Query psy2244
Match_columns 73
No_of_seqs 105 out of 175
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 19:50:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2244.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2244hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00659 RPOLCX RNA polymera 99.9 4.1E-22 8.8E-27 115.4 5.2 43 16-58 1-43 (44)
2 KOG3507|consensus 99.9 3.3E-23 7.2E-28 128.7 0.3 47 12-58 15-61 (62)
3 PF03604 DNA_RNApol_7kD: DNA d 99.8 3.4E-19 7.4E-24 97.9 2.4 32 18-49 1-32 (32)
4 COG1996 RPC10 DNA-directed RNA 99.7 1.1E-16 2.3E-21 95.6 4.5 45 14-58 3-48 (49)
5 PRK00398 rpoP DNA-directed RNA 99.2 2.7E-11 5.8E-16 69.0 3.9 39 16-54 2-41 (46)
6 smart00834 CxxC_CXXC_SSSS Puta 97.5 8.2E-05 1.8E-09 40.1 2.0 28 16-43 4-35 (41)
7 TIGR02605 CxxC_CxxC_SSSS putat 97.3 0.00024 5.2E-09 40.4 3.0 27 16-42 4-34 (52)
8 PF09723 Zn-ribbon_8: Zinc rib 97.3 0.00026 5.7E-09 39.8 2.5 27 16-42 4-34 (42)
9 TIGR02098 MJ0042_CXXC MJ0042 f 97.2 0.00045 9.9E-09 37.3 3.2 30 16-45 1-36 (38)
10 smart00531 TFIIE Transcription 96.5 0.003 6.5E-08 42.9 3.4 39 13-51 95-140 (147)
11 PF13717 zinc_ribbon_4: zinc-r 96.3 0.006 1.3E-07 33.5 3.0 29 16-44 1-35 (36)
12 PRK03824 hypA hydrogenase nick 96.2 0.004 8.6E-08 42.4 2.5 31 13-43 66-116 (135)
13 PF13248 zf-ribbon_3: zinc-rib 96.2 0.0014 3.1E-08 33.7 0.2 26 16-44 1-26 (26)
14 PF13719 zinc_ribbon_5: zinc-r 96.1 0.0087 1.9E-07 32.9 3.1 29 16-44 1-35 (37)
15 PRK00564 hypA hydrogenase nick 96.0 0.0041 8.9E-08 41.4 1.9 31 14-44 68-98 (117)
16 PF10571 UPF0547: Uncharacteri 95.9 0.0038 8.2E-08 32.7 1.0 22 19-43 2-23 (26)
17 PF13240 zinc_ribbon_2: zinc-r 95.8 0.0031 6.8E-08 32.0 0.5 23 19-44 1-23 (23)
18 COG2888 Predicted Zn-ribbon RN 95.8 0.011 2.5E-07 36.9 3.1 35 8-42 15-58 (61)
19 PRK03681 hypA hydrogenase nick 95.7 0.0081 1.8E-07 39.8 2.3 30 14-43 67-96 (114)
20 PF01155 HypA: Hydrogenase exp 95.7 0.0037 8.1E-08 41.2 0.5 29 14-43 67-95 (113)
21 COG1579 Zn-ribbon protein, pos 95.6 0.0029 6.4E-08 47.5 -0.1 30 18-48 198-234 (239)
22 cd00350 rubredoxin_like Rubred 95.6 0.0099 2.1E-07 31.8 2.0 25 17-42 1-25 (33)
23 TIGR01206 lysW lysine biosynth 95.4 0.014 3E-07 35.1 2.3 33 16-48 1-36 (54)
24 PF07295 DUF1451: Protein of u 95.3 0.014 2.9E-07 40.8 2.3 39 5-44 101-140 (146)
25 PF09538 FYDLN_acid: Protein o 95.3 0.01 2.2E-07 39.7 1.5 27 16-42 8-34 (108)
26 cd00729 rubredoxin_SM Rubredox 95.2 0.02 4.3E-07 31.2 2.3 26 16-42 1-26 (34)
27 PF09297 zf-NADH-PPase: NADH p 95.2 0.018 3.9E-07 30.4 2.1 26 19-44 5-31 (32)
28 PRK14890 putative Zn-ribbon RN 94.8 0.039 8.4E-07 34.2 3.1 27 19-45 9-36 (59)
29 PRK12380 hydrogenase nickel in 94.8 0.025 5.5E-07 37.4 2.4 28 15-43 68-95 (113)
30 PF08274 PhnA_Zn_Ribbon: PhnA 94.6 0.02 4.4E-07 31.0 1.3 26 19-44 4-29 (30)
31 TIGR00100 hypA hydrogenase nic 94.5 0.033 7E-07 36.9 2.3 29 14-43 67-95 (115)
32 smart00661 RPOL9 RNA polymeras 94.4 0.069 1.5E-06 29.8 3.2 23 20-42 3-28 (52)
33 PF07754 DUF1610: Domain of un 94.0 0.043 9.4E-07 28.5 1.7 23 20-42 1-24 (24)
34 COG1439 Predicted nucleic acid 93.9 0.056 1.2E-06 39.4 2.7 33 16-51 138-170 (177)
35 TIGR00373 conserved hypothetic 93.8 0.044 9.4E-07 38.0 2.0 34 13-46 105-140 (158)
36 PRK06266 transcription initiat 93.8 0.04 8.7E-07 39.1 1.9 35 13-47 113-149 (178)
37 PF10058 DUF2296: Predicted in 93.7 0.054 1.2E-06 32.3 2.0 38 5-42 7-52 (54)
38 PRK00762 hypA hydrogenase nick 93.6 0.049 1.1E-06 36.6 2.0 28 14-42 67-100 (124)
39 PF14353 CpXC: CpXC protein 93.3 0.14 3E-06 33.5 3.7 42 19-60 3-70 (128)
40 PRK12496 hypothetical protein; 93.3 0.048 1E-06 38.1 1.5 28 17-45 127-154 (164)
41 TIGR02300 FYDLN_acid conserved 92.9 0.063 1.4E-06 37.6 1.6 29 16-44 8-36 (129)
42 PF08271 TF_Zn_Ribbon: TFIIB z 92.5 0.11 2.3E-06 28.9 2.0 27 18-44 1-29 (43)
43 PF13451 zf-trcl: Probable zin 92.2 0.049 1.1E-06 32.4 0.4 28 15-42 2-41 (49)
44 PF01396 zf-C4_Topoisom: Topoi 92.2 0.23 4.9E-06 27.6 3.0 34 35-72 2-35 (39)
45 PF12773 DZR: Double zinc ribb 92.1 0.063 1.4E-06 30.0 0.7 34 9-43 5-38 (50)
46 PRK11032 hypothetical protein; 92.0 0.15 3.2E-06 36.4 2.5 39 5-44 113-152 (160)
47 PF10263 SprT-like: SprT-like 91.5 0.23 5.1E-06 32.7 3.0 34 14-47 120-156 (157)
48 PF08792 A2L_zn_ribbon: A2L zi 91.4 0.2 4.3E-06 27.3 2.1 26 17-42 3-29 (33)
49 PF12773 DZR: Double zinc ribb 91.3 0.1 2.2E-06 29.1 1.0 31 8-41 18-50 (50)
50 PRK14890 putative Zn-ribbon RN 91.2 0.22 4.8E-06 30.8 2.4 36 8-43 13-57 (59)
51 PF07282 OrfB_Zn_ribbon: Putat 91.0 0.2 4.2E-06 29.5 2.1 25 19-43 30-55 (69)
52 PRK00432 30S ribosomal protein 90.9 0.19 4.1E-06 29.5 1.9 26 19-44 22-47 (50)
53 COG1592 Rubrerythrin [Energy p 90.7 0.19 4.2E-06 36.0 2.2 25 17-43 134-158 (166)
54 COG1096 Predicted RNA-binding 90.6 0.34 7.3E-06 35.7 3.4 35 12-47 144-178 (188)
55 COG1571 Predicted DNA-binding 90.6 0.12 2.7E-06 41.8 1.2 32 19-50 352-383 (421)
56 PF09855 DUF2082: Nucleic-acid 90.5 0.22 4.8E-06 30.8 2.0 21 33-53 35-55 (64)
57 PHA00626 hypothetical protein 90.2 0.27 5.9E-06 30.6 2.2 26 19-44 2-33 (59)
58 PRK14714 DNA polymerase II lar 89.7 0.22 4.7E-06 45.3 2.1 29 17-45 692-720 (1337)
59 PRK00420 hypothetical protein; 89.4 0.39 8.4E-06 32.6 2.7 32 18-49 24-55 (112)
60 PF02318 FYVE_2: FYVE-type zin 89.4 0.31 6.8E-06 32.0 2.2 29 16-44 53-81 (118)
61 PRK06450 threonine synthase; V 89.2 0.35 7.6E-06 36.8 2.6 29 16-46 2-30 (338)
62 COG3357 Predicted transcriptio 89.1 0.19 4.1E-06 33.9 1.0 25 18-42 59-84 (97)
63 PF14446 Prok-RING_1: Prokaryo 89.1 0.26 5.5E-06 29.9 1.5 26 16-42 4-29 (54)
64 PRK07591 threonine synthase; V 89.0 0.34 7.3E-06 37.8 2.5 26 17-44 18-43 (421)
65 TIGR00686 phnA alkylphosphonat 88.8 0.27 5.9E-06 33.6 1.6 25 19-43 4-28 (109)
66 smart00731 SprT SprT homologue 88.6 0.58 1.3E-05 31.4 3.1 32 15-46 110-145 (146)
67 cd01675 RNR_III Class III ribo 88.3 0.31 6.8E-06 39.6 1.9 39 15-59 517-555 (555)
68 PF14369 zf-RING_3: zinc-finge 87.9 0.67 1.5E-05 25.3 2.5 29 17-45 2-32 (35)
69 COG0375 HybF Zn finger protein 87.8 0.39 8.4E-06 32.9 1.8 28 14-42 67-94 (115)
70 PRK09521 exosome complex RNA-b 87.6 0.78 1.7E-05 32.1 3.4 35 11-45 143-177 (189)
71 COG1326 Uncharacterized archae 87.2 0.5 1.1E-05 35.3 2.3 29 14-42 3-38 (201)
72 PF07191 zinc-ribbons_6: zinc- 87.1 0.36 7.8E-06 30.6 1.3 51 9-64 8-59 (70)
73 PF09082 DUF1922: Domain of un 87.0 0.6 1.3E-05 29.6 2.3 33 16-50 2-35 (68)
74 PF05191 ADK_lid: Adenylate ki 86.8 0.54 1.2E-05 25.9 1.8 28 18-45 2-32 (36)
75 TIGR01384 TFS_arch transcripti 86.6 0.5 1.1E-05 29.9 1.8 24 19-43 2-25 (104)
76 PRK00464 nrdR transcriptional 86.4 0.42 9.2E-06 33.6 1.5 27 18-44 1-38 (154)
77 PRK10220 hypothetical protein; 86.4 0.53 1.2E-05 32.3 1.9 25 19-43 5-29 (111)
78 COG1645 Uncharacterized Zn-fin 86.4 0.79 1.7E-05 32.1 2.8 30 17-47 28-57 (131)
79 PRK04351 hypothetical protein; 86.2 1 2.3E-05 31.3 3.4 34 15-48 110-146 (149)
80 PF10122 Mu-like_Com: Mu-like 86.2 0.38 8.2E-06 29.1 1.0 26 17-42 4-32 (51)
81 COG2816 NPY1 NTP pyrophosphohy 86.2 0.47 1E-05 36.6 1.8 26 19-44 113-139 (279)
82 cd00730 rubredoxin Rubredoxin; 85.9 0.53 1.1E-05 27.7 1.5 26 17-42 1-42 (50)
83 COG2888 Predicted Zn-ribbon RN 85.8 0.76 1.6E-05 28.7 2.2 30 18-47 10-40 (61)
84 PRK06260 threonine synthase; V 85.7 0.9 2E-05 34.9 3.1 27 17-44 3-29 (397)
85 KOG2846|consensus 85.4 0.35 7.5E-06 38.3 0.7 55 5-61 208-267 (328)
86 PRK00415 rps27e 30S ribosomal 85.2 1.3 2.9E-05 27.2 3.1 30 15-44 9-40 (59)
87 PF02591 DUF164: Putative zinc 85.1 0.5 1.1E-05 27.3 1.1 24 18-41 23-53 (56)
88 PF13408 Zn_ribbon_recom: Reco 85.1 1.4 3E-05 24.5 2.9 21 33-53 4-24 (58)
89 PRK04173 glycyl-tRNA synthetas 84.8 0.86 1.9E-05 36.2 2.7 47 15-61 84-166 (456)
90 PRK15103 paraquat-inducible me 84.7 0.63 1.4E-05 36.9 1.9 32 18-50 11-45 (419)
91 COG3364 Zn-ribbon containing p 84.7 0.22 4.7E-06 34.3 -0.6 33 16-48 1-35 (112)
92 PRK04136 rpl40e 50S ribosomal 84.2 0.48 1E-05 28.3 0.8 24 17-43 14-37 (48)
93 COG2051 RPS27A Ribosomal prote 84.1 2.6 5.6E-05 26.7 4.1 30 16-45 18-49 (67)
94 COG1379 PHP family phosphoeste 84.0 0.27 5.8E-06 39.8 -0.4 26 19-44 248-275 (403)
95 PRK14559 putative protein seri 83.7 0.67 1.5E-05 38.9 1.7 22 19-43 29-50 (645)
96 PF14690 zf-ISL3: zinc-finger 83.7 1.3 2.7E-05 24.2 2.3 31 34-65 2-32 (47)
97 PF12760 Zn_Tnp_IS1595: Transp 82.8 0.87 1.9E-05 25.5 1.5 25 18-42 19-45 (46)
98 PF02150 RNA_POL_M_15KD: RNA p 82.2 1.2 2.7E-05 24.2 1.9 24 20-43 4-29 (35)
99 COG1503 eRF1 Peptide chain rel 81.9 1 2.2E-05 36.5 2.0 39 6-44 315-358 (411)
100 smart00709 Zpr1 Duplicated dom 81.2 0.59 1.3E-05 32.9 0.4 11 33-43 28-38 (160)
101 PF14319 Zn_Tnp_IS91: Transpos 81.1 1.9 4.1E-05 28.5 2.8 36 8-43 33-69 (111)
102 PRK08351 DNA-directed RNA poly 80.8 0.85 1.8E-05 28.2 1.0 21 19-44 5-25 (61)
103 PF14803 Nudix_N_2: Nudix N-te 80.5 1 2.2E-05 24.7 1.2 23 20-42 3-30 (34)
104 PHA02942 putative transposase; 80.2 1.5 3.2E-05 34.3 2.4 24 19-42 327-350 (383)
105 PF03367 zf-ZPR1: ZPR1 zinc-fi 80.1 0.62 1.4E-05 32.6 0.3 25 19-43 3-39 (161)
106 PF11781 RRN7: RNA polymerase 80.0 1.3 2.9E-05 24.4 1.5 24 20-43 11-34 (36)
107 PF00301 Rubredoxin: Rubredoxi 79.9 1.8 3.9E-05 25.2 2.1 27 17-43 1-43 (47)
108 COG3091 SprT Zn-dependent meta 79.9 1.9 4E-05 31.2 2.6 33 15-48 115-154 (156)
109 COG2331 Uncharacterized protei 79.7 0.53 1.2E-05 30.9 -0.2 28 16-43 11-42 (82)
110 TIGR00155 pqiA_fam integral me 79.6 2 4.3E-05 33.9 2.9 27 18-44 14-43 (403)
111 TIGR00416 sms DNA repair prote 79.3 1.6 3.6E-05 34.6 2.4 31 15-48 5-35 (454)
112 PF07503 zf-HYPF: HypF finger; 79.3 0.35 7.6E-06 26.7 -1.0 26 19-44 1-31 (35)
113 COG0675 Transposase and inacti 79.2 1.4 3.1E-05 30.7 1.9 23 16-42 308-330 (364)
114 PF09845 DUF2072: Zn-ribbon co 79.0 0.79 1.7E-05 32.1 0.5 28 18-45 2-30 (131)
115 PF13597 NRDD: Anaerobic ribon 78.9 0.68 1.5E-05 37.7 0.2 38 16-59 490-527 (546)
116 PF14255 Cys_rich_CPXG: Cystei 78.7 0.99 2.1E-05 26.9 0.8 14 35-48 1-14 (52)
117 PRK04860 hypothetical protein; 78.6 2.9 6.2E-05 29.5 3.2 32 15-48 117-157 (160)
118 PRK11823 DNA repair protein Ra 78.6 1.8 3.8E-05 34.2 2.4 32 15-49 5-36 (446)
119 PRK06393 rpoE DNA-directed RNA 78.5 1 2.2E-05 28.1 0.9 20 19-43 7-26 (64)
120 PF02146 SIR2: Sir2 family; I 78.3 2.2 4.7E-05 29.1 2.5 28 16-43 104-138 (178)
121 PF12172 DUF35_N: Rubredoxin-l 78.2 2.3 5E-05 22.6 2.1 26 15-43 9-34 (37)
122 TIGR03844 cysteate_syn cysteat 78.1 1.8 3.8E-05 33.9 2.3 25 17-43 2-26 (398)
123 PRK08329 threonine synthase; V 78.0 1.7 3.8E-05 32.8 2.1 27 18-47 2-28 (347)
124 TIGR00155 pqiA_fam integral me 76.7 1.6 3.5E-05 34.4 1.7 26 17-44 215-240 (403)
125 COG4530 Uncharacterized protei 76.7 1.4 3E-05 30.9 1.2 26 17-42 9-34 (129)
126 TIGR01053 LSD1 zinc finger dom 76.6 2.7 5.8E-05 22.6 2.1 24 19-42 3-27 (31)
127 TIGR00375 conserved hypothetic 76.4 1 2.3E-05 35.6 0.6 25 19-44 242-268 (374)
128 PRK08271 anaerobic ribonucleos 76.3 0.83 1.8E-05 38.3 0.0 42 18-65 567-608 (623)
129 cd01121 Sms Sms (bacterial rad 76.2 1.6 3.5E-05 33.9 1.6 29 18-49 1-29 (372)
130 PRK14559 putative protein seri 76.1 1.6 3.4E-05 36.8 1.6 31 8-44 7-37 (645)
131 PRK08197 threonine synthase; V 75.8 2.9 6.3E-05 32.1 2.8 29 17-47 7-35 (394)
132 PF14599 zinc_ribbon_6: Zinc-r 75.6 2.4 5.2E-05 25.9 1.9 36 7-42 15-56 (61)
133 PF00130 C1_1: Phorbol esters/ 75.5 3.6 7.7E-05 22.8 2.5 27 18-44 12-38 (53)
134 COG0846 SIR2 NAD-dependent pro 75.4 3.3 7.1E-05 31.1 3.0 41 16-60 121-168 (250)
135 COG1552 RPL40A Ribosomal prote 75.2 0.39 8.5E-06 29.0 -1.6 26 17-45 14-39 (50)
136 PRK12775 putative trifunctiona 74.8 2 4.3E-05 37.4 1.9 45 5-51 811-855 (1006)
137 COG1545 Predicted nucleic-acid 74.8 2.1 4.6E-05 29.2 1.7 27 15-44 27-53 (140)
138 smart00647 IBR In Between Ring 74.6 3.6 7.9E-05 22.9 2.4 29 19-47 20-53 (64)
139 PF05207 zf-CSL: CSL zinc fing 74.6 1.4 3E-05 26.0 0.6 33 13-46 14-52 (55)
140 TIGR00340 zpr1_rel ZPR1-relate 74.5 1.6 3.5E-05 30.9 1.1 11 33-43 27-37 (163)
141 TIGR02487 NrdD anaerobic ribon 74.4 1.8 3.8E-05 35.6 1.4 36 19-59 526-561 (579)
142 PRK07111 anaerobic ribonucleos 74.4 1.6 3.4E-05 37.1 1.2 36 19-60 682-717 (735)
143 CHL00174 accD acetyl-CoA carbo 74.4 1.5 3.3E-05 33.9 1.0 39 5-43 26-66 (296)
144 PF06677 Auto_anti-p27: Sjogre 74.2 3.3 7.1E-05 23.5 2.1 23 19-41 19-41 (41)
145 TIGR00310 ZPR1_znf ZPR1 zinc f 74.0 1.7 3.6E-05 31.5 1.1 10 34-43 30-39 (192)
146 PF01780 Ribosomal_L37ae: Ribo 73.6 0.98 2.1E-05 29.8 -0.2 33 12-44 30-63 (90)
147 PF04161 Arv1: Arv1-like famil 73.6 1.6 3.5E-05 31.2 0.9 25 18-42 1-32 (208)
148 TIGR02827 RNR_anaer_Bdell anae 73.5 2.6 5.7E-05 35.2 2.2 38 18-60 533-570 (586)
149 smart00350 MCM minichromosome 73.4 3.7 8E-05 32.8 2.9 31 14-44 34-71 (509)
150 PF11023 DUF2614: Protein of u 73.3 2.2 4.7E-05 29.4 1.5 31 14-45 66-96 (114)
151 PF06943 zf-LSD1: LSD1 zinc fi 73.2 4.5 9.7E-05 21.1 2.3 23 20-42 1-24 (25)
152 COG2995 PqiA Uncharacterized p 72.2 3.3 7.2E-05 33.9 2.5 37 9-45 10-49 (418)
153 TIGR00515 accD acetyl-CoA carb 72.1 1.8 3.9E-05 33.0 0.9 34 10-43 19-54 (285)
154 PF01667 Ribosomal_S27e: Ribos 71.9 6.8 0.00015 23.7 3.2 29 16-44 6-36 (55)
155 PRK14892 putative transcriptio 71.9 4.9 0.00011 26.6 2.8 29 14-43 18-51 (99)
156 PF08772 NOB1_Zn_bind: Nin one 71.8 3.6 7.8E-05 26.0 2.1 30 17-48 9-38 (73)
157 TIGR00354 polC DNA polymerase, 71.8 3 6.6E-05 37.6 2.3 42 15-57 1010-1051(1095)
158 PRK09710 lar restriction allev 71.7 6.3 0.00014 24.7 3.1 27 36-62 8-34 (64)
159 PRK14714 DNA polymerase II lar 71.4 3.1 6.8E-05 38.2 2.3 36 14-50 1250-1285(1337)
160 PF09332 Mcm10: Mcm10 replicat 71.0 2.8 6.1E-05 33.1 1.8 26 17-42 285-311 (344)
161 PF08996 zf-DNA_Pol: DNA Polym 70.8 4.1 8.8E-05 28.7 2.4 29 14-42 15-53 (188)
162 PRK08579 anaerobic ribonucleos 70.5 0.97 2.1E-05 37.8 -0.9 37 18-59 569-605 (625)
163 PRK15103 paraquat-inducible me 70.1 3 6.6E-05 33.1 1.8 24 18-44 222-245 (419)
164 PF01485 IBR: IBR domain; Int 70.1 4.2 9E-05 22.6 1.9 26 19-44 20-50 (64)
165 cd07973 Spt4 Transcription elo 70.0 2.1 4.6E-05 28.3 0.8 46 19-64 5-50 (98)
166 TIGR03831 YgiT_finger YgiT-typ 69.7 3.6 7.9E-05 21.8 1.6 20 26-45 24-43 (46)
167 PRK13130 H/ACA RNA-protein com 69.5 3.3 7.2E-05 25.1 1.5 22 17-43 5-26 (56)
168 PHA02768 hypothetical protein; 68.9 1.6 3.5E-05 26.4 0.1 26 17-42 5-39 (55)
169 PRK04023 DNA polymerase II lar 68.7 3.9 8.4E-05 37.0 2.3 38 15-53 1035-1072(1121)
170 PF05495 zf-CHY: CHY zinc fing 68.7 3.5 7.6E-05 25.2 1.5 26 17-42 41-69 (71)
171 PF14205 Cys_rich_KTR: Cystein 68.5 4.8 0.0001 24.7 2.1 21 35-55 5-25 (55)
172 PF11672 DUF3268: Protein of u 68.3 3.4 7.3E-05 27.6 1.5 13 34-46 2-14 (102)
173 PRK09678 DNA-binding transcrip 68.2 2.7 5.8E-05 26.5 0.9 12 19-30 3-14 (72)
174 COG1675 TFA1 Transcription ini 68.1 1.7 3.8E-05 31.4 0.1 35 12-46 108-144 (176)
175 PTZ00255 60S ribosomal protein 68.0 2.1 4.6E-05 28.2 0.5 34 11-44 30-64 (90)
176 PRK05638 threonine synthase; V 68.0 4.4 9.5E-05 31.6 2.3 24 18-44 2-25 (442)
177 PRK04011 peptide chain release 67.9 5.9 0.00013 31.3 3.0 43 1-43 310-359 (411)
178 cd01407 SIR2-fam SIR2 family o 67.7 3.7 8.1E-05 29.0 1.7 27 17-43 109-142 (218)
179 PRK14715 DNA polymerase II lar 67.6 4.1 8.9E-05 38.1 2.3 34 15-50 1540-1573(1627)
180 COG0551 TopA Zn-finger domain 67.5 8 0.00017 25.6 3.2 32 33-66 100-131 (140)
181 PF10263 SprT-like: SprT-like 67.3 5.4 0.00012 26.1 2.3 32 31-63 120-151 (157)
182 cd01413 SIR2_Af2 SIR2_Af2: Arc 67.3 3.8 8.3E-05 29.3 1.7 27 17-43 113-145 (222)
183 PF10276 zf-CHCC: Zinc-finger 67.2 3.9 8.4E-05 23.2 1.4 16 28-43 22-38 (40)
184 PF14311 DUF4379: Domain of un 67.2 6.3 0.00014 22.5 2.3 27 14-40 25-55 (55)
185 PF09526 DUF2387: Probable met 67.1 4.2 9.1E-05 25.4 1.7 26 18-43 9-39 (71)
186 PRK00241 nudC NADH pyrophospha 67.1 6.8 0.00015 29.0 3.0 25 19-43 101-126 (256)
187 PF14205 Cys_rich_KTR: Cystein 66.7 19 0.0004 22.1 4.4 43 18-60 5-54 (55)
188 COG1933 Archaeal DNA polymeras 66.7 1.8 4E-05 33.3 -0.0 41 16-57 166-206 (253)
189 PRK00481 NAD-dependent deacety 66.6 3.9 8.4E-05 29.4 1.6 28 16-43 121-151 (242)
190 TIGR02443 conserved hypothetic 66.4 4.5 9.8E-05 25.0 1.7 27 18-44 10-41 (59)
191 PF09963 DUF2197: Uncharacteri 66.3 2.3 5E-05 26.0 0.4 30 17-46 2-43 (56)
192 PRK03976 rpl37ae 50S ribosomal 66.2 2.1 4.5E-05 28.3 0.2 34 11-44 30-64 (90)
193 COG1997 RPL43A Ribosomal prote 66.0 4.5 9.7E-05 26.9 1.7 32 13-44 31-63 (89)
194 COG4031 Predicted metal-bindin 65.8 2.9 6.4E-05 31.7 0.9 20 19-43 2-21 (227)
195 COG1066 Sms Predicted ATP-depe 65.7 4.6 9.9E-05 33.4 2.0 25 16-43 6-30 (456)
196 PF04216 FdhE: Protein involve 65.6 4.2 9.1E-05 30.1 1.7 27 13-42 193-219 (290)
197 TIGR00280 L37a ribosomal prote 65.4 2.3 5.1E-05 28.1 0.3 34 11-44 29-63 (91)
198 PRK05654 acetyl-CoA carboxylas 65.3 3 6.5E-05 31.9 0.9 34 11-44 21-56 (292)
199 PTZ00083 40S ribosomal protein 64.8 12 0.00026 24.7 3.5 39 6-44 24-64 (85)
200 PLN00209 ribosomal protein S27 64.2 11 0.00023 24.9 3.2 38 7-44 26-65 (86)
201 PRK12495 hypothetical protein; 63.0 4.9 0.00011 30.5 1.6 28 16-44 41-68 (226)
202 PF10083 DUF2321: Uncharacteri 63.0 1.2 2.6E-05 32.1 -1.5 27 13-45 24-50 (158)
203 PF06397 Desulfoferrod_N: Desu 62.3 4.5 9.7E-05 22.6 1.0 22 16-37 5-28 (36)
204 COG4311 SoxD Sarcosine oxidase 62.3 3.6 7.9E-05 27.7 0.8 10 34-43 3-12 (97)
205 PF09862 DUF2089: Protein of u 62.3 5.8 0.00012 27.0 1.7 22 20-44 1-22 (113)
206 COG4481 Uncharacterized protei 62.0 5.8 0.00013 24.7 1.6 15 33-47 33-47 (60)
207 PF04606 Ogr_Delta: Ogr/Delta- 62.0 6.4 0.00014 22.2 1.6 12 36-47 1-12 (47)
208 PF15616 TerY-C: TerY-C metal 62.0 10 0.00023 26.3 3.0 26 22-47 93-118 (131)
209 COG1656 Uncharacterized conser 61.9 3.2 6.8E-05 30.1 0.4 16 17-32 97-112 (165)
210 PF06906 DUF1272: Protein of u 61.7 2.7 5.8E-05 26.0 0.0 36 8-45 11-52 (57)
211 cd00924 Cyt_c_Oxidase_Vb Cytoc 61.5 9.9 0.00022 25.0 2.7 21 27-47 72-92 (97)
212 KOG3134|consensus 61.5 3.4 7.3E-05 31.4 0.5 25 18-42 1-32 (225)
213 PF06750 DiS_P_DiS: Bacterial 61.2 4.8 0.0001 25.8 1.2 26 19-44 35-68 (92)
214 PF10005 DUF2248: Uncharacteri 61.0 7.5 0.00016 31.0 2.4 39 19-60 1-39 (343)
215 PF09788 Tmemb_55A: Transmembr 60.6 9.5 0.00021 29.4 2.8 36 12-47 152-190 (256)
216 PF09334 tRNA-synt_1g: tRNA sy 60.3 8.6 0.00019 29.9 2.6 38 18-55 150-187 (391)
217 cd00246 RabGEF Nucleotide exch 60.1 5.9 0.00013 26.8 1.5 12 34-45 2-13 (103)
218 PF01096 TFIIS_C: Transcriptio 59.9 5.2 0.00011 22.0 1.0 10 35-44 1-10 (39)
219 cd01411 SIR2H SIR2H: Uncharact 59.7 7.7 0.00017 27.8 2.1 27 17-43 118-145 (225)
220 PF00096 zf-C2H2: Zinc finger, 59.7 5.2 0.00011 18.6 0.9 11 18-28 1-11 (23)
221 PRK04023 DNA polymerase II lar 59.2 6.2 0.00013 35.8 1.8 23 16-43 625-647 (1121)
222 COG4357 Zinc finger domain con 59.2 2.4 5.1E-05 29.0 -0.6 31 14-44 59-90 (105)
223 PRK14873 primosome assembly pr 59.1 8.6 0.00019 32.4 2.6 27 17-43 392-419 (665)
224 PHA02998 RNA polymerase subuni 59.0 7.5 0.00016 29.0 2.0 32 12-43 138-180 (195)
225 COG1779 C4-type Zn-finger prot 58.8 4.1 8.8E-05 30.4 0.6 28 16-43 13-52 (201)
226 PF05876 Terminase_GpA: Phage 58.1 6 0.00013 32.3 1.5 34 18-51 201-246 (557)
227 cd04476 RPA1_DBD_C RPA1_DBD_C: 58.0 13 0.00029 24.9 3.0 30 15-44 32-61 (166)
228 PRK00423 tfb transcription ini 57.8 6 0.00013 29.8 1.3 28 15-42 9-38 (310)
229 PF06107 DUF951: Bacterial pro 57.5 8.7 0.00019 23.6 1.8 15 33-47 30-44 (57)
230 COG4098 comFA Superfamily II D 56.7 6 0.00013 32.5 1.3 51 15-67 37-89 (441)
231 COG4640 Predicted membrane pro 56.6 5.6 0.00012 33.0 1.1 22 20-44 4-25 (465)
232 PF09986 DUF2225: Uncharacteri 56.3 17 0.00037 26.2 3.4 36 33-68 4-39 (214)
233 cd01412 SIRT5_Af1_CobB SIRT5_A 56.0 7.7 0.00017 27.4 1.6 27 17-43 109-139 (224)
234 PRK12286 rpmF 50S ribosomal pr 56.0 12 0.00026 22.4 2.2 26 13-42 23-48 (57)
235 COG1110 Reverse gyrase [DNA re 55.9 4.9 0.00011 36.6 0.7 26 18-46 695-720 (1187)
236 cd00029 C1 Protein kinase C co 55.8 6.7 0.00015 20.9 1.0 25 19-43 13-37 (50)
237 PLN02294 cytochrome c oxidase 55.7 12 0.00027 27.4 2.6 21 27-47 134-154 (174)
238 PF08646 Rep_fac-A_C: Replicat 55.7 9 0.00019 25.3 1.8 31 14-44 15-47 (146)
239 COG1998 RPS31 Ribosomal protei 55.5 8.3 0.00018 23.4 1.4 26 18-43 20-46 (51)
240 smart00109 C1 Protein kinase C 55.4 6 0.00013 20.8 0.7 24 19-43 13-36 (49)
241 COG1773 Rubredoxin [Energy pro 55.3 9.7 0.00021 23.2 1.7 26 17-42 3-44 (55)
242 COG4391 Uncharacterized protei 55.0 9.7 0.00021 23.8 1.7 16 29-44 43-58 (62)
243 PRK09263 anaerobic ribonucleos 54.7 7.8 0.00017 32.9 1.7 41 18-58 642-684 (711)
244 TIGR00595 priA primosomal prot 54.7 10 0.00023 30.4 2.3 7 36-42 255-261 (505)
245 TIGR01385 TFSII transcription 54.4 10 0.00023 29.1 2.2 31 14-44 255-296 (299)
246 COG5254 ARV1 Predicted membran 54.0 4.5 9.7E-05 30.9 0.1 25 18-42 1-32 (239)
247 PF13894 zf-C2H2_4: C2H2-type 53.7 8.7 0.00019 17.2 1.1 10 18-27 1-10 (24)
248 PRK05452 anaerobic nitric oxid 53.3 14 0.0003 29.6 2.8 31 13-43 421-467 (479)
249 PF09567 RE_MamI: MamI restric 53.3 6 0.00013 31.2 0.7 31 18-51 83-114 (314)
250 PF03884 DUF329: Domain of unk 53.2 8.2 0.00018 23.4 1.2 12 35-46 3-14 (57)
251 TIGR01562 FdhE formate dehydro 52.9 35 0.00076 26.5 4.8 26 14-42 207-232 (305)
252 PRK14873 primosome assembly pr 52.8 13 0.00029 31.3 2.7 21 18-43 411-431 (665)
253 COG2956 Predicted N-acetylgluc 52.6 4.7 0.0001 32.7 0.1 43 6-51 343-385 (389)
254 PRK14704 anaerobic ribonucleos 52.5 8.4 0.00018 32.3 1.5 37 18-58 560-597 (618)
255 PF13453 zf-TFIIB: Transcripti 52.4 15 0.00033 19.9 2.1 24 20-43 2-28 (41)
256 COG1594 RPB9 DNA-directed RNA 52.3 11 0.00025 25.0 1.9 28 20-47 5-35 (113)
257 PF14354 Lar_restr_allev: Rest 52.3 13 0.00028 21.1 1.9 25 18-42 4-37 (61)
258 PF06221 zf-C2HC5: Putative zi 52.3 8.4 0.00018 23.4 1.1 33 15-47 16-48 (57)
259 cd00065 FYVE FYVE domain; Zinc 52.3 10 0.00023 21.0 1.5 24 19-43 4-27 (57)
260 cd01408 SIRT1 SIRT1: Eukaryoti 52.0 7.2 0.00016 28.2 0.9 27 17-43 116-149 (235)
261 PHA00732 hypothetical protein 52.0 6.2 0.00013 24.8 0.5 28 18-45 2-38 (79)
262 PF05605 zf-Di19: Drought indu 51.9 5.7 0.00012 22.6 0.3 27 17-43 2-40 (54)
263 PF03119 DNA_ligase_ZBD: NAD-d 51.7 13 0.00027 19.3 1.6 19 20-38 2-21 (28)
264 COG2824 PhnA Uncharacterized Z 51.7 9.7 0.00021 26.3 1.5 23 20-42 6-28 (112)
265 COG1867 TRM1 N2,N2-dimethylgua 51.6 11 0.00024 30.5 2.0 27 17-43 240-266 (380)
266 PRK14138 NAD-dependent deacety 51.5 13 0.00027 27.2 2.1 27 17-43 119-152 (244)
267 PF05180 zf-DNL: DNL zinc fing 51.4 9 0.00019 23.9 1.2 31 16-46 3-41 (66)
268 PRK04338 N(2),N(2)-dimethylgua 51.3 16 0.00035 28.5 2.8 29 16-44 243-271 (382)
269 PF04981 NMD3: NMD3 family ; 51.0 12 0.00026 27.1 1.9 36 7-42 3-43 (236)
270 TIGR00595 priA primosomal prot 50.5 13 0.00027 30.0 2.1 14 31-44 237-250 (505)
271 smart00653 eIF2B_5 domain pres 50.4 12 0.00026 25.0 1.7 25 19-43 82-110 (110)
272 COG5257 GCD11 Translation init 50.4 11 0.00025 30.8 1.9 27 16-44 56-82 (415)
273 PF01363 FYVE: FYVE zinc finge 50.1 14 0.00029 21.5 1.8 25 17-42 9-33 (69)
274 PRK05580 primosome assembly pr 49.7 13 0.00027 31.0 2.1 8 36-43 423-430 (679)
275 PRK07219 DNA topoisomerase I; 49.6 27 0.0006 29.9 4.1 30 34-67 688-717 (822)
276 PF01783 Ribosomal_L32p: Ribos 49.6 8.8 0.00019 22.5 0.9 27 16-49 25-51 (56)
277 KOG2907|consensus 49.0 7.6 0.00016 26.9 0.6 37 19-55 9-46 (116)
278 TIGR00311 aIF-2beta translatio 48.1 14 0.00029 25.5 1.8 25 19-43 99-127 (133)
279 TIGR00354 polC DNA polymerase, 47.3 13 0.00028 33.8 1.9 26 14-44 622-647 (1095)
280 PF04810 zf-Sec23_Sec24: Sec23 47.2 8.5 0.00018 21.1 0.5 10 33-42 1-10 (40)
281 PRK11595 DNA utilization prote 46.6 6.4 0.00014 28.1 -0.0 34 7-43 10-43 (227)
282 KOG2462|consensus 46.3 17 0.00037 28.4 2.2 32 12-43 125-170 (279)
283 COG2260 Predicted Zn-ribbon RN 46.3 11 0.00024 23.4 1.0 24 16-44 4-27 (59)
284 PRK11788 tetratricopeptide rep 46.3 14 0.00031 26.4 1.7 30 17-49 354-383 (389)
285 smart00154 ZnF_AN1 AN1-like Zi 46.2 17 0.00037 20.0 1.7 21 20-43 1-21 (39)
286 PRK05580 primosome assembly pr 46.0 13 0.00028 30.9 1.7 28 18-45 391-419 (679)
287 smart00238 BIR Baculoviral inh 45.9 12 0.00027 21.7 1.1 15 32-46 34-48 (71)
288 TIGR01374 soxD sarcosine oxida 45.8 9.1 0.0002 24.9 0.6 9 35-43 2-10 (84)
289 PLN02569 threonine synthase 45.7 15 0.00033 29.7 2.0 27 17-45 49-75 (484)
290 PF01927 Mut7-C: Mut7-C RNAse 45.2 14 0.00031 24.9 1.5 8 35-42 92-99 (147)
291 smart00064 FYVE Protein presen 45.0 15 0.00032 21.2 1.4 25 18-43 11-35 (68)
292 PF01215 COX5B: Cytochrome c o 44.7 15 0.00032 25.7 1.5 19 28-46 106-124 (136)
293 PF13912 zf-C2H2_6: C2H2-type 44.7 12 0.00027 17.9 0.9 11 18-28 2-12 (27)
294 PF00653 BIR: Inhibitor of Apo 44.5 13 0.00028 21.9 1.1 13 32-44 34-46 (70)
295 PF01921 tRNA-synt_1f: tRNA sy 44.5 7.2 0.00016 31.0 -0.0 36 15-50 172-215 (360)
296 PRK05776 DNA topoisomerase I; 44.1 15 0.00033 30.8 1.8 35 34-70 596-634 (670)
297 KOG2463|consensus 43.9 13 0.00029 30.1 1.3 28 18-47 243-270 (376)
298 PF10609 ParA: ParA/MinD ATPas 43.9 12 0.00026 23.9 0.9 15 30-44 61-75 (81)
299 TIGR03830 CxxCG_CxxCG_HTH puta 43.7 19 0.0004 22.7 1.8 23 22-45 20-42 (127)
300 TIGR00108 eRF peptide chain re 43.7 26 0.00057 27.7 2.9 44 1-44 306-356 (409)
301 TIGR00308 TRM1 tRNA(guanine-26 43.7 22 0.00049 27.8 2.5 29 16-44 232-262 (374)
302 COG4888 Uncharacterized Zn rib 43.6 21 0.00045 24.4 2.1 32 14-45 19-57 (104)
303 PRK00448 polC DNA polymerase I 43.2 19 0.00041 33.3 2.3 62 5-67 894-966 (1437)
304 PF10080 DUF2318: Predicted me 43.1 15 0.00032 24.4 1.3 27 18-44 36-62 (102)
305 PF01020 Ribosomal_L40e: Ribos 43.0 18 0.00038 21.9 1.5 23 17-42 17-41 (52)
306 cd01410 SIRT7 SIRT7: Eukaryoti 43.0 13 0.00028 26.5 1.1 27 17-43 95-129 (206)
307 PF12647 RNHCP: RNHCP domain; 42.9 13 0.00029 24.6 1.1 26 17-42 4-32 (92)
308 PF00628 PHD: PHD-finger; Int 42.7 27 0.00058 18.9 2.1 22 19-42 1-22 (51)
309 PRK03988 translation initiatio 42.6 19 0.0004 25.0 1.8 25 19-43 104-132 (138)
310 TIGR00244 transcriptional regu 42.5 10 0.00023 27.0 0.5 8 35-42 1-8 (147)
311 PRK12336 translation initiatio 42.4 17 0.00038 26.1 1.7 27 18-44 99-129 (201)
312 PF07967 zf-C3HC: C3HC zinc fi 42.3 21 0.00045 23.6 1.9 29 18-48 29-57 (133)
313 PRK08402 replication factor A; 42.2 36 0.00078 26.8 3.5 27 16-42 211-238 (355)
314 KOG2324|consensus 41.9 19 0.00041 29.8 2.0 46 5-50 215-263 (457)
315 TIGR00319 desulf_FeS4 desulfof 41.7 18 0.00038 18.9 1.2 15 16-30 6-20 (34)
316 PF01873 eIF-5_eIF-2B: Domain 41.7 24 0.00051 24.0 2.1 25 19-43 95-123 (125)
317 PRK08270 anaerobic ribonucleos 41.7 20 0.00042 30.3 2.1 21 19-43 628-648 (656)
318 PF03833 PolC_DP2: DNA polymer 41.6 8.7 0.00019 34.2 0.0 21 18-43 681-701 (900)
319 PF04267 SoxD: Sarcosine oxida 41.5 10 0.00022 24.7 0.3 9 35-43 2-10 (84)
320 cd00974 DSRD Desulforedoxin (D 41.3 18 0.00039 18.9 1.2 13 17-29 4-16 (34)
321 KOG3352|consensus 41.1 14 0.0003 26.6 1.0 16 29-44 128-143 (153)
322 PRK11088 rrmA 23S rRNA methylt 41.0 17 0.00038 26.0 1.5 25 17-43 2-26 (272)
323 PF00684 DnaJ_CXXCXGXG: DnaJ c 40.9 65 0.0014 18.9 3.8 47 20-66 1-52 (66)
324 smart00714 LITAF Possible memb 40.6 21 0.00046 21.0 1.6 16 34-49 3-18 (67)
325 COG1241 MCM2 Predicted ATPase 40.6 20 0.00043 30.8 1.9 29 12-40 124-157 (682)
326 KOG3854|consensus 40.4 17 0.00038 30.5 1.5 47 15-61 406-459 (505)
327 COG1743 Adenine-specific DNA m 40.2 26 0.00056 31.3 2.6 30 34-63 178-214 (875)
328 cd01409 SIRT4 SIRT4: Eukaryoti 40.0 29 0.00063 25.6 2.5 12 17-28 118-129 (260)
329 PF02207 zf-UBR: Putative zinc 39.8 18 0.00039 21.7 1.2 31 15-50 11-48 (71)
330 cd04367 IlGF_insulin_like IlGF 39.8 2.2 4.7E-05 27.3 -3.0 25 3-27 1-25 (79)
331 COG1198 PriA Primosomal protei 39.7 28 0.00062 30.1 2.8 13 31-43 459-471 (730)
332 PF04828 GFA: Glutathione-depe 39.6 67 0.0015 18.5 3.7 17 31-47 45-61 (92)
333 PF13397 DUF4109: Domain of un 39.6 35 0.00076 23.1 2.7 29 14-43 25-59 (105)
334 PTZ00043 cytochrome c oxidase 39.4 24 0.00052 27.4 2.1 16 28-43 175-190 (268)
335 PTZ00408 NAD-dependent deacety 39.2 20 0.00043 26.3 1.6 26 17-42 117-145 (242)
336 COG2093 DNA-directed RNA polym 39.1 16 0.00035 23.0 0.9 21 20-43 7-27 (64)
337 COG2401 ABC-type ATPase fused 39.1 18 0.00038 30.8 1.4 37 5-44 118-154 (593)
338 PF06054 CoiA: Competence prot 39.0 35 0.00076 26.6 3.0 26 32-57 28-53 (375)
339 KOG3623|consensus 39.0 12 0.00026 33.5 0.4 29 16-44 280-319 (1007)
340 PHA00616 hypothetical protein 39.0 7 0.00015 22.7 -0.7 11 18-28 2-12 (44)
341 PF07649 C1_3: C1-like domain; 38.9 19 0.00042 18.3 1.1 17 8-24 6-22 (30)
342 COG4260 Membrane protease subu 38.7 12 0.00027 29.9 0.4 25 19-43 317-343 (345)
343 PRK05978 hypothetical protein; 38.7 18 0.00038 25.5 1.2 24 19-42 35-60 (148)
344 TIGR01405 polC_Gram_pos DNA po 38.6 16 0.00034 33.2 1.1 62 5-67 669-741 (1213)
345 PRK08665 ribonucleotide-diphos 38.6 18 0.00039 31.0 1.4 23 19-42 726-748 (752)
346 PF03107 C1_2: C1 domain; Int 38.6 23 0.0005 18.2 1.3 8 17-24 15-22 (30)
347 PF05129 Elf1: Transcription e 38.4 16 0.00035 23.0 0.9 33 15-47 20-59 (81)
348 TIGR01031 rpmF_bact ribosomal 38.1 38 0.00083 20.0 2.4 23 15-41 24-46 (55)
349 cd00022 BIR Baculoviral inhibi 37.9 20 0.00043 20.7 1.1 15 32-46 32-46 (69)
350 COG2995 PqiA Uncharacterized p 37.4 14 0.0003 30.4 0.6 30 18-50 221-250 (418)
351 TIGR02159 PA_CoA_Oxy4 phenylac 37.3 15 0.00034 25.4 0.7 10 34-43 105-114 (146)
352 PRK14891 50S ribosomal protein 37.1 45 0.00098 23.5 3.0 35 17-62 4-38 (131)
353 TIGR00143 hypF [NiFe] hydrogen 37.1 14 0.00031 31.3 0.6 35 15-49 116-155 (711)
354 PF04502 DUF572: Family of unk 37.0 24 0.00051 27.0 1.7 18 34-51 77-94 (324)
355 PF01194 RNA_pol_N: RNA polyme 36.9 12 0.00026 23.1 0.1 12 33-44 3-14 (60)
356 PRK03564 formate dehydrogenase 36.8 40 0.00086 26.3 2.9 27 13-42 208-234 (309)
357 KOG0478|consensus 36.7 16 0.00034 32.3 0.8 27 16-42 263-294 (804)
358 KOG2807|consensus 36.4 21 0.00045 29.0 1.4 39 6-44 334-377 (378)
359 COG0777 AccD Acetyl-CoA carbox 35.4 24 0.00052 27.8 1.6 30 14-43 25-56 (294)
360 PF10601 zf-LITAF-like: LITAF- 35.4 34 0.00074 20.4 1.9 16 34-49 58-73 (73)
361 PF03833 PolC_DP2: DNA polymer 35.4 12 0.00027 33.2 0.0 28 11-43 649-676 (900)
362 PTZ00410 NAD-dependent SIR2; P 35.3 30 0.00064 27.4 2.1 27 17-43 147-180 (349)
363 COG1328 NrdD Oxygen-sensitive 35.1 26 0.00055 30.3 1.8 36 19-59 643-678 (700)
364 PF13465 zf-H2C2_2: Zinc-finge 34.7 23 0.00049 17.5 0.9 11 17-27 14-24 (26)
365 PRK14894 glycyl-tRNA synthetas 34.5 25 0.00054 29.7 1.6 36 14-50 85-120 (539)
366 PRK14715 DNA polymerase II lar 34.4 25 0.00055 33.2 1.7 30 14-48 671-700 (1627)
367 COG1198 PriA Primosomal protei 34.4 27 0.00058 30.2 1.8 23 17-43 462-484 (730)
368 PRK07218 replication factor A; 34.2 23 0.00051 28.5 1.4 24 14-42 294-317 (423)
369 PF04438 zf-HIT: HIT zinc fing 34.0 48 0.001 17.4 2.2 9 35-43 14-22 (30)
370 smart00249 PHD PHD zinc finger 33.8 37 0.0008 17.0 1.7 21 20-42 2-22 (47)
371 PF13913 zf-C2HC_2: zinc-finge 33.1 21 0.00046 17.8 0.7 10 34-43 2-11 (25)
372 PF01258 zf-dskA_traR: Prokary 32.7 6.4 0.00014 20.9 -1.4 11 20-30 6-16 (36)
373 PRK00418 DNA gyrase inhibitor; 32.6 25 0.00054 21.8 1.0 13 34-46 6-18 (62)
374 cd00296 SIR2 SIR2 superfamily 31.9 29 0.00063 23.9 1.4 26 18-43 114-143 (222)
375 PHA00733 hypothetical protein 31.9 23 0.0005 23.7 0.9 29 15-43 71-108 (128)
376 TIGR03829 YokU_near_AblA uncha 31.7 25 0.00054 23.1 1.0 19 26-44 27-45 (89)
377 cd02249 ZZ Zinc finger, ZZ typ 31.6 31 0.00067 19.0 1.2 8 16-23 13-20 (46)
378 PF02005 TRM: N2,N2-dimethylgu 31.6 36 0.00078 26.7 2.0 29 16-44 239-269 (377)
379 PF14570 zf-RING_4: RING/Ubox 31.3 33 0.00071 20.2 1.3 8 33-40 36-43 (48)
