-value=0.97 Score=27.57 Aligned_cols=17 Identities=24% Similarity=0.362 Sum_probs=12.5
Q ss_pred CCceecCCCCCeEEEee
Q 035423 8 GDVIQCRECGYRILYKK 24 (35)
Q Consensus 8 ~~~irC~~CG~RIlyK~ 24 (35)
.+.-.||.||++++-|.
T Consensus 151 ~~~~~Cp~CG~~~~~~~ 167 (177)
T COG1439 151 EPKDFCPICGSPLKRKR 167 (177)
T ss_pred CCCCcCCCCCCceEEee
Confidence 45567999999955543
No 49
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=81.91 E-value=0.66 Score=28.00 Aligned_cols=15 Identities=33% Similarity=0.722 Sum_probs=11.7
Q ss_pred CCCceecCCCCCeEE
Q 035423 7 PGDVIQCRECGYRIL 21 (35)
Q Consensus 7 ~~~~irC~~CG~RIl 21 (35)
.++.+-||+|||--+
T Consensus 45 ~Y~V~vCP~CgyA~~ 59 (214)
T PF09986_consen 45 FYEVWVCPHCGYAAF 59 (214)
T ss_pred eeeEEECCCCCCccc
Confidence 467889999998643
No 50
>PF06054 CoiA: Competence protein CoiA-like family; InterPro: IPR010330 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterised protein.
Probab=81.90 E-value=2 Score=27.88 Aligned_cols=25 Identities=24% Similarity=0.582 Sum_probs=21.3
Q ss_pred CCceecCCCCCeEEEeecCCceEEE
Q 035423 8 GDVIQCRECGYRILYKKRTRRIVQY 32 (35)
Q Consensus 8 ~~~irC~~CG~RIlyK~R~~~~~~~ 32 (35)
.....||.||..++.|.-..+.-.|
T Consensus 28 ~~~~~CP~C~~~v~lk~G~~k~~HF 52 (375)
T PF06054_consen 28 KGKYFCPGCGEPVILKKGKKKIPHF 52 (375)
T ss_pred CCcEECCCCCCeeEEEEcCccccee
Confidence 7789999999999999877766655
No 51
>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=81.87 E-value=1 Score=19.80 Aligned_cols=11 Identities=27% Similarity=0.920 Sum_probs=6.3
Q ss_pred ecCCCCCeEEE
Q 035423 12 QCRECGYRILY 22 (35)
Q Consensus 12 rC~~CG~RIly 22 (35)
.||.||..++.
T Consensus 1 ~CP~C~s~l~~ 11 (28)
T PF03119_consen 1 TCPVCGSKLVR 11 (28)
T ss_dssp B-TTT--BEEE
T ss_pred CcCCCCCEeEc
Confidence 49999999773
No 52
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=81.76 E-value=2.5 Score=22.21 Aligned_cols=21 Identities=19% Similarity=0.286 Sum_probs=15.6
Q ss_pred ecCCCCCeEEEeecCCceEEE
Q 035423 12 QCRECGYRILYKKRTRRIVQY 32 (35)
Q Consensus 12 rC~~CG~RIlyK~R~~~~~~~ 32 (35)
-||.||+.++.-+.+...-++
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v 28 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRA 28 (64)
T ss_pred CCCCCCCceeEEEecCceEEE
Confidence 399999999887776554443
No 53
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=80.92 E-value=1.1 Score=20.15 Aligned_cols=17 Identities=24% Similarity=0.626 Sum_probs=12.8
Q ss_pred cCCCCceecCCCCCeEE
Q 035423 5 LKPGDVIQCRECGYRIL 21 (35)
Q Consensus 5 lk~~~~irC~~CG~RIl 21 (35)
++..+...|+.||-.++
T Consensus 27 i~~vp~~~C~~CGE~~~ 43 (46)
T TIGR03831 27 IENVPALVCPQCGEEYL 43 (46)
T ss_pred EeCCCccccccCCCEee
Confidence 45566778999998764
No 54
>TIGR01374 soxD sarcosine oxidase, delta subunit family, heterotetrameric form. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) form
Probab=80.66 E-value=0.73 Score=25.18 Aligned_cols=9 Identities=56% Similarity=1.161 Sum_probs=7.8
Q ss_pred eecCCCCCe
Q 035423 11 IQCRECGYR 19 (35)
Q Consensus 11 irC~~CG~R 19 (35)
|.||.||-|
T Consensus 2 I~CP~CG~R 10 (84)
T TIGR01374 2 IPCPYCGPR 10 (84)
T ss_pred ccCCCCCCc
Confidence 789999976
No 55
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=80.60 E-value=0.89 Score=26.77 Aligned_cols=10 Identities=50% Similarity=1.484 Sum_probs=8.7
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
...|++||||
T Consensus 29 sf~C~~CGyk 38 (160)
T smart00709 29 SFECEHCGYR 38 (160)
T ss_pred EEECCCCCCc
Confidence 5689999998
No 56
>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
Probab=80.17 E-value=1.1 Score=22.09 Aligned_cols=13 Identities=38% Similarity=0.915 Sum_probs=11.4
Q ss_pred CCceecCCCCCeE
Q 035423 8 GDVIQCRECGYRI 20 (35)
Q Consensus 8 ~~~irC~~CG~RI 20 (35)
+|.++|.+||..+
T Consensus 34 ~d~v~C~~C~~~l 46 (71)
T smart00238 34 GDEVKCFFCGGEL 46 (71)
T ss_pred CCEEEeCCCCCCc
Confidence 6789999999875
No 57
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=80.14 E-value=0.99 Score=26.08 Aligned_cols=26 Identities=31% Similarity=0.703 Sum_probs=18.8
Q ss_pred ccccCCCCceecCCCCCe--EEEeecCC
Q 035423 2 ENTLKPGDVIQCRECGYR--ILYKKRTR 27 (35)
Q Consensus 2 ~~~lk~~~~irC~~CG~R--IlyK~R~~ 27 (35)
|+.|+......||.||++ ++|-.++.
T Consensus 65 DPTLPrts~~~C~~C~~~eavffQ~~~~ 92 (113)
T KOG2691|consen 65 DPTLPRTSDKHCPKCGHREAVFFQAQTR 92 (113)
T ss_pred CCCcCccccccCCccCCcceEEEecccc
Confidence 455677678899999997 55655544
No 58
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=80.02 E-value=0.84 Score=21.99 Aligned_cols=9 Identities=33% Similarity=0.885 Sum_probs=6.0
Q ss_pred ceecCCCCC
Q 035423 10 VIQCRECGY 18 (35)
Q Consensus 10 ~irC~~CG~ 18 (35)
...||+||.
T Consensus 2 ~f~CP~C~~ 10 (54)
T PF05605_consen 2 SFTCPYCGK 10 (54)
T ss_pred CcCCCCCCC
Confidence 456777775
No 59
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=79.78 E-value=0.99 Score=26.77 Aligned_cols=10 Identities=50% Similarity=1.368 Sum_probs=8.8
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
...|++||||
T Consensus 28 sf~C~~CGyr 37 (163)
T TIGR00340 28 TYICEKCGYR 37 (163)
T ss_pred EEECCCCCCc
Confidence 5789999998
No 60
>PF00653 BIR: Inhibitor of Apoptosis domain; InterPro: IPR001370 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The baculovirus inhibitor of apoptosis protein repeat (BIR) is a domain of tandem repeats separated by a variable length linker that seems to confer cell death-preventing activity [, ]. The BIR domains characterise the Inhibitor of Apoptosis (IAP) family of proteins (MEROPS proteinase inhibitor family I32, clan IV) that suppress apoptosis by interacting with and inhibiting the enzymatic activity of both initiator and effector caspases (MEROPS peptidase family C14, IPR002398 from INTERPRO). Several distinct mammalian IAPs including XIAP, c-IAP1, c-IAP2, and ML-IAP, have been identified, and they all exhibit antiapoptotic activity in cell culture. The functional unit in each IAP protein is the baculoviral IAP repeat (BIR), which contains approximately 80 amino acids folded around a zinc atom. Most mammalian IAPs have more than one BIR domain, with the different BIR domains performing distinct functions. For example, in XIAP, the third BIR domain (BIR3) potently inhibits the catalytic activity of caspase-9, whereas the linker sequences immediately preceding the second BIR domain (BIR2) selectively targets caspase-3 or -7. The first-recognised members of family MEROPS inhibitor family I32 were viral proteins that inhibited the apoptosis of infected cells: Cp-IAP from Cydia pomonella granulosis virus (CpGV) [] and Op-IAP from Orgyia pseudotsugata multicapsid polyhedrosis virus(OpMNPV) []. The discovery of homologous proteins in mammals followed soon after with the recognition that mutations in the gene for neuronal apoptosis inhibitory protein (NIAP) underlie spinal muscular atrophy []. The inhibitors in family I32 all possess one or more 80-residue domains known as BIR (baculovirus inhibitor repeat) domains and have accordingly been termed 'BIR-containing' or 'BIRC' proteins as well as IAP proteins. The mechanism of inhibition of caspases by the IAP proteins is complex, and reactive site residues cannot yet be identified with any confidence. Despite the conservation of the BIR or IAP (inhibitor of apoptosis) domains throughout the family it seems clear that other parts of the molecules also make essential contributions to inhibitory activity. Homologs of most components in the mammalian apoptotic pathway have been identified in fruit flies. The Drosophila Apaf-1, known as Dapaf-1, HAC-1 or Dark, shares significant sequence similarity with its mammalian counterpart, and is critically important for the activation of the Drosophila initiator caspase Dronc. Dronc, in turn, cleaves and activates the effector caspase DrICE. The Drosophila IAP, DIAP1, binds to and in-activates both DrICE and Dronc through its BIR1 and BIR2 domains. During apoptosis, the anti-death function of DIAP1 is countered by at least four pro-apoptotic proteins, Reaper, Hid, Grim, and sickle, through direct physical interactions. These four proteins represent the functional homologs of the mammalian protein Smac, and they all share a conserved IAP-binding motif at their N termini. The three proteins Reaper, Hid, and Grim are collectively referred to as the RHG proteins [, ]. Both XIAP and DIAP1 contain a RING domain at their C termini, and can act as an E3 ubiquitin ligase. Indeed, both XIAP and DIAP1 have been shown to promote self-ubiquitination and degradation as well as to negatively regulate the target caspases. Nonetheless, important differences exist between XIAP and DIAP1. The primary function of XIAP is thought to inhibit the catalytic activities of caspases; to what extent the ubiquitinating activity of XIAP contributes to its function remains unclear. For DIAP1, however, the ubiquitinating activity appears to be essential for its function. Recently a Drosophila p53 protein has been identified that mediates apoptosis via a novel pathway involving the activation of the Reaper gene and subsequent inhibition of the inhibitors of apoptosis (IAPs). CIAP1, a major mammalian homologue of Drosophila IAPs, is irreversibly inhibited (cleaved) during p53-dependent apoptosis and this cleavage is mediated by a serine protease. Serine protease inhibitors that block CIAP1 cleavage inhibit p53-dependent apoptosis. Furthermore, activation of the p53 protein increases the transcription of the HTRA2 gene, which encodes a serine protease that interacts with CIAP1 and potentiates apoptosis. Therefore mammalian p53 protein activates apoptosis through a novel pathway functionally similar to that in Drosophila, which involves HTRA2 and subsequent inhibition of CIAP1 by cleavage [].; GO: 0005622 intracellular; PDB: 3HL5_B 3UW5_A 3CM7_A 1G3F_A 1G73_C 3G76_G 3CM2_C 2VSL_A 2OPZ_B 3CLX_A ....
Probab=79.23 E-value=1.3 Score=22.11 Aligned_cols=13 Identities=38% Similarity=1.045 Sum_probs=11.7
Q ss_pred CCceecCCCCCeE
Q 035423 8 GDVIQCRECGYRI 20 (35)
Q Consensus 8 ~~~irC~~CG~RI 20 (35)
.+.++|-+||..|
T Consensus 34 ~d~v~C~~C~~~l 46 (70)
T PF00653_consen 34 GDRVRCFYCGLEL 46 (70)
T ss_dssp TTEEEETTTTEEE
T ss_pred CCEEEEeccCCEE
Confidence 6899999999886
No 61
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=79.13 E-value=0.94 Score=21.15 Aligned_cols=11 Identities=36% Similarity=0.824 Sum_probs=8.1
Q ss_pred ecCCCCCeEEE
Q 035423 12 QCRECGYRILY 22 (35)
Q Consensus 12 rC~~CG~RIly 22 (35)
.||.||++=.+
T Consensus 2 ~Cp~C~~~~a~ 12 (40)
T smart00440 2 PCPKCGNREAT 12 (40)
T ss_pred cCCCCCCCeEE
Confidence 69999987443
No 62
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=79.11 E-value=1.1 Score=23.79 Aligned_cols=12 Identities=25% Similarity=0.913 Sum_probs=9.4
Q ss_pred ceecCCCCCeEE
Q 035423 10 VIQCRECGYRIL 21 (35)
Q Consensus 10 ~irC~~CG~RIl 21 (35)
-|+||.||+.=.
T Consensus 19 ~VkCpdC~N~q~ 30 (67)
T COG2051 19 RVKCPDCGNEQV 30 (67)
T ss_pred EEECCCCCCEEE
Confidence 489999998643
No 63
>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=78.86 E-value=1 Score=26.40 Aligned_cols=10 Identities=40% Similarity=1.418 Sum_probs=5.7
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
...|++||||
T Consensus 30 sf~C~~CGyk 39 (161)
T PF03367_consen 30 SFECEHCGYK 39 (161)
T ss_dssp EEE-TTT--E
T ss_pred EeECCCCCCE
Confidence 4689999998
No 64
>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=78.28 E-value=1.8 Score=20.06 Aligned_cols=10 Identities=30% Similarity=1.055 Sum_probs=7.7
Q ss_pred eecCCCCCeE
Q 035423 11 IQCRECGYRI 20 (35)
Q Consensus 11 irC~~CG~RI 20 (35)
.+||+||..-
T Consensus 1 m~Cp~Cg~~~ 10 (43)
T PF08271_consen 1 MKCPNCGSKE 10 (43)
T ss_dssp ESBTTTSSSE
T ss_pred CCCcCCcCCc
Confidence 3699999874
No 65
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=77.98 E-value=1.6 Score=22.17 Aligned_cols=12 Identities=42% Similarity=1.055 Sum_probs=10.5
Q ss_pred CCCceecCCCCC
Q 035423 7 PGDVIQCRECGY 18 (35)
Q Consensus 7 ~~~~irC~~CG~ 18 (35)
..|.|.||.||-
T Consensus 18 ~dDiVvCp~Cga 29 (54)
T PF14446_consen 18 GDDIVVCPECGA 29 (54)
T ss_pred CCCEEECCCCCC
Confidence 678999999994
No 66
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=77.97 E-value=1.4 Score=29.10 Aligned_cols=23 Identities=26% Similarity=0.546 Sum_probs=17.2
Q ss_pred ccCCCCceecCCCCCeEEEeecCC
Q 035423 4 TLKPGDVIQCRECGYRILYKKRTR 27 (35)
Q Consensus 4 ~lk~~~~irC~~CG~RIlyK~R~~ 27 (35)
.+.++...+||.||+. ||..++.
T Consensus 24 ~l~~g~~a~CpRCg~~-L~~~~~~ 46 (419)
T PRK15103 24 RLEHGQKAACPRCGTT-LTVRWDE 46 (419)
T ss_pred CCCCCCeeECCCCCCC-CcCCCCC
Confidence 4567888999999999 4655543
No 67
>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=77.84 E-value=1.2 Score=26.21 Aligned_cols=12 Identities=8% Similarity=-0.053 Sum_probs=10.4
Q ss_pred CceecCCCCCeE
Q 035423 9 DVIQCRECGYRI 20 (35)
Q Consensus 9 ~~irC~~CG~RI 20 (35)
++|.||+||.-.
T Consensus 25 ~p~vcP~cg~~~ 36 (129)
T TIGR02300 25 RPAVSPYTGEQF 36 (129)
T ss_pred CCccCCCcCCcc
Confidence 789999999863
No 68
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=77.81 E-value=1.2 Score=26.96 Aligned_cols=10 Identities=50% Similarity=1.311 Sum_probs=8.7
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
...|++||||
T Consensus 30 sf~C~~CGyr 39 (192)
T TIGR00310 30 STICEHCGYR 39 (192)
T ss_pred EEECCCCCCc
Confidence 5689999998
No 69
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=77.59 E-value=1.1 Score=23.65 Aligned_cols=15 Identities=27% Similarity=0.536 Sum_probs=10.3
Q ss_pred eecCCCCCeEEEeecCC
Q 035423 11 IQCRECGYRILYKKRTR 27 (35)
Q Consensus 11 irC~~CG~RIlyK~R~~ 27 (35)
++||.||+.- +.|+.
T Consensus 2 m~CP~Cg~~a--~irtS 16 (72)
T PRK09678 2 FHCPLCQHAA--HARTS 16 (72)
T ss_pred ccCCCCCCcc--EEEEC
Confidence 5789999886 44443
No 70
>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=77.58 E-value=1.3 Score=25.63 Aligned_cols=14 Identities=21% Similarity=0.631 Sum_probs=10.5
Q ss_pred CceecCCCCCeEEE
Q 035423 9 DVIQCRECGYRILY 22 (35)
Q Consensus 9 ~~irC~~CG~RIly 22 (35)
-.|.||+||+....
T Consensus 68 v~V~CP~C~K~TKm 81 (114)
T PF11023_consen 68 VQVECPNCGKQTKM 81 (114)
T ss_pred eeeECCCCCChHhh
Confidence 46899999986533
No 71
>PF04267 SoxD: Sarcosine oxidase, delta subunit family ; InterPro: IPR006279 These sequences represent the delta subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Rhizobium loti (Mesorhizobium loti) and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate []. Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the heterotetrameric form.; GO: 0008115 sarcosine oxidase activity, 0046653 tetrahydrofolate metabolic process; PDB: 3AD7_D 1X31_D 1VRQ_D 3AD8_D 3ADA_D 3AD9_D 2GAG_D 2GAH_D.
Probab=77.27 E-value=0.89 Score=24.78 Aligned_cols=9 Identities=56% Similarity=1.276 Sum_probs=7.8
Q ss_pred eecCCCCCe
Q 035423 11 IQCRECGYR 19 (35)
Q Consensus 11 irC~~CG~R 19 (35)
|.||.||-|
T Consensus 2 I~CP~CG~R 10 (84)
T PF04267_consen 2 IPCPHCGPR 10 (84)
T ss_dssp EEETTTEEE
T ss_pred ccCCCCCcc
Confidence 789999976
No 72
>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=77.23 E-value=2.3 Score=19.60 Aligned_cols=17 Identities=29% Similarity=0.626 Sum_probs=12.9
Q ss_pred CCCceecCCCCCeEEEee
Q 035423 7 PGDVIQCRECGYRILYKK 24 (35)
Q Consensus 7 ~~~~irC~~CG~RIlyK~ 24 (35)
.++.+.|+.||.+ +|..
T Consensus 5 ~~~~~~C~~C~~~-~~~~ 21 (36)
T PF11781_consen 5 RGPNEPCPVCGSR-WFYS 21 (36)
T ss_pred ccCCCcCCCCCCe-EeEc
Confidence 4566789999999 6654
No 73
>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=77.11 E-value=4 Score=20.11 Aligned_cols=24 Identities=21% Similarity=0.502 Sum_probs=13.8
Q ss_pred CceecCCCCCeEEEe-ecCCceEEE
Q 035423 9 DVIQCRECGYRILYK-KRTRRIVQY 32 (35)
Q Consensus 9 ~~irC~~CG~RIlyK-~R~~~~~~~ 32 (35)
.-..|+.||..|++- ...+....+
T Consensus 47 ~r~FC~~CGs~l~~~~~~~~~~~~V 71 (92)
T PF04828_consen 47 ERYFCPTCGSPLFSEDERDPDLVGV 71 (92)
T ss_dssp EEEEETTT--EEEEEESSTTTEEEE
T ss_pred cCcccCCCCCeeecccCCCCCEEEE
Confidence 457899999999863 333344443
No 74
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=76.93 E-value=1.1 Score=27.47 Aligned_cols=14 Identities=50% Similarity=1.044 Sum_probs=10.7
Q ss_pred cCCCC-ceecCCCCC
Q 035423 5 LKPGD-VIQCRECGY 18 (35)
Q Consensus 5 lk~~~-~irC~~CG~ 18 (35)
|+..+ ..+||.|||
T Consensus 87 Lk~k~nl~~CP~CGh 101 (176)
T KOG4080|consen 87 LKPKDNLNTCPACGH 101 (176)
T ss_pred ccchhccccCcccCc
Confidence 45555 678999998
No 75
>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=76.49 E-value=1.6 Score=28.67 Aligned_cols=22 Identities=23% Similarity=0.512 Sum_probs=16.3
Q ss_pred ccCCCCceecCCCCCeEEEeecC
Q 035423 4 TLKPGDVIQCRECGYRILYKKRT 26 (35)
Q Consensus 4 ~lk~~~~irC~~CG~RIlyK~R~ 26 (35)
.+++++..+||.||+. ||..++
T Consensus 27 ~l~~g~~a~CpRCg~~-L~~~~~ 48 (403)
T TIGR00155 27 RIESGQKAACPRCGTT-LTVGWD 48 (403)
T ss_pred CCCCCCeeECCCCCCC-CcCCCC
Confidence 4567888999999998 565443
No 76
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=76.42 E-value=1.6 Score=23.52 Aligned_cols=15 Identities=33% Similarity=0.685 Sum_probs=8.4
Q ss_pred CCCCceecCCCCCeE
Q 035423 6 KPGDVIQCRECGYRI 20 (35)
Q Consensus 6 k~~~~irC~~CG~RI 20 (35)
+......||.||+++
T Consensus 61 ENMs~~~Cp~Cg~~~ 75 (81)
T PF10609_consen 61 ENMSYFVCPHCGERI 75 (81)
T ss_dssp ECT-EEE-TTT--EE
T ss_pred ECCCccCCCCCCCee
Confidence 445678999999985
No 77
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=75.57 E-value=0.91 Score=23.51 Aligned_cols=11 Identities=36% Similarity=0.878 Sum_probs=8.5
Q ss_pred ceecCCCCCeE
Q 035423 10 VIQCRECGYRI 20 (35)
Q Consensus 10 ~irC~~CG~RI 20 (35)
||||..||.-|
T Consensus 4 PVRCFTCGkvi 14 (60)
T PF01194_consen 4 PVRCFTCGKVI 14 (60)
T ss_dssp SSS-STTTSBT
T ss_pred ceecCCCCCCh
Confidence 79999999765
No 78
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=75.51 E-value=1.6 Score=28.30 Aligned_cols=15 Identities=27% Similarity=0.600 Sum_probs=12.6
Q ss_pred cCCCCceecCCCCCe
Q 035423 5 LKPGDVIQCRECGYR 19 (35)
Q Consensus 5 lk~~~~irC~~CG~R 19 (35)
+..+.+-||++||+=
T Consensus 176 LrEGkpqRCpECGqV 190 (268)
T PTZ00043 176 CREGFLYRCGECDQI 190 (268)
T ss_pred ecCCCCccCCCCCcE
Confidence 567889999999984
No 79
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=74.68 E-value=0.93 Score=24.19 Aligned_cols=26 Identities=27% Similarity=0.585 Sum_probs=20.6
Q ss_pred ccccCCCCceecCCCCCeEEEeecCC
Q 035423 2 ENTLKPGDVIQCRECGYRILYKKRTR 27 (35)
Q Consensus 2 ~~~lk~~~~irC~~CG~RIlyK~R~~ 27 (35)
|++.+..-.|-|..|||-=+|+.-+-
T Consensus 32 dvq~n~f~~itCk~CgYtEfY~a~~s 57 (68)
T COG3478 32 DVQNNKFIVITCKNCGYTEFYSAKIS 57 (68)
T ss_pred EecccEEEEEEeccCCchhheecccc
Confidence 45667777899999999999987543
No 80
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=73.99 E-value=1.4 Score=26.60 Aligned_cols=7 Identities=43% Similarity=1.146 Sum_probs=4.4
Q ss_pred ecCCCCC
Q 035423 12 QCRECGY 18 (35)
Q Consensus 12 rC~~CG~ 18 (35)
+||+|||
T Consensus 2 ~CPfC~~ 8 (156)
T COG1327 2 KCPFCGH 8 (156)
T ss_pred CCCCCCC
Confidence 5666665
No 81
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=73.69 E-value=2 Score=20.15 Aligned_cols=10 Identities=30% Similarity=0.933 Sum_probs=8.2
Q ss_pred CceecCCCCC
Q 035423 9 DVIQCRECGY 18 (35)
Q Consensus 9 ~~irC~~CG~ 18 (35)
..+.|+.||-
T Consensus 12 ~~~~C~~CgM 21 (41)
T PF13878_consen 12 GATTCPTCGM 21 (41)
T ss_pred CCcCCCCCCC
Confidence 3689999993
No 82
>cd00022 BIR Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
Probab=73.27 E-value=2.3 Score=20.83 Aligned_cols=13 Identities=38% Similarity=1.017 Sum_probs=11.1
Q ss_pred CCceecCCCCCeE
Q 035423 8 GDVIQCRECGYRI 20 (35)
Q Consensus 8 ~~~irC~~CG~RI 20 (35)
.+.++|.+||..+
T Consensus 32 ~d~v~C~~C~~~~ 44 (69)
T cd00022 32 GDEVKCFFCGLEL 44 (69)
T ss_pred CCEEEeCCCCCCc
Confidence 5789999999875
No 83
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=73.25 E-value=2.9 Score=20.80 Aligned_cols=16 Identities=13% Similarity=0.426 Sum_probs=12.7
Q ss_pred ceecCCCCCeEEEeec
Q 035423 10 VIQCRECGYRILYKKR 25 (35)
Q Consensus 10 ~irC~~CG~RIlyK~R 25 (35)
.+.||.|+.++.=..+
T Consensus 3 ~i~Cp~C~~~~~T~v~ 18 (67)
T smart00714 3 QLFCPRCQNNVTTRVE 18 (67)
T ss_pred ceECCCCCCEEEEEEE
Confidence 5899999999875544
No 84
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=72.80 E-value=2.3 Score=22.14 Aligned_cols=15 Identities=20% Similarity=0.643 Sum_probs=12.6
Q ss_pred CceecCCCCCeEEEe
Q 035423 9 DVIQCRECGYRILYK 23 (35)
Q Consensus 9 ~~irC~~CG~RIlyK 23 (35)
..++||.||..+.|.
T Consensus 5 ~~v~CP~C~k~~~w~ 19 (62)
T PRK00418 5 ITVNCPTCGKPVEWG 19 (62)
T ss_pred ccccCCCCCCccccc
Confidence 468999999998764
No 85
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=72.60 E-value=2.5 Score=19.40 Aligned_cols=12 Identities=25% Similarity=0.675 Sum_probs=5.5
Q ss_pred cCCCCCeEEEee
Q 035423 13 CRECGYRILYKK 24 (35)
Q Consensus 13 C~~CG~RIlyK~ 24 (35)
||.||..+-++.
T Consensus 3 C~~CG~~l~~~i 14 (34)
T PF14803_consen 3 CPQCGGPLERRI 14 (34)
T ss_dssp -TTT--B-EEE-
T ss_pred cccccChhhhhc
Confidence 999999965553
No 86
>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=72.54 E-value=1.6 Score=20.20 Aligned_cols=10 Identities=30% Similarity=0.926 Sum_probs=3.7
Q ss_pred CceecCCCCC
Q 035423 9 DVIQCRECGY 18 (35)
Q Consensus 9 ~~irC~~CG~ 18 (35)
+++||..|+.
T Consensus 1 ~p~rC~~C~a 10 (40)
T PF04810_consen 1 GPVRCRRCRA 10 (40)
T ss_dssp -S-B-TTT--
T ss_pred CccccCCCCC
Confidence 3577777764
No 87
>PHA00626 hypothetical protein
Probab=71.91 E-value=2.8 Score=21.82 Aligned_cols=12 Identities=33% Similarity=0.783 Sum_probs=8.9
Q ss_pred ecCCCCCeEEEe
Q 035423 12 QCRECGYRILYK 23 (35)
Q Consensus 12 rC~~CG~RIlyK 23 (35)
.||.||+.=++|
T Consensus 2 ~CP~CGS~~Ivr 13 (59)
T PHA00626 2 SCPKCGSGNIAK 13 (59)
T ss_pred CCCCCCCceeee
Confidence 599999974554
No 88
>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=71.43 E-value=2.3 Score=22.51 Aligned_cols=18 Identities=22% Similarity=0.368 Sum_probs=7.6
Q ss_pred CCCceecCCCCCeEEEee
Q 035423 7 PGDVIQCRECGYRILYKK 24 (35)
Q Consensus 7 ~~~~irC~~CG~RIlyK~ 24 (35)
..+..-||.||+.-|.|.
T Consensus 21 ~~~k~FCp~CGn~TL~rv 38 (73)
T PF08772_consen 21 DMTKQFCPKCGNATLKRV 38 (73)
T ss_dssp -SS--S-SSS--S--EEE
T ss_pred CCCceeCcccCCCcceEE
Confidence 456678999999877664
No 89
>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=70.80 E-value=1.9 Score=24.99 Aligned_cols=10 Identities=40% Similarity=1.046 Sum_probs=8.8
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
.+.||+||..
T Consensus 105 ~~~cp~c~s~ 114 (146)
T TIGR02159 105 SVQCPRCGSA 114 (146)
T ss_pred CCcCCCCCCC
Confidence 5999999975
No 90
>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=70.63 E-value=2.4 Score=19.17 Aligned_cols=11 Identities=36% Similarity=0.724 Sum_probs=8.2
Q ss_pred eecCCCCCeEE
Q 035423 11 IQCRECGYRIL 21 (35)
Q Consensus 11 irC~~CG~RIl 21 (35)
-+|+.|||-.-
T Consensus 3 ~~C~~CG~i~~ 13 (34)
T cd00729 3 WVCPVCGYIHE 13 (34)
T ss_pred EECCCCCCEeE
Confidence 57999998644
No 91
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=70.60 E-value=3 Score=26.26 Aligned_cols=18 Identities=33% Similarity=0.975 Sum_probs=12.2
Q ss_pred cCCCCceecCCCCC-eEEE
Q 035423 5 LKPGDVIQCRECGY-RILY 22 (35)
Q Consensus 5 lk~~~~irC~~CG~-RIly 22 (35)
+......+||+||. .|++
T Consensus 6 ~~~~~~~~Cp~Cg~~~iv~ 24 (310)
T PRK00423 6 LEEEEKLVCPECGSDKLIY 24 (310)
T ss_pred hhcccCCcCcCCCCCCeeE
Confidence 34556678999997 4444
No 92
>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 Score=15.83 Aligned_cols=9 Identities=44% Similarity=1.014 Sum_probs=5.4
Q ss_pred ecCCCCCeE
Q 035423 12 QCRECGYRI 20 (35)
Q Consensus 12 rC~~CG~RI 20 (35)
.|+.||...
T Consensus 2 ~C~~C~~~~ 10 (24)
T PF13894_consen 2 QCPICGKSF 10 (24)
T ss_dssp E-SSTS-EE
T ss_pred CCcCCCCcC
Confidence 699999863
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=69.33 E-value=2.9 Score=20.97 Aligned_cols=9 Identities=44% Similarity=1.306 Sum_probs=5.4
Q ss_pred ecCCCCCeE
Q 035423 12 QCRECGYRI 20 (35)
Q Consensus 12 rC~~CG~RI 20 (35)
.||.||.-|
T Consensus 4 ~CP~CG~~i 12 (54)
T TIGR01206 4 ECPDCGAEI 12 (54)
T ss_pred CCCCCCCEE
Confidence 566666654
No 94
>PRK12496 hypothetical protein; Provisional
Probab=69.20 E-value=1.6 Score=25.56 Aligned_cols=10 Identities=30% Similarity=0.743 Sum_probs=8.3
Q ss_pred eecCCCCCeE
Q 035423 11 IQCRECGYRI 20 (35)
Q Consensus 11 irC~~CG~RI 20 (35)
-.||.||+.+
T Consensus 144 ~~C~~CG~~~ 153 (164)
T PRK12496 144 DVCEICGSPV 153 (164)
T ss_pred CcCCCCCChh
Confidence 4699999985
No 95
>PF07967 zf-C3HC: C3HC zinc finger-like ; InterPro: IPR012935 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc-finger like domain is distributed throughout the eukaryotic kingdom in NIPA (Nuclear interacting partner of ALK) and other proteins. NIPA is thought to perform an antiapoptotic role in nucleophosmin-anaplastic lymphoma kinase (ALK) mediated signalling events []. The domain is often repeated, with the second domain usually containing a large insert (approximately 90 residues) after the first three cysteine residues. The Schizosaccharomyces pombe protein containing this domain (O94506 from SWISSPROT) is involved in mRNA export from the nucleus []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=69.10 E-value=5.2 Score=22.23 Aligned_cols=16 Identities=38% Similarity=0.949 Sum_probs=14.8
Q ss_pred CCceecCCCCCeEEEe
Q 035423 8 GDVIQCRECGYRILYK 23 (35)
Q Consensus 8 ~~~irC~~CG~RIlyK 23 (35)
.+.++|..||..+.++
T Consensus 41 ~d~l~C~~C~~~l~~~ 56 (133)
T PF07967_consen 41 KDMLKCESCGARLCVK 56 (133)
T ss_pred CCEEEeCCCCCEEEEe
Confidence 6789999999999998
No 96
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=69.08 E-value=2.5 Score=17.91 Aligned_cols=10 Identities=30% Similarity=1.052 Sum_probs=8.1
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
-+.|+.||-.
T Consensus 2 l~~C~~CgR~ 11 (25)
T PF13913_consen 2 LVPCPICGRK 11 (25)
T ss_pred CCcCCCCCCE
Confidence 4689999965
No 97
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=69.04 E-value=2.1 Score=28.95 Aligned_cols=17 Identities=24% Similarity=0.763 Sum_probs=14.2
Q ss_pred ccCCCCceecCCCCCeE
Q 035423 4 TLKPGDVIQCRECGYRI 20 (35)
Q Consensus 4 ~lk~~~~irC~~CG~RI 20 (35)
.|+.....||.+||++.