380 PF00641 zf-RanBP: Zn-finger i 31.2 36 0.00079 17.1 1.4 23 17-42 4-26 (30)
381 TIGR03676 aRF1/eRF1 peptide ch 30.8 58 0.0013 25.8 3.1 43 1-43 302-351 (403)
382 PF11331 DUF3133: Protein of u 30.7 35 0.00077 19.9 1.4 31 19-49 8-46 (46)
383 COG4896 Uncharacterized protei 30.2 13 0.00028 23.7 -0.5 29 19-47 4-44 (68)
384 KOG3993|consensus 30.1 25 0.00054 29.5 0.9 14 15-28 293-306 (500)
385 TIGR01057 topA_arch DNA topois 30.0 53 0.0012 27.1 2.8 27 35-66 590-617 (618)
386 PRK05333 NAD-dependent deacety 29.3 48 0.001 24.6 2.2 12 16-27 127-138 (285)
387 KOG2593|consensus 29.3 29 0.00063 28.7 1.2 33 13-45 124-164 (436)
388 PRK06386 replication factor A; 29.2 38 0.00082 26.9 1.8 24 14-42 233-256 (358)
389 smart00290 ZnF_UBP Ubiquitin C 28.9 37 0.00081 18.4 1.3 8 17-24 11-18 (50)
390 PTZ00409 Sir2 (Silent Informat 28.8 37 0.0008 25.5 1.6 12 17-28 137-148 (271)
391 smart00401 ZnF_GATA zinc finge 28.8 34 0.00075 19.7 1.1 28 17-44 3-35 (52)
392 PF08209 Sgf11: Sgf11 (transcr 28.5 43 0.00094 18.2 1.4 11 34-44 4-14 (33)
393 TIGR00320 dfx_rbo desulfoferro 28.4 51 0.0011 22.3 2.1 21 17-37 7-29 (125)
394 COG0498 ThrC Threonine synthas 28.4 22 0.00048 28.6 0.3 26 16-42 4-29 (411)
395 PF12322 T4_baseplate: T4 bact 28.3 37 0.00079 24.7 1.4 23 15-37 76-99 (205)
396 PF14569 zf-UDP: Zinc-binding 28.1 32 0.00069 22.5 1.0 29 16-44 8-38 (80)
397 KOG1812|consensus 27.5 29 0.00063 27.3 0.9 31 18-49 307-338 (384)
398 PF08063 PADR1: PADR1 (NUC008) 27.5 22 0.00047 21.0 0.1 17 33-49 13-30 (55)
399 COG1405 SUA7 Transcription ini 27.4 35 0.00075 26.1 1.2 24 19-42 3-28 (285)
400 KOG1105|consensus 26.3 44 0.00096 26.1 1.6 27 17-43 255-292 (296)
401 PF06524 NOA36: NOA36 protein; 26.2 31 0.00066 27.4 0.8 18 28-45 203-220 (314)
402 TIGR02420 dksA RNA polymerase- 25.8 16 0.00035 23.6 -0.7 23 18-40 81-107 (110)
403 PF13901 DUF4206: Domain of un 25.6 45 0.00097 23.8 1.5 26 17-42 152-180 (202)
404 TIGR00577 fpg formamidopyrimid 25.6 51 0.0011 24.4 1.8 12 35-46 246-257 (272)
405 PLN02638 cellulose synthase A 25.4 48 0.001 30.2 1.9 28 17-44 17-46 (1079)
406 COG5216 Uncharacterized conser 25.4 40 0.00087 21.3 1.0 26 16-42 21-52 (67)
407 PF13878 zf-C2H2_3: zinc-finge 25.3 43 0.00092 18.5 1.1 8 34-41 13-20 (41)
408 COG0317 SpoT Guanosine polypho 25.2 37 0.00079 29.4 1.1 28 45-72 288-316 (701)
409 PRK14810 formamidopyrimidine-D 25.2 51 0.0011 24.5 1.7 9 36-44 246-254 (272)
410 PF14122 YokU: YokU-like prote 25.1 47 0.001 22.0 1.4 18 25-42 26-43 (87)
411 PF13005 zf-IS66: zinc-finger 25.0 43 0.00094 18.1 1.0 12 34-45 2-13 (47)
412 PF12677 DUF3797: Domain of un 24.9 40 0.00086 20.2 0.9 12 34-45 13-24 (49)
413 TIGR00627 tfb4 transcription f 24.7 56 0.0012 25.0 1.9 26 15-43 253-278 (279)
414 PRK14811 formamidopyrimidine-D 24.7 53 0.0011 24.4 1.8 23 19-41 237-262 (269)
415 TIGR00622 ssl1 transcription f 24.6 59 0.0013 22.1 1.8 25 18-45 2-26 (112)
416 PRK00807 50S ribosomal protein 24.6 1.1E+02 0.0024 17.8 2.8 19 44-62 17-35 (52)
417 cd02335 ZZ_ADA2 Zinc finger, Z 24.6 52 0.0011 18.5 1.4 13 11-23 9-21 (49)
418 KOG4080|consensus 24.5 34 0.00073 25.2 0.7 9 34-42 93-101 (176)
419 COG4307 Uncharacterized protei 24.4 19 0.00042 28.8 -0.6 26 17-45 3-28 (349)
420 KOG2691|consensus 24.4 66 0.0014 22.2 2.1 20 33-52 72-93 (113)
421 PRK10996 thioredoxin 2; Provis 24.3 67 0.0015 21.0 2.0 28 18-45 3-33 (139)
422 COG1327 Predicted transcriptio 24.2 32 0.00069 24.9 0.5 7 36-42 2-8 (156)
423 COG5132 BUD31 Cell cycle contr 24.2 21 0.00046 25.5 -0.4 12 32-43 129-140 (146)
424 PRK01103 formamidopyrimidine/5 24.1 55 0.0012 24.1 1.8 10 36-45 247-256 (274)
425 PRK10445 endonuclease VIII; Pr 24.0 56 0.0012 24.1 1.8 15 35-49 236-250 (263)
426 PF02176 zf-TRAF: TRAF-type zi 23.8 62 0.0013 17.9 1.6 6 34-39 9-14 (60)
427 TIGR00398 metG methionyl-tRNA 23.6 39 0.00085 26.7 0.9 36 19-54 151-186 (530)
428 PRK13945 formamidopyrimidine-D 23.6 57 0.0012 24.3 1.7 22 19-40 256-280 (282)
429 TIGR03655 anti_R_Lar restricti 23.4 52 0.0011 18.7 1.2 8 36-43 28-35 (53)
430 KOG3404|consensus 23.3 34 0.00074 24.5 0.5 15 29-43 126-140 (145)
431 smart00355 ZnF_C2H2 zinc finge 23.2 29 0.00063 15.3 0.1 10 18-27 1-10 (26)
432 KOG0482|consensus 23.2 46 0.001 29.0 1.3 49 13-61 177-237 (721)
433 cd02337 ZZ_CBP Zinc finger, ZZ 23.1 56 0.0012 18.1 1.3 20 18-41 1-20 (41)
434 PF14952 zf-tcix: Putative tre 22.9 50 0.0011 19.4 1.1 22 18-42 12-35 (44)
435 COG3809 Uncharacterized protei 22.8 1E+02 0.0023 20.4 2.7 41 19-59 3-55 (88)
436 smart00078 IlGF Insulin / insu 22.6 6.4 0.00014 23.8 -2.9 20 5-24 1-20 (66)
437 PF14768 RPA_interact_C: Repli 22.5 77 0.0017 19.6 2.0 25 19-44 1-25 (82)
438 PF10764 Gin: Inhibitor of sig 22.5 52 0.0011 18.9 1.1 20 7-26 4-27 (46)
439 PLN02189 cellulose synthase 22.5 62 0.0013 29.5 2.0 29 16-44 33-63 (1040)
440 PF09706 Cas_CXXC_CXXC: CRISPR 22.2 53 0.0011 20.0 1.2 18 33-50 4-21 (69)
441 PF15494 SRCR_2: Scavenger rec 22.2 45 0.00098 20.7 0.9 25 15-43 73-97 (98)
442 PRK08173 DNA topoisomerase III 22.1 58 0.0013 28.4 1.7 26 18-44 625-650 (862)
443 PF13909 zf-H2C2_5: C2H2-type 22.1 52 0.0011 15.4 0.9 9 36-44 2-10 (24)
444 PF09158 MotCF: Bacteriophage 21.8 84 0.0018 21.3 2.2 18 42-59 32-49 (103)
445 PLN02195 cellulose synthase A 21.8 61 0.0013 29.3 1.8 25 19-43 8-34 (977)
446 PF13824 zf-Mss51: Zinc-finger 21.8 42 0.00092 20.3 0.6 16 11-26 8-23 (55)
447 smart00547 ZnF_RBZ Zinc finger 21.5 48 0.001 15.9 0.7 22 18-42 3-24 (26)
448 COG3478 Predicted nucleic-acid 21.5 34 0.00075 21.8 0.2 19 33-51 39-57 (68)
449 PRK02935 hypothetical protein; 21.4 63 0.0014 22.3 1.5 27 16-43 69-95 (110)
450 KOG0480|consensus 21.3 1.2E+02 0.0025 27.0 3.3 45 12-57 152-203 (764)
451 KOG0402|consensus 21.2 21 0.00045 23.9 -0.9 31 11-41 30-61 (92)
452 TIGR00201 comF comF family pro 21.2 44 0.00096 23.0 0.7 22 20-44 1-22 (190)
453 KOG4684|consensus 21.1 52 0.0011 25.6 1.1 31 12-42 165-197 (275)
454 cd00085 HNHc HNH nucleases; HN 20.8 88 0.0019 16.1 1.7 10 35-44 12-21 (57)
455 PF01844 HNH: HNH endonuclease 20.6 62 0.0013 16.9 1.1 26 37-64 1-26 (47)
456 COG5349 Uncharacterized protei 20.5 42 0.0009 23.6 0.5 17 30-46 17-33 (126)
457 KOG2767|consensus 20.5 34 0.00073 28.0 0.0 33 19-51 98-135 (400)
458 COG5347 GTPase-activating prot 20.5 55 0.0012 25.6 1.2 24 18-42 21-48 (319)
459 PF14996 RMP: Retinal Maintena 20.4 63 0.0014 23.0 1.4 15 32-46 66-80 (146)
460 PF07975 C1_4: TFIIH C1-like d 20.3 72 0.0016 18.9 1.4 15 16-30 20-34 (51)
461 PRK07220 DNA topoisomerase I; 20.3 1.1E+02 0.0024 26.0 3.0 12 18-29 590-601 (740)
462 PF01283 Ribosomal_S26e: Ribos 20.2 51 0.0011 22.6 0.8 21 33-56 19-39 (113)
463 COG3677 Transposase and inacti 20.2 63 0.0014 21.8 1.3 9 34-42 53-61 (129)
464 PRK06319 DNA topoisomerase I/S 20.1 93 0.002 27.0 2.5 12 34-45 592-603 (860)
465 PLN02436 cellulose synthase A 20.1 74 0.0016 29.2 2.0 29 16-44 35-65 (1094)
466 PF02892 zf-BED: BED zinc fing 20.0 63 0.0014 17.1 1.0 16 32-47 14-29 (45)
No 1
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=99.86 E-value=4.1e-22 Score=115.38 Aligned_cols=43 Identities=53% Similarity=0.888 Sum_probs=41.4
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEee
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFK 58 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~~ 58 (73)
|.|+|++||.+++++..++||||+||||||||+||++++||.+
T Consensus 1 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~rIlyK~R~~~~~~~~A 43 (44)
T smart00659 1 MIYICGECGRENEIKSKDVVRCRECGYRILYKKRTKRLVEVKA 43 (44)
T ss_pred CEEECCCCCCEeecCCCCceECCCCCceEEEEeCCCceEEEEc
Confidence 6799999999999999999999999999999999999999975
No 2
>KOG3507|consensus
Probab=99.86 E-value=3.3e-23 Score=128.75 Aligned_cols=47 Identities=45% Similarity=0.784 Sum_probs=45.1
Q ss_pred CCcceEEEcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEee
Q psy2244 12 LPGDIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFK 58 (73)
Q Consensus 12 ~~~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~~ 58 (73)
-++.|.|+|++||.+|.|+.+|.|||++||||||||+|+++++||++
T Consensus 15 r~~~miYiCgdC~~en~lk~~D~irCReCG~RIlyKkRtkrlvqfea 61 (62)
T KOG3507|consen 15 RTATMIYICGDCGQENTLKRGDVIRCRECGYRILYKKRTKRLVQFEA 61 (62)
T ss_pred CcccEEEEeccccccccccCCCcEehhhcchHHHHHHHHhhhheeec
Confidence 56789999999999999999999999999999999999999999986
No 3
>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=99.75 E-value=3.4e-19 Score=97.93 Aligned_cols=32 Identities=59% Similarity=1.064 Sum_probs=27.7
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeEEEeee
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRIMYKKR 49 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkR 49 (73)
|+|++||++++++..|+|||++||||||||+|
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R 32 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECGHRILYKKR 32 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS-SEEBE--
T ss_pred CCCCcCCCeeEcCCCCcEECCcCCCeEEEecC
Confidence 89999999999999999999999999999998
No 4
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=99.66 E-value=1.1e-16 Score=95.56 Aligned_cols=45 Identities=31% Similarity=0.346 Sum_probs=40.5
Q ss_pred cceEEEcCcCCccee-cCCCCCeecCCCCCeEEEeeeCCeeEEEee
Q psy2244 14 GDIEKYYLECHFENE-IRPRDPIRCRECGYRIMYKKRTKRCILYFK 58 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~-ik~~d~IRC~~CG~RILyKkRt~r~vqf~~ 58 (73)
..++|+|++||++++ +...+.||||+||||||+|.|++.+.+|.+
T Consensus 3 ~~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~K~R~~~~krvkA 48 (49)
T COG1996 3 AMMEYKCARCGREVELDQETRGIRCPYCGSRILVKERPKVPKRVKA 48 (49)
T ss_pred ceEEEEhhhcCCeeehhhccCceeCCCCCcEEEEeccCCccEEEec
Confidence 458999999999999 557899999999999999999999888764
No 5
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=99.19 E-value=2.7e-11 Score=68.96 Aligned_cols=39 Identities=33% Similarity=0.604 Sum_probs=35.1
Q ss_pred eEEEcCcCCcceecCCCC-CeecCCCCCeEEEeeeCCeeE
Q psy2244 16 IEKYYLECHFENEIRPRD-PIRCRECGYRIMYKKRTKRCI 54 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d-~IRC~~CG~RILyKkRt~r~v 54 (73)
++|+|.+||++++++... .++||+||++++||.|++.+-
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~~~~v~ 41 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGYRILFKERPPVVK 41 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCCeEEEccCCCcce
Confidence 589999999999999765 899999999999999998543
No 6
>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=97.47 E-value=8.2e-05 Score=40.12 Aligned_cols=28 Identities=25% Similarity=0.396 Sum_probs=23.0
Q ss_pred eEEEcCcCCcceecCC----CCCeecCCCCCe
Q psy2244 16 IEKYYLECHFENEIRP----RDPIRCRECGYR 43 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~----~d~IRC~~CG~R 43 (73)
.+|.|.+||..+++.. .+.+.||+||..
T Consensus 4 Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred EEEEcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence 5799999999877542 568999999984
No 7
>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=97.34 E-value=0.00024 Score=40.41 Aligned_cols=27 Identities=26% Similarity=0.400 Sum_probs=22.0
Q ss_pred eEEEcCcCCcceecC----CCCCeecCCCCC
Q psy2244 16 IEKYYLECHFENEIR----PRDPIRCRECGY 42 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik----~~d~IRC~~CG~ 42 (73)
-+|+|.+||.++++. ..+.+.||.||.
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 479999999987764 235689999998
No 8
>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=97.26 E-value=0.00026 Score=39.80 Aligned_cols=27 Identities=41% Similarity=0.721 Sum_probs=22.3
Q ss_pred eEEEcCcCCcceecC----CCCCeecCCCCC
Q psy2244 16 IEKYYLECHFENEIR----PRDPIRCRECGY 42 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik----~~d~IRC~~CG~ 42 (73)
-+|+|.+||..++.- ..+.+.||.||.
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 479999999887643 346899999999
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=97.23 E-value=0.00045 Score=37.26 Aligned_cols=30 Identities=17% Similarity=0.389 Sum_probs=24.2
Q ss_pred eEEEcCcCCcceecCC------CCCeecCCCCCeEE
Q psy2244 16 IEKYYLECHFENEIRP------RDPIRCRECGYRIM 45 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~------~d~IRC~~CG~RIL 45 (73)
|...|.+|++.+.+.. +..++|++||+.+.
T Consensus 1 M~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 1 MRIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred CEEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 5688999999988873 23599999999764
No 10
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=96.54 E-value=0.003 Score=42.93 Aligned_cols=39 Identities=10% Similarity=0.247 Sum_probs=30.1
Q ss_pred CcceEEEcCcCCcceecC-------CCCCeecCCCCCeEEEeeeCC
Q psy2244 13 PGDIEKYYLECHFENEIR-------PRDPIRCRECGYRIMYKKRTK 51 (73)
Q Consensus 13 ~~~v~YiC~~Cg~e~~ik-------~~d~IRC~~CG~RILyKkRt~ 51 (73)
.+...|+|..||..++.. +.....||+||..+.....+.
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn~~ 140 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEEDDNSE 140 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEcCchh
Confidence 456799999999987753 222399999999998876654
No 11
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=96.26 E-value=0.006 Score=33.54 Aligned_cols=29 Identities=24% Similarity=0.506 Sum_probs=23.3
Q ss_pred eEEEcCcCCcceecCC------CCCeecCCCCCeE
Q psy2244 16 IEKYYLECHFENEIRP------RDPIRCRECGYRI 44 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~------~d~IRC~~CG~RI 44 (73)
|.-.|.+|++..+++. +..++|+.||+.+
T Consensus 1 M~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 1 MIITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred CEEECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 4567999999988872 3569999999864
No 12
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=96.21 E-value=0.004 Score=42.38 Aligned_cols=31 Identities=19% Similarity=0.427 Sum_probs=24.8
Q ss_pred CcceEEEcCcCCcceecCC--------------------CCCeecCCCCCe
Q psy2244 13 PGDIEKYYLECHFENEIRP--------------------RDPIRCRECGYR 43 (73)
Q Consensus 13 ~~~v~YiC~~Cg~e~~ik~--------------------~d~IRC~~CG~R 43 (73)
..+..+.|.+||..+.+.. ....+||.||.+
T Consensus 66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 3458899999999988862 345789999985
No 13
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=96.18 E-value=0.0014 Score=33.65 Aligned_cols=26 Identities=27% Similarity=0.631 Sum_probs=19.6
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
|+-.|.+||++++. +.--|++||.++
T Consensus 1 m~~~Cp~Cg~~~~~---~~~fC~~CG~~L 26 (26)
T PF13248_consen 1 MEMFCPNCGAEIDP---DAKFCPNCGAKL 26 (26)
T ss_pred CcCCCcccCCcCCc---ccccChhhCCCC
Confidence 35579999996533 457899999875
No 14
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=96.11 E-value=0.0087 Score=32.86 Aligned_cols=29 Identities=17% Similarity=0.417 Sum_probs=23.5
Q ss_pred eEEEcCcCCcceecCC------CCCeecCCCCCeE
Q psy2244 16 IEKYYLECHFENEIRP------RDPIRCRECGYRI 44 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~------~d~IRC~~CG~RI 44 (73)
|.-.|.+|++.+++.. +..+||++|++..
T Consensus 1 M~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 1 MIITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred CEEECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 4557999999988773 4679999999865
No 15
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=96.03 E-value=0.0041 Score=41.40 Aligned_cols=31 Identities=16% Similarity=0.230 Sum_probs=25.7
Q ss_pred cceEEEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 14 GDIEKYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
.+....|.+||..+.+....-.+||.||.+-
T Consensus 68 vp~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 68 EKVELECKDCSHVFKPNALDYGVCEKCHSKN 98 (117)
T ss_pred cCCEEEhhhCCCccccCCccCCcCcCCCCCc
Confidence 4577899999999988866667899999853
No 16
>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=95.89 E-value=0.0038 Score=32.67 Aligned_cols=22 Identities=32% Similarity=0.561 Sum_probs=18.0
Q ss_pred EcCcCCcceecCCCCCeecCCCCCe
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
.|.+|++++.. ....||+|||.
T Consensus 2 ~CP~C~~~V~~---~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPE---SAKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchh---hcCcCCCCCCC
Confidence 58899999954 45789999985
No 17
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=95.84 E-value=0.0031 Score=31.99 Aligned_cols=23 Identities=35% Similarity=0.632 Sum_probs=18.2
Q ss_pred EcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
.|.+||++++- +..-|++||.+|
T Consensus 1 ~Cp~CG~~~~~---~~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEIED---DAKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCCCC---cCcchhhhCCcC
Confidence 48899999853 457799999875
No 18
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=95.83 E-value=0.011 Score=36.87 Aligned_cols=35 Identities=29% Similarity=0.705 Sum_probs=20.6
Q ss_pred ccccC-Ccc--eEEEcCcCCcceecC------CCCCeecCCCCC
Q psy2244 8 VGKCL-PGD--IEKYYLECHFENEIR------PRDPIRCRECGY 42 (73)
Q Consensus 8 ~~~~~-~~~--v~YiC~~Cg~e~~ik------~~d~IRC~~CG~ 42 (73)
||..+ |.. +.+.|.+||.+.-.+ .+.+-+||+||+
T Consensus 15 Cg~~i~p~e~~v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 15 CGREIAPGETAVKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred CCCEeccCCceeEeeCCCCCceeeehhhhHHHcCCceECCCcCc
Confidence 45555 332 667777777544332 456677777775
No 19
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=95.73 E-value=0.0081 Score=39.84 Aligned_cols=30 Identities=17% Similarity=0.313 Sum_probs=25.1
Q ss_pred cceEEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 14 GDIEKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
.|....|.+||..+.+......+||.||..
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 67 QEAECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred eCcEEEcccCCCeeecCCccCCcCcCcCCC
Confidence 457889999999998876666789999975
No 20
>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=95.66 E-value=0.0037 Score=41.15 Aligned_cols=29 Identities=24% Similarity=0.377 Sum_probs=22.1
Q ss_pred cceEEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 14 GDIEKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
.|....|.+||.+++++... ..||.||.+
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~-~~CP~Cgs~ 95 (113)
T PF01155_consen 67 VPARARCRDCGHEFEPDEFD-FSCPRCGSP 95 (113)
T ss_dssp E--EEEETTTS-EEECHHCC-HH-SSSSSS
T ss_pred cCCcEECCCCCCEEecCCCC-CCCcCCcCC
Confidence 35778999999999998777 889999996
No 21
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=95.63 E-value=0.0029 Score=47.48 Aligned_cols=30 Identities=27% Similarity=0.627 Sum_probs=22.6
Q ss_pred EEcCcCCcceec-------CCCCCeecCCCCCeEEEee
Q psy2244 18 KYYLECHFENEI-------RPRDPIRCRECGYRIMYKK 48 (73)
Q Consensus 18 YiC~~Cg~e~~i-------k~~d~IRC~~CG~RILyKk 48 (73)
=.|+.|+..... +..+.|.||+|| ||||..
T Consensus 198 ~~C~GC~m~l~~~~~~~V~~~d~iv~CP~Cg-RILy~~ 234 (239)
T COG1579 198 RVCGGCHMKLPSQTLSKVRKKDEIVFCPYCG-RILYYD 234 (239)
T ss_pred CcccCCeeeecHHHHHHHhcCCCCccCCccc-hHHHhh
Confidence 369999877542 266889999998 787754
No 22
>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=95.62 E-value=0.0099 Score=31.85 Aligned_cols=25 Identities=20% Similarity=0.409 Sum_probs=20.7
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCC
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
.|+|..||-..+.+. ++-+||.||.
T Consensus 1 ~~~C~~CGy~y~~~~-~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYDGEE-APWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEECCCc-CCCcCcCCCC
Confidence 489999999876544 6679999997
No 23
>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=95.43 E-value=0.014 Score=35.14 Aligned_cols=33 Identities=21% Similarity=0.424 Sum_probs=26.2
Q ss_pred eEEEcCcCCcceecCC---CCCeecCCCCCeEEEee
Q psy2244 16 IEKYYLECHFENEIRP---RDPIRCRECGYRIMYKK 48 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~---~d~IRC~~CG~RILyKk 48 (73)
|...|..||.++++.. +..+.|+.||..+-.-.
T Consensus 1 ~~~~CP~CG~~iev~~~~~GeiV~Cp~CGaeleVv~ 36 (54)
T TIGR01206 1 MQFECPDCGAEIELENPELGELVICDECGAELEVVS 36 (54)
T ss_pred CccCCCCCCCEEecCCCccCCEEeCCCCCCEEEEEe
Confidence 3578999999999874 67899999999664433
No 24
>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=95.31 E-value=0.014 Score=40.84 Aligned_cols=39 Identities=23% Similarity=0.327 Sum_probs=31.3
Q ss_pred ceeccccCCcceEEEcCcCCcceecC-CCCCeecCCCCCeE
Q psy2244 5 QVLVGKCLPGDIEKYYLECHFENEIR-PRDPIRCRECGYRI 44 (73)
Q Consensus 5 ~~l~~~~~~~~v~YiC~~Cg~e~~ik-~~d~IRC~~CG~RI 44 (73)
.|-+| +.+++-.|.|-+||..+.+. +.....||+||+.-
T Consensus 101 ~Y~sG-E~~g~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~ 140 (146)
T PF07295_consen 101 VYHSG-EVVGPGTLVCENCGHEVELTHPERLPPCPKCGHTE 140 (146)
T ss_pred CeecC-cEecCceEecccCCCEEEecCCCcCCCCCCCCCCe
Confidence 45555 56788899999999999988 44567899999864
No 25
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=95.27 E-value=0.01 Score=39.72 Aligned_cols=27 Identities=26% Similarity=0.496 Sum_probs=22.7
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCC
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
..-+|.+||+.|-==.+++|.||+||.
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~ 34 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGT 34 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCC
Confidence 567899999997655559999999998
No 26
>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=95.22 E-value=0.02 Score=31.16 Aligned_cols=26 Identities=23% Similarity=0.392 Sum_probs=20.5
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCC
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
+.|+|..||...+-+. .+-+||.||.
T Consensus 1 ~~~~C~~CG~i~~g~~-~p~~CP~Cg~ 26 (34)
T cd00729 1 KVWVCPVCGYIHEGEE-APEKCPICGA 26 (34)
T ss_pred CeEECCCCCCEeECCc-CCCcCcCCCC
Confidence 3699999998876442 4569999998
No 27
>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=95.20 E-value=0.018 Score=30.42 Aligned_cols=26 Identities=23% Similarity=0.454 Sum_probs=16.3
Q ss_pred EcCcCCcceecCCC-CCeecCCCCCeE
Q psy2244 19 YYLECHFENEIRPR-DPIRCRECGYRI 44 (73)
Q Consensus 19 iC~~Cg~e~~ik~~-d~IRC~~CG~RI 44 (73)
-|+.||....+... -..+|+.||+..
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-EE
T ss_pred ccCcCCccccCCCCcCEeECCCCcCEe
Confidence 38999999887754 779999999864
No 28
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=94.83 E-value=0.039 Score=34.16 Aligned_cols=27 Identities=26% Similarity=0.444 Sum_probs=12.5
Q ss_pred EcCcCCcceecCC-CCCeecCCCCCeEE
Q psy2244 19 YYLECHFENEIRP-RDPIRCRECGYRIM 45 (73)
Q Consensus 19 iC~~Cg~e~~ik~-~d~IRC~~CG~RIL 45 (73)
+|..||..+.... ...-.||+||.-+|
T Consensus 9 ~CtSCg~~i~~~~~~~~F~CPnCG~~~I 36 (59)
T PRK14890 9 KCTSCGIEIAPREKAVKFLCPNCGEVII 36 (59)
T ss_pred cccCCCCcccCCCccCEeeCCCCCCeeE
Confidence 4555555544332 34445555555433
No 29
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=94.80 E-value=0.025 Score=37.42 Aligned_cols=28 Identities=21% Similarity=0.495 Sum_probs=22.5
Q ss_pred ceEEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 15 DIEKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
|....|.+||.++.+.... .+||.||..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~-~~CP~Cgs~ 95 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQHD-AQCPHCHGE 95 (113)
T ss_pred CcEEEcccCCCEEecCCcC-ccCcCCCCC
Confidence 5678999999999887544 459999974
No 30
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=94.63 E-value=0.02 Score=30.96 Aligned_cols=26 Identities=23% Similarity=0.381 Sum_probs=16.4
Q ss_pred EcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
+|..|+.+.....+...-|+.|||-|
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCPECGHEW 29 (30)
T ss_dssp --TTT-----EE-SSSEEETTTTEEE
T ss_pred CCCCCCCcceeccCCEEeCCcccccC
Confidence 68999999999999999999999865
No 31
>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=94.46 E-value=0.033 Score=36.93 Aligned_cols=29 Identities=21% Similarity=0.214 Sum_probs=23.4
Q ss_pred cceEEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 14 GDIEKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
.+....|.+||.++.+.... .+||.||..
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~-~~CP~Cgs~ 95 (115)
T TIGR00100 67 EPVECECEDCSEEVSPEIDL-YRCPKCHGI 95 (115)
T ss_pred eCcEEEcccCCCEEecCCcC-ccCcCCcCC
Confidence 35778999999999887543 779999984
No 32
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=94.38 E-value=0.069 Score=29.81 Aligned_cols=23 Identities=26% Similarity=0.543 Sum_probs=18.1
Q ss_pred cCcCCcceecCCC---CCeecCCCCC
Q psy2244 20 YLECHFENEIRPR---DPIRCRECGY 42 (73)
Q Consensus 20 C~~Cg~e~~ik~~---d~IRC~~CG~ 42 (73)
|.+||.....+.. ....|+.|||
T Consensus 3 Cp~Cg~~l~~~~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 3 CPKCGNMLIPKEGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCccccccCCCCCEEECCcCCC
Confidence 8899998776643 3588999998
No 33
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=94.00 E-value=0.043 Score=28.54 Aligned_cols=23 Identities=26% Similarity=0.616 Sum_probs=16.2
Q ss_pred cCcCCcceecCC-CCCeecCCCCC
Q psy2244 20 YLECHFENEIRP-RDPIRCRECGY 42 (73)
Q Consensus 20 C~~Cg~e~~ik~-~d~IRC~~CG~ 42 (73)
|..||..+..+. .-.-.||+||.
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 567777766554 56678888884
No 34
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=93.86 E-value=0.056 Score=39.37 Aligned_cols=33 Identities=15% Similarity=0.134 Sum_probs=26.2
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCCeEEEeeeCC
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTK 51 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~ 51 (73)
-.|+|-.|++.+. .+.-.||.||++++-|....
T Consensus 138 w~~rC~GC~~~f~---~~~~~Cp~CG~~~~~~~~~~ 170 (177)
T COG1439 138 WRLRCHGCKRIFP---EPKDFCPICGSPLKRKRVKS 170 (177)
T ss_pred eeEEEecCceecC---CCCCcCCCCCCceEEeeech
Confidence 4699999999998 55568999999976665443
No 35
>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=93.84 E-value=0.044 Score=38.03 Aligned_cols=34 Identities=12% Similarity=0.183 Sum_probs=27.1
Q ss_pred CcceEEEcCcCCcceecC--CCCCeecCCCCCeEEE
Q psy2244 13 PGDIEKYYLECHFENEIR--PRDPIRCRECGYRIMY 46 (73)
Q Consensus 13 ~~~v~YiC~~Cg~e~~ik--~~d~IRC~~CG~RILy 46 (73)
.+...|+|..|+...+.. ....-.||.||.-..+
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAMELNFTCPRCGAMLDY 140 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHHcCCcCCCCCCEeee
Confidence 456899999999887766 3356899999997655
No 36
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=93.82 E-value=0.04 Score=39.08 Aligned_cols=35 Identities=17% Similarity=0.366 Sum_probs=27.8
Q ss_pred CcceEEEcCcCCcceecC--CCCCeecCCCCCeEEEe
Q psy2244 13 PGDIEKYYLECHFENEIR--PRDPIRCRECGYRIMYK 47 (73)
Q Consensus 13 ~~~v~YiC~~Cg~e~~ik--~~d~IRC~~CG~RILyK 47 (73)
.+...|+|.+||...... ....-.||.||.-..+-
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~~ 149 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEEY 149 (178)
T ss_pred cCCCEEECCCCCcEEeHHHHhhcCCcCCCCCCCCeec
Confidence 346899999999998766 34568999999987763
No 37
>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=93.66 E-value=0.054 Score=32.30 Aligned_cols=38 Identities=26% Similarity=0.468 Sum_probs=28.6
Q ss_pred ceeccccC---CcceEEEcCcCCcceecCC-----CCCeecCCCCC
Q psy2244 5 QVLVGKCL---PGDIEKYYLECHFENEIRP-----RDPIRCRECGY 42 (73)
Q Consensus 5 ~~l~~~~~---~~~v~YiC~~Cg~e~~ik~-----~d~IRC~~CG~ 42 (73)
++|+|++- .....-||.+|..-+.+-+ .-.-||++||+
T Consensus 7 d~L~G~d~~~~~~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 7 DVLLGDDPTSPSNRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred HHHhCCCCccccCceeEECcccchhhcccccccCCceEEEcCCCCC
Confidence 67888887 6678889999987765542 12578999996
No 38
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=93.65 E-value=0.049 Score=36.58 Aligned_cols=28 Identities=29% Similarity=0.593 Sum_probs=21.0
Q ss_pred cceEEEcCcCCcceecCCCC------CeecCCCCC
Q psy2244 14 GDIEKYYLECHFENEIRPRD------PIRCRECGY 42 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~~d------~IRC~~CG~ 42 (73)
.+....| +||.++.+...+ ...||.||.
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs 100 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGN 100 (124)
T ss_pred cCeeEEe-eCcCcccccccchhccccCCcCcCCCC
Confidence 4678899 999997765221 267999996
No 39
>PF14353 CpXC: CpXC protein
Probab=93.32 E-value=0.14 Score=33.48 Aligned_cols=42 Identities=24% Similarity=0.590 Sum_probs=33.3
Q ss_pred EcCcCCcceecCC-------C-------------CCeecCCCCC------eEEEeeeCCeeEEEeecc
Q psy2244 19 YYLECHFENEIRP-------R-------------DPIRCRECGY------RIMYKKRTKRCILYFKPQ 60 (73)
Q Consensus 19 iC~~Cg~e~~ik~-------~-------------d~IRC~~CG~------RILyKkRt~r~vqf~~~~ 60 (73)
.|..||..++.+. . -...||+||+ .+||--..++.+-|..|+
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~~~~~~i~~~P~ 70 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYHDPEKKFMIYYFPD 70 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEEcCCCCEEEEEcCC
Confidence 5888988876541 1 3588999997 678988889888888888
No 40
>PRK12496 hypothetical protein; Provisional
Probab=93.25 E-value=0.048 Score=38.15 Aligned_cols=28 Identities=21% Similarity=0.303 Sum_probs=22.0
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCeEE
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYRIM 45 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~RIL 45 (73)
.|+|..||+.++..... -.||.||+++-
T Consensus 127 ~~~C~gC~~~~~~~~~~-~~C~~CG~~~~ 154 (164)
T PRK12496 127 RKVCKGCKKKYPEDYPD-DVCEICGSPVK 154 (164)
T ss_pred eEECCCCCccccCCCCC-CcCCCCCChhh
Confidence 59999999998765422 48999999763
No 41
>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=92.90 E-value=0.063 Score=37.60 Aligned_cols=29 Identities=10% Similarity=-0.042 Sum_probs=24.3
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
...+|..||+.|---.+++|.||+||.-.
T Consensus 8 tKr~Cp~cg~kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred ccccCCCcCccccccCCCCccCCCcCCcc
Confidence 56789999999876666999999999843
No 42
>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=92.53 E-value=0.11 Score=28.86 Aligned_cols=27 Identities=19% Similarity=0.468 Sum_probs=18.4
Q ss_pred EEcCcCCcce-ecC-CCCCeecCCCCCeE
Q psy2244 18 KYYLECHFEN-EIR-PRDPIRCRECGYRI 44 (73)
Q Consensus 18 YiC~~Cg~e~-~ik-~~d~IRC~~CG~RI 44 (73)
|+|..||... ..+ ....+.|++||.=|
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVL 29 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBE
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEe
Confidence 6899999875 223 44668999998643
No 43
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=92.22 E-value=0.049 Score=32.41 Aligned_cols=28 Identities=25% Similarity=0.464 Sum_probs=22.3
Q ss_pred ceEEEcCcCCcceecCC------------CCCeecCCCCC
Q psy2244 15 DIEKYYLECHFENEIRP------------RDPIRCRECGY 42 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~------------~d~IRC~~CG~ 42 (73)
+....|-+||+++.+.. ..+.||+.|..
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR~ 41 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCRQ 41 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHHH
Confidence 46789999999987663 47899999854
No 44
>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=92.19 E-value=0.23 Score=27.55 Aligned_cols=34 Identities=21% Similarity=0.538 Sum_probs=24.6
Q ss_pred eecCCCCCeEEEeeeCCeeEEEeeccCCCCCcceeeee
Q psy2244 35 IRCRECGYRIMYKKRTKRCILYFKPQTGGFPKLKTTVT 72 (73)
Q Consensus 35 IRC~~CG~RILyKkRt~r~vqf~~~~~~~~~~~~~~~~ 72 (73)
..||.||..++.|.-... .|+ .|.+||.=+.|..
T Consensus 2 ~~CP~Cg~~lv~r~~k~g--~F~--~Cs~yP~C~~~~~ 35 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG--KFL--GCSNYPECKYTEP 35 (39)
T ss_pred cCCCCCCceeEEEECCCC--CEE--ECCCCCCcCCeEe
Confidence 579999976666555555 664 7999998877653
No 45
>PF12773 DZR: Double zinc ribbon
Probab=92.13 E-value=0.063 Score=29.99 Aligned_cols=34 Identities=24% Similarity=0.418 Sum_probs=20.9
Q ss_pred cccCCcceEEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 9 GKCLPGDIEKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 9 ~~~~~~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
|..++... =.|..||..+.......+.|+.||..
T Consensus 5 g~~~~~~~-~fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 5 GTPNPDDA-KFCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred CCcCCccc-cCChhhcCChhhccCCCCCCcCCcCC
Confidence 44444332 34777777776555566778877774
No 46
>PRK11032 hypothetical protein; Provisional
Probab=91.96 E-value=0.15 Score=36.43 Aligned_cols=39 Identities=21% Similarity=0.252 Sum_probs=30.9
Q ss_pred ceeccccCCcceEEEcCcCCcceecC-CCCCeecCCCCCeE
Q psy2244 5 QVLVGKCLPGDIEKYYLECHFENEIR-PRDPIRCRECGYRI 44 (73)
Q Consensus 5 ~~l~~~~~~~~v~YiC~~Cg~e~~ik-~~d~IRC~~CG~RI 44 (73)
.|-.| ++.++-...|-+||....+. +.....||+||+.-
T Consensus 113 ~Y~sG-Evvg~G~LvC~~Cg~~~~~~~p~~i~pCp~C~~~~ 152 (160)
T PRK11032 113 VYHSG-EVVGLGNLVCEKCHHHLAFYTPEVLPLCPKCGHDQ 152 (160)
T ss_pred eeecc-eeeecceEEecCCCCEEEecCCCcCCCCCCCCCCe
Confidence 45555 56677789999999999887 56667999999853
No 47
>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=91.53 E-value=0.23 Score=32.67 Aligned_cols=34 Identities=21% Similarity=0.308 Sum_probs=23.9
Q ss_pred cceEEEcCcCCcceecCCC---CCeecCCCCCeEEEe
Q psy2244 14 GDIEKYYLECHFENEIRPR---DPIRCRECGYRIMYK 47 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~~---d~IRC~~CG~RILyK 47 (73)
..-.|.|..|+.++.-... ...+|+.||..+-..
T Consensus 120 ~~~~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~l~~~ 156 (157)
T PF10263_consen 120 KKYVYRCPSCGREYKRHRRSKRKRYRCGRCGGPLVQV 156 (157)
T ss_pred cceEEEcCCCCCEeeeecccchhhEECCCCCCEEEEc
Confidence 4468899999887655433 456899999776543
No 48
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=91.38 E-value=0.2 Score=27.32 Aligned_cols=26 Identities=23% Similarity=0.305 Sum_probs=20.9
Q ss_pred EEEcCcCCcceec-CCCCCeecCCCCC
Q psy2244 17 EKYYLECHFENEI-RPRDPIRCRECGY 42 (73)
Q Consensus 17 ~YiC~~Cg~e~~i-k~~d~IRC~~CG~ 42 (73)
.++|..|+.+..+ +..+-..|++||.
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGS 29 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCc
Confidence 4678888888777 7778888988885
No 49
>PF12773 DZR: Double zinc ribbon
Probab=91.34 E-value=0.1 Score=29.09 Aligned_cols=31 Identities=32% Similarity=0.573 Sum_probs=18.7
Q ss_pred ccccCC--cceEEEcCcCCcceecCCCCCeecCCCC
Q psy2244 8 VGKCLP--GDIEKYYLECHFENEIRPRDPIRCRECG 41 (73)
Q Consensus 8 ~~~~~~--~~v~YiC~~Cg~e~~ik~~d~IRC~~CG 41 (73)
+|..++ .....+|..||+.+... .--|++||
T Consensus 18 CG~~l~~~~~~~~~C~~Cg~~~~~~---~~fC~~CG 50 (50)
T PF12773_consen 18 CGTPLPPPDQSKKICPNCGAENPPN---AKFCPNCG 50 (50)
T ss_pred hcCChhhccCCCCCCcCCcCCCcCC---cCccCccc
Confidence 455555 45567777777764333 35677776
No 50
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=91.17 E-value=0.22 Score=30.81 Aligned_cols=36 Identities=19% Similarity=0.457 Sum_probs=25.7
Q ss_pred ccccCC--c-ceEEEcCcCCcceecC------CCCCeecCCCCCe
Q psy2244 8 VGKCLP--G-DIEKYYLECHFENEIR------PRDPIRCRECGYR 43 (73)
Q Consensus 8 ~~~~~~--~-~v~YiC~~Cg~e~~ik------~~d~IRC~~CG~R 43 (73)
||..+. + -+.+.|.+||.++--+ ...+.+||+||+.
T Consensus 13 Cg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CGF~ 57 (59)
T PRK14890 13 CGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGFE 57 (59)
T ss_pred CCCcccCCCccCEeeCCCCCCeeEeechhHHhcCCceECCCCCCc
Confidence 455554 3 4889999999873322 5678999999974
No 51
>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=91.00 E-value=0.2 Score=29.52 Aligned_cols=25 Identities=24% Similarity=0.626 Sum_probs=18.2
Q ss_pred EcCcCCcceec-CCCCCeecCCCCCe
Q psy2244 19 YYLECHFENEI-RPRDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e~~i-k~~d~IRC~~CG~R 43 (73)
.|..||....- .......|++||+.
T Consensus 30 ~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCcccccccccccceEEcCCCCCE
Confidence 47888877766 45567888888875
No 52
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=90.92 E-value=0.19 Score=29.49 Aligned_cols=26 Identities=23% Similarity=0.484 Sum_probs=20.8
Q ss_pred EcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
-|.+||.++.....+...|..||+..
T Consensus 22 fCP~Cg~~~m~~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSGFMAEHLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCCCcchheccCCcEECCCcCCEE
Confidence 68999987555566889999999864
No 53
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=90.74 E-value=0.19 Score=36.05 Aligned_cols=25 Identities=24% Similarity=0.403 Sum_probs=21.7
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
.|+|..||-...- -.|-+||.||.+
T Consensus 134 ~~vC~vCGy~~~g--e~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHEG--EAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCcccC--CCCCcCCCCCCh
Confidence 8999999999876 577899999963
No 54
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=90.65 E-value=0.34 Score=35.73 Aligned_cols=35 Identities=20% Similarity=0.245 Sum_probs=27.9
Q ss_pred CCcceEEEcCcCCcceecCCCCCeecCCCCCeEEEe
Q psy2244 12 LPGDIEKYYLECHFENEIRPRDPIRCRECGYRIMYK 47 (73)
Q Consensus 12 ~~~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyK 47 (73)
-.+.+.-+|++|+..... .++..+||+||+.-.=|
T Consensus 144 dlGVI~A~CsrC~~~L~~-~~~~l~Cp~Cg~tEkRK 178 (188)
T COG1096 144 DLGVIYARCSRCRAPLVK-KGNMLKCPNCGNTEKRK 178 (188)
T ss_pred cceEEEEEccCCCcceEE-cCcEEECCCCCCEEeee
Confidence 345677899999999877 78889999999965433
No 55
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=90.59 E-value=0.12 Score=41.76 Aligned_cols=32 Identities=22% Similarity=0.362 Sum_probs=26.1
Q ss_pred EcCcCCcceecCCCCCeecCCCCCeEEEeeeC
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYRIMYKKRT 50 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt 50 (73)
+|..||...+..-...-||+.||+|+=.+.+.
T Consensus 352 ~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 352 VCPRCGGRMKSAGRNGFRCKKCGTRARETLIK 383 (421)
T ss_pred CCCccCCchhhcCCCCcccccccccCCccccc
Confidence 79999999888866699999999987554443
No 56
>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=90.45 E-value=0.22 Score=30.75 Aligned_cols=21 Identities=33% Similarity=0.857 Sum_probs=17.7
Q ss_pred CCeecCCCCCeEEEeeeCCee
Q psy2244 33 DPIRCRECGYRIMYKKRTKRC 53 (73)
Q Consensus 33 d~IRC~~CG~RILyKkRt~r~ 53 (73)
..+.|++|||-=+|+..+...
T Consensus 35 ~~v~C~~CGYTE~Y~~~~~~~ 55 (64)
T PF09855_consen 35 TTVSCTNCGYTEFYKAKTSNG 55 (64)
T ss_pred EEEECCCCCCEEEEeecCccc
Confidence 568999999999999877654
No 57
>PHA00626 hypothetical protein
Probab=90.21 E-value=0.27 Score=30.58 Aligned_cols=26 Identities=27% Similarity=0.469 Sum_probs=17.6
Q ss_pred EcCcCCcceecC------CCCCeecCCCCCeE
Q psy2244 19 YYLECHFENEIR------PRDPIRCRECGYRI 44 (73)
Q Consensus 19 iC~~Cg~e~~ik------~~d~IRC~~CG~RI 44 (73)
.|.+||..+-++ ....-.|+.|||+-
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence 477888753333 35778899999853
No 58
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=89.68 E-value=0.22 Score=45.30 Aligned_cols=29 Identities=14% Similarity=0.308 Sum_probs=18.1
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCeEE
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYRIM 45 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~RIL 45 (73)
.|.|.+||+++..+.....+||+||....
T Consensus 692 vy~CPsCGaev~~des~a~~CP~CGtplv 720 (1337)
T PRK14714 692 VYVCPDCGAEVPPDESGRVECPRCDVELT 720 (1337)
T ss_pred ceeCccCCCccCCCccccccCCCCCCccc
Confidence 45777777766555444667777776443
No 59
>PRK00420 hypothetical protein; Validated
Probab=89.37 E-value=0.39 Score=32.58 Aligned_cols=32 Identities=16% Similarity=0.101 Sum_probs=24.7
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeEEEeee
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRIMYKKR 49 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkR 49 (73)
--|..||.+.--.....+.||.||..+.-+..
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v~~~ 55 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVYIVKSD 55 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCeeeeccH
Confidence 57999998865435667999999997776543
No 60
>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=89.36 E-value=0.31 Score=31.99 Aligned_cols=29 Identities=17% Similarity=0.207 Sum_probs=23.3
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
....|+.|+..+.+-.+....|.+|+++|
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~V 81 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRV 81 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccc
Confidence 45689999999888777789999999987
No 61
>PRK06450 threonine synthase; Validated
Probab=89.18 E-value=0.35 Score=36.78 Aligned_cols=29 Identities=28% Similarity=0.579 Sum_probs=21.9
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCCeEEE
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGYRIMY 46 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILy 46 (73)
+.++|.+||++... ....+|+.||..+..
T Consensus 2 ~~~~C~~Cg~~~~~--~~~~~C~~cg~~l~~ 30 (338)
T PRK06450 2 VKEVCMKCGKERES--IYEIRCKKCGGPFEI 30 (338)
T ss_pred ceeEECCcCCcCCC--cccccCCcCCCEeEE
Confidence 46899999999754 334799999975443
No 62
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=89.15 E-value=0.19 Score=33.85 Aligned_cols=25 Identities=28% Similarity=0.557 Sum_probs=20.7
Q ss_pred EEcCcCCcceecC-CCCCeecCCCCC
Q psy2244 18 KYYLECHFENEIR-PRDPIRCRECGY 42 (73)
Q Consensus 18 YiC~~Cg~e~~ik-~~d~IRC~~CG~ 42 (73)
-.|.+||-++..+ ...+-|||.|-+
T Consensus 59 a~CkkCGfef~~~~ik~pSRCP~CKS 84 (97)
T COG3357 59 ARCKKCGFEFRDDKIKKPSRCPKCKS 84 (97)
T ss_pred hhhcccCccccccccCCcccCCcchh
Confidence 4699999998874 566899999976
No 63
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=89.15 E-value=0.26 Score=29.94 Aligned_cols=26 Identities=23% Similarity=0.266 Sum_probs=20.4
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCC
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
...+|..||..+.. ..|.|.||.||-
T Consensus 4 ~~~~C~~Cg~~~~~-~dDiVvCp~Cga 29 (54)
T PF14446_consen 4 EGCKCPVCGKKFKD-GDDIVVCPECGA 29 (54)
T ss_pred cCccChhhCCcccC-CCCEEECCCCCC
Confidence 34689999998743 458899999984
No 64
>PRK07591 threonine synthase; Validated
Probab=88.97 E-value=0.34 Score=37.76 Aligned_cols=26 Identities=27% Similarity=0.369 Sum_probs=21.7
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
.++|.+||++..+... .+||.||.-+
T Consensus 18 ~l~C~~Cg~~~~~~~~--~~C~~cg~~l 43 (421)
T PRK07591 18 ALKCRECGAEYPLGPI--HVCEECFGPL 43 (421)
T ss_pred EEEeCCCCCcCCCCCC--ccCCCCCCeE
Confidence 5899999999987743 9999999744
No 65
>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=88.79 E-value=0.27 Score=33.61 Aligned_cols=25 Identities=20% Similarity=0.425 Sum_probs=22.2
Q ss_pred EcCcCCcceecCCCCCeecCCCCCe
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
-|..|+.+..-..++..-||+|||-
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~E 28 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYE 28 (109)
T ss_pred cCCcCCCcceEecCCeeECcccccc
Confidence 4889999999888999999999994
No 66
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=88.60 E-value=0.58 Score=31.39 Aligned_cols=32 Identities=16% Similarity=0.297 Sum_probs=23.6
Q ss_pred ceEEEcCcCCcceecC-CC---CCeecCCCCCeEEE
Q psy2244 15 DIEKYYLECHFENEIR-PR---DPIRCRECGYRIMY 46 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik-~~---d~IRC~~CG~RILy 46 (73)
.-.|.|..|+....-. .. ...+|..||.++.+
T Consensus 110 ~~~y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~l~~ 145 (146)
T smart00731 110 KYPYRCTGCGQRYLRVRRSNNVSRYRCGKCGGKLIL 145 (146)
T ss_pred eEEEECCCCCCCCceEccccCcceEEcCCCCCEEEe
Confidence 4689999999775422 11 45899999999875
No 67
>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=88.29 E-value=0.31 Score=39.64 Aligned_cols=39 Identities=23% Similarity=0.525 Sum_probs=26.8
Q ss_pred ceEEEcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEeec
Q psy2244 15 DIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKP 59 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~~~ 59 (73)
++. +|.+||.... +..-.||.||.+- -.+-+|++-|+.|
T Consensus 517 p~~-~C~~CG~~~~---~~~~~CP~CGs~~--~~~~~Rv~GYl~~ 555 (555)
T cd01675 517 PID-ICNDCGYIGE---GEGFKCPKCGSED--VEVISRITGYLGP 555 (555)
T ss_pred CCc-cCCCCCCCCc---CCCCCCcCCCCcC--ceEEEeeeeecCC
Confidence 444 9999998553 3447899999874 3445567777643
No 68
>PF14369 zf-RING_3: zinc-finger
Probab=87.89 E-value=0.67 Score=25.34 Aligned_cols=29 Identities=17% Similarity=0.429 Sum_probs=22.4
Q ss_pred EEEcCcCCcceecC--CCCCeecCCCCCeEE
Q psy2244 17 EKYYLECHFENEIR--PRDPIRCRECGYRIM 45 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik--~~d~IRC~~CG~RIL 45 (73)
.|=|-.|.+.+.+. ..+.+.||+|+...|
T Consensus 2 ~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFv 32 (35)
T PF14369_consen 2 RYWCHQCNRFVRIAPSPDSDVACPRCHGGFV 32 (35)
T ss_pred CEeCccCCCEeEeCcCCCCCcCCcCCCCcEe
Confidence 48899999999985 345566999997654
No 69
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=87.76 E-value=0.39 Score=32.85 Aligned_cols=28 Identities=32% Similarity=0.584 Sum_probs=23.9
Q ss_pred cceEEEcCcCCcceecCCCCCeecCCCCC
Q psy2244 14 GDIEKYYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
.|..-.|.+|+.++.+...+.. ||.||.
T Consensus 67 ~p~~~~C~~C~~~~~~e~~~~~-CP~C~s 94 (115)
T COG0375 67 EPAECWCLDCGQEVELEELDYR-CPKCGS 94 (115)
T ss_pred eccEEEeccCCCeecchhheeE-CCCCCC
Confidence 4577899999999998887766 999996
No 70
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=87.64 E-value=0.78 Score=32.08 Aligned_cols=35 Identities=17% Similarity=0.256 Sum_probs=27.6
Q ss_pred cCCcceEEEcCcCCcceecCCCCCeecCCCCCeEE
Q psy2244 11 CLPGDIEKYYLECHFENEIRPRDPIRCRECGYRIM 45 (73)
Q Consensus 11 ~~~~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RIL 45 (73)
+..+.+.=+|..||........+.+.|++||.+-.
T Consensus 143 ~~lGvv~a~~~~~g~~~~~~~~~~~~c~~~~~~e~ 177 (189)
T PRK09521 143 KDLGVIYAMCSRCRTPLVKKGENELKCPNCGNIET 177 (189)
T ss_pred CCceEEEEEccccCCceEECCCCEEECCCCCCEEe
Confidence 33456677899999998777768899999997643
No 71
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=87.24 E-value=0.5 Score=35.27 Aligned_cols=29 Identities=31% Similarity=0.562 Sum_probs=20.6
Q ss_pred cceEEEcCcCCccee----cCC---CCCeecCCCCC
Q psy2244 14 GDIEKYYLECHFENE----IRP---RDPIRCRECGY 42 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~----ik~---~d~IRC~~CG~ 42 (73)
+...+.|..||.+-. ++. ...+||.+||+
T Consensus 3 ~~iy~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~ 38 (201)
T COG1326 3 EEIYIECPSCGSEEVSHEVIKERGREPLVRCEECGT 38 (201)
T ss_pred ceEEEECCCCCcchhhHHHHHhcCCceEEEccCCCc
Confidence 457889999993321 232 24799999998
No 72
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=87.14 E-value=0.36 Score=30.63 Aligned_cols=51 Identities=16% Similarity=0.239 Sum_probs=26.8
Q ss_pred cccCCcc-eEEEcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEeeccCCCC
Q psy2244 9 GKCLPGD-IEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKPQTGGF 64 (73)
Q Consensus 9 ~~~~~~~-v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~~~~~~~~ 64 (73)
..++.+. ..|.|..|+.++... ..||+||..+- +.+.=..+.|+=-.++|.
T Consensus 8 ~~~L~~~~~~~~C~~C~~~~~~~----a~CPdC~~~Le-~LkACGAvdYFC~~c~gL 59 (70)
T PF07191_consen 8 QQELEWQGGHYHCEACQKDYKKE----AFCPDCGQPLE-VLKACGAVDYFCNHCHGL 59 (70)
T ss_dssp -SBEEEETTEEEETTT--EEEEE----EE-TTT-SB-E-EEEETTEEEEE-TTTT-E
T ss_pred CCccEEeCCEEECccccccceec----ccCCCcccHHH-HHHHhcccceeeccCCce
Confidence 3444444 389999999988776 78999987642 333444455555555543
No 73
>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=87.00 E-value=0.6 Score=29.57 Aligned_cols=33 Identities=18% Similarity=0.316 Sum_probs=22.0
Q ss_pred eEEEcCcCCcceecC-CCCCeecCCCCCeEEEeeeC
Q psy2244 16 IEKYYLECHFENEIR-PRDPIRCRECGYRIMYKKRT 50 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik-~~d~IRC~~CG~RILyKkRt 50 (73)
+.+.| +||.-.-.+ ....-+| .||++|=.|+|.
T Consensus 2 lifrC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~~r 35 (68)
T PF09082_consen 2 LIFRC-DCGRYLYAKEGAKTKKC-VCGKTLKVKERR 35 (68)
T ss_dssp EEEEE-TTS--EEEETT-SEEEE-TTTEEEE--SSS
T ss_pred EEEEe-cCCCEEEecCCcceeEe-cCCCeeeeeeEE
Confidence 46899 899986655 4466889 999998887775
No 74
>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=86.83 E-value=0.54 Score=25.93 Aligned_cols=28 Identities=21% Similarity=0.470 Sum_probs=21.9
Q ss_pred EEcCcCCcceecC---CCCCeecCCCCCeEE
Q psy2244 18 KYYLECHFENEIR---PRDPIRCRECGYRIM 45 (73)
Q Consensus 18 YiC~~Cg~e~~ik---~~d~IRC~~CG~RIL 45 (73)
.+|..||+...+. +...-.|..||..++
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGGELV 32 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTEBEB
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCCeeE
Confidence 5799999998776 456789999999653
No 75
>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=86.58 E-value=0.5 Score=29.89 Aligned_cols=24 Identities=21% Similarity=0.540 Sum_probs=18.7
Q ss_pred EcCcCCcceecCCCCCeecCCCCCe
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
-|.+||.....+ .+.+.|+.||+.
T Consensus 2 fC~~Cg~~l~~~-~~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPK-NGVYVCPSCGYE 25 (104)
T ss_pred CCcccCcccccC-CCeEECcCCCCc
Confidence 388999888654 357999999975
No 76
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=86.42 E-value=0.42 Score=33.63 Aligned_cols=27 Identities=26% Similarity=0.539 Sum_probs=17.0
Q ss_pred EEcCcCCcce----ecC---CCCCe----ecCCCCCeE
Q psy2244 18 KYYLECHFEN----EIR---PRDPI----RCRECGYRI 44 (73)
Q Consensus 18 YiC~~Cg~e~----~ik---~~d~I----RC~~CG~RI 44 (73)
++|..||.+. +.+ ++..| +|++||++-
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 4799999643 222 22235 499999963
No 77
>PRK10220 hypothetical protein; Provisional
Probab=86.41 E-value=0.53 Score=32.33 Aligned_cols=25 Identities=20% Similarity=0.355 Sum_probs=21.7
Q ss_pred EcCcCCcceecCCCCCeecCCCCCe
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
.|..|+.+..-..++..-||+|+|-
T Consensus 5 ~CP~C~seytY~d~~~~vCpeC~hE 29 (111)
T PRK10220 5 HCPKCNSEYTYEDNGMYICPECAHE 29 (111)
T ss_pred cCCCCCCcceEcCCCeEECCcccCc
Confidence 4889999988888888999999984
No 78
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=86.37 E-value=0.79 Score=32.07 Aligned_cols=30 Identities=23% Similarity=0.351 Sum_probs=22.8
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCeEEEe
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYRIMYK 47 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyK 47 (73)
.+-|..||...-- ....|-||.||+|.--.
T Consensus 28 ~~hCp~Cg~PLF~-KdG~v~CPvC~~~~~~v 57 (131)
T COG1645 28 AKHCPKCGTPLFR-KDGEVFCPVCGYREVVV 57 (131)
T ss_pred HhhCcccCCccee-eCCeEECCCCCceEEEe
Confidence 3679999999544 45569999999976544
No 79
>PRK04351 hypothetical protein; Provisional
Probab=86.22 E-value=1 Score=31.29 Aligned_cols=34 Identities=12% Similarity=0.206 Sum_probs=25.0
Q ss_pred ceEEEcCcCCcceecC---CCCCeecCCCCCeEEEee
Q psy2244 15 DIEKYYLECHFENEIR---PRDPIRCRECGYRIMYKK 48 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik---~~d~IRC~~CG~RILyKk 48 (73)
.-.|.|.+||....-. ....-+|..|+.++.++.
T Consensus 110 ~y~Y~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~L~~~~ 146 (149)
T PRK04351 110 NYLYECQSCGQQYLRKRRINTKRYRCGKCRGKLKLIN 146 (149)
T ss_pred eEEEECCCCCCEeeeeeecCCCcEEeCCCCcEeeecc
Confidence 3679999999764322 225589999999988763
No 80
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=86.20 E-value=0.38 Score=29.06 Aligned_cols=26 Identities=19% Similarity=0.193 Sum_probs=16.5
Q ss_pred EEEcCcCCcceec-CCC--CCeecCCCCC
Q psy2244 17 EKYYLECHFENEI-RPR--DPIRCRECGY 42 (73)
Q Consensus 17 ~YiC~~Cg~e~~i-k~~--d~IRC~~CG~ 42 (73)
++.|+.|++..-. ... -.|+||.||-
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCc
Confidence 4678888766433 222 3588888875
No 81
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=86.19 E-value=0.47 Score=36.62 Aligned_cols=26 Identities=19% Similarity=0.318 Sum_probs=21.6
Q ss_pred EcCcCCcceecCC-CCCeecCCCCCeE
Q psy2244 19 YYLECHFENEIRP-RDPIRCRECGYRI 44 (73)
Q Consensus 19 iC~~Cg~e~~ik~-~d~IRC~~CG~RI 44 (73)
-|+.||.+..... +....|++||++.
T Consensus 113 FCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 113 FCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred CCCCCCCcCccccCceeeeCCCCCCcc
Confidence 4999999988885 4678999999963
No 82
>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=85.88 E-value=0.53 Score=27.71 Aligned_cols=26 Identities=19% Similarity=0.321 Sum_probs=19.6
Q ss_pred EEEcCcCCcceecCCC----------------CCeecCCCCC
Q psy2244 17 EKYYLECHFENEIRPR----------------DPIRCRECGY 42 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~----------------d~IRC~~CG~ 42 (73)
.|+|..||-.-+...+ +.-+||.||.
T Consensus 1 ~y~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a 42 (50)
T cd00730 1 KYECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGA 42 (50)
T ss_pred CcCCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCC
Confidence 3899999988776533 3349999986
No 83
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=85.78 E-value=0.76 Score=28.73 Aligned_cols=30 Identities=20% Similarity=0.358 Sum_probs=23.9
Q ss_pred EEcCcCCcceecC-CCCCeecCCCCCeEEEe
Q psy2244 18 KYYLECHFENEIR-PRDPIRCRECGYRIMYK 47 (73)
Q Consensus 18 YiC~~Cg~e~~ik-~~d~IRC~~CG~RILyK 47 (73)
=.|..||.++.+. ..-.--||+||.-++|.
T Consensus 10 ~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~R 40 (61)
T COG2888 10 PVCTSCGREIAPGETAVKFPCPNCGEVEIYR 40 (61)
T ss_pred ceeccCCCEeccCCceeEeeCCCCCceeeeh
Confidence 3799999999555 45667899999888874
No 84
>PRK06260 threonine synthase; Validated
Probab=85.72 E-value=0.9 Score=34.86 Aligned_cols=27 Identities=26% Similarity=0.356 Sum_probs=21.7
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
.++|.+||.+..++.. ..+||.||.-+
T Consensus 3 ~~~C~~cg~~~~~~~~-~~~Cp~cg~~l 29 (397)
T PRK06260 3 WLKCIECGKEYDPDEI-IYTCPECGGLL 29 (397)
T ss_pred EEEECCCCCCCCCCCc-cccCCCCCCeE
Confidence 5899999999876644 47899999753
No 85
>KOG2846|consensus
Probab=85.45 E-value=0.35 Score=38.26 Aligned_cols=55 Identities=20% Similarity=0.277 Sum_probs=40.9
Q ss_pred ceeccccCCcceEEEcCcCCcceecCC-----CCCeecCCCCCeEEEeeeCCeeEEEeeccC
Q psy2244 5 QVLVGKCLPGDIEKYYLECHFENEIRP-----RDPIRCRECGYRIMYKKRTKRCILYFKPQT 61 (73)
Q Consensus 5 ~~l~~~~~~~~v~YiC~~Cg~e~~ik~-----~d~IRC~~CG~RILyKkRt~r~vqf~~~~~ 61 (73)
+||+|++....---||+.|+.-+.+-. .-.-+|++|++- -+.|..+...+++|+.
T Consensus 208 d~lvGdsP~~ryALIC~~C~~HNGla~~ee~~yi~F~C~~Cn~L--N~~~k~~e~s~~~~~~ 267 (328)
T KOG2846|consen 208 DYLVGDSPNNRYALICSQCHHHNGLARKEEYEYITFRCPHCNAL--NPAKKSPENSLEAPQP 267 (328)
T ss_pred HHHhcCCCcchhhhcchhhccccCcCChhhcCceEEECcccccc--CCCcCCcccccccCCC
Confidence 789999888888889999998887653 345799999974 4555555666666553
No 86
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=85.19 E-value=1.3 Score=27.24 Aligned_cols=30 Identities=20% Similarity=0.454 Sum_probs=23.3
Q ss_pred ceEEEcCcCCcceec--CCCCCeecCCCCCeE
Q psy2244 15 DIEKYYLECHFENEI--RPRDPIRCRECGYRI 44 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~i--k~~d~IRC~~CG~RI 44 (73)
=+.=+|.+|+.+.-+ .....++|..||.-+
T Consensus 9 F~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L 40 (59)
T PRK00415 9 FLKVKCPDCGNEQVVFSHASTVVRCLVCGKTL 40 (59)
T ss_pred EEEEECCCCCCeEEEEecCCcEEECcccCCCc
Confidence 367799999998543 366889999999744
No 87
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=85.06 E-value=0.5 Score=27.34 Aligned_cols=24 Identities=29% Similarity=0.596 Sum_probs=18.1
Q ss_pred EEcCcCCcceec------CCC-CCeecCCCC
Q psy2244 18 KYYLECHFENEI------RPR-DPIRCRECG 41 (73)
Q Consensus 18 YiC~~Cg~e~~i------k~~-d~IRC~~CG 41 (73)
-.|+.|+..+.. +.. ..+.||+||
T Consensus 23 ~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~Cg 53 (56)
T PF02591_consen 23 GTCSGCHMELPPQELNEIRKGDEIVFCPNCG 53 (56)
T ss_pred CccCCCCEEcCHHHHHHHHcCCCeEECcCCC
Confidence 379999887653 333 679999998
No 88
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=85.06 E-value=1.4 Score=24.48 Aligned_cols=21 Identities=29% Similarity=0.746 Sum_probs=16.9
Q ss_pred CCeecCCCCCeEEEeeeCCee
Q psy2244 33 DPIRCRECGYRIMYKKRTKRC 53 (73)
Q Consensus 33 d~IRC~~CG~RILyKkRt~r~ 53 (73)
..|+|.+||++...+.++++-
T Consensus 4 g~l~C~~CG~~m~~~~~~~~~ 24 (58)
T PF13408_consen 4 GLLRCGHCGSKMTRRKRKGKY 24 (58)
T ss_pred CcEEcccCCcEeEEEECCCCc
Confidence 568999999998888877544
No 89
>PRK04173 glycyl-tRNA synthetase; Provisional
Probab=84.80 E-value=0.86 Score=36.21 Aligned_cols=47 Identities=26% Similarity=0.530 Sum_probs=32.4
Q ss_pred ceEEEcCcCCcceecCC----------------------CCCeecCCCCCe---------EEEeee-----CCeeEEEee
Q psy2244 15 DIEKYYLECHFENEIRP----------------------RDPIRCRECGYR---------IMYKKR-----TKRCILYFK 58 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~----------------------~d~IRC~~CG~R---------ILyKkR-----t~r~vqf~~ 58 (73)
+.+|.|..|+.....+. ..+++||+||.- .||+-+ ..+.-.|+.
T Consensus 84 d~m~~~~~~~~~~r~d~~~~~~~~~~~~~~~~~~~~~~~~~~m~cp~~~~~~~~~~~~f~l~f~~~~g~~~~~~~~~~lR 163 (456)
T PRK04173 84 DPLVECKKCKKRYRADHLIEELGIDAEGLSNEELKELIRENDIKCPECGGENWTEVRQFNLMFKTFIGPVEDSKSLGYLR 163 (456)
T ss_pred CceeEeCCCCCEeechhhhHHHhhhhccccHHHHHHHHHHhCCCCCCCCCCCCcCccchhhceeecccCccCCCcceeec
Confidence 46788999987654332 137999999865 888866 445566776
Q ss_pred ccC
Q psy2244 59 PQT 61 (73)
Q Consensus 59 ~~~ 61 (73)
|.+
T Consensus 164 pet 166 (456)
T PRK04173 164 PET 166 (456)
T ss_pred ccc
Confidence 643
No 90
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=84.75 E-value=0.63 Score=36.90 Aligned_cols=32 Identities=13% Similarity=0.328 Sum_probs=24.4
Q ss_pred EEcCcCCcceecC---CCCCeecCCCCCeEEEeeeC
Q psy2244 18 KYYLECHFENEIR---PRDPIRCRECGYRIMYKKRT 50 (73)
Q Consensus 18 YiC~~Cg~e~~ik---~~d~IRC~~CG~RILyKkRt 50 (73)
-.|.+|+..++.. ++...+||.||+.+ |..++
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L-~~~~~ 45 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTL-TVRWD 45 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCC-cCCCC
Confidence 4599999887654 56779999999987 44433
No 91
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=84.69 E-value=0.22 Score=34.31 Aligned_cols=33 Identities=15% Similarity=0.259 Sum_probs=22.6
Q ss_pred eEEEcCcCCcceecC-CCCCeecCCCCCeE-EEee
Q psy2244 16 IEKYYLECHFENEIR-PRDPIRCRECGYRI-MYKK 48 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik-~~d~IRC~~CG~RI-LyKk 48 (73)
|..+|.+||..++-- ..-.--||+||.|- +|-+
T Consensus 1 MpH~CtrCG~vf~~g~~~il~GCp~CG~nkF~yv~ 35 (112)
T COG3364 1 MPHQCTRCGEVFDDGSEEILSGCPKCGCNKFLYVP 35 (112)
T ss_pred CCceecccccccccccHHHHccCccccchheEecc
Confidence 456899999998753 22334699999963 4433
No 92
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=84.16 E-value=0.48 Score=28.34 Aligned_cols=24 Identities=38% Similarity=0.996 Sum_probs=20.5
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
..||-.|++.+.++ +.+|+.|||.
T Consensus 14 k~ICrkC~ARnp~~---A~~CRKCg~~ 37 (48)
T PRK04136 14 KKICMRCNARNPWR---ATKCRKCGYK 37 (48)
T ss_pred ccchhcccCCCCcc---ccccccCCCC
Confidence 57999999998766 5899999995
No 93
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=84.11 E-value=2.6 Score=26.75 Aligned_cols=30 Identities=17% Similarity=0.372 Sum_probs=23.1
Q ss_pred eEEEcCcCCccee--cCCCCCeecCCCCCeEE
Q psy2244 16 IEKYYLECHFENE--IRPRDPIRCRECGYRIM 45 (73)
Q Consensus 16 v~YiC~~Cg~e~~--ik~~d~IRC~~CG~RIL 45 (73)
+.-+|.+|+.+.- ..+...|+|..||--|.
T Consensus 18 l~VkCpdC~N~q~vFshast~V~C~~CG~~l~ 49 (67)
T COG2051 18 LRVKCPDCGNEQVVFSHASTVVTCLICGTTLA 49 (67)
T ss_pred EEEECCCCCCEEEEeccCceEEEecccccEEE
Confidence 6678999998844 34678899999996443
No 94
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=84.05 E-value=0.27 Score=39.76 Aligned_cols=26 Identities=23% Similarity=0.519 Sum_probs=21.1
Q ss_pred EcCcCCcceecCCCCC--eecCCCCCeE
Q psy2244 19 YYLECHFENEIRPRDP--IRCRECGYRI 44 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~--IRC~~CG~RI 44 (73)
-|.+|.+..++..... -|||+||.+|
T Consensus 248 AC~rC~t~y~le~A~~~~wrCpkCGg~i 275 (403)
T COG1379 248 ACSRCYTRYSLEEAKSLRWRCPKCGGKI 275 (403)
T ss_pred HHHHhhhccCcchhhhhcccCcccccch
Confidence 3999999998886544 8999999944
No 95
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=83.72 E-value=0.67 Score=38.94 Aligned_cols=22 Identities=23% Similarity=0.523 Sum_probs=15.2
Q ss_pred EcCcCCcceecCCCCCeecCCCCCe
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
.|.+||+++... .--|++||.+
T Consensus 29 ~Cp~CG~~~~~~---~~fC~~CG~~ 50 (645)
T PRK14559 29 PCPQCGTEVPVD---EAHCPNCGAE 50 (645)
T ss_pred cCCCCCCCCCcc---cccccccCCc
Confidence 577777775443 3578888885
No 96
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=83.67 E-value=1.3 Score=24.15 Aligned_cols=31 Identities=26% Similarity=0.458 Sum_probs=18.1
Q ss_pred CeecCCCCCeEEEeeeCCeeEEEeeccCCCCC
Q psy2244 34 PIRCRECGYRIMYKKRTKRCILYFKPQTGGFP 65 (73)
Q Consensus 34 ~IRC~~CG~RILyKkRt~r~vqf~~~~~~~~~ 65 (73)
+.+||+||...+++. ..+...+.-.+..|+|
T Consensus 2 ~~~Cp~Cg~~~~~~~-g~~~r~i~~l~~~~~~ 32 (47)
T PF14690_consen 2 PPRCPHCGSPSVHRH-GYKTRRIRHLPIGGRP 32 (47)
T ss_pred CccCCCcCCCceECC-ceEEEEEeecccCCEE
Confidence 568999998875542 2233334444555554
No 97
>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=82.76 E-value=0.87 Score=25.53 Aligned_cols=25 Identities=20% Similarity=0.474 Sum_probs=12.1
Q ss_pred EEcCcCCcc--eecCCCCCeecCCCCC
Q psy2244 18 KYYLECHFE--NEIRPRDPIRCRECGY 42 (73)
Q Consensus 18 YiC~~Cg~e--~~ik~~d~IRC~~CG~ 42 (73)
..|..||.. ..++....-+|..|++
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 446666543 2233334455555554
No 98
>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=82.17 E-value=1.2 Score=24.18 Aligned_cols=24 Identities=29% Similarity=0.609 Sum_probs=14.9
Q ss_pred cCcCCcceecCC--CCCeecCCCCCe
Q psy2244 20 YLECHFENEIRP--RDPIRCRECGYR 43 (73)
Q Consensus 20 C~~Cg~e~~ik~--~d~IRC~~CG~R 43 (73)
|.+||.....+. ...++|+.|||-
T Consensus 4 Cp~C~nlL~p~~~~~~~~~C~~C~Y~ 29 (35)
T PF02150_consen 4 CPECGNLLYPKEDKEKRVACRTCGYE 29 (35)
T ss_dssp ETTTTSBEEEEEETTTTEEESSSS-E
T ss_pred CCCCCccceEcCCCccCcCCCCCCCc
Confidence 778887765552 233378888873
No 99
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=81.90 E-value=1 Score=36.55 Aligned_cols=39 Identities=28% Similarity=0.561 Sum_probs=28.6
Q ss_pred eeccccCCcc-eEEEcCcCCcceecCC----CCCeecCCCCCeE
Q psy2244 6 VLVGKCLPGD-IEKYYLECHFENEIRP----RDPIRCRECGYRI 44 (73)
Q Consensus 6 ~l~~~~~~~~-v~YiC~~Cg~e~~ik~----~d~IRC~~CG~RI 44 (73)
.|+.+++... +.|.|..||.++.... ....+||+||--+
T Consensus 315 llv~Edl~~~r~~~~c~~~~~e~~~t~~~~~~~~~~~~~~~~e~ 358 (411)
T COG1503 315 LLVSEDLEKERVTYKCPTCGYENLKSKREFEQKRFRCPECGSEM 358 (411)
T ss_pred EEeeccccccceeecCCCcchhhhhcccccccccccCccccccc
Confidence 4667777765 9999999999986542 1234999999743
No 100
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=81.16 E-value=0.59 Score=32.89 Aligned_cols=11 Identities=45% Similarity=1.262 Sum_probs=7.2
Q ss_pred CCeecCCCCCe
Q psy2244 33 DPIRCRECGYR 43 (73)
Q Consensus 33 d~IRC~~CG~R 43 (73)
....|++||||
T Consensus 28 ~sf~C~~CGyk 38 (160)
T smart00709 28 MSFECEHCGYR 38 (160)
T ss_pred EEEECCCCCCc
Confidence 35667777774
No 101
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=81.11 E-value=1.9 Score=28.46 Aligned_cols=36 Identities=14% Similarity=0.186 Sum_probs=26.3
Q ss_pred ccccCCcceEEEcCcCCcceecCCC-CCeecCCCCCe
Q psy2244 8 VGKCLPGDIEKYYLECHFENEIRPR-DPIRCRECGYR 43 (73)
Q Consensus 8 ~~~~~~~~v~YiC~~Cg~e~~ik~~-d~IRC~~CG~R 43 (73)
|+....+-..|.|.+||.+..+-.. ..=-||.||.+
T Consensus 33 Crt~~~G~~~~~C~~Cg~~~~~~~SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 33 CRTEALGFHRYRCEDCGHEKIVYNSCKNRHCPSCQAK 69 (111)
T ss_pred cCCccCCcceeecCCCCceEEecCcccCcCCCCCCCh
Confidence 6677778899999999998655432 12278999974
No 102
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=80.75 E-value=0.85 Score=28.16 Aligned_cols=21 Identities=33% Similarity=0.687 Sum_probs=16.3
Q ss_pred EcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
-|-+|+..++-+ +||+||..-
T Consensus 5 AC~~C~~i~~~~-----~CP~Cgs~~ 25 (61)
T PRK08351 5 ACRHCHYITTED-----RCPVCGSRD 25 (61)
T ss_pred hhhhCCcccCCC-----cCCCCcCCc
Confidence 488999888433 799999954
No 103
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=80.50 E-value=1 Score=24.69 Aligned_cols=23 Identities=30% Similarity=0.676 Sum_probs=13.0
Q ss_pred cCcCCcceecC-----CCCCeecCCCCC
Q psy2244 20 YLECHFENEIR-----PRDPIRCRECGY 42 (73)
Q Consensus 20 C~~Cg~e~~ik-----~~d~IRC~~CG~ 42 (73)
|..||..++.+ ...-..|+.||+
T Consensus 3 C~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 3 CPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred cccccChhhhhcCCCCCccceECCCCCC
Confidence 78898887764 235577999985
No 104
>PHA02942 putative transposase; Provisional
Probab=80.18 E-value=1.5 Score=34.27 Aligned_cols=24 Identities=21% Similarity=0.477 Sum_probs=12.0
Q ss_pred EcCcCCcceecCCCCCeecCCCCC
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
.|..||....-......+|++||+
T Consensus 327 ~Cs~CG~~~~~l~~r~f~C~~CG~ 350 (383)
T PHA02942 327 SCPKCGHKMVEIAHRYFHCPSCGY 350 (383)
T ss_pred cCCCCCCccCcCCCCEEECCCCCC
Confidence 466666544311223456666665
No 105
>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=80.14 E-value=0.62 Score=32.61 Aligned_cols=25 Identities=24% Similarity=0.591 Sum_probs=13.6
Q ss_pred EcCcCCcceecCC------------CCCeecCCCCCe
Q psy2244 19 YYLECHFENEIRP------------RDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e~~ik~------------~d~IRC~~CG~R 43 (73)
.|..||.....+. -....|++||||
T Consensus 3 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk 39 (161)
T PF03367_consen 3 LCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYK 39 (161)
T ss_dssp E-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--E
T ss_pred cCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCE
Confidence 5888887744331 155689999985
No 106
>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=79.97 E-value=1.3 Score=24.35 Aligned_cols=24 Identities=17% Similarity=0.229 Sum_probs=18.1
Q ss_pred cCcCCcceecCCCCCeecCCCCCe
Q psy2244 20 YLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 20 C~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
|+.|+...........-|..||+-
T Consensus 11 C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 11 CPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CCCCCCeEeEccCCEEEhhhCceE
Confidence 888888866666666888888874
No 107
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=79.91 E-value=1.8 Score=25.19 Aligned_cols=27 Identities=19% Similarity=0.340 Sum_probs=18.7
Q ss_pred EEEcCcCCcceecCCC----------------CCeecCCCCCe
Q psy2244 17 EKYYLECHFENEIRPR----------------DPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~----------------d~IRC~~CG~R 43 (73)
.|+|..||-.-+...+ +.-+||.||..
T Consensus 1 ky~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred CcCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 4899999987665544 44699999863
No 108
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=79.88 E-value=1.9 Score=31.18 Aligned_cols=33 Identities=24% Similarity=0.515 Sum_probs=23.8
Q ss_pred ceEEEcCcCCccee-c------CCCCCeecCCCCCeEEEee
Q psy2244 15 DIEKYYLECHFENE-I------RPRDPIRCRECGYRIMYKK 48 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~-i------k~~d~IRC~~CG~RILyKk 48 (73)
.-.|.|. |+.-.. + ..+...||..|+.+++++.