T Consensus 348 ~l~~~~~YRC~~CGF~a 364 (389)
T COG2956 348 QLRRKPRYRCQNCGFTA 364 (389)
T ss_pred HHhhcCCceecccCCcc
Confidence 46778899999999974
No 98
>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=68.88 E-value=2.6 Score=21.01 Aligned_cols=9 Identities=33% Similarity=0.855 Sum_probs=6.3
Q ss_pred ceecCCCCC
Q 035423 10 VIQCRECGY 18 (35)
Q Consensus 10 ~irC~~CG~ 18 (35)
.-+|++||+
T Consensus 44 ~y~C~~Cg~ 52 (54)
T PF10058_consen 44 QYRCPYCGA 52 (54)
T ss_pred EEEcCCCCC
Confidence 467777775
No 99
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=68.06 E-value=3 Score=23.17 Aligned_cols=10 Identities=20% Similarity=0.564 Sum_probs=7.2
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
..+||.||..
T Consensus 88 ~~~CP~Cgs~ 97 (117)
T PRK00564 88 YGVCEKCHSK 97 (117)
T ss_pred CCcCcCCCCC
Confidence 3468888875
No 100
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=68.03 E-value=4.1 Score=19.61 Aligned_cols=15 Identities=20% Similarity=0.494 Sum_probs=10.8
Q ss_pred ecCCCCCeEEEeecC
Q 035423 12 QCRECGYRILYKKRT 26 (35)
Q Consensus 12 rC~~CG~RIlyK~R~ 26 (35)
-||.||...+.....
T Consensus 5 PCPFCG~~~~~~~~~ 19 (61)
T PF14354_consen 5 PCPFCGSADVLIRQD 19 (61)
T ss_pred CCCCCCCcceEeecc
Confidence 399999877665543
No 101
>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=67.74 E-value=4 Score=21.58 Aligned_cols=13 Identities=23% Similarity=0.751 Sum_probs=10.6
Q ss_pred CceecCCCCCeEE
Q 035423 9 DVIQCRECGYRIL 21 (35)
Q Consensus 9 ~~irC~~CG~RIl 21 (35)
..++||.||++=.
T Consensus 61 ~~~~Cp~Cg~~~a 73 (104)
T TIGR01384 61 TRVECPKCGHKEA 73 (104)
T ss_pred ccCCCCCCCCCee
Confidence 3589999999864
No 102
>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=67.51 E-value=3.1 Score=18.47 Aligned_cols=8 Identities=50% Similarity=1.277 Sum_probs=5.8
Q ss_pred ecCCCCCe
Q 035423 12 QCRECGYR 19 (35)
Q Consensus 12 rC~~CG~R 19 (35)
+|+.|||-
T Consensus 3 ~C~~CGy~ 10 (33)
T cd00350 3 VCPVCGYI 10 (33)
T ss_pred ECCCCCCE
Confidence 67788874
No 103
>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=67.11 E-value=2.3 Score=22.91 Aligned_cols=10 Identities=30% Similarity=0.780 Sum_probs=6.1
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
.-+|++|+++
T Consensus 33 rS~C~~C~~~ 42 (92)
T PF06750_consen 33 RSHCPHCGHP 42 (92)
T ss_pred CCcCcCCCCc
Confidence 4566666664
No 104
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=67.11 E-value=3.1 Score=20.03 Aligned_cols=14 Identities=29% Similarity=0.821 Sum_probs=9.8
Q ss_pred eecCCCCCeEEEeecC
Q 035423 11 IQCRECGYRILYKKRT 26 (35)
Q Consensus 11 irC~~CG~RIlyK~R~ 26 (35)
=+|+.|||. |+.+.
T Consensus 29 W~C~~Cgh~--w~~~v 42 (55)
T PF14311_consen 29 WKCPKCGHE--WKASV 42 (55)
T ss_pred EECCCCCCe--eEccH
Confidence 389999995 55433
No 105
>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=67.04 E-value=3.2 Score=17.39 Aligned_cols=11 Identities=27% Similarity=0.703 Sum_probs=9.0
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
.+..|+.||..
T Consensus 13 k~~~C~~C~k~ 23 (26)
T PF13465_consen 13 KPYKCPYCGKS 23 (26)
T ss_dssp SSEEESSSSEE
T ss_pred CCCCCCCCcCe
Confidence 45899999975
No 106
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=66.86 E-value=2.9 Score=23.89 Aligned_cols=12 Identities=25% Similarity=0.526 Sum_probs=8.5
Q ss_pred CCceecCCCCCe
Q 035423 8 GDVIQCRECGYR 19 (35)
Q Consensus 8 ~~~irC~~CG~R 19 (35)
....+|+.||+-
T Consensus 27 l~g~kC~~CG~v 38 (140)
T COG1545 27 LLGTKCKKCGRV 38 (140)
T ss_pred EEEEEcCCCCeE
Confidence 346788888864
No 107
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.81 E-value=3.3 Score=21.89 Aligned_cols=16 Identities=19% Similarity=0.634 Sum_probs=13.1
Q ss_pred CCCceecCCCCCeEEE
Q 035423 7 PGDVIQCRECGYRILY 22 (35)
Q Consensus 7 ~~~~irC~~CG~RIly 22 (35)
....+.||.||.-+..
T Consensus 4 ~~~~v~CP~Cgkpv~w 19 (65)
T COG3024 4 LRITVPCPTCGKPVVW 19 (65)
T ss_pred ccccccCCCCCCcccc
Confidence 3457899999999887
No 108
>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=66.38 E-value=3.5 Score=23.63 Aligned_cols=14 Identities=29% Similarity=0.762 Sum_probs=10.9
Q ss_pred CCCCceecCCCCCe
Q 035423 6 KPGDVIQCRECGYR 19 (35)
Q Consensus 6 k~~~~irC~~CG~R 19 (35)
..++..-||+|||-
T Consensus 15 ~dg~~~iCpeC~~E 28 (109)
T TIGR00686 15 HDGTQLICPSCLYE 28 (109)
T ss_pred ecCCeeECcccccc
Confidence 45667889999985
No 109
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=66.33 E-value=4.7 Score=25.72 Aligned_cols=17 Identities=29% Similarity=0.774 Sum_probs=13.0
Q ss_pred eecCCCCCeEEEeecCC
Q 035423 11 IQCRECGYRILYKKRTR 27 (35)
Q Consensus 11 irC~~CG~RIlyK~R~~ 27 (35)
++|+.|+.-|-+|-=|+
T Consensus 78 ~kC~~C~~~i~~kTDPk 94 (324)
T PF04502_consen 78 IKCPRCSNEIEFKTDPK 94 (324)
T ss_pred EEcCCCCCEEeeecCCC
Confidence 68999999888875443
No 110
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=66.33 E-value=5.3 Score=18.48 Aligned_cols=10 Identities=50% Similarity=1.371 Sum_probs=8.5
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
-..|+.|||-
T Consensus 20 ~~vC~~Cg~~ 29 (52)
T smart00661 20 RFVCRKCGYE 29 (52)
T ss_pred EEECCcCCCe
Confidence 6789999985
No 111
>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=66.12 E-value=5.5 Score=18.26 Aligned_cols=13 Identities=23% Similarity=0.856 Sum_probs=8.7
Q ss_pred CCceecCCCCCeE
Q 035423 8 GDVIQCRECGYRI 20 (35)
Q Consensus 8 ~~~irC~~CG~RI 20 (35)
.+.+.|++||--|
T Consensus 2 ~~~~~C~nC~R~v 14 (33)
T PF08209_consen 2 SPYVECPNCGRPV 14 (33)
T ss_dssp S-EEE-TTTSSEE
T ss_pred CCeEECCCCcCCc
Confidence 3568999999765
No 112
>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=66.12 E-value=3.6 Score=20.72 Aligned_cols=12 Identities=25% Similarity=0.755 Sum_probs=9.5
Q ss_pred ceecCCCCCeEE
Q 035423 10 VIQCRECGYRIL 21 (35)
Q Consensus 10 ~irC~~CG~RIl 21 (35)
-..||.||...+
T Consensus 13 Y~~Cp~CGN~~v 24 (49)
T PF12677_consen 13 YCKCPKCGNDKV 24 (49)
T ss_pred hccCcccCCcEe
Confidence 368999998765
No 113
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=66.10 E-value=2.7 Score=24.37 Aligned_cols=8 Identities=38% Similarity=1.232 Sum_probs=7.0
Q ss_pred ecCCCCCe
Q 035423 12 QCRECGYR 19 (35)
Q Consensus 12 rC~~CG~R 19 (35)
+||.|||-
T Consensus 76 kCpkCghe 83 (116)
T KOG2907|consen 76 KCPKCGHE 83 (116)
T ss_pred cCcccCCc
Confidence 79999985
No 114
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=66.05 E-value=5.7 Score=20.37 Aligned_cols=18 Identities=22% Similarity=0.447 Sum_probs=9.4
Q ss_pred cccCCCCceecCCCCCeE
Q 035423 3 NTLKPGDVIQCRECGYRI 20 (35)
Q Consensus 3 ~~lk~~~~irC~~CG~RI 20 (35)
+.++...+-.||.||.-|
T Consensus 17 ~~~~S~~PatCP~C~a~~ 34 (54)
T PF09237_consen 17 SKSQSEQPATCPICGAVI 34 (54)
T ss_dssp CCCTTS--EE-TTT--EE
T ss_pred HhhccCCCCCCCcchhhc
Confidence 456677889999999653
No 115
>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=65.67 E-value=3.4 Score=20.87 Aligned_cols=10 Identities=30% Similarity=0.690 Sum_probs=8.2
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
.|+||.||.-
T Consensus 24 eIKCpRC~ti 33 (51)
T PF10122_consen 24 EIKCPRCKTI 33 (51)
T ss_pred EEECCCCCcc
Confidence 6899999863
No 116
>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=65.47 E-value=6.3 Score=17.19 Aligned_cols=15 Identities=27% Similarity=0.519 Sum_probs=9.7
Q ss_pred CCCCceecCCCCCeE
Q 035423 6 KPGDVIQCRECGYRI 20 (35)
Q Consensus 6 k~~~~irC~~CG~RI 20 (35)
..+-..+|+.||+..
T Consensus 17 ~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 17 PGGWARRCPSCGHEH 31 (32)
T ss_dssp SSSS-EEESSSS-EE
T ss_pred CCcCEeECCCCcCEe
Confidence 345678999999863
No 117
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=64.99 E-value=2.9 Score=20.66 Aligned_cols=9 Identities=33% Similarity=1.117 Sum_probs=6.6
Q ss_pred ceecCCCCC
Q 035423 10 VIQCRECGY 18 (35)
Q Consensus 10 ~irC~~CG~ 18 (35)
.-+||.||.
T Consensus 11 irkCp~CGt 19 (44)
T PF14952_consen 11 IRKCPKCGT 19 (44)
T ss_pred cccCCcCcC
Confidence 347999984
No 118
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=64.91 E-value=3.9 Score=16.38 Aligned_cols=10 Identities=30% Similarity=1.022 Sum_probs=6.0
Q ss_pred eecCCCCCeE
Q 035423 11 IQCRECGYRI 20 (35)
Q Consensus 11 irC~~CG~RI 20 (35)
.+|+.|.|.-
T Consensus 1 y~C~~C~y~t 10 (24)
T PF13909_consen 1 YKCPHCSYST 10 (24)
T ss_dssp EE-SSSS-EE
T ss_pred CCCCCCCCcC
Confidence 3799999863
No 119
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=64.88 E-value=4.5 Score=20.33 Aligned_cols=16 Identities=31% Similarity=0.760 Sum_probs=10.0
Q ss_pred cCCCCceecCCCCCeE
Q 035423 5 LKPGDVIQCRECGYRI 20 (35)
Q Consensus 5 lk~~~~irC~~CG~RI 20 (35)
+..-..+.|+.||.-.
T Consensus 22 l~~~~l~~C~~CG~~~ 37 (57)
T PRK12286 22 LKAPGLVECPNCGEPK 37 (57)
T ss_pred ccCCcceECCCCCCcc
Confidence 4445566788777643
No 120
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=64.77 E-value=3.9 Score=21.10 Aligned_cols=12 Identities=25% Similarity=0.761 Sum_probs=9.2
Q ss_pred CceecCCCCCeE
Q 035423 9 DVIQCRECGYRI 20 (35)
Q Consensus 9 ~~irC~~CG~RI 20 (35)
..|+||.|+.--
T Consensus 10 ~~VkCp~C~n~q 21 (59)
T PRK00415 10 LKVKCPDCGNEQ 21 (59)
T ss_pred EEEECCCCCCeE
Confidence 358999999754
No 121
>PF13395 HNH_4: HNH endonuclease
Probab=64.74 E-value=2.9 Score=20.17 Aligned_cols=9 Identities=44% Similarity=0.922 Sum_probs=7.4
Q ss_pred cCCCCCeEE
Q 035423 13 CRECGYRIL 21 (35)
Q Consensus 13 C~~CG~RIl 21 (35)
|+|||-.|=
T Consensus 1 C~Y~g~~i~ 9 (54)
T PF13395_consen 1 CPYCGKPIS 9 (54)
T ss_pred CCCCCCCCC
Confidence 899998864
No 122
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=64.54 E-value=2.8 Score=23.81 Aligned_cols=10 Identities=40% Similarity=1.235 Sum_probs=8.0
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
..+||.||..
T Consensus 107 ~~~CP~Cgs~ 116 (135)
T PRK03824 107 FLKCPKCGSR 116 (135)
T ss_pred CcCCcCCCCC
Confidence 4679999975
No 123
>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=64.38 E-value=3.4 Score=16.17 Aligned_cols=8 Identities=38% Similarity=1.049 Sum_probs=6.5
Q ss_pred ecCCCCCe
Q 035423 12 QCRECGYR 19 (35)
Q Consensus 12 rC~~CG~R 19 (35)
.|+.||..
T Consensus 2 ~C~~C~~~ 9 (23)
T PF00096_consen 2 KCPICGKS 9 (23)
T ss_dssp EETTTTEE
T ss_pred CCCCCCCc
Confidence 69999965
No 124
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=63.71 E-value=4 Score=25.18 Aligned_cols=17 Identities=29% Similarity=0.759 Sum_probs=13.3
Q ss_pred CCCCceecCCCCCeEEE
Q 035423 6 KPGDVIQCRECGYRILY 22 (35)
Q Consensus 6 k~~~~irC~~CG~RIly 22 (35)
+.+...+||.||+.-.=
T Consensus 161 ~~~~~l~Cp~Cg~tEkR 177 (188)
T COG1096 161 KKGNMLKCPNCGNTEKR 177 (188)
T ss_pred EcCcEEECCCCCCEEee
Confidence 46788999999987443
No 125
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=63.68 E-value=2.7 Score=23.76 Aligned_cols=11 Identities=27% Similarity=1.138 Sum_probs=8.8
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
.+-+|+.|||-
T Consensus 57 ~Pa~CkkCGfe 67 (97)
T COG3357 57 RPARCKKCGFE 67 (97)
T ss_pred cChhhcccCcc
Confidence 36789999985
No 126
>PF09158 MotCF: Bacteriophage T4 MotA, C-terminal; InterPro: IPR015241 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the C-terminal domain of MotA factors, which adopts a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. It contains a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end [].; PDB: 1KAF_B.
Probab=63.41 E-value=8.4 Score=21.85 Aligned_cols=17 Identities=53% Similarity=0.843 Sum_probs=15.0
Q ss_pred CeEEEeecCCceEEEEe
Q 035423 18 YRILYKKRTRRIVQYEA 34 (35)
Q Consensus 18 ~RIlyK~R~~~~~~~~A 34 (35)
+-|++++|+....|||-
T Consensus 32 ~~i~f~KRt~GirqfEi 48 (103)
T PF09158_consen 32 YEIRFKKRTKGIRQFEI 48 (103)
T ss_dssp EEEEEEEEETTEEEEEE
T ss_pred eEEeeecccCceeEEEE
Confidence 56899999999999984
No 127
>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=63.05 E-value=4.1 Score=18.81 Aligned_cols=14 Identities=36% Similarity=0.745 Sum_probs=7.9
Q ss_pred CCCceecCCCCCeE
Q 035423 7 PGDVIQCRECGYRI 20 (35)
Q Consensus 7 ~~~~irC~~CG~RI 20 (35)
-...+-|++||=|.
T Consensus 18 ~~~~isC~~CGPr~ 31 (35)
T PF07503_consen 18 HYQFISCTNCGPRY 31 (35)
T ss_dssp T-TT--BTTCC-SC
T ss_pred cCcCccCCCCCCCE
Confidence 35689999999764
No 128
>PF14369 zf-RING_3: zinc-finger
Probab=62.40 E-value=6.7 Score=17.88 Aligned_cols=14 Identities=14% Similarity=0.465 Sum_probs=9.9
Q ss_pred CCceecCCCCCeEE
Q 035423 8 GDVIQCRECGYRIL 21 (35)
Q Consensus 8 ~~~irC~~CG~RIl 21 (35)
.+.+-||+|+...|
T Consensus 19 ~~~~~CP~C~~gFv 32 (35)
T PF14369_consen 19 DSDVACPRCHGGFV 32 (35)
T ss_pred CCCcCCcCCCCcEe
Confidence 44456999997654
No 129
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=62.13 E-value=5.4 Score=19.50 Aligned_cols=8 Identities=38% Similarity=0.983 Sum_probs=5.4
Q ss_pred ecCCCCCe
Q 035423 12 QCRECGYR 19 (35)
Q Consensus 12 rC~~CG~R 19 (35)
-||.||..
T Consensus 22 fCP~Cg~~ 29 (50)
T PRK00432 22 FCPRCGSG 29 (50)
T ss_pred cCcCCCcc
Confidence 57777765
No 130
>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=61.95 E-value=5.5 Score=19.64 Aligned_cols=15 Identities=33% Similarity=0.899 Sum_probs=9.5
Q ss_pred cCCCCceecCCCCCe
Q 035423 5 LKPGDVIQCRECGYR 19 (35)
Q Consensus 5 lk~~~~irC~~CG~R 19 (35)
|+.-..+.|+.||.-
T Consensus 21 l~~~~l~~c~~cg~~ 35 (56)
T PF01783_consen 21 LKAPNLVKCPNCGEP 35 (56)
T ss_dssp --TTSEEESSSSSSE
T ss_pred ccccceeeeccCCCE
Confidence 455567788888864
No 131
>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=61.54 E-value=3.3 Score=20.21 Aligned_cols=13 Identities=38% Similarity=0.700 Sum_probs=9.9
Q ss_pred CCCCceecCCCCC
Q 035423 6 KPGDVIQCRECGY 18 (35)
Q Consensus 6 k~~~~irC~~CG~ 18 (35)
+....+.||-||-
T Consensus 5 ~~ltG~~CPgCG~ 17 (52)
T PF10825_consen 5 KALTGIPCPGCGM 17 (52)
T ss_pred hhhhCCCCCCCcH
Confidence 4556789999994
No 132
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=61.45 E-value=4.2 Score=25.42 Aligned_cols=11 Identities=36% Similarity=1.072 Sum_probs=9.2
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
..++|.+||+=
T Consensus 29 ~lvrC~eCG~V 39 (201)
T COG1326 29 PLVRCEECGTV 39 (201)
T ss_pred eEEEccCCCcE
Confidence 37999999984
No 133
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=61.17 E-value=9 Score=22.42 Aligned_cols=15 Identities=33% Similarity=0.813 Sum_probs=10.9
Q ss_pred CCCceecCCCCCeEE
Q 035423 7 PGDVIQCRECGYRIL 21 (35)
Q Consensus 7 ~~~~irC~~CG~RIl 21 (35)
....|-||.||++.-
T Consensus 41 KdG~v~CPvC~~~~~ 55 (131)
T COG1645 41 KDGEVFCPVCGYREV 55 (131)
T ss_pred eCCeEECCCCCceEE
Confidence 445688999998743
No 134
>KOG3404 consensus G10 protein/predicted nuclear transcription regulator [Transcription]
Probab=60.98 E-value=3.5 Score=24.62 Aligned_cols=16 Identities=31% Similarity=0.870 Sum_probs=13.3
Q ss_pred ccCCCCceecCCCCCe
Q 035423 4 TLKPGDVIQCRECGYR 19 (35)
Q Consensus 4 ~lk~~~~irC~~CG~R 19 (35)
.|.....+.|.+||+|
T Consensus 125 ~ld~~~~~~C~hCGCr 140 (145)
T KOG3404|consen 125 KLDVERIVECVHCGCR 140 (145)
T ss_pred hcChhheeeeeccCcC
Confidence 4667778999999987
No 135
>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=60.74 E-value=5.6 Score=18.58 Aligned_cols=10 Identities=30% Similarity=1.049 Sum_probs=8.4
Q ss_pred eecCCCCCeE
Q 035423 11 IQCRECGYRI 20 (35)
Q Consensus 11 irC~~CG~RI 20 (35)
+.|+.||+.+
T Consensus 41 ~~C~~C~~~f 50 (64)
T PF01485_consen 41 VTCPSCGTEF 50 (64)
T ss_dssp CCTTSCCSEE
T ss_pred eECCCCCCcC
Confidence 8899999864
No 136
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=60.71 E-value=5.3 Score=23.89 Aligned_cols=17 Identities=35% Similarity=0.837 Sum_probs=10.7
Q ss_pred ecCCCCCeE--EEeecCCc
Q 035423 12 QCRECGYRI--LYKKRTRR 28 (35)
Q Consensus 12 rC~~CG~RI--lyK~R~~~ 28 (35)
+|-+||+.+ ||++=++.
T Consensus 2 iCIeCg~~v~~Ly~~Ys~~ 20 (208)
T PF04161_consen 2 ICIECGHPVKSLYRQYSPG 20 (208)
T ss_pred EeccCCCcchhhhhccCCC
Confidence 688888876 55544443
No 137
>PF12773 DZR: Double zinc ribbon
Probab=60.67 E-value=4.5 Score=18.76 Aligned_cols=11 Identities=27% Similarity=0.685 Sum_probs=6.1
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
..+.|+.||..
T Consensus 28 ~~~~C~~Cg~~ 38 (50)
T PF12773_consen 28 SKKICPNCGAE 38 (50)
T ss_pred CCCCCcCCcCC
Confidence 34556666654
No 138
>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=60.52 E-value=9.5 Score=19.15 Aligned_cols=17 Identities=29% Similarity=0.366 Sum_probs=13.5
Q ss_pred CceecCCCCCeEEEeec
Q 035423 9 DVIQCRECGYRILYKKR 25 (35)
Q Consensus 9 ~~irC~~CG~RIlyK~R 25 (35)
-.-.||+||..|=.++|
T Consensus 57 ~~H~Cp~C~~~lg~~~r 73 (73)
T PF10601_consen 57 VYHYCPNCGAFLGTYKR 73 (73)
T ss_pred ceEECCCCCCEeEEEeC
Confidence 34689999999877765
No 139
>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=60.37 E-value=4.2 Score=22.40 Aligned_cols=17 Identities=29% Similarity=0.708 Sum_probs=13.4
Q ss_pred ccCCCCceecCCCCCeE
Q 035423 4 TLKPGDVIQCRECGYRI 20 (35)
Q Consensus 4 ~lk~~~~irC~~CG~RI 20 (35)
.|+.-+.+.|++||--.
T Consensus 29 vIknVPa~~C~~CGe~y 45 (89)
T TIGR03829 29 EIKETPSISCSHCGMEY 45 (89)
T ss_pred EEecCCcccccCCCcEe
Confidence 46777899999999653
No 140
>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=60.34 E-value=4.3 Score=19.55 Aligned_cols=10 Identities=30% Similarity=0.600 Sum_probs=8.5
Q ss_pred ecCCCCCeEE
Q 035423 12 QCRECGYRIL 21 (35)
Q Consensus 12 rC~~CG~RIl 21 (35)
-||.||..-.
T Consensus 3 PCPfCGg~~~ 12 (53)
T TIGR03655 3 PCPFCGGADV 12 (53)
T ss_pred CCCCCCCcce
Confidence 4999999876
No 141
>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=60.23 E-value=3.8 Score=27.14 Aligned_cols=10 Identities=50% Similarity=1.109 Sum_probs=8.2
Q ss_pred ceecCCCCCeE
Q 035423 10 VIQCRECGYRI 20 (35)
Q Consensus 10 ~irC~~CG~RI 20 (35)
..+|| ||.+|
T Consensus 259 ~~~Cp-CG~~i 268 (374)
T TIGR00375 259 CANCP-CGGRI 268 (374)
T ss_pred CCCCC-CCCcc
Confidence 36899 99994
No 142
>PRK10220 hypothetical protein; Provisional
Probab=60.10 E-value=6.4 Score=22.64 Aligned_cols=14 Identities=21% Similarity=0.581 Sum_probs=10.7
Q ss_pred CCCCceecCCCCCe
Q 035423 6 KPGDVIQCRECGYR 19 (35)
Q Consensus 6 k~~~~irC~~CG~R 19 (35)
..++..-||+|||-
T Consensus 16 ~d~~~~vCpeC~hE 29 (111)
T PRK10220 16 EDNGMYICPECAHE 29 (111)
T ss_pred cCCCeEECCcccCc
Confidence 45667889999985
No 143
>PRK00807 50S ribosomal protein L24e; Validated
Probab=59.83 E-value=5.3 Score=19.66 Aligned_cols=10 Identities=40% Similarity=0.833 Sum_probs=8.3
Q ss_pred ecCCCCCeEE
Q 035423 12 QCRECGYRIL 21 (35)
Q Consensus 12 rC~~CG~RIl 21 (35)
.|-+||+.|-
T Consensus 3 ~C~fcG~~I~ 12 (52)
T PRK00807 3 TCSFCGKEIE 12 (52)
T ss_pred ccCCCCCeEc
Confidence 5999999974
No 144
>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=59.78 E-value=5.3 Score=21.16 Aligned_cols=16 Identities=31% Similarity=0.694 Sum_probs=9.8
Q ss_pred ceecCCCCCeEEEeecC
Q 035423 10 VIQCRECGYRILYKKRT 26 (35)
Q Consensus 10 ~irC~~CG~RIlyK~R~ 26 (35)
.=+| .||++|=.|+|.
T Consensus 20 TkkC-~CG~~l~vk~~r 35 (68)
T PF09082_consen 20 TKKC-VCGKTLKVKERR 35 (68)
T ss_dssp EEEE-TTTEEEE--SSS
T ss_pred eeEe-cCCCeeeeeeEE
Confidence 3468 888887777654
No 145
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=59.70 E-value=4.3 Score=27.61 Aligned_cols=17 Identities=24% Similarity=0.501 Sum_probs=12.8
Q ss_pred ceecCCCCCeEEEeecC
Q 035423 10 VIQCRECGYRILYKKRT 26 (35)
Q Consensus 10 ~irC~~CG~RIlyK~R~ 26 (35)
..||+.||+|+=.....
T Consensus 367 g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 367 GFRCKKCGTRARETLIK 383 (421)
T ss_pred CcccccccccCCccccc
Confidence 78999999996544443
No 146
>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=59.35 E-value=4.1 Score=27.71 Aligned_cols=14 Identities=21% Similarity=0.707 Sum_probs=10.2
Q ss_pred ceecCCCCCeEEEe
Q 035423 10 VIQCRECGYRILYK 23 (35)
Q Consensus 10 ~irC~~CG~RIlyK 23 (35)
-+.||+||+.-...
T Consensus 200 ~vpCPhCg~~~~l~ 213 (557)
T PF05876_consen 200 YVPCPHCGEEQVLE 213 (557)
T ss_pred EccCCCCCCCcccc
Confidence 47899999876544
No 147
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=59.28 E-value=9.2 Score=17.87 Aligned_cols=16 Identities=19% Similarity=0.814 Sum_probs=12.0
Q ss_pred CCCceecCCCCCeEEE
Q 035423 7 PGDVIQCRECGYRILY 22 (35)
Q Consensus 7 ~~~~irC~~CG~RIly 22 (35)
....+.|+.||+..-+
T Consensus 37 ~~~~v~C~~C~~~fC~ 52 (64)
T smart00647 37 GCNRVTCPKCGFSFCF 52 (64)
T ss_pred CCCeeECCCCCCeECC
Confidence 4457999999987644
No 148
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=59.12 E-value=4.5 Score=20.65 Aligned_cols=10 Identities=30% Similarity=0.640 Sum_probs=8.1
Q ss_pred eecCCCCCeE
Q 035423 11 IQCRECGYRI 20 (35)
Q Consensus 11 irC~~CG~RI 20 (35)
.-||.||.|+
T Consensus 40 ngCPfC~~~~ 49 (55)
T PF14447_consen 40 NGCPFCGTPF 49 (55)
T ss_pred cCCCCCCCcc
Confidence 4599999886
No 149
>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=58.73 E-value=8.1 Score=18.91 Aligned_cols=11 Identities=36% Similarity=1.186 Sum_probs=6.2
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
....|+.||+.
T Consensus 45 r~~~C~~Cg~~ 55 (69)
T PF07282_consen 45 RVFTCPNCGFE 55 (69)
T ss_pred ceEEcCCCCCE
Confidence 34556666654
No 150
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=58.54 E-value=9.9 Score=21.05 Aligned_cols=16 Identities=25% Similarity=0.659 Sum_probs=10.5
Q ss_pred CCCCceecCCCCCeEE
Q 035423 6 KPGDVIQCRECGYRIL 21 (35)
Q Consensus 6 k~~~~irC~~CG~RIl 21 (35)
+....+.||+||...|
T Consensus 17 klpt~f~CP~Cge~~v 32 (99)
T PRK14892 17 KLPKIFECPRCGKVSI 32 (99)
T ss_pred CCCcEeECCCCCCeEe
Confidence 3445677888886544
No 151
>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=58.02 E-value=5.7 Score=20.14 Aligned_cols=10 Identities=20% Similarity=0.507 Sum_probs=6.1
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
.|+||.|+.-
T Consensus 7 ~VkCp~C~~~ 16 (55)
T PF01667_consen 7 DVKCPGCYNI 16 (55)
T ss_dssp EEE-TTT-SE
T ss_pred EEECCCCCCe
Confidence 5889999874
No 152
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=57.92 E-value=3.9 Score=23.57 Aligned_cols=9 Identities=33% Similarity=0.984 Sum_probs=7.4
Q ss_pred ecCCCCCeE
Q 035423 12 QCRECGYRI 20 (35)
Q Consensus 12 rC~~CG~RI 20 (35)
=||+||.+-
T Consensus 22 GCp~CG~nk 30 (112)
T COG3364 22 GCPKCGCNK 30 (112)
T ss_pred cCccccchh
Confidence 499999983
No 153
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=57.72 E-value=10 Score=17.81 Aligned_cols=14 Identities=14% Similarity=0.498 Sum_probs=6.2
Q ss_pred CCceecCC-CCCeEE
Q 035423 8 GDVIQCRE-CGYRIL 21 (35)
Q Consensus 8 ~~~irC~~-CG~RIl 21 (35)
...|.||+ ||..+|
T Consensus 7 ~~~v~C~~~cc~~~i 21 (60)
T PF02176_consen 7 FRPVPCPNGCCNEMI 21 (60)
T ss_dssp TSEEE-TT--S-BEE
T ss_pred CCEeeCCCCCcccce
Confidence 34677777 554433
No 154
>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=57.72 E-value=5 Score=17.87 Aligned_cols=13 Identities=31% Similarity=0.680 Sum_probs=7.0
Q ss_pred ceecCCCCCeEEE
Q 035423 10 VIQCRECGYRILY 22 (35)
Q Consensus 10 ~irC~~CG~RIly 22 (35)
.-+|+.||.-.++
T Consensus 11 ~~rC~~Cg~~~~p 23 (37)
T PF12172_consen 11 GQRCRDCGRVQFP 23 (37)
T ss_dssp EEE-TTT--EEES
T ss_pred EEEcCCCCCEecC
Confidence 4689999987553
No 155
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=57.51 E-value=6.6 Score=21.02 Aligned_cols=13 Identities=38% Similarity=0.838 Sum_probs=10.6
Q ss_pred eecCCCCCeEEEe
Q 035423 11 IQCRECGYRILYK 23 (35)
Q Consensus 11 irC~~CG~RIlyK 23 (35)
+.||=|||..|-.
T Consensus 2 ~~CPCCg~~Tl~~ 14 (78)
T PF14206_consen 2 YPCPCCGYYTLEE 14 (78)
T ss_pred ccCCCCCcEEecc
Confidence 5799999998743
No 156
>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=57.42 E-value=11 Score=20.72 Aligned_cols=20 Identities=25% Similarity=0.536 Sum_probs=15.0
Q ss_pred CCCceecCCCCCeEEEeecC
Q 035423 7 PGDVIQCRECGYRILYKKRT 26 (35)
Q Consensus 7 ~~~~irC~~CG~RIlyK~R~ 26 (35)
.....+|+.||..+-.+.+.
T Consensus 120 ~~~~~~C~~C~~~~~r~~~~ 139 (157)
T PF10263_consen 120 KKYVYRCPSCGREYKRHRRS 139 (157)
T ss_pred cceEEEcCCCCCEeeeeccc
Confidence 34578899999998666665
No 157
>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=57.29 E-value=8 Score=19.22 Aligned_cols=15 Identities=27% Similarity=0.665 Sum_probs=10.7
Q ss_pred cCCCCceecCCCCCe
Q 035423 5 LKPGDVIQCRECGYR 19 (35)
Q Consensus 5 lk~~~~irC~~CG~R 19 (35)
|+.-..+.|+.||.-
T Consensus 21 l~~p~l~~C~~cG~~ 35 (55)
T TIGR01031 21 LTAPTLVVCPNCGEF 35 (55)
T ss_pred ccCCcceECCCCCCc
Confidence 555667788888853
No 158
>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=57.21 E-value=6.9 Score=17.93 Aligned_cols=12 Identities=25% Similarity=0.670 Sum_probs=8.8
Q ss_pred ceecCCCCCeEE
Q 035423 10 VIQCRECGYRIL 21 (35)
Q Consensus 10 ~irC~~CG~RIl 21 (35)
+-.|+.||...-
T Consensus 2 ~~~C~~Cg~~l~ 13 (47)
T PF13005_consen 2 PRACPDCGGELK 13 (47)
T ss_pred CCcCCCCCceee
Confidence 346999999743
No 159
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=56.83 E-value=5.5 Score=24.84 Aligned_cols=10 Identities=50% Similarity=1.228 Sum_probs=8.6
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
...|..||||
T Consensus 43 t~~C~~CgYR 52 (201)
T COG1779 43 TGVCERCGYR 52 (201)
T ss_pred EEEccccCCc
Confidence 4689999998
No 160
>smart00746 TRASH metallochaperone-like domain.