T Consensus 115 ~~~Y~C~-C~q~~l~~RRhn~~~~g~~YrC~~C~gkL~~~~ 154 (156)
T COG3091 115 TYPYRCQ-CQQHYLRIRRHNTVRRGEVYRCGKCGGKLVFKG 154 (156)
T ss_pred ceeEEee-cCCccchhhhcccccccceEEeccCCceEEecc
Confidence 3579999 987632 2 2334578999999999863
No 109
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.74 E-value=0.53 Score=30.90 Aligned_cols=28 Identities=25% Similarity=0.450 Sum_probs=22.4
Q ss_pred eEEEcCcCCcceec----CCCCCeecCCCCCe
Q psy2244 16 IEKYYLECHFENEI----RPRDPIRCRECGYR 43 (73)
Q Consensus 16 v~YiC~~Cg~e~~i----k~~d~IRC~~CG~R 43 (73)
-.|.|-+||..+++ ......-|++||.|
T Consensus 11 Y~Y~c~~cg~~~dvvq~~~ddplt~ce~c~a~ 42 (82)
T COG2331 11 YSYECTECGNRFDVVQAMTDDPLTTCEECGAR 42 (82)
T ss_pred eEEeecccchHHHHHHhcccCccccChhhChH
Confidence 57999999998764 34566899999985
No 110
>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=79.56 E-value=2 Score=33.91 Aligned_cols=27 Identities=15% Similarity=0.439 Sum_probs=22.3
Q ss_pred EEcCcCCcceecC---CCCCeecCCCCCeE
Q psy2244 18 KYYLECHFENEIR---PRDPIRCRECGYRI 44 (73)
Q Consensus 18 YiC~~Cg~e~~ik---~~d~IRC~~CG~RI 44 (73)
=.|.+|+..++.. +++..+||.||+.+
T Consensus 14 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 14 ILCSQCDMLVALPRIESGQKAACPRCGTTL 43 (403)
T ss_pred eeCCCCCCcccccCCCCCCeeECCCCCCCC
Confidence 3599999887654 67889999999987
No 111
>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=79.35 E-value=1.6 Score=34.62 Aligned_cols=31 Identities=10% Similarity=0.156 Sum_probs=23.6
Q ss_pred ceEEEcCcCCcceecCCCCCeecCCCCCeEEEee
Q psy2244 15 DIEKYYLECHFENEIRPRDPIRCRECGYRIMYKK 48 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKk 48 (73)
+..|.|.+||.+.. .-.-|||.||.+==+++
T Consensus 5 ~~~y~C~~Cg~~~~---~~~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 5 KSKFVCQHCGADSP---KWQGKCPACHAWNTITE 35 (454)
T ss_pred CCeEECCcCCCCCc---cccEECcCCCCccccch
Confidence 45799999998753 34479999999765555
No 112
>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=79.31 E-value=0.35 Score=26.73 Aligned_cols=26 Identities=27% Similarity=0.376 Sum_probs=13.8
Q ss_pred EcCcCCccee-cC----CCCCeecCCCCCeE
Q psy2244 19 YYLECHFENE-IR----PRDPIRCRECGYRI 44 (73)
Q Consensus 19 iC~~Cg~e~~-ik----~~d~IRC~~CG~RI 44 (73)
+|.+|-+|.. .. ....|.|++||-|+
T Consensus 1 lC~~C~~Ey~~p~~RR~~~~~isC~~CGPr~ 31 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFHYQFISCTNCGPRY 31 (35)
T ss_dssp --HHHHHHHCSTTSTTTT-TT--BTTCC-SC
T ss_pred CCHHHHHHHcCCCCCcccCcCccCCCCCCCE
Confidence 4677777642 22 24889999999875
No 113
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=79.24 E-value=1.4 Score=30.66 Aligned_cols=23 Identities=22% Similarity=0.546 Sum_probs=14.9
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCC
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
..=.|..||. .......|+.||+
T Consensus 308 tS~~C~~cg~----~~~r~~~C~~cg~ 330 (364)
T COG0675 308 TSKTCPCCGH----LSGRLFKCPRCGF 330 (364)
T ss_pred CcccccccCC----ccceeEECCCCCC
Confidence 3345777777 3345577888886
No 114
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=79.03 E-value=0.79 Score=32.13 Aligned_cols=28 Identities=21% Similarity=0.332 Sum_probs=20.5
Q ss_pred EEcCcCCcceecCCCC-CeecCCCCCeEE
Q psy2244 18 KYYLECHFENEIRPRD-PIRCRECGYRIM 45 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d-~IRC~~CG~RIL 45 (73)
.+|.+||+.++-...+ .-=||+||.+-.
T Consensus 2 H~Ct~Cg~~f~dgs~eil~GCP~CGg~kF 30 (131)
T PF09845_consen 2 HQCTKCGRVFEDGSKEILSGCPECGGNKF 30 (131)
T ss_pred cccCcCCCCcCCCcHHHHccCcccCCcce
Confidence 4799999999855433 245999998643
No 115
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=78.87 E-value=0.68 Score=37.71 Aligned_cols=38 Identities=18% Similarity=0.368 Sum_probs=16.9
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEeec
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKP 59 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~~~ 59 (73)
-.=+|.+||..... .-.||.||..- -.+-+|++-|+.|
T Consensus 490 ~~~~C~~CG~~~~~----~~~CP~CGs~~--~~~~~Rv~GYl~~ 527 (546)
T PF13597_consen 490 PIDICPDCGYIGGE----GDKCPKCGSEN--IEVYSRVTGYLRP 527 (546)
T ss_dssp -EEEETTT---S------EEE-CCC------EEEEB-SSSS-BT
T ss_pred CcccccCCCcCCCC----CCCCCCCCCcc--cceEEEeeccccC
Confidence 34589999986543 57899999994 2344555666664
No 116
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=78.67 E-value=0.99 Score=26.88 Aligned_cols=14 Identities=36% Similarity=0.596 Sum_probs=10.8
Q ss_pred eecCCCCCeEEEee
Q psy2244 35 IRCRECGYRIMYKK 48 (73)
Q Consensus 35 IRC~~CG~RILyKk 48 (73)
|.||+||..|-.-.
T Consensus 1 i~CPyCge~~~~~i 14 (52)
T PF14255_consen 1 IQCPYCGEPIEILI 14 (52)
T ss_pred CCCCCCCCeeEEEE
Confidence 57999999876543
No 117
>PRK04860 hypothetical protein; Provisional
Probab=78.61 E-value=2.9 Score=29.47 Aligned_cols=32 Identities=22% Similarity=0.538 Sum_probs=23.3
Q ss_pred ceEEEcCcCCcceecC---------CCCCeecCCCCCeEEEee
Q psy2244 15 DIEKYYLECHFENEIR---------PRDPIRCRECGYRIMYKK 48 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik---------~~d~IRC~~CG~RILyKk 48 (73)
.-.|.|. |+.- .++ ...+.+|.+|+.++.++.
T Consensus 117 ~~~Y~C~-C~~~-~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 117 TFPYRCK-CQEH-QLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEEcC-CCCe-eCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 3679998 9763 221 135699999999998874
No 118
>PRK11823 DNA repair protein RadA; Provisional
Probab=78.56 E-value=1.8 Score=34.25 Aligned_cols=32 Identities=25% Similarity=0.318 Sum_probs=24.8
Q ss_pred ceEEEcCcCCcceecCCCCCeecCCCCCeEEEeee
Q psy2244 15 DIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKR 49 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkR 49 (73)
+..|.|.+||.+.. .-.-+||.||.+==+++.
T Consensus 5 ~~~y~C~~Cg~~~~---~~~g~Cp~C~~w~t~~e~ 36 (446)
T PRK11823 5 KTAYVCQECGAESP---KWLGRCPECGAWNTLVEE 36 (446)
T ss_pred CCeEECCcCCCCCc---ccCeeCcCCCCccceeee
Confidence 56799999998753 334799999998777763
No 119
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=78.49 E-value=1 Score=28.13 Aligned_cols=20 Identities=15% Similarity=0.154 Sum_probs=15.7
Q ss_pred EcCcCCcceecCCCCCeecCCCCCe
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
-|-+|+..++- -.||.||..
T Consensus 7 AC~~C~~i~~~-----~~Cp~Cgs~ 26 (64)
T PRK06393 7 ACKKCKRLTPE-----KTCPVHGDE 26 (64)
T ss_pred hHhhCCcccCC-----CcCCCCCCC
Confidence 38899988842 299999984
No 120
>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=78.33 E-value=2.2 Score=29.08 Aligned_cols=28 Identities=25% Similarity=0.498 Sum_probs=21.2
Q ss_pred eEEEcCcCCcceecC-------CCCCeecCCCCCe
Q psy2244 16 IEKYYLECHFENEIR-------PRDPIRCRECGYR 43 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik-------~~d~IRC~~CG~R 43 (73)
-...|..|+.+...+ ....-+|+.||..
T Consensus 104 ~~~~C~~C~~~~~~~~~~~~~~~~~~~~C~~C~~~ 138 (178)
T PF02146_consen 104 FRLRCSKCGKEYDREDIVDSIDEEEPPRCPKCGGL 138 (178)
T ss_dssp EEEEETTTSBEEEGHHHHHHHHTTSSCBCTTTSCB
T ss_pred ceeeecCCCccccchhhcccccccccccccccCcc
Confidence 357899999987544 3455699999994
No 121
>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=78.18 E-value=2.3 Score=22.62 Aligned_cols=26 Identities=15% Similarity=0.225 Sum_probs=14.6
Q ss_pred ceEEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 15 DIEKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
-+.-.|.+||...-... ..|++||..
T Consensus 9 l~~~rC~~Cg~~~~pPr---~~Cp~C~s~ 34 (37)
T PF12172_consen 9 LLGQRCRDCGRVQFPPR---PVCPHCGSD 34 (37)
T ss_dssp EEEEE-TTT--EEES-----SEETTTT--
T ss_pred EEEEEcCCCCCEecCCC---cCCCCcCcc
Confidence 35678999998854432 789999863
No 122
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=78.15 E-value=1.8 Score=33.89 Aligned_cols=25 Identities=8% Similarity=-0.156 Sum_probs=19.6
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
.++|.+||++.. +. ...+||.|+..
T Consensus 2 ~l~C~~Cg~~~~-~~-~~~~C~~c~g~ 26 (398)
T TIGR03844 2 TLRCPGCGEVLP-DH-YTLSCPLDCGL 26 (398)
T ss_pred EEEeCCCCCccC-Cc-cccCCCCCCCc
Confidence 479999999986 33 36899998853
No 123
>PRK08329 threonine synthase; Validated
Probab=78.01 E-value=1.7 Score=32.80 Aligned_cols=27 Identities=22% Similarity=0.503 Sum_probs=20.6
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeEEEe
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRIMYK 47 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RILyK 47 (73)
++|.+||.+...+ ...+| .||..+...
T Consensus 2 l~C~~Cg~~~~~~--~~~~C-~c~~~l~~~ 28 (347)
T PRK08329 2 LRCTKCGRTYEEK--FKLRC-DCGGTLLVE 28 (347)
T ss_pred cCcCCCCCCcCCC--Cceec-CCCCcEEEE
Confidence 7899999999753 33899 799865544
No 124
>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=76.71 E-value=1.6 Score=34.42 Aligned_cols=26 Identities=19% Similarity=0.402 Sum_probs=21.0
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
.-.|.+|+..+ .++...+||.||+.+
T Consensus 215 ~~~C~~Cd~~~--~~~~~a~CpRC~~~L 240 (403)
T TIGR00155 215 LRSCSACHTTI--LPAQEPVCPRCSTPL 240 (403)
T ss_pred CCcCCCCCCcc--CCCCCcCCcCCCCcc
Confidence 34599999965 457778999999987
No 125
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=76.70 E-value=1.4 Score=30.92 Aligned_cols=26 Identities=23% Similarity=0.060 Sum_probs=23.0
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCC
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
.-||.+||+.+---.+++|-||+||.
T Consensus 9 KridPetg~KFYDLNrdPiVsPytG~ 34 (129)
T COG4530 9 KRIDPETGKKFYDLNRDPIVSPYTGK 34 (129)
T ss_pred cccCccccchhhccCCCccccCcccc
Confidence 45899999998877889999999997
No 126
>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=76.55 E-value=2.7 Score=22.63 Aligned_cols=24 Identities=17% Similarity=0.241 Sum_probs=18.9
Q ss_pred EcCcCCcceecCCC-CCeecCCCCC
Q psy2244 19 YYLECHFENEIRPR-DPIRCRECGY 42 (73)
Q Consensus 19 iC~~Cg~e~~ik~~-d~IRC~~CG~ 42 (73)
.|+.|+......++ ..+||..|..
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCALCQT 27 (31)
T ss_pred CcCCCCcEeecCCCCCeEECCCCCe
Confidence 58899998887765 6699999953
No 127
>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=76.40 E-value=1 Score=35.62 Aligned_cols=25 Identities=24% Similarity=0.332 Sum_probs=19.1
Q ss_pred EcCcCCcceecCCC--CCeecCCCCCeE
Q psy2244 19 YYLECHFENEIRPR--DPIRCRECGYRI 44 (73)
Q Consensus 19 iC~~Cg~e~~ik~~--d~IRC~~CG~RI 44 (73)
-|.+|+...+.+.. ...+|| ||.+|
T Consensus 242 ~c~~C~~~~~~~~~~~~~~~Cp-CG~~i 268 (374)
T TIGR00375 242 ACEACGEPAVSEDAETACANCP-CGGRI 268 (374)
T ss_pred hhcccCCcCCchhhhhcCCCCC-CCCcc
Confidence 58999988776632 357899 99994
No 128
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=76.32 E-value=0.83 Score=38.31 Aligned_cols=42 Identities=29% Similarity=0.516 Sum_probs=30.0
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEeeccCCCCC
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKPQTGGFP 65 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~~~~~~~~~ 65 (73)
=+|.+||... .+..-.||.||..-+ .+.+|++-|+.|. ..|-
T Consensus 567 ~iC~~CG~~~---~g~~~~CP~CGs~~~--ev~~RV~GYl~~v-~~wN 608 (623)
T PRK08271 567 TICNDCHHID---KRTGKRCPICGSENI--DYYTRVIGYLKRV-SAFS 608 (623)
T ss_pred ccCCCCCCcC---CCCCcCCcCCCCcch--hHHHHHhhhhcCc-cccc
Confidence 3799999752 334578999997533 5778889998875 3443
No 129
>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=76.18 E-value=1.6 Score=33.93 Aligned_cols=29 Identities=24% Similarity=0.432 Sum_probs=22.7
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeEEEeee
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRIMYKKR 49 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkR 49 (73)
|.|.+||.+. +.-.-|||.||.+==+++.
T Consensus 1 ~~c~~cg~~~---~~~~g~cp~c~~w~~~~e~ 29 (372)
T cd01121 1 YVCSECGYVS---PKWLGKCPECGEWNTLVEE 29 (372)
T ss_pred CCCCCCCCCC---CCccEECcCCCCceeeeeh
Confidence 7899999875 3345799999998777764
No 130
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=76.14 E-value=1.6 Score=36.77 Aligned_cols=31 Identities=16% Similarity=0.373 Sum_probs=15.4
Q ss_pred ccccCCcceEEEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 8 VGKCLPGDIEKYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 8 ~~~~~~~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
||.+++.... -|.+||.... ...|++||..+
T Consensus 7 Cg~~n~~~ak-FC~~CG~~l~-----~~~Cp~CG~~~ 37 (645)
T PRK14559 7 CQFENPNNNR-FCQKCGTSLT-----HKPCPQCGTEV 37 (645)
T ss_pred CCCcCCCCCc-cccccCCCCC-----CCcCCCCCCCC
Confidence 3444444433 2555555442 23577777764
No 131
>PRK08197 threonine synthase; Validated
Probab=75.80 E-value=2.9 Score=32.09 Aligned_cols=29 Identities=14% Similarity=0.314 Sum_probs=21.8
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCeEEEe
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYRIMYK 47 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyK 47 (73)
.++|.+||.+..++.. ..+| .||..+..-
T Consensus 7 ~~~C~~Cg~~~~~~~~-~~~C-~cg~~l~~~ 35 (394)
T PRK08197 7 HLECSKCGETYDADQV-HNLC-KCGKPLLVR 35 (394)
T ss_pred EEEECCCCCCCCCCCc-ceec-CCCCeeEEE
Confidence 4999999999876654 4789 899864433
No 132
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=75.63 E-value=2.4 Score=25.95 Aligned_cols=36 Identities=17% Similarity=0.397 Sum_probs=14.7
Q ss_pred eccccCCcc-----eEEEcCcCCcceecCC-CCCeecCCCCC
Q psy2244 7 LVGKCLPGD-----IEKYYLECHFENEIRP-RDPIRCRECGY 42 (73)
Q Consensus 7 l~~~~~~~~-----v~YiC~~Cg~e~~ik~-~d~IRC~~CG~ 42 (73)
++.++.|++ +.-.|.+|++..+... -=..+|.+||+
T Consensus 15 i~~~pmP~~Y~~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~S 56 (61)
T PF14599_consen 15 IAATPMPEEYRNKKVWILCNDCNAKSEVPFHFLGHKCSHCGS 56 (61)
T ss_dssp -------------EEEEEESSS--EEEEE--TT----TTTS-
T ss_pred HHhCCCCHHHhCCEEEEECCCCCCccceeeeHhhhcCCCCCC
Confidence 344445543 5566999999877663 35689999986
No 133
>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=75.54 E-value=3.6 Score=22.79 Aligned_cols=27 Identities=22% Similarity=0.212 Sum_probs=18.5
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
-.|..|+..+--....+.+|..|+..+
T Consensus 12 ~~C~~C~~~i~g~~~~g~~C~~C~~~~ 38 (53)
T PF00130_consen 12 TYCDVCGKFIWGLGKQGYRCSWCGLVC 38 (53)
T ss_dssp EB-TTSSSBECSSSSCEEEETTTT-EE
T ss_pred CCCcccCcccCCCCCCeEEECCCCChH
Confidence 368888888755666788888888654
No 134
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=75.36 E-value=3.3 Score=31.08 Aligned_cols=41 Identities=20% Similarity=0.330 Sum_probs=26.4
Q ss_pred eEEEcCcCCccee-------cCCCCCeecCCCCCeEEEeeeCCeeEEEeecc
Q psy2244 16 IEKYYLECHFENE-------IRPRDPIRCRECGYRIMYKKRTKRCILYFKPQ 60 (73)
Q Consensus 16 v~YiC~~Cg~e~~-------ik~~d~IRC~~CG~RILyKkRt~r~vqf~~~~ 60 (73)
-...|..||.... ++..+.-+|+.||..+| | ++++-|-++-
T Consensus 121 ~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~~l---r-P~VV~fGE~l 168 (250)
T COG0846 121 KRVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGPVL---R-PDVVWFGEPL 168 (250)
T ss_pred eeeEeCCCcCccchhhhhhhcccCCCCcCccCCCccc---c-CCEEEeCCCC
Confidence 4567999987765 22345689999999721 2 3455555543
No 135
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=75.20 E-value=0.39 Score=29.00 Aligned_cols=26 Identities=35% Similarity=0.802 Sum_probs=20.9
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCeEE
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYRIM 45 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~RIL 45 (73)
..||.+|++.+.++ +.+|+.||++=|
T Consensus 14 kkIC~rC~Arnp~~---A~kCRkC~~k~L 39 (50)
T COG1552 14 KKICRRCYARNPPR---ATKCRKCGYKNL 39 (50)
T ss_pred HHHHHHhcCCCCcc---hhHHhhccCCCc
Confidence 46899999987554 689999999765
No 136
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=74.81 E-value=2 Score=37.36 Aligned_cols=45 Identities=16% Similarity=0.163 Sum_probs=31.4
Q ss_pred ceeccccCCcceEEEcCcCCcceecCCCCCeecCCCCCeEEEeeeCC
Q psy2244 5 QVLVGKCLPGDIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTK 51 (73)
Q Consensus 5 ~~l~~~~~~~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~ 51 (73)
+|+|- ..+...|+|-+||+..+-..-+--+||+||...-.-+|-+
T Consensus 811 ~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 855 (1006)
T PRK12775 811 EYVCC--ATSELQWRCDDCGKVSEGFAFPYGMCPACGGKLQALDRRK 855 (1006)
T ss_pred eeEEe--cCcceeeehhhhccccccccCCcCcCcccccchhhhhccC
Confidence 55542 3456778999999887655555579999999865555443
No 137
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=74.76 E-value=2.1 Score=29.19 Aligned_cols=27 Identities=15% Similarity=0.188 Sum_probs=21.0
Q ss_pred ceEEEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 15 DIEKYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
-+-=+|.+||+..-... ..|++||.+.
T Consensus 27 l~g~kC~~CG~v~~PPr---~~Cp~C~~~~ 53 (140)
T COG1545 27 LLGTKCKKCGRVYFPPR---AYCPKCGSET 53 (140)
T ss_pred EEEEEcCCCCeEEcCCc---ccCCCCCCCC
Confidence 35568999999875543 6799999984
No 138
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=74.64 E-value=3.6 Score=22.93 Aligned_cols=29 Identities=14% Similarity=0.615 Sum_probs=22.0
Q ss_pred EcC--cCCcceecC---CCCCeecCCCCCeEEEe
Q psy2244 19 YYL--ECHFENEIR---PRDPIRCRECGYRIMYK 47 (73)
Q Consensus 19 iC~--~Cg~e~~ik---~~d~IRC~~CG~RILyK 47 (73)
-|. +|+..+... ....+.|+.||++.-++
T Consensus 20 ~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~ 53 (64)
T smart00647 20 WCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFR 53 (64)
T ss_pred CCCCCCCcceEEecCCCCCCeeECCCCCCeECCC
Confidence 387 898887765 35679999999887554
No 139
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=74.57 E-value=1.4 Score=26.03 Aligned_cols=33 Identities=24% Similarity=0.326 Sum_probs=24.7
Q ss_pred CcceEEEcCcCCcceecCCC------CCeecCCCCCeEEE
Q psy2244 13 PGDIEKYYLECHFENEIRPR------DPIRCRECGYRIMY 46 (73)
Q Consensus 13 ~~~v~YiC~~Cg~e~~ik~~------d~IRC~~CG~RILy 46 (73)
.+.-.|-| +||..+.+... ..+.|+.|+-.|..
T Consensus 14 ~~~~~y~C-RCG~~f~i~e~~l~~~~~iv~C~sCSL~I~V 52 (55)
T PF05207_consen 14 EGVYSYPC-RCGGEFEISEEDLEEGEVIVQCDSCSLWIRV 52 (55)
T ss_dssp TTEEEEEE-TTSSEEEEEHHHHHCT--EEEETTTTEEEEE
T ss_pred CCEEEEcC-CCCCEEEEcchhccCcCEEEECCCCccEEEE
Confidence 34478999 99999887632 45999999987753
No 140
>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=74.47 E-value=1.6 Score=30.91 Aligned_cols=11 Identities=45% Similarity=1.247 Sum_probs=6.9
Q ss_pred CCeecCCCCCe
Q psy2244 33 DPIRCRECGYR 43 (73)
Q Consensus 33 d~IRC~~CG~R 43 (73)
....|++||||
T Consensus 27 ~sf~C~~CGyr 37 (163)
T TIGR00340 27 STYICEKCGYR 37 (163)
T ss_pred EEEECCCCCCc
Confidence 34567777764
No 141
>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=74.44 E-value=1.8 Score=35.60 Aligned_cols=36 Identities=22% Similarity=0.418 Sum_probs=24.7
Q ss_pred EcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEeec
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKP 59 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~~~ 59 (73)
+|.+||..-+.. .-.||.||.+- -.+-+|++-|+.|
T Consensus 526 ~C~~CG~~g~~~---~~~CP~Cgs~~--~~~~~Rv~GYl~~ 561 (579)
T TIGR02487 526 VCEDCGYTGEGL---NDKCPKCGSHD--IEVISRITGYLGP 561 (579)
T ss_pred cCCCCCCCCCCC---CCcCcCCCCcc--ceehhhhhhhhcc
Confidence 799999732221 24799999763 4566777778764
No 142
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=74.44 E-value=1.6 Score=37.14 Aligned_cols=36 Identities=22% Similarity=0.415 Sum_probs=26.4
Q ss_pred EcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEeecc
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKPQ 60 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~~~~ 60 (73)
+|.+||....+. -.||.||..- -.+.+|++-|+.|-
T Consensus 682 ~C~~CG~~~~~~----~~CP~CG~~~--~~~~~Ri~GYl~~v 717 (735)
T PRK07111 682 RCPVCGYLGVIE----DKCPKCGSTN--IQRIRRITGYLGTL 717 (735)
T ss_pred ecCCCCCCCCcC----ccCcCCCCcc--ceeeehhhhhccch
Confidence 799999755443 6899999732 35677888888663
No 143
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=74.36 E-value=1.5 Score=33.94 Aligned_cols=39 Identities=15% Similarity=0.110 Sum_probs=29.5
Q ss_pred ceeccccCCcceEEEcCcCCcceecCC--CCCeecCCCCCe
Q psy2244 5 QVLVGKCLPGDIEKYYLECHFENEIRP--RDPIRCRECGYR 43 (73)
Q Consensus 5 ~~l~~~~~~~~v~YiC~~Cg~e~~ik~--~d~IRC~~CG~R 43 (73)
++-.+.+.|+..--+|.+|+..+..+. ...--||+|||-
T Consensus 26 ~~~~~~~~p~~lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h 66 (296)
T CHL00174 26 KYSWNTQKYKHLWVQCENCYGLNYKKFLKSKMNICEQCGYH 66 (296)
T ss_pred ccccCCCCCCCCeeECCCccchhhHHHHHHcCCCCCCCCCC
Confidence 344456788888999999999877663 244689999993
No 144
>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=74.20 E-value=3.3 Score=23.53 Aligned_cols=23 Identities=22% Similarity=0.378 Sum_probs=15.1
Q ss_pred EcCcCCcceecCCCCCeecCCCC
Q psy2244 19 YYLECHFENEIRPRDPIRCRECG 41 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG 41 (73)
.|.+||...--+....+.|+.|+
T Consensus 19 ~Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred ccCCCCCeeEEecCCCEECCCCC
Confidence 47778776554445567788775
No 145
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=74.03 E-value=1.7 Score=31.53 Aligned_cols=10 Identities=50% Similarity=1.341 Sum_probs=6.4
Q ss_pred CeecCCCCCe
Q psy2244 34 PIRCRECGYR 43 (73)
Q Consensus 34 ~IRC~~CG~R 43 (73)
...|++||||
T Consensus 30 sf~C~~CGyr 39 (192)
T TIGR00310 30 STICEHCGYR 39 (192)
T ss_pred EEECCCCCCc
Confidence 4567777764
No 146
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=73.58 E-value=0.98 Score=29.81 Aligned_cols=33 Identities=15% Similarity=0.347 Sum_probs=23.5
Q ss_pred CCcceEEEcCcCCcceecC-CCCCeecCCCCCeE
Q psy2244 12 LPGDIEKYYLECHFENEIR-PRDPIRCRECGYRI 44 (73)
Q Consensus 12 ~~~~v~YiC~~Cg~e~~ik-~~d~IRC~~CG~RI 44 (73)
..+...|.|..||++.--+ ....-.|..||..+
T Consensus 30 ~~q~~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 30 ISQHAKYTCPFCGKTSVKRVATGIWKCKKCGKKF 63 (90)
T ss_dssp HHHHS-BEESSSSSSEEEEEETTEEEETTTTEEE
T ss_pred HHHhCCCcCCCCCCceeEEeeeEEeecCCCCCEE
Confidence 4455789999999986333 44557999999754
No 147
>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=73.55 E-value=1.6 Score=31.22 Aligned_cols=25 Identities=24% Similarity=0.590 Sum_probs=17.2
Q ss_pred EEcCcCCcceec---C--C--CCCeecCCCCC
Q psy2244 18 KYYLECHFENEI---R--P--RDPIRCRECGY 42 (73)
Q Consensus 18 YiC~~Cg~e~~i---k--~--~d~IRC~~CG~ 42 (73)
++|-+||.+++- + + -.--+|++||.
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~ 32 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGK 32 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCC
Confidence 579999999752 1 1 13368999995
No 148
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=73.54 E-value=2.6 Score=35.21 Aligned_cols=38 Identities=29% Similarity=0.433 Sum_probs=26.2
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEeecc
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKPQ 60 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~~~~ 60 (73)
=+|.+||.. .....-.||.||..- -.+-+|++-|+.|.
T Consensus 533 siC~~CGy~---~g~~~~~CP~CGs~~--~ev~sRv~GYl~~v 570 (586)
T TIGR02827 533 TICNDCHHI---DKRTLHRCPVCGSAN--IDYGTRVIGYLKRV 570 (586)
T ss_pred eecCCCCCc---CCCcCCcCcCCCCcc--ceEEEeecceecCc
Confidence 379999982 211236999999752 24567888888875
No 149
>smart00350 MCM minichromosome maintenance proteins.
Probab=73.36 E-value=3.7 Score=32.77 Aligned_cols=31 Identities=13% Similarity=0.180 Sum_probs=23.2
Q ss_pred cceEEEcCcCCcceecC-----CCCCeecCC--CCCeE
Q psy2244 14 GDIEKYYLECHFENEIR-----PRDPIRCRE--CGYRI 44 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik-----~~d~IRC~~--CG~RI 44 (73)
....|.|..||.++... ...+..|++ |+.+-
T Consensus 34 ~~~~f~C~~C~~~~~~~~~~~~~~~p~~C~~~~C~~~~ 71 (509)
T smart00350 34 KRASFTCEKCGATLGPEIQSGRETEPTVCPPRECQSPT 71 (509)
T ss_pred EEEEEEecCCCCEEeEEecCCcccCCCcCCCCcCCCCC
Confidence 34789999999875433 237789998 99763
No 150
>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=73.30 E-value=2.2 Score=29.44 Aligned_cols=31 Identities=13% Similarity=0.245 Sum_probs=22.6
Q ss_pred cceEEEcCcCCcceecCCCCCeecCCCCCeEE
Q psy2244 14 GDIEKYYLECHFENEIRPRDPIRCRECGYRIM 45 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RIL 45 (73)
..+..+|.+||+....-.+. -+|.+|+....
T Consensus 66 kav~V~CP~C~K~TKmLGr~-D~CM~C~~pLT 96 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLGRV-DACMHCKEPLT 96 (114)
T ss_pred cceeeECCCCCChHhhhchh-hccCcCCCcCc
Confidence 34778899999998654333 39999997654
No 151
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=73.25 E-value=4.5 Score=21.11 Aligned_cols=23 Identities=17% Similarity=0.241 Sum_probs=17.8
Q ss_pred cCcCCcceecCCC-CCeecCCCCC
Q psy2244 20 YLECHFENEIRPR-DPIRCRECGY 42 (73)
Q Consensus 20 C~~Cg~e~~ik~~-d~IRC~~CG~ 42 (73)
|+.|........+ ..|||.-|..
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCc
Confidence 7788888776655 6699999863
No 152
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=72.23 E-value=3.3 Score=33.87 Aligned_cols=37 Identities=19% Similarity=0.348 Sum_probs=29.2
Q ss_pred cccCCcceEEEcCcCCcceecC---CCCCeecCCCCCeEE
Q psy2244 9 GKCLPGDIEKYYLECHFENEIR---PRDPIRCRECGYRIM 45 (73)
Q Consensus 9 ~~~~~~~v~YiC~~Cg~e~~ik---~~d~IRC~~CG~RIL 45 (73)
.++.+..-.-.|.+|+..+++. .+..--||.|||.|-
T Consensus 10 ~~~~~~~~~~~C~eCd~~~~~P~l~~~q~A~CPRC~~~l~ 49 (418)
T COG2995 10 TEELPPGHLILCPECDMLVSLPRLDSGQSAYCPRCGHTLT 49 (418)
T ss_pred cccCCccceecCCCCCceeccccCCCCCcccCCCCCCccc
Confidence 3456666777899999998865 567899999999773
No 153
>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=72.10 E-value=1.8 Score=33.01 Aligned_cols=34 Identities=15% Similarity=0.234 Sum_probs=26.5
Q ss_pred ccCCcceEEEcCcCCcceecCC--CCCeecCCCCCe
Q psy2244 10 KCLPGDIEKYYLECHFENEIRP--RDPIRCRECGYR 43 (73)
Q Consensus 10 ~~~~~~v~YiC~~Cg~e~~ik~--~d~IRC~~CG~R 43 (73)
.+.|+..-.+|.+|+..+..+. .+---||+|||.
T Consensus 19 ~~~~~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h 54 (285)
T TIGR00515 19 AEVPEGVWTKCPKCGQVLYTKELERNLEVCPKCDHH 54 (285)
T ss_pred CCCCCCCeeECCCCcchhhHHHHHhhCCCCCCCCCc
Confidence 4577788899999999876652 244689999994
No 154
>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=71.87 E-value=6.8 Score=23.70 Aligned_cols=29 Identities=14% Similarity=0.415 Sum_probs=18.2
Q ss_pred eEEEcCcCCcceec--CCCCCeecCCCCCeE
Q psy2244 16 IEKYYLECHFENEI--RPRDPIRCRECGYRI 44 (73)
Q Consensus 16 v~YiC~~Cg~e~~i--k~~d~IRC~~CG~RI 44 (73)
|.=+|.+|+.+.-+ .....|+|..||.-+
T Consensus 6 m~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L 36 (55)
T PF01667_consen 6 MDVKCPGCYNIQTVFSHAQTVVKCVVCGTVL 36 (55)
T ss_dssp EEEE-TTT-SEEEEETT-SS-EE-SSSTSEE
T ss_pred EEEECCCCCCeeEEEecCCeEEEcccCCCEe
Confidence 56789999988553 366889999999743
No 155
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=71.85 E-value=4.9 Score=26.63 Aligned_cols=29 Identities=21% Similarity=0.185 Sum_probs=20.6
Q ss_pred cceEEEcCcCCcceecC-----CCCCeecCCCCCe
Q psy2244 14 GDIEKYYLECHFENEIR-----PRDPIRCRECGYR 43 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik-----~~d~IRC~~CG~R 43 (73)
-+..+.|..||.. .+. ...-+.|+.||+.
T Consensus 18 lpt~f~CP~Cge~-~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 18 LPKIFECPRCGKV-SISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred CCcEeECCCCCCe-EeeeecCCCcceEECCCCCCc
Confidence 3578999999942 221 2356999999985
No 156
>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=71.85 E-value=3.6 Score=25.99 Aligned_cols=30 Identities=13% Similarity=0.222 Sum_probs=13.8
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCeEEEee
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYRIMYKK 48 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKk 48 (73)
.++|..|-+... ..+..-||.||+.-|.|.
T Consensus 9 vlrC~aCf~~t~--~~~k~FCp~CGn~TL~rv 38 (73)
T PF08772_consen 9 VLRCHACFKITK--DMTKQFCPKCGNATLKRV 38 (73)
T ss_dssp EEE-SSS--EES---SS--S-SSS--S--EEE
T ss_pred eEEccccccCcC--CCCceeCcccCCCcceEE
Confidence 578888866554 456689999999877664
No 157
>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=71.81 E-value=3 Score=37.59 Aligned_cols=42 Identities=17% Similarity=0.325 Sum_probs=30.2
Q ss_pred ceEEEcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEe
Q psy2244 15 DIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYF 57 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~ 57 (73)
.-.++|.+||+...--+.. -+|+.||.+|+...=.-.+..|+
T Consensus 1010 rQ~fRC~kC~~kYRR~PL~-G~C~kCGg~lilTV~~GsV~KYl 1051 (1095)
T TIGR00354 1010 RQEVRCTKCNTKYRRIPLV-GKCLKCGNNLTLTVSKGSVMKYL 1051 (1095)
T ss_pred ccceeecccCCccccCCCC-CcccccCCeEEEEEecchhHhhH
Confidence 4568999999987655544 58999999998766544444443
No 158
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=71.72 E-value=6.3 Score=24.70 Aligned_cols=27 Identities=15% Similarity=0.063 Sum_probs=21.7
Q ss_pred ecCCCCCeEEEeeeCCeeEEEeeccCC
Q psy2244 36 RCRECGYRIMYKKRTKRCILYFKPQTG 62 (73)
Q Consensus 36 RC~~CG~RILyKkRt~r~vqf~~~~~~ 62 (73)
-||.||..++.-+.+....+|.=.+|+
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v~C~~Cg 34 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRAKCNGCE 34 (64)
T ss_pred CCCCCCCceeEEEecCceEEEEcCCCC
Confidence 499999998888888888877766664
No 159
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=71.40 E-value=3.1 Score=38.23 Aligned_cols=36 Identities=28% Similarity=0.467 Sum_probs=27.4
Q ss_pred cceEEEcCcCCcceecCCCCCeecCCCCCeEEEeeeC
Q psy2244 14 GDIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRT 50 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt 50 (73)
+.-+++|.+||+...--|.. -+|+.||.+|+...=.
T Consensus 1250 srQ~~RC~kC~~kyRR~PL~-G~C~kCGg~iilTv~~ 1285 (1337)
T PRK14714 1250 SRQEFRCLKCGTKYRRMPLA-GKCRKCGGRIILTVHE 1285 (1337)
T ss_pred hccceeecccCcccccCCCC-CcccccCCeEEEEEec
Confidence 34578999999987655544 5899999999876543
No 160
>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=71.03 E-value=2.8 Score=33.11 Aligned_cols=26 Identities=15% Similarity=0.275 Sum_probs=13.6
Q ss_pred EEEcCcCCcc-eecCCCCCeecCCCCC
Q psy2244 17 EKYYLECHFE-NEIRPRDPIRCRECGY 42 (73)
Q Consensus 17 ~YiC~~Cg~e-~~ik~~d~IRC~~CG~ 42 (73)
-+.|.+|+.. +.+...+...|++||.
T Consensus 285 FFkC~~C~~Rt~sl~r~P~~~C~~Cg~ 311 (344)
T PF09332_consen 285 FFKCKDCGNRTISLERLPKKHCSNCGS 311 (344)
T ss_dssp EEE-T-TS-EEEESSSS--S--TTT-S
T ss_pred eEECCCCCCeeeecccCCCCCCCcCCc
Confidence 4789999775 5566777789999997
No 161
>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=70.79 E-value=4.1 Score=28.71 Aligned_cols=29 Identities=17% Similarity=0.349 Sum_probs=17.0
Q ss_pred cceEEEcCcCCcceecCC----------CCCeecCCCCC
Q psy2244 14 GDIEKYYLECHFENEIRP----------RDPIRCRECGY 42 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~----------~d~IRC~~CG~ 42 (73)
++....|..|+.++.+.. ...+.|++|+.
T Consensus 15 ~~l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~ 53 (188)
T PF08996_consen 15 EPLKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCST 53 (188)
T ss_dssp --EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--
T ss_pred CceEeECCCCCCCccccccccCCccccccCcCcCCCCCC
Confidence 567889999999987752 24789999998
No 162
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=70.47 E-value=0.97 Score=37.83 Aligned_cols=37 Identities=24% Similarity=0.404 Sum_probs=27.3
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEeec
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKP 59 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~~~ 59 (73)
=+|.+||.+. .+..-.||.||.+- -.+.+|++-|+.|
T Consensus 569 ~~C~~CG~~~---~g~~~~CP~CGs~~--~~v~~Rv~GYl~~ 605 (625)
T PRK08579 569 TVCNKCGRST---TGLYTRCPRCGSED--VEVWSRIIGYYRP 605 (625)
T ss_pred ccCCCCCCcc---CCCCCcCcCCCCch--hHHHHHHHhhhcc
Confidence 4799999854 23346999999753 3577788888876
No 163
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=70.15 E-value=3 Score=33.11 Aligned_cols=24 Identities=21% Similarity=0.317 Sum_probs=19.1
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
-.|.+|+..+ +++..+||.||+.+
T Consensus 222 ~~C~~Cd~l~---~~~~a~CpRC~~~L 245 (419)
T PRK15103 222 RSCSCCTAIL---PADQPVCPRCHTKG 245 (419)
T ss_pred CcCCCCCCCC---CCCCCCCCCCCCcC
Confidence 3599999865 34556999999987
No 164
>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=70.09 E-value=4.2 Score=22.61 Aligned_cols=26 Identities=19% Similarity=0.535 Sum_probs=15.1
Q ss_pred EcCc--CCcceecCCCC-C--eecCCCCCeE
Q psy2244 19 YYLE--CHFENEIRPRD-P--IRCRECGYRI 44 (73)
Q Consensus 19 iC~~--Cg~e~~ik~~d-~--IRC~~CG~RI 44 (73)
.|.. |+..+...... . ++|+.|++.+
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCSEE
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCCcC
Confidence 7865 99988877553 2 8999999875
No 165
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=70.00 E-value=2.1 Score=28.32 Aligned_cols=46 Identities=17% Similarity=0.219 Sum_probs=28.1
Q ss_pred EcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEeeccCCCC
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKPQTGGF 64 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~~~~~~~~ 64 (73)
-|..|+.....+.-..-.||+|+.=+=++-...++..+.-+.-.|+
T Consensus 5 AC~~C~~I~~~~qf~~~gCpnC~~~l~~~g~~~~v~~~tT~~f~G~ 50 (98)
T cd07973 5 ACLLCSLIKTEDQFERDGCPNCEGYLDMKGNHERVYDCTSPNFEGI 50 (98)
T ss_pred hhccCCcccccccccCCCCCCCcchhccCCCccccccccCCCcceE
Confidence 4889998887766566789999733333333334444444444444
No 166
>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=69.67 E-value=3.6 Score=21.83 Aligned_cols=20 Identities=20% Similarity=0.411 Sum_probs=14.4
Q ss_pred ceecCCCCCeecCCCCCeEE
Q psy2244 26 ENEIRPRDPIRCRECGYRIM 45 (73)
Q Consensus 26 e~~ik~~d~IRC~~CG~RIL 45 (73)
.+.++..+...|+.||-.++
T Consensus 24 ~~~i~~vp~~~C~~CGE~~~ 43 (46)
T TIGR03831 24 LIVIENVPALVCPQCGEEYL 43 (46)
T ss_pred EEEEeCCCccccccCCCEee
Confidence 34455667778999998765
No 167
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=69.54 E-value=3.3 Score=25.06 Aligned_cols=22 Identities=18% Similarity=0.324 Sum_probs=16.2
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
+-+|.+||.-.- ...||.||..
T Consensus 5 mr~C~~CgvYTL-----k~~CP~CG~~ 26 (56)
T PRK13130 5 IRKCPKCGVYTL-----KEICPVCGGK 26 (56)
T ss_pred ceECCCCCCEEc-----cccCcCCCCC
Confidence 457888887765 3678999863
No 168
>PHA02768 hypothetical protein; Provisional
Probab=68.95 E-value=1.6 Score=26.41 Aligned_cols=26 Identities=12% Similarity=0.041 Sum_probs=20.7
Q ss_pred EEEcCcCCcceecCC---------CCCeecCCCCC
Q psy2244 17 EKYYLECHFENEIRP---------RDPIRCRECGY 42 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~---------~d~IRC~~CG~ 42 (73)
-|.|..||+.+.... ..+-+|.+||-
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k 39 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHNTNLKLSNCKR 39 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcCCcccCCcccc
Confidence 389999999987552 14789999997
No 169
>PRK04023 DNA polymerase II large subunit; Validated
Probab=68.74 E-value=3.9 Score=37.05 Aligned_cols=38 Identities=16% Similarity=0.298 Sum_probs=28.2
Q ss_pred ceEEEcCcCCcceecCCCCCeecCCCCCeEEEeeeCCee
Q psy2244 15 DIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRC 53 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~ 53 (73)
.-.++|.+||+...--+.. -+|+.||.+|+...=.-.+
T Consensus 1035 rQ~fRC~kC~~kYRR~PL~-G~C~kCGg~lilTVh~GsV 1072 (1121)
T PRK04023 1035 RQEFRCTKCGAKYRRPPLS-GKCPKCGGNLILTVHKGSV 1072 (1121)
T ss_pred ccceeecccCcccccCCCC-CcCccCCCeEEEEEecchH
Confidence 4568999999987655544 5899999999876544333
No 170
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=68.70 E-value=3.5 Score=25.16 Aligned_cols=26 Identities=23% Similarity=0.392 Sum_probs=14.7
Q ss_pred EEEcCcCCcceecCCC---CCeecCCCCC
Q psy2244 17 EKYYLECHFENEIRPR---DPIRCRECGY 42 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~---d~IRC~~CG~ 42 (73)
.=+|+.|+.+..++.. ....|+.|+.
T Consensus 41 ~v~Cg~C~~~~~~~~~~c~~~~~C~~C~~ 69 (71)
T PF05495_consen 41 RVICGKCRTEQPIDEYSCGADYFCPICGL 69 (71)
T ss_dssp EEEETTT--EEES-SBTT--SEEETTTTE
T ss_pred CeECCCCCCccChhhhhcCCCccCcCcCC
Confidence 4567788777777654 2357777764
No 171
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=68.48 E-value=4.8 Score=24.68 Aligned_cols=21 Identities=29% Similarity=0.532 Sum_probs=11.8
Q ss_pred eecCCCCCeEEEeeeCCeeEE
Q psy2244 35 IRCRECGYRIMYKKRTKRCIL 55 (73)
Q Consensus 35 IRC~~CG~RILyKkRt~r~vq 55 (73)
|.||.||++-.-|.|..-.+.
T Consensus 5 i~CP~CgnKTR~kir~DT~Lk 25 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLK 25 (55)
T ss_pred EECCCCCCccceeeecCceec
Confidence 456666666555555554443
No 172
>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=68.31 E-value=3.4 Score=27.62 Aligned_cols=13 Identities=38% Similarity=0.705 Sum_probs=11.6
Q ss_pred CeecCCCCCeEEE
Q psy2244 34 PIRCRECGYRIMY 46 (73)
Q Consensus 34 ~IRC~~CG~RILy 46 (73)
+++|++||..+.+
T Consensus 2 p~~CpYCg~~~~l 14 (102)
T PF11672_consen 2 PIICPYCGGPAEL 14 (102)
T ss_pred CcccCCCCCeeEE
Confidence 6899999998877
No 173
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=68.19 E-value=2.7 Score=26.52 Aligned_cols=12 Identities=17% Similarity=0.246 Sum_probs=5.4
Q ss_pred EcCcCCcceecC
Q psy2244 19 YYLECHFENEIR 30 (73)
Q Consensus 19 iC~~Cg~e~~ik 30 (73)
.|..||....+.
T Consensus 3 ~CP~Cg~~a~ir 14 (72)
T PRK09678 3 HCPLCQHAAHAR 14 (72)
T ss_pred cCCCCCCccEEE
Confidence 344454444333
No 174
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=68.12 E-value=1.7 Score=31.38 Aligned_cols=35 Identities=14% Similarity=0.236 Sum_probs=26.9
Q ss_pred CCcceEEEcCcCCcceecC--CCCCeecCCCCCeEEE
Q psy2244 12 LPGDIEKYYLECHFENEIR--PRDPIRCRECGYRIMY 46 (73)
Q Consensus 12 ~~~~v~YiC~~Cg~e~~ik--~~d~IRC~~CG~RILy 46 (73)
..+.+.|.|..|+..++++ ....-.||.||.-+-|
T Consensus 108 ~~~~~~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L~~ 144 (176)
T COG1675 108 ETENNYYVCPNCHVKYSFDEAMELGFTCPKCGEDLEE 144 (176)
T ss_pred hccCCceeCCCCCCcccHHHHHHhCCCCCCCCchhhh
Confidence 4567889999999888877 2345899999985543
No 175
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=68.00 E-value=2.1 Score=28.21 Aligned_cols=34 Identities=15% Similarity=0.268 Sum_probs=24.7
Q ss_pred cCCcceEEEcCcCCcceecC-CCCCeecCCCCCeE
Q psy2244 11 CLPGDIEKYYLECHFENEIR-PRDPIRCRECGYRI 44 (73)
Q Consensus 11 ~~~~~v~YiC~~Cg~e~~ik-~~d~IRC~~CG~RI 44 (73)
+..+...|.|..||.+.--+ ....-.|..||..+
T Consensus 30 e~~q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 30 EISQHAKYFCPFCGKHAVKRQAVGIWRCKGCKKTV 64 (90)
T ss_pred HHHHhCCccCCCCCCCceeeeeeEEEEcCCCCCEE
Confidence 44566789999999764333 44668999999854
No 176
>PRK05638 threonine synthase; Validated
Probab=67.96 E-value=4.4 Score=31.64 Aligned_cols=24 Identities=25% Similarity=0.336 Sum_probs=18.2
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
++|.+||.+.... ...+| .||..+
T Consensus 2 l~C~~Cg~~~~~~--~~~~C-~c~~~l 25 (442)
T PRK05638 2 MKCPKCGREYNSY--IPPFC-ICGELL 25 (442)
T ss_pred eEeCCCCCCCCCC--Cceec-CCCCcE
Confidence 6899999998633 34889 899744
No 177
>PRK04011 peptide chain release factor 1; Provisional
Probab=67.86 E-value=5.9 Score=31.31 Aligned_cols=43 Identities=23% Similarity=0.439 Sum_probs=29.6
Q ss_pred CCcccee-ccccCCc-ceEEEcCcCCcceec-----CCCCCeecCCCCCe
Q psy2244 1 MGYSQVL-VGKCLPG-DIEKYYLECHFENEI-----RPRDPIRCRECGYR 43 (73)
Q Consensus 1 ~~~~~~l-~~~~~~~-~v~YiC~~Cg~e~~i-----k~~d~IRC~~CG~R 43 (73)
|||-+-| +.+.+.. .+.|+|.+||.+... ...+.-.||+||..
T Consensus 310 ~GAVetLLV~d~l~~~r~~~~c~~c~~~~~~~~~~~~~~~~~~c~~~~~~ 359 (411)
T PRK04011 310 MGAVDTLLISEDLRKDRVTYKCPNCGYEEEKTVKRREELPEKTCPKCGSE 359 (411)
T ss_pred cCCceEEEEeccccceeEEEEcCCCCcceeeecccccccccccCcccCcc
Confidence 4555444 6666654 589999999987543 13456799999976
No 178
>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=67.67 E-value=3.7 Score=29.00 Aligned_cols=27 Identities=22% Similarity=0.351 Sum_probs=19.2
Q ss_pred EEEcCcCCcceecC-------CCCCeecCCCCCe
Q psy2244 17 EKYYLECHFENEIR-------PRDPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik-------~~d~IRC~~CG~R 43 (73)
...|..|+...... ....-+|+.||..
T Consensus 109 ~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~ 142 (218)
T cd01407 109 RVRCTKCGKEYPRDELQADIDREEVPRCPKCGGL 142 (218)
T ss_pred cceeCCCcCCCcHHHHhHhhccCCCCcCCCCCCc
Confidence 46799998876532 2345689999975
No 179
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=67.57 E-value=4.1 Score=38.08 Aligned_cols=34 Identities=18% Similarity=0.383 Sum_probs=25.9
Q ss_pred ceEEEcCcCCcceecCCCCCeecCCCCCeEEEeeeC
Q psy2244 15 DIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRT 50 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt 50 (73)
.-+++| +||+...--+.. -+||.||.+|+...-.
T Consensus 1540 rQ~~RC-kC~~kyRR~PL~-G~C~kCGg~~ilTV~k 1573 (1627)
T PRK14715 1540 RQEFRC-KCGAKYRRVPLK-GKCPKCGSKLILTVSK 1573 (1627)
T ss_pred ccceee-cCCCccccCCCC-CcCcccCCeEEEEEec
Confidence 457899 999987655544 5899999999876543
No 180
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=67.50 E-value=8 Score=25.63 Aligned_cols=32 Identities=19% Similarity=0.287 Sum_probs=19.9
Q ss_pred CCeecCCCCCeEEEeeeCCeeEEEeeccCCCCCc
Q psy2244 33 DPIRCRECGYRIMYKKRTKRCILYFKPQTGGFPK 66 (73)
Q Consensus 33 d~IRC~~CG~RILyKkRt~r~vqf~~~~~~~~~~ 66 (73)
...+||.||.+.|-+++ ...+...++++++|-
T Consensus 100 ~~~~cp~c~~~~~~~k~--~~~~~~~~~c~~~~~ 131 (140)
T COG0551 100 KEKKCPKCGSRKLVEKK--EKKKGVFLECSNKPC 131 (140)
T ss_pred ccccCCcCCCceeEEEe--eecceEEEecCCCcc
Confidence 44669999986666633 334445566777664
No 181
>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=67.28 E-value=5.4 Score=26.13 Aligned_cols=32 Identities=25% Similarity=0.472 Sum_probs=25.9
Q ss_pred CCCCeecCCCCCeEEEeeeCCeeEEEeeccCCC
Q psy2244 31 PRDPIRCRECGYRIMYKKRTKRCILYFKPQTGG 63 (73)
Q Consensus 31 ~~d~IRC~~CG~RILyKkRt~r~vqf~~~~~~~ 63 (73)
.....+|+.||..+-.+.|. +..+|.=+.|+|
T Consensus 120 ~~~~~~C~~C~~~~~r~~~~-~~~~~~C~~C~~ 151 (157)
T PF10263_consen 120 KKYVYRCPSCGREYKRHRRS-KRKRYRCGRCGG 151 (157)
T ss_pred cceEEEcCCCCCEeeeeccc-chhhEECCCCCC
Confidence 34678999999999777776 777788888886
No 182
>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=67.28 E-value=3.8 Score=29.30 Aligned_cols=27 Identities=22% Similarity=0.605 Sum_probs=19.0
Q ss_pred EEEcCcCCcceecC------CCCCeecCCCCCe
Q psy2244 17 EKYYLECHFENEIR------PRDPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik------~~d~IRC~~CG~R 43 (73)
...|..|+.....+ ....-+|+.||..
T Consensus 113 ~~~C~~C~~~~~~~~~~~~~~~~~p~C~~Cgg~ 145 (222)
T cd01413 113 TAYCVNCGSKYDLEEVKYAKKHEVPRCPKCGGI 145 (222)
T ss_pred cceECCCCCCcchhHHHHhccCCCCcCCCCCCc
Confidence 46799998876544 2234689999975
No 183
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=67.16 E-value=3.9 Score=23.19 Aligned_cols=16 Identities=31% Similarity=0.848 Sum_probs=10.7
Q ss_pred ecCCC-CCeecCCCCCe
Q psy2244 28 EIRPR-DPIRCRECGYR 43 (73)
Q Consensus 28 ~ik~~-d~IRC~~CG~R 43 (73)
+++.. ..+.|++||-+
T Consensus 22 ~l~~~~~~~~CpYCg~~ 38 (40)
T PF10276_consen 22 NLDDEPGPVVCPYCGTR 38 (40)
T ss_dssp E-TTTTCEEEETTTTEE
T ss_pred ecCCCCCeEECCCCCCE
Confidence 34442 46999999965
No 184
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=67.15 E-value=6.3 Score=22.50 Aligned_cols=27 Identities=19% Similarity=0.230 Sum_probs=18.6
Q ss_pred cceEEEcCcCCcceecCC----CCCeecCCC
Q psy2244 14 GDIEKYYLECHFENEIRP----RDPIRCREC 40 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~----~d~IRC~~C 40 (73)
..+-.+|..||.+...+. ...-.||+|
T Consensus 25 ~~v~W~C~~Cgh~w~~~v~~R~~~~~~CP~C 55 (55)
T PF14311_consen 25 KKVWWKCPKCGHEWKASVNDRTRRGKGCPYC 55 (55)
T ss_pred CEEEEECCCCCCeeEccHhhhccCCCCCCCC
Confidence 346688899988866542 356678877
No 185
>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=67.13 E-value=4.2 Score=25.43 Aligned_cols=26 Identities=27% Similarity=0.616 Sum_probs=19.9
Q ss_pred EEcCcCCcceecC-----CCCCeecCCCCCe
Q psy2244 18 KYYLECHFENEIR-----PRDPIRCRECGYR 43 (73)
Q Consensus 18 YiC~~Cg~e~~ik-----~~d~IRC~~CG~R 43 (73)
-.|..|++--.|. ..+-+-|..|||+
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~ 39 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYT 39 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCe
Confidence 5799998765443 4577999999995
No 186
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=67.07 E-value=6.8 Score=28.97 Aligned_cols=25 Identities=16% Similarity=0.292 Sum_probs=17.6
Q ss_pred EcCcCCcceecC-CCCCeecCCCCCe
Q psy2244 19 YYLECHFENEIR-PRDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e~~ik-~~d~IRC~~CG~R 43 (73)
-|+.||...... ..-..+|+.||.+
T Consensus 101 fC~~CG~~~~~~~~~~~~~C~~c~~~ 126 (256)
T PRK00241 101 FCGYCGHPMHPSKTEWAMLCPHCRER 126 (256)
T ss_pred cccccCCCCeecCCceeEECCCCCCE
Confidence 488888886654 3455678888863
No 187
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=66.69 E-value=19 Score=22.09 Aligned_cols=43 Identities=12% Similarity=0.305 Sum_probs=32.2
Q ss_pred EEcCcCCcceecCC-------CCCeecCCCCCeEEEeeeCCeeEEEeecc
Q psy2244 18 KYYLECHFENEIRP-------RDPIRCRECGYRIMYKKRTKRCILYFKPQ 60 (73)
Q Consensus 18 YiC~~Cg~e~~ik~-------~d~IRC~~CG~RILyKkRt~r~vqf~~~~ 60 (73)
..|.-||....++. +-++-||.|-.-.|.-...-.+..--+||
T Consensus 5 i~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI~v~~~~i~vikepd 54 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKNFPLYCPKCKQETLIDVKQLKITVIKEPD 54 (55)
T ss_pred EECCCCCCccceeeecCceeccccccCCCCCceEEEEeeccEEEEEeCCC
Confidence 57999997765552 36789999999988887766666666665
No 188
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=66.68 E-value=1.8 Score=33.29 Aligned_cols=41 Identities=22% Similarity=0.358 Sum_probs=27.4
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEe
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYF 57 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~ 57 (73)
-+..|+.|++...--+.. .+|+.||..+.--.=+.+.+.|+
T Consensus 166 q~~rc~~c~~k~rr~pl~-g~c~kcg~~~~ltv~~g~v~kyL 206 (253)
T COG1933 166 QEFRCVKCNTKFRRPPLD-GKCPICGGKIVLTVSKGAIEKYL 206 (253)
T ss_pred heeehHhhhhhhcCCCcc-ccccccCCeEEEEEeccHHHHHH
Confidence 467899998887554443 79999999665544444444443
No 189
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=66.58 E-value=3.9 Score=29.42 Aligned_cols=28 Identities=21% Similarity=0.548 Sum_probs=18.3
Q ss_pred eEEEcCcCCcceecC---CCCCeecCCCCCe
Q psy2244 16 IEKYYLECHFENEIR---PRDPIRCRECGYR 43 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik---~~d~IRC~~CG~R 43 (73)
-...|..|+...+.+ ..+..+|+.||..
T Consensus 121 ~~~~C~~C~~~~~~~~~~~~~~p~C~~Cgg~ 151 (242)
T PRK00481 121 LRARCTKCGQTYDLDEYLKPEPPRCPKCGGI 151 (242)
T ss_pred CceeeCCCCCCcChhhhccCCCCCCCCCCCc
Confidence 346799998765433 2244569999864
No 190
>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=66.36 E-value=4.5 Score=25.00 Aligned_cols=27 Identities=22% Similarity=0.607 Sum_probs=19.8
Q ss_pred EEcCcCCcceecC-----CCCCeecCCCCCeE
Q psy2244 18 KYYLECHFENEIR-----PRDPIRCRECGYRI 44 (73)
Q Consensus 18 YiC~~Cg~e~~ik-----~~d~IRC~~CG~RI 44 (73)
-.|..|+.--.|. ..+.+-|..|||+=
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 5789998764443 33669999999974
No 191
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=66.27 E-value=2.3 Score=25.96 Aligned_cols=30 Identities=27% Similarity=0.402 Sum_probs=22.0
Q ss_pred EEEcCcCCcceecCC------------CCCeecCCCCCeEEE
Q psy2244 17 EKYYLECHFENEIRP------------RDPIRCRECGYRIMY 46 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~------------~d~IRC~~CG~RILy 46 (73)
.-+|.-|++.++|+. -..-.|.+|-+||=.
T Consensus 2 ~vkC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~RI~~ 43 (56)
T PF09963_consen 2 RVKCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKERIRE 43 (56)
T ss_pred eeEEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHHHhH
Confidence 457888988888763 255679999888743
No 192
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=66.23 E-value=2.1 Score=28.26 Aligned_cols=34 Identities=18% Similarity=0.239 Sum_probs=24.8
Q ss_pred cCCcceEEEcCcCCcceecC-CCCCeecCCCCCeE
Q psy2244 11 CLPGDIEKYYLECHFENEIR-PRDPIRCRECGYRI 44 (73)
Q Consensus 11 ~~~~~v~YiC~~Cg~e~~ik-~~d~IRC~~CG~RI 44 (73)
+..+...|.|..||+..--+ ....-.|..||+-+
T Consensus 30 e~~q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 64 (90)
T PRK03976 30 EEKMRAKHVCPVCGRPKVKRVGTGIWECRKCGAKF 64 (90)
T ss_pred HHHHhcCccCCCCCCCceEEEEEEEEEcCCCCCEE
Confidence 44566789999998774443 44667999999865
No 193
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=65.96 E-value=4.5 Score=26.91 Aligned_cols=32 Identities=19% Similarity=0.368 Sum_probs=23.3
Q ss_pred CcceEEEcCcCCcceecC-CCCCeecCCCCCeE
Q psy2244 13 PGDIEKYYLECHFENEIR-PRDPIRCRECGYRI 44 (73)
Q Consensus 13 ~~~v~YiC~~Cg~e~~ik-~~d~IRC~~CG~RI 44 (73)
.+...|.|..||...-.+ ....-+|+.||+..
T Consensus 31 ~~~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 31 QQRAKHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred HHhcCCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 345679999999994444 34557999999854
No 194
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=65.79 E-value=2.9 Score=31.67 Aligned_cols=20 Identities=30% Similarity=0.539 Sum_probs=16.2
Q ss_pred EcCcCCcceecCCCCCeecCCCCCe
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
+| +||.+.+.. ..|++||-+
T Consensus 2 ~C-rCG~~l~~p----~~Cl~Cg~~ 21 (227)
T COG4031 2 IC-RCGAELSSP----AFCLNCGRR 21 (227)
T ss_pred cc-ccCCccccc----chhcccCCc
Confidence 58 899988764 789999975
No 195
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=65.67 E-value=4.6 Score=33.41 Aligned_cols=25 Identities=24% Similarity=0.489 Sum_probs=19.8
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
..|+|.+||... +.-.=+||+||-+
T Consensus 6 t~f~C~~CG~~s---~KW~GkCp~Cg~W 30 (456)
T COG1066 6 TAFVCQECGYVS---PKWLGKCPACGAW 30 (456)
T ss_pred cEEEcccCCCCC---ccccccCCCCCCc
Confidence 679999999875 3445689999963
No 196
>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=65.60 E-value=4.2 Score=30.07 Aligned_cols=27 Identities=26% Similarity=0.366 Sum_probs=14.7
Q ss_pred CcceEEEcCcCCcceecCCCCCeecCCCCC
Q psy2244 13 PGDIEKYYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 13 ~~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
.+.-...|+-||.+-.... ++|++||.
T Consensus 193 ~G~R~L~Cs~C~t~W~~~R---~~Cp~Cg~ 219 (290)
T PF04216_consen 193 EGKRYLHCSLCGTEWRFVR---IKCPYCGN 219 (290)
T ss_dssp --EEEEEETTT--EEE--T---TS-TTT--
T ss_pred CccEEEEcCCCCCeeeecC---CCCcCCCC
Confidence 3556778999999977664 68999998
No 197
>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=65.37 E-value=2.3 Score=28.12 Aligned_cols=34 Identities=18% Similarity=0.310 Sum_probs=24.6
Q ss_pred cCCcceEEEcCcCCcceecC-CCCCeecCCCCCeE
Q psy2244 11 CLPGDIEKYYLECHFENEIR-PRDPIRCRECGYRI 44 (73)
Q Consensus 11 ~~~~~v~YiC~~Cg~e~~ik-~~d~IRC~~CG~RI 44 (73)
+..+...|.|..||++.--+ ....-.|..||..+
T Consensus 29 e~~q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 29 EIQQKAKYVCPFCGKKTVKRGSTGIWTCRKCGAKF 63 (91)
T ss_pred HHHHhcCccCCCCCCCceEEEeeEEEEcCCCCCEE
Confidence 44556789999999774333 44668999999854
No 198
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=65.34 E-value=3 Score=31.86 Aligned_cols=34 Identities=15% Similarity=0.227 Sum_probs=26.1
Q ss_pred cCCcceEEEcCcCCcceecCCC--CCeecCCCCCeE
Q psy2244 11 CLPGDIEKYYLECHFENEIRPR--DPIRCRECGYRI 44 (73)
Q Consensus 11 ~~~~~v~YiC~~Cg~e~~ik~~--d~IRC~~CG~RI 44 (73)
+.|+..--+|.+|+..+-.+.. +.--||+|||-.
T Consensus 21 ~~~~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 21 EVPEGLWTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred CCCCCCeeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 5778888999999998765532 346899999944
No 199
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=64.80 E-value=12 Score=24.67 Aligned_cols=39 Identities=13% Similarity=0.189 Sum_probs=28.2
Q ss_pred eeccccCCcceEEEcCcCCcceec--CCCCCeecCCCCCeE
Q psy2244 6 VLVGKCLPGDIEKYYLECHFENEI--RPRDPIRCRECGYRI 44 (73)
Q Consensus 6 ~l~~~~~~~~v~YiC~~Cg~e~~i--k~~d~IRC~~CG~RI 44 (73)
-|+-++..-=|.=+|.+|+.+..+ .....|.|..||.-+
T Consensus 24 ~Lv~~PnS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L 64 (85)
T PTZ00083 24 RLVQGPNSYFMDVKCPGCSQITTVFSHAQTVVLCGGCSSQL 64 (85)
T ss_pred eEecCCCCeEEEEECCCCCCeeEEEecCceEEEccccCCEe
Confidence 344455555578899999988554 366889999999643
No 200
>PLN00209 ribosomal protein S27; Provisional
Probab=64.17 E-value=11 Score=24.92 Aligned_cols=38 Identities=13% Similarity=0.183 Sum_probs=27.6
Q ss_pred eccccCCcceEEEcCcCCcceec--CCCCCeecCCCCCeE
Q psy2244 7 LVGKCLPGDIEKYYLECHFENEI--RPRDPIRCRECGYRI 44 (73)
Q Consensus 7 l~~~~~~~~v~YiC~~Cg~e~~i--k~~d~IRC~~CG~RI 44 (73)
|.-++..-=|.=+|.+|+.+..+ .....|.|..||.-+
T Consensus 26 Lv~~PnS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L 65 (86)
T PLN00209 26 LVQSPNSFFMDVKCQGCFNITTVFSHSQTVVVCGSCQTVL 65 (86)
T ss_pred eecCCCCEEEEEECCCCCCeeEEEecCceEEEccccCCEe
Confidence 44444555578899999998554 366889999999644
No 201
>PRK12495 hypothetical protein; Provisional
Probab=62.96 E-value=4.9 Score=30.53 Aligned_cols=28 Identities=18% Similarity=0.169 Sum_probs=22.2
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
..+.|..||..+- .....++|+.|+..+
T Consensus 41 sa~hC~~CG~PIp-a~pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 41 TNAHCDECGDPIF-RHDGQEFCPTCQQPV 68 (226)
T ss_pred chhhcccccCccc-CCCCeeECCCCCCcc
Confidence 4578999999987 445679999999654
No 202
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=62.96 E-value=1.2 Score=32.14 Aligned_cols=27 Identities=26% Similarity=0.492 Sum_probs=19.5
Q ss_pred CcceEEEcCcCCcceecCCCCCeecCCCCCeEE
Q psy2244 13 PGDIEKYYLECHFENEIRPRDPIRCRECGYRIM 45 (73)
Q Consensus 13 ~~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RIL 45 (73)
|+...=-|.+||+++- ..||+|+..|-
T Consensus 24 p~~~~~fC~kCG~~tI------~~Cp~C~~~Ir 50 (158)
T PF10083_consen 24 PELREKFCSKCGAKTI------TSCPNCSTPIR 50 (158)
T ss_pred chHHHHHHHHhhHHHH------HHCcCCCCCCC
Confidence 4555667888988862 56888888774
No 203
>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=62.32 E-value=4.5 Score=22.62 Aligned_cols=22 Identities=18% Similarity=0.161 Sum_probs=12.0
Q ss_pred eEEEcCcCCcceecC--CCCCeec
Q psy2244 16 IEKYYLECHFENEIR--PRDPIRC 37 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik--~~d~IRC 37 (73)
-.|+|..||..+++- ...++-|
T Consensus 5 ~~YkC~~CGniVev~~~g~g~lvC 28 (36)
T PF06397_consen 5 EFYKCEHCGNIVEVVHDGGGPLVC 28 (36)
T ss_dssp EEEE-TTT--EEEEEE--SS-EEE
T ss_pred cEEEccCCCCEEEEEECCCCCEEe
Confidence 469999999998754 2344555
No 204
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=62.32 E-value=3.6 Score=27.73 Aligned_cols=10 Identities=50% Similarity=0.959 Sum_probs=8.6
Q ss_pred CeecCCCCCe
Q psy2244 34 PIRCRECGYR 43 (73)
Q Consensus 34 ~IRC~~CG~R 43 (73)
.|.||+||-|
T Consensus 3 LI~CP~Cg~R 12 (97)
T COG4311 3 LIPCPYCGER 12 (97)
T ss_pred eecCCCCCCC
Confidence 5899999975
No 205
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=62.26 E-value=5.8 Score=26.97 Aligned_cols=22 Identities=27% Similarity=0.573 Sum_probs=13.1
Q ss_pred cCcCCcceecCCCCCeecCCCCCeE
Q psy2244 20 YLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 20 C~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
|..||.+..+. .++|++|+-.|
T Consensus 1 CPvCg~~l~vt---~l~C~~C~t~i 22 (113)
T PF09862_consen 1 CPVCGGELVVT---RLKCPSCGTEI 22 (113)
T ss_pred CCCCCCceEEE---EEEcCCCCCEE
Confidence 55666665554 26677776544
No 206
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=61.99 E-value=5.8 Score=24.70 Aligned_cols=15 Identities=33% Similarity=0.831 Sum_probs=12.1
Q ss_pred CCeecCCCCCeEEEe
Q psy2244 33 DPIRCRECGYRIMYK 47 (73)
Q Consensus 33 d~IRC~~CG~RILyK 47 (73)
-.|+|.+|||-||.-
T Consensus 33 IkikC~nC~h~vm~p 47 (60)
T COG4481 33 IKIKCENCGHSVMMP 47 (60)
T ss_pred EEEEecCCCcEEEec
Confidence 348999999988863
No 207
>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=61.98 E-value=6.4 Score=22.20 Aligned_cols=12 Identities=33% Similarity=0.946 Sum_probs=8.1
Q ss_pred ecCCCCCeEEEe
Q psy2244 36 RCRECGYRIMYK 47 (73)
Q Consensus 36 RC~~CG~RILyK 47 (73)
+||+||.+....
T Consensus 1 ~CP~Cg~~a~ir 12 (47)
T PF04606_consen 1 RCPHCGSKARIR 12 (47)
T ss_pred CcCCCCCeeEEE
Confidence 578888876444
No 208
>PF15616 TerY-C: TerY-C metal binding domain
Probab=61.97 E-value=10 Score=26.31 Aligned_cols=26 Identities=19% Similarity=0.304 Sum_probs=22.2
Q ss_pred cCCcceecCCCCCeecCCCCCeEEEe
Q psy2244 22 ECHFENEIRPRDPIRCRECGYRIMYK 47 (73)
Q Consensus 22 ~Cg~e~~ik~~d~IRC~~CG~RILyK 47 (73)
.||+..=++..+.+-||-||..+.|-
T Consensus 93 ~CGkl~Ci~g~~~~~CPwCg~~g~~~ 118 (131)
T PF15616_consen 93 GCGKLFCIDGEGEVTCPWCGNEGSFG 118 (131)
T ss_pred cCCCEEEeCCCCCEECCCCCCeeeec
Confidence 78888888888899999999987663
No 209
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=61.88 E-value=3.2 Score=30.10 Aligned_cols=16 Identities=31% Similarity=0.166 Sum_probs=9.5
Q ss_pred EEEcCcCCcceecCCC
Q psy2244 17 EKYYLECHFENEIRPR 32 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~ 32 (73)
.=.|..|+.+...-+.
T Consensus 97 ~~RCp~CN~~L~~vs~ 112 (165)
T COG1656 97 FSRCPECNGELEKVSR 112 (165)
T ss_pred cccCcccCCEeccCcH
Confidence 4467777776554433
No 210
>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=61.72 E-value=2.7 Score=25.97 Aligned_cols=36 Identities=25% Similarity=0.266 Sum_probs=19.6
Q ss_pred ccccCCcce--EEEcC----cCCcceecCCCCCeecCCCCCeEE
Q psy2244 8 VGKCLPGDI--EKYYL----ECHFENEIRPRDPIRCRECGYRIM 45 (73)
Q Consensus 8 ~~~~~~~~v--~YiC~----~Cg~e~~ik~~d~IRC~~CG~RIL 45 (73)
|++++|... -|||. -|..=.+... .-.||+||.-.+
T Consensus 11 C~~dLp~~s~~A~ICSfECTFC~~C~e~~l--~~~CPNCgGelv 52 (57)
T PF06906_consen 11 CDKDLPPDSPEAYICSFECTFCADCAETML--NGVCPNCGGELV 52 (57)
T ss_pred cCCCCCCCCCcceEEeEeCcccHHHHHHHh--cCcCcCCCCccc
Confidence 455666554 55554 3322222111 368999998765
No 211
>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=61.49 E-value=9.9 Score=25.03 Aligned_cols=21 Identities=29% Similarity=0.506 Sum_probs=16.1
Q ss_pred eecCCCCCeecCCCCCeEEEe
Q psy2244 27 NEIRPRDPIRCRECGYRIMYK 47 (73)
Q Consensus 27 ~~ik~~d~IRC~~CG~RILyK 47 (73)
+.+..+.+-||++||+-...+
T Consensus 72 ~~l~~g~~~rC~eCG~~fkL~ 92 (97)
T cd00924 72 MWLEKGKPKRCPECGHVFKLV 92 (97)
T ss_pred EEEeCCCceeCCCCCcEEEEE
Confidence 346677899999999966554
No 212
>KOG3134|consensus
Probab=61.47 E-value=3.4 Score=31.38 Aligned_cols=25 Identities=20% Similarity=0.300 Sum_probs=17.5
Q ss_pred EEcCcCCcceecC---CC----CCeecCCCCC
Q psy2244 18 KYYLECHFENEIR---PR----DPIRCRECGY 42 (73)
Q Consensus 18 YiC~~Cg~e~~ik---~~----d~IRC~~CG~ 42 (73)
|+|-+||.+++.= -. .-.+|++|+-
T Consensus 1 ~~CVeCg~~vksLy~~Ys~g~irlt~C~nC~e 32 (225)
T KOG3134|consen 1 YRCVECGSEVKSLYTQYSPGNIRLTKCPNCQE 32 (225)
T ss_pred CcccccCchHHHHHHhcCCCcEEEeeCCchhh
Confidence 6899999997632 11 3367999974
No 213
>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=61.23 E-value=4.8 Score=25.80 Aligned_cols=26 Identities=27% Similarity=0.304 Sum_probs=16.7
Q ss_pred EcCcCCcceecCCC--------CCeecCCCCCeE
Q psy2244 19 YYLECHFENEIRPR--------DPIRCRECGYRI 44 (73)
Q Consensus 19 iC~~Cg~e~~ik~~--------d~IRC~~CG~RI 44 (73)
.|..|++....... -.-||++|+.+|
T Consensus 35 ~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~I 68 (92)
T PF06750_consen 35 HCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAPI 68 (92)
T ss_pred cCcCCCCcCcccccchHHHHHHhCCCCcccCCCC
Confidence 57777777655433 334788887766
No 214
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=61.02 E-value=7.5 Score=30.97 Aligned_cols=39 Identities=13% Similarity=0.245 Sum_probs=32.9
Q ss_pred EcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEeecc
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKPQ 60 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~~~~ 60 (73)
.|..||..+-++. .+|-.||+++=|-+-...|+.+....
T Consensus 1 ~C~~Cg~~v~FeN---t~C~~Cg~~LGf~p~~~~~~al~~~~ 39 (343)
T PF10005_consen 1 SCPNCGQPVFFEN---TRCLSCGSALGFDPDRREMVALEPDG 39 (343)
T ss_pred CCCCCCCcceeCC---CccccCCccccCCCCCCcEEeeccCC
Confidence 3889999887764 78999999999999998998887643
No 215
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=60.60 E-value=9.5 Score=29.42 Aligned_cols=36 Identities=17% Similarity=0.218 Sum_probs=26.4
Q ss_pred CCcceEEEcCcCCcceecC---CCCCeecCCCCCeEEEe
Q psy2244 12 LPGDIEKYYLECHFENEIR---PRDPIRCRECGYRIMYK 47 (73)
Q Consensus 12 ~~~~v~YiC~~Cg~e~~ik---~~d~IRC~~CG~RILyK 47 (73)
.|.....+|+.|...+... .....|||+|....-..
T Consensus 152 ~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG 190 (256)
T PF09788_consen 152 QPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVG 190 (256)
T ss_pred CCCceeEECCCCCCcEeccCCCCCccccCCCCceecccc
Confidence 3455789999999997765 24567999998655443
No 216
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=60.27 E-value=8.6 Score=29.93 Aligned_cols=38 Identities=13% Similarity=0.104 Sum_probs=26.9
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEE
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCIL 55 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vq 55 (73)
..|-.||..++......-+|+.||.....++.+.-...
T Consensus 150 ~~Ce~cG~~~~~~~l~~p~~~~~g~~~~~r~e~~~ff~ 187 (391)
T PF09334_consen 150 DQCENCGRPLEPEELINPVCKICGSPPEVREEENYFFK 187 (391)
T ss_dssp TEETTTSSBEECCCSECEEETTTS-B-EEEEEEEEEE-
T ss_pred CcccCCCCCcccccccCCccccccccCccccceEEEEe
Confidence 45668899998888888899999999887766554443
No 217
>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=60.15 E-value=5.9 Score=26.79 Aligned_cols=12 Identities=33% Similarity=1.148 Sum_probs=11.1
Q ss_pred CeecCCCCCeEE
Q psy2244 34 PIRCRECGYRIM 45 (73)
Q Consensus 34 ~IRC~~CG~RIL 45 (73)
.|+|+.|++.||
T Consensus 2 ~v~C~~C~S~VL 13 (103)
T cd00246 2 AVLCQRCGSRVL 13 (103)
T ss_pred ceECCCCCCEEE
Confidence 489999999999
No 218
>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=59.86 E-value=5.2 Score=21.96 Aligned_cols=10 Identities=40% Similarity=1.065 Sum_probs=5.2
Q ss_pred eecCCCCCeE
Q psy2244 35 IRCRECGYRI 44 (73)
Q Consensus 35 IRC~~CG~RI 44 (73)
|.||+||++-
T Consensus 1 ~~Cp~Cg~~~ 10 (39)
T PF01096_consen 1 IKCPKCGHNE 10 (39)
T ss_dssp S--SSS-SSE
T ss_pred CCCcCCCCCe
Confidence 5799999853
No 219
>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=59.73 E-value=7.7 Score=27.84 Aligned_cols=27 Identities=15% Similarity=0.167 Sum_probs=18.6
Q ss_pred EEEcCcCCcceecCC-CCCeecCCCCCe
Q psy2244 17 EKYYLECHFENEIRP-RDPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~-~d~IRC~~CG~R 43 (73)
...|..|+...+... ...-+|+.||..
T Consensus 118 ~~~C~~C~~~~~~~~~~~~p~C~~Cgg~ 145 (225)
T cd01411 118 RIYCTVCGKTVDWEEYLKSPYHAKCGGV 145 (225)
T ss_pred eeEeCCCCCccchhhcCCCCCCCCCCCE
Confidence 357999987765442 234689999974
No 220
>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=59.70 E-value=5.2 Score=18.59 Aligned_cols=11 Identities=9% Similarity=-0.167 Sum_probs=7.5
Q ss_pred EEcCcCCccee
Q psy2244 18 KYYLECHFENE 28 (73)
Q Consensus 18 YiC~~Cg~e~~ 28 (73)
|.|..|+..+.
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 67777776654
No 221
>PRK04023 DNA polymerase II large subunit; Validated
Probab=59.25 E-value=6.2 Score=35.80 Aligned_cols=23 Identities=26% Similarity=0.335 Sum_probs=12.4
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
-...|.+||... ...+||+||..
T Consensus 625 g~RfCpsCG~~t-----~~frCP~CG~~ 647 (1121)
T PRK04023 625 GRRKCPSCGKET-----FYRRCPFCGTH 647 (1121)
T ss_pred cCccCCCCCCcC-----CcccCCCCCCC
Confidence 445666666653 23456666554
No 222
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=59.24 E-value=2.4 Score=28.98 Aligned_cols=31 Identities=10% Similarity=-0.081 Sum_probs=22.6
Q ss_pred cceEEEcCcCCcceecCC-CCCeecCCCCCeE
Q psy2244 14 GDIEKYYLECHFENEIRP-RDPIRCRECGYRI 44 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~-~d~IRC~~CG~RI 44 (73)
++-.-+||-|..+..... ++..+||+|.+|.
T Consensus 59 ~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~spF 90 (105)
T COG4357 59 NPKAIICGVCRKLLTRAEYGMCGSCPYCQSPF 90 (105)
T ss_pred CCccEEhhhhhhhhhHHHHhhcCCCCCcCCCC
Confidence 344468889988877664 4678999998863
No 223
>PRK14873 primosome assembly protein PriA; Provisional
Probab=59.13 E-value=8.6 Score=32.39 Aligned_cols=27 Identities=22% Similarity=0.353 Sum_probs=15.2
Q ss_pred EEEcCcCCcceec-CCCCCeecCCCCCe
Q psy2244 17 EKYYLECHFENEI-RPRDPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~i-k~~d~IRC~~CG~R 43 (73)
...|.+|+..... +.....+|.+||+.
T Consensus 392 ~~~C~~C~~~L~~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 392 PARCRHCTGPLGLPSAGGTPRCRWCGRA 419 (665)
T ss_pred eeECCCCCCceeEecCCCeeECCCCcCC
Confidence 4556666555444 33445667777764
No 224
>PHA02998 RNA polymerase subunit; Provisional
Probab=59.00 E-value=7.5 Score=29.03 Aligned_cols=32 Identities=22% Similarity=0.425 Sum_probs=17.9
Q ss_pred CCcceEEEcCcCCcc------eecCCCCC-----eecCCCCCe
Q psy2244 12 LPGDIEKYYLECHFE------NEIRPRDP-----IRCRECGYR 43 (73)
Q Consensus 12 ~~~~v~YiC~~Cg~e------~~ik~~d~-----IRC~~CG~R 43 (73)
+|....-.|..||.. .++++.|. .+|.+||++
T Consensus 138 lpkkt~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~ 180 (195)
T PHA02998 138 LDEKYNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKH 180 (195)
T ss_pred cCcccCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCc
Confidence 344455677778665 22332221 378888875
No 225
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=58.81 E-value=4.1 Score=30.44 Aligned_cols=28 Identities=21% Similarity=0.301 Sum_probs=19.0
Q ss_pred eEEEcCcCCcceecCC------------CCCeecCCCCCe
Q psy2244 16 IEKYYLECHFENEIRP------------RDPIRCRECGYR 43 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~------------~d~IRC~~CG~R 43 (73)
..-.|.-||....... -....|.+||||
T Consensus 13 ~~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR 52 (201)
T COG1779 13 TRIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYR 52 (201)
T ss_pred eeecCCcccceeeEEEeeecCCccceEEEEEEEccccCCc
Confidence 4456888888544331 156889999996
No 226
>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=58.06 E-value=6 Score=32.29 Aligned_cols=34 Identities=18% Similarity=0.297 Sum_probs=22.6
Q ss_pred EEcCcCCcceecCC------------CCCeecCCCCCeEEEeeeCC
Q psy2244 18 KYYLECHFENEIRP------------RDPIRCRECGYRIMYKKRTK 51 (73)
Q Consensus 18 YiC~~Cg~e~~ik~------------~d~IRC~~CG~RILyKkRt~ 51 (73)
-.|..||....++- .--..|+.||+.|--..|..
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~ 246 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRR 246 (557)
T ss_pred ccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhh
Confidence 35888888877651 12367889998876654433
No 227
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=58.04 E-value=13 Score=24.88 Aligned_cols=30 Identities=13% Similarity=0.189 Sum_probs=23.9
Q ss_pred ceEEEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 15 DIEKYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
-...-|..|++.+.....+.-+|+.|+..+
T Consensus 32 ~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 32 WWYPACPGCNKKVVEEGNGTYRCEKCNKSV 61 (166)
T ss_pred eEEccccccCcccEeCCCCcEECCCCCCcC
Confidence 345569999999876655789999999876
No 228
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=57.76 E-value=6 Score=29.78 Aligned_cols=28 Identities=25% Similarity=0.516 Sum_probs=19.4
Q ss_pred ceEEEcCcCCccee-cC-CCCCeecCCCCC
Q psy2244 15 DIEKYYLECHFENE-IR-PRDPIRCRECGY 42 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~-ik-~~d~IRC~~CG~ 42 (73)
....+|.+||...- .+ ....+-|.+||.
T Consensus 9 ~~~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~ 38 (310)
T PRK00423 9 EEKLVCPECGSDKLIYDYERGEIVCADCGL 38 (310)
T ss_pred ccCCcCcCCCCCCeeEECCCCeEeecccCC
Confidence 34568999997322 12 446699999998
No 229
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=57.50 E-value=8.7 Score=23.57 Aligned_cols=15 Identities=40% Similarity=0.806 Sum_probs=12.5
Q ss_pred CCeecCCCCCeEEEe
Q psy2244 33 DPIRCRECGYRIMYK 47 (73)
Q Consensus 33 d~IRC~~CG~RILyK 47 (73)
-.++|..||+.||.-
T Consensus 30 ikikC~gCg~~imlp 44 (57)
T PF06107_consen 30 IKIKCLGCGRQIMLP 44 (57)
T ss_pred EEEEECCCCCEEEEe
Confidence 458999999999874
No 230
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=56.75 E-value=6 Score=32.55 Aligned_cols=51 Identities=22% Similarity=0.355 Sum_probs=34.4
Q ss_pred ceEEEcCcCCcc-eecCCCCCeecCCCCCeEEEeee-CCeeEEEeeccCCCCCcc
Q psy2244 15 DIEKYYLECHFE-NEIRPRDPIRCRECGYRIMYKKR-TKRCILYFKPQTGGFPKL 67 (73)
Q Consensus 15 ~v~YiC~~Cg~e-~~ik~~d~IRC~~CG~RILyKkR-t~r~vqf~~~~~~~~~~~ 67 (73)
.-.|+|.+||.. .+....-++-|-||..-|++..- +.+.+-|.+ -.-|||-
T Consensus 37 ~gk~~C~RC~~~~~~~~~~lp~~~~YCr~Cl~mgRv~sd~~Ly~~~--~~~fp~~ 89 (441)
T COG4098 37 NGKYRCNRCGNTHIELFAKLPCGCLYCRNCLMMGRVRSDQKLYYWK--PYAFPKK 89 (441)
T ss_pred cCcEEehhcCCcchhhhcccccceEeehhhhhcccccccceeeecC--CcCCCcc
Confidence 356999999944 45555666778888888888754 445555555 4567763
No 231
>COG4640 Predicted membrane protein [Function unknown]
Probab=56.65 E-value=5.6 Score=32.96 Aligned_cols=22 Identities=23% Similarity=0.708 Sum_probs=15.3
Q ss_pred cCcCCcceecCCCCCeecCCCCCeE
Q psy2244 20 YLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 20 C~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
|..||....- |.+.|+.||+.+
T Consensus 4 C~kcG~qk~E---d~~qC~qCG~~~ 25 (465)
T COG4640 4 CPKCGSQKAE---DDVQCTQCGHKF 25 (465)
T ss_pred cccccccccc---ccccccccCCcC
Confidence 7888855433 346699999865
No 232
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=56.25 E-value=17 Score=26.18 Aligned_cols=36 Identities=25% Similarity=0.376 Sum_probs=27.2
Q ss_pred CCeecCCCCCeEEEeeeCCeeEEEeeccCCCCCcce
Q psy2244 33 DPIRCRECGYRIMYKKRTKRCILYFKPQTGGFPKLK 68 (73)
Q Consensus 33 d~IRC~~CG~RILyKkRt~r~vqf~~~~~~~~~~~~ 68 (73)
..+.||.|+...--|+=..+-+...+.+.|.+|+-+
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~ 39 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYK 39 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccC
Confidence 458999999988777655566666688888888754
No 233
>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=56.04 E-value=7.7 Score=27.36 Aligned_cols=27 Identities=22% Similarity=0.438 Sum_probs=18.4
Q ss_pred EEEcCcCCcceecC----CCCCeecCCCCCe
Q psy2244 17 EKYYLECHFENEIR----PRDPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik----~~d~IRC~~CG~R 43 (73)
...|..|+.+.... ....-+|+.||..