Probab=56.82 E-value=5.7 Score=15.49 Aligned_cols=9 Identities=44% Similarity=1.003 Sum_probs=7.1
Q ss_pred cCCCCCeEE
Q 035423 13 CRECGYRIL 21 (35)
Q Consensus 13 C~~CG~RIl 21 (35)
|+.||..|.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 788988864
No 161
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=56.49 E-value=6.2 Score=23.69 Aligned_cols=12 Identities=50% Similarity=1.154 Sum_probs=7.3
Q ss_pred CCceecCCCCCe
Q 035423 8 GDVIQCRECGYR 19 (35)
Q Consensus 8 ~~~irC~~CG~R 19 (35)
+..-+|+.|||-
T Consensus 132 ~~~~vC~vCGy~ 143 (166)
T COG1592 132 GKVWVCPVCGYT 143 (166)
T ss_pred CCEEEcCCCCCc
Confidence 335667777763
No 162
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=56.30 E-value=7.5 Score=17.53 Aligned_cols=17 Identities=29% Similarity=0.647 Sum_probs=10.1
Q ss_pred CCCceecCCCCCeEEEe
Q 035423 7 PGDVIQCRECGYRILYK 23 (35)
Q Consensus 7 ~~~~irC~~CG~RIlyK 23 (35)
....++|.+|+..+-+.
T Consensus 13 ~~~~a~C~~C~~~~~~~ 29 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYS 29 (45)
T ss_dssp CSS-EEETTTTEE----
T ss_pred CcCeEEeCCCCeEEeeC
Confidence 35679999999887665
No 163
>COG4640 Predicted membrane protein [Function unknown]
Probab=56.14 E-value=5 Score=27.74 Aligned_cols=15 Identities=40% Similarity=0.953 Sum_probs=11.6
Q ss_pred CCCCceecCCCCCeE
Q 035423 6 KPGDVIQCRECGYRI 20 (35)
Q Consensus 6 k~~~~irC~~CG~RI 20 (35)
+..|.+.|+.||+.+
T Consensus 11 k~Ed~~qC~qCG~~~ 25 (465)
T COG4640 11 KAEDDVQCTQCGHKF 25 (465)
T ss_pred cccccccccccCCcC
Confidence 445678899999975
No 164
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=56.02 E-value=11 Score=20.92 Aligned_cols=17 Identities=24% Similarity=0.432 Sum_probs=13.1
Q ss_pred CCceecCCCCCeEEEee
Q 035423 8 GDVIQCRECGYRILYKK 24 (35)
Q Consensus 8 ~~~irC~~CG~RIlyK~ 24 (35)
.....||.||...+++.
T Consensus 15 ~~~~~Cp~Cg~~m~~~~ 31 (140)
T COG0551 15 KTGQICPKCGKNMVKKF 31 (140)
T ss_pred ccCccCCcCCCeeEEEE
Confidence 34679999999966654
No 165
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=55.90 E-value=10 Score=18.73 Aligned_cols=15 Identities=27% Similarity=0.441 Sum_probs=10.1
Q ss_pred CCCCceecCCCCCeE
Q 035423 6 KPGDVIQCRECGYRI 20 (35)
Q Consensus 6 k~~~~irC~~CG~RI 20 (35)
+.....||-||+..+
T Consensus 31 ~~~~~~rC~YCe~~~ 45 (52)
T PF02748_consen 31 KEPIKLRCHYCERII 45 (52)
T ss_dssp TTTCEEEETTT--EE
T ss_pred CCCCEEEeeCCCCEe
Confidence 456778999999765
No 166
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=55.75 E-value=4.5 Score=27.48 Aligned_cols=11 Identities=36% Similarity=0.918 Sum_probs=8.9
Q ss_pred ceecCCCCCeE
Q 035423 10 VIQCRECGYRI 20 (35)
Q Consensus 10 ~irC~~CG~RI 20 (35)
.-+||.||.+|
T Consensus 265 ~wrCpkCGg~i 275 (403)
T COG1379 265 RWRCPKCGGKI 275 (403)
T ss_pred cccCcccccch
Confidence 37899999954
No 167
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 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 archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=55.66 E-value=6.5 Score=20.68 Aligned_cols=11 Identities=36% Similarity=0.830 Sum_probs=7.0
Q ss_pred ceecCCCCCeE
Q 035423 10 VIQCRECGYRI 20 (35)
Q Consensus 10 ~irC~~CG~RI 20 (35)
.-.|.+||+.|
T Consensus 3 ~~~C~Fsg~~I 13 (71)
T PF01246_consen 3 TEKCSFSGYKI 13 (71)
T ss_dssp SEE-TTT-SEE
T ss_pred eEEecccCCcc
Confidence 35799999986
No 168
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=55.41 E-value=6.7 Score=21.06 Aligned_cols=10 Identities=50% Similarity=1.235 Sum_probs=8.3
Q ss_pred eecCCCCCeE
Q 035423 11 IQCRECGYRI 20 (35)
Q Consensus 11 irC~~CG~RI 20 (35)
..|++||.+|
T Consensus 5 Y~CRHCg~~I 14 (76)
T PF10955_consen 5 YYCRHCGTKI 14 (76)
T ss_pred EEecCCCCEE
Confidence 4699999886
No 169
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=54.80 E-value=6.3 Score=18.88 Aligned_cols=14 Identities=36% Similarity=0.601 Sum_probs=6.9
Q ss_pred cCCCCceecCCCCCe
Q 035423 5 LKPGDVIQCRECGYR 19 (35)
Q Consensus 5 lk~~~~irC~~CG~R 19 (35)
|+..++ .||-||.-
T Consensus 16 l~~~~~-~CPlC~r~ 29 (54)
T PF04423_consen 16 LKEAKG-CCPLCGRP 29 (54)
T ss_dssp HTT-SE-E-TTT--E
T ss_pred HhcCCC-cCCCCCCC
Confidence 444555 99999965
No 170
>PF00471 Ribosomal_L33: Ribosomal protein L33; InterPro: IPR001705 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 L33 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L33 has been shown to be on the surface of 50S subunit. L33 belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , ], groups: Eubacterial L33. Algal and plant chloroplast L33. Cyanelle L33. L33 is a small protein of 49 to 66 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3PIO_1 3PIP_1 3PYT_3 3MS1_3 3F1F_6 3F1H_6 3MRZ_3 3PYO_3 3D5B_6 3D5D_6 ....
Probab=54.64 E-value=12 Score=18.26 Aligned_cols=13 Identities=31% Similarity=0.613 Sum_probs=11.1
Q ss_pred ecCCCCCeEEEee
Q 035423 12 QCRECGYRILYKK 24 (35)
Q Consensus 12 rC~~CG~RIlyK~ 24 (35)
-||.|+-..|+++
T Consensus 34 ycp~~~khtlhkE 46 (48)
T PF00471_consen 34 YCPRCRKHTLHKE 46 (48)
T ss_dssp EETSSSSEEEEEC
T ss_pred cCCCCCCEecEEE
Confidence 4899999999886
No 171
>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=54.51 E-value=14 Score=19.58 Aligned_cols=19 Identities=21% Similarity=0.370 Sum_probs=11.9
Q ss_pred cCCCCCeEEEeecCCceEE
Q 035423 13 CRECGYRILYKKRTRRIVQ 31 (35)
Q Consensus 13 C~~CG~RIlyK~R~~~~~~ 31 (35)
|+.||.--+++........
T Consensus 1 C~~C~~~~~~~~~~~~~~~ 19 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYT 19 (127)
T ss_pred CCCCCCccceeeeecceEE
Confidence 8899976566555544433
No 172
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=54.51 E-value=5.5 Score=20.35 Aligned_cols=9 Identities=44% Similarity=1.073 Sum_probs=7.5
Q ss_pred ecCCCCCeE
Q 035423 12 QCRECGYRI 20 (35)
Q Consensus 12 rC~~CG~RI 20 (35)
.|+.||.-|
T Consensus 5 HC~~CG~~I 13 (59)
T PF09889_consen 5 HCPVCGKPI 13 (59)
T ss_pred cCCcCCCcC
Confidence 599999776
No 173
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=54.32 E-value=7.8 Score=19.78 Aligned_cols=16 Identities=31% Similarity=0.571 Sum_probs=10.1
Q ss_pred cCCCCceecCCCCCeE
Q 035423 5 LKPGDVIQCRECGYRI 20 (35)
Q Consensus 5 lk~~~~irC~~CG~RI 20 (35)
|+.-..+.|++||.-.
T Consensus 22 l~~~~~~~c~~cG~~~ 37 (57)
T COG0333 22 LKAPTLSVCPNCGEYK 37 (57)
T ss_pred hhCccceeccCCCCcc
Confidence 3344467888888654
No 174
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=54.28 E-value=6.5 Score=19.70 Aligned_cols=11 Identities=45% Similarity=1.174 Sum_probs=8.8
Q ss_pred ceecCCCCCeE
Q 035423 10 VIQCRECGYRI 20 (35)
Q Consensus 10 ~irC~~CG~RI 20 (35)
.-.|..||++|
T Consensus 3 ~~~C~f~g~~I 13 (54)
T cd00472 3 TEKCSFCGYKI 13 (54)
T ss_pred EEEecCcCCee
Confidence 35799999986
No 175
>PHA02998 RNA polymerase subunit; Provisional
Probab=54.24 E-value=7.2 Score=24.35 Aligned_cols=13 Identities=15% Similarity=0.330 Sum_probs=9.3
Q ss_pred CceecCCCCCeEE
Q 035423 9 DVIQCRECGYRIL 21 (35)
Q Consensus 9 ~~irC~~CG~RIl 21 (35)
..+.||.||++=.
T Consensus 142 t~v~CPkCg~~~A 154 (195)
T PHA02998 142 YNTPCPNCKSKNT 154 (195)
T ss_pred cCCCCCCCCCCce
Confidence 4578888888633
No 176
>COG5132 BUD31 Cell cycle control protein, G10 family [Transcription / Cell division and chromosome partitioning]
Probab=53.95 E-value=3.7 Score=24.47 Aligned_cols=15 Identities=33% Similarity=0.893 Sum_probs=11.6
Q ss_pred cCCCCceecCCCCCe
Q 035423 5 LKPGDVIQCRECGYR 19 (35)
Q Consensus 5 lk~~~~irC~~CG~R 19 (35)
|.....++|.+||+|
T Consensus 126 ld~~qr~kC~hCGCr 140 (146)
T COG5132 126 LDVSQRLKCDHCGCR 140 (146)
T ss_pred cCHHHhccccccCCC
Confidence 445567889999987
No 177
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=53.42 E-value=3.5 Score=22.95 Aligned_cols=17 Identities=18% Similarity=0.305 Sum_probs=12.3
Q ss_pred ccCCCCceecCCCCCeE
Q 035423 4 TLKPGDVIQCRECGYRI 20 (35)
Q Consensus 4 ~lk~~~~irC~~CG~RI 20 (35)
+.+..+.-.||.||...
T Consensus 29 e~~~~~~~~Cp~C~~~~ 45 (89)
T COG1997 29 EAQQRAKHVCPFCGRTT 45 (89)
T ss_pred HHHHhcCCcCCCCCCcc
Confidence 44556777899999874
No 178
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=53.38 E-value=12 Score=22.60 Aligned_cols=20 Identities=30% Similarity=0.956 Sum_probs=15.4
Q ss_pred cCCCCceecCCCCCeEEEee
Q 035423 5 LKPGDVIQCRECGYRILYKK 24 (35)
Q Consensus 5 lk~~~~irC~~CG~RIlyK~ 24 (35)
...+...+|..||-+++++.
T Consensus 135 ~~~g~~YrC~~C~gkL~~~~ 154 (156)
T COG3091 135 VRRGEVYRCGKCGGKLVFKG 154 (156)
T ss_pred ccccceEEeccCCceEEecc
Confidence 34556789999999988763
No 179
>PRK11866 2-oxoacid ferredoxin oxidoreductase subunit beta; Provisional
Probab=53.31 E-value=2.3 Score=26.88 Aligned_cols=15 Identities=27% Similarity=0.463 Sum_probs=12.0
Q ss_pred CCceecCCCCCeEEE
Q 035423 8 GDVIQCRECGYRILY 22 (35)
Q Consensus 8 ~~~irC~~CG~RIly 22 (35)
.++.-||-|||++++
T Consensus 5 r~~~~CpGCg~~~il 19 (279)
T PRK11866 5 RPPIWCPGCGNYGIL 19 (279)
T ss_pred CCCCCCCCCCChHHH
Confidence 467899999998554
No 180
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=53.16 E-value=7.2 Score=21.56 Aligned_cols=9 Identities=22% Similarity=0.637 Sum_probs=7.4
Q ss_pred eecCCCCCe
Q 035423 11 IQCRECGYR 19 (35)
Q Consensus 11 irC~~CG~R 19 (35)
..||.||..
T Consensus 88 ~~CP~Cgs~ 96 (114)
T PRK03681 88 RRCPQCHGD 96 (114)
T ss_pred CcCcCcCCC
Confidence 679999965
No 181
>PHA00616 hypothetical protein
Probab=52.90 E-value=4.7 Score=19.64 Aligned_cols=11 Identities=36% Similarity=0.673 Sum_probs=8.2
Q ss_pred eecCCCCCeEE
Q 035423 11 IQCRECGYRIL 21 (35)
Q Consensus 11 irC~~CG~RIl 21 (35)
-+|+.||..-.
T Consensus 2 YqC~~CG~~F~ 12 (44)
T PHA00616 2 YQCLRCGGIFR 12 (44)
T ss_pred CccchhhHHHh
Confidence 47999997643
No 182
>PRK04860 hypothetical protein; Provisional
Probab=52.86 E-value=14 Score=21.77 Aligned_cols=17 Identities=35% Similarity=0.915 Sum_probs=13.9
Q ss_pred CCceecCCCCCeEEEee
Q 035423 8 GDVIQCRECGYRILYKK 24 (35)
Q Consensus 8 ~~~irC~~CG~RIlyK~ 24 (35)
..+.+|..|+..+.|+.
T Consensus 141 ~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 141 EAVYRCRRCGETLVFKG 157 (160)
T ss_pred CccEECCCCCceeEEec
Confidence 34689999999988864
No 183
>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=52.78 E-value=15 Score=16.61 Aligned_cols=12 Identities=42% Similarity=0.805 Sum_probs=8.3
Q ss_pred ecCCCCCeEEEe
Q 035423 12 QCRECGYRILYK 23 (35)
Q Consensus 12 rC~~CG~RIlyK 23 (35)
-||+||.=.+.+
T Consensus 3 FCp~C~nlL~p~ 14 (35)
T PF02150_consen 3 FCPECGNLLYPK 14 (35)
T ss_dssp BETTTTSBEEEE
T ss_pred eCCCCCccceEc
Confidence 499999864433
No 184
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=52.64 E-value=10 Score=17.84 Aligned_cols=16 Identities=19% Similarity=0.603 Sum_probs=12.6
Q ss_pred CceecCCCCCeEEEee
Q 035423 9 DVIQCRECGYRILYKK 24 (35)
Q Consensus 9 ~~irC~~CG~RIlyK~ 24 (35)
+.+.|.+||..+=+..
T Consensus 17 ~~a~C~~C~~~l~~~~ 32 (50)
T smart00614 17 QRAKCKYCGKKLSRSS 32 (50)
T ss_pred eEEEecCCCCEeeeCC
Confidence 4699999999876543
No 185
>PRK00595 rpmG 50S ribosomal protein L33; Validated
Probab=52.54 E-value=14 Score=18.32 Aligned_cols=12 Identities=17% Similarity=-0.017 Sum_probs=10.0
Q ss_pred cCCCCCeEEEee
Q 035423 13 CRECGYRILYKK 24 (35)
Q Consensus 13 C~~CG~RIlyK~ 24 (35)
||.|+...|+|+
T Consensus 40 cp~~~khtlhkE 51 (53)
T PRK00595 40 DPVLRKHVLHKE 51 (53)
T ss_pred CCCCCCEEeEEe
Confidence 888888888876
No 186
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=52.12 E-value=8 Score=19.35 Aligned_cols=13 Identities=46% Similarity=1.288 Sum_probs=10.2
Q ss_pred CCCceecCCCCCe
Q 035423 7 PGDVIQCRECGYR 19 (35)
Q Consensus 7 ~~~~irC~~CG~R 19 (35)
+-...+|..|||.
T Consensus 25 p~~A~~CRKCg~~ 37 (48)
T PRK04136 25 PWRATKCRKCGYK 37 (48)
T ss_pred CccccccccCCCC
Confidence 3456899999996
No 187
>PF14122 YokU: YokU-like protein
Probab=52.08 E-value=8.8 Score=21.26 Aligned_cols=15 Identities=27% Similarity=0.725 Sum_probs=12.9
Q ss_pred ccCCCCceecCCCCC
Q 035423 4 TLKPGDVIQCRECGY 18 (35)
Q Consensus 4 ~lk~~~~irC~~CG~ 18 (35)
+|+..+.+-|.+||-
T Consensus 29 eI~~tP~i~C~~Cgm 43 (87)
T PF14122_consen 29 EITDTPAIICSNCGM 43 (87)
T ss_pred EecCCceeeecCCCc
Confidence 577889999999995
No 188
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=52.03 E-value=6.4 Score=20.73 Aligned_cols=9 Identities=33% Similarity=1.232 Sum_probs=7.4
Q ss_pred ceecCCCCC
Q 035423 10 VIQCRECGY 18 (35)
Q Consensus 10 ~irC~~CG~ 18 (35)
-.+||.||.
T Consensus 17 ~lrCPRC~~ 25 (65)
T COG4049 17 FLRCPRCGM 25 (65)
T ss_pred eeeCCchhH
Confidence 479999994
No 189
>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=51.76 E-value=20 Score=16.97 Aligned_cols=16 Identities=25% Similarity=0.746 Sum_probs=10.5
Q ss_pred eecCCCCCeEEEeecCC
Q 035423 11 IQCRECGYRILYKKRTR 27 (35)
Q Consensus 11 irC~~CG~RIlyK~R~~ 27 (35)
-.||.||.. |++.+..
T Consensus 18 ~~Cp~C~~P-L~~~k~g 33 (41)
T PF06677_consen 18 EHCPDCGTP-LMRDKDG 33 (41)
T ss_pred CccCCCCCe-eEEecCC
Confidence 469999865 6654443
No 190
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=51.72 E-value=6.2 Score=23.15 Aligned_cols=10 Identities=40% Similarity=0.916 Sum_probs=7.8
Q ss_pred ecCCCCCeEE
Q 035423 12 QCRECGYRIL 21 (35)
Q Consensus 12 rC~~CG~RIl 21 (35)
=||.||.+-+
T Consensus 21 GCP~CGg~kF 30 (131)
T PF09845_consen 21 GCPECGGNKF 30 (131)
T ss_pred cCcccCCcce
Confidence 4999998843
No 191
>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=51.58 E-value=12 Score=21.85 Aligned_cols=16 Identities=19% Similarity=0.657 Sum_probs=12.8
Q ss_pred CceecCCCCCeEEEee
Q 035423 9 DVIQCRECGYRILYKK 24 (35)
Q Consensus 9 ~~irC~~CG~RIlyK~ 24 (35)
....|..|||.+-|..
T Consensus 111 G~l~C~~Cg~~~~~~~ 126 (146)
T PF07295_consen 111 GTLVCENCGHEVELTH 126 (146)
T ss_pred ceEecccCCCEEEecC
Confidence 4578999999988865
No 192
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=51.40 E-value=9.9 Score=22.21 Aligned_cols=12 Identities=25% Similarity=0.769 Sum_probs=10.0
Q ss_pred CceecCCCCCeE
Q 035423 9 DVIQCRECGYRI 20 (35)
Q Consensus 9 ~~irC~~CG~RI 20 (35)
..+.|++||++-
T Consensus 165 ~~~~c~~~~~~e 176 (189)
T PRK09521 165 NELKCPNCGNIE 176 (189)
T ss_pred CEEECCCCCCEE
Confidence 679999999763
No 193
>PF10533 Plant_zn_clust: Plant zinc cluster domain; InterPro: IPR018872 This zinc binding domain is found associated with the WRKY domain IPR003657 from INTERPRO [].
Probab=51.35 E-value=13 Score=18.47 Aligned_cols=25 Identities=24% Similarity=0.489 Sum_probs=18.7
Q ss_pred CCCceecCCCCCeEEEeecCCceEEEEe
Q 035423 7 PGDVIQCRECGYRILYKKRTRRIVQYEA 34 (35)
Q Consensus 7 ~~~~irC~~CG~RIlyK~R~~~~~~~~A 34 (35)
-...-+| +|..+ =|.|-++++.+.|
T Consensus 16 ~sssgrC-HCsKk--RK~RvKR~irVPA 40 (47)
T PF10533_consen 16 CSSSGRC-HCSKK--RKSRVKRTIRVPA 40 (47)
T ss_pred cCCCCcc-cCCCc--ccccceeeEEeec
Confidence 3456688 89886 5778888888876
No 194
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=51.34 E-value=3.9 Score=22.57 Aligned_cols=17 Identities=18% Similarity=0.323 Sum_probs=12.7
Q ss_pred cccCCCCceecCCCCCe
Q 035423 3 NTLKPGDVIQCRECGYR 19 (35)
Q Consensus 3 ~~lk~~~~irC~~CG~R 19 (35)
.+++....-.||.||.-
T Consensus 29 ie~~q~a~y~CpfCgk~ 45 (90)
T PTZ00255 29 IEISQHAKYFCPFCGKH 45 (90)
T ss_pred HHHHHhCCccCCCCCCC
Confidence 45667778889999854
No 195
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=51.18 E-value=15 Score=20.60 Aligned_cols=24 Identities=25% Similarity=0.551 Sum_probs=17.1
Q ss_pred CCceecCCCCCeEEEeecCCceEE
Q 035423 8 GDVIQCRECGYRILYKKRTRRIVQ 31 (35)
Q Consensus 8 ~~~irC~~CG~RIlyK~R~~~~~~ 31 (35)
.-.-+|..||..++...|...+.+
T Consensus 110 ~~~y~C~~C~~~~~~~rr~~~~~~ 133 (146)
T smart00731 110 KYPYRCTGCGQRYLRVRRSNNVSR 133 (146)
T ss_pred eEEEECCCCCCCCceEccccCcce
Confidence 346788889988887777766433
No 196
>cd02772 MopB_NDH-1_NuoG2 MopB_NDH-1_NuoG2: The second domain of the NuoG subunit of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1), found in beta- and gammaproteobacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain (this CD), is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Although only vestigial sequence evidence remains of a molybdopterin binding site, this protein domain belongs to t
Probab=50.66 E-value=26 Score=22.01 Aligned_cols=23 Identities=4% Similarity=0.176 Sum_probs=19.0
Q ss_pred ecCCC--CCeEEEeecCCceEEEEe
Q 035423 12 QCREC--GYRILYKKRTRRIVQYEA 34 (35)
Q Consensus 12 rC~~C--G~RIlyK~R~~~~~~~~A 34 (35)
-|+.| |+-|+...+..+++.++.
T Consensus 3 ~C~~C~~gC~i~v~~~~g~i~~v~~ 27 (414)
T cd02772 3 VSPHDALGSNLVVHVKNNKVMRVVP 27 (414)
T ss_pred cCCCCCCCCCeEEEEECCEEEEEEc
Confidence 38888 888999999888888764
No 197
>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=50.50 E-value=11 Score=17.35 Aligned_cols=14 Identities=21% Similarity=0.501 Sum_probs=11.1
Q ss_pred ceecCCCCCeE-EEe
Q 035423 10 VIQCRECGYRI-LYK 23 (35)
Q Consensus 10 ~irC~~CG~RI-lyK 23 (35)
.|.||.|+.-= +||
T Consensus 5 ~v~CP~C~s~~~v~k 19 (36)
T PF03811_consen 5 DVHCPRCQSTEGVKK 19 (36)
T ss_pred eeeCCCCCCCCccee
Confidence 58999999876 555
No 198
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=50.47 E-value=7.6 Score=20.04 Aligned_cols=9 Identities=44% Similarity=1.010 Sum_probs=7.5
Q ss_pred ecCCCCCeE
Q 035423 12 QCRECGYRI 20 (35)
Q Consensus 12 rC~~CG~RI 20 (35)
+||.||..-
T Consensus 17 ~CP~Cgs~~ 25 (61)
T PRK08351 17 RCPVCGSRD 25 (61)
T ss_pred cCCCCcCCc
Confidence 799999863
No 199
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=50.43 E-value=6.5 Score=20.68 Aligned_cols=12 Identities=33% Similarity=0.708 Sum_probs=9.8
Q ss_pred CceecCCCCCeE
Q 035423 9 DVIQCRECGYRI 20 (35)
Q Consensus 9 ~~irC~~CG~RI 20 (35)
-||||=.||.-|
T Consensus 3 iPiRCFsCGkvi 14 (63)
T COG1644 3 IPVRCFSCGKVI 14 (63)
T ss_pred CceEeecCCCCH
Confidence 479999999754
No 200
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=50.37 E-value=12 Score=21.04 Aligned_cols=13 Identities=31% Similarity=0.692 Sum_probs=10.9
Q ss_pred ceecCCCCCeEEE
Q 035423 10 VIQCRECGYRILY 22 (35)
Q Consensus 10 ~irC~~CG~RIly 22 (35)
-.+|.+||+.+.-
T Consensus 68 r~~Ct~Cgkah~~ 80 (94)
T COG1631 68 RLRCTECGKAHQR 80 (94)
T ss_pred EEEehhhcccccc
Confidence 4689999999775
No 201
>PRK01343 zinc-binding protein; Provisional
Probab=50.19 E-value=7.2 Score=19.96 Aligned_cols=18 Identities=22% Similarity=0.355 Sum_probs=12.8
Q ss_pred CCceecCCCCCeEEEeec
Q 035423 8 GDVIQCRECGYRILYKKR 25 (35)
Q Consensus 8 ~~~irC~~CG~RIlyK~R 25 (35)
...++||.||.......|
T Consensus 7 ~p~~~CP~C~k~~~~~~r 24 (57)
T PRK01343 7 RPTRPCPECGKPSTREAY 24 (57)
T ss_pred CCCCcCCCCCCcCcCCCC
Confidence 357899999987654433
No 202
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=50.13 E-value=7.7 Score=22.05 Aligned_cols=16 Identities=31% Similarity=0.860 Sum_probs=10.7
Q ss_pred ccCCCCceecCCCCCeE
Q 035423 4 TLKPGDVIQCRECGYRI 20 (35)
Q Consensus 4 ~lk~~~~irC~~CG~RI 20 (35)
++..++ ..||.||.-+
T Consensus 42 eIevG~-~~cP~Cge~~ 57 (102)
T PF04475_consen 42 EIEVGD-TICPKCGEEL 57 (102)
T ss_pred EEecCc-ccCCCCCCcc
Confidence 344443 7899999863
No 203
>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=50.01 E-value=7 Score=21.58 Aligned_cols=10 Identities=20% Similarity=0.604 Sum_probs=7.6
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
...||.||..
T Consensus 86 ~~~CP~Cgs~ 95 (115)
T TIGR00100 86 LYRCPKCHGI 95 (115)
T ss_pred CccCcCCcCC
Confidence 4679999964
No 204
>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=49.61 E-value=9.3 Score=24.54 Aligned_cols=15 Identities=20% Similarity=0.561 Sum_probs=11.3
Q ss_pred CCCCceecCCCCCeE
Q 035423 6 KPGDVIQCRECGYRI 20 (35)
Q Consensus 6 k~~~~irC~~CG~RI 20 (35)
...+.+.|+.||++=
T Consensus 254 ~~t~~~~C~~C~~~~ 268 (299)
T TIGR01385 254 AVTDLFTCGKCKQKK 268 (299)
T ss_pred CCcccccCCCCCCcc
Confidence 345678999999873
No 205
>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=49.56 E-value=6.8 Score=20.74 Aligned_cols=11 Identities=27% Similarity=0.685 Sum_probs=4.0
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
..-.||.|||.
T Consensus 21 ~~F~CPfC~~~ 31 (81)
T PF05129_consen 21 KVFDCPFCNHE 31 (81)
T ss_dssp S----TTT--S
T ss_pred ceEcCCcCCCC
Confidence 45689999965
No 206
>TIGR01023 rpmG_bact ribosomal protein L33, bacterial type. This model describes bacterial ribosomal protein L33 and its chloroplast and mitochondrial equivalents.
Probab=49.42 E-value=16 Score=18.18 Aligned_cols=12 Identities=33% Similarity=0.750 Sum_probs=9.9
Q ss_pred cCCCCCeEEEee
Q 035423 13 CRECGYRILYKK 24 (35)
Q Consensus 13 C~~CG~RIlyK~ 24 (35)
||.|+...|+|+
T Consensus 41 cp~~~khtlhkE 52 (54)
T TIGR01023 41 CPVCRKHVLHKE 52 (54)
T ss_pred CCCCCCeEeEEe
Confidence 788888888876
No 207
>COG1743 Adenine-specific DNA methylase containing a Zn-ribbon [DNA replication, recombination, and repair]
Probab=48.98 E-value=8.6 Score=28.49 Aligned_cols=10 Identities=30% Similarity=0.926 Sum_probs=8.4
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
.|+||.||+-
T Consensus 178 ~VkCP~CG~~ 187 (875)
T COG1743 178 EVKCPRCGRL 187 (875)
T ss_pred EEecCCcCcc
Confidence 4899999974
No 208
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=48.81 E-value=9.2 Score=18.01 Aligned_cols=11 Identities=36% Similarity=0.927 Sum_probs=8.1
Q ss_pred ecCCCCCeEEE
Q 035423 12 QCRECGYRILY 22 (35)
Q Consensus 12 rC~~CG~RIly 22 (35)
-||.||--+|-
T Consensus 3 lcpkcgvgvl~ 13 (36)
T PF09151_consen 3 LCPKCGVGVLE 13 (36)
T ss_dssp B-TTTSSSBEE
T ss_pred cCCccCceEEE
Confidence 49999988874
No 209
>PF15494 SRCR_2: Scavenger receptor cysteine-rich domain
Probab=48.73 E-value=9.4 Score=20.03 Aligned_cols=10 Identities=50% Similarity=1.305 Sum_probs=8.2
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
.++|-.||.|
T Consensus 88 sL~C~~CG~r 97 (98)
T PF15494_consen 88 SLQCSDCGKR 97 (98)
T ss_pred EEECcccCCc
Confidence 4789999976
No 210
>PRK00420 hypothetical protein; Validated
Probab=48.64 E-value=17 Score=20.63 Aligned_cols=16 Identities=19% Similarity=0.293 Sum_probs=10.6
Q ss_pred CCceecCCCCCeEEEe
Q 035423 8 GDVIQCRECGYRILYK 23 (35)
Q Consensus 8 ~~~irC~~CG~RIlyK 23 (35)
...+.||.||.-+..+
T Consensus 38 ~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 38 DGEVVCPVHGKVYIVK 53 (112)
T ss_pred CCceECCCCCCeeeec
Confidence 4467788888765543
No 211
>PRK02935 hypothetical protein; Provisional
Probab=48.25 E-value=10 Score=21.83 Aligned_cols=11 Identities=18% Similarity=0.465 Sum_probs=8.8
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
.+|.||+|+.-
T Consensus 69 vqV~CP~C~K~ 79 (110)
T PRK02935 69 VQVICPSCEKP 79 (110)
T ss_pred eeeECCCCCch
Confidence 46899999864
No 212
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=48.22 E-value=11 Score=21.04 Aligned_cols=11 Identities=27% Similarity=0.776 Sum_probs=8.4
Q ss_pred ceecCCCCCeE
Q 035423 10 VIQCRECGYRI 20 (35)
Q Consensus 10 ~irC~~CG~RI 20 (35)
.+.||.||++=
T Consensus 72 ~~~CpkCg~~e 82 (113)
T COG1594 72 KEKCPKCGNKE 82 (113)
T ss_pred cccCCCCCCce
Confidence 46799999873
No 213
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=48.20 E-value=7.5 Score=21.77 Aligned_cols=8 Identities=50% Similarity=1.294 Sum_probs=6.7
Q ss_pred eecCCCCC
Q 035423 11 IQCRECGY 18 (35)
Q Consensus 11 irC~~CG~ 18 (35)
..||.||.
T Consensus 93 ~~CP~Cgs 100 (124)
T PRK00762 93 IECPVCGN 100 (124)
T ss_pred CcCcCCCC
Confidence 57999994
No 214
>PF03330 DPBB_1: Rare lipoprotein A (RlpA)-like double-psi beta-barrel; InterPro: IPR009009 Beta barrels are commonly observed in protein structures. They are classified in terms of two integral parameters: the number of strands in the sheet, n, and the shear number, S, a measure of the stagger of the strands in the beta-sheet. These two parameters have been shown to determine the major geometrical features of beta-barrels. Six-stranded beta-barrels with a pseudo-twofold axis are found in several proteins. One involving parallel strands forming two psi structures is known as the double-psi barrel. The first psi structure consists of the loop connecting strands beta1 and beta2 (a 'psi loop') and the strand beta5, whereas the second psi structure consists of the loop connecting strands beta4 and beta5 and the strand beta2. All the psi structures in double-psi barrels have a unique handedness, in that beta1 (beta4), beta2 (beta5) and the loop following beta5 (beta2) form a right-handed helix. The unique handedness may be related to the fact that the twisting angle between the parallel pair of strands is always larger than that between the antiparallel pair [].; PDB: 1N10_B 3D30_A 2BH0_A 2HCZ_X.
Probab=48.11 E-value=13 Score=18.65 Aligned_cols=11 Identities=27% Similarity=0.498 Sum_probs=7.9
Q ss_pred eecCCCCCeEE
Q 035423 11 IQCRECGYRIL 21 (35)
Q Consensus 11 irC~~CG~RIl 21 (35)
-+||.|+.+.|
T Consensus 46 D~Cp~~~~~~l 56 (78)
T PF03330_consen 46 DRCPGCPPNHL 56 (78)
T ss_dssp EE-TTSSSSEE
T ss_pred ccCCCCcCCEE
Confidence 47999998876
No 215
>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=47.96 E-value=6.2 Score=24.42 Aligned_cols=10 Identities=40% Similarity=0.929 Sum_probs=4.0
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
-+.||+||..
T Consensus 211 R~~Cp~Cg~~ 220 (290)
T PF04216_consen 211 RIKCPYCGNT 220 (290)
T ss_dssp TTS-TTT---
T ss_pred CCCCcCCCCC
Confidence 3567888753
No 216
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=47.84 E-value=6.9 Score=18.82 Aligned_cols=8 Identities=38% Similarity=1.481 Sum_probs=6.3
Q ss_pred eecCCCCC
Q 035423 11 IQCRECGY 18 (35)
Q Consensus 11 irC~~CG~ 18 (35)
++|..||-
T Consensus 2 ~kC~~CG~ 9 (40)
T PF15288_consen 2 VKCKNCGA 9 (40)
T ss_pred cccccccc
Confidence 68999973
No 217
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=47.41 E-value=12 Score=22.52 Aligned_cols=16 Identities=38% Similarity=0.904 Sum_probs=12.5
Q ss_pred ccCCCCceecCCCCCe
Q 035423 4 TLKPGDVIQCRECGYR 19 (35)
Q Consensus 4 ~lk~~~~irC~~CG~R 19 (35)
.+++.+...|.+||+.