T Consensus 109 ~~~C~~C~~~~~~~~~~~~~~~p~C~~Cgg~ 139 (224)
T cd01412 109 RVRCSSCGYVGENNEEIPEEELPRCPKCGGL 139 (224)
T ss_pred ccccCCCCCCCCcchhhhccCCCCCCCCCCc
Confidence 45688998876543 2234689999974
No 234
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=56.01 E-value=12 Score=22.40 Aligned_cols=26 Identities=19% Similarity=0.231 Sum_probs=17.6
Q ss_pred CcceEEEcCcCCcceecCCCCCeecCCCCC
Q psy2244 13 PGDIEKYYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 13 ~~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
.-+..-.|.+||..... -.-|++||+
T Consensus 23 ~~~~l~~C~~CG~~~~~----H~vC~~CG~ 48 (57)
T PRK12286 23 KAPGLVECPNCGEPKLP----HRVCPSCGY 48 (57)
T ss_pred cCCcceECCCCCCccCC----eEECCCCCc
Confidence 34555678888876532 477888984
No 235
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=55.88 E-value=4.9 Score=36.62 Aligned_cols=26 Identities=27% Similarity=0.464 Sum_probs=20.0
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeEEE
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRIMY 46 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RILy 46 (73)
-+|.+||.-+.-. .+ .||.||.+.+-
T Consensus 695 KrC~dcg~q~~~~-~~--~cP~Cgs~~v~ 720 (1187)
T COG1110 695 KRCRDCGEQFVDS-ED--KCPRCGSRNVE 720 (1187)
T ss_pred HHHhhcCceeccc-cc--cCCCCCCcccc
Confidence 4799999987665 33 89999996553
No 236
>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=55.76 E-value=6.7 Score=20.90 Aligned_cols=25 Identities=16% Similarity=0.250 Sum_probs=16.1
Q ss_pred EcCcCCcceecCCCCCeecCCCCCe
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
.|.-|+..+-.-.....+|+.|+..
T Consensus 13 ~C~~C~~~i~~~~~~~~~C~~C~~~ 37 (50)
T cd00029 13 FCDVCRKSIWGLFKQGLRCSWCKVK 37 (50)
T ss_pred ChhhcchhhhccccceeEcCCCCCc
Confidence 3677766654434567788888754
No 237
>PLN02294 cytochrome c oxidase subunit Vb
Probab=55.70 E-value=12 Score=27.40 Aligned_cols=21 Identities=10% Similarity=0.197 Sum_probs=16.2
Q ss_pred eecCCCCCeecCCCCCeEEEe
Q psy2244 27 NEIRPRDPIRCRECGYRIMYK 47 (73)
Q Consensus 27 ~~ik~~d~IRC~~CG~RILyK 47 (73)
+.+..+.+.||++||+-...|
T Consensus 134 f~L~kGkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 134 FWLEKGKSFECPVCTQYFELE 154 (174)
T ss_pred EEecCCCceeCCCCCCEEEEE
Confidence 346678999999999976554
No 238
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=55.67 E-value=9 Score=25.29 Aligned_cols=31 Identities=13% Similarity=0.235 Sum_probs=21.5
Q ss_pred cceEEEcC--cCCcceecCCCCCeecCCCCCeE
Q psy2244 14 GDIEKYYL--ECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 14 ~~v~YiC~--~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
.....-|. .|++.+.....+.-+|+.|+.-+
T Consensus 15 ~~~Y~aC~~~~C~kKv~~~~~~~y~C~~C~~~~ 47 (146)
T PF08646_consen 15 NWYYPACPNEKCNKKVTENGDGSYRCEKCNKTV 47 (146)
T ss_dssp TTEEEE-TSTTTS-B-EEETTTEEEETTTTEEE
T ss_pred CcEECCCCCccCCCEeecCCCcEEECCCCCCcC
Confidence 34566799 99998877755678999999654
No 239
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=55.50 E-value=8.3 Score=23.37 Aligned_cols=26 Identities=23% Similarity=0.565 Sum_probs=18.4
Q ss_pred EEcCcCCc-ceecCCCCCeecCCCCCe
Q psy2244 18 KYYLECHF-ENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 18 YiC~~Cg~-e~~ik~~d~IRC~~CG~R 43 (73)
=.|.+||. .+--.-.|-..|-.|||-
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CGkCgyT 46 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACGKCGYT 46 (51)
T ss_pred ccCCCCCCcchhhhcCceeEeccccce
Confidence 35888886 444556677888888873
No 240
>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=55.43 E-value=6 Score=20.80 Aligned_cols=24 Identities=17% Similarity=0.185 Sum_probs=16.5
Q ss_pred EcCcCCcceecCCCCCeecCCCCCe
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
.|.-|+..+.... ...+|+.|+..
T Consensus 13 ~C~~C~~~i~~~~-~~~~C~~C~~~ 36 (49)
T smart00109 13 KCCVCRKSIWGSF-QGLRCSWCKVK 36 (49)
T ss_pred CccccccccCcCC-CCcCCCCCCch
Confidence 5778877765433 57888888753
No 241
>COG1773 Rubredoxin [Energy production and conversion]
Probab=55.31 E-value=9.7 Score=23.15 Aligned_cols=26 Identities=23% Similarity=0.422 Sum_probs=18.6
Q ss_pred EEEcCcCCcceecCCC----------------CCeecCCCCC
Q psy2244 17 EKYYLECHFENEIRPR----------------DPIRCRECGY 42 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~----------------d~IRC~~CG~ 42 (73)
.|+|..||-..+...+ +.-.||.||-
T Consensus 3 ~~~C~~CG~vYd~e~Gdp~~gi~pgT~fedlPd~w~CP~Cg~ 44 (55)
T COG1773 3 RWRCSVCGYVYDPEKGDPRCGIAPGTPFEDLPDDWVCPECGV 44 (55)
T ss_pred ceEecCCceEeccccCCccCCCCCCCchhhCCCccCCCCCCC
Confidence 5889999887665533 4457899984
No 242
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.03 E-value=9.7 Score=23.83 Aligned_cols=16 Identities=19% Similarity=0.497 Sum_probs=12.2
Q ss_pred cCCCCCeecCCCCCeE
Q psy2244 29 IRPRDPIRCRECGYRI 44 (73)
Q Consensus 29 ik~~d~IRC~~CG~RI 44 (73)
+.....+.||+||-|-
T Consensus 43 mg~~gev~CPYC~t~y 58 (62)
T COG4391 43 MGDEGEVVCPYCSTRY 58 (62)
T ss_pred cCCCCcEecCccccEE
Confidence 4455779999999764
No 243
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=54.69 E-value=7.8 Score=32.93 Aligned_cols=41 Identities=24% Similarity=0.418 Sum_probs=25.5
Q ss_pred EEcCcCCcceecCC-CCCeecCCCCCeE-EEeeeCCeeEEEee
Q psy2244 18 KYYLECHFENEIRP-RDPIRCRECGYRI-MYKKRTKRCILYFK 58 (73)
Q Consensus 18 YiC~~Cg~e~~ik~-~d~IRC~~CG~RI-LyKkRt~r~vqf~~ 58 (73)
=+|.+||..-+++. ...-.||.||.+- .=-.+-+|+.-|+.
T Consensus 642 ~~C~~CG~~Ge~~~~~~~~~CP~CG~~~~~~~~v~~Ri~GYl~ 684 (711)
T PRK09263 642 DECYECGFTGEFECTEKGFTCPKCGNHDPKTVSVTRRTCGYLG 684 (711)
T ss_pred cccCCCCCCccccCCCCCCcCcCCCCCCCcceeEEEeeccccC
Confidence 47999998544432 2236899999752 00134567777874
No 244
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=54.67 E-value=10 Score=30.44 Aligned_cols=7 Identities=43% Similarity=1.345 Sum_probs=3.0
Q ss_pred ecCCCCC
Q psy2244 36 RCRECGY 42 (73)
Q Consensus 36 RC~~CG~ 42 (73)
+||+||.
T Consensus 255 ~Cp~C~s 261 (505)
T TIGR00595 255 TCPQCGS 261 (505)
T ss_pred CCCCCCC
Confidence 3444444
No 245
>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=54.38 E-value=10 Score=29.12 Aligned_cols=31 Identities=23% Similarity=0.304 Sum_probs=19.5
Q ss_pred cceEEEcCcCCccee------cCC-C----CCeecCCCCCeE
Q psy2244 14 GDIEKYYLECHFENE------IRP-R----DPIRCRECGYRI 44 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~------ik~-~----d~IRC~~CG~RI 44 (73)
....+.|++||...- .+. . --+.|.+||||-
T Consensus 255 ~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w 296 (299)
T TIGR01385 255 VTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRW 296 (299)
T ss_pred CcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCee
Confidence 345689999976522 221 1 225899999874
No 246
>COG5254 ARV1 Predicted membrane protein [Function unknown]
Probab=54.03 E-value=4.5 Score=30.94 Aligned_cols=25 Identities=20% Similarity=0.373 Sum_probs=18.1
Q ss_pred EEcCcCCcceecC-------CCCCeecCCCCC
Q psy2244 18 KYYLECHFENEIR-------PRDPIRCRECGY 42 (73)
Q Consensus 18 YiC~~Cg~e~~ik-------~~d~IRC~~CG~ 42 (73)
|+|-+||++++.- .-.--|||+|.-
T Consensus 1 mvCIeCg~~vdsLyt~ysts~iqls~Cp~C~~ 32 (239)
T COG5254 1 MVCIECGSRVDSLYTRYSTSAIQLSRCPSCNR 32 (239)
T ss_pred CeeeEcCCccceeeeeccCcceehhcCchHHH
Confidence 5899999998743 224468999964
No 247
>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=53.70 E-value=8.7 Score=17.16 Aligned_cols=10 Identities=10% Similarity=-0.217 Sum_probs=4.8
Q ss_pred EEcCcCCcce
Q psy2244 18 KYYLECHFEN 27 (73)
Q Consensus 18 YiC~~Cg~e~ 27 (73)
|.|..|+..+
T Consensus 1 ~~C~~C~~~~ 10 (24)
T PF13894_consen 1 FQCPICGKSF 10 (24)
T ss_dssp EE-SSTS-EE
T ss_pred CCCcCCCCcC
Confidence 5666666554
No 248
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=53.33 E-value=14 Score=29.58 Aligned_cols=31 Identities=16% Similarity=0.249 Sum_probs=23.5
Q ss_pred CcceEEEcCcCCcceecCCC----------------CCeecCCCCCe
Q psy2244 13 PGDIEKYYLECHFENEIRPR----------------DPIRCRECGYR 43 (73)
Q Consensus 13 ~~~v~YiC~~Cg~e~~ik~~----------------d~IRC~~CG~R 43 (73)
.....|+|..||-.-+...+ +.-+||-||..
T Consensus 421 ~~~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 421 DLGPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred CCCCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 35578999999988776533 34699999963
No 249
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=53.27 E-value=6 Score=31.23 Aligned_cols=31 Identities=23% Similarity=0.322 Sum_probs=22.0
Q ss_pred EEcCcCCcceecCCCCCeecCCCCC-eEEEeeeCC
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGY-RIMYKKRTK 51 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~-RILyKkRt~ 51 (73)
=+|.+||+.+..=. -.||+||. .|.-|-+++
T Consensus 83 ~~C~~CGa~V~~~e---~~Cp~C~StnI~r~DdSk 114 (314)
T PF09567_consen 83 GKCNNCGANVSRLE---ESCPNCGSTNIKRKDDSK 114 (314)
T ss_pred hhhccccceeeehh---hcCCCCCcccccccCCcc
Confidence 46999999986432 56999998 555555544
No 250
>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=53.25 E-value=8.2 Score=23.41 Aligned_cols=12 Identities=25% Similarity=0.944 Sum_probs=4.1
Q ss_pred eecCCCCCeEEE
Q psy2244 35 IRCRECGYRIMY 46 (73)
Q Consensus 35 IRC~~CG~RILy 46 (73)
++||.||..+.+
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 455555555444
No 251
>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=52.88 E-value=35 Score=26.46 Aligned_cols=26 Identities=19% Similarity=0.244 Sum_probs=20.2
Q ss_pred cceEEEcCcCCcceecCCCCCeecCCCCC
Q psy2244 14 GDIEKYYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
+.-...|+-|+.+=... -++|++||.
T Consensus 207 G~RyL~CslC~teW~~~---R~~C~~Cg~ 232 (305)
T TIGR01562 207 GLRYLSCSLCATEWHYV---RVKCSHCEE 232 (305)
T ss_pred CceEEEcCCCCCccccc---CccCCCCCC
Confidence 34567899998886655 489999998
No 252
>PRK14873 primosome assembly protein PriA; Provisional
Probab=52.85 E-value=13 Score=31.30 Aligned_cols=21 Identities=24% Similarity=0.408 Sum_probs=10.7
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
-+|--||... .+-+||+||..
T Consensus 411 l~Ch~CG~~~-----~p~~Cp~Cgs~ 431 (665)
T PRK14873 411 PRCRWCGRAA-----PDWRCPRCGSD 431 (665)
T ss_pred eECCCCcCCC-----cCccCCCCcCC
Confidence 3466666531 13466666654
No 253
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=52.59 E-value=4.7 Score=32.73 Aligned_cols=43 Identities=19% Similarity=0.207 Sum_probs=32.5
Q ss_pred eeccccCCcceEEEcCcCCcceecCCCCCeecCCCCCeEEEeeeCC
Q psy2244 6 VLVGKCLPGDIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTK 51 (73)
Q Consensus 6 ~l~~~~~~~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~ 51 (73)
-++|+-+.....|.|-+||.....= --.||.|..+=-+|++..
T Consensus 343 ~mvge~l~~~~~YRC~~CGF~a~~l---~W~CPsC~~W~TikPir~ 385 (389)
T COG2956 343 DMVGEQLRRKPRYRCQNCGFTAHTL---YWHCPSCRAWETIKPIRG 385 (389)
T ss_pred HHHHHHHhhcCCceecccCCcceee---eeeCCCcccccccCCccc
Confidence 3578888888999999998764322 267999998888877643
No 254
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=52.51 E-value=8.4 Score=32.33 Aligned_cols=37 Identities=22% Similarity=0.375 Sum_probs=22.3
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeEEE-eeeCCeeEEEee
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRIMY-KKRTKRCILYFK 58 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RILy-KkRt~r~vqf~~ 58 (73)
=+|.+||..-++. -.||.||.+--- -.+-+|+.-|+.
T Consensus 560 ~~C~~CGy~g~~~----~~CP~CG~~d~~~~~v~~Ri~GYl~ 597 (618)
T PRK14704 560 DRCKCCSYHGVIG----NECPSCGNEDEANIERIRRITGYLV 597 (618)
T ss_pred eecCCCCCCCCcC----ccCcCCCCCCcchhHHHHHHHhHhc
Confidence 4799999743332 589999974100 024456666664
No 255
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=52.42 E-value=15 Score=19.91 Aligned_cols=24 Identities=25% Similarity=0.268 Sum_probs=11.5
Q ss_pred cCcCCcceecC---CCCCeecCCCCCe
Q psy2244 20 YLECHFENEIR---PRDPIRCRECGYR 43 (73)
Q Consensus 20 C~~Cg~e~~ik---~~d~IRC~~CG~R 43 (73)
|..|+...+.. ....-+|+.||.-
T Consensus 2 CP~C~~~l~~~~~~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 2 CPRCGTELEPVRLGDVEIDVCPSCGGI 28 (41)
T ss_pred cCCCCcccceEEECCEEEEECCCCCeE
Confidence 56665542221 2233457777653
No 256
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=52.34 E-value=11 Score=24.98 Aligned_cols=28 Identities=21% Similarity=0.394 Sum_probs=19.8
Q ss_pred cCcCCcceecC---CCCCeecCCCCCeEEEe
Q psy2244 20 YLECHFENEIR---PRDPIRCRECGYRIMYK 47 (73)
Q Consensus 20 C~~Cg~e~~ik---~~d~IRC~~CG~RILyK 47 (73)
|.+||.-.-.+ .+....|+.|||-.-..
T Consensus 5 Cp~Cgsll~p~~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 5 CPKCGSLLYPKKDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred cCCccCeeEEeEcCCCcEEECCCCCcchhcc
Confidence 77888876664 34578899999854433
No 257
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=52.34 E-value=13 Score=21.14 Aligned_cols=25 Identities=28% Similarity=0.490 Sum_probs=14.8
Q ss_pred EEcCcCCccee-cCCC--------CCeecCCCCC
Q psy2244 18 KYYLECHFENE-IRPR--------DPIRCRECGY 42 (73)
Q Consensus 18 YiC~~Cg~e~~-ik~~--------d~IRC~~CG~ 42 (73)
.-|.-||.... ++.. --|.|.+||.
T Consensus 4 kPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred cCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 44777875532 2211 2488999987
No 258
>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=52.33 E-value=8.4 Score=23.38 Aligned_cols=33 Identities=15% Similarity=0.143 Sum_probs=25.0
Q ss_pred ceEEEcCcCCcceecCCCCCeecCCCCCeEEEe
Q psy2244 15 DIEKYYLECHFENEIRPRDPIRCRECGYRIMYK 47 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyK 47 (73)
++.=.|..||+.+=...+..--|+.||..++-+
T Consensus 16 ~~~~NCl~CGkIiC~~Eg~~~pC~fCg~~l~~~ 48 (57)
T PF06221_consen 16 PYAPNCLNCGKIICEQEGPLGPCPFCGTPLLSS 48 (57)
T ss_pred cccccccccChhhcccccCcCcCCCCCCcccCH
Confidence 345579999999877766567899999877644
No 259
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=52.28 E-value=10 Score=21.01 Aligned_cols=24 Identities=25% Similarity=0.531 Sum_probs=15.9
Q ss_pred EcCcCCcceecCCCCCeecCCCCCe
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
.|..|++.+.+- .....|+.||..
T Consensus 4 ~C~~C~~~F~~~-~rk~~Cr~Cg~~ 27 (57)
T cd00065 4 SCMGCGKPFTLT-RRRHHCRNCGRI 27 (57)
T ss_pred cCcccCccccCC-ccccccCcCcCC
Confidence 477888887764 334667777763
No 260
>cd01408 SIRT1 SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; 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, 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 nuclear SIRT1 has been shown to target the p53 tumor suppressor protein for deacetylation to suppress DNA damage, and the cytoplasmic SIRT2 homolog has been shown to target alpha-tubulin for deacetylation for the maintenance of cell integrity.
Probab=52.04 E-value=7.2 Score=28.24 Aligned_cols=27 Identities=15% Similarity=0.394 Sum_probs=17.7
Q ss_pred EEEcCcCCcceecC-------CCCCeecCCCCCe
Q psy2244 17 EKYYLECHFENEIR-------PRDPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik-------~~d~IRC~~CG~R 43 (73)
...|..|+...+.+ ..+.-+|+.||..
T Consensus 116 ~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cgg~ 149 (235)
T cd01408 116 TAHCIKCKHKYPGDWMREDIFNQEVPKCPRCGGL 149 (235)
T ss_pred ccccccCCCcCCHHHHHHHHhCCCCccCCCCCCC
Confidence 45788998865432 2234689999864
No 261
>PHA00732 hypothetical protein
Probab=52.04 E-value=6.2 Score=24.80 Aligned_cols=28 Identities=14% Similarity=0.208 Sum_probs=19.1
Q ss_pred EEcCcCCcceecC---------CCCCeecCCCCCeEE
Q psy2244 18 KYYLECHFENEIR---------PRDPIRCRECGYRIM 45 (73)
Q Consensus 18 YiC~~Cg~e~~ik---------~~d~IRC~~CG~RIL 45 (73)
|.|..||..+.-. .-.+-+|+.||.+--
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~ 38 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYR 38 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeC
Confidence 7899998886532 112348999998654
No 262
>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=51.85 E-value=5.7 Score=22.62 Aligned_cols=27 Identities=15% Similarity=0.154 Sum_probs=18.7
Q ss_pred EEEcCcCCcceecC------------CCCCeecCCCCCe
Q psy2244 17 EKYYLECHFENEIR------------PRDPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik------------~~d~IRC~~CG~R 43 (73)
.|.|.-||+.++.. ....+.||-|..+
T Consensus 2 ~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSR 40 (54)
T ss_pred CcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhh
Confidence 47788888865522 2356999999863
No 263
>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=51.72 E-value=13 Score=19.34 Aligned_cols=19 Identities=21% Similarity=0.221 Sum_probs=6.2
Q ss_pred cCcCCcceecCC-CCCeecC
Q psy2244 20 YLECHFENEIRP-RDPIRCR 38 (73)
Q Consensus 20 C~~Cg~e~~ik~-~d~IRC~ 38 (73)
|..||.++.-.. .-.+||+
T Consensus 2 CP~C~s~l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 2 CPVCGSKLVREEGEVDIRCP 21 (28)
T ss_dssp -TTT--BEEE-CCTTCEEE-
T ss_pred cCCCCCEeEcCCCCEeEECC
Confidence 455555544222 2235554
No 264
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=51.68 E-value=9.7 Score=26.27 Aligned_cols=23 Identities=22% Similarity=0.475 Sum_probs=13.5
Q ss_pred cCcCCcceecCCCCCeecCCCCC
Q psy2244 20 YLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 20 C~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
|..|+.+..-..+...-||+|+|
T Consensus 6 cp~c~sEytYed~~~~~cpec~~ 28 (112)
T COG2824 6 CPKCNSEYTYEDGGQLICPECAH 28 (112)
T ss_pred CCccCCceEEecCceEeCchhcc
Confidence 55566655555555566666665
No 265
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=51.56 E-value=11 Score=30.46 Aligned_cols=27 Identities=15% Similarity=0.125 Sum_probs=19.2
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
.|.|..||..+..-..-.-+||.||..
T Consensus 240 ~~~c~~cg~~~~~~~~~~~~c~~Cg~~ 266 (380)
T COG1867 240 IYHCSRCGEIVGSFREVDEKCPHCGGK 266 (380)
T ss_pred EEEcccccceecccccccccCCccccc
Confidence 499999994444334444789999973
No 266
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=51.49 E-value=13 Score=27.21 Aligned_cols=27 Identities=26% Similarity=0.544 Sum_probs=18.7
Q ss_pred EEEcCcCCcceecC-------CCCCeecCCCCCe
Q psy2244 17 EKYYLECHFENEIR-------PRDPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik-------~~d~IRC~~CG~R 43 (73)
...|..|+...+.+ ..+.-+||.||..
T Consensus 119 ~~~C~~C~~~~~~~~~~~~~~~~~~p~Cp~Cgg~ 152 (244)
T PRK14138 119 EYYCVRCGKRYTVEDVIEKLEKSDVPRCDDCSGL 152 (244)
T ss_pred eeEECCCCCcccHHHHHHHHhcCCCCCCCCCCCe
Confidence 45799999876543 2245679999963
No 267
>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=51.43 E-value=9 Score=23.90 Aligned_cols=31 Identities=13% Similarity=0.211 Sum_probs=19.6
Q ss_pred eEEEcCcCCcceecC--------CCCCeecCCCCCeEEE
Q psy2244 16 IEKYYLECHFENEIR--------PRDPIRCRECGYRIMY 46 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik--------~~d~IRC~~CG~RILy 46 (73)
+.|.|..|+....-. ..=-|+||.|..+=|.
T Consensus 3 l~FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~HlI 41 (66)
T PF05180_consen 3 LTFTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRHLI 41 (66)
T ss_dssp EEEEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EEES
T ss_pred EEEEcCCCCCccceeeCHHHHhCCeEEEECCCCcceeee
Confidence 679999998775532 1245899999987553
No 268
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=51.27 E-value=16 Score=28.51 Aligned_cols=29 Identities=24% Similarity=0.597 Sum_probs=20.4
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
-.|.|..|+..........-.|++||.+.
T Consensus 243 ~~~~C~~c~~~~~~~~~~~~~C~~c~~~~ 271 (382)
T PRK04338 243 YVYYCPKCLYREEVEGLPPEECPVCGGKF 271 (382)
T ss_pred eEEECCCCCcEEEecCCCCCCCCCCCCcc
Confidence 46789999987554433345799999864
No 269
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=51.02 E-value=12 Score=27.06 Aligned_cols=36 Identities=22% Similarity=0.421 Sum_probs=24.3
Q ss_pred eccccCCcceEEEcCcCCcc----eecC-CCCCeecCCCCC
Q psy2244 7 LVGKCLPGDIEKYYLECHFE----NEIR-PRDPIRCRECGY 42 (73)
Q Consensus 7 l~~~~~~~~v~YiC~~Cg~e----~~ik-~~d~IRC~~CG~ 42 (73)
+||.+...-..=+|.+|=.+ ++++ ......|+.||.
T Consensus 3 ~CG~~~~~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~ 43 (236)
T PF04981_consen 3 RCGREIEPLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGR 43 (236)
T ss_pred CCCCCCCCcccccChHHhcccCCeeecCCccCceECCCCCC
Confidence 57776555555689999433 3333 347799999996
No 270
>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=50.47 E-value=13 Score=30.00 Aligned_cols=14 Identities=36% Similarity=0.973 Sum_probs=7.7
Q ss_pred CCCCeecCCCCCeE
Q psy2244 31 PRDPIRCRECGYRI 44 (73)
Q Consensus 31 ~~d~IRC~~CG~RI 44 (73)
.....+|.+||++.
T Consensus 237 ~~~~l~Ch~Cg~~~ 250 (505)
T TIGR00595 237 KEGKLRCHYCGYQE 250 (505)
T ss_pred CCCeEEcCCCcCcC
Confidence 34456666666543
No 271
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=50.39 E-value=12 Score=24.97 Aligned_cols=25 Identities=28% Similarity=0.517 Sum_probs=15.8
Q ss_pred EcCcCCcc-eecC---CCCCeecCCCCCe
Q psy2244 19 YYLECHFE-NEIR---PRDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e-~~ik---~~d~IRC~~CG~R 43 (73)
+|..|+.. .++. ..-.++|..||.+
T Consensus 82 lC~~C~spdT~l~k~~r~~~l~C~aCGa~ 110 (110)
T smart00653 82 LCPECGSPDTELIKENRLFFLKCEACGAR 110 (110)
T ss_pred ECCCCCCCCcEEEEeCCeEEEEccccCCC
Confidence 68888776 2222 2345788888874
No 272
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=50.38 E-value=11 Score=30.80 Aligned_cols=27 Identities=19% Similarity=0.244 Sum_probs=20.0
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
..|+|.+|.... .....-.|++||..-
T Consensus 56 ~i~kC~~c~~~~--~y~~~~~C~~cg~~~ 82 (415)
T COG5257 56 KIYKCPECYRPE--CYTTEPKCPNCGAET 82 (415)
T ss_pred ceEeCCCCCCCc--ccccCCCCCCCCCCc
Confidence 469999998762 233456899999865
No 273
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=50.07 E-value=14 Score=21.45 Aligned_cols=25 Identities=24% Similarity=0.511 Sum_probs=10.5
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCC
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
.=.|..|++.+.+- ...-.|+.||.
T Consensus 9 ~~~C~~C~~~F~~~-~rrhhCr~CG~ 33 (69)
T PF01363_consen 9 ASNCMICGKKFSLF-RRRHHCRNCGR 33 (69)
T ss_dssp -SB-TTT--B-BSS-S-EEE-TTT--
T ss_pred CCcCcCcCCcCCCc-eeeEccCCCCC
Confidence 34688888888664 34466666665
No 274
>PRK05580 primosome assembly protein PriA; Validated
Probab=49.73 E-value=13 Score=31.05 Aligned_cols=8 Identities=50% Similarity=1.232 Sum_probs=3.9
Q ss_pred ecCCCCCe
Q psy2244 36 RCRECGYR 43 (73)
Q Consensus 36 RC~~CG~R 43 (73)
+||+||..
T Consensus 423 ~Cp~Cg~~ 430 (679)
T PRK05580 423 ACPECGST 430 (679)
T ss_pred CCCCCcCC
Confidence 45555444
No 275
>PRK07219 DNA topoisomerase I; Validated
Probab=49.61 E-value=27 Score=29.86 Aligned_cols=30 Identities=23% Similarity=0.445 Sum_probs=17.5
Q ss_pred CeecCCCCCeEEEeeeCCeeEEEeeccCCCCCcc
Q psy2244 34 PIRCRECGYRIMYKKRTKRCILYFKPQTGGFPKL 67 (73)
Q Consensus 34 ~IRC~~CG~RILyKkRt~r~vqf~~~~~~~~~~~ 67 (73)
...||.||..++.| +.+.-. |+ .|.+||+-
T Consensus 688 ~~~CP~Cg~~l~~k-~gr~G~-F~--~Cs~yp~C 717 (822)
T PRK07219 688 IGPCPKCGGELAIK-QLKYGS-FL--GCTNYPKC 717 (822)
T ss_pred cccCCCCCCeeEEE-cCCCCC-ee--eCCCCCCC
Confidence 57899999876654 333222 44 45555554
No 276
>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=49.58 E-value=8.8 Score=22.52 Aligned_cols=27 Identities=26% Similarity=0.363 Sum_probs=16.2
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCCeEEEeee
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGYRIMYKKR 49 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkR 49 (73)
..-.|..||.....- --|++|| .||.|
T Consensus 25 ~l~~c~~cg~~~~~H----~vc~~cG---~y~~r 51 (56)
T PF01783_consen 25 NLVKCPNCGEPKLPH----RVCPSCG---YYKGR 51 (56)
T ss_dssp SEEESSSSSSEESTT----SBCTTTB---BSSSS
T ss_pred ceeeeccCCCEeccc----EeeCCCC---eECCE
Confidence 446788888443222 5688887 45544
No 277
>KOG2907|consensus
Probab=49.01 E-value=7.6 Score=26.92 Aligned_cols=37 Identities=11% Similarity=0.204 Sum_probs=27.1
Q ss_pred EcCcCCcceecCC-CCCeecCCCCCeEEEeeeCCeeEE
Q psy2244 19 YYLECHFENEIRP-RDPIRCRECGYRIMYKKRTKRCIL 55 (73)
Q Consensus 19 iC~~Cg~e~~ik~-~d~IRC~~CG~RILyKkRt~r~vq 55 (73)
-|++||....... .+.+-|..|+.++--+.+..+.+.
T Consensus 9 FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~~~~~~~v~ 46 (116)
T KOG2907|consen 9 FCSDCGSLLEEPSAQSTVLCIRCKIEYPVSQFSGLVVE 46 (116)
T ss_pred hhhhhhhhcccccccCceEeccccccCCHHHhCCeeEE
Confidence 4889999988774 466779999987766665555443
No 278
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=48.10 E-value=14 Score=25.48 Aligned_cols=25 Identities=24% Similarity=0.574 Sum_probs=15.7
Q ss_pred EcCcCCcc-eecC---CCCCeecCCCCCe
Q psy2244 19 YYLECHFE-NEIR---PRDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e-~~ik---~~d~IRC~~CG~R 43 (73)
+|..|+.. .++. ....++|..||++
T Consensus 99 lC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 99 ICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred ECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 68889775 2222 1234689999974
No 279
>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=47.34 E-value=13 Score=33.80 Aligned_cols=26 Identities=19% Similarity=0.258 Sum_probs=20.5
Q ss_pred cceEEEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 14 GDIEKYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
+--..+|.+||... -..+||.||.+.
T Consensus 622 ev~~RKCPkCG~yT-----lk~rCP~CG~~T 647 (1095)
T TIGR00354 622 EIAIRKCPQCGKES-----FWLKCPVCGELT 647 (1095)
T ss_pred EEEEEECCCCCccc-----ccccCCCCCCcc
Confidence 34578999999885 337999999874
No 280
>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=47.23 E-value=8.5 Score=21.10 Aligned_cols=10 Identities=50% Similarity=1.345 Sum_probs=4.1
Q ss_pred CCeecCCCCC
Q psy2244 33 DPIRCRECGY 42 (73)
Q Consensus 33 d~IRC~~CG~ 42 (73)
+++||..|+.
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 4688888875
No 281
>PRK11595 DNA utilization protein GntX; Provisional
Probab=46.56 E-value=6.4 Score=28.10 Aligned_cols=34 Identities=18% Similarity=0.148 Sum_probs=20.8
Q ss_pred eccccCCcceEEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 7 LVGKCLPGDIEKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 7 l~~~~~~~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
+||+.+......+|..|......- .-+|+.||..
T Consensus 10 ~C~~~~~~~~~~lC~~C~~~l~~~---~~~C~~Cg~~ 43 (227)
T PRK11595 10 LCRMPLALSHWGICSVCSRALRTL---KTCCPQCGLP 43 (227)
T ss_pred cCCCccCCCCCcccHHHHhhCCcc---cCcCccCCCc
Confidence 567665443345788886665431 2478888854
No 282
>KOG2462|consensus
Probab=46.34 E-value=17 Score=28.39 Aligned_cols=32 Identities=16% Similarity=0.293 Sum_probs=23.2
Q ss_pred CCcceEEEcCcCCcceecC--------------CCCCeecCCCCCe
Q psy2244 12 LPGDIEKYYLECHFENEIR--------------PRDPIRCRECGYR 43 (73)
Q Consensus 12 ~~~~v~YiC~~Cg~e~~ik--------------~~d~IRC~~CG~R 43 (73)
....-.|+|.+||+.-.-. ....-+|++||..
T Consensus 125 ~~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~ 170 (279)
T KOG2462|consen 125 AAKHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKV 170 (279)
T ss_pred cccCCceeccccccccccccccchhhcccccccccccccCCCCCce
Confidence 4456789999999874332 2567889999964
No 283
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=46.31 E-value=11 Score=23.38 Aligned_cols=24 Identities=17% Similarity=0.290 Sum_probs=16.3
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
+..+|.+||.-.-- -.||.||...
T Consensus 4 ~~rkC~~cg~YTLk-----e~Cp~CG~~t 27 (59)
T COG2260 4 LIRKCPKCGRYTLK-----EKCPVCGGDT 27 (59)
T ss_pred hhhcCcCCCceeec-----ccCCCCCCcc
Confidence 45678888765422 3699999754
No 284
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=46.30 E-value=14 Score=26.45 Aligned_cols=30 Identities=17% Similarity=0.185 Sum_probs=16.6
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCeEEEeee
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYRIMYKKR 49 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkR 49 (73)
.|.|..||....- -.-+||+||..==++.|
T Consensus 354 ~~~c~~cg~~~~~---~~~~c~~c~~~~~~~~~ 383 (389)
T PRK11788 354 RYRCRNCGFTART---LYWHCPSCKAWETIKPI 383 (389)
T ss_pred CEECCCCCCCCcc---ceeECcCCCCccCcCCc
Confidence 3777777665321 23567777764433333
No 285
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=46.17 E-value=17 Score=20.00 Aligned_cols=21 Identities=24% Similarity=0.580 Sum_probs=11.9
Q ss_pred cCcCCcceecCCCCCeecCCCCCe
Q psy2244 20 YLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 20 C~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
|..|++...+- +..|+.|+..
T Consensus 1 C~~C~~~~~l~---~f~C~~C~~~ 21 (39)
T smart00154 1 CHFCRKKVGLT---GFKCRHCGNL 21 (39)
T ss_pred CcccCCccccc---CeECCccCCc
Confidence 44555544443 5677777754
No 286
>PRK05580 primosome assembly protein PriA; Validated
Probab=45.98 E-value=13 Score=30.93 Aligned_cols=28 Identities=25% Similarity=0.566 Sum_probs=18.1
Q ss_pred EEcCcCCcceec-CCCCCeecCCCCCeEE
Q psy2244 18 KYYLECHFENEI-RPRDPIRCRECGYRIM 45 (73)
Q Consensus 18 YiC~~Cg~e~~i-k~~d~IRC~~CG~RIL 45 (73)
.+|.+|+..... +.....+|.+||++.-
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~ 419 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCGYQEP 419 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCcCCCC
Confidence 345555544332 4567799999998754
No 287
>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=45.93 E-value=12 Score=21.69 Aligned_cols=15 Identities=27% Similarity=0.585 Sum_probs=12.2
Q ss_pred CCCeecCCCCCeEEE
Q psy2244 32 RDPIRCRECGYRIMY 46 (73)
Q Consensus 32 ~d~IRC~~CG~RILy 46 (73)
+|.++|..||..|--
T Consensus 34 ~d~v~C~~C~~~l~~ 48 (71)
T smart00238 34 GDEVKCFFCGGELDN 48 (71)
T ss_pred CCEEEeCCCCCCcCC
Confidence 568999999988644
No 288
>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=45.76 E-value=9.1 Score=24.93 Aligned_cols=9 Identities=56% Similarity=1.136 Sum_probs=7.5
Q ss_pred eecCCCCCe
Q psy2244 35 IRCRECGYR 43 (73)
Q Consensus 35 IRC~~CG~R 43 (73)
|.||.||-|
T Consensus 2 I~CP~CG~R 10 (84)
T TIGR01374 2 IPCPYCGPR 10 (84)
T ss_pred ccCCCCCCc
Confidence 789999954
No 289
>PLN02569 threonine synthase
Probab=45.68 E-value=15 Score=29.68 Aligned_cols=27 Identities=7% Similarity=-0.212 Sum_probs=21.1
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCeEE
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYRIM 45 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~RIL 45 (73)
-+.|.+||++..++... .+| .||..+-
T Consensus 49 ~l~C~~Cg~~y~~~~~~-~~C-~cgg~l~ 75 (484)
T PLN02569 49 FLECPLTGEKYSLDEVV-YRS-KSGGLLD 75 (484)
T ss_pred ccEeCCCCCcCCCcccc-ccC-CCCCeEE
Confidence 38899999998887653 699 7987553
No 290
>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=45.19 E-value=14 Score=24.89 Aligned_cols=8 Identities=38% Similarity=0.941 Sum_probs=4.0
Q ss_pred eecCCCCC
Q psy2244 35 IRCRECGY 42 (73)
Q Consensus 35 IRC~~CG~ 42 (73)
-||+.|+.
T Consensus 92 sRC~~CN~ 99 (147)
T PF01927_consen 92 SRCPKCNG 99 (147)
T ss_pred CccCCCCc
Confidence 45555554
No 291
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the 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=44.73 E-value=15 Score=25.74 Aligned_cols=19 Identities=32% Similarity=0.643 Sum_probs=14.2
Q ss_pred ecCCCCCeecCCCCCeEEE
Q psy2244 28 EIRPRDPIRCRECGYRIMY 46 (73)
Q Consensus 28 ~ik~~d~IRC~~CG~RILy 46 (73)
.+..+.+-||++||+-...
T Consensus 106 ~l~~g~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 106 WLHKGKPQRCPECGQVFKL 124 (136)
T ss_dssp EEETTSEEEETTTEEEEEE
T ss_pred EEeCCCccCCCCCCeEEEE
Confidence 3557788999999985433
No 293
>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=44.70 E-value=12 Score=17.90 Aligned_cols=11 Identities=18% Similarity=-0.091 Sum_probs=8.7
Q ss_pred EEcCcCCccee
Q psy2244 18 KYYLECHFENE 28 (73)
Q Consensus 18 YiC~~Cg~e~~ 28 (73)
|.|..|+..+.
T Consensus 2 ~~C~~C~~~F~ 12 (27)
T PF13912_consen 2 FECDECGKTFS 12 (27)
T ss_dssp EEETTTTEEES
T ss_pred CCCCccCCccC
Confidence 78899987764
No 294
>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=44.50 E-value=13 Score=21.94 Aligned_cols=13 Identities=38% Similarity=0.961 Sum_probs=11.7
Q ss_pred CCCeecCCCCCeE
Q psy2244 32 RDPIRCRECGYRI 44 (73)
Q Consensus 32 ~d~IRC~~CG~RI 44 (73)
.|.|+|.+||..|
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 6889999999887
No 295
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=44.47 E-value=7.2 Score=31.01 Aligned_cols=36 Identities=19% Similarity=0.245 Sum_probs=18.2
Q ss_pred ceEEEcCcCCcc--eecCC----C--CCeecCCCCCeEEEeeeC
Q psy2244 15 DIEKYYLECHFE--NEIRP----R--DPIRCRECGYRIMYKKRT 50 (73)
Q Consensus 15 ~v~YiC~~Cg~e--~~ik~----~--d~IRC~~CG~RILyKkRt 50 (73)
|..=+|.+||+. +.+.. . =.-+|+.|||+.--..|.
T Consensus 172 Pf~piC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~~~i~~ 215 (360)
T PF01921_consen 172 PFLPICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGEVDITG 215 (360)
T ss_dssp SEEEEETTTEE--EEEEEEE--SSSEEEEE--TTS---EEETTT
T ss_pred eeeeeccccCCcccceeeEeecCCCEEEEEecCCCCEEEEecCC
Confidence 466689999983 22221 1 236899999987655544
No 296
>PRK05776 DNA topoisomerase I; Provisional
Probab=44.08 E-value=15 Score=30.85 Aligned_cols=35 Identities=20% Similarity=0.136 Sum_probs=21.7
Q ss_pred CeecCCCCCeE----EEeeeCCeeEEEeeccCCCCCcceee
Q psy2244 34 PIRCRECGYRI----MYKKRTKRCILYFKPQTGGFPKLKTT 70 (73)
Q Consensus 34 ~IRC~~CG~RI----LyKkRt~r~vqf~~~~~~~~~~~~~~ 70 (73)
..+||.||... +.|.-.+..-.|.. |.|||+-+.+
T Consensus 596 ~~~Cp~Cg~~l~~~~~~~~~~~~~~~f~~--c~~~p~c~~~ 634 (670)
T PRK05776 596 VGKCKICGREAYKDGLCKYHYEAKKRLVK--AYEEWKERTG 634 (670)
T ss_pred CCcCCCCCCccccCceEEecccCCcccee--cCCCccccCC
Confidence 36899999866 55543333234554 7788876554
No 297
>KOG2463|consensus
Probab=43.88 E-value=13 Score=30.12 Aligned_cols=28 Identities=18% Similarity=0.258 Sum_probs=19.5
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeEEEe
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRIMYK 47 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RILyK 47 (73)
-+|-.|-+.+ +.+..+-||.||++.|-|
T Consensus 243 LRCh~Cfsit--~~m~k~FCp~CG~~TL~K 270 (376)
T KOG2463|consen 243 LRCHGCFSIT--SEMPKDFCPSCGHKTLTK 270 (376)
T ss_pred eEeeeeeEec--CccchhcccccCCCeeeE
Confidence 4566665544 344578999999987754
No 298
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=43.88 E-value=12 Score=23.93 Aligned_cols=15 Identities=33% Similarity=0.651 Sum_probs=7.8
Q ss_pred CCCCCeecCCCCCeE
Q psy2244 30 RPRDPIRCRECGYRI 44 (73)
Q Consensus 30 k~~d~IRC~~CG~RI 44 (73)
+.+...+|+.||+++
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 345678888888875
No 299
>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=43.74 E-value=19 Score=22.67 Aligned_cols=23 Identities=17% Similarity=0.190 Sum_probs=16.7
Q ss_pred cCCcceecCCCCCeecCCCCCeEE
Q psy2244 22 ECHFENEIRPRDPIRCRECGYRIM 45 (73)
Q Consensus 22 ~Cg~e~~ik~~d~IRC~~CG~RIL 45 (73)
.+|.++.+ ..+...|+.||-.++
T Consensus 20 ~~G~~~~v-~~~~~~C~~CGe~~~ 42 (127)
T TIGR03830 20 YKGESITI-GVPGWYCPACGEELL 42 (127)
T ss_pred EcCEEEEE-eeeeeECCCCCCEEE
Confidence 35666666 667788999998664
No 300
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=43.72 E-value=26 Score=27.71 Aligned_cols=44 Identities=23% Similarity=0.310 Sum_probs=27.4
Q ss_pred CCcccee-ccccCCc-ceEEEcCcCCcceecCC-----CCCeecCCCCCeE
Q psy2244 1 MGYSQVL-VGKCLPG-DIEKYYLECHFENEIRP-----RDPIRCRECGYRI 44 (73)
Q Consensus 1 ~~~~~~l-~~~~~~~-~v~YiC~~Cg~e~~ik~-----~d~IRC~~CG~RI 44 (73)
|||-+-| +.+.+.- ...++|..|+.+..+.. .....||+||...