T Consensus 348 ~~~~~p~~~c~~cg~~ 363 (389)
T PRK11788 348 QLKRKPRYRCRNCGFT 363 (389)
T ss_pred HHhCCCCEECCCCCCC
Confidence 3677778889999975
No 218
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=47.37 E-value=22 Score=15.51 Aligned_cols=16 Identities=31% Similarity=0.690 Sum_probs=12.7
Q ss_pred CCceecCCCCCeEEEe
Q 035423 8 GDVIQCRECGYRILYK 23 (35)
Q Consensus 8 ~~~irC~~CG~RIlyK 23 (35)
..-.+|..||.-+..-
T Consensus 5 ~~~ykC~~Cgniv~v~ 20 (34)
T TIGR00319 5 GQVYKCEVCGNIVEVL 20 (34)
T ss_pred CcEEEcCCCCcEEEEE
Confidence 5578999999987654
No 219
>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=47.32 E-value=11 Score=20.88 Aligned_cols=15 Identities=40% Similarity=1.108 Sum_probs=12.9
Q ss_pred CCCCceecCCCCCeE
Q 035423 6 KPGDVIQCRECGYRI 20 (35)
Q Consensus 6 k~~~~irC~~CG~RI 20 (35)
..++.+-|..||-|+
T Consensus 48 q~g~~lvC~~C~~~~ 62 (102)
T PF10080_consen 48 QEGDQLVCKNCGVRF 62 (102)
T ss_pred EECCEEEEecCCCEE
Confidence 467899999999985
No 220
>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=47.24 E-value=23 Score=15.53 Aligned_cols=16 Identities=25% Similarity=0.590 Sum_probs=12.0
Q ss_pred CceecCCCCCeEEEee
Q 035423 9 DVIQCRECGYRILYKK 24 (35)
Q Consensus 9 ~~irC~~CG~RIlyK~ 24 (35)
.-.+|..||.-+..-.
T Consensus 3 ~~ykC~~CGniv~v~~ 18 (34)
T cd00974 3 EVYKCEICGNIVEVLN 18 (34)
T ss_pred cEEEcCCCCcEEEEEE
Confidence 4578999999886543
No 221
>cd02768 MopB_NADH-Q-OR-NuoG2 MopB_NADH-Q-OR-NuoG2: The NuoG/Nad11/75-kDa subunit (second domain) of the NADH-quinone oxidoreductase (NADH-Q-OR)/respiratory complex I/NADH dehydrogenase-1 (NDH-1). The NADH-Q-OR is the first energy-transducting complex in the respiratory chains of many prokaryotes and eukaryotes. Mitochondrial complex I and its bacterial counterpart, NDH-1, function as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. The atomic structure of complex I is not known and the mechanisms of electron transfer and proton pumping are not established. The nad11 gene codes for the largest (75-kDa) subunit of the mitochondrial NADH:ubiquinone oxidoreductase, it constitutes the electron input part of the enzyme, or the so-called NADH dehydrogenase fragment. In Escherichia coli, this subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the 'minimal' fun
Probab=46.81 E-value=32 Score=21.21 Aligned_cols=23 Identities=13% Similarity=0.011 Sum_probs=17.0
Q ss_pred ecCCC--CCeEEEeecCCceEEEEe
Q 035423 12 QCREC--GYRILYKKRTRRIVQYEA 34 (35)
Q Consensus 12 rC~~C--G~RIlyK~R~~~~~~~~A 34 (35)
-|+.| |+-|.+..|..+++.++.
T Consensus 3 ~C~~C~~gC~i~v~~~~g~i~~i~~ 27 (386)
T cd02768 3 IDVHDALGSNIRVDVRGGEVMRILP 27 (386)
T ss_pred cCCCCCCCCCeEEEEECCEEEEEeC
Confidence 48888 778888888777766653
No 222
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.78 E-value=5.4 Score=23.41 Aligned_cols=18 Identities=33% Similarity=0.645 Sum_probs=12.5
Q ss_pred cCCCCceecCCCCCeEEE
Q 035423 5 LKPGDVIQCRECGYRILY 22 (35)
Q Consensus 5 lk~~~~irC~~CG~RIly 22 (35)
|+.+-.-+||.||.-=||
T Consensus 16 i~~Gl~grCP~CGeGrLF 33 (126)
T COG5349 16 IKRGLRGRCPRCGEGRLF 33 (126)
T ss_pred HHHHhcCCCCCCCCchhh
Confidence 555666789999965444
No 223
>PRK11032 hypothetical protein; Provisional
Probab=46.29 E-value=17 Score=21.69 Aligned_cols=16 Identities=13% Similarity=0.532 Sum_probs=10.8
Q ss_pred CceecCCCCCeEEEee
Q 035423 9 DVIQCRECGYRILYKK 24 (35)
Q Consensus 9 ~~irC~~CG~RIlyK~ 24 (35)
....|.+|||.+-|..
T Consensus 123 G~LvC~~Cg~~~~~~~ 138 (160)
T PRK11032 123 GNLVCEKCHHHLAFYT 138 (160)
T ss_pred ceEEecCCCCEEEecC
Confidence 3467888888776643
No 224
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=46.22 E-value=6 Score=23.96 Aligned_cols=18 Identities=22% Similarity=0.438 Sum_probs=13.8
Q ss_pred ceecCCCCCeEEEeecCC
Q 035423 10 VIQCRECGYRILYKKRTR 27 (35)
Q Consensus 10 ~irC~~CG~RIlyK~R~~ 27 (35)
.-|||+|+-.+.-..+..
T Consensus 97 ~~RCp~CN~~L~~vs~ee 114 (165)
T COG1656 97 FSRCPECNGELEKVSREE 114 (165)
T ss_pred cccCcccCCEeccCcHHH
Confidence 579999999977655554
No 225
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=46.15 E-value=11 Score=22.31 Aligned_cols=19 Identities=21% Similarity=0.539 Sum_probs=14.4
Q ss_pred CCCCceecCCCCCeEEEee
Q 035423 6 KPGDVIQCRECGYRILYKK 24 (35)
Q Consensus 6 k~~~~irC~~CG~RIlyK~ 24 (35)
.....|-||.||.--+-|.
T Consensus 28 ~~~glv~CP~Cgs~~V~K~ 46 (148)
T PF06676_consen 28 QARGLVSCPVCGSTEVSKA 46 (148)
T ss_pred HHcCCccCCCCCCCeEeee
Confidence 3456799999999877663
No 226
>PRK04173 glycyl-tRNA synthetase; Provisional
Probab=45.82 E-value=10 Score=25.26 Aligned_cols=15 Identities=40% Similarity=1.006 Sum_probs=12.0
Q ss_pred ceecCCCCCe---------EEEee
Q 035423 10 VIQCRECGYR---------ILYKK 24 (35)
Q Consensus 10 ~irC~~CG~R---------IlyK~ 24 (35)
+++||.||.- .||+-
T Consensus 125 ~m~cp~~~~~~~~~~~~f~l~f~~ 148 (456)
T PRK04173 125 DIKCPECGGENWTEVRQFNLMFKT 148 (456)
T ss_pred CCCCCCCCCCCCcCccchhhceee
Confidence 6999999865 78773
No 227
>PF09706 Cas_CXXC_CXXC: CRISPR-associated protein (Cas_CXXC_CXXC); InterPro: IPR019121 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved domain of about 65 amino acids found in otherwise highly divergent proteins encoded in CRISPR-associated regions. This domain features two CXXC motifs.
Probab=45.66 E-value=14 Score=18.91 Aligned_cols=20 Identities=30% Similarity=0.411 Sum_probs=15.4
Q ss_pred CCCceecCCCCCeEEEeecC
Q 035423 7 PGDVIQCRECGYRILYKKRT 26 (35)
Q Consensus 7 ~~~~irC~~CG~RIlyK~R~ 26 (35)
..+.-.|-.||-|+.++...
T Consensus 2 ~k~~~~C~~Cg~r~~~~~k~ 21 (69)
T PF09706_consen 2 SKKKYNCIFCGERPSKKKKG 21 (69)
T ss_pred CCCCCcCcCCCCcccccccc
Confidence 35567899999998777655
No 228
>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=45.41 E-value=11 Score=18.36 Aligned_cols=8 Identities=63% Similarity=1.522 Sum_probs=5.6
Q ss_pred eecCCCCC
Q 035423 11 IQCRECGY 18 (35)
Q Consensus 11 irC~~CG~ 18 (35)
-+|+.|||
T Consensus 2 y~C~~Cgy 9 (47)
T PF00301_consen 2 YQCPVCGY 9 (47)
T ss_dssp EEETTTSB
T ss_pred cCCCCCCE
Confidence 36788886
No 229
>cd02753 MopB_Formate-Dh-H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. Members of the MopB_Formate-Dh-H CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=45.27 E-value=34 Score=22.19 Aligned_cols=23 Identities=26% Similarity=0.475 Sum_probs=17.7
Q ss_pred ecCCC--CCeEEEeecCCceEEEEe
Q 035423 12 QCREC--GYRILYKKRTRRIVQYEA 34 (35)
Q Consensus 12 rC~~C--G~RIlyK~R~~~~~~~~A 34 (35)
-|+.| |+-|....|..+++.++.
T Consensus 3 ~C~~C~~~C~i~v~v~~g~v~ri~g 27 (512)
T cd02753 3 VCPYCGVGCGLELWVKDNKIVGVEP 27 (512)
T ss_pred cCCCCCCCCCEEEEEECCeEEEeec
Confidence 37777 678998888888877764
No 230
>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=45.20 E-value=16 Score=19.59 Aligned_cols=14 Identities=29% Similarity=0.738 Sum_probs=10.1
Q ss_pred ceecCCCCCeEEEe
Q 035423 10 VIQCRECGYRILYK 23 (35)
Q Consensus 10 ~irC~~CG~RIlyK 23 (35)
-.+|.+||+..+..
T Consensus 53 rl~C~~C~~~~~~~ 66 (77)
T PF00935_consen 53 RLECTECGKAHMRP 66 (77)
T ss_dssp EEEETTTS-EEEEE
T ss_pred EEEeCCCCcccccc
Confidence 46899999987643
No 231
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=45.19 E-value=12 Score=21.91 Aligned_cols=11 Identities=27% Similarity=0.486 Sum_probs=8.9
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
....||+||+-
T Consensus 97 G~l~CpetG~v 107 (124)
T KOG1088|consen 97 GELVCPETGRV 107 (124)
T ss_pred ceEecCCCCcE
Confidence 35889999975
No 232
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=45.10 E-value=14 Score=24.99 Aligned_cols=17 Identities=29% Similarity=0.419 Sum_probs=13.2
Q ss_pred CCCceecCCCCCeEEEe
Q 035423 7 PGDVIQCRECGYRILYK 23 (35)
Q Consensus 7 ~~~~irC~~CG~RIlyK 23 (35)
....+-||.||++-|-|
T Consensus 254 ~m~k~FCp~CG~~TL~K 270 (376)
T KOG2463|consen 254 EMPKDFCPSCGHKTLTK 270 (376)
T ss_pred ccchhcccccCCCeeeE
Confidence 34467899999997765
No 233
>PF14577 SEO_C: Sieve element occlusion C-terminus
Probab=44.98 E-value=12 Score=23.61 Aligned_cols=13 Identities=38% Similarity=0.785 Sum_probs=10.1
Q ss_pred CCCceecCCCCCe
Q 035423 7 PGDVIQCRECGYR 19 (35)
Q Consensus 7 ~~~~irC~~CG~R 19 (35)
.-+.|.||+||..
T Consensus 211 ipe~i~CpeC~R~ 223 (235)
T PF14577_consen 211 IPETIVCPECGRP 223 (235)
T ss_pred CCceeECCCCCCc
Confidence 4467999999964
No 234
>cd02008 TPP_IOR_alpha Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as indolepyruvate or phenylpyruvate, which are generated by the transamination of aromatic amino acids, to the corresponding aryl acetyl-CoA.
Probab=44.88 E-value=4.4 Score=23.05 Aligned_cols=17 Identities=18% Similarity=0.208 Sum_probs=13.2
Q ss_pred CCceecCCCCCeEEEee
Q 035423 8 GDVIQCRECGYRILYKK 24 (35)
Q Consensus 8 ~~~irC~~CG~RIlyK~ 24 (35)
.++--|+-|+|++++..
T Consensus 2 ~~~~~c~gc~~~~~~~~ 18 (178)
T cd02008 2 RPPGLCPGCPHRPSFYA 18 (178)
T ss_pred CCCCcCCCCCChHHHHH
Confidence 35678999999987654
No 235
>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=44.82 E-value=16 Score=21.17 Aligned_cols=13 Identities=31% Similarity=0.784 Sum_probs=7.5
Q ss_pred ceecCCCCCeEEE
Q 035423 10 VIQCRECGYRILY 22 (35)
Q Consensus 10 ~irC~~CG~RIly 22 (35)
.-.||.||.-..+
T Consensus 128 ~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 128 NFTCPRCGAMLDY 140 (158)
T ss_pred CCcCCCCCCEeee
Confidence 3566666665443
No 236
>PF05265 DUF723: Protein of unknown function (DUF723); InterPro: IPR007929 This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA binding.
Probab=44.75 E-value=10 Score=19.66 Aligned_cols=6 Identities=67% Similarity=1.735 Sum_probs=4.5
Q ss_pred ecCCCC
Q 035423 12 QCRECG 17 (35)
Q Consensus 12 rC~~CG 17 (35)
=||+||
T Consensus 55 GCP~Cg 60 (60)
T PF05265_consen 55 GCPECG 60 (60)
T ss_pred CCCCCC
Confidence 488886
No 237
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=44.72 E-value=17 Score=21.38 Aligned_cols=15 Identities=20% Similarity=0.669 Sum_probs=8.8
Q ss_pred ceecCCCCCeEEEee
Q 035423 10 VIQCRECGYRILYKK 24 (35)
Q Consensus 10 ~irC~~CG~RIlyK~ 24 (35)
.++||.||+...|.-
T Consensus 18 ~~~C~~C~~~~~f~g 32 (188)
T PF08996_consen 18 KLTCPSCGTEFEFPG 32 (188)
T ss_dssp EEE-TTT--EEEE-S
T ss_pred EeECCCCCCCccccc
Confidence 478999999988753
No 238
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=44.71 E-value=26 Score=21.64 Aligned_cols=15 Identities=40% Similarity=0.576 Sum_probs=11.2
Q ss_pred ceecCCCCCeEEEee
Q 035423 10 VIQCRECGYRILYKK 24 (35)
Q Consensus 10 ~irC~~CG~RIlyK~ 24 (35)
.--||.||..|.--+
T Consensus 245 g~pC~~Cg~~I~~~~ 259 (274)
T PRK01103 245 GEPCRRCGTPIEKIK 259 (274)
T ss_pred CCCCCCCCCeeEEEE
Confidence 345999999986544
No 239
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=44.70 E-value=15 Score=23.11 Aligned_cols=14 Identities=29% Similarity=0.717 Sum_probs=10.2
Q ss_pred CCCCceecCCCCCe
Q 035423 6 KPGDVIQCRECGYR 19 (35)
Q Consensus 6 k~~~~irC~~CG~R 19 (35)
..++.-+|+.||..
T Consensus 142 ~~~~~p~C~~Cg~~ 155 (250)
T COG0846 142 EDGLIPRCPKCGGP 155 (250)
T ss_pred ccCCCCcCccCCCc
Confidence 34456789999985
No 240
>PRK05978 hypothetical protein; Provisional
Probab=44.69 E-value=10 Score=22.37 Aligned_cols=15 Identities=27% Similarity=0.561 Sum_probs=11.8
Q ss_pred CceecCCCCCeEEEe
Q 035423 9 DVIQCRECGYRILYK 23 (35)
Q Consensus 9 ~~irC~~CG~RIlyK 23 (35)
-.-|||.||.-=||+
T Consensus 32 l~grCP~CG~G~LF~ 46 (148)
T PRK05978 32 FRGRCPACGEGKLFR 46 (148)
T ss_pred HcCcCCCCCCCcccc
Confidence 346899999887775
No 241
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a 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). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=44.62 E-value=10 Score=20.01 Aligned_cols=8 Identities=38% Similarity=0.983 Sum_probs=6.0
Q ss_pred ceecCCCC
Q 035423 10 VIQCRECG 17 (35)
Q Consensus 10 ~irC~~CG 17 (35)
.-+||.||
T Consensus 84 np~C~~C~ 91 (91)
T cd04482 84 NPVCPKCG 91 (91)
T ss_pred CCcCCCCC
Confidence 45788887
No 242
>PRK11823 DNA repair protein RadA; Provisional
Probab=44.59 E-value=15 Score=24.31 Aligned_cols=14 Identities=36% Similarity=0.769 Sum_probs=9.8
Q ss_pred CCCCceecCCCCCe
Q 035423 6 KPGDVIQCRECGYR 19 (35)
Q Consensus 6 k~~~~irC~~CG~R 19 (35)
+.....+|.+|||.
T Consensus 3 ~~~~~y~C~~Cg~~ 16 (446)
T PRK11823 3 KKKTAYVCQECGAE 16 (446)
T ss_pred CCCCeEECCcCCCC
Confidence 34556788888875
No 243
>cd00368 Molybdopterin-Binding Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is
Probab=44.44 E-value=39 Score=20.47 Aligned_cols=23 Identities=30% Similarity=0.590 Sum_probs=17.0
Q ss_pred ecCCC--CCeEEEeecCCceEEEEe
Q 035423 12 QCREC--GYRILYKKRTRRIVQYEA 34 (35)
Q Consensus 12 rC~~C--G~RIlyK~R~~~~~~~~A 34 (35)
-|+.| |+-|....|..+++.++.
T Consensus 3 ~C~~C~~gC~i~v~~~~g~i~ri~~ 27 (374)
T cd00368 3 VCPFCGVGCGILVYVKDGKVVRIEG 27 (374)
T ss_pred CCCCCcCCCCEEEEEECCEEEEEEC
Confidence 47777 677888888777777654
No 244
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=44.17 E-value=14 Score=19.41 Aligned_cols=13 Identities=38% Similarity=0.810 Sum_probs=10.0
Q ss_pred CCCceecCCCCCe
Q 035423 7 PGDVIQCRECGYR 19 (35)
Q Consensus 7 ~~~~irC~~CG~R 19 (35)
+.|.-.||.||..
T Consensus 15 ~~d~e~CP~Cgs~ 27 (64)
T COG2093 15 PEDTEICPVCGST 27 (64)
T ss_pred CCCCccCCCCCCc
Confidence 4555679999987
No 245
>PRK10445 endonuclease VIII; Provisional
Probab=43.75 E-value=27 Score=21.57 Aligned_cols=19 Identities=26% Similarity=0.368 Sum_probs=13.0
Q ss_pred ceecCCCCCeEEEeecCCc
Q 035423 10 VIQCRECGYRILYKKRTRR 28 (35)
Q Consensus 10 ~irC~~CG~RIlyK~R~~~ 28 (35)
.--||.||..|.-.+-..+
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR 253 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSR 253 (263)
T ss_pred CCCCCCCCCEeEEEEECCC
Confidence 4569999999875544333
No 246
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=43.68 E-value=11 Score=22.23 Aligned_cols=10 Identities=30% Similarity=0.464 Sum_probs=8.3
Q ss_pred eecCCCCCeE
Q 035423 11 IQCRECGYRI 20 (35)
Q Consensus 11 irC~~CG~RI 20 (35)
-.|.+||++|
T Consensus 5 e~CsFcG~kI 14 (131)
T PRK14891 5 RTCDYTGEEI 14 (131)
T ss_pred eeecCcCCcc
Confidence 4699999886
No 247
>PF14996 RMP: Retinal Maintenance
Probab=43.48 E-value=16 Score=21.78 Aligned_cols=16 Identities=25% Similarity=0.877 Sum_probs=13.0
Q ss_pred CCCceecCCCCCeEEE
Q 035423 7 PGDVIQCRECGYRILY 22 (35)
Q Consensus 7 ~~~~irC~~CG~RIly 22 (35)
.=+.+||..|-++|+.
T Consensus 65 ~C~~LrC~~CDf~V~~ 80 (146)
T PF14996_consen 65 ACDNLRCTKCDFRVVR 80 (146)
T ss_pred cCCCCEEecCCcEEEE
Confidence 3467899999999874
No 248
>cd02771 MopB_NDH-1_NuoG2-N7 MopB_NDH-1_NuoG2-N7: The second domain of the NuoG subunit (with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain (this CD), is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups in this domain
Probab=43.09 E-value=35 Score=21.89 Aligned_cols=23 Identities=26% Similarity=0.540 Sum_probs=18.4
Q ss_pred ecCCC--CCeEEEeecCCceEEEEe
Q 035423 12 QCREC--GYRILYKKRTRRIVQYEA 34 (35)
Q Consensus 12 rC~~C--G~RIlyK~R~~~~~~~~A 34 (35)
-|++| |+-|.+..|..+++.++.
T Consensus 3 ~C~~C~~gC~i~v~v~dg~v~rv~~ 27 (472)
T cd02771 3 ICHHCSVGCNISLGERYGELRRVEN 27 (472)
T ss_pred cCcCcccCCCcEEEEECCEEEEEEC
Confidence 48888 688998888888887764
No 249
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=43.06 E-value=16 Score=24.31 Aligned_cols=13 Identities=23% Similarity=0.680 Sum_probs=8.6
Q ss_pred CCCceecCCCCCe
Q 035423 7 PGDVIQCRECGYR 19 (35)
Q Consensus 7 ~~~~irC~~CG~R 19 (35)
.....+|.+|||.
T Consensus 4 ~~~~y~C~~Cg~~ 16 (454)
T TIGR00416 4 AKSKFVCQHCGAD 16 (454)
T ss_pred CCCeEECCcCCCC
Confidence 3455778788775
No 250
>smart00355 ZnF_C2H2 zinc finger.
Probab=42.86 E-value=12 Score=13.97 Aligned_cols=8 Identities=50% Similarity=1.236 Sum_probs=6.3
Q ss_pred ecCCCCCe
Q 035423 12 QCRECGYR 19 (35)
Q Consensus 12 rC~~CG~R 19 (35)
.|+.|+..
T Consensus 2 ~C~~C~~~ 9 (26)
T smart00355 2 RCPECGKV 9 (26)
T ss_pred CCCCCcch
Confidence 68999865
No 251
>PRK06386 replication factor A; Reviewed
Probab=42.61 E-value=11 Score=24.88 Aligned_cols=11 Identities=27% Similarity=0.573 Sum_probs=8.7
Q ss_pred eecCCCCCeEE
Q 035423 11 IQCRECGYRIL 21 (35)
Q Consensus 11 irC~~CG~RIl 21 (35)
-|||+|+-.+-
T Consensus 237 ~rCP~C~R~l~ 247 (358)
T PRK06386 237 TKCSVCNKIIE 247 (358)
T ss_pred ecCcCCCeEcc
Confidence 58999987754
No 252
>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=42.43 E-value=16 Score=24.14 Aligned_cols=12 Identities=33% Similarity=1.140 Sum_probs=6.4
Q ss_pred eecCCCCCeEEE
Q 035423 11 IQCRECGYRILY 22 (35)
Q Consensus 11 irC~~CG~RIly 22 (35)
.+|+.||+|..-
T Consensus 286 FkC~~C~~Rt~s 297 (344)
T PF09332_consen 286 FKCKDCGNRTIS 297 (344)
T ss_dssp EE-T-TS-EEEE
T ss_pred EECCCCCCeeee
Confidence 578889988653
No 253
>PF06957 COPI_C: Coatomer (COPI) alpha subunit C-terminus; InterPro: IPR010714 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit [, ]. This domain is found along with the IPR006692 from INTERPRO domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat; PDB: 3MKR_B 3MV2_E 3MKQ_B 3MV3_A.
Probab=42.39 E-value=15 Score=24.88 Aligned_cols=13 Identities=23% Similarity=0.746 Sum_probs=7.2
Q ss_pred CCceecCCCCCeE
Q 035423 8 GDVIQCRECGYRI 20 (35)
Q Consensus 8 ~~~irC~~CG~RI 20 (35)
.+.++||+||.+-
T Consensus 378 ~~~v~CP~cgA~y 390 (422)
T PF06957_consen 378 SPSVKCPYCGAKY 390 (422)
T ss_dssp S-EEE-TTT--EE
T ss_pred CCCeeCCCCCCcc
Confidence 4779999999873
No 254
>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=42.26 E-value=14 Score=24.42 Aligned_cols=15 Identities=40% Similarity=1.048 Sum_probs=12.3
Q ss_pred CCCCceecCCCCCeE
Q 035423 6 KPGDVIQCRECGYRI 20 (35)
Q Consensus 6 k~~~~irC~~CG~RI 20 (35)
..+.++.||.|||-.
T Consensus 205 ~k~k~~PCPKCg~et 219 (314)
T PF06524_consen 205 EKGKPIPCPKCGYET 219 (314)
T ss_pred ccCCCCCCCCCCCcc
Confidence 456889999999973
No 255
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=42.16 E-value=22 Score=17.90 Aligned_cols=16 Identities=13% Similarity=0.005 Sum_probs=10.0
Q ss_pred cCCCCceecCCCCCeE
Q 035423 5 LKPGDVIQCRECGYRI 20 (35)
Q Consensus 5 lk~~~~irC~~CG~RI 20 (35)
++.-..+.|+.||.-+
T Consensus 22 ~~~~~~~~c~~cg~~~ 37 (60)
T PRK01110 22 LTAPTLSVDKTTGEYH 37 (60)
T ss_pred ccCCceeEcCCCCcee
Confidence 3444567788887544
No 256
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=42.10 E-value=11 Score=19.40 Aligned_cols=11 Identities=27% Similarity=0.625 Sum_probs=8.5
Q ss_pred ceecCCCCCeE
Q 035423 10 VIQCRECGYRI 20 (35)
Q Consensus 10 ~irC~~CG~RI 20 (35)
.-.||+||.-.
T Consensus 41 ~~~CPNCgGel 51 (57)
T PF06906_consen 41 NGVCPNCGGEL 51 (57)
T ss_pred cCcCcCCCCcc
Confidence 35799999874
No 257
>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=41.94 E-value=17 Score=17.98 Aligned_cols=17 Identities=18% Similarity=0.632 Sum_probs=9.4
Q ss_pred CCceecCCCCC-eEEEee
Q 035423 8 GDVIQCRECGY-RILYKK 24 (35)
Q Consensus 8 ~~~irC~~CG~-RIlyK~ 24 (35)
+..-.||.|+. .+.|..
T Consensus 12 Gal~~Cp~C~~~~l~~~~ 29 (55)
T PF08063_consen 12 GALEPCPKCKGGQLYFDG 29 (55)
T ss_dssp TEE---SSSSE-EEEEET
T ss_pred cCCCCCCCCCCCeEEecC
Confidence 44568999999 555543
No 258
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=41.86 E-value=14 Score=20.37 Aligned_cols=11 Identities=18% Similarity=0.471 Sum_probs=7.7
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
...+|+.||+.
T Consensus 69 ~~~~C~~Cg~~ 79 (113)
T PRK12380 69 AQAWCWDCSQV 79 (113)
T ss_pred cEEEcccCCCE
Confidence 35778888864
No 259
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=41.77 E-value=13 Score=19.32 Aligned_cols=12 Identities=33% Similarity=0.700 Sum_probs=9.9
Q ss_pred CceecCCCCCeE
Q 035423 9 DVIQCRECGYRI 20 (35)
Q Consensus 9 ~~irC~~CG~RI 20 (35)
-||||-.||.=|
T Consensus 3 iPvRCFTCGkvi 14 (62)
T PRK04016 3 IPVRCFTCGKVI 14 (62)
T ss_pred CCeEecCCCCCh
Confidence 479999999754
No 260
>cd03375 TPP_OGFOR Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR catalyzes the oxidative decarboxylation of 2-oxoglutarate to succinyl-CoA. In the reductive tricarboxylic acid cycle found in the anaerobic autotroph Hydrogenobacter thermophilus, OGFOR catalyzes the reductive carboxylation of succinyl-CoA to produce 2-oxoglutarate. Thauera aromatica OGFOR has been shown to provide reduced ferredoxin to benzoyl-CoA reductase, a key enzyme in the anaerobic metabolism of aromatic compounds. OGFOR is dependent on TPP and a divalent metal cation for activity.
Probab=41.73 E-value=3.4 Score=24.09 Aligned_cols=11 Identities=36% Similarity=0.857 Sum_probs=9.2
Q ss_pred cCCCCCeEEEe
Q 035423 13 CRECGYRILYK 23 (35)
Q Consensus 13 C~~CG~RIlyK 23 (35)
|+-||||+.|+
T Consensus 2 c~gc~~~~~~~ 12 (193)
T cd03375 2 CPGCGDGSILK 12 (193)
T ss_pred CCCCCcHHHHH
Confidence 88999998775
No 261
>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=41.60 E-value=13 Score=20.29 Aligned_cols=9 Identities=44% Similarity=1.328 Sum_probs=4.2
Q ss_pred eecCCCCCe
Q 035423 11 IQCRECGYR 19 (35)
Q Consensus 11 irC~~CG~R 19 (35)
.+|+.||+.
T Consensus 71 ~~C~~Cg~~ 79 (113)
T PF01155_consen 71 ARCRDCGHE 79 (113)
T ss_dssp EEETTTS-E
T ss_pred EECCCCCCE
Confidence 455555543
No 262
>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=41.24 E-value=14 Score=21.32 Aligned_cols=9 Identities=44% Similarity=1.423 Sum_probs=7.8
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
.|+| .|||-
T Consensus 24 ~vkc-~CGh~ 32 (112)
T PF08882_consen 24 VVKC-DCGHE 32 (112)
T ss_pred eeec-cCCCe
Confidence 7999 99985
No 263
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.16 E-value=13 Score=21.80 Aligned_cols=12 Identities=25% Similarity=0.133 Sum_probs=10.0
Q ss_pred CCceecCCCCCe
Q 035423 8 GDVIQCRECGYR 19 (35)
Q Consensus 8 ~~~irC~~CG~R 19 (35)
.++|-||+||..
T Consensus 24 rdPiVsPytG~s 35 (129)
T COG4530 24 RDPIVSPYTGKS 35 (129)
T ss_pred CCccccCccccc
Confidence 578999999974
No 264
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=41.07 E-value=13 Score=19.39 Aligned_cols=9 Identities=22% Similarity=0.353 Sum_probs=7.5
Q ss_pred eecCCCCCe
Q 035423 11 IQCRECGYR 19 (35)
Q Consensus 11 irC~~CG~R 19 (35)
-.||.||..
T Consensus 18 ~~Cp~Cgs~ 26 (64)
T PRK06393 18 KTCPVHGDE 26 (64)
T ss_pred CcCCCCCCC
Confidence 389999985
No 265
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=41.02 E-value=12 Score=25.99 Aligned_cols=10 Identities=30% Similarity=1.042 Sum_probs=8.2
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
..-||+||++
T Consensus 68 SF~CpHCG~k 77 (460)
T KOG2703|consen 68 SFECPHCGHK 77 (460)
T ss_pred EeecCccCCc
Confidence 4679999986
No 266
>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=40.89 E-value=6.6 Score=21.74 Aligned_cols=17 Identities=18% Similarity=0.419 Sum_probs=12.2
Q ss_pred cccCCCCceecCCCCCe
Q 035423 3 NTLKPGDVIQCRECGYR 19 (35)
Q Consensus 3 ~~lk~~~~irC~~CG~R 19 (35)
.++++...-.||.||.-
T Consensus 28 ie~~q~a~y~CpfCgk~ 44 (91)
T TIGR00280 28 IEIQQKAKYVCPFCGKK 44 (91)
T ss_pred HHHHHhcCccCCCCCCC
Confidence 45566777889999853
No 267
>PHA02768 hypothetical protein; Provisional
Probab=40.82 E-value=12 Score=19.00 Aligned_cols=9 Identities=33% Similarity=0.811 Sum_probs=6.7
Q ss_pred eecCCCCCe
Q 035423 11 IQCRECGYR 19 (35)
Q Consensus 11 irC~~CG~R 19 (35)
-.|++||.+
T Consensus 6 y~C~~CGK~ 14 (55)
T PHA02768 6 YECPICGEI 14 (55)
T ss_pred cCcchhCCe
Confidence 478888876
No 268
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=40.76 E-value=13 Score=19.35 Aligned_cols=9 Identities=33% Similarity=0.789 Sum_probs=7.2
Q ss_pred eecCCCCCe
Q 035423 11 IQCRECGYR 19 (35)
Q Consensus 11 irC~~CG~R 19 (35)
-.||.||..