T Consensus 306 ~GAVetLLV~d~l~~~r~~~r~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~ 356 (409)
T TIGR00108 306 LGAVETLIVSEDLEYIRVTYKCAECGEVIEKTVRELKDKKFAICPACGQEM 356 (409)
T ss_pred hCCCcEEEEeccccceeEEEEcCCCCceeecccccccccccccCcccCccc
Confidence 4555444 6666643 47899999997522221 1235799999764
No 301
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=43.66 E-value=22 Score=27.80 Aligned_cols=29 Identities=21% Similarity=0.456 Sum_probs=19.6
Q ss_pred eEEEcCcCCcceecC--CCCCeecCCCCCeE
Q psy2244 16 IEKYYLECHFENEIR--PRDPIRCRECGYRI 44 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik--~~d~IRC~~CG~RI 44 (73)
..|.|..|+...... ....-+|++||.+.
T Consensus 232 ~v~~C~~c~~~~~~~~~~~~~~~C~~c~~~~ 262 (374)
T TIGR00308 232 YTYHCSRCLHNKPVNGISQRKGRCKECGGEY 262 (374)
T ss_pred eEEECCCcccccccccccCCCCCCCCCCCcc
Confidence 357799998764433 22345799999864
No 302
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=43.61 E-value=21 Score=24.37 Aligned_cols=32 Identities=16% Similarity=0.219 Sum_probs=23.8
Q ss_pred cceEEEcCcCCcceec----C---CCCCeecCCCCCeEE
Q psy2244 14 GDIEKYYLECHFENEI----R---PRDPIRCRECGYRIM 45 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~i----k---~~d~IRC~~CG~RIL 45 (73)
=+..+-|..||.+... + ....+-|.+||-+--
T Consensus 19 L~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred CCceEecCccCCeeeeEEEEEecCceeEEEcccCcceEE
Confidence 3578999999998554 2 346689999997643
No 303
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=43.21 E-value=19 Score=33.26 Aligned_cols=62 Identities=11% Similarity=0.264 Sum_probs=38.2
Q ss_pred ceeccccCCcce--EEEcCcCCcceecCC--------CCCeecCCCCCeEEEeeeCCee-EEEeeccCCCCCcc
Q psy2244 5 QVLVGKCLPGDI--EKYYLECHFENEIRP--------RDPIRCRECGYRIMYKKRTKRC-ILYFKPQTGGFPKL 67 (73)
Q Consensus 5 ~~l~~~~~~~~v--~YiC~~Cg~e~~ik~--------~d~IRC~~CG~RILyKkRt~r~-vqf~~~~~~~~~~~ 67 (73)
-|+.|.--..|. -|+|.+|+...-+.. .+.-.||+||.. |.|-.-.-. -.|+-|+-+-.|-+
T Consensus 894 Ay~lgITeVdPL~phy~C~~C~~~ef~~~~~~~sG~Dlpdk~Cp~Cg~~-~~kdg~~l~FErFL~~~r~~~PDI 966 (1437)
T PRK00448 894 ATMIGITEVNPLPPHYVCPNCKYSEFFTDGSVGSGFDLPDKDCPKCGTK-LKKDGHDIPFETFLGFKGDKVPDI 966 (1437)
T ss_pred HHHhcCCCcCCCCccccCcccccccccccccccccccCccccCcccccc-ccccCCCceeeeccCCCCCCCCCC
Confidence 466666666665 499999965433322 245689999874 444443322 24777777776654
No 304
>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=43.12 E-value=15 Score=24.36 Aligned_cols=27 Identities=22% Similarity=0.493 Sum_probs=21.1
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
=.|.-|+..--...++.+-|.+||-|+
T Consensus 36 daCeiC~~~GY~q~g~~lvC~~C~~~~ 62 (102)
T PF10080_consen 36 DACEICGPKGYYQEGDQLVCKNCGVRF 62 (102)
T ss_pred EeccccCCCceEEECCEEEEecCCCEE
Confidence 357788766556678899999999876
No 305
>PF01020 Ribosomal_L40e: Ribosomal L40e family; InterPro: IPR001975 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the L40 ribosomal protein from both archaea and eukaryotes. Bovine ribosomal protein L40 has been identified as a secondary RNA binding protein []. L40 is fused to a ubiquitin protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZS_p 3IZR_p 2AYJ_A 4A1B_K 4A19_K 4A18_K 4A1D_K.
Probab=43.03 E-value=18 Score=21.95 Aligned_cols=23 Identities=26% Similarity=0.535 Sum_probs=15.0
Q ss_pred EEEcCcCCcceecCCCCCeecCC--CCC
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRE--CGY 42 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~--CG~ 42 (73)
..||-.|.+.+-++ ++.|+. |||
T Consensus 17 k~ICrkCyarl~~~---A~nCRKkkCGh 41 (52)
T PF01020_consen 17 KMICRKCYARLPPR---ATNCRKKKCGH 41 (52)
T ss_dssp -EEETTT--EE-TT---SSS-TSSSCTS
T ss_pred ceecccccCcCCCC---ccceecccCCC
Confidence 57999999888665 588997 997
No 306
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, 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.
Probab=42.97 E-value=13 Score=26.46 Aligned_cols=27 Identities=22% Similarity=0.288 Sum_probs=18.1
Q ss_pred EEEcCcCCcceecC--------CCCCeecCCCCCe
Q psy2244 17 EKYYLECHFENEIR--------PRDPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik--------~~d~IRC~~CG~R 43 (73)
...|..|+.....+ .....+|+.||.-
T Consensus 95 ~~~C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cgg~ 129 (206)
T cd01410 95 IEVCKSCGPEYVRDDVVETRGDKETGRRCHACGGI 129 (206)
T ss_pred cccCCCCCCccchHHHHHHhhcCCCCCcCCCCcCc
Confidence 45699999765432 1234689999975
No 307
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=42.90 E-value=13 Score=24.62 Aligned_cols=26 Identities=12% Similarity=0.193 Sum_probs=18.7
Q ss_pred EEEcCcCCcceecCCC---CCeecCCCCC
Q psy2244 17 EKYYLECHFENEIRPR---DPIRCRECGY 42 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~---d~IRC~~CG~ 42 (73)
.+.|..||.++..... --.-||+|=+
T Consensus 4 ~F~C~~CG~~V~p~~~g~~~RNHCP~CL~ 32 (92)
T PF12647_consen 4 SFTCVHCGLTVSPLAAGSAHRNHCPSCLS 32 (92)
T ss_pred ccCccccCCCcccCCCCCCccCcCccccc
Confidence 5789999999877533 2356888744
No 308
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=42.67 E-value=27 Score=18.92 Aligned_cols=22 Identities=27% Similarity=0.520 Sum_probs=15.0
Q ss_pred EcCcCCcceecCCCCCeecCCCCC
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
+|.-|+. .....+.|.|-.|+.
T Consensus 1 ~C~vC~~--~~~~~~~i~C~~C~~ 22 (51)
T PF00628_consen 1 YCPVCGQ--SDDDGDMIQCDSCNR 22 (51)
T ss_dssp EBTTTTS--SCTTSSEEEBSTTSC
T ss_pred eCcCCCC--cCCCCCeEEcCCCCh
Confidence 3666777 444667788888874
No 309
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=42.65 E-value=19 Score=24.95 Aligned_cols=25 Identities=20% Similarity=0.456 Sum_probs=15.6
Q ss_pred EcCcCCcce-ecC---CCCCeecCCCCCe
Q psy2244 19 YYLECHFEN-EIR---PRDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e~-~ik---~~d~IRC~~CG~R 43 (73)
+|..||... ++. ..-.++|..||.+
T Consensus 104 lC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 104 ICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred ECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 688887652 222 2235788888874
No 310
>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=42.47 E-value=10 Score=26.96 Aligned_cols=8 Identities=25% Similarity=0.754 Sum_probs=5.8
Q ss_pred eecCCCCC
Q psy2244 35 IRCRECGY 42 (73)
Q Consensus 35 IRC~~CG~ 42 (73)
++||+||+
T Consensus 1 M~CP~C~~ 8 (147)
T TIGR00244 1 MHCPFCQH 8 (147)
T ss_pred CCCCCCCC
Confidence 36788877
No 311
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=42.44 E-value=17 Score=26.10 Aligned_cols=27 Identities=22% Similarity=0.438 Sum_probs=17.4
Q ss_pred EEcCcCCcc-eecC---CCCCeecCCCCCeE
Q psy2244 18 KYYLECHFE-NEIR---PRDPIRCRECGYRI 44 (73)
Q Consensus 18 YiC~~Cg~e-~~ik---~~d~IRC~~CG~RI 44 (73)
=+|..|+.. .++. ..-.++|..||.+=
T Consensus 99 V~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~ 129 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRVLMLRCDACGAHR 129 (201)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCCCc
Confidence 379999876 2222 22346999999843
No 312
>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=42.32 E-value=21 Score=23.63 Aligned_cols=29 Identities=21% Similarity=0.380 Sum_probs=21.5
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeEEEee
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRIMYKK 48 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKk 48 (73)
..|+.-|=.+. ..+.++|..||.++.++.
T Consensus 29 l~cA~~GW~~~--~~d~l~C~~C~~~l~~~~ 57 (133)
T PF07967_consen 29 LECARRGWICV--SKDMLKCESCGARLCVKL 57 (133)
T ss_pred HHHHHcCCCcC--CCCEEEeCCCCCEEEEec
Confidence 45665555552 268899999999999984
No 313
>PRK08402 replication factor A; Reviewed
Probab=42.23 E-value=36 Score=26.77 Aligned_cols=27 Identities=22% Similarity=0.330 Sum_probs=21.4
Q ss_pred eEEEcCcCCcceecC-CCCCeecCCCCC
Q psy2244 16 IEKYYLECHFENEIR-PRDPIRCRECGY 42 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik-~~d~IRC~~CG~ 42 (73)
....|..|.+.+..+ ..+.-+|+.||.
T Consensus 211 ~y~aCp~CnKkv~~~~~~~~~~Ce~~~~ 238 (355)
T PRK08402 211 VYDACPECRRKVDYDPATDTWICPEHGE 238 (355)
T ss_pred eEecCCCCCeEEEEecCCCCEeCCCCCC
Confidence 567899999999744 446789999984
No 314
>KOG2324|consensus
Probab=41.86 E-value=19 Score=29.84 Aligned_cols=46 Identities=11% Similarity=0.229 Sum_probs=30.6
Q ss_pred ceeccccCCcceEEEcCcCCcc---eecCCCCCeecCCCCCeEEEeeeC
Q psy2244 5 QVLVGKCLPGDIEKYYLECHFE---NEIRPRDPIRCRECGYRIMYKKRT 50 (73)
Q Consensus 5 ~~l~~~~~~~~v~YiC~~Cg~e---~~ik~~d~IRC~~CG~RILyKkRt 50 (73)
||--=-++-|+..+.|..||-. ..++...++.||.|...-|=|.+.
T Consensus 215 Efhl~~~vgED~l~~C~~C~~s~n~e~~~~sk~~~Cp~C~~~~L~~~~~ 263 (457)
T KOG2324|consen 215 EFHLIHPVGEDTLMSCPSCGYSKNSEDLDLSKIASCPKCNEGRLTKTKS 263 (457)
T ss_pred eEeccCccCccceeecCcCCccCchhhhcCCccccCCcccCCCcccccc
Confidence 3333345667889999999655 345555669999999854444443
No 315
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=41.70 E-value=18 Score=18.92 Aligned_cols=15 Identities=13% Similarity=-0.144 Sum_probs=11.8
Q ss_pred eEEEcCcCCcceecC
Q psy2244 16 IEKYYLECHFENEIR 30 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik 30 (73)
-.|+|..||..+..-
T Consensus 6 ~~ykC~~Cgniv~v~ 20 (34)
T TIGR00319 6 QVYKCEVCGNIVEVL 20 (34)
T ss_pred cEEEcCCCCcEEEEE
Confidence 369999999987643
No 316
>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=41.68 E-value=24 Score=23.96 Aligned_cols=25 Identities=24% Similarity=0.510 Sum_probs=17.2
Q ss_pred EcCcCCcc-eec---CCCCCeecCCCCCe
Q psy2244 19 YYLECHFE-NEI---RPRDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e-~~i---k~~d~IRC~~CG~R 43 (73)
+|..|+.. ..+ +..-.++|..||.+
T Consensus 95 lC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 95 LCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp SCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred EcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 68899765 222 24466899999975
No 317
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=41.65 E-value=20 Score=30.31 Aligned_cols=21 Identities=14% Similarity=0.327 Sum_probs=15.7
Q ss_pred EcCcCCcceecCCCCCeecCCCCCe
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
+|.+||... +..-.||.||..
T Consensus 628 ~C~~CG~~~----g~~~~CP~CG~~ 648 (656)
T PRK08270 628 ICPKHGYLS----GEHEFCPKCGEE 648 (656)
T ss_pred ccCCCCCcC----CCCCCCcCCcCc
Confidence 689999742 335789999976
No 318
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=41.60 E-value=8.7 Score=34.19 Aligned_cols=21 Identities=29% Similarity=0.615 Sum_probs=0.0
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
|.|.+|+.+++.+ .|+.||-.
T Consensus 681 ~~Cp~C~~~~~~~-----~C~~C~~~ 701 (900)
T PF03833_consen 681 YVCPDCGIEVEED-----ECPKCGRE 701 (900)
T ss_dssp --------------------------
T ss_pred eeccccccccCcc-----cccccccc
Confidence 5555555544332 66666654
No 319
>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=41.51 E-value=10 Score=24.66 Aligned_cols=9 Identities=56% Similarity=1.250 Sum_probs=7.6
Q ss_pred eecCCCCCe
Q psy2244 35 IRCRECGYR 43 (73)
Q Consensus 35 IRC~~CG~R 43 (73)
|.||.||-|
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 789999965
No 320
>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=41.34 E-value=18 Score=18.92 Aligned_cols=13 Identities=15% Similarity=-0.082 Sum_probs=10.8
Q ss_pred EEEcCcCCcceec
Q psy2244 17 EKYYLECHFENEI 29 (73)
Q Consensus 17 ~YiC~~Cg~e~~i 29 (73)
.|+|..||..+..
T Consensus 4 ~ykC~~CGniv~v 16 (34)
T cd00974 4 VYKCEICGNIVEV 16 (34)
T ss_pred EEEcCCCCcEEEE
Confidence 6999999998763
No 321
>KOG3352|consensus
Probab=41.09 E-value=14 Score=26.64 Aligned_cols=16 Identities=31% Similarity=0.760 Sum_probs=13.3
Q ss_pred cCCCCCeecCCCCCeE
Q psy2244 29 IRPRDPIRCRECGYRI 44 (73)
Q Consensus 29 ik~~d~IRC~~CG~RI 44 (73)
+..++.-||++|||--
T Consensus 128 l~Kge~~rc~eCG~~f 143 (153)
T KOG3352|consen 128 LEKGETQRCPECGHYF 143 (153)
T ss_pred EEcCCcccCCcccceE
Confidence 5578999999999953
No 322
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=41.00 E-value=17 Score=26.05 Aligned_cols=25 Identities=12% Similarity=0.205 Sum_probs=19.7
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
.+.|..|+....... ...+|.+ ||+
T Consensus 2 ~~~CP~C~~~l~~~~-~~~~C~~-~h~ 26 (272)
T PRK11088 2 SYQCPLCHQPLTLEE-NSWICPQ-NHQ 26 (272)
T ss_pred cccCCCCCcchhcCC-CEEEcCC-CCC
Confidence 488999998876543 5699988 776
No 323
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=40.94 E-value=65 Score=18.92 Aligned_cols=47 Identities=19% Similarity=0.371 Sum_probs=23.3
Q ss_pred cCcCCcceecCCCCCeecCCCCC--eEEEeeeCCe---eEEEeeccCCCCCc
Q psy2244 20 YLECHFENEIRPRDPIRCRECGY--RIMYKKRTKR---CILYFKPQTGGFPK 66 (73)
Q Consensus 20 C~~Cg~e~~ik~~d~IRC~~CG~--RILyKkRt~r---~vqf~~~~~~~~~~ 66 (73)
|..|.-.=..+......|+.|+. ++....|+.- ..+-.=|+++|.=+
T Consensus 1 C~~C~G~G~~~~~~~~~C~~C~G~G~~~~~~~~~~~~~~~~~~C~~C~G~G~ 52 (66)
T PF00684_consen 1 CPKCNGTGAKPGKKPKTCPQCNGSGQVTRRQQTPGGVFQMQQTCPKCGGTGK 52 (66)
T ss_dssp -CCCTTTSB-STTT-EE-TTSSSSSEEEEEEESSSTTEEEEEE-TTTSSSSE
T ss_pred CCcCCCcccCCCCCCcCCcCCCCeeEEEEEEeCCCeEEEEEEECCCCcceee
Confidence 45664444445567788999976 4555555332 23333356666543
No 324
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=40.60 E-value=21 Score=20.99 Aligned_cols=16 Identities=13% Similarity=0.455 Sum_probs=12.2
Q ss_pred CeecCCCCCeEEEeee
Q psy2244 34 PIRCRECGYRIMYKKR 49 (73)
Q Consensus 34 ~IRC~~CG~RILyKkR 49 (73)
.+.||.|+.+++=+.+
T Consensus 3 ~i~Cp~C~~~~~T~v~ 18 (67)
T smart00714 3 QLFCPRCQNNVTTRVE 18 (67)
T ss_pred ceECCCCCCEEEEEEE
Confidence 4899999998765443
No 325
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=40.57 E-value=20 Score=30.84 Aligned_cols=29 Identities=21% Similarity=0.332 Sum_probs=22.4
Q ss_pred CCcceEEEcCcCCcceecCCC-----CCeecCCC
Q psy2244 12 LPGDIEKYYLECHFENEIRPR-----DPIRCREC 40 (73)
Q Consensus 12 ~~~~v~YiC~~Cg~e~~ik~~-----d~IRC~~C 40 (73)
......|.|..||.++..... ++..|++|
T Consensus 124 ~~~~~~~~C~~Cg~~~~~~~~~~~~~~~~~C~~~ 157 (682)
T COG1241 124 RLKKAVFECPKCGREVEVEQSEFRVEPPRECENC 157 (682)
T ss_pred eeEEEEEEcCCCCCEEEEEeccccccCCccCCCc
Confidence 345688999999999776533 56779999
No 326
>KOG3854|consensus
Probab=40.36 E-value=17 Score=30.49 Aligned_cols=47 Identities=21% Similarity=0.350 Sum_probs=32.4
Q ss_pred ceEEEcCcCCcceecCCC----CCeecCCCCCeEEE---eeeCCeeEEEeeccC
Q psy2244 15 DIEKYYLECHFENEIRPR----DPIRCRECGYRIMY---KKRTKRCILYFKPQT 61 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~~----d~IRC~~CG~RILy---KkRt~r~vqf~~~~~ 61 (73)
+..|.|..|++....... ...||.+|-.+|.. |++...-++-+-|.+
T Consensus 406 Kf~Y~C~~C~~~~~~~skSl~t~~~~C~~Ckg~i~l~~~~kk~~~~~~~~d~~~ 459 (505)
T KOG3854|consen 406 KFKYTCTKCNKLSGGHSKSLDTSRLRCRYCKGEISLKPVKKKQMTRIVISDPTM 459 (505)
T ss_pred eEEEEecccCcccccccccccHhHHHHHhcccceEEEeeeeccCCceeecCccc
Confidence 478999999888765432 55899999998764 455554445444444
No 327
>COG1743 Adenine-specific DNA methylase containing a Zn-ribbon [DNA replication, recombination, and repair]
Probab=40.25 E-value=26 Score=31.26 Aligned_cols=30 Identities=17% Similarity=0.557 Sum_probs=21.6
Q ss_pred CeecCCCCC-------eEEEeeeCCeeEEEeeccCCC
Q psy2244 34 PIRCRECGY-------RIMYKKRTKRCILYFKPQTGG 63 (73)
Q Consensus 34 ~IRC~~CG~-------RILyKkRt~r~vqf~~~~~~~ 63 (73)
.|+||.||+ +=|.++|-...+-|.+|..+|
T Consensus 178 ~VkCP~CG~~tP~vgn~wlar~k~~~~~~y~~~~~eG 214 (875)
T COG1743 178 EVKCPRCGRLTPLVGNWWLARVKRGKRVAYMDVEEEG 214 (875)
T ss_pred EEecCCcCccccCccceeehccccCceeEEecccccC
Confidence 489999987 445555544667778888877
No 328
>cd01409 SIRT4 SIRT4: Eukaryotic and prokaryotic group (class2) which includes human sirtuin SIRT4 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.
Probab=39.96 E-value=29 Score=25.61 Aligned_cols=12 Identities=25% Similarity=0.523 Sum_probs=8.9
Q ss_pred EEEcCcCCccee
Q psy2244 17 EKYYLECHFENE 28 (73)
Q Consensus 17 ~YiC~~Cg~e~~ 28 (73)
...|..|+....
T Consensus 118 ~~~C~~C~~~~~ 129 (260)
T cd01409 118 RVVCLSCGFRTP 129 (260)
T ss_pred EEEeCCCcCccC
Confidence 467999998653
No 329
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 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 N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=39.84 E-value=18 Score=21.69 Aligned_cols=31 Identities=29% Similarity=0.660 Sum_probs=21.5
Q ss_pred ceEEEcCcCCcceecCCCCCeecCCC-------CCeEEEeeeC
Q psy2244 15 DIEKYYLECHFENEIRPRDPIRCREC-------GYRIMYKKRT 50 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~~d~IRC~~C-------G~RILyKkRt 50 (73)
...|.|..|..+ ...+-|.+| ||++.+..-+
T Consensus 11 q~~y~C~tC~~~-----~~~~iC~~CF~~~~H~gH~~~~~~~~ 48 (71)
T PF02207_consen 11 QIFYRCLTCSLD-----ESSGICEECFANSCHEGHRVVYYRSS 48 (71)
T ss_dssp -EEEEETTTBSS-----TT-BBEHHHHCTSGGGGSSEEEEE--
T ss_pred CEEEECccCCCC-----CCEEEchhhCCCCCcCCCcEEEEEeC
Confidence 688999999772 235788888 8888876544
No 330
>cd04367 IlGF_insulin_like IlGF_like family, insulin_like subgroup, specific to vertebrates. Members include a number of peptides including insulin and insulin-like growth factors I and II, which play a variety of roles in controlling processes such as metabolism, growth and differentiation, and reproduction. On a cellular level they affect cell cycle, apoptosis, cell migration, and differentiation. With the exception of the insulin-like growth factors, the active forms of these peptide hormones are composed of two chains (A and B) linked by two disulfide bonds; the arrangement of four cysteines is conserved in the "A" chain: Cys1 is linked by a disulfide bond to Cys3, Cys2 and Cys4 are linked by interchain disulfide bonds to cysteines in the "B" chain. This alignment contains both chains, plus the intervening linker region, arranged as found in the propeptide form. Propeptides are cleaved to yield two separate chains linked covalently by the two disulfide bonds.
Probab=39.80 E-value=2.2 Score=27.34 Aligned_cols=25 Identities=20% Similarity=0.065 Sum_probs=20.3
Q ss_pred ccceeccccCCcceEEEcCcCCcce
Q psy2244 3 YSQVLVGKCLPGDIEKYYLECHFEN 27 (73)
Q Consensus 3 ~~~~l~~~~~~~~v~YiC~~Cg~e~ 27 (73)
.+|+|||.+|.+....+|++=|--.
T Consensus 1 ~~q~LCGs~LvdaL~~VCG~RGF~~ 25 (79)
T cd04367 1 VNQHLCGSHLVDALYLVCGDRGFFY 25 (79)
T ss_pred CCccchHHHHHHHHHHHHccCCccc
Confidence 4799999999999988888766443
No 331
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=39.69 E-value=28 Score=30.06 Aligned_cols=13 Identities=38% Similarity=1.135 Sum_probs=7.5
Q ss_pred CCCCeecCCCCCe
Q psy2244 31 PRDPIRCRECGYR 43 (73)
Q Consensus 31 ~~d~IRC~~CG~R 43 (73)
....++|.+||+.
T Consensus 459 ~~~~L~CH~Cg~~ 471 (730)
T COG1198 459 ATGQLRCHYCGYQ 471 (730)
T ss_pred CCCeeEeCCCCCC
Confidence 3455666666664
No 332
>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=39.62 E-value=67 Score=18.53 Aligned_cols=17 Identities=18% Similarity=0.468 Sum_probs=11.5
Q ss_pred CCCCeecCCCCCeEEEe
Q psy2244 31 PRDPIRCRECGYRIMYK 47 (73)
Q Consensus 31 ~~d~IRC~~CG~RILyK 47 (73)
...-..|++||..|.+-
T Consensus 45 ~~~r~FC~~CGs~l~~~ 61 (92)
T PF04828_consen 45 GVERYFCPTCGSPLFSE 61 (92)
T ss_dssp SCEEEEETTT--EEEEE
T ss_pred cCcCcccCCCCCeeecc
Confidence 34558899999999974
No 333
>PF13397 DUF4109: Domain of unknown function (DUF4109)
Probab=39.62 E-value=35 Score=23.10 Aligned_cols=29 Identities=17% Similarity=0.374 Sum_probs=21.6
Q ss_pred cceEEEcCcCCcceecCC------CCCeecCCCCCe
Q psy2244 14 GDIEKYYLECHFENEIRP------RDPIRCRECGYR 43 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~------~d~IRC~~CG~R 43 (73)
..+.|.|.+ |.++.+.. -+..-|+.||.-
T Consensus 25 ~~v~Y~C~~-Gh~~~v~Fa~eAevP~~WeC~~cG~~ 59 (105)
T PF13397_consen 25 QRVSYWCPN-GHETEVPFAAEAEVPATWECPRCGLP 59 (105)
T ss_pred eEEEEECCC-CCEEeccccccCCCCCceeCCCCCCc
Confidence 458999999 77766552 256789999974
No 334
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=39.44 E-value=24 Score=27.45 Aligned_cols=16 Identities=31% Similarity=0.445 Sum_probs=13.2
Q ss_pred ecCCCCCeecCCCCCe
Q psy2244 28 EIRPRDPIRCRECGYR 43 (73)
Q Consensus 28 ~ik~~d~IRC~~CG~R 43 (73)
.++.+.+-||++||+-
T Consensus 175 wLrEGkpqRCpECGqV 190 (268)
T PTZ00043 175 RCREGFLYRCGECDQI 190 (268)
T ss_pred EecCCCCccCCCCCcE
Confidence 4567889999999984
No 335
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=39.25 E-value=20 Score=26.33 Aligned_cols=26 Identities=15% Similarity=0.266 Sum_probs=17.6
Q ss_pred EEEcCcCCcceecC---CCCCeecCCCCC
Q psy2244 17 EKYYLECHFENEIR---PRDPIRCRECGY 42 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik---~~d~IRC~~CG~ 42 (73)
...|..|+...+.. ....-+|+.||.
T Consensus 117 ~~~C~~C~~~~~~~~~~~~~~p~C~~Cg~ 145 (242)
T PTZ00408 117 KVRCTATGHVFDWTEDVVHGSSRCKCCGC 145 (242)
T ss_pred eEEECCCCcccCchhhhhcCCCccccCCC
Confidence 46799999876543 123467999984
No 336
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=39.11 E-value=16 Score=23.02 Aligned_cols=21 Identities=24% Similarity=0.464 Sum_probs=15.1
Q ss_pred cCcCCcceecCCCCCeecCCCCCe
Q psy2244 20 YLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 20 C~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
|-+|+..++ .|.-.||.||..
T Consensus 7 C~~Ck~l~~---~d~e~CP~Cgs~ 27 (64)
T COG2093 7 CKNCKRLTP---EDTEICPVCGST 27 (64)
T ss_pred HhhccccCC---CCCccCCCCCCc
Confidence 778876654 344669999986
No 337
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=39.10 E-value=18 Score=30.83 Aligned_cols=37 Identities=16% Similarity=0.180 Sum_probs=24.9
Q ss_pred ceeccccCCcceEEEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 5 QVLVGKCLPGDIEKYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 5 ~~l~~~~~~~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
||--+-.........|.+||..++-...+ -| .||.+|
T Consensus 118 qyhyas~k~~va~w~c~~cg~~iean~kp--~c-~cg~~~ 154 (593)
T COG2401 118 QYHYASQKEKVALWRCEKCGTIIEANTKP--EC-KCGSHV 154 (593)
T ss_pred HhhhccccceEEEEecchhchhhhhcCCc--cc-CCCCce
Confidence 34333333445679999999987665544 68 899865
No 338
>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=39.01 E-value=35 Score=26.58 Aligned_cols=26 Identities=23% Similarity=0.473 Sum_probs=20.9
Q ss_pred CCCeecCCCCCeEEEeeeCCeeEEEe
Q psy2244 32 RDPIRCRECGYRIMYKKRTKRCILYF 57 (73)
Q Consensus 32 ~d~IRC~~CG~RILyKkRt~r~vqf~ 57 (73)
...-.||.||.+++.|.-..+.--|-
T Consensus 28 ~~~~~CP~C~~~v~lk~G~~k~~HFA 53 (375)
T PF06054_consen 28 KGKYFCPGCGEPVILKKGKKKIPHFA 53 (375)
T ss_pred CCcEECCCCCCeeEEEEcCcccceee
Confidence 67789999999999988877666654
No 339
>KOG3623|consensus
Probab=38.99 E-value=12 Score=33.51 Aligned_cols=29 Identities=21% Similarity=0.433 Sum_probs=22.4
Q ss_pred eEEEcCcCCcceecC-----------CCCCeecCCCCCeE
Q psy2244 16 IEKYYLECHFENEIR-----------PRDPIRCRECGYRI 44 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik-----------~~d~IRC~~CG~RI 44 (73)
-.++|.+||+-+..+ .-.+.-|++|+.|.
T Consensus 280 RKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRF 319 (1007)
T KOG3623|consen 280 RKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRF 319 (1007)
T ss_pred ccccccccchhhhhHHHHHhhheeecCCCCcCCccccccc
Confidence 468999999988765 12567899998873
No 340
>PHA00616 hypothetical protein
Probab=38.97 E-value=7 Score=22.69 Aligned_cols=11 Identities=18% Similarity=-0.010 Sum_probs=7.9
Q ss_pred EEcCcCCccee
Q psy2244 18 KYYLECHFENE 28 (73)
Q Consensus 18 YiC~~Cg~e~~ 28 (73)
|.|.+||..+.
T Consensus 2 YqC~~CG~~F~ 12 (44)
T PHA00616 2 YQCLRCGGIFR 12 (44)
T ss_pred CccchhhHHHh
Confidence 77888877654
No 341
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=38.93 E-value=19 Score=18.26 Aligned_cols=17 Identities=29% Similarity=0.370 Sum_probs=5.5
Q ss_pred ccccCCcceEEEcCcCC
Q psy2244 8 VGKCLPGDIEKYYLECH 24 (73)
Q Consensus 8 ~~~~~~~~v~YiC~~Cg 24 (73)
||+.......|.|..|.
T Consensus 6 C~~~~~~~~~Y~C~~Cd 22 (30)
T PF07649_consen 6 CGKPIDGGWFYRCSECD 22 (30)
T ss_dssp TS----S--EEE-TTT-
T ss_pred CCCcCCCCceEECccCC
Confidence 44445455666666664
No 342
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=38.69 E-value=12 Score=29.95 Aligned_cols=25 Identities=24% Similarity=0.582 Sum_probs=17.0
Q ss_pred EcCcCC--cceecCCCCCeecCCCCCe
Q psy2244 19 YYLECH--FENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg--~e~~ik~~d~IRC~~CG~R 43 (73)
-|.+|| +..+++.+.+--||+||..
T Consensus 317 fc~ncG~~~t~~~~ng~a~fcp~cgq~ 343 (345)
T COG4260 317 FCLNCGCGTTADFDNGKAKFCPECGQG 343 (345)
T ss_pred cccccCcccccCCccchhhhChhhcCC
Confidence 466665 4455667777888888853
No 343
>PRK05978 hypothetical protein; Provisional
Probab=38.66 E-value=18 Score=25.54 Aligned_cols=24 Identities=21% Similarity=0.355 Sum_probs=10.5
Q ss_pred EcCcCCcceecC--CCCCeecCCCCC
Q psy2244 19 YYLECHFENEIR--PRDPIRCRECGY 42 (73)
Q Consensus 19 iC~~Cg~e~~ik--~~d~IRC~~CG~ 42 (73)
+|.+||.---.+ ..-.-+|+.||-
T Consensus 35 rCP~CG~G~LF~g~Lkv~~~C~~CG~ 60 (148)
T PRK05978 35 RCPACGEGKLFRAFLKPVDHCAACGE 60 (148)
T ss_pred cCCCCCCCcccccccccCCCccccCC
Confidence 455554443222 122345555554
No 344
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=38.61 E-value=16 Score=33.16 Aligned_cols=62 Identities=13% Similarity=0.236 Sum_probs=37.3
Q ss_pred ceeccccCCcceE--EEcCcCCcceecCC--------CCCeecCCCCCeEEEeeeCCee-EEEeeccCCCCCcc
Q psy2244 5 QVLVGKCLPGDIE--KYYLECHFENEIRP--------RDPIRCRECGYRIMYKKRTKRC-ILYFKPQTGGFPKL 67 (73)
Q Consensus 5 ~~l~~~~~~~~v~--YiC~~Cg~e~~ik~--------~d~IRC~~CG~RILyKkRt~r~-vqf~~~~~~~~~~~ 67 (73)
-|+.|.--..|.. |+|.+|....-+.. .+.-.||+||. .|-|---.-. -.|+-|.-+-.|-+
T Consensus 669 Ay~lgITeVdPL~phy~c~~c~~~ef~~~~~~~sg~dlp~k~cp~c~~-~~~~dg~~L~FErFLn~er~~~PDI 741 (1213)
T TIGR01405 669 ATMTGITEVNPLPPHYLCPNCKYSEFITDGSVGSGFDLPDKDCPKCGA-PLKKDGQDIPFETFLGFKGDKVPDI 741 (1213)
T ss_pred HHHhcCCCcCCCcccccCcccccccccccccccccccCccccCccccc-cccccCCCceeeeccCCCCCCCCCC
Confidence 4666766666764 99999965433332 25578999985 2333322211 24777777766654
No 345
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=38.56 E-value=18 Score=30.99 Aligned_cols=23 Identities=30% Similarity=0.561 Sum_probs=15.7
Q ss_pred EcCcCCcceecCCCCCeecCCCCC
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
.|.+||...... ..=..|+.|||
T Consensus 726 ~Cp~Cg~~l~~~-~GC~~C~~CG~ 748 (752)
T PRK08665 726 ACPECGSILEHE-EGCVVCHSCGY 748 (752)
T ss_pred CCCCCCcccEEC-CCCCcCCCCCC
Confidence 599998543333 34478999987
No 346
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=38.55 E-value=23 Score=18.17 Aligned_cols=8 Identities=25% Similarity=0.127 Sum_probs=4.8
Q ss_pred EEEcCcCC
Q psy2244 17 EKYYLECH 24 (73)
Q Consensus 17 ~YiC~~Cg 24 (73)
.|.|.+|.
T Consensus 15 ~Y~C~~c~ 22 (30)
T PF03107_consen 15 FYHCSECC 22 (30)
T ss_pred eEEeCCCC
Confidence 56666665
No 347
>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=38.44 E-value=16 Score=23.03 Aligned_cols=33 Identities=24% Similarity=0.297 Sum_probs=16.5
Q ss_pred ceEEEcCcCCcc----eecCC---CCCeecCCCCCeEEEe
Q psy2244 15 DIEKYYLECHFE----NEIRP---RDPIRCRECGYRIMYK 47 (73)
Q Consensus 15 ~v~YiC~~Cg~e----~~ik~---~d~IRC~~CG~RILyK 47 (73)
+..+.|..|+.+ ++++. ...+.|..||-.--++
T Consensus 20 ~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp SS----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred CceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence 467999999955 33432 3669999998765544
No 348
>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=38.12 E-value=38 Score=19.98 Aligned_cols=23 Identities=17% Similarity=0.208 Sum_probs=14.5
Q ss_pred ceEEEcCcCCcceecCCCCCeecCCCC
Q psy2244 15 DIEKYYLECHFENEIRPRDPIRCRECG 41 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~~d~IRC~~CG 41 (73)
+..-.|.+||.... .---|+.||
T Consensus 24 p~l~~C~~cG~~~~----~H~vc~~cG 46 (55)
T TIGR01031 24 PTLVVCPNCGEFKL----PHRVCPSCG 46 (55)
T ss_pred CcceECCCCCCccc----CeeECCccC
Confidence 44456888876432 235688888
No 349
>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=37.86 E-value=20 Score=20.69 Aligned_cols=15 Identities=27% Similarity=0.709 Sum_probs=11.9
Q ss_pred CCCeecCCCCCeEEE
Q psy2244 32 RDPIRCRECGYRIMY 46 (73)
Q Consensus 32 ~d~IRC~~CG~RILy 46 (73)
.|.++|..|+..+--
T Consensus 32 ~d~v~C~~C~~~~~~ 46 (69)
T cd00022 32 GDEVKCFFCGLELKN 46 (69)
T ss_pred CCEEEeCCCCCCccC
Confidence 467999999987643
No 350
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=37.42 E-value=14 Score=30.35 Aligned_cols=30 Identities=30% Similarity=0.695 Sum_probs=22.3
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeEEEeeeC
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRIMYKKRT 50 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt 50 (73)
=-|..|+.....+ +..+||.||.++ |-.|+
T Consensus 221 ~~C~~C~~~~~~~--~~~~CpRC~~~L-y~rr~ 250 (418)
T COG2995 221 RSCLCCHYILPHD--AEPRCPRCGSKL-YVRRR 250 (418)
T ss_pred eecccccccCCHh--hCCCCCCCCChh-hccCh
Confidence 3588998777665 779999999985 44443
No 351
>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=37.27 E-value=15 Score=25.37 Aligned_cols=10 Identities=30% Similarity=1.052 Sum_probs=8.9
Q ss_pred CeecCCCCCe
Q psy2244 34 PIRCRECGYR 43 (73)
Q Consensus 34 ~IRC~~CG~R 43 (73)
.++||+||+.
T Consensus 105 ~~~cp~c~s~ 114 (146)
T TIGR02159 105 SVQCPRCGSA 114 (146)
T ss_pred CCcCCCCCCC
Confidence 6999999984
No 352
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=37.06 E-value=45 Score=23.53 Aligned_cols=35 Identities=11% Similarity=0.108 Sum_probs=26.2
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEeeccCC
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKPQTG 62 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~~~~~~ 62 (73)
..+|.-||..+ +-|+-++|=++..+++.|...+|.
T Consensus 4 ~e~CsFcG~kI-----------yPG~G~~fVR~DGkvf~FcssKC~ 38 (131)
T PRK14891 4 TRTCDYTGEEI-----------EPGTGTMFVRKDGTVLHFVDSKCE 38 (131)
T ss_pred eeeecCcCCcc-----------cCCCCcEEEecCCCEEEEecHHHH
Confidence 35666666555 556677899999999999988774
No 353
>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=37.06 E-value=14 Score=31.33 Aligned_cols=35 Identities=23% Similarity=0.419 Sum_probs=25.3
Q ss_pred ceEEEcCcCCcceecC-----CCCCeecCCCCCeEEEeee
Q psy2244 15 DIEKYYLECHFENEIR-----PRDPIRCRECGYRIMYKKR 49 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik-----~~d~IRC~~CG~RILyKkR 49 (73)
+.-=+|.+|-+|..-. -..++.|++||-|+-+...
T Consensus 116 ~~f~~C~~C~~ey~~p~~rr~h~~~~~C~~Cgp~l~l~~~ 155 (711)
T TIGR00143 116 ADFPLCPDCAKEYKDPLDRRFHAQPIACPRCGPQLNFVSR 155 (711)
T ss_pred CCCcCCHHHHHHhcCCccccCCCCCccCCCCCcEEEEEeC
Confidence 4445799998885322 2388999999999977543
No 354
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=37.05 E-value=24 Score=26.98 Aligned_cols=18 Identities=33% Similarity=0.720 Sum_probs=14.4
Q ss_pred CeecCCCCCeEEEeeeCC
Q psy2244 34 PIRCRECGYRIMYKKRTK 51 (73)
Q Consensus 34 ~IRC~~CG~RILyKkRt~ 51 (73)
-|+|+.|++.|-+|-=++
T Consensus 77 ~~kC~~C~~~i~~kTDPk 94 (324)
T PF04502_consen 77 YIKCPRCSNEIEFKTDPK 94 (324)
T ss_pred EEEcCCCCCEEeeecCCC
Confidence 489999999999885443
No 355
>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=36.93 E-value=12 Score=23.06 Aligned_cols=12 Identities=50% Similarity=1.049 Sum_probs=8.4
Q ss_pred CCeecCCCCCeE
Q psy2244 33 DPIRCRECGYRI 44 (73)
Q Consensus 33 d~IRC~~CG~RI 44 (73)
-||||.-||.-|
T Consensus 3 iPVRCFTCGkvi 14 (60)
T PF01194_consen 3 IPVRCFTCGKVI 14 (60)
T ss_dssp -SSS-STTTSBT
T ss_pred CceecCCCCCCh
Confidence 379999999765
No 356
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=36.82 E-value=40 Score=26.30 Aligned_cols=27 Identities=19% Similarity=0.290 Sum_probs=20.7
Q ss_pred CcceEEEcCcCCcceecCCCCCeecCCCCC
Q psy2244 13 PGDIEKYYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 13 ~~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
.+.-...|+-|+.+=... -++|++||.
T Consensus 208 ~G~RyL~CslC~teW~~~---R~~C~~Cg~ 234 (309)
T PRK03564 208 QGLRYLHCNLCESEWHVV---RVKCSNCEQ 234 (309)
T ss_pred CCceEEEcCCCCCccccc---CccCCCCCC
Confidence 345667899998886655 489999997
No 357
>KOG0478|consensus
Probab=36.73 E-value=16 Score=32.26 Aligned_cols=27 Identities=26% Similarity=0.552 Sum_probs=21.0
Q ss_pred eEEEcCcCCcceecC-----CCCCeecCCCCC
Q psy2244 16 IEKYYLECHFENEIR-----PRDPIRCRECGY 42 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik-----~~d~IRC~~CG~ 42 (73)
-.+.|..|+.+.... ..+++.|++|+.