T Consensus 18 e~Cp~CG~~ 26 (59)
T COG2260 18 EKCPVCGGD 26 (59)
T ss_pred ccCCCCCCc
Confidence 379999976
No 269
>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=40.76 E-value=12 Score=18.28 Aligned_cols=8 Identities=63% Similarity=1.680 Sum_probs=5.8
Q ss_pred eecCCCCC
Q 035423 11 IQCRECGY 18 (35)
Q Consensus 11 irC~~CG~ 18 (35)
-+|..|||
T Consensus 2 y~C~~Cgy 9 (50)
T cd00730 2 YECRICGY 9 (50)
T ss_pred cCCCCCCe
Confidence 36888886
No 270
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=40.59 E-value=17 Score=25.00 Aligned_cols=16 Identities=31% Similarity=0.800 Sum_probs=10.9
Q ss_pred cCCCCceecCCCCCeE
Q 035423 5 LKPGDVIQCRECGYRI 20 (35)
Q Consensus 5 lk~~~~irC~~CG~RI 20 (35)
|..+...-||.|||.|
T Consensus 33 l~~~q~A~CPRC~~~l 48 (418)
T COG2995 33 LDSGQSAYCPRCGHTL 48 (418)
T ss_pred CCCCCcccCCCCCCcc
Confidence 5566667777777763
No 271
>CHL00104 rpl33 ribosomal protein L33
Probab=40.48 E-value=24 Score=18.35 Aligned_cols=12 Identities=25% Similarity=0.509 Sum_probs=10.0
Q ss_pred cCCCCCeEEEee
Q 035423 13 CRECGYRILYKK 24 (35)
Q Consensus 13 C~~CG~RIlyK~ 24 (35)
||.|.-..|+|+
T Consensus 52 cp~c~kHtlhkE 63 (66)
T CHL00104 52 CPYCYKHTIHKE 63 (66)
T ss_pred CCCCCCEeeEee
Confidence 888888888876
No 272
>PRK08116 hypothetical protein; Validated
Probab=40.33 E-value=18 Score=22.27 Aligned_cols=18 Identities=28% Similarity=0.396 Sum_probs=12.9
Q ss_pred CCCCceecCCCCCeEEEe
Q 035423 6 KPGDVIQCRECGYRILYK 23 (35)
Q Consensus 6 k~~~~irC~~CG~RIlyK 23 (35)
.......|+.||..+.++
T Consensus 12 ~~~~~~~C~~Cg~~~~~~ 29 (268)
T PRK08116 12 EEDGGEYCEVCGKRIEKV 29 (268)
T ss_pred ccccCccCcCCCCcceee
Confidence 344566799999987653
No 273
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=40.20 E-value=7.3 Score=21.51 Aligned_cols=17 Identities=24% Similarity=0.247 Sum_probs=12.1
Q ss_pred cccCCCCceecCCCCCe
Q 035423 3 NTLKPGDVIQCRECGYR 19 (35)
Q Consensus 3 ~~lk~~~~irC~~CG~R 19 (35)
.+++....-.||.||.-
T Consensus 29 ie~~q~a~y~CpfCgk~ 45 (90)
T PRK03976 29 IEEKMRAKHVCPVCGRP 45 (90)
T ss_pred HHHHHhcCccCCCCCCC
Confidence 45566777889999754
No 274
>PRK07218 replication factor A; Provisional
Probab=39.81 E-value=12 Score=25.18 Aligned_cols=10 Identities=50% Similarity=1.042 Sum_probs=8.2
Q ss_pred eecCCCCCeE
Q 035423 11 IQCRECGYRI 20 (35)
Q Consensus 11 irC~~CG~RI 20 (35)
-|||+|+-.+
T Consensus 298 ~rCP~C~r~v 307 (423)
T PRK07218 298 ERCPECGRVI 307 (423)
T ss_pred ecCcCccccc
Confidence 5899998775
No 275
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=39.76 E-value=16 Score=27.77 Aligned_cols=13 Identities=23% Similarity=0.669 Sum_probs=9.9
Q ss_pred eecCCCCCeEEEe
Q 035423 11 IQCRECGYRILYK 23 (35)
Q Consensus 11 irC~~CG~RIlyK 23 (35)
-+|+.||.+|+.-
T Consensus 1029 G~C~kCGg~lilT 1041 (1095)
T TIGR00354 1029 GKCLKCGNNLTLT 1041 (1095)
T ss_pred CcccccCCeEEEE
Confidence 3688999988753
No 276
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=39.70 E-value=27 Score=20.22 Aligned_cols=18 Identities=28% Similarity=0.728 Sum_probs=15.5
Q ss_pred CCCCceecCCCCCeEEEe
Q 035423 6 KPGDVIQCRECGYRILYK 23 (35)
Q Consensus 6 k~~~~irC~~CG~RIlyK 23 (35)
.+++..-|..||.++.|-
T Consensus 24 ~~~~~~tC~~Cg~~L~lh 41 (128)
T PF11682_consen 24 APYDHWTCHSCGCPLILH 41 (128)
T ss_pred CCCCeEEEecCCceEEEe
Confidence 367889999999999886
No 277
>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=39.51 E-value=17 Score=19.00 Aligned_cols=12 Identities=42% Similarity=1.162 Sum_probs=9.7
Q ss_pred CCceecCCCCCe
Q 035423 8 GDVIQCRECGYR 19 (35)
Q Consensus 8 ~~~irC~~CG~R 19 (35)
.+.+-|-.|||.
T Consensus 28 ve~vECV~CGy~ 39 (71)
T PF09526_consen 28 VEYVECVECGYT 39 (71)
T ss_pred ceEEEecCCCCe
Confidence 456789999997
No 278
>PRK11869 2-oxoacid ferredoxin oxidoreductase subunit beta; Provisional
Probab=39.44 E-value=5 Score=25.42 Aligned_cols=18 Identities=22% Similarity=0.399 Sum_probs=13.8
Q ss_pred CCCCceecCCCCCeEEEe
Q 035423 6 KPGDVIQCRECGYRILYK 23 (35)
Q Consensus 6 k~~~~irC~~CG~RIlyK 23 (35)
...+.+-||-|||+++++
T Consensus 4 ~~~~~~~CpGCg~~~i~~ 21 (280)
T PRK11869 4 EKYDIAWCPGCGNFGIRN 21 (280)
T ss_pred ccCCCCCCcCCCCHHHHH
Confidence 456678899999987653
No 279
>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=39.34 E-value=33 Score=21.25 Aligned_cols=15 Identities=40% Similarity=0.576 Sum_probs=11.5
Q ss_pred ceecCCCCCeEEEee
Q 035423 10 VIQCRECGYRILYKK 24 (35)
Q Consensus 10 ~irC~~CG~RIlyK~ 24 (35)
.--||.||..|...+
T Consensus 245 g~pC~~Cg~~I~~~~ 259 (272)
T TIGR00577 245 GEPCRRCGTPIEKIK 259 (272)
T ss_pred CCCCCCCCCeeEEEE
Confidence 446999999986544
No 280
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=39.28 E-value=14 Score=18.74 Aligned_cols=10 Identities=30% Similarity=0.770 Sum_probs=7.0
Q ss_pred eecCCCCCeE
Q 035423 11 IQCRECGYRI 20 (35)
Q Consensus 11 irC~~CG~RI 20 (35)
-.||.||--+
T Consensus 20 ~~CPrCG~gv 29 (51)
T COG1998 20 RFCPRCGPGV 29 (51)
T ss_pred ccCCCCCCcc
Confidence 3599999543
No 281
>COG0267 RpmG Ribosomal protein L33 [Translation, ribosomal structure and biogenesis]
Probab=39.23 E-value=25 Score=17.50 Aligned_cols=12 Identities=33% Similarity=0.647 Sum_probs=9.1
Q ss_pred cCCCCCeEEEee
Q 035423 13 CRECGYRILYKK 24 (35)
Q Consensus 13 C~~CG~RIlyK~ 24 (35)
||.|+.-+|+|+
T Consensus 37 cp~~~khtlhkE 48 (50)
T COG0267 37 CPVCRKHTLHKE 48 (50)
T ss_pred CcccccEEEEee
Confidence 777887777775
No 282
>cd00085 HNHc HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.
Probab=39.20 E-value=14 Score=16.32 Aligned_cols=10 Identities=30% Similarity=0.414 Sum_probs=8.5
Q ss_pred eecCCCCCeE
Q 035423 11 IQCRECGYRI 20 (35)
Q Consensus 11 irC~~CG~RI 20 (35)
-+|.+||..+
T Consensus 12 ~~C~~c~~~~ 21 (57)
T cd00085 12 GLCPYCGKPG 21 (57)
T ss_pred CcCccCCCcC
Confidence 5799999876
No 283
>PLN00209 ribosomal protein S27; Provisional
Probab=39.16 E-value=18 Score=19.97 Aligned_cols=10 Identities=20% Similarity=0.547 Sum_probs=8.0
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
.|+||.|+.-
T Consensus 36 ~VkCp~C~n~ 45 (86)
T PLN00209 36 DVKCQGCFNI 45 (86)
T ss_pred EEECCCCCCe
Confidence 5899999874
No 284
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=39.15 E-value=22 Score=18.93 Aligned_cols=15 Identities=40% Similarity=0.762 Sum_probs=12.7
Q ss_pred cCCCCceec----CCCCCe
Q 035423 5 LKPGDVIQC----RECGYR 19 (35)
Q Consensus 5 lk~~~~irC----~~CG~R 19 (35)
|...++..| +.|+|.
T Consensus 75 Lp~~~G~~C~~~~~~C~y~ 93 (109)
T PF12013_consen 75 LPVYDGYRCQCDPPHCGYI 93 (109)
T ss_pred CCCCCCeeeecCCCCCCcE
Confidence 566789999 999985
No 285
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=39.12 E-value=21 Score=19.51 Aligned_cols=13 Identities=23% Similarity=0.542 Sum_probs=10.4
Q ss_pred CCceecCCCCCeE
Q 035423 8 GDVIQCRECGYRI 20 (35)
Q Consensus 8 ~~~irC~~CG~RI 20 (35)
..+..|.+|+++|
T Consensus 69 ~~~~~C~~C~~~V 81 (118)
T PF02318_consen 69 NRGRVCVDCKHRV 81 (118)
T ss_dssp TTCEEETTTTEEE
T ss_pred CCCCcCCcCCccc
Confidence 4468999999886
No 286
>PF09696 Ctf8: Ctf8; InterPro: IPR018607 Ctf8 (chromosome transmissions fidelity 8) is a component of the Ctf18 RFC-like complex which is a DNA clamp loader involved in sister chromatid cohesion.
Probab=39.08 E-value=14 Score=20.71 Aligned_cols=12 Identities=33% Similarity=0.863 Sum_probs=10.0
Q ss_pred CCCeEEEeecCC
Q 035423 16 CGYRILYKKRTR 27 (35)
Q Consensus 16 CG~RIlyK~R~~ 27 (35)
.-++|+||.||.
T Consensus 109 I~~KiiFk~RP~ 120 (122)
T PF09696_consen 109 IRYKIIFKTRPK 120 (122)
T ss_pred eeeeeEccCCCC
Confidence 458999999986
No 287
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=38.93 E-value=17 Score=19.44 Aligned_cols=11 Identities=36% Similarity=0.878 Sum_probs=9.6
Q ss_pred ceecCCCCCeE
Q 035423 10 VIQCRECGYRI 20 (35)
Q Consensus 10 ~irC~~CG~RI 20 (35)
||||=.||.=|
T Consensus 4 PVRCFTCGkvi 14 (71)
T PLN00032 4 PVRCFTCGKVI 14 (71)
T ss_pred ceeecCCCCCc
Confidence 79999999765
No 288
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=38.92 E-value=51 Score=18.85 Aligned_cols=16 Identities=19% Similarity=0.572 Sum_probs=10.4
Q ss_pred ecCCCCCeEEEeecCC
Q 035423 12 QCRECGYRILYKKRTR 27 (35)
Q Consensus 12 rC~~CG~RIlyK~R~~ 27 (35)
-||.||.=++++.-..
T Consensus 3 FCP~Cgn~Live~g~~ 18 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGES 18 (105)
T ss_pred ccCCCCCEEEEecCCe
Confidence 3777777777765443
No 289
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=38.69 E-value=22 Score=20.78 Aligned_cols=8 Identities=38% Similarity=0.941 Sum_probs=4.0
Q ss_pred ceecCCCC
Q 035423 10 VIQCRECG 17 (35)
Q Consensus 10 ~irC~~CG 17 (35)
...|+.||
T Consensus 309 S~~C~~cg 316 (364)
T COG0675 309 SKTCPCCG 316 (364)
T ss_pred cccccccC
Confidence 34455555
No 290
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=38.66 E-value=15 Score=18.70 Aligned_cols=12 Identities=25% Similarity=0.722 Sum_probs=9.1
Q ss_pred CCceecCCCCCe
Q 035423 8 GDVIQCRECGYR 19 (35)
Q Consensus 8 ~~~irC~~CG~R 19 (35)
.-..-||.||.-
T Consensus 12 ~v~~~Cp~cGip 23 (55)
T PF13824_consen 12 HVNFECPDCGIP 23 (55)
T ss_pred ccCCcCCCCCCc
Confidence 445779999964
No 291
>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=38.46 E-value=14 Score=22.32 Aligned_cols=13 Identities=23% Similarity=0.746 Sum_probs=11.0
Q ss_pred ecCCCCCeEEEee
Q 035423 12 QCRECGYRILYKK 24 (35)
Q Consensus 12 rC~~CG~RIlyK~ 24 (35)
-|+.||..|++..
T Consensus 91 FC~~CGS~L~~~~ 103 (182)
T TIGR02820 91 ACKGCGTHMYGRI 103 (182)
T ss_pred cCCCCCCcccccc
Confidence 3999999987765
No 292
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=38.46 E-value=14 Score=19.67 Aligned_cols=11 Identities=45% Similarity=0.905 Sum_probs=9.4
Q ss_pred ceecCCCCCeE
Q 035423 10 VIQCRECGYRI 20 (35)
Q Consensus 10 ~irC~~CG~RI 20 (35)
+|||-.||.-|
T Consensus 4 PiRCFtCGKvi 14 (69)
T KOG3497|consen 4 PIRCFTCGKVI 14 (69)
T ss_pred eeEeeeccccc
Confidence 79999999765
No 293
>PRK05767 rpl44e 50S ribosomal protein L44e; Validated
Probab=38.44 E-value=23 Score=19.62 Aligned_cols=14 Identities=29% Similarity=0.596 Sum_probs=10.8
Q ss_pred ceecCCCCCeEEEe
Q 035423 10 VIQCRECGYRILYK 23 (35)
Q Consensus 10 ~irC~~CG~RIlyK 23 (35)
-.+|.+||+..+..
T Consensus 67 r~~C~~C~~~~~~~ 80 (92)
T PRK05767 67 RYRCTECGKAHTRE 80 (92)
T ss_pred EEEecccChhhccc
Confidence 46899999986654
No 294
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=38.39 E-value=18 Score=16.68 Aligned_cols=12 Identities=25% Similarity=0.780 Sum_probs=8.1
Q ss_pred CceecCCCCCeE
Q 035423 9 DVIQCRECGYRI 20 (35)
Q Consensus 9 ~~irC~~CG~RI 20 (35)
-++.|+.||..-
T Consensus 12 ~~~~C~~C~~~F 23 (43)
T PF01428_consen 12 LPFKCKHCGKSF 23 (43)
T ss_dssp SHEE-TTTS-EE
T ss_pred CCeECCCCCccc
Confidence 589999999763
No 295
>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=38.39 E-value=17 Score=18.80 Aligned_cols=11 Identities=45% Similarity=1.506 Sum_probs=9.2
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
+.+-|-.|||+
T Consensus 30 e~vECv~Cg~~ 40 (59)
T TIGR02443 30 ELVECVECGYQ 40 (59)
T ss_pred eEEEeccCCCc
Confidence 45889999997
No 296
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=38.32 E-value=16 Score=21.63 Aligned_cols=13 Identities=23% Similarity=0.578 Sum_probs=7.0
Q ss_pred ceecCCCCCeEEE
Q 035423 10 VIQCRECGYRILY 22 (35)
Q Consensus 10 ~irC~~CG~RIly 22 (35)
.-.||.||.-..+
T Consensus 136 ~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 136 GFRCPQCGEMLEE 148 (178)
T ss_pred CCcCCCCCCCCee
Confidence 3456666655443
No 297
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=38.24 E-value=17 Score=20.36 Aligned_cols=13 Identities=38% Similarity=0.966 Sum_probs=10.3
Q ss_pred CCceecCCCCCeE
Q 035423 8 GDVIQCRECGYRI 20 (35)
Q Consensus 8 ~~~irC~~CG~RI 20 (35)
...|+|.+||--+
T Consensus 18 v~~V~C~nCgr~v 30 (95)
T PRK09335 18 VGYVQCDNCGRRV 30 (95)
T ss_pred CccEEeCCCCCcC
Confidence 3579999999764
No 298
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=38.08 E-value=18 Score=22.50 Aligned_cols=13 Identities=23% Similarity=0.299 Sum_probs=10.1
Q ss_pred ceecCCCCCeEEE
Q 035423 10 VIQCRECGYRILY 22 (35)
Q Consensus 10 ~irC~~CG~RIly 22 (35)
.--||.||..|.-
T Consensus 244 g~pCprCG~~I~~ 256 (272)
T PRK14810 244 GEPCLNCKTPIRR 256 (272)
T ss_pred CCcCCCCCCeeEE
Confidence 4569999998843
No 299
>cd02759 MopB_Acetylene-hydratase The MopB_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=38.02 E-value=52 Score=21.35 Aligned_cols=23 Identities=26% Similarity=0.634 Sum_probs=17.5
Q ss_pred ecCCC--CCeEEEeecCCceEEEEe
Q 035423 12 QCREC--GYRILYKKRTRRIVQYEA 34 (35)
Q Consensus 12 rC~~C--G~RIlyK~R~~~~~~~~A 34 (35)
-|++| |+-|+...+..+++.++.
T Consensus 3 ~C~~C~~~C~l~v~v~~g~v~~v~g 27 (477)
T cd02759 3 TCPGCHSGCGVLVYVKDGKLVKVEG 27 (477)
T ss_pred cCcCCcCCCCEEEEEECCEEEEEEc
Confidence 48888 567999888877777653
No 300
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=37.97 E-value=13 Score=19.99 Aligned_cols=10 Identities=30% Similarity=0.926 Sum_probs=8.0
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
.-+|+.||-.
T Consensus 8 ~~~C~~CG~d 17 (86)
T PF06170_consen 8 APRCPHCGLD 17 (86)
T ss_pred CCcccccCCc
Confidence 3489999976
No 301
>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=37.76 E-value=25 Score=18.34 Aligned_cols=12 Identities=42% Similarity=0.949 Sum_probs=6.1
Q ss_pred ceecCCCCCeEE
Q 035423 10 VIQCRECGYRIL 21 (35)
Q Consensus 10 ~irC~~CG~RIl 21 (35)
-|+||.|..+=|
T Consensus 29 iv~C~gC~~~Hl 40 (66)
T PF05180_consen 29 IVQCPGCKNRHL 40 (66)
T ss_dssp EEE-TTS--EEE
T ss_pred EEECCCCcceee
Confidence 378888887644
No 302
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=37.71 E-value=11 Score=19.67 Aligned_cols=17 Identities=47% Similarity=0.966 Sum_probs=12.0
Q ss_pred CCceecCCCCCeEEEeec
Q 035423 8 GDVIQCRECGYRILYKKR 25 (35)
Q Consensus 8 ~~~irC~~CG~RIlyK~R 25 (35)
..-++|.-||.+ -|-.+
T Consensus 14 ~tH~~CRRCGr~-syhv~ 30 (61)
T COG2126 14 KTHIRCRRCGRR-SYHVR 30 (61)
T ss_pred cceehhhhccch-heeec
Confidence 456899999987 44443
No 303
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=37.70 E-value=15 Score=23.80 Aligned_cols=7 Identities=57% Similarity=1.787 Sum_probs=4.4
Q ss_pred ecCCCCC
Q 035423 12 QCRECGY 18 (35)
Q Consensus 12 rC~~CG~ 18 (35)
-||+|||
T Consensus 59 vcp~c~~ 65 (296)
T CHL00174 59 ICEQCGY 65 (296)
T ss_pred CCCCCCC
Confidence 4666666
No 304
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=37.63 E-value=18 Score=28.04 Aligned_cols=13 Identities=46% Similarity=1.027 Sum_probs=9.9
Q ss_pred eecCCCCCeEEEe
Q 035423 11 IQCRECGYRILYK 23 (35)
Q Consensus 11 irC~~CG~RIlyK 23 (35)
-+|+.||.+|+.-
T Consensus 1270 G~C~kCGg~iilT 1282 (1337)
T PRK14714 1270 GKCRKCGGRIILT 1282 (1337)
T ss_pred CcccccCCeEEEE
Confidence 3688999988753
No 305
>TIGR02177 PorB_KorB 2-oxoacid:acceptor oxidoreductase, beta subunit, pyruvate/2-ketoisovalerate family. Several related four-subunit enzymes may exist in the same species. This model describes a subfamily of beta subunits, representing mostly pyruvate and 2-ketoisovalerate specific enzymes.
Probab=37.60 E-value=4.8 Score=25.59 Aligned_cols=12 Identities=25% Similarity=0.382 Sum_probs=9.1
Q ss_pred eecCCCCCeEEE
Q 035423 11 IQCRECGYRILY 22 (35)
Q Consensus 11 irC~~CG~RIly 22 (35)
+-||-|||++++
T Consensus 2 ~~CpGCg~~~i~ 13 (287)
T TIGR02177 2 DWCPGCGDFGIL 13 (287)
T ss_pred CcCCCCCChHHH
Confidence 469999996543
No 306
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=37.47 E-value=21 Score=18.08 Aligned_cols=12 Identities=25% Similarity=0.562 Sum_probs=7.2
Q ss_pred eecCCCCCeEEE
Q 035423 11 IQCRECGYRILY 22 (35)
Q Consensus 11 irC~~CG~RIly 22 (35)
-.||+|...|=.
T Consensus 56 G~CP~C~~~i~~ 67 (70)
T PF11793_consen 56 GECPYCSSPISW 67 (70)
T ss_dssp EE-TTT-SEEEG
T ss_pred cCCcCCCCeeeE
Confidence 469999988743
No 307
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=37.42 E-value=9.9 Score=19.20 Aligned_cols=16 Identities=44% Similarity=1.138 Sum_probs=12.8
Q ss_pred CCCCceecCCCCCeEE
Q 035423 6 KPGDVIQCRECGYRIL 21 (35)
Q Consensus 6 k~~~~irC~~CG~RIl 21 (35)
.+-+..+|+.|||.=|
T Consensus 24 np~~A~kCRkC~~k~L 39 (50)
T COG1552 24 NPPRATKCRKCGYKNL 39 (50)
T ss_pred CCcchhHHhhccCCCc
Confidence 4567789999999855
No 308
>PF01283 Ribosomal_S26e: Ribosomal protein S26e; InterPro: IPR000892 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 ribosomal proteins can be grouped on the basis of sequence similarities. One of these families, the S26E family, includes mammalian S26 []; Octopus S26 []; Drosophila S26 (DS31) []; plant cytoplasmic S26; and fungal S26 []. These proteins have 114 to 127 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3U5G_a 3U5C_a 2XZM_5 2XZN_5.
Probab=37.15 E-value=20 Score=20.56 Aligned_cols=13 Identities=23% Similarity=0.761 Sum_probs=7.8
Q ss_pred CCceecCCCCCeE
Q 035423 8 GDVIQCRECGYRI 20 (35)
Q Consensus 8 ~~~irC~~CG~RI 20 (35)
...|+|.+||.-+
T Consensus 18 v~~V~C~nCgr~v 30 (113)
T PF01283_consen 18 VQPVRCDNCGRCV 30 (113)
T ss_dssp --EEE-TTTB-EE
T ss_pred CcCEeeCcccccC
Confidence 3579999999875
No 309
>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=37.06 E-value=31 Score=15.83 Aligned_cols=14 Identities=21% Similarity=0.423 Sum_probs=8.3
Q ss_pred CCCceecCCCCCeE
Q 035423 7 PGDVIQCRECGYRI 20 (35)
Q Consensus 7 ~~~~irC~~CG~RI 20 (35)
...+.+|..|+..+
T Consensus 25 ~~~g~~C~~C~~~~ 38 (53)
T PF00130_consen 25 GKQGYRCSWCGLVC 38 (53)
T ss_dssp SSCEEEETTTT-EE
T ss_pred CCCeEEECCCCChH
Confidence 45567777777653
No 310
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=37.03 E-value=15 Score=20.89 Aligned_cols=13 Identities=23% Similarity=0.669 Sum_probs=9.7
Q ss_pred ceecCCCCCeEEE
Q 035423 10 VIQCRECGYRILY 22 (35)
Q Consensus 10 ~irC~~CG~RIly 22 (35)
..-||.|||--+-
T Consensus 22 ~FtCp~Cghe~vs 34 (104)
T COG4888 22 TFTCPRCGHEKVS 34 (104)
T ss_pred eEecCccCCeeee
Confidence 3679999997543
No 311
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.82 E-value=11 Score=20.11 Aligned_cols=15 Identities=33% Similarity=0.662 Sum_probs=11.9
Q ss_pred CceecCCCCCeEEEe
Q 035423 9 DVIQCRECGYRILYK 23 (35)
Q Consensus 9 ~~irC~~CG~RIlyK 23 (35)
-...|++|.+||--|
T Consensus 30 rtymC~eC~~Rva~k 44 (68)
T COG4896 30 RTYMCPECEHRVAIK 44 (68)
T ss_pred eeEechhhHhhhchh
Confidence 345799999998766
No 312
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=36.80 E-value=18 Score=22.47 Aligned_cols=15 Identities=27% Similarity=0.361 Sum_probs=11.1
Q ss_pred ceecCCCCCeEEEee
Q 035423 10 VIQCRECGYRILYKK 24 (35)
Q Consensus 10 ~irC~~CG~RIlyK~ 24 (35)
.--||.||..|.-.+
T Consensus 235 g~pC~~Cg~~I~~~~ 249 (269)
T PRK14811 235 GQPCPRCGTPIEKIV 249 (269)
T ss_pred cCCCCcCCCeeEEEE
Confidence 345999999986544
No 313
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=36.62 E-value=12 Score=22.45 Aligned_cols=12 Identities=33% Similarity=0.495 Sum_probs=0.0
Q ss_pred CceecCCCCCeE
Q 035423 9 DVIQCRECGYRI 20 (35)
Q Consensus 9 ~~irC~~CG~RI 20 (35)
.-+.||.||-.|
T Consensus 167 ~~~~cPitGe~I 178 (229)
T PF12230_consen 167 KMIICPITGEMI 178 (229)
T ss_dssp ------------
T ss_pred cccccccccccc
Confidence 458999999876
No 314
>PF13575 DUF4135: Domain of unknown function (DUF4135)
Probab=36.55 E-value=23 Score=22.52 Aligned_cols=12 Identities=42% Similarity=0.764 Sum_probs=9.8
Q ss_pred CCCeEEEeecCC
Q 035423 16 CGYRILYKKRTR 27 (35)
Q Consensus 16 CG~RIlyK~R~~ 27 (35)
-|.+|+||.|+-
T Consensus 69 ~g~kivYKPRsl 80 (370)
T PF13575_consen 69 SGKKIVYKPRSL 80 (370)
T ss_pred CCCEEEEeCccc
Confidence 467999999974
No 315
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=36.49 E-value=16 Score=21.19 Aligned_cols=9 Identities=33% Similarity=0.959 Sum_probs=7.4
Q ss_pred eecCCCCCe
Q 035423 11 IQCRECGYR 19 (35)
Q Consensus 11 irC~~CG~R 19 (35)
-.||.||.-
T Consensus 50 t~CP~Cg~~ 58 (115)
T COG1885 50 TSCPKCGEP 58 (115)
T ss_pred ccCCCCCCc
Confidence 579999974
No 316
>PRK05320 rhodanese superfamily protein; Provisional
Probab=36.40 E-value=23 Score=21.94 Aligned_cols=18 Identities=22% Similarity=0.388 Sum_probs=14.0
Q ss_pred cccCCCCceecCCCCCeE
Q 035423 3 NTLKPGDVIQCRECGYRI 20 (35)
Q Consensus 3 ~~lk~~~~irC~~CG~RI 20 (35)
..++++....|..||+.+
T Consensus 237 ~~~~~~~~~~c~~c~~~~ 254 (257)
T PRK05320 237 PQLAPLVDVTCFACRAVV 254 (257)
T ss_pred CCCccCccceecCCCCcC
Confidence 456777778899999864
No 317
>PF01125 G10: G10 protein; InterPro: IPR001748 A Xenopus protein known as G10 [] has been found to be highly conserved in a wide range of eukaryotic species. The function of G10 is still unknown. G10 is a protein of about 17 to 18 kDa (143 to 157 residues) which is hydrophilic and whose C-terminal half is rich in cysteines and could be involved in metal-binding.; GO: 0005634 nucleus
Probab=36.10 E-value=17 Score=21.55 Aligned_cols=16 Identities=31% Similarity=0.868 Sum_probs=12.4
Q ss_pred ccCCCCceecCCCCCe
Q 035423 4 TLKPGDVIQCRECGYR 19 (35)
Q Consensus 4 ~lk~~~~irC~~CG~R 19 (35)
++..+..+.|..||++
T Consensus 126 ~l~~~~~~~c~~CGC~ 141 (145)
T PF01125_consen 126 KLEEKQFVECVHCGCR 141 (145)
T ss_pred HhccCcccccCCCCCC
Confidence 3555677899999986
No 318
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=36.04 E-value=19 Score=24.00 Aligned_cols=11 Identities=27% Similarity=1.132 Sum_probs=6.8
Q ss_pred ecCCCCCeEEE
Q 035423 12 QCRECGYRILY 22 (35)
Q Consensus 12 rC~~CG~RIly 22 (35)
.|+.||..+.|
T Consensus 1 ~C~~Cg~~v~F 11 (343)
T PF10005_consen 1 SCPNCGQPVFF 11 (343)
T ss_pred CCCCCCCccee
Confidence 36677766554
No 319
>PRK04023 DNA polymerase II large subunit; Validated
Probab=35.96 E-value=23 Score=27.08 Aligned_cols=13 Identities=23% Similarity=0.741 Sum_probs=9.8
Q ss_pred eecCCCCCeEEEe
Q 035423 11 IQCRECGYRILYK 23 (35)
Q Consensus 11 irC~~CG~RIlyK 23 (35)
-+|+.||.+|+.-
T Consensus 1054 G~C~kCGg~lilT 1066 (1121)
T PRK04023 1054 GKCPKCGGNLILT 1066 (1121)
T ss_pred CcCccCCCeEEEE
Confidence 3688899888753
No 320
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=35.56 E-value=17 Score=18.40 Aligned_cols=10 Identities=30% Similarity=0.640 Sum_probs=6.9
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
...||.||-.
T Consensus 17 k~~CP~CG~~ 26 (56)
T PRK13130 17 KEICPVCGGK 26 (56)
T ss_pred cccCcCCCCC
Confidence 4568888854
No 321
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=35.45 E-value=19 Score=25.81 Aligned_cols=9 Identities=33% Similarity=1.099 Sum_probs=6.1
Q ss_pred eecCCCCCe
Q 035423 11 IQCRECGYR 19 (35)
Q Consensus 11 irC~~CG~R 19 (35)
+.||+||+.
T Consensus 228 vpCPHCGe~ 236 (611)
T COG5525 228 VPCPHCGEE 236 (611)
T ss_pred eeCCCCCch
Confidence 567777765
No 322
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=35.37 E-value=43 Score=15.56 Aligned_cols=17 Identities=24% Similarity=0.661 Sum_probs=9.6
Q ss_pred CCCceecCCCCCeEEEe
Q 035423 7 PGDVIQCRECGYRILYK 23 (35)
Q Consensus 7 ~~~~irC~~CG~RIlyK 23 (35)
...-.+|..||.=|..-
T Consensus 3 ~~~~YkC~~CGniVev~ 19 (36)
T PF06397_consen 3 KGEFYKCEHCGNIVEVV 19 (36)
T ss_dssp TTEEEE-TTT--EEEEE
T ss_pred cccEEEccCCCCEEEEE
Confidence 45567999999876543
No 323
>COG1468 CRISPR-associated protein Cas4 (RecB family exonuclease) [Defense mechanisms]
Probab=35.20 E-value=31 Score=20.67 Aligned_cols=19 Identities=26% Similarity=0.667 Sum_probs=15.0
Q ss_pred cCCCCceecCCCCCeEEEe
Q 035423 5 LKPGDVIQCRECGYRILYK 23 (35)
Q Consensus 5 lk~~~~irC~~CG~RIlyK 23 (35)
..+..+-+|..|+++-+.+
T Consensus 169 p~~~~~~~C~~C~y~~iC~ 187 (190)
T COG1468 169 PPPKKKKKCKKCAYREICF 187 (190)
T ss_pred CCCCCCCcCCCCCcceecc
Confidence 4566788999999997754
No 324
>PLN03166 60S ribosomal protein L34; Provisional
Probab=35.19 E-value=23 Score=19.65 Aligned_cols=15 Identities=33% Similarity=0.452 Sum_probs=11.4
Q ss_pred CCCCceecCCCCCeE
Q 035423 6 KPGDVIQCRECGYRI 20 (35)
Q Consensus 6 k~~~~irC~~CG~RI 20 (35)
|....-+|..||-++
T Consensus 37 K~~~~pkC~~cg~~L 51 (96)
T PLN03166 37 KRASGPKCPVTGKRI 51 (96)
T ss_pred cCCCCCcCCCCCCcc
Confidence 455677899999874
No 325
>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=34.78 E-value=24 Score=15.63 Aligned_cols=12 Identities=17% Similarity=0.551 Sum_probs=9.2
Q ss_pred CCceecCCCCCe
Q 035423 8 GDVIQCRECGYR 19 (35)
Q Consensus 8 ~~~irC~~CG~R 19 (35)
..+.+|..|+..
T Consensus 26 ~~~~~C~~C~~~ 37 (50)
T cd00029 26 KQGLRCSWCKVK 37 (50)
T ss_pred cceeEcCCCCCc
Confidence 467889888865
No 326
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=34.47 E-value=21 Score=20.44 Aligned_cols=13 Identities=23% Similarity=0.754 Sum_probs=10.2
Q ss_pred CCceecCCCCCeE
Q 035423 8 GDVIQCRECGYRI 20 (35)
Q Consensus 8 ~~~irC~~CG~RI 20 (35)
...|+|.+||--+
T Consensus 18 v~~V~C~nCgr~v 30 (108)
T PTZ00172 18 VKPVRCSNCGRCV 30 (108)
T ss_pred CccEEeCCccccc
Confidence 3579999999754
No 327
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=34.42 E-value=23 Score=19.45 Aligned_cols=10 Identities=20% Similarity=0.644 Sum_probs=7.9
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
.|+||.|+.-
T Consensus 35 ~VkCp~C~n~ 44 (85)
T PTZ00083 35 DVKCPGCSQI 44 (85)
T ss_pred EEECCCCCCe
Confidence 5889999864
No 328
>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=34.39 E-value=20 Score=16.67 Aligned_cols=9 Identities=33% Similarity=0.700 Sum_probs=6.9
Q ss_pred ceecCCCCC
Q 035423 10 VIQCRECGY 18 (35)
Q Consensus 10 ~irC~~CG~ 18 (35)
..-||.||-
T Consensus 3 ~~pCP~CGG 11 (37)
T smart00778 3 HGPCPNCGG 11 (37)
T ss_pred ccCCCCCCC
Confidence 356999986
No 329
>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=34.36 E-value=44 Score=14.04 Aligned_cols=11 Identities=27% Similarity=0.461 Sum_probs=5.3
Q ss_pred ecCCCCCeEEE
Q 035423 12 QCRECGYRILY 22 (35)
Q Consensus 12 rC~~CG~RIly 22 (35)
.|+-||.-|.=
T Consensus 3 ~C~rC~~~~~~ 13 (30)
T PF06827_consen 3 KCPRCWNYIED 13 (30)
T ss_dssp B-TTT--BBEE
T ss_pred cCccCCCcceE
Confidence 68888877543
No 330
>PF03691 UPF0167: Uncharacterised protein family (UPF0167); InterPro: IPR005363 The proteins in this family are about 200 amino acids long and each contain 3 CXXC motifs.
Probab=34.23 E-value=30 Score=20.90 Aligned_cols=13 Identities=38% Similarity=1.025 Sum_probs=11.2
Q ss_pred ceecCCCCCeEEE
Q 035423 10 VIQCRECGYRILY 22 (35)
Q Consensus 10 ~irC~~CG~RIly 22 (35)
.-||.+||...||
T Consensus 160 lFrClhCgk~~l~ 172 (176)
T PF03691_consen 160 LFRCLHCGKHRLY 172 (176)
T ss_pred EEEcCcCCcEEEE
Confidence 4699999998887
No 331
>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=34.01 E-value=19 Score=23.32 Aligned_cols=10 Identities=20% Similarity=0.737 Sum_probs=7.7
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
-++|++||..
T Consensus 224 R~~C~~Cg~~ 233 (305)
T TIGR01562 224 RVKCSHCEES 233 (305)
T ss_pred CccCCCCCCC
Confidence 4789999973
No 332
>COG1773 Rubredoxin [Energy production and conversion]
Probab=33.90 E-value=18 Score=18.35 Aligned_cols=8 Identities=50% Similarity=1.456 Sum_probs=4.9
Q ss_pred eecCCCCC
Q 035423 11 IQCRECGY 18 (35)
Q Consensus 11 irC~~CG~ 18 (35)
-+|..|||
T Consensus 4 ~~C~~CG~ 11 (55)
T COG1773 4 WRCSVCGY 11 (55)
T ss_pred eEecCCce
Confidence 45666665
No 333
>PF11648 RIG-I_C-RD: C-terminal domain of RIG-I; InterPro: IPR021673 This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependent dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity []. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2RQB_A 3GA3_A 2W4R_D 3EQT_A 2RQA_A 2RMJ_A 3NCU_A 2QFD_C 2QFB_D 3TMI_A ....
Probab=33.87 E-value=16 Score=20.49 Aligned_cols=15 Identities=33% Similarity=0.962 Sum_probs=11.6
Q ss_pred cCCCCceecCCCCCe
Q 035423 5 LKPGDVIQCRECGYR 19 (35)
Q Consensus 5 lk~~~~irC~~CG~R 19 (35)
..++..|.|..||+.
T Consensus 55 ~~~~~~I~C~~C~~~ 69 (123)
T PF11648_consen 55 WEPNGKIHCKNCGQD 69 (123)
T ss_dssp SEEEEEEEETSTSBE
T ss_pred eEeCCEEEcCCCChH
Confidence 345567999999986
No 334
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=33.79 E-value=16 Score=18.55 Aligned_cols=16 Identities=19% Similarity=0.426 Sum_probs=11.9
Q ss_pred CCCceecCCCCCeEEE
Q 035423 7 PGDVIQCRECGYRILY 22 (35)
Q Consensus 7 ~~~~irC~~CG~RIly 22 (35)
..+.-.|+-||.+|..
T Consensus 75 i~~~~~C~vC~k~l~~ 90 (109)
T PF10367_consen 75 ITESTKCSVCGKPLGN 90 (109)
T ss_pred ECCCCCccCcCCcCCC
Confidence 3456679999999754
No 335
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=33.55 E-value=24 Score=19.38 Aligned_cols=15 Identities=20% Similarity=0.534 Sum_probs=10.5
Q ss_pred CCCceecCCCCCeEE
Q 035423 7 PGDVIQCRECGYRIL 21 (35)
Q Consensus 7 ~~~~irC~~CG~RIl 21 (35)
.+...+|+.||+.-+
T Consensus 39 G~~~~~C~~Cg~~~~ 53 (111)
T PF14319_consen 39 GFHRYRCEDCGHEKI 53 (111)
T ss_pred CcceeecCCCCceEE
Confidence 345678999998643
No 336
>TIGR02652 conserved hypothetical protein TIGR02652, cyanobacterial. Members of this family of conserved hypothetical proteins are found, so far, only in the Cyanobacteria. Members are about 170 amino acids long and share a motif CxxCx(14)CxxH near the amino end.
Probab=33.50 E-value=14 Score=22.43 Aligned_cols=14 Identities=36% Similarity=0.710 Sum_probs=10.8
Q ss_pred CCCceecCCCCCeE
Q 035423 7 PGDVIQCRECGYRI 20 (35)
Q Consensus 7 ~~~~irC~~CG~RI 20 (35)
-+..|.||+|.--|
T Consensus 6 FGpei~CPhCRQ~i 19 (163)
T TIGR02652 6 FGPEIRCPHCRQNI 19 (163)
T ss_pred cCCcCcCchhhccc
Confidence 36789999997654
No 337
>PF08295 Sin3_corepress: Sin3 family co-repressor; InterPro: IPR013194 This domain is found on transcriptional regulators. It forms interactions with histone deacetylases [].
Probab=33.46 E-value=13 Score=20.62 Aligned_cols=14 Identities=50% Similarity=1.160 Sum_probs=10.5
Q ss_pred ecCCCC--CeEEEeec
Q 035423 12 QCRECG--YRILYKKR 25 (35)
Q Consensus 12 rC~~CG--~RIlyK~R 25 (35)
.|..|| ||.|-|.=
T Consensus 1 ~c~~~gpSYr~LP~~~ 16 (101)
T PF08295_consen 1 NCERCGPSYRLLPKSY 16 (101)
T ss_pred CCCcCccchhhCCccc
Confidence 388999 88886643
No 338
>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=33.37 E-value=19 Score=16.96 Aligned_cols=8 Identities=38% Similarity=0.721 Sum_probs=4.1
Q ss_pred eecCCCCC
Q 035423 11 IQCRECGY 18 (35)
Q Consensus 11 irC~~CG~ 18 (35)
.-||.||-
T Consensus 4 ~pCP~CGG 11 (40)
T PF08273_consen 4 GPCPICGG 11 (40)
T ss_dssp E--TTTT-
T ss_pred CCCCCCcC
Confidence 45999985
No 339
>PLN00186 ribosomal protein S26; Provisional
Probab=33.18 E-value=23 Score=20.32 Aligned_cols=13 Identities=31% Similarity=0.764 Sum_probs=10.1
Q ss_pred CCceecCCCCCeE
Q 035423 8 GDVIQCRECGYRI 20 (35)
Q Consensus 8 ~~~irC~~CG~RI 20 (35)
-..|+|.+||--+
T Consensus 18 v~~V~C~nCgr~v 30 (109)
T PLN00186 18 VKRIRCSNCGKCV 30 (109)
T ss_pred CcceeeCCCcccc
Confidence 3579999999753
No 340
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=33.18 E-value=21 Score=15.15 Aligned_cols=10 Identities=30% Similarity=0.750 Sum_probs=8.3
Q ss_pred eecCCCCCeE
Q 035423 11 IQCRECGYRI 20 (35)
Q Consensus 11 irC~~CG~RI 20 (35)
+.||-|+..+
T Consensus 2 v~CPiC~~~v 11 (26)
T smart00734 2 VQCPVCFREV 11 (26)
T ss_pred CcCCCCcCcc
Confidence 5799999875
No 341
>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=33.05 E-value=18 Score=21.88 Aligned_cols=10 Identities=30% Similarity=0.806 Sum_probs=8.2
Q ss_pred eecCCCCCeE
Q 035423 11 IQCRECGYRI 20 (35)
Q Consensus 11 irC~~CG~RI 20 (35)
..||+|++.|
T Consensus 40 ~~Cp~C~~~I 49 (158)
T PF10083_consen 40 TSCPNCSTPI 49 (158)
T ss_pred HHCcCCCCCC
Confidence 4699999876
No 342
>PRK04059 rpl34e 50S ribosomal protein L34e; Validated
Probab=32.98 E-value=26 Score=19.20 Aligned_cols=15 Identities=27% Similarity=0.592 Sum_probs=11.3
Q ss_pred CCCCceecCCCCCeE
Q 035423 6 KPGDVIQCRECGYRI 20 (35)
Q Consensus 6 k~~~~irC~~CG~RI 20 (35)
+....-+|..||.++
T Consensus 30 K~~~~pkC~~c~~~L 44 (88)
T PRK04059 30 KKPSKAKCAICGKPL 44 (88)
T ss_pred cCCCCCcCCCCCCcc
Confidence 455667899999874
No 343
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=32.95 E-value=36 Score=19.32 Aligned_cols=9 Identities=33% Similarity=1.029 Sum_probs=6.8
Q ss_pred cCCCCCeEE
Q 035423 13 CRECGYRIL 21 (35)
Q Consensus 13 C~~CG~RIl 21 (35)
||-||....
T Consensus 1 CPvCg~~l~ 9 (113)
T PF09862_consen 1 CPVCGGELV 9 (113)
T ss_pred CCCCCCceE
Confidence 888887754
No 344
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=32.69 E-value=27 Score=27.67 Aligned_cols=13 Identities=23% Similarity=0.856 Sum_probs=10.2
Q ss_pred eecCCCCCeEEEe
Q 035423 11 IQCRECGYRILYK 23 (35)
Q Consensus 11 irC~~CG~RIlyK 23 (35)
-+||.||.+|+.-
T Consensus 1558 G~C~kCGg~~ilT 1570 (1627)
T PRK14715 1558 GKCPKCGSKLILT 1570 (1627)
T ss_pred CcCcccCCeEEEE
Confidence 4799999998753
No 345
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=32.50 E-value=31 Score=19.28 Aligned_cols=16 Identities=19% Similarity=0.590 Sum_probs=12.5
Q ss_pred eecCCCCCeEEEeecC
Q 035423 11 IQCRECGYRILYKKRT 26 (35)
Q Consensus 11 irC~~CG~RIlyK~R~ 26 (35)
.-|+.||....+.-..
T Consensus 70 ~FC~~CGs~l~~~~~~ 85 (133)
T COG3791 70 GFCPTCGSPLFWRGPD 85 (133)
T ss_pred eecccCCCceEEecCC
Confidence 3799999998777444
No 346
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=32.42 E-value=26 Score=19.87 Aligned_cols=12 Identities=25% Similarity=0.631 Sum_probs=8.8
Q ss_pred CCceecCCCCCe
Q 035423 8 GDVIQCRECGYR 19 (35)
Q Consensus 8 ~~~irC~~CG~R 19 (35)
...-+|+.||..
T Consensus 127 ~~~~~C~~C~~~ 138 (178)
T PF02146_consen 127 EEPPRCPKCGGL 138 (178)
T ss_dssp TSSCBCTTTSCB
T ss_pred cccccccccCcc
Confidence 344589999985
No 347
>PRK00504 rpmG 50S ribosomal protein L33; Validated
Probab=32.30 E-value=41 Score=16.54 Aligned_cols=12 Identities=33% Similarity=0.750 Sum_probs=8.3
Q ss_pred cCCCCCeEEEee
Q 035423 13 CRECGYRILYKK 24 (35)
Q Consensus 13 C~~CG~RIlyK~ 24 (35)
||.|+-..|+|+
T Consensus 37 cp~c~khtlhkE 48 (50)
T PRK00504 37 CPRCNKHTLHKE 48 (50)
T ss_pred CCCCCCeEeeee
Confidence 677777777665
No 348
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=32.25 E-value=21 Score=16.73 Aligned_cols=8 Identities=50% Similarity=1.124 Sum_probs=5.2
Q ss_pred cCCCCCeE
Q 035423 13 CRECGYRI 20 (35)
Q Consensus 13 C~~CG~RI 20 (35)
|.+||.-|
T Consensus 1 Cd~CG~~I 8 (37)
T PF08394_consen 1 CDYCGGEI 8 (37)
T ss_pred CCccCCcc
Confidence 67787543
No 349
>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=32.24 E-value=6.9 Score=21.60 Aligned_cols=17 Identities=18% Similarity=0.378 Sum_probs=10.9
Q ss_pred ccCCCCceecCCCCCeE
Q 035423 4 TLKPGDVIQCRECGYRI 20 (35)
Q Consensus 4 ~lk~~~~irC~~CG~RI 20 (35)
+++....-.||.||.--
T Consensus 29 e~~q~~ky~Cp~Cgk~~ 45 (90)
T PF01780_consen 29 EISQHAKYTCPFCGKTS 45 (90)
T ss_dssp HHHHHS-BEESSSSSSE
T ss_pred HHHHhCCCcCCCCCCce
Confidence 34445567899998765
No 350
>COG4830 RPS26B Ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=32.22 E-value=22 Score=20.43 Aligned_cols=12 Identities=25% Similarity=0.960 Sum_probs=10.0
Q ss_pred CceecCCCCCeE
Q 035423 9 DVIQCRECGYRI 20 (35)
Q Consensus 9 ~~irC~~CG~RI 20 (35)
..|+|-+||..+
T Consensus 19 ~~v~CdnCg~~v 30 (108)
T COG4830 19 KYVRCDNCGKAV 30 (108)
T ss_pred cceeeccccccC
Confidence 469999999874
No 351
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=31.99 E-value=22 Score=14.75 Aligned_cols=10 Identities=20% Similarity=0.368 Sum_probs=6.1
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
..+||.|+..
T Consensus 35 ~~~Cp~C~~~ 44 (45)
T cd00162 35 KNTCPLCRTP 44 (45)
T ss_pred cCCCCCCCCc
Confidence 4567777643
No 352
>PF14149 YhfH: YhfH-like protein
Probab=31.72 E-value=6.1 Score=18.76 Aligned_cols=15 Identities=33% Similarity=0.658 Sum_probs=10.4
Q ss_pred CCCCceecCCCCCeE
Q 035423 6 KPGDVIQCRECGYRI 20 (35)
Q Consensus 6 k~~~~irC~~CG~RI 20 (35)
+..+.-.|++||.-|
T Consensus 9 rnLp~K~C~~CG~~i 23 (37)
T PF14149_consen 9 RNLPPKKCTECGKEI 23 (37)
T ss_pred HhCCCcccHHHHHHH
Confidence 345566899999654
No 353
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=31.67 E-value=21 Score=21.77 Aligned_cols=9 Identities=33% Similarity=0.922 Sum_probs=7.1
Q ss_pred ecCCCCCeE
Q 035423 12 QCRECGYRI 20 (35)
Q Consensus 12 rC~~CG~RI 20 (35)
.||.||.-|
T Consensus 156 ~CPlCg~Pl 164 (171)
T PF11290_consen 156 PCPLCGEPL 164 (171)
T ss_pred CCCCCCCCC
Confidence 599999763
No 354
>PHA02942 putative transposase; Provisional
Probab=31.64 E-value=28 Score=22.77 Aligned_cols=10 Identities=40% Similarity=1.271 Sum_probs=6.1
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
...|+.||+.
T Consensus 342 ~f~C~~CG~~ 351 (383)
T PHA02942 342 YFHCPSCGYE 351 (383)
T ss_pred EEECCCCCCE
Confidence 4566666664
No 355
>PF12322 T4_baseplate: T4 bacteriophage base plate protein; InterPro: IPR024364 Proteins in this family are found in T4-like viruses. They have a single completely conserved residue S that may be functionally important. The family includes the two base plate proteins from bacteriophage T4: Gp51 and Gp26, encoded by late genes []. Gp26 is a structural component of central hub of the baseplate. It associates with Gp25 (tail lysozyme) in the assembly process. Gp51 is essential for the formation of the central hub of the phage baseplate, playing a catalytic role for the central hub formation. It may be also a structural component of the hub.
Probab=31.49 E-value=23 Score=21.54 Aligned_cols=12 Identities=25% Similarity=0.789 Sum_probs=9.0
Q ss_pred CCCceecCCCCCe
Q 035423 7 PGDVIQCRECGYR 19 (35)
Q Consensus 7 ~~~~irC~~CG~R 19 (35)
..-+|+| +||+.
T Consensus 181 ~~v~vkC-~cg~~ 192 (205)
T PF12322_consen 181 HAVPVKC-KCGKE 192 (205)
T ss_pred EEEEEee-cCCcc
Confidence 3447899 99975
No 356
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=31.47 E-value=23 Score=19.02 Aligned_cols=11 Identities=36% Similarity=0.981 Sum_probs=8.7
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
+.-+|..||+-
T Consensus 79 ~~~~C~~CG~p 89 (104)
T TIGR00269 79 DLRRCERCGEP 89 (104)
T ss_pred cCCcCCcCcCc
Confidence 45789999974
No 357
>PRK03954 ribonuclease P protein component 4; Validated
Probab=31.47 E-value=26 Score=20.02 Aligned_cols=11 Identities=55% Similarity=0.936 Sum_probs=8.8
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
-.+.|-+||+-
T Consensus 92 vvitCl~CG~~ 102 (121)
T PRK03954 92 VVITCLECGHI 102 (121)
T ss_pred EEEECccCCCE
Confidence 35789999984
No 358
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=31.23 E-value=25 Score=25.14 Aligned_cols=13 Identities=31% Similarity=0.572 Sum_probs=9.8
Q ss_pred eecCCCCCeEEEe
Q 035423 11 IQCRECGYRILYK 23 (35)
Q Consensus 11 irC~~CG~RIlyK 23 (35)
..||+||..+.|.
T Consensus 725 ~~Cp~Cg~~l~~~ 737 (752)
T PRK08665 725 GACPECGSILEHE 737 (752)
T ss_pred CCCCCCCcccEEC
Confidence 4799999876653
No 359
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=31.21 E-value=21 Score=26.70 Aligned_cols=12 Identities=33% Similarity=0.606 Sum_probs=9.1
Q ss_pred CceecCCCCCeE
Q 035423 9 DVIQCRECGYRI 20 (35)
Q Consensus 9 ~~irC~~CG~RI 20 (35)
-.-.||+||..|
T Consensus 6 y~~~CPnCgg~i 17 (1171)
T TIGR01054 6 YSNLCPNCGGEI 17 (1171)
T ss_pred hcCCCCCCCCcc
Confidence 345799999874
No 360
>PTZ00157 60S ribosomal protein L36a; Provisional
Probab=31.14 E-value=34 Score=18.75 Aligned_cols=13 Identities=15% Similarity=0.524 Sum_probs=10.3
Q ss_pred ceecCCCCCeEEE
Q 035423 10 VIQCRECGYRILY 22 (35)
Q Consensus 10 ~irC~~CG~RIly 22 (35)
-.+|.+||+..+.
T Consensus 69 rl~C~~C~~~~~~ 81 (84)
T PTZ00157 69 KLECTKCKSKRQK 81 (84)
T ss_pred EEEecccCceeEe
Confidence 4689999998663
No 361
>PF09814 HECT_2: HECT-like Ubiquitin-conjugating enzyme (E2)-binding; InterPro: IPR019193 This entry consists of E3 ubiquitin-protein ligases which accept ubiquitin from specific E2 ubiquitin-conjugating enzymes, and transfer it to substrates, generally promoting their degradation by the proteasome [].
Probab=31.03 E-value=30 Score=21.50 Aligned_cols=17 Identities=29% Similarity=0.735 Sum_probs=13.2
Q ss_pred cCCCC-ceecCCCCCeEE
Q 035423 5 LKPGD-VIQCRECGYRIL 21 (35)
Q Consensus 5 lk~~~-~irC~~CG~RIl 21 (35)
++... .+.|..|+..|+
T Consensus 100 l~~~~~~~~C~~C~~~li 117 (354)
T PF09814_consen 100 LKSESFSLCCRNCKNPLI 117 (354)
T ss_pred hcCCceEEECCCCCCccc
Confidence 44445 799999999975
No 362
>PF06769 Plasmid_Txe: Plasmid encoded toxin Txe; InterPro: IPR009614 The Axe-Txe pair in Enterococcus faecium (Streptococcus faecium) and the homologous YefM-YoeB pair in Escherichia coli have been shown to act as an antitoxin-toxin pair. This family describes the toxin component. Nearly every example found is next to an identifiable antitoxin, as indicated by match to IPR006442 from INTERPRO [].; GO: 0004519 endonuclease activity, 0006401 RNA catabolic process; PDB: 3OEI_L 2A6R_F 2A6Q_E 2A6S_D.
Probab=30.90 E-value=74 Score=16.83 Aligned_cols=19 Identities=21% Similarity=0.352 Sum_probs=13.5
Q ss_pred CCeEEEeecCCceEEEEeC
Q 035423 17 GYRILYKKRTRRIVQYEAR 35 (35)
Q Consensus 17 G~RIlyK~R~~~~~~~~Ar 35 (35)
.||++|+.-...+.-+.|+
T Consensus 59 ~hRLVY~v~~~~i~I~s~~ 77 (80)
T PF06769_consen 59 KHRLVYEVDDDTITILSCR 77 (80)
T ss_dssp SEEEEEEEESSEEEEEESS
T ss_pred CceEEEEEeCCEEEEEEee
Confidence 5899999976666555543
No 363
>TIGR00598 rad14 DNA repair protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.89 E-value=37 Score=20.66 Aligned_cols=12 Identities=33% Similarity=0.863 Sum_probs=10.2
Q ss_pred eecCCCCCeEEE
Q 035423 11 IQCRECGYRILY 22 (35)
Q Consensus 11 irC~~CG~RIly 22 (35)
-+|..||+.+=|
T Consensus 158 k~C~~Cg~e~~~ 169 (172)
T TIGR00598 158 RTCTTCGLEETY 169 (172)
T ss_pred eecCCCCceEEE
Confidence 579999999866
No 364
>PRK11867 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed
Probab=30.89 E-value=6.8 Score=24.67 Aligned_cols=15 Identities=20% Similarity=0.443 Sum_probs=11.2
Q ss_pred CCceecCCCCCeEEE
Q 035423 8 GDVIQCRECGYRILY 22 (35)
Q Consensus 8 ~~~irC~~CG~RIly 22 (35)
..+.-||-||+.+++
T Consensus 15 ~~~~~CpGCg~~~il 29 (286)
T PRK11867 15 QEPRWCPGCGDGSIL 29 (286)
T ss_pred CCCCcCCCCCCHHHH
Confidence 345689999998654
No 365
>cd02750 MopB_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. Members of the MopB_Nitrate-R-NarG-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=30.63 E-value=82 Score=20.43 Aligned_cols=24 Identities=8% Similarity=0.059 Sum_probs=18.2
Q ss_pred eecCCC--CCeEEEeecCCceEEEEe
Q 035423 11 IQCREC--GYRILYKKRTRRIVQYEA 34 (35)
Q Consensus 11 irC~~C--G~RIlyK~R~~~~~~~~A 34 (35)
.-|++| |+-|....|..+++.++.
T Consensus 7 ~~c~~C~~gC~i~~~v~dg~v~~v~g 32 (461)
T cd02750 7 THGVNCTGSCSWNVYVKNGIVTREEQ 32 (461)
T ss_pred CCCCCCCCCCceEEEEECCEEEEEec
Confidence 448888 578888888888777753
No 366
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=30.61 E-value=23 Score=16.02 Aligned_cols=8 Identities=38% Similarity=1.211 Sum_probs=5.9
Q ss_pred ecCCCCCe
Q 035423 12 QCRECGYR 19 (35)
Q Consensus 12 rC~~CG~R 19 (35)
.||.|+..
T Consensus 1 ~CP~C~~~ 8 (41)
T PF13453_consen 1 KCPRCGTE 8 (41)
T ss_pred CcCCCCcc
Confidence 48888873
No 367
>COG1060 ThiH Thiamine biosynthesis enzyme ThiH and related uncharacterized enzymes [Coenzyme metabolism / General function prediction only]
Probab=30.60 E-value=20 Score=23.58 Aligned_cols=11 Identities=27% Similarity=0.661 Sum_probs=8.9
Q ss_pred ceecCCCCCeE
Q 035423 10 VIQCRECGYRI 20 (35)
Q Consensus 10 ~irC~~CG~RI 20 (35)
..+|.+|+++-
T Consensus 70 ~~~C~fCaF~~ 80 (370)
T COG1060 70 VNDCTFCAFYR 80 (370)
T ss_pred cCCCCcccccc
Confidence 36899999984
No 368
>PF09654 DUF2396: Protein of unknown function (DUF2396); InterPro: IPR013472 These conserved hypothetical proteins have so far been found only in the Cyanobacteria. They are about 170 amino acids long and contain a CxxCx(14)CxxH motif near the N terminus.
Probab=30.56 E-value=17 Score=22.03 Aligned_cols=13 Identities=46% Similarity=0.879 Sum_probs=10.3
Q ss_pred CCceecCCCCCeE
Q 035423 8 GDVIQCRECGYRI 20 (35)
Q Consensus 8 ~~~irC~~CG~RI 20 (35)
+..|.||+|.--|
T Consensus 4 Gpei~CPhCRq~i 16 (161)
T PF09654_consen 4 GPEIQCPHCRQTI 16 (161)
T ss_pred CCcCcCchhhccc
Confidence 6789999997654
No 369
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=30.54 E-value=31 Score=24.89 Aligned_cols=10 Identities=40% Similarity=0.909 Sum_probs=4.7
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
+..||+||..
T Consensus 475 p~~Cp~Cgs~ 484 (730)
T COG1198 475 PQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCC
Confidence 3445555544
No 370
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=30.53 E-value=22 Score=21.86 Aligned_cols=9 Identities=44% Similarity=0.999 Sum_probs=7.3
Q ss_pred ecCCCCCeE
Q 035423 12 QCRECGYRI 20 (35)
Q Consensus 12 rC~~CG~RI 20 (35)
.||.||.-|
T Consensus 158 ~CPlCg~Pl 166 (177)
T TIGR03847 158 PCPLCGRPI 166 (177)
T ss_pred CCCCCCCCC
Confidence 699999864
No 371
>PF12653 DUF3785: Protein of unknown function (DUF3785); InterPro: IPR024210 This family of proteins is functionally uncharacterised. Proteins in this family are approximately 140 amino acids in length and share two CXXC motifs suggesting these are zinc binding proteins. In clostridia proteins are found in an operon with three signalling proteins, suggesting that they are involved in DNA-binding transcription regulator downstream of an as yet unknown signalling pathway.
Probab=30.52 E-value=43 Score=19.93 Aligned_cols=13 Identities=31% Similarity=0.777 Sum_probs=10.3
Q ss_pred ceecCCCCCeEEE
Q 035423 10 VIQCRECGYRILY 22 (35)
Q Consensus 10 ~irC~~CG~RIly 22 (35)
.+-||+||--++.
T Consensus 120 i~VC~nCG~y~i~ 132 (138)
T PF12653_consen 120 IIVCPNCGNYSIE 132 (138)
T ss_pred EEECCCCCceEEE
Confidence 5789999987654
No 372
>PF03243 MerB: Alkylmercury lyase; InterPro: IPR004927 Mercury is a highly toxic metal. Toxicity can result from three different mercurial forms: elemental, inorganic ion and organomercurial compounds. The ability of bacteria to detoxify mercurial compounds by reduction and volatilisation is conferred by the Mer genes, which are usually plasmid encoded (although chromosome resistance determinants have also occasionally been identified) []. Organomercurial lyase (MerB), also known as alkylmercury lyase, mediates the first of the two steps in the microbial detoxification of organomercurial salts (the other catalysed by mercuric reductase). Organomercurial lyase catalyses the protonolysis of the C-Hg bond in a wide range of organomercurial salts (primary, secondary, tertiary, alkyl, vinyl, allyl and aryl) to Hg(II) and the respective organic compound []: RHg(+) + H(+) = RH + Hg(2+) Hg(II) is subsequently detoxified by mercuric reductase. The enzyme has been purified to homogeneity in Escherichia coli and has been found to be a 22.4kDa monomer with no detectable cofactors or metal ions.; GO: 0018836 alkylmercury lyase activity, 0046413 organomercury catabolic process; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=30.52 E-value=1e+02 Score=17.08 Aligned_cols=21 Identities=19% Similarity=0.251 Sum_probs=13.2
Q ss_pred eecCCCCCeEEEeecCCceEE
Q 035423 11 IQCRECGYRILYKKRTRRIVQ 31 (35)
Q Consensus 11 irC~~CG~RIlyK~R~~~~~~ 31 (35)
-+||.||-.|=...++..+..
T Consensus 40 S~cp~tg~pI~l~v~~~~i~~ 60 (127)
T PF03243_consen 40 SRCPATGEPIRLTVDPGGITD 60 (127)
T ss_dssp EE-TTT--EEEEEE-SSSEEE
T ss_pred EcCCCCCCeEEEEEeCCceee
Confidence 589999999999988765544
No 373
>COG0635 HemN Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]
Probab=30.48 E-value=29 Score=22.90 Aligned_cols=17 Identities=29% Similarity=0.591 Sum_probs=13.1
Q ss_pred ceecCCCCCeEEEeecC
Q 035423 10 VIQCRECGYRILYKKRT 26 (35)
Q Consensus 10 ~irC~~CG~RIlyK~R~ 26 (35)
.-+|+||++..+.....
T Consensus 45 ~~~C~YC~fn~~~~~~~ 61 (416)
T COG0635 45 VSKCPYCDFNSHVTKRG 61 (416)
T ss_pred cccCCCCCCeeeccCCC
Confidence 35899999998776653
No 374
>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=30.47 E-value=50 Score=22.22 Aligned_cols=8 Identities=25% Similarity=0.808 Sum_probs=3.1
Q ss_pred ecCCCCCe
Q 035423 12 QCRECGYR 19 (35)
Q Consensus 12 rC~~CG~R 19 (35)
+||+|+-.
T Consensus 224 ~C~~C~~~ 231 (505)
T TIGR00595 224 CCPNCDVS 231 (505)
T ss_pred CCCCCCCc
Confidence 33444333
No 375
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=30.16 E-value=13 Score=18.94 Aligned_cols=16 Identities=38% Similarity=0.698 Sum_probs=12.0
Q ss_pred CCCCceecCCCCCeEE
Q 035423 6 KPGDVIQCRECGYRIL 21 (35)
Q Consensus 6 k~~~~irC~~CG~RIl 21 (35)
++-....|.+|.+||=
T Consensus 27 rPi~tYmC~eC~~RI~ 42 (56)
T PF09963_consen 27 RPIHTYMCDECKERIR 42 (56)
T ss_pred CCCcceeChhHHHHHh
Confidence 3555678999999974
No 376
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=29.99 E-value=22 Score=22.96 Aligned_cols=15 Identities=27% Similarity=0.627 Sum_probs=7.7
Q ss_pred ccCCCCceecCCCCC
Q 035423 4 TLKPGDVIQCRECGY 18 (35)
Q Consensus 4 ~lk~~~~irC~~CG~ 18 (35)
++.+...+.||.|.|
T Consensus 186 ~~~~~~alIC~~C~h 200 (251)
T COG5415 186 DLSPFKALICPQCHH 200 (251)
T ss_pred ccCchhhhccccccc
Confidence 344455555555544
No 377
>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=29.79 E-value=21 Score=23.08 Aligned_cols=14 Identities=36% Similarity=0.755 Sum_probs=5.5
Q ss_pred ceecCCCCCeEEEe
Q 035423 10 VIQCRECGYRILYK 23 (35)
Q Consensus 10 ~irC~~CG~RIlyK 23 (35)
.+-||.||..-|=+
T Consensus 31 n~yCP~Cg~~~L~~ 44 (254)
T PF06044_consen 31 NMYCPNCGSKPLSK 44 (254)
T ss_dssp H---TTT--SS-EE
T ss_pred CCcCCCCCChhHhh
Confidence 35799999885543
No 378
>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=29.78 E-value=18 Score=15.82 Aligned_cols=11 Identities=18% Similarity=0.634 Sum_probs=7.9
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
.+.+|..|+..
T Consensus 26 ~~~~C~~C~~~ 36 (49)
T smart00109 26 QGLRCSWCKVK 36 (49)
T ss_pred CCcCCCCCCch
Confidence 46788888754
No 379
>smart00507 HNHc HNH nucleases.
Probab=29.70 E-value=22 Score=15.32 Aligned_cols=11 Identities=27% Similarity=0.437 Sum_probs=9.0
Q ss_pred eecCCCCCeEE
Q 035423 11 IQCRECGYRIL 21 (35)
Q Consensus 11 irC~~CG~RIl 21 (35)
-.|.+||..+-
T Consensus 11 ~~C~~C~~~~~ 21 (52)
T smart00507 11 GVCAYCGKPAS 21 (52)
T ss_pred CCCcCCcCCCC
Confidence 68999998763
No 380
>cd02018 TPP_PFOR Thiamine pyrophosphate (TPP family), Pyruvate ferredoxin/flavodoxin oxidoreductase (PFOR) subfamily, TPP-binding module; PFOR catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA, a crucial step in many metabolic pathways. Archaea, anaerobic bacteria and eukaryotes that lack mitochondria (and therefore pyruvate dehydrogenase) use PFOR to oxidatively decarboxylate pyruvate, with ferredoxin or flavodoxin as the electron acceptor. PFORs can be homodimeric, heterodimeric, or heterotetrameric, depending on the organism. These enzymes are dependent on TPP and a divalent metal cation as cofactors.
Probab=29.53 E-value=7.1 Score=23.64 Aligned_cols=14 Identities=21% Similarity=0.404 Sum_probs=10.7
Q ss_pred eecCCCCCeEEEee
Q 035423 11 IQCRECGYRILYKK 24 (35)
Q Consensus 11 irC~~CG~RIlyK~ 24 (35)
--||-|||.++++.
T Consensus 6 ~~c~gc~~~~~~~~ 19 (237)
T cd02018 6 GACAGCGEVTAVRV 19 (237)
T ss_pred ccCcCCCcHHHHHH
Confidence 45999999887654
No 381
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=29.48 E-value=24 Score=15.55 Aligned_cols=10 Identities=30% Similarity=0.534 Sum_probs=3.7
Q ss_pred cCCCCCeEEE
Q 035423 13 CRECGYRILY 22 (35)
Q Consensus 13 C~~CG~RIly 22 (35)
|++||..+-+
T Consensus 1 C~~C~~~~~~ 10 (47)
T PF01844_consen 1 CQYCGKPGSD 10 (47)
T ss_dssp -TTT--B--G
T ss_pred CCCCCCcCcc
Confidence 7888877543
No 382
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=29.42 E-value=23 Score=21.47 Aligned_cols=8 Identities=50% Similarity=1.277 Sum_probs=6.7
Q ss_pred eecCCCCC
Q 035423 11 IQCRECGY 18 (35)
Q Consensus 11 irC~~CG~ 18 (35)
..||+||.
T Consensus 121 ficpecg~ 128 (165)
T COG4647 121 FICPECGI 128 (165)
T ss_pred hhCccccc
Confidence 56999996
No 383
>PF15616 TerY-C: TerY-C metal binding domain
Probab=29.42 E-value=57 Score=18.96 Aligned_cols=16 Identities=19% Similarity=0.445 Sum_probs=10.3
Q ss_pred CCceecCCCCCeEEEe
Q 035423 8 GDVIQCRECGYRILYK 23 (35)
Q Consensus 8 ~~~irC~~CG~RIlyK 23 (35)
.+.+-||-||..+-|-
T Consensus 103 ~~~~~CPwCg~~g~~~ 118 (131)
T PF15616_consen 103 EGEVTCPWCGNEGSFG 118 (131)
T ss_pred CCCEECCCCCCeeeec
Confidence 3457777777776553
No 384
>TIGR02646 conserved hypothetical protein TIGR02646. Members of this uncharacterized protein family are found exclusively in bacteria. Neighboring genes in various genomes are also uncharacterized or may annotated as similar to restriction system proteins.
Probab=29.41 E-value=22 Score=19.98 Aligned_cols=12 Identities=25% Similarity=0.362 Sum_probs=9.4
Q ss_pred CceecCCCCCeE
Q 035423 9 DVIQCRECGYRI 20 (35)
Q Consensus 9 ~~irC~~CG~RI 20 (35)
..-+|.||+.+|
T Consensus 23 ~~~~C~YC~~~~ 34 (144)
T TIGR02646 23 QGGLCAYCEREI 34 (144)
T ss_pred hCCCcCccCCCc
Confidence 356899999965
No 385
>PRK14873 primosome assembly protein PriA; Provisional
Probab=29.40 E-value=60 Score=22.95 Aligned_cols=10 Identities=40% Similarity=0.883 Sum_probs=4.9
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
..+|.+||+.
T Consensus 410 ~l~Ch~CG~~ 419 (665)
T PRK14873 410 TPRCRWCGRA 419 (665)
T ss_pred eeECCCCcCC
Confidence 4455555543
No 386
>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=29.20 E-value=39 Score=15.08 Aligned_cols=13 Identities=23% Similarity=0.782 Sum_probs=9.7
Q ss_pred eecCCCCCeEEEe
Q 035423 11 IQCRECGYRILYK 23 (35)
Q Consensus 11 irC~~CG~RIlyK 23 (35)
+.|..|+--++|=
T Consensus 2 ~~C~~C~t~L~yP 14 (31)
T TIGR01053 2 VVCGGCRTLLMYP 14 (31)
T ss_pred cCcCCCCcEeecC
Confidence 6788888877763
No 387
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 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. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=29.16 E-value=40 Score=14.85 Aligned_cols=15 Identities=20% Similarity=0.257 Sum_probs=8.4
Q ss_pred CCCceecCCCCCeEE
Q 035423 7 PGDVIQCRECGYRIL 21 (35)
Q Consensus 7 ~~~~irC~~CG~RIl 21 (35)
......|.+|+.-|-
T Consensus 3 ~~~~~~C~~C~~~~~ 17 (43)
T PF06467_consen 3 NLKMKTCSYCKKYIP 17 (43)
T ss_dssp G-SCEE-TTT--EEE
T ss_pred CCcCCcCcccCCccc
Confidence 356789999999874
No 388
>TIGR03129 one_C_dehyd_B formylmethanofuran dehydrogenase subunit B. Members of this largely archaeal protein family are subunit B of the formylmethanofuran dehydrogenase. Nomenclature in some bacteria may reflect inclusion of the formyltransferase described by TIGR03119 as part of the complex, and therefore call this protein formyltransferase/hydrolase complex Fhc subunit C. Note that this model does not distinguish tungsten (FwdB) from molybdenum-containing (FmdB) forms of this enzyme.
Probab=29.13 E-value=83 Score=19.51 Aligned_cols=22 Identities=23% Similarity=0.369 Sum_probs=15.9
Q ss_pred eecCCC--CCe-EEEeecCCceEEE
Q 035423 11 IQCREC--GYR-ILYKKRTRRIVQY 32 (35)
Q Consensus 11 irC~~C--G~R-IlyK~R~~~~~~~ 32 (35)
+-|+.| |+- |..+.+..+++.+
T Consensus 2 ~~C~~C~~gC~~l~v~v~~g~v~~v 26 (421)
T TIGR03129 2 VVCPFCGCLCDDIEVEVEGNKIVKV 26 (421)
T ss_pred cccCCcccccCeEEEEEECCEEEEE
Confidence 468888 565 8888887766554
No 389
>cd02754 MopB_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. Members of the MopB_Nitrate-R-NapA CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=29.13 E-value=88 Score=20.62 Aligned_cols=23 Identities=17% Similarity=0.462 Sum_probs=17.3
Q ss_pred ecCCC--CCeEEEeecCCceEEEEe
Q 035423 12 QCREC--GYRILYKKRTRRIVQYEA 34 (35)
Q Consensus 12 rC~~C--G~RIlyK~R~~~~~~~~A 34 (35)
-|+.| |+-|....|..+++.++.
T Consensus 3 ~C~~C~~~C~i~v~v~dg~i~ri~g 27 (565)
T cd02754 3 TCPYCGVGCGVEIGVKDGKVVAVRG 27 (565)
T ss_pred CCCCCCCCCCEEEEEECCEEEEEEC
Confidence 37777 578888888888877764
No 390
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.10 E-value=27 Score=19.21 Aligned_cols=12 Identities=42% Similarity=1.019 Sum_probs=6.2
Q ss_pred CCceecCCCCCe
Q 035423 8 GDVIQCRECGYR 19 (35)
Q Consensus 8 ~~~irC~~CG~R 19 (35)
.+..-|++||-+
T Consensus 31 dplt~ce~c~a~ 42 (82)
T COG2331 31 DPLTTCEECGAR 42 (82)
T ss_pred CccccChhhChH
Confidence 334456666554
No 391
>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=29.03 E-value=27 Score=17.45 Aligned_cols=9 Identities=44% Similarity=1.065 Sum_probs=5.0
Q ss_pred ceecCCCCC
Q 035423 10 VIQCRECGY 18 (35)
Q Consensus 10 ~irC~~CG~ 18 (35)
.+.|-.||+
T Consensus 77 ~~~C~~C~~ 85 (85)
T PF04032_consen 77 VYTCLNCGH 85 (85)
T ss_dssp EEEETTTTE
T ss_pred EEEccccCC
Confidence 355666654
No 392
>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=29.02 E-value=32 Score=18.05 Aligned_cols=13 Identities=31% Similarity=0.830 Sum_probs=9.9
Q ss_pred CCCCceecCCCCC
Q 035423 6 KPGDVIQCRECGY 18 (35)
Q Consensus 6 k~~~~irC~~CG~ 18 (35)
++..++.||.|+.
T Consensus 1 ~~~~~~~CPRC~S 13 (63)
T PF02701_consen 1 KPEQPLPCPRCDS 13 (63)
T ss_pred CCccCCCCCCcCC
Confidence 3567789999975
No 393
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=28.94 E-value=32 Score=19.87 Aligned_cols=10 Identities=40% Similarity=0.986 Sum_probs=7.8
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
=|.|++||..
T Consensus 102 yVlC~~C~sp 111 (138)
T PRK03988 102 YVICPECGSP 111 (138)
T ss_pred cEECCCCCCC
Confidence 4789999874
No 394
>cd04511 Nudix_Hydrolase_4 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, U=I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specifici
Probab=28.83 E-value=27 Score=18.50 Aligned_cols=7 Identities=57% Similarity=1.749 Sum_probs=5.9
Q ss_pred cCCCCCe
Q 035423 13 CRECGYR 19 (35)
Q Consensus 13 C~~CG~R 19 (35)
||.||..
T Consensus 1 c~~~~~~ 7 (130)
T cd04511 1 CPDCGYI 7 (130)
T ss_pred CCCCccc
Confidence 8999984
No 395
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=28.77 E-value=25 Score=17.95 Aligned_cols=8 Identities=38% Similarity=1.132 Sum_probs=2.6
Q ss_pred eecCCCCC
Q 035423 11 IQCRECGY 18 (35)
Q Consensus 11 irC~~CG~ 18 (35)
.+|.+||.
T Consensus 49 ~KC~~C~S 56 (61)
T PF14599_consen 49 HKCSHCGS 56 (61)
T ss_dssp ---TTTS-
T ss_pred hcCCCCCC
Confidence 45666653
No 396
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=28.72 E-value=29 Score=21.58 Aligned_cols=14 Identities=36% Similarity=0.581 Sum_probs=10.7
Q ss_pred ceecCCCCCeEEEe
Q 035423 10 VIQCRECGYRILYK 23 (35)
Q Consensus 10 ~irC~~CG~RIlyK 23 (35)
.--|+.||..|.-.
T Consensus 254 g~pC~~Cg~~I~~~ 267 (282)
T PRK13945 254 GKPCRKCGTPIERI 267 (282)
T ss_pred cCCCCcCCCeeEEE
Confidence 44699999998643
No 397
>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=28.43 E-value=30 Score=17.16 Aligned_cols=11 Identities=36% Similarity=0.908 Sum_probs=8.8
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
....||+||..
T Consensus 52 g~L~Cp~c~r~ 62 (68)
T PF03966_consen 52 GELICPECGRE 62 (68)
T ss_dssp TEEEETTTTEE
T ss_pred CEEEcCCCCCE
Confidence 56899999864
No 398
>PRK03922 hypothetical protein; Provisional
Probab=28.40 E-value=27 Score=20.18 Aligned_cols=10 Identities=30% Similarity=0.853 Sum_probs=8.1
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
..-||.||.-
T Consensus 49 ~~~cP~cge~ 58 (113)
T PRK03922 49 LTICPKCGEP 58 (113)
T ss_pred cccCCCCCCc
Confidence 3679999975
No 399
>PF01199 Ribosomal_L34e: Ribosomal protein L34e; InterPro: IPR008195 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 archaebacterial ribosomal proteins belong to the L34e family. These include, vertebrate L34, mosquito L31 [], plant L34 [], yeast putative ribosomal protein YIL052c and archaebacterial L34e.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_i 3IZS_i 4A19_L 4A1D_L 4A18_L 4A1B_L.
Probab=28.25 E-value=28 Score=19.18 Aligned_cols=15 Identities=27% Similarity=0.663 Sum_probs=7.8
Q ss_pred CCCCceecCCCCCeE
Q 035423 6 KPGDVIQCRECGYRI 20 (35)
Q Consensus 6 k~~~~irC~~CG~RI 20 (35)
+.....+|..||..+
T Consensus 37 K~~~~pkC~~cg~~L 51 (94)
T PF01199_consen 37 KKPKKPKCGDCGKPL 51 (94)
T ss_dssp --TT--BSTSSS-BS
T ss_pred ccCCCCCcCccCCcc
Confidence 445677899999763
No 400
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=28.13 E-value=48 Score=18.78 Aligned_cols=14 Identities=43% Similarity=0.797 Sum_probs=10.9
Q ss_pred CceecCCCCCeEEE
Q 035423 9 DVIQCRECGYRILY 22 (35)
Q Consensus 9 ~~irC~~CG~RIly 22 (35)
-.+.|.+||+-.-|
T Consensus 81 v~vtC~~CG~~~R~ 94 (105)
T COG2023 81 VVVTCLECGTIRRY 94 (105)
T ss_pred EEEEecCCCcEEEe
Confidence 46899999986554
No 401
>cd02752 MopB_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. Members of the MopB_Formate-Dh-Na-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=27.81 E-value=91 Score=21.93 Aligned_cols=22 Identities=23% Similarity=0.394 Sum_probs=16.8
Q ss_pred ecCCC--CCeEEEeecCCceEEEE
Q 035423 12 QCREC--GYRILYKKRTRRIVQYE 33 (35)
Q Consensus 12 rC~~C--G~RIlyK~R~~~~~~~~ 33 (35)
-|++| |+-|....+..+++.++
T Consensus 3 vC~~C~~gCgi~v~v~dg~iv~ve 26 (649)
T cd02752 3 ICPYCSVGCGLIAYVQNGVWVHQE 26 (649)
T ss_pred cCcCcccCCCeEEEEECCEEEEEE
Confidence 38888 78888877777777665
No 402
>PRK07726 DNA topoisomerase III; Provisional
Probab=27.80 E-value=32 Score=23.95 Aligned_cols=14 Identities=29% Similarity=0.636 Sum_probs=11.0
Q ss_pred ceecCCCCCeEEEe
Q 035423 10 VIQCRECGYRILYK 23 (35)
Q Consensus 10 ~irC~~CG~RIlyK 23 (35)
...||.||..++++
T Consensus 610 ~~~CP~C~~~~~~~ 623 (658)
T PRK07726 610 GPKCPDCGKPMLKV 623 (658)
T ss_pred cccccccCccceee
Confidence 46799999987654
No 403
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=27.71 E-value=31 Score=15.60 Aligned_cols=10 Identities=30% Similarity=0.969 Sum_probs=7.9
Q ss_pred CCceecCCCC
Q 035423 8 GDVIQCRECG 17 (35)
Q Consensus 8 ~~~irC~~CG 17 (35)
...+.||.|+
T Consensus 34 ~~~~~CP~C~ 43 (44)
T PF14634_consen 34 GKSVKCPICR 43 (44)
T ss_pred CCCCCCcCCC
Confidence 4578999987
No 404
>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=27.71 E-value=44 Score=18.89 Aligned_cols=15 Identities=27% Similarity=0.538 Sum_probs=11.9
Q ss_pred CCceecCCCCCeEEE
Q 035423 8 GDVIQCRECGYRILY 22 (35)
Q Consensus 8 ~~~irC~~CG~RIly 22 (35)
..-.+|+.||.-++.
T Consensus 5 ~~fYkC~~CGniv~v 19 (125)
T TIGR00320 5 LQVYKCEVCGNIVEV 19 (125)
T ss_pred CcEEECCCCCcEEEE
Confidence 456899999998853
No 405
>TIGR03336 IOR_alpha indolepyruvate ferredoxin oxidoreductase, alpha subunit. Indolepyruvate ferredoxin oxidoreductase (IOR) is an alpha 2/beta 2 tetramer related to ketoacid oxidoreductases for pyruvate (1.2.7.1, POR), 2-ketoglutarate (1.2.7.3, KOR), and 2-oxoisovalerate (1.2.7.7, VOR). These multi-subunit enzymes typically are found in anaerobes and are inactiviated by oxygen. IOR in Pyrococcus acts in fermentation of all three aromatic amino acids, following removal of the amino group by transamination. In Methanococcus maripaludis, by contrast, IOR acts in the opposite direction, in pathways of amino acid biosynthesis from phenylacetate, indoleacetate, and p-hydroxyphenylacetate. In M. maripaludis and many other species, iorA and iorB are found next to an apparent phenylacetate-CoA ligase.
Probab=27.55 E-value=14 Score=25.01 Aligned_cols=18 Identities=22% Similarity=0.375 Sum_probs=14.9
Q ss_pred cCCCCceecCCCCCeEEE
Q 035423 5 LKPGDVIQCRECGYRILY 22 (35)
Q Consensus 5 lk~~~~irC~~CG~RIly 22 (35)
+...++.-|+-|+||.++
T Consensus 351 ~~~r~~~~C~GCp~~~~~ 368 (595)
T TIGR03336 351 LPVRPPSLCAGCPHRATF 368 (595)
T ss_pred cCCCCCCCCCCCCChHHH
Confidence 455678899999999876
No 406
>TIGR01591 Fdh-alpha formate dehydrogenase, alpha subunit, archaeal-type. This model is well-defined, with only a single fragmentary sequence falling between trusted and noise. The alpha subunit of a version of nitrate reductase is closely related.
Probab=27.54 E-value=95 Score=20.90 Aligned_cols=22 Identities=27% Similarity=0.573 Sum_probs=16.9
Q ss_pred cCCC--CCeEEEeecCCceEEEEe
Q 035423 13 CREC--GYRILYKKRTRRIVQYEA 34 (35)
Q Consensus 13 C~~C--G~RIlyK~R~~~~~~~~A 34 (35)
|+.| |+-|....|..+++.++.
T Consensus 3 C~~C~~~C~i~v~~~~g~i~rv~~ 26 (671)
T TIGR01591 3 CPYCGVGCSLNLVVKDGKIVRVEP 26 (671)
T ss_pred CCCCCCCCCEEEEEECCEEEEeec
Confidence 7777 578888888888877764
No 407
>PF10891 DUF2719: Protein of unknown function (DUF2719); InterPro: IPR020122 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf56; it is a family of uncharacterised viral proteins.
Probab=27.48 E-value=37 Score=18.60 Aligned_cols=12 Identities=25% Similarity=0.833 Sum_probs=9.8
Q ss_pred CCCceecCCCCC
Q 035423 7 PGDVIQCRECGY 18 (35)
Q Consensus 7 ~~~~irC~~CG~ 18 (35)
..+.|.|+.|.+
T Consensus 19 ~~qVV~C~~C~F 30 (81)
T PF10891_consen 19 ENQVVYCPKCYF 30 (81)
T ss_pred cCCEEEccccce
Confidence 456899999976
No 408
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=27.44 E-value=28 Score=17.65 Aligned_cols=12 Identities=33% Similarity=0.719 Sum_probs=8.6
Q ss_pred ceecCCCCCeEE
Q 035423 10 VIQCRECGYRIL 21 (35)
Q Consensus 10 ~irC~~CG~RIl 21 (35)
.--|++||..++
T Consensus 35 ~~pC~fCg~~l~ 46 (57)
T PF06221_consen 35 LGPCPFCGTPLL 46 (57)
T ss_pred cCcCCCCCCccc
Confidence 356889987655
No 409
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=27.43 E-value=29 Score=22.61 Aligned_cols=9 Identities=22% Similarity=0.881 Sum_probs=7.1
Q ss_pred ceecCCCCC
Q 035423 10 VIQCRECGY 18 (35)
Q Consensus 10 ~irC~~CG~ 18 (35)
-++|++||.
T Consensus 226 R~~C~~Cg~ 234 (309)
T PRK03564 226 RVKCSNCEQ 234 (309)
T ss_pred CccCCCCCC
Confidence 468899986
No 410
>cd02762 MopB_1 The MopB_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=27.39 E-value=90 Score=20.64 Aligned_cols=23 Identities=13% Similarity=0.362 Sum_probs=15.9
Q ss_pred ecCCCC--CeEEEeecCCceEEEEe
Q 035423 12 QCRECG--YRILYKKRTRRIVQYEA 34 (35)
Q Consensus 12 rC~~CG--~RIlyK~R~~~~~~~~A 34 (35)
-|+.|+ +.|....+..+++.++.
T Consensus 3 ~C~~C~~~C~i~v~v~~g~ivkv~g 27 (539)
T cd02762 3 ACILCEANCGLVVTVEDGRVASIRG 27 (539)
T ss_pred cCCCcccCCCeEEEEECCEEEEEEC
Confidence 377775 77888777777766653
No 411
>PRK09401 reverse gyrase; Reviewed
Probab=27.32 E-value=27 Score=26.22 Aligned_cols=11 Identities=36% Similarity=0.757 Sum_probs=8.2
Q ss_pred ceecCCCCCeE
Q 035423 10 VIQCRECGYRI 20 (35)
Q Consensus 10 ~irC~~CG~RI 20 (35)
.--||+||..|
T Consensus 7 ~~~cpnc~g~i 17 (1176)
T PRK09401 7 KNSCPNCGGDI 17 (1176)
T ss_pred cccCCCCCCcC
Confidence 34699999765
No 412
>PRK11865 pyruvate ferredoxin oxidoreductase subunit beta; Provisional
Probab=27.10 E-value=8.4 Score=24.74 Aligned_cols=14 Identities=29% Similarity=0.622 Sum_probs=10.9
Q ss_pred ceecCCCCCeEEEe
Q 035423 10 VIQCRECGYRILYK 23 (35)
Q Consensus 10 ~irC~~CG~RIlyK 23 (35)
.--|+-||+++.++
T Consensus 18 ~~~C~GCg~~~~~~ 31 (299)
T PRK11865 18 HRACAGCGAAIAMR 31 (299)
T ss_pred CCCCcCCCcHHHHH
Confidence 34699999997665
No 413
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=27.01 E-value=21 Score=22.79 Aligned_cols=17 Identities=41% Similarity=0.849 Sum_probs=10.9
Q ss_pred CCCceecCCCCCeEEEee
Q 035423 7 PGDVIQCRECGYRILYKK 24 (35)
Q Consensus 7 ~~~~irC~~CG~RIlyK~ 24 (35)
.+--++||.|+.- +|++
T Consensus 24 ~~~~~~c~~c~~~-~~~~ 40 (292)
T PRK05654 24 EGLWTKCPSCGQV-LYRK 40 (292)
T ss_pred CCCeeECCCccch-hhHH
Confidence 3346788888875 4443
No 414
>TIGR02116 toxin_Txe_YoeB toxin-antitoxin system, toxin component, Txe/YoeB family. The Axe-Txe pair in Enterococcus faecium and the homologous YefM-YoeB pair in Escherichia coli have been shown to act as an antitoxin-toxin pair. This model describes the toxin component. Nearly every example found is next to an identifiable antitoxin, as indicated by matches to TIGR01552 and/or pfam02604.
Probab=26.88 E-value=95 Score=15.52 Aligned_cols=24 Identities=17% Similarity=0.253 Sum_probs=18.0
Q ss_pred eecCCC-CCeEEEeecCCceEEEEe
Q 035423 11 IQCREC-GYRILYKKRTRRIVQYEA 34 (35)
Q Consensus 11 irC~~C-G~RIlyK~R~~~~~~~~A 34 (35)
-+|.-- .|||+|..-.+.+.-+.+
T Consensus 52 ~r~rig~dyRIIY~i~~~~~~i~~~ 76 (80)
T TIGR02116 52 WSRRITDEHRLVYRVTDDEVLILAA 76 (80)
T ss_pred EEEEcCCCeEEEEEEECCEEEEEEe
Confidence 477766 699999988877666654
No 415
>cd02755 MopB_Thiosulfate-R-like The MopB_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Members of the MopB_Thiosulfate-R-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=26.71 E-value=90 Score=20.17 Aligned_cols=22 Identities=27% Similarity=0.575 Sum_probs=16.3
Q ss_pred ecCCC--CCeEEEeecCCceEEEE
Q 035423 12 QCREC--GYRILYKKRTRRIVQYE 33 (35)
Q Consensus 12 rC~~C--G~RIlyK~R~~~~~~~~ 33 (35)
-|++| |+-|+...+.-+++.++
T Consensus 4 ~C~~C~~~C~l~v~v~dG~v~~v~ 27 (454)
T cd02755 4 ICEMCSSRCGILARVEDGRVVKID 27 (454)
T ss_pred cCcCcccCCCcEEEEECCEEEEEE
Confidence 58888 57788887777776665
No 416
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=26.67 E-value=29 Score=21.09 Aligned_cols=12 Identities=33% Similarity=1.010 Sum_probs=9.9
Q ss_pred ecCCCCCeEEEe
Q 035423 12 QCRECGYRILYK 23 (35)
Q Consensus 12 rC~~CG~RIlyK 23 (35)
-|+.||..+.+.
T Consensus 95 FC~~CGS~L~~~ 106 (191)
T PRK05417 95 ACKECGVHMYGR 106 (191)
T ss_pred eCCCCCCccccc
Confidence 499999997664
No 417
>TIGR02174 CXXU_selWTH selT/selW/selH selenoprotein domain. This model represents a domain found in both bacteria and animals, including animal proteins SelT, SelW, and SelH, all of which are selenoproteins. In a CXXC motif near the N-terminus of the domain, selenocysteine may replace the second Cys. Proteins with this domain may include an insert of about 70 amino acids. This model is broader than the current SelW model pfam05169 in Pfam.
Probab=26.58 E-value=30 Score=17.47 Aligned_cols=9 Identities=44% Similarity=1.291 Sum_probs=6.5
Q ss_pred eecCCCCCe
Q 035423 11 IQCRECGYR 19 (35)
Q Consensus 11 irC~~CG~R 19 (35)
.-|..|||+
T Consensus 4 eyC~~C~y~ 12 (72)
T TIGR02174 4 EYCGSCGYK 12 (72)
T ss_pred EECCCCCCh
Confidence 458899954
No 418
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 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 proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=26.57 E-value=57 Score=16.60 Aligned_cols=13 Identities=38% Similarity=0.810 Sum_probs=9.1
Q ss_pred CceecCCCCCeEE
Q 035423 9 DVIQCRECGYRIL 21 (35)
Q Consensus 9 ~~irC~~CG~RIl 21 (35)
.-+.|+-||.+-+
T Consensus 14 tH~~CrRCG~~sy 26 (55)
T PF01907_consen 14 THTLCRRCGRRSY 26 (55)
T ss_dssp SEEE-TTTSSEEE
T ss_pred cEeeecccCCeee
Confidence 5688999998843
No 419
>PF01930 Cas_Cas4: Domain of unknown function DUF83; InterPro: IPR022765 This entry represents an uncharacterised domain found in several proteins, including DNA replication helicase Dna2, clustered regularly interspaced short palindromic repeats (CRISPR)-associated exonuclease Cas4 and putative RecB family exonuclease proteins.
Probab=26.57 E-value=40 Score=18.56 Aligned_cols=12 Identities=42% Similarity=1.132 Sum_probs=9.1
Q ss_pred CCceecCCCCCe
Q 035423 8 GDVIQCRECGYR 19 (35)
Q Consensus 8 ~~~irC~~CG~R 19 (35)
...-+|..|+|+
T Consensus 146 ~~~~~C~~C~y~ 157 (162)
T PF01930_consen 146 ENSKKCRRCSYR 157 (162)
T ss_pred CCCCCCCCCCCc
Confidence 334589999987
No 420
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=26.49 E-value=32 Score=13.45 Aligned_cols=7 Identities=43% Similarity=1.241 Sum_probs=5.0
Q ss_pred ecCCCCC
Q 035423 12 QCRECGY 18 (35)
Q Consensus 12 rC~~CG~ 18 (35)
+|-+||-
T Consensus 2 ~C~~C~~ 8 (18)
T PF00098_consen 2 KCFNCGE 8 (18)
T ss_dssp BCTTTSC
T ss_pred cCcCCCC
Confidence 6788874
No 421
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=26.44 E-value=39 Score=18.81 Aligned_cols=10 Identities=40% Similarity=0.996 Sum_probs=7.9
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
=|.|++||..
T Consensus 80 yVlC~~C~sp 89 (110)
T smart00653 80 YVLCPECGSP 89 (110)
T ss_pred cEECCCCCCC
Confidence 3889999874
No 422
>cd04792 LanM-like LanM-like proteins. LanM is a bifunctional enzyme, involved in the synthesis of class II lantibiotics. It is responsible for both the dehydration and the cyclization of the precursor-peptide during lantibiotic synthesis. The C-terminal domain shows similarity to LanC, the cyclase component of the lan operon, but the N terminus seems to be unrelated to the dehydratase, LanB.
Probab=26.34 E-value=36 Score=23.56 Aligned_cols=12 Identities=33% Similarity=0.780 Sum_probs=10.0
Q ss_pred CCeEEEeecCCc
Q 035423 17 GYRILYKKRTRR 28 (35)
Q Consensus 17 G~RIlyK~R~~~ 28 (35)
|.+|+||+|+-.
T Consensus 113 g~kivYKPr~l~ 124 (825)
T cd04792 113 GLKLVYKPRSLS 124 (825)
T ss_pred CCEEEECCCCch
Confidence 789999999753
No 423
>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=25.90 E-value=50 Score=14.46 Aligned_cols=11 Identities=36% Similarity=0.921 Sum_probs=5.5
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
...+||.||-+
T Consensus 12 ~kY~Cp~C~~~ 22 (30)
T PF04438_consen 12 AKYRCPRCGAR 22 (30)
T ss_dssp ESEE-TTT--E
T ss_pred CEEECCCcCCc
Confidence 34688888865
No 424
>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=25.82 E-value=42 Score=13.32 Aligned_cols=9 Identities=44% Similarity=1.232 Sum_probs=6.6
Q ss_pred eecCCCCCe
Q 035423 11 IQCRECGYR 19 (35)
Q Consensus 11 irC~~CG~R 19 (35)
-.|..|+-.
T Consensus 2 ~~C~~C~~~ 10 (27)
T PF13912_consen 2 FECDECGKT 10 (27)
T ss_dssp EEETTTTEE
T ss_pred CCCCccCCc
Confidence 478999854
No 425
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=25.77 E-value=32 Score=19.41 Aligned_cols=10 Identities=30% Similarity=0.836 Sum_probs=7.6
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
.-||.+||..
T Consensus 88 ~~rC~nCG~~ 97 (98)
T PF10164_consen 88 ERRCSNCGAT 97 (98)
T ss_pred ccccCCCCcc
Confidence 4689999863
No 426
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.50 E-value=32 Score=18.90 Aligned_cols=13 Identities=23% Similarity=0.741 Sum_probs=9.7
Q ss_pred ecCCCCCeEEEee
Q 035423 12 QCRECGYRILYKK 24 (35)
Q Consensus 12 rC~~CG~RIlyK~ 24 (35)
-||+||.-++-..
T Consensus 43 ~CPnCGGelv~RP 55 (84)
T COG3813 43 LCPNCGGELVARP 55 (84)
T ss_pred cCCCCCchhhcCc
Confidence 5999998866443
No 427
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=25.32 E-value=33 Score=20.22 Aligned_cols=11 Identities=27% Similarity=0.821 Sum_probs=8.3
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
..-+||.||..
T Consensus 129 ~~p~C~~Cgg~ 139 (224)
T cd01412 129 ELPRCPKCGGL 139 (224)
T ss_pred CCCCCCCCCCc
Confidence 34689999975
No 428
>COG1856 Uncharacterized homolog of biotin synthetase [Function unknown]
Probab=25.28 E-value=8.1 Score=25.16 Aligned_cols=13 Identities=31% Similarity=0.795 Sum_probs=10.3
Q ss_pred ceecCCCCCeEEE
Q 035423 10 VIQCRECGYRILY 22 (35)
Q Consensus 10 ~irC~~CG~RIly 22 (35)
...|++||.++|.
T Consensus 22 ~lnC~HCg~~~L~ 34 (275)
T COG1856 22 SLNCPHCGRHYLE 34 (275)
T ss_pred EecChHHHHHHHH
Confidence 4679999988763
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=25.08 E-value=31 Score=23.62 Aligned_cols=12 Identities=33% Similarity=1.024 Sum_probs=8.7
Q ss_pred CCceecCCCCCe
Q 035423 8 GDVIQCRECGYR 19 (35)
Q Consensus 8 ~~~irC~~CG~R 19 (35)
+..-.||.||.+
T Consensus 530 ~~~~~CP~CGs~ 541 (555)
T cd01675 530 GEGFKCPKCGSE 541 (555)
T ss_pred CCCCCCcCCCCc
Confidence 344689999965
No 430
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=25.05 E-value=34 Score=18.09 Aligned_cols=10 Identities=30% Similarity=0.796 Sum_probs=7.8
Q ss_pred CceecCCCCC
Q 035423 9 DVIQCRECGY 18 (35)
Q Consensus 9 ~~irC~~CG~ 18 (35)
...|||.|+-
T Consensus 43 ~VArCPSCSL 52 (67)
T COG5216 43 VVARCPSCSL 52 (67)
T ss_pred eEEEcCCceE
Confidence 4569999984
No 431
>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=24.99 E-value=27 Score=22.29 Aligned_cols=12 Identities=25% Similarity=0.678 Sum_probs=8.2
Q ss_pred CceecCCCCCeE
Q 035423 9 DVIQCRECGYRI 20 (35)
Q Consensus 9 ~~irC~~CG~RI 20 (35)
--++||+||.-|
T Consensus 25 ~~~~c~~c~~~~ 36 (285)
T TIGR00515 25 VWTKCPKCGQVL 36 (285)
T ss_pred CeeECCCCcchh
Confidence 357888887653
No 432
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=24.69 E-value=46 Score=15.25 Aligned_cols=11 Identities=36% Similarity=0.948 Sum_probs=9.0
Q ss_pred ceecCCCCCeE
Q 035423 10 VIQCRECGYRI 20 (35)
Q Consensus 10 ~irC~~CG~RI 20 (35)
+..|++||..-
T Consensus 12 ~f~C~~C~~~F 22 (39)
T smart00154 12 GFKCRHCGNLF 22 (39)
T ss_pred CeECCccCCcc
Confidence 78999999754
No 433
>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=24.59 E-value=33 Score=15.62 Aligned_cols=7 Identities=43% Similarity=1.246 Sum_probs=4.4
Q ss_pred ecCCCCC
Q 035423 12 QCRECGY 18 (35)
Q Consensus 12 rC~~CG~ 18 (35)
.|+.||.
T Consensus 3 ~C~~Cg~ 9 (36)
T PF05191_consen 3 ICPKCGR 9 (36)
T ss_dssp EETTTTE
T ss_pred CcCCCCC
Confidence 4777773
No 434
>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=24.50 E-value=33 Score=19.45 Aligned_cols=9 Identities=44% Similarity=1.147 Sum_probs=7.0
Q ss_pred eecCCCCCe
Q 035423 11 IQCRECGYR 19 (35)
Q Consensus 11 irC~~CG~R 19 (35)
|.|+.||..
T Consensus 94 VlC~~C~sp 102 (125)
T PF01873_consen 94 VLCPECGSP 102 (125)
T ss_dssp SSCTSTSSS
T ss_pred EEcCCCCCC
Confidence 778888863
No 435
>KOG3456 consensus NADH:ubiquinone oxidoreductase, NDUFS6/13 kDa subunit [Energy production and conversion]
Probab=24.30 E-value=35 Score=19.88 Aligned_cols=13 Identities=31% Similarity=0.580 Sum_probs=9.9
Q ss_pred CCCceecCCCCCe
Q 035423 7 PGDVIQCRECGYR 19 (35)
Q Consensus 7 ~~~~irC~~CG~R 19 (35)
.-.+-.|.|||-|
T Consensus 101 k~~~~~CgYCGlr 113 (120)
T KOG3456|consen 101 KPGPHICGYCGLR 113 (120)
T ss_pred CCCCcccccchhh
Confidence 3445789999988
No 436
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=24.15 E-value=56 Score=14.34 Aligned_cols=10 Identities=40% Similarity=0.936 Sum_probs=7.6
Q ss_pred cCCCCCeEEE
Q 035423 13 CRECGYRILY 22 (35)
Q Consensus 13 C~~CG~RIly 22 (35)
|..||--|..
T Consensus 6 C~~CGe~I~~ 15 (36)
T PF01258_consen 6 CEDCGEPIPE 15 (36)
T ss_dssp -TTTSSBEEH
T ss_pred ccccCChHHH
Confidence 9999998864
No 437
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=24.15 E-value=57 Score=19.44 Aligned_cols=14 Identities=14% Similarity=0.434 Sum_probs=10.9
Q ss_pred CCCceecCCCCCeE
Q 035423 7 PGDVIQCRECGYRI 20 (35)
Q Consensus 7 ~~~~irC~~CG~RI 20 (35)
.....||.||+.-+
T Consensus 131 ~~~~~rC~YCe~~~ 144 (152)
T PRK00893 131 EPIKLRCKYCEKEF 144 (152)
T ss_pred CCCEEEeeCCCCEe
Confidence 44578999999864
No 438
>PRK02048 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Provisional
Probab=23.95 E-value=46 Score=23.85 Aligned_cols=18 Identities=33% Similarity=0.748 Sum_probs=13.4
Q ss_pred ccCCCCceecCCCCCeEEE
Q 035423 4 TLKPGDVIQCRECGYRILY 22 (35)
Q Consensus 4 ~lk~~~~irC~~CG~RIly 22 (35)
.+...+=|.||.||-- ||
T Consensus 512 R~sKTEyISCPsCGRT-Lf 529 (611)
T PRK02048 512 RTSKTEYISCPGCGRT-LY 529 (611)
T ss_pred ccccceEEECCCCCcc-hh
Confidence 3556778999999954 54
No 439
>COG4307 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.81 E-value=48 Score=22.23 Aligned_cols=15 Identities=27% Similarity=0.968 Sum_probs=12.0
Q ss_pred eecCCCCCeEEEeec
Q 035423 11 IQCRECGYRILYKKR 25 (35)
Q Consensus 11 irC~~CG~RIlyK~R 25 (35)
..|+.||-++.|-.+
T Consensus 4 FhC~~CgQ~v~FeN~ 18 (349)
T COG4307 4 FHCPNCGQRVAFENS 18 (349)
T ss_pred ccCCCCCCeeeecch
Confidence 579999999887643
No 440
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=23.76 E-value=43 Score=16.49 Aligned_cols=12 Identities=25% Similarity=0.634 Sum_probs=7.7
Q ss_pred CCCceecCCCCC
Q 035423 7 PGDVIQCRECGY 18 (35)
Q Consensus 7 ~~~~irC~~CG~ 18 (35)
..++|+...|||
T Consensus 21 ~~~PV~s~~C~H 32 (57)
T PF11789_consen 21 FEDPVKSKKCGH 32 (57)
T ss_dssp -SSEEEESSS--
T ss_pred hhCCcCcCCCCC
Confidence 457899999998
No 441
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=23.54 E-value=35 Score=21.82 Aligned_cols=10 Identities=40% Similarity=1.002 Sum_probs=7.6
Q ss_pred eecCCCCCeE
Q 035423 11 IQCRECGYRI 20 (35)
Q Consensus 11 irC~~CG~RI 20 (35)
..||+||.--
T Consensus 2 ~~CpeCg~~~ 11 (285)
T COG1405 2 MSCPECGSTN 11 (285)
T ss_pred CCCCCCCCcc
Confidence 4699999763
No 442
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.46 E-value=42 Score=20.06 Aligned_cols=12 Identities=25% Similarity=0.797 Sum_probs=9.6
Q ss_pred CCceecCCCCCe
Q 035423 8 GDVIQCRECGYR 19 (35)
Q Consensus 8 ~~~irC~~CG~R 19 (35)
...+-||-||+-
T Consensus 30 rgLv~CPvCgs~ 41 (142)
T COG5319 30 RGLVTCPVCGST 41 (142)
T ss_pred cCceeCCCCCcH
Confidence 456899999984
No 443
>cd01411 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=23.43 E-value=43 Score=20.09 Aligned_cols=10 Identities=20% Similarity=0.205 Sum_probs=7.7
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
.-+|+.||..
T Consensus 136 ~p~C~~Cgg~ 145 (225)
T cd01411 136 SPYHAKCGGV 145 (225)
T ss_pred CCCCCCCCCE
Confidence 3579999975
No 444
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=23.40 E-value=31 Score=23.62 Aligned_cols=17 Identities=29% Similarity=0.761 Sum_probs=13.7
Q ss_pred cccCCCCceecCCCCCe
Q 035423 3 NTLKPGDVIQCRECGYR 19 (35)
Q Consensus 3 ~~lk~~~~irC~~CG~R 19 (35)
..|...|+-+||.||-.
T Consensus 277 e~L~g~d~W~CpkC~~k 293 (415)
T COG5533 277 EKLEGKDAWRCPKCGRK 293 (415)
T ss_pred HhhcCcccccCchhccc
Confidence 34778899999999954
No 445
>PTZ00033 60S ribosomal protein L24; Provisional
Probab=23.38 E-value=36 Score=19.87 Aligned_cols=11 Identities=18% Similarity=0.549 Sum_probs=8.6
Q ss_pred ceecCCCCCeE
Q 035423 10 VIQCRECGYRI 20 (35)
Q Consensus 10 ~irC~~CG~RI 20 (35)
...|-+||+.|
T Consensus 3 ~~~C~Fsg~~I 13 (125)
T PTZ00033 3 TIACEFSHFAV 13 (125)
T ss_pred eeEecCcCCcc
Confidence 35799999886
No 446
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=23.31 E-value=1.1e+02 Score=17.48 Aligned_cols=9 Identities=33% Similarity=0.977 Sum_probs=6.4
Q ss_pred eecCCCCCe
Q 035423 11 IQCRECGYR 19 (35)
Q Consensus 11 irC~~CG~R 19 (35)
.+||.||..
T Consensus 87 ~~CP~C~s~ 95 (115)
T COG0375 87 YRCPKCGSI 95 (115)
T ss_pred eECCCCCCC
Confidence 349999854
No 447
>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=23.26 E-value=66 Score=18.08 Aligned_cols=15 Identities=20% Similarity=0.408 Sum_probs=10.6
Q ss_pred ceecCCCCCeEEEeec
Q 035423 10 VIQCRECGYRILYKKR 25 (35)
Q Consensus 10 ~irC~~CG~RIlyK~R 25 (35)
..||+.|+.. |-+..
T Consensus 91 ~sRC~~CN~~-L~~v~ 105 (147)
T PF01927_consen 91 FSRCPKCNGP-LRPVS 105 (147)
T ss_pred CCccCCCCcE-eeech
Confidence 5799999995 54443
No 448
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.25 E-value=32 Score=23.48 Aligned_cols=14 Identities=21% Similarity=0.529 Sum_probs=9.3
Q ss_pred cCCCCc--eecCCCCC
Q 035423 5 LKPGDV--IQCRECGY 18 (35)
Q Consensus 5 lk~~~~--irC~~CG~ 18 (35)
|..+.. .+||||--
T Consensus 367 LS~ng~~sfKCPYCP~ 382 (394)
T KOG2817|consen 367 LSKNGSQSFKCPYCPV 382 (394)
T ss_pred HhhCCCeeeeCCCCCc
Confidence 334444 89999964
No 449
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=23.24 E-value=37 Score=22.13 Aligned_cols=8 Identities=50% Similarity=1.107 Sum_probs=3.5
Q ss_pred eecCCCCC
Q 035423 11 IQCRECGY 18 (35)
Q Consensus 11 irC~~CG~ 18 (35)
-+||.||.
T Consensus 15 g~cp~c~~ 22 (372)
T cd01121 15 GKCPECGE 22 (372)
T ss_pred EECcCCCC
Confidence 03555554
No 450
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=23.24 E-value=62 Score=16.20 Aligned_cols=15 Identities=20% Similarity=0.574 Sum_probs=10.8
Q ss_pred CCCceecCCCCCeEE
Q 035423 7 PGDVIQCRECGYRIL 21 (35)
Q Consensus 7 ~~~~irC~~CG~RIl 21 (35)
+..-..|+.|+-.|.
T Consensus 4 ks~Ra~Ck~C~~~I~ 18 (82)
T PF00645_consen 4 KSGRAKCKGCKKKIA 18 (82)
T ss_dssp SSSTEBETTTSCBE-
T ss_pred CCCCccCcccCCcCC
Confidence 345578999998874
No 451
>PRK05776 DNA topoisomerase I; Provisional
Probab=23.14 E-value=58 Score=22.93 Aligned_cols=11 Identities=36% Similarity=0.842 Sum_probs=9.1
Q ss_pred ceecCCCCCeE
Q 035423 10 VIQCRECGYRI 20 (35)
Q Consensus 10 ~irC~~CG~RI 20 (35)
...||.||...
T Consensus 596 ~~~Cp~Cg~~l 606 (670)
T PRK05776 596 VGKCKICGREA 606 (670)
T ss_pred CCcCCCCCCcc
Confidence 45899999876
No 452
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=23.13 E-value=34 Score=21.14 Aligned_cols=11 Identities=27% Similarity=0.537 Sum_probs=7.9
Q ss_pred ecCCCCCeEEE
Q 035423 12 QCRECGYRILY 22 (35)
Q Consensus 12 rC~~CG~RIly 22 (35)
-|+.||.....
T Consensus 101 fC~~CG~~~~~ 111 (256)
T PRK00241 101 FCGYCGHPMHP 111 (256)
T ss_pred cccccCCCCee
Confidence 58888887543
No 453
>PTZ00074 60S ribosomal protein L34; Provisional
Probab=23.13 E-value=48 Score=19.49 Aligned_cols=15 Identities=27% Similarity=0.647 Sum_probs=11.2
Q ss_pred CCCCceecCCCCCeE
Q 035423 6 KPGDVIQCRECGYRI 20 (35)
Q Consensus 6 k~~~~irC~~CG~RI 20 (35)
+....-+|..||-++
T Consensus 37 K~~~~pkC~~cg~~L 51 (135)
T PTZ00074 37 KKSSGPKCGDCGKVL 51 (135)
T ss_pred cCCCCCCCCCCCCcc
Confidence 345667899999874
No 454
>PHA02325 hypothetical protein
Probab=23.02 E-value=63 Score=17.31 Aligned_cols=13 Identities=46% Similarity=0.905 Sum_probs=9.6
Q ss_pred CceecCCCCCeEE
Q 035423 9 DVIQCRECGYRIL 21 (35)
Q Consensus 9 ~~irC~~CG~RIl 21 (35)
+.-.||.||-+-|
T Consensus 2 ~~k~CPkC~A~Wl 14 (72)
T PHA02325 2 DTKICPKCGARWL 14 (72)
T ss_pred CccccCccCCEeE
Confidence 3457999998754
No 455
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=22.89 E-value=84 Score=15.29 Aligned_cols=18 Identities=11% Similarity=0.429 Sum_probs=14.4
Q ss_pred CCceecCCCCCeEEEeec
Q 035423 8 GDVIQCRECGYRILYKKR 25 (35)
Q Consensus 8 ~~~irC~~CG~RIlyK~R 25 (35)
...+||-.|+.=|-|+.|
T Consensus 29 ~~klrCGaCs~vl~~s~~ 46 (46)
T PF11331_consen 29 QQKLRCGACSEVLSFSLP 46 (46)
T ss_pred eeEEeCCCCceeEEEecC
Confidence 457899999998888754
No 456
>PRK07219 DNA topoisomerase I; Validated
Probab=22.86 E-value=52 Score=23.58 Aligned_cols=16 Identities=25% Similarity=0.696 Sum_probs=12.8
Q ss_pred ceecCCCCCeEEEeec
Q 035423 10 VIQCRECGYRILYKKR 25 (35)
Q Consensus 10 ~irC~~CG~RIlyK~R 25 (35)
...||.||..++++.-
T Consensus 602 ~~~CP~Cg~~l~~r~~ 617 (822)
T PRK07219 602 IGKCPECGGDLIIIRT 617 (822)
T ss_pred cCcCCCCCCcceeeec
Confidence 4689999998887753
No 457
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=22.77 E-value=47 Score=19.58 Aligned_cols=11 Identities=36% Similarity=0.869 Sum_probs=8.5
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
..-+||.||..
T Consensus 132 ~~p~C~~Cg~~ 142 (218)
T cd01407 132 EVPRCPKCGGL 142 (218)
T ss_pred CCCcCCCCCCc
Confidence 45689999976
No 458
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.76 E-value=36 Score=21.13 Aligned_cols=12 Identities=25% Similarity=0.639 Sum_probs=9.2
Q ss_pred ceecCCCCCeEE
Q 035423 10 VIQCRECGYRIL 21 (35)
Q Consensus 10 ~irC~~CG~RIl 21 (35)
...||-|+.+|=
T Consensus 167 ~~~CP~C~kkIt 178 (187)
T KOG0320|consen 167 TNKCPTCRKKIT 178 (187)
T ss_pred CCCCCCcccccc
Confidence 568999998763
No 459
>TIGR00433 bioB biotin synthetase. Catalyzes the last step of the biotin biosynthesis pathway.
Probab=22.72 E-value=31 Score=20.69 Aligned_cols=16 Identities=25% Similarity=0.389 Sum_probs=12.5
Q ss_pred CCceecCCCCCeEEEe
Q 035423 8 GDVIQCRECGYRILYK 23 (35)
Q Consensus 8 ~~~irC~~CG~RIlyK 23 (35)
+=+.+|.+|+....++
T Consensus 38 ~C~~~C~fC~~~~~~~ 53 (296)
T TIGR00433 38 GCPEDCKYCSQSSRSK 53 (296)
T ss_pred CCCCCCcCCCCcccCC
Confidence 3467899999988774
No 460
>PF10238 Eapp_C: E2F-associated phosphoprotein; InterPro: IPR019370 This entry represents E2F binding proteins. E2F transcription factors play an essential role in cell proliferation and apoptosis and their activity is frequently deregulated in human cancers. E2F activity is regulated by a variety of mechanisms, frequently mediated by proteins binding to individual members or a subgroup of the family. E2F-associated phosphoprotein (EAPP)interacts with a subset of E2F factors and influences E2F-dependent promoter activity. EAPP is present throughout the cell cycle but disappears during mitosis [].
Probab=22.61 E-value=54 Score=19.06 Aligned_cols=20 Identities=15% Similarity=0.463 Sum_probs=15.6
Q ss_pred CCCCceecCCCCCeEEEeec
Q 035423 6 KPGDVIQCRECGYRILYKKR 25 (35)
Q Consensus 6 k~~~~irC~~CG~RIlyK~R 25 (35)
...-+|.|..|+.-|=+--.
T Consensus 105 e~yhPV~Cs~C~TeVaV~D~ 124 (136)
T PF10238_consen 105 ETYHPVKCSECSTEVAVYDK 124 (136)
T ss_pred ccEeceecccCCCEEEEEec
Confidence 35668999999998876653
No 461
>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=22.54 E-value=64 Score=22.29 Aligned_cols=14 Identities=29% Similarity=0.631 Sum_probs=10.7
Q ss_pred eecCCCCCeEEEee
Q 035423 11 IQCRECGYRILYKK 24 (35)
Q Consensus 11 irC~~CG~RIlyK~ 24 (35)
..||.||..++.++
T Consensus 575 ~~CP~Cg~~~~~~~ 588 (610)
T TIGR01051 575 QDCPLCGRPMVVKL 588 (610)
T ss_pred CCCCCCCCeeEEEe
Confidence 57999999876433
No 462
>PRK07220 DNA topoisomerase I; Validated
Probab=22.52 E-value=62 Score=23.00 Aligned_cols=15 Identities=20% Similarity=0.749 Sum_probs=11.4
Q ss_pred ceecCCCCCeEEEee
Q 035423 10 VIQCRECGYRILYKK 24 (35)
Q Consensus 10 ~irC~~CG~RIlyK~ 24 (35)
...||.||..++.+.
T Consensus 589 ~~~CP~Cg~~l~~r~ 603 (740)
T PRK07220 589 IGKCPLCGSDLMVRR 603 (740)
T ss_pred ccccccCCCeeeEEe
Confidence 358999998877653
No 463
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=22.45 E-value=42 Score=18.47 Aligned_cols=11 Identities=45% Similarity=0.884 Sum_probs=8.0
Q ss_pred eecCCCCCeEE
Q 035423 11 IQCRECGYRIL 21 (35)
Q Consensus 11 irC~~CG~RIl 21 (35)
-.|..||..||
T Consensus 70 GiCamCGKki~ 80 (90)
T PF10235_consen 70 GICAMCGKKIL 80 (90)
T ss_pred CcccccCCeec
Confidence 36788888775
No 464
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=22.36 E-value=51 Score=18.94 Aligned_cols=10 Identities=40% Similarity=0.969 Sum_probs=7.7
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
=|-|+.||..
T Consensus 97 yVlC~~C~sP 106 (133)
T TIGR00311 97 YVICRECNRP 106 (133)
T ss_pred eEECCCCCCC
Confidence 4789999874
No 465
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=22.29 E-value=35 Score=22.47 Aligned_cols=16 Identities=38% Similarity=0.821 Sum_probs=11.1
Q ss_pred CCCceecCCCCCeEEEe
Q 035423 7 PGDVIQCRECGYRILYK 23 (35)
Q Consensus 7 ~~~~irC~~CG~RIlyK 23 (35)
.+--++||.||.= ||.
T Consensus 25 e~lw~KCp~c~~~-~y~ 40 (294)
T COG0777 25 EGLWTKCPSCGEM-LYR 40 (294)
T ss_pred CCceeECCCccce-eeH
Confidence 3445799999985 443
No 466
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=22.25 E-value=78 Score=15.59 Aligned_cols=13 Identities=23% Similarity=1.124 Sum_probs=9.9
Q ss_pred ceecCCCCCeEEE
Q 035423 10 VIQCRECGYRILY 22 (35)
Q Consensus 10 ~irC~~CG~RIly 22 (35)
.+.|..||..-++
T Consensus 4 ~l~C~dCg~~Fvf 16 (49)
T PF13451_consen 4 TLTCKDCGAEFVF 16 (49)
T ss_pred eEEcccCCCeEEE
Confidence 5789999987554
No 467
>PF01430 HSP33: Hsp33 protein; InterPro: IPR000397 Hsp33 is a molecular chaperone, distinguished from all other known chaperones by its mode of functional regulation. Its activity is redox regulated. Hsp33 is a cytoplasmically localized protein with highly reactive cysteines that respond quickly to changes in the redox environment. Oxidizing conditions like H2O2 cause disulphide bonds to form in Hsp33, a process that leads to the activation of its chaperone function [].; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0005737 cytoplasm; PDB: 1VZY_B 1VQ0_A 1I7F_A 3M7M_X 1XJH_A 1HW7_A.
Probab=22.20 E-value=63 Score=20.00 Aligned_cols=14 Identities=21% Similarity=0.626 Sum_probs=8.4
Q ss_pred CceecCCCCCeEEE
Q 035423 9 DVIQCRECGYRILY 22 (35)
Q Consensus 9 ~~irC~~CG~RIly 22 (35)
-.|.|.+||.+-.|
T Consensus 265 iev~C~fC~~~Y~f 278 (280)
T PF01430_consen 265 IEVTCEFCGKKYRF 278 (280)
T ss_dssp EEEE-TTT--EEEE
T ss_pred EEEEeeCCCCEEEe
Confidence 46899999988655
No 468
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=22.13 E-value=44 Score=16.73 Aligned_cols=8 Identities=38% Similarity=1.032 Sum_probs=6.4
Q ss_pred ecCCCCCe
Q 035423 12 QCRECGYR 19 (35)
Q Consensus 12 rC~~CG~R 19 (35)
.||.||.-
T Consensus 19 ~cp~cG~~ 26 (53)
T PF04135_consen 19 KCPPCGGP 26 (53)
T ss_dssp BBTTTSSB
T ss_pred ccCCCCCC
Confidence 79999964
No 469
>PF04060 FeS: Putative Fe-S cluster; InterPro: IPR007202 These proteins contain a domain with four conserved cysteines that probably form an Fe-S redox cluster.; GO: 0051536 iron-sulfur cluster binding; PDB: 2YCL_A 4DJF_E 4DJD_C 4DJE_C.
Probab=21.96 E-value=42 Score=15.09 Aligned_cols=11 Identities=36% Similarity=0.957 Sum_probs=4.7
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
+..-|-.|||.
T Consensus 3 P~~nCg~CG~~ 13 (35)
T PF04060_consen 3 PGTNCGACGYP 13 (35)
T ss_dssp -S----TTSSS
T ss_pred CCCcCCCCCCc
Confidence 45679999985
No 470
>PRK12495 hypothetical protein; Provisional
Probab=21.87 E-value=34 Score=21.76 Aligned_cols=12 Identities=42% Similarity=0.927 Sum_probs=10.1
Q ss_pred ceecCCCCCeEE
Q 035423 10 VIQCRECGYRIL 21 (35)
Q Consensus 10 ~irC~~CG~RIl 21 (35)
...|+.||.-|.
T Consensus 42 a~hC~~CG~PIp 53 (226)
T PRK12495 42 NAHCDECGDPIF 53 (226)
T ss_pred hhhcccccCccc
Confidence 457999999987
No 471
>KOG3125 consensus Thymidine kinase [Nucleotide transport and metabolism]
Probab=21.84 E-value=56 Score=20.95 Aligned_cols=24 Identities=25% Similarity=0.452 Sum_probs=19.2
Q ss_pred ceecCCCCCeEEEeecCCceEEEE
Q 035423 10 VIQCRECGYRILYKKRTRRIVQYE 33 (35)
Q Consensus 10 ~irC~~CG~RIlyK~R~~~~~~~~ 33 (35)
.++|-+||++-.|-.|...-+.++
T Consensus 165 tavC~~Cg~~a~Ft~R~~~~K~ve 188 (234)
T KOG3125|consen 165 TAVCEECGADARFTLRKTNDKEVE 188 (234)
T ss_pred hhhhhhhcccceeEeeecCCceeE
Confidence 378999999999999987655543
No 472
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=21.75 E-value=52 Score=22.09 Aligned_cols=20 Identities=25% Similarity=0.617 Sum_probs=15.6
Q ss_pred ceecCCCCCeEEEeecCCce
Q 035423 10 VIQCRECGYRILYKKRTRRI 29 (35)
Q Consensus 10 ~irC~~CG~RIlyK~R~~~~ 29 (35)
...||.||..++.|.=+.++
T Consensus 25 ~ffCPaC~~~l~lK~G~~k~ 44 (342)
T COG4469 25 RFFCPACGSQLILKQGLIKI 44 (342)
T ss_pred ccccCCCCCeeeeecCcccc
Confidence 47899999999988654443
No 473
>cd00296 SIR2 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic
Probab=21.75 E-value=41 Score=19.37 Aligned_cols=11 Identities=27% Similarity=0.646 Sum_probs=8.0
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
..-+|+.||..
T Consensus 133 ~~p~C~~C~~~ 143 (222)
T cd00296 133 KPPRCPKCGGL 143 (222)
T ss_pred CCCCCCCCCCc
Confidence 34579999875
No 474
>PRK04351 hypothetical protein; Provisional
Probab=21.65 E-value=1.1e+02 Score=17.68 Aligned_cols=15 Identities=33% Similarity=0.795 Sum_probs=10.1
Q ss_pred CceecCCCCCeEEEe
Q 035423 9 DVIQCRECGYRILYK 23 (35)
Q Consensus 9 ~~irC~~CG~RIlyK 23 (35)
-..+|..||+-++=.
T Consensus 111 y~Y~C~~Cg~~~~r~ 125 (149)
T PRK04351 111 YLYECQSCGQQYLRK 125 (149)
T ss_pred EEEECCCCCCEeeee
Confidence 346888888766543
No 475
>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=21.64 E-value=42 Score=13.73 Aligned_cols=10 Identities=40% Similarity=0.949 Sum_probs=6.7
Q ss_pred ecCCCCCeEE
Q 035423 12 QCRECGYRIL 21 (35)
Q Consensus 12 rC~~CG~RIl 21 (35)
+|..|+..|.
T Consensus 1 ~C~~C~~~i~ 10 (39)
T smart00132 1 KCAGCGKPIR 10 (39)
T ss_pred CccccCCccc
Confidence 5777777654
No 476
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=21.41 E-value=42 Score=23.16 Aligned_cols=9 Identities=33% Similarity=0.973 Sum_probs=7.1
Q ss_pred eecCCCCCe
Q 035423 11 IQCRECGYR 19 (35)
Q Consensus 11 irC~~CG~R 19 (35)
-.||.||.+
T Consensus 539 ~~CP~Cgs~ 547 (579)
T TIGR02487 539 DKCPKCGSH 547 (579)
T ss_pred CcCcCCCCc
Confidence 379999964
No 477
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=21.19 E-value=68 Score=22.86 Aligned_cols=17 Identities=24% Similarity=0.671 Sum_probs=14.1
Q ss_pred CCceecCCCCCeEEEee
Q 035423 8 GDVIQCRECGYRILYKK 24 (35)
Q Consensus 8 ~~~irC~~CG~RIlyK~ 24 (35)
..++-|+.||=|+.+..
T Consensus 138 ~~~~~C~~Cgp~l~l~~ 154 (711)
T TIGR00143 138 AQPIACPRCGPQLNFVS 154 (711)
T ss_pred CCCccCCCCCcEEEEEe
Confidence 47899999999987744
No 478
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=21.00 E-value=47 Score=19.64 Aligned_cols=9 Identities=44% Similarity=1.387 Sum_probs=7.1
Q ss_pred ceecCCCCC
Q 035423 10 VIQCRECGY 18 (35)
Q Consensus 10 ~irC~~CG~ 18 (35)
-++|+.||.
T Consensus 105 yv~C~~c~s 113 (151)
T COG1601 105 YVKCKECGS 113 (151)
T ss_pred eeEeccCCC
Confidence 478999986
No 479
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=20.98 E-value=46 Score=19.89 Aligned_cols=11 Identities=36% Similarity=0.863 Sum_probs=8.3
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
..-+||.||..
T Consensus 135 ~~p~C~~Cgg~ 145 (222)
T cd01413 135 EVPRCPKCGGI 145 (222)
T ss_pred CCCcCCCCCCc
Confidence 34689999975
No 480
>PF03470 zf-XS: XS zinc finger domain; InterPro: IPR005381 This domain is a putative nucleic acid binding zinc finger and is found at the N terminus of proteins that also contain an adjacent XS domain IPR005380 from INTERPRO and in some proteins a C-terminal XH domain IPR005379 from INTERPRO.
Probab=20.90 E-value=43 Score=16.25 Aligned_cols=7 Identities=29% Similarity=0.728 Sum_probs=5.3
Q ss_pred cCCCCCe
Q 035423 13 CRECGYR 19 (35)
Q Consensus 13 C~~CG~R 19 (35)
||+|-.+
T Consensus 1 CP~C~~k 7 (43)
T PF03470_consen 1 CPFCPGK 7 (43)
T ss_pred CCCCCCC
Confidence 8899664
No 481
>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=20.86 E-value=44 Score=22.68 Aligned_cols=19 Identities=37% Similarity=0.679 Sum_probs=13.6
Q ss_pred cCCCCceecCCCCCeEEEee
Q 035423 5 LKPGDVIQCRECGYRILYKK 24 (35)
Q Consensus 5 lk~~~~irC~~CG~RIlyK~ 24 (35)
|...-..||+.|.| ||.|.
T Consensus 293 L~~KrSkRC~~C~h-~L~KP 311 (483)
T PF05502_consen 293 LRTKRSKRCRQCRH-ILSKP 311 (483)
T ss_pred eeceeehhhhcccC-ceECC
Confidence 44555679999987 56664
No 482
>PRK08780 DNA topoisomerase I; Provisional
Probab=20.74 E-value=77 Score=22.75 Aligned_cols=14 Identities=7% Similarity=-0.073 Sum_probs=11.4
Q ss_pred eecCCCCCeEEEee
Q 035423 11 IQCRECGYRILYKK 24 (35)
Q Consensus 11 irC~~CG~RIlyK~ 24 (35)
-.||.||..++.+.
T Consensus 592 G~cP~CG~~l~~r~ 605 (780)
T PRK08780 592 GTDPKSGKPVSVRI 605 (780)
T ss_pred CCCCCCCCEEEEEe
Confidence 38999999987764
No 483
>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=20.61 E-value=83 Score=15.44 Aligned_cols=10 Identities=50% Similarity=0.919 Sum_probs=5.3
Q ss_pred cCCCCCeEEE
Q 035423 13 CRECGYRILY 22 (35)
Q Consensus 13 C~~CG~RIly 22 (35)
|+.||...|-
T Consensus 1 CR~Cgs~~l~ 10 (62)
T PF08421_consen 1 CRICGSSDLK 10 (62)
T ss_dssp -TTTS-E-EE
T ss_pred CCCCCCCccc
Confidence 7889988653
No 484
>cd02757 MopB_Arsenate-R This CD includes the respiratory arsenate reductase, As(V), catalytic subunit (ArrA) and other related proteins. These members belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=20.60 E-value=1.5e+02 Score=19.73 Aligned_cols=23 Identities=17% Similarity=0.407 Sum_probs=16.6
Q ss_pred ecCCCC--CeEEEeecCCceEEEEe
Q 035423 12 QCRECG--YRILYKKRTRRIVQYEA 34 (35)
Q Consensus 12 rC~~CG--~RIlyK~R~~~~~~~~A 34 (35)
-|+.|+ +-|+...+..+++.++.
T Consensus 5 ~C~~C~~~C~l~v~v~dg~v~kv~g 29 (523)
T cd02757 5 TCQGCTAWCGLQAYVEDGRVTKVEG 29 (523)
T ss_pred cCcCCcCCCCeEEEEECCEEEEEEC
Confidence 477776 56888888777777653
No 485
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.59 E-value=43 Score=23.53 Aligned_cols=9 Identities=33% Similarity=0.992 Sum_probs=6.8
Q ss_pred eecCCCCCe
Q 035423 11 IQCRECGYR 19 (35)
Q Consensus 11 irC~~CG~R 19 (35)
-.||.||..
T Consensus 573 ~~CP~CG~~ 581 (618)
T PRK14704 573 NECPSCGNE 581 (618)
T ss_pred ccCcCCCCC
Confidence 379999963
No 486
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.56 E-value=34 Score=22.30 Aligned_cols=14 Identities=36% Similarity=0.534 Sum_probs=11.3
Q ss_pred CCCCceecCCCCCe
Q 035423 6 KPGDVIQCRECGYR 19 (35)
Q Consensus 6 k~~~~irC~~CG~R 19 (35)
-.++.+-||.|+|-
T Consensus 58 ~fY~VvvCP~C~yA 71 (267)
T COG1655 58 YFYDVVVCPICYYA 71 (267)
T ss_pred ceeEEEEcchhhHH
Confidence 45678999999974
No 487
>KOG3940 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.53 E-value=58 Score=22.00 Aligned_cols=11 Identities=45% Similarity=1.126 Sum_probs=9.2
Q ss_pred CceecCCCCCe
Q 035423 9 DVIQCRECGYR 19 (35)
Q Consensus 9 ~~irC~~CG~R 19 (35)
+.+.||+||-|
T Consensus 321 s~~~Cp~cg~r 331 (351)
T KOG3940|consen 321 SYVQCPHCGRR 331 (351)
T ss_pred CcccCcccccc
Confidence 45899999987
No 488
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=20.40 E-value=57 Score=19.60 Aligned_cols=10 Identities=40% Similarity=1.072 Sum_probs=7.3
Q ss_pred ceecCCCCCe
Q 035423 10 VIQCRECGYR 19 (35)
Q Consensus 10 ~irC~~CG~R 19 (35)
=|.|++||.-
T Consensus 98 yV~C~~C~~p 107 (201)
T PRK12336 98 YVICSECGLP 107 (201)
T ss_pred eEECCCCCCC
Confidence 4788888863
No 489
>PRK09129 NADH dehydrogenase subunit G; Validated
Probab=20.26 E-value=1.5e+02 Score=20.74 Aligned_cols=24 Identities=8% Similarity=0.171 Sum_probs=18.1
Q ss_pred eecCCC--CCeEEEeecCCceEEEEe
Q 035423 11 IQCREC--GYRILYKKRTRRIVQYEA 34 (35)
Q Consensus 11 irC~~C--G~RIlyK~R~~~~~~~~A 34 (35)
--|++| |+.|.+..+..+++.++.
T Consensus 220 t~C~~C~~gC~i~v~v~~g~i~rv~g 245 (776)
T PRK09129 220 SVSPHDSLGSNLVVHVKNNRVMRVVP 245 (776)
T ss_pred ccCCCCCCCCCeEEEEECCEEEEeec
Confidence 359999 678888888777777653
No 490
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=20.23 E-value=45 Score=19.05 Aligned_cols=12 Identities=25% Similarity=0.415 Sum_probs=9.1
Q ss_pred CCceecCCCCCe
Q 035423 8 GDVIQCRECGYR 19 (35)
Q Consensus 8 ~~~irC~~CG~R 19 (35)
++...||+|.++
T Consensus 78 ~~~~~Cp~C~sp 89 (105)
T COG4357 78 GMCGSCPYCQSP 89 (105)
T ss_pred hhcCCCCCcCCC
Confidence 346789999876
No 491
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=20.22 E-value=74 Score=21.81 Aligned_cols=13 Identities=31% Similarity=0.588 Sum_probs=5.9
Q ss_pred ceecCCCCCe-EEE
Q 035423 10 VIQCRECGYR-ILY 22 (35)
Q Consensus 10 ~irC~~CG~R-Ily 22 (35)
.-.||.||.. |-+
T Consensus 504 ~~~CP~CGs~~~~~ 517 (546)
T PF13597_consen 504 GDKCPKCGSENIEV 517 (546)
T ss_dssp EEE-CCC----EEE
T ss_pred CCCCCCCCCcccce
Confidence 5579999988 443
No 492
>cd02763 MopB_2 The MopB_2 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins
Probab=20.03 E-value=1.4e+02 Score=21.11 Aligned_cols=23 Identities=17% Similarity=0.330 Sum_probs=17.2
Q ss_pred ecCCC--CCeEEEeecCCceEEEEe
Q 035423 12 QCREC--GYRILYKKRTRRIVQYEA 34 (35)
Q Consensus 12 rC~~C--G~RIlyK~R~~~~~~~~A 34 (35)
-|++| |+.|....|.-+++.++.
T Consensus 3 ~C~~C~~gCgi~v~v~dG~v~~I~g 27 (679)
T cd02763 3 TCYMCACRCGIRVHLRDGKVRYIKG 27 (679)
T ss_pred cCCCCcCCCCeEEEEECCEEEEEEc
Confidence 37777 788888888777777663
No 493
>smart00532 LIGANc Ligase N family.
Probab=20.01 E-value=61 Score=21.85 Aligned_cols=14 Identities=21% Similarity=0.619 Sum_probs=11.4
Q ss_pred CceecCCCCCeEEE
Q 035423 9 DVIQCRECGYRILY 22 (35)
Q Consensus 9 ~~irC~~CG~RIly 22 (35)
.+-.||.||..+..
T Consensus 398 ~P~~CP~C~s~l~~ 411 (441)
T smart00532 398 MPTHCPSCGSELVR 411 (441)
T ss_pred CCCCCCCCCCEeEe
Confidence 47899999999753
Done!