T Consensus 263 afFrC~vC~~~~~ve~drg~i~eP~~C~~C~~ 294 (804)
T KOG0478|consen 263 AFFRCSVCGHEIAVESDRGRIKEPMLCKECGT 294 (804)
T ss_pred HhhhhhhcCceEEEEeecCccCCCcccccccC
Confidence 458999999885544 348999999965
No 358
>KOG2807|consensus
Probab=36.39 E-value=21 Score=29.01 Aligned_cols=39 Identities=10% Similarity=0.009 Sum_probs=29.3
Q ss_pred eeccccCCcceEEEcCcCCcceecCC-----CCCeecCCCCCeE
Q psy2244 6 VLVGKCLPGDIEKYYLECHFENEIRP-----RDPIRCRECGYRI 44 (73)
Q Consensus 6 ~l~~~~~~~~v~YiC~~Cg~e~~ik~-----~d~IRC~~CG~RI 44 (73)
|-|++.+....-|.|..|...+=++= ...--||.|-|++
T Consensus 334 f~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCeh~~ 377 (378)
T KOG2807|consen 334 FACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCEHKP 377 (378)
T ss_pred eeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcCCCC
Confidence 56778888889999999988876662 2345688887763
No 359
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=35.43 E-value=24 Score=27.82 Aligned_cols=30 Identities=13% Similarity=0.173 Sum_probs=22.8
Q ss_pred cceEEEcCcCCcceecC--CCCCeecCCCCCe
Q psy2244 14 GDIEKYYLECHFENEIR--PRDPIRCRECGYR 43 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik--~~d~IRC~~CG~R 43 (73)
+..--+|..|+...--+ ..+.-.||+|||-
T Consensus 25 e~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h 56 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKELESNLKVCPKCGHH 56 (294)
T ss_pred CCceeECCCccceeeHHHHHhhhhcccccCcc
Confidence 56778999999886555 2346789999993
No 360
>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=35.40 E-value=34 Score=20.35 Aligned_cols=16 Identities=31% Similarity=0.424 Sum_probs=11.9
Q ss_pred CeecCCCCCeEEEeee
Q psy2244 34 PIRCRECGYRIMYKKR 49 (73)
Q Consensus 34 ~IRC~~CG~RILyKkR 49 (73)
.-.||+||..|=.++|
T Consensus 58 ~H~Cp~C~~~lg~~~r 73 (73)
T PF10601_consen 58 YHYCPNCGAFLGTYKR 73 (73)
T ss_pred eEECCCCCCEeEEEeC
Confidence 3678888888777665
No 361
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=35.35 E-value=12 Score=33.25 Aligned_cols=28 Identities=25% Similarity=0.260 Sum_probs=0.0
Q ss_pred cCCcceEEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 11 CLPGDIEKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 11 ~~~~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
-..+--..+|.+||.+.- ..+|+.||.+
T Consensus 649 i~vei~~r~Cp~Cg~~t~-----~~~Cp~CG~~ 676 (900)
T PF03833_consen 649 IEVEIGRRRCPKCGKETF-----YNRCPECGSH 676 (900)
T ss_dssp ---------------------------------
T ss_pred eEEeeecccCcccCCcch-----hhcCcccCCc
Confidence 334455678888887742 3567777765
No 362
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=35.27 E-value=30 Score=27.39 Aligned_cols=27 Identities=26% Similarity=0.525 Sum_probs=18.0
Q ss_pred EEEcCcCCcceecCC-------CCCeecCCCCCe
Q psy2244 17 EKYYLECHFENEIRP-------RDPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~-------~d~IRC~~CG~R 43 (73)
...|..|+...+++. ...-+|+.||..
T Consensus 147 ~~~C~~C~~~~~~~~~~~~~~~~~vP~C~~CgG~ 180 (349)
T PTZ00410 147 AASCIECHTPYDIEQAYLEARSGKVPHCSTCGGI 180 (349)
T ss_pred eeEeCCCCCCcchhHHHHHhhcCCCCCCCCCCCc
Confidence 357999997765431 234579999863
No 363
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=35.12 E-value=26 Score=30.29 Aligned_cols=36 Identities=19% Similarity=0.336 Sum_probs=24.3
Q ss_pred EcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEeec
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKP 59 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~~~ 59 (73)
.|.+||...+..... ||.||.+= ..=.+|+.-|+.|
T Consensus 643 ~C~~cg~~~~~~~~~---Cp~CG~~d--ve~~~Ri~GYl~~ 678 (700)
T COG1328 643 VCNRCGYSGEGLRTR---CPKCGSED--VEVFSRITGYLQN 678 (700)
T ss_pred eeccCCccccccccc---CCCCCCcc--ceeeeeecccccC
Confidence 689999886644333 99999753 4445566666664
No 364
>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=34.66 E-value=23 Score=17.50 Aligned_cols=11 Identities=9% Similarity=-0.188 Sum_probs=7.1
Q ss_pred EEEcCcCCcce
Q psy2244 17 EKYYLECHFEN 27 (73)
Q Consensus 17 ~YiC~~Cg~e~ 27 (73)
.|.|..|+..+
T Consensus 14 ~~~C~~C~k~F 24 (26)
T PF13465_consen 14 PYKCPYCGKSF 24 (26)
T ss_dssp SEEESSSSEEE
T ss_pred CCCCCCCcCee
Confidence 37777776654
No 365
>PRK14894 glycyl-tRNA synthetase; Provisional
Probab=34.46 E-value=25 Score=29.70 Aligned_cols=36 Identities=19% Similarity=0.287 Sum_probs=24.9
Q ss_pred cceEEEcCcCCcceecCCCCCeecCCCCCeEEEeeeC
Q psy2244 14 GDIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRT 50 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt 50 (73)
.+.+=.|.+|+..+..+... ++||+||..-|=.+|+
T Consensus 85 ~DpmV~CkkCk~ryRaD~Li-ikCP~CGs~dLTe~~~ 120 (539)
T PRK14894 85 NDPLVDCRDCKMRWRADHIQ-GVCPNCGSRDLTEPRP 120 (539)
T ss_pred CCceeECCCCCccccCccce-eeCCCCCCcCCCccee
Confidence 44566899999988766543 7899999644444443
No 366
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=34.39 E-value=25 Score=33.20 Aligned_cols=30 Identities=20% Similarity=0.102 Sum_probs=22.1
Q ss_pred cceEEEcCcCCcceecCCCCCeecCCCCCeEEEee
Q psy2244 14 GDIEKYYLECHFENEIRPRDPIRCRECGYRIMYKK 48 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKk 48 (73)
+--..+|.+||... -..+||.||.++--+.
T Consensus 671 ei~~~~Cp~Cg~~~-----~~~~Cp~CG~~~~~~~ 700 (1627)
T PRK14715 671 EIAFFKCPKCGKVG-----LYHVCPFCGTRVELKP 700 (1627)
T ss_pred EEEeeeCCCCCCcc-----ccccCcccCCcccCCC
Confidence 44568999999874 3479999999844333
No 367
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=34.37 E-value=27 Score=30.20 Aligned_cols=23 Identities=26% Similarity=0.611 Sum_probs=16.9
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
...|-.||... .-+.+||+||..
T Consensus 462 ~L~CH~Cg~~~----~~p~~Cp~Cgs~ 484 (730)
T COG1198 462 QLRCHYCGYQE----PIPQSCPECGSE 484 (730)
T ss_pred eeEeCCCCCCC----CCCCCCCCCCCC
Confidence 45677777663 345899999998
No 368
>PRK07218 replication factor A; Provisional
Probab=34.21 E-value=23 Score=28.52 Aligned_cols=24 Identities=21% Similarity=0.267 Sum_probs=17.6
Q ss_pred cceEEEcCcCCcceecCCCCCeecCCCCC
Q psy2244 14 GDIEKYYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
+...++|..|++.++. -.|+.||-
T Consensus 294 sgli~rCP~C~r~v~~-----~~C~~hG~ 317 (423)
T PRK07218 294 SGLIERCPECGRVIQK-----GQCRSHGA 317 (423)
T ss_pred CcceecCcCccccccC-----CcCCCCCC
Confidence 3466889999887733 58998884
No 369
>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=34.01 E-value=48 Score=17.38 Aligned_cols=9 Identities=56% Similarity=1.316 Sum_probs=3.2
Q ss_pred eecCCCCCe
Q psy2244 35 IRCRECGYR 43 (73)
Q Consensus 35 IRC~~CG~R 43 (73)
.+||.||-+
T Consensus 14 Y~Cp~C~~~ 22 (30)
T PF04438_consen 14 YRCPRCGAR 22 (30)
T ss_dssp EE-TTT--E
T ss_pred EECCCcCCc
Confidence 555555543
No 370
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=33.12 E-value=21 Score=17.80 Aligned_cols=10 Identities=30% Similarity=0.893 Sum_probs=7.8
Q ss_pred CeecCCCCCe
Q psy2244 34 PIRCRECGYR 43 (73)
Q Consensus 34 ~IRC~~CG~R 43 (73)
.+.|+.||-+
T Consensus 2 l~~C~~CgR~ 11 (25)
T PF13913_consen 2 LVPCPICGRK 11 (25)
T ss_pred CCcCCCCCCE
Confidence 4789999965
No 372
>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=32.72 E-value=6.4 Score=20.91 Aligned_cols=11 Identities=9% Similarity=-0.013 Sum_probs=6.8
Q ss_pred cCcCCcceecC
Q psy2244 20 YLECHFENEIR 30 (73)
Q Consensus 20 C~~Cg~e~~ik 30 (73)
|.+||..+...
T Consensus 6 C~~CGe~I~~~ 16 (36)
T PF01258_consen 6 CEDCGEPIPEE 16 (36)
T ss_dssp -TTTSSBEEHH
T ss_pred ccccCChHHHH
Confidence 77777776644
No 373
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=32.59 E-value=25 Score=21.78 Aligned_cols=13 Identities=23% Similarity=0.879 Sum_probs=7.5
Q ss_pred CeecCCCCCeEEE
Q psy2244 34 PIRCRECGYRIMY 46 (73)
Q Consensus 34 ~IRC~~CG~RILy 46 (73)
.++||.||..+.+
T Consensus 6 ~v~CP~C~k~~~w 18 (62)
T PRK00418 6 TVNCPTCGKPVEW 18 (62)
T ss_pred cccCCCCCCcccc
Confidence 3566666665554
No 374
>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=31.94 E-value=29 Score=23.89 Aligned_cols=26 Identities=27% Similarity=0.443 Sum_probs=16.8
Q ss_pred EEcCcCCcceecCC----CCCeecCCCCCe
Q psy2244 18 KYYLECHFENEIRP----RDPIRCRECGYR 43 (73)
Q Consensus 18 YiC~~Cg~e~~ik~----~d~IRC~~CG~R 43 (73)
..|..|+....... ...-+|+.||..
T Consensus 114 ~~C~~C~~~~~~~~~~~~~~~p~C~~C~~~ 143 (222)
T cd00296 114 VRCTSCGKEYPRDEVLEREKPPRCPKCGGL 143 (222)
T ss_pred cEECCCCCCcchhhhhhccCCCCCCCCCCc
Confidence 45888886544332 234679999875
No 375
>PHA00733 hypothetical protein
Probab=31.93 E-value=23 Score=23.73 Aligned_cols=29 Identities=14% Similarity=0.142 Sum_probs=18.8
Q ss_pred ceEEEcCcCCcceecCC---------CCCeecCCCCCe
Q psy2244 15 DIEKYYLECHFENEIRP---------RDPIRCRECGYR 43 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~---------~d~IRC~~CG~R 43 (73)
...|.|..||..+.-.. ..+..|+.||..
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~ 108 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKE 108 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCc
Confidence 34688888887755321 234688888764
No 376
>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=31.67 E-value=25 Score=23.10 Aligned_cols=19 Identities=32% Similarity=0.695 Sum_probs=15.0
Q ss_pred ceecCCCCCeecCCCCCeE
Q psy2244 26 ENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 26 e~~ik~~d~IRC~~CG~RI 44 (73)
.+.|+..+.+.|++||--.
T Consensus 27 ~IvIknVPa~~C~~CGe~y 45 (89)
T TIGR03829 27 AIEIKETPSISCSHCGMEY 45 (89)
T ss_pred EEEEecCCcccccCCCcEe
Confidence 4567778999999999743
No 377
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=31.63 E-value=31 Score=19.04 Aligned_cols=8 Identities=25% Similarity=0.513 Sum_probs=4.0
Q ss_pred eEEEcCcC
Q psy2244 16 IEKYYLEC 23 (73)
Q Consensus 16 v~YiC~~C 23 (73)
..|.|.+|
T Consensus 13 ~r~~C~~C 20 (46)
T cd02249 13 VRYHCLVC 20 (46)
T ss_pred CEEECCCC
Confidence 44555555
No 378
>PF02005 TRM: N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA: S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs []. The enzyme is found in both eukaryotes and archaea [].; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing; PDB: 2YTZ_B 2DUL_A 2EJU_A 2EJT_A 3AXT_A 3AXS_A.
Probab=31.60 E-value=36 Score=26.69 Aligned_cols=29 Identities=24% Similarity=0.630 Sum_probs=16.6
Q ss_pred eEEEcCcCCcceecCCC--CCeecCCCCCeE
Q psy2244 16 IEKYYLECHFENEIRPR--DPIRCRECGYRI 44 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~--d~IRC~~CG~RI 44 (73)
-.|.|..|+........ ....|++||.+.
T Consensus 239 ~v~~C~~C~~~~~~~~~~~~~~~c~~cg~~~ 269 (377)
T PF02005_consen 239 YVYYCPSCGYREEVKGLQKLKSKCPECGSKL 269 (377)
T ss_dssp EEEEETTT--EECCT-GCC--CEETTT-SCC
T ss_pred EEEECCCccccccccCccccCCcCCCCCCcc
Confidence 57899999754332221 138999999865
No 379
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=31.30 E-value=33 Score=20.17 Aligned_cols=8 Identities=38% Similarity=0.941 Sum_probs=3.2
Q ss_pred CCeecCCC
Q psy2244 33 DPIRCREC 40 (73)
Q Consensus 33 d~IRC~~C 40 (73)
..-+||.|
T Consensus 36 ~~g~CPgC 43 (48)
T PF14570_consen 36 EGGRCPGC 43 (48)
T ss_dssp S-SB-TTT
T ss_pred cCCCCCCC
Confidence 34556655
No 380
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=31.22 E-value=36 Score=17.14 Aligned_cols=23 Identities=26% Similarity=0.557 Sum_probs=14.6
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCC
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
.-.|..|...|... ..+|..||.
T Consensus 4 ~W~C~~C~~~N~~~---~~~C~~C~~ 26 (30)
T PF00641_consen 4 DWKCPSCTFMNPAS---RSKCVACGA 26 (30)
T ss_dssp SEEETTTTEEEESS---SSB-TTT--
T ss_pred CccCCCCcCCchHH---hhhhhCcCC
Confidence 45788998777655 367888874
No 381
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=30.82 E-value=58 Score=25.82 Aligned_cols=43 Identities=26% Similarity=0.490 Sum_probs=26.6
Q ss_pred CCcccee-ccccCC-cceEEEcCcCCcceecC--CC---CCeecCCCCCe
Q psy2244 1 MGYSQVL-VGKCLP-GDIEKYYLECHFENEIR--PR---DPIRCRECGYR 43 (73)
Q Consensus 1 ~~~~~~l-~~~~~~-~~v~YiC~~Cg~e~~ik--~~---d~IRC~~CG~R 43 (73)
|||-+-| +-+.+. ....++|..||.+...- +. +.-.|++||..
T Consensus 302 ~GAVetLLV~d~l~~~r~~~rc~~c~~~~~~~~~~~~~~~~~~~~~~~~~ 351 (403)
T TIGR03676 302 MGAVDTLLISEDLRKIRVTFKCPNCGYEEEKTVKPEEGDKSEACPKCGSE 351 (403)
T ss_pred hCCCcEEEEEccccceeEEEEcCCCCcceeeecccccccccccCcccCcc
Confidence 4555444 555553 34789999999875432 11 12458999876
No 382
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=30.73 E-value=35 Score=19.91 Aligned_cols=31 Identities=13% Similarity=0.353 Sum_probs=21.0
Q ss_pred EcCcCCcceecCC--------CCCeecCCCCCeEEEeee
Q psy2244 19 YYLECHFENEIRP--------RDPIRCRECGYRIMYKKR 49 (73)
Q Consensus 19 iC~~Cg~e~~ik~--------~d~IRC~~CG~RILyKkR 49 (73)
.|.+|-....+.. ...+||-.|..=|-|+-|
T Consensus 8 ~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~s~~ 46 (46)
T PF11331_consen 8 VCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSFSLP 46 (46)
T ss_pred ECccHHHHHcCCCccCCCccceeEEeCCCCceeEEEecC
Confidence 5777866554431 246899999988877654
No 383
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.22 E-value=13 Score=23.66 Aligned_cols=29 Identities=34% Similarity=0.639 Sum_probs=20.7
Q ss_pred EcCcCCcceecCCC---------CC---eecCCCCCeEEEe
Q psy2244 19 YYLECHFENEIRPR---------DP---IRCRECGYRIMYK 47 (73)
Q Consensus 19 iC~~Cg~e~~ik~~---------d~---IRC~~CG~RILyK 47 (73)
+|.-|.+...|+.. .| ..|++|-+||--|
T Consensus 4 kCiiCd~v~~iD~rt~~tKrLrN~PIrtymC~eC~~Rva~k 44 (68)
T COG4896 4 KCIICDRVDEIDNRTFKTKRLRNKPIRTYMCPECEHRVAIK 44 (68)
T ss_pred eEEEecceeeecchhHHHHHhhCCCceeEechhhHhhhchh
Confidence 57778777666632 33 4599999998776
No 384
>KOG3993|consensus
Probab=30.09 E-value=25 Score=29.52 Aligned_cols=14 Identities=21% Similarity=0.188 Sum_probs=11.2
Q ss_pred ceEEEcCcCCccee
Q psy2244 15 DIEKYYLECHFENE 28 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ 28 (73)
.++|+|.+|++.++
T Consensus 293 ~vEYrCPEC~KVFs 306 (500)
T KOG3993|consen 293 HVEYRCPECDKVFS 306 (500)
T ss_pred EeeecCCccccccc
Confidence 37899999988774
No 385
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=30.01 E-value=53 Score=27.11 Aligned_cols=27 Identities=19% Similarity=0.594 Sum_probs=17.5
Q ss_pred eecCCCCCeEEEe-eeCCeeEEEeeccCCCCCc
Q psy2244 35 IRCRECGYRIMYK-KRTKRCILYFKPQTGGFPK 66 (73)
Q Consensus 35 IRC~~CG~RILyK-kRt~r~vqf~~~~~~~~~~ 66 (73)
..||.||+.++.+ .+.. .| ..|.|||+
T Consensus 590 ~~CPkCg~~l~~~~~k~g---~f--~gCs~yp~ 617 (618)
T TIGR01057 590 GKCPKCGGKLVSKYAKKG---RF--VGCSNYPE 617 (618)
T ss_pred CCCCcCCCeeeeeecCCc---cE--EECCCCCC
Confidence 5699999987754 2222 23 35888875
No 386
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=29.32 E-value=48 Score=24.63 Aligned_cols=12 Identities=8% Similarity=0.080 Sum_probs=8.5
Q ss_pred eEEEcCcCCcce
Q psy2244 16 IEKYYLECHFEN 27 (73)
Q Consensus 16 v~YiC~~Cg~e~ 27 (73)
-...|..|+...
T Consensus 127 ~~~~C~~C~~~~ 138 (285)
T PRK05333 127 DGVRCMGCGARH 138 (285)
T ss_pred CEEEECCCCCcC
Confidence 347799998553
No 387
>KOG2593|consensus
Probab=29.29 E-value=29 Score=28.66 Aligned_cols=33 Identities=12% Similarity=0.355 Sum_probs=24.3
Q ss_pred CcceEEEcCcCCccee-cC------C-CCCeecCCCCCeEE
Q psy2244 13 PGDIEKYYLECHFENE-IR------P-RDPIRCRECGYRIM 45 (73)
Q Consensus 13 ~~~v~YiC~~Cg~e~~-ik------~-~d~IRC~~CG~RIL 45 (73)
..+-.|.|..|.+... |+ . .+.-+|..||.-++
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelv 164 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELV 164 (436)
T ss_pred cccccccCCccccchhhhHHHHhhcccCceEEEecCCCchh
Confidence 4566799999998843 22 2 36799999998654
No 388
>PRK06386 replication factor A; Reviewed
Probab=29.18 E-value=38 Score=26.88 Aligned_cols=24 Identities=17% Similarity=0.032 Sum_probs=17.5
Q ss_pred cceEEEcCcCCcceecCCCCCeecCCCCC
Q psy2244 14 GDIEKYYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 14 ~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
+-..++|.+|++.++- -+|++||-
T Consensus 233 sgli~rCP~C~R~l~~-----g~C~~HG~ 256 (358)
T PRK06386 233 SRIFTKCSVCNKIIED-----GVCKDHPD 256 (358)
T ss_pred cEeEecCcCCCeEccC-----CcCCCCCC
Confidence 4466888888888762 38888884
No 389
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=28.90 E-value=37 Score=18.38 Aligned_cols=8 Identities=25% Similarity=0.302 Sum_probs=3.9
Q ss_pred EEEcCcCC
Q psy2244 17 EKYYLECH 24 (73)
Q Consensus 17 ~YiC~~Cg 24 (73)
.|+|..|+
T Consensus 11 l~~CL~C~ 18 (50)
T smart00290 11 LWLCLTCG 18 (50)
T ss_pred eEEecCCC
Confidence 45555554
No 390
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=28.81 E-value=37 Score=25.47 Aligned_cols=12 Identities=17% Similarity=0.193 Sum_probs=8.5
Q ss_pred EEEcCcCCccee
Q psy2244 17 EKYYLECHFENE 28 (73)
Q Consensus 17 ~YiC~~Cg~e~~ 28 (73)
...|..|+....
T Consensus 137 ~~~C~~C~~~~~ 148 (271)
T PTZ00409 137 EARCCTCRKTIQ 148 (271)
T ss_pred cceeCCCCCCcc
Confidence 456888887655
No 391
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=28.77 E-value=34 Score=19.67 Aligned_cols=28 Identities=14% Similarity=0.331 Sum_probs=19.6
Q ss_pred EEEcCcCCcceecC-----CCCCeecCCCCCeE
Q psy2244 17 EKYYLECHFENEIR-----PRDPIRCRECGYRI 44 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik-----~~d~IRC~~CG~RI 44 (73)
...|..|+...... .+..+-|..||-+.
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~ 35 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYY 35 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHH
Confidence 36799999876654 23348899998643
No 392
>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=28.51 E-value=43 Score=18.21 Aligned_cols=11 Identities=27% Similarity=0.920 Sum_probs=6.3
Q ss_pred CeecCCCCCeE
Q psy2244 34 PIRCRECGYRI 44 (73)
Q Consensus 34 ~IRC~~CG~RI 44 (73)
.+.|++|+--|
T Consensus 4 ~~~C~nC~R~v 14 (33)
T PF08209_consen 4 YVECPNCGRPV 14 (33)
T ss_dssp EEE-TTTSSEE
T ss_pred eEECCCCcCCc
Confidence 46677777544
No 393
>TIGR00320 dfx_rbo desulfoferrodoxin. This protein is described in some articles as rubredoxin oxidoreductase (rbo), and its gene shares an operon with the rubredoxin gene in Desulfovibrio vulgaris Hildenborough.
Probab=28.43 E-value=51 Score=22.29 Aligned_cols=21 Identities=14% Similarity=0.093 Sum_probs=14.6
Q ss_pred EEEcCcCCccee-cC-CCCCeec
Q psy2244 17 EKYYLECHFENE-IR-PRDPIRC 37 (73)
Q Consensus 17 ~YiC~~Cg~e~~-ik-~~d~IRC 37 (73)
.|+|..||..+. +. ....+.|
T Consensus 7 fYkC~~CGniv~v~~~g~~~l~C 29 (125)
T TIGR00320 7 VYKCEVCGNIVEVLNAGIGQLVC 29 (125)
T ss_pred EEECCCCCcEEEEEECCCcceee
Confidence 799999999885 22 3334666
No 394
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=28.41 E-value=22 Score=28.57 Aligned_cols=26 Identities=23% Similarity=0.376 Sum_probs=18.7
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCC
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
+.-+|.+||.++..... ..+|++||.
T Consensus 4 ~~~rc~~cg~~f~~a~~-~~~c~~cGl 29 (411)
T COG0498 4 VSLRCLKCGREFSQALL-QGLCPDCGL 29 (411)
T ss_pred eEeecCCCCcchhhHHh-hCcCCcCCc
Confidence 34579999977653322 588999998
No 395
>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=28.29 E-value=37 Score=24.72 Aligned_cols=23 Identities=17% Similarity=0.245 Sum_probs=17.3
Q ss_pred ceEEEcCcCCcceecC-CCCCeec
Q psy2244 15 DIEKYYLECHFENEIR-PRDPIRC 37 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik-~~d~IRC 37 (73)
++.|.|.+||.+++.. ..+.+.+
T Consensus 76 ~~~~~C~~cg~~~~~~i~l~~~~l 99 (205)
T PF12322_consen 76 PVNYTCPDCGEEVKVPINLDQIKL 99 (205)
T ss_pred eEEEECCCCCcEEEEEecchhccc
Confidence 5889999999987766 3355565
No 396
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=28.10 E-value=32 Score=22.51 Aligned_cols=29 Identities=14% Similarity=0.391 Sum_probs=10.0
Q ss_pred eEEEcCcCCcceecCCCC--CeecCCCCCeE
Q psy2244 16 IEKYYLECHFENEIRPRD--PIRCRECGYRI 44 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d--~IRC~~CG~RI 44 (73)
..-+|--||.++.+.... -|-|.+|++-|
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPv 38 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPV 38 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS----
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCcc
Confidence 335788888888877442 26777777644
No 397
>KOG1812|consensus
Probab=27.53 E-value=29 Score=27.32 Aligned_cols=31 Identities=26% Similarity=0.625 Sum_probs=24.8
Q ss_pred EEcCcCCcceecCCC-CCeecCCCCCeEEEeee
Q psy2244 18 KYYLECHFENEIRPR-DPIRCRECGYRIMYKKR 49 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~-d~IRC~~CG~RILyKkR 49 (73)
=.|..|+..+++..+ .-+.|+ |||..-|.-.
T Consensus 307 r~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~ 338 (384)
T KOG1812|consen 307 RQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCG 338 (384)
T ss_pred CcCcccceeeeecCCcceEEee-ccccchhhcC
Confidence 468899988887766 679999 9998877665
No 398
>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=27.46 E-value=22 Score=21.05 Aligned_cols=17 Identities=12% Similarity=0.401 Sum_probs=9.0
Q ss_pred CCeecCCCCC-eEEEeee
Q psy2244 33 DPIRCRECGY-RIMYKKR 49 (73)
Q Consensus 33 d~IRC~~CG~-RILyKkR 49 (73)
..-.||.|+. .+.|...
T Consensus 13 al~~Cp~C~~~~l~~~~~ 30 (55)
T PF08063_consen 13 ALEPCPKCKGGQLYFDGS 30 (55)
T ss_dssp EE---SSSSE-EEEEETT
T ss_pred CCCCCCCCCCCeEEecCC
Confidence 3467999998 5555443
No 399
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=27.36 E-value=35 Score=26.13 Aligned_cols=24 Identities=38% Similarity=0.674 Sum_probs=12.7
Q ss_pred EcCcCCcceecC--CCCCeecCCCCC
Q psy2244 19 YYLECHFENEIR--PRDPIRCRECGY 42 (73)
Q Consensus 19 iC~~Cg~e~~ik--~~d~IRC~~CG~ 42 (73)
.|.+||.++-.. ....+-|..||.
T Consensus 3 ~CpeCg~~~~~~d~~~ge~VC~~CG~ 28 (285)
T COG1405 3 SCPECGSTNIITDYERGEIVCADCGL 28 (285)
T ss_pred CCCCCCCccceeeccCCeEEeccCCE
Confidence 466666662222 234466666665
No 400
>KOG1105|consensus
Probab=26.28 E-value=44 Score=26.14 Aligned_cols=27 Identities=30% Similarity=0.449 Sum_probs=19.8
Q ss_pred EEEcCcCCcceec------C-----CCCCeecCCCCCe
Q psy2244 17 EKYYLECHFENEI------R-----PRDPIRCRECGYR 43 (73)
Q Consensus 17 ~YiC~~Cg~e~~i------k-----~~d~IRC~~CG~R 43 (73)
.++|+.|+..+-. + ...-+-|.+||.|
T Consensus 255 ~fkcgkckk~~cty~q~Qtrs~DePmtTfv~C~ecgnr 292 (296)
T KOG1105|consen 255 LFKCGKCKKKNCTYTQLQTRSADEPMTTFVTCNECGNR 292 (296)
T ss_pred ceeeccccccceeEEeeccCCCCCCcceeeeecccCCc
Confidence 6999999886432 1 2345899999987
No 401
>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=26.15 E-value=31 Score=27.43 Aligned_cols=18 Identities=33% Similarity=0.870 Sum_probs=13.6
Q ss_pred ecCCCCCeecCCCCCeEE
Q psy2244 28 EIRPRDPIRCRECGYRIM 45 (73)
Q Consensus 28 ~ik~~d~IRC~~CG~RIL 45 (73)
....+.++.||.|||.+-
T Consensus 203 ky~k~k~~PCPKCg~et~ 220 (314)
T PF06524_consen 203 KYEKGKPIPCPKCGYETQ 220 (314)
T ss_pred ccccCCCCCCCCCCCccc
Confidence 344568999999999653
No 402
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=25.79 E-value=16 Score=23.60 Aligned_cols=23 Identities=30% Similarity=0.557 Sum_probs=15.5
Q ss_pred EEcCcCCcceecCCC----CCeecCCC
Q psy2244 18 KYYLECHFENEIRPR----DPIRCREC 40 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~----d~IRC~~C 40 (73)
=+|-+||.++..... ...+|..|
T Consensus 81 G~C~~Cge~I~~~RL~a~P~a~~Cv~C 107 (110)
T TIGR02420 81 GYCEECGEEIGLRRLEARPTATLCIDC 107 (110)
T ss_pred CchhccCCcccHHHHhhCCCccccHHh
Confidence 478899988876632 34567666
No 403
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=25.63 E-value=45 Score=23.80 Aligned_cols=26 Identities=15% Similarity=0.374 Sum_probs=15.3
Q ss_pred EEEcCcCCccee---cCCCCCeecCCCCC
Q psy2244 17 EKYYLECHFENE---IRPRDPIRCRECGY 42 (73)
Q Consensus 17 ~YiC~~Cg~e~~---ik~~d~IRC~~CG~ 42 (73)
-++|.-|..+.- ......+||+.|+.
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~~C~~ 180 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCPKCKS 180 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCCcCcc
Confidence 367777765422 22346678887764
No 404
>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=25.58 E-value=51 Score=24.42 Aligned_cols=12 Identities=42% Similarity=0.783 Sum_probs=6.5
Q ss_pred eecCCCCCeEEE
Q psy2244 35 IRCRECGYRIMY 46 (73)
Q Consensus 35 IRC~~CG~RILy 46 (73)
--|+.||..|..
T Consensus 246 ~pC~~Cg~~I~~ 257 (272)
T TIGR00577 246 EPCRRCGTPIEK 257 (272)
T ss_pred CCCCCCCCeeEE
Confidence 346666655543
No 405
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=25.38 E-value=48 Score=30.23 Aligned_cols=28 Identities=14% Similarity=0.390 Sum_probs=20.8
Q ss_pred EEEcCcCCcceecCCCC-C-eecCCCCCeE
Q psy2244 17 EKYYLECHFENEIRPRD-P-IRCRECGYRI 44 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d-~-IRC~~CG~RI 44 (73)
.-+|--||.++.+.... + |-|.+||+-+
T Consensus 17 ~qiCqICGD~vg~~~~Ge~FVAC~eC~FPV 46 (1079)
T PLN02638 17 GQVCQICGDNVGKTVDGEPFVACDVCAFPV 46 (1079)
T ss_pred CceeeecccccCcCCCCCEEEEeccCCCcc
Confidence 34899999999888542 2 8888888743
No 406
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=25.36 E-value=40 Score=21.35 Aligned_cols=26 Identities=23% Similarity=0.322 Sum_probs=18.6
Q ss_pred eEEEcCcCCcceecCC------CCCeecCCCCC
Q psy2244 16 IEKYYLECHFENEIRP------RDPIRCRECGY 42 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~------~d~IRC~~CG~ 42 (73)
-.|-| -||..++|.. -...|||.|.-
T Consensus 21 ftyPC-PCGDRFeIsLeDl~~GE~VArCPSCSL 52 (67)
T COG5216 21 FTYPC-PCGDRFEISLEDLRNGEVVARCPSCSL 52 (67)
T ss_pred EEecC-CCCCEeEEEHHHhhCCceEEEcCCceE
Confidence 34556 4999888763 25689999985
No 407
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=25.27 E-value=43 Score=18.52 Aligned_cols=8 Identities=38% Similarity=1.169 Sum_probs=6.7
Q ss_pred CeecCCCC
Q psy2244 34 PIRCRECG 41 (73)
Q Consensus 34 ~IRC~~CG 41 (73)
.+.|+.||
T Consensus 13 ~~~C~~Cg 20 (41)
T PF13878_consen 13 ATTCPTCG 20 (41)
T ss_pred CcCCCCCC
Confidence 57899998
No 408
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=25.21 E-value=37 Score=29.44 Aligned_cols=28 Identities=29% Similarity=0.476 Sum_probs=25.1
Q ss_pred EEeeeCCeeEEEee-ccCCCCCcceeeee
Q psy2244 45 MYKKRTKRCILYFK-PQTGGFPKLKTTVT 72 (73)
Q Consensus 45 LyKkRt~r~vqf~~-~~~~~~~~~~~~~~ 72 (73)
+||+.+.|.--|.+ |+.|||-.|-|||-
T Consensus 288 ~~kp~PgrFKDYIA~PK~NgYQSlHTtv~ 316 (701)
T COG0317 288 LWKPIPGEFDDYIANPKPNGYQSLHTTVI 316 (701)
T ss_pred cCcCCCCccccccccCCCCCCceeEEEEE
Confidence 68899999999886 99999999999984
No 409
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.17 E-value=51 Score=24.48 Aligned_cols=9 Identities=33% Similarity=0.774 Sum_probs=4.8
Q ss_pred ecCCCCCeE
Q psy2244 36 RCRECGYRI 44 (73)
Q Consensus 36 RC~~CG~RI 44 (73)
-||.||..|
T Consensus 246 pCprCG~~I 254 (272)
T PRK14810 246 PCLNCKTPI 254 (272)
T ss_pred cCCCCCCee
Confidence 455555544
No 410
>PF14122 YokU: YokU-like protein
Probab=25.08 E-value=47 Score=21.99 Aligned_cols=18 Identities=33% Similarity=0.589 Sum_probs=14.3
Q ss_pred cceecCCCCCeecCCCCC
Q psy2244 25 FENEIRPRDPIRCRECGY 42 (73)
Q Consensus 25 ~e~~ik~~d~IRC~~CG~ 42 (73)
+.++|+..+.+.|.+||-
T Consensus 26 raIeI~~tP~i~C~~Cgm 43 (87)
T PF14122_consen 26 RAIEITDTPAIICSNCGM 43 (87)
T ss_pred eEEEecCCceeeecCCCc
Confidence 356777888899999985
No 411
>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=24.98 E-value=43 Score=18.06 Aligned_cols=12 Identities=33% Similarity=0.938 Sum_probs=9.1
Q ss_pred CeecCCCCCeEE
Q psy2244 34 PIRCRECGYRIM 45 (73)
Q Consensus 34 ~IRC~~CG~RIL 45 (73)
+-.|+.||..+-
T Consensus 2 ~~~C~~Cg~~l~ 13 (47)
T PF13005_consen 2 PRACPDCGGELK 13 (47)
T ss_pred CCcCCCCCceee
Confidence 346999999665
No 412
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=24.90 E-value=40 Score=20.23 Aligned_cols=12 Identities=25% Similarity=0.728 Sum_probs=8.7
Q ss_pred CeecCCCCCeEE
Q psy2244 34 PIRCRECGYRIM 45 (73)
Q Consensus 34 ~IRC~~CG~RIL 45 (73)
-..||.||...+
T Consensus 13 Y~~Cp~CGN~~v 24 (49)
T PF12677_consen 13 YCKCPKCGNDKV 24 (49)
T ss_pred hccCcccCCcEe
Confidence 367999998544
No 413
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.69 E-value=56 Score=24.99 Aligned_cols=26 Identities=15% Similarity=0.093 Sum_probs=19.4
Q ss_pred ceEEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 15 DIEKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
.+-|.|..|...+-.- ++.|+-||-+
T Consensus 253 ~~GyvCs~Clsi~C~~---p~~C~~Cgt~ 278 (279)
T TIGR00627 253 SIGFVCSVCLSVLCQY---TPICKTCKTA 278 (279)
T ss_pred cceEECCCccCCcCCC---CCCCCCCCCC
Confidence 3559999998876433 3599999965
No 414
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=24.66 E-value=53 Score=24.39 Aligned_cols=23 Identities=22% Similarity=0.275 Sum_probs=11.4
Q ss_pred EcCcCCcceecC---CCCCeecCCCC
Q psy2244 19 YYLECHFENEIR---PRDPIRCRECG 41 (73)
Q Consensus 19 iC~~Cg~e~~ik---~~d~IRC~~CG 41 (73)
.|..||..+.-. .+...-||.|-
T Consensus 237 pC~~Cg~~I~~~~~~gR~ty~Cp~CQ 262 (269)
T PRK14811 237 PCPRCGTPIEKIVVGGRGTHFCPQCQ 262 (269)
T ss_pred CCCcCCCeeEEEEECCCCcEECCCCc
Confidence 455565554322 34555555553
No 415
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.64 E-value=59 Score=22.15 Aligned_cols=25 Identities=20% Similarity=0.600 Sum_probs=18.9
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeEE
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRIM 45 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RIL 45 (73)
|.|.+|+..+--- ++.||-||=-++
T Consensus 2 Y~CPrC~skvC~L---P~~CpiCgLtLV 26 (112)
T TIGR00622 2 YFCPQCRAKVCEL---PVECPICGLTLI 26 (112)
T ss_pred ccCCCCCCCccCC---CCcCCcCCCEEe
Confidence 8999998876432 488999987653
No 416
>PRK00807 50S ribosomal protein L24e; Validated
Probab=24.59 E-value=1.1e+02 Score=17.77 Aligned_cols=19 Identities=16% Similarity=0.345 Sum_probs=11.4
Q ss_pred EEEeeeCCeeEEEeeccCC
Q psy2244 44 IMYKKRTKRCILYFKPQTG 62 (73)
Q Consensus 44 ILyKkRt~r~vqf~~~~~~ 62 (73)
++|=....++..|...++-
T Consensus 17 ~~~vr~Dgkv~~Fcs~KC~ 35 (52)
T PRK00807 17 KMYVKKDGTILYFCSSKCE 35 (52)
T ss_pred eEEEEeCCcEEEEeCHHHH
Confidence 4455556667777666553
No 417
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=24.55 E-value=52 Score=18.47 Aligned_cols=13 Identities=31% Similarity=0.511 Sum_probs=6.5
Q ss_pred cCCcceEEEcCcC
Q psy2244 11 CLPGDIEKYYLEC 23 (73)
Q Consensus 11 ~~~~~v~YiC~~C 23 (73)
++.+..-|+|.+|
T Consensus 9 ~~~~g~r~~C~~C 21 (49)
T cd02335 9 DITGTIRIKCAEC 21 (49)
T ss_pred CCCCCcEEECCCC
Confidence 3333455555555
No 418
>KOG4080|consensus
Probab=24.54 E-value=34 Score=25.25 Aligned_cols=9 Identities=33% Similarity=0.785 Sum_probs=8.0
Q ss_pred CeecCCCCC
Q psy2244 34 PIRCRECGY 42 (73)
Q Consensus 34 ~IRC~~CG~ 42 (73)
..+||.|||
T Consensus 93 l~~CP~CGh 101 (176)
T KOG4080|consen 93 LNTCPACGH 101 (176)
T ss_pred cccCcccCc
Confidence 678999998
No 419
>COG4307 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.44 E-value=19 Score=28.76 Aligned_cols=26 Identities=15% Similarity=0.303 Sum_probs=20.8
Q ss_pred EEEcCcCCcceecCCCCCeecCCCCCeEE
Q psy2244 17 EKYYLECHFENEIRPRDPIRCRECGYRIM 45 (73)
Q Consensus 17 ~YiC~~Cg~e~~ik~~d~IRC~~CG~RIL 45 (73)
.+-|.+||..+-++. .+|-.||+++=
T Consensus 3 ~FhC~~CgQ~v~FeN---~~C~~Cg~~Lg 28 (349)
T COG4307 3 DFHCPNCGQRVAFEN---SACLSCGSALG 28 (349)
T ss_pred cccCCCCCCeeeecc---hHHHhhhhHhh
Confidence 467999999887764 78999999765
No 420
>KOG2691|consensus
Probab=24.37 E-value=66 Score=22.24 Aligned_cols=20 Identities=30% Similarity=0.883 Sum_probs=14.5
Q ss_pred CCeecCCCCCe--EEEeeeCCe
Q psy2244 33 DPIRCRECGYR--IMYKKRTKR 52 (73)
Q Consensus 33 d~IRC~~CG~R--ILyKkRt~r 52 (73)
....||.||+| +.|-.+++|
T Consensus 72 s~~~C~~C~~~eavffQ~~~~r 93 (113)
T KOG2691|consen 72 SDKHCPKCGHREAVFFQAQTRR 93 (113)
T ss_pred ccccCCccCCcceEEEeccccc
Confidence 55789999995 666666654
No 421
>PRK10996 thioredoxin 2; Provisional
Probab=24.31 E-value=67 Score=20.96 Aligned_cols=28 Identities=21% Similarity=0.580 Sum_probs=21.6
Q ss_pred EEcCcCCcceecCC---CCCeecCCCCCeEE
Q psy2244 18 KYYLECHFENEIRP---RDPIRCRECGYRIM 45 (73)
Q Consensus 18 YiC~~Cg~e~~ik~---~d~IRC~~CG~RIL 45 (73)
-.|..|..++++.+ -+...|+-||..+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 33 (139)
T PRK10996 3 TVCTSCQAINRLPDERIEDAAKCGRCGHDLF 33 (139)
T ss_pred EECCCCCCcCCCCCccccCCCcCCCCCCccC
Confidence 46888988887763 47788999988665
No 422
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=24.25 E-value=32 Score=24.90 Aligned_cols=7 Identities=43% Similarity=1.203 Sum_probs=4.1
Q ss_pred ecCCCCC
Q psy2244 36 RCRECGY 42 (73)
Q Consensus 36 RC~~CG~ 42 (73)
+||.|+|
T Consensus 2 ~CPfC~~ 8 (156)
T COG1327 2 KCPFCGH 8 (156)
T ss_pred CCCCCCC
Confidence 5666665
No 423
>COG5132 BUD31 Cell cycle control protein, G10 family [Transcription / Cell division and chromosome partitioning]
Probab=24.21 E-value=21 Score=25.46 Aligned_cols=12 Identities=33% Similarity=1.088 Sum_probs=9.8
Q ss_pred CCCeecCCCCCe
Q psy2244 32 RDPIRCRECGYR 43 (73)
Q Consensus 32 ~d~IRC~~CG~R 43 (73)
...++|.+||+|
T Consensus 129 ~qr~kC~hCGCr 140 (146)
T COG5132 129 SQRLKCDHCGCR 140 (146)
T ss_pred HHhccccccCCC
Confidence 356899999987
No 424
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=24.12 E-value=55 Score=24.15 Aligned_cols=10 Identities=50% Similarity=1.099 Sum_probs=5.2
Q ss_pred ecCCCCCeEE
Q psy2244 36 RCRECGYRIM 45 (73)
Q Consensus 36 RC~~CG~RIL 45 (73)
-|+.||..|.
T Consensus 247 pC~~Cg~~I~ 256 (274)
T PRK01103 247 PCRRCGTPIE 256 (274)
T ss_pred CCCCCCCeeE
Confidence 3555555554
No 425
>PRK10445 endonuclease VIII; Provisional
Probab=24.04 E-value=56 Score=24.12 Aligned_cols=15 Identities=27% Similarity=0.414 Sum_probs=8.8
Q ss_pred eecCCCCCeEEEeee
Q psy2244 35 IRCRECGYRIMYKKR 49 (73)
Q Consensus 35 IRC~~CG~RILyKkR 49 (73)
-.||.||..|.-.+-
T Consensus 236 ~~Cp~Cg~~I~~~~~ 250 (263)
T PRK10445 236 EACERCGGIIEKTTL 250 (263)
T ss_pred CCCCCCCCEeEEEEE
Confidence 357777776654433
No 426
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=23.77 E-value=62 Score=17.90 Aligned_cols=6 Identities=33% Similarity=1.182 Sum_probs=2.5
Q ss_pred CeecCC
Q psy2244 34 PIRCRE 39 (73)
Q Consensus 34 ~IRC~~ 39 (73)
.|.|++
T Consensus 9 ~v~C~~ 14 (60)
T PF02176_consen 9 PVPCPN 14 (60)
T ss_dssp EEE-TT
T ss_pred EeeCCC
Confidence 355554
No 427
>TIGR00398 metG methionyl-tRNA synthetase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma
Probab=23.57 E-value=39 Score=26.70 Aligned_cols=36 Identities=17% Similarity=0.185 Sum_probs=22.3
Q ss_pred EcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeE
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCI 54 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~v 54 (73)
+|-.||..++......-+|..||..+.+++...-.+
T Consensus 151 ~ce~cg~~~~~~~l~~p~~~~~~~~~e~~~~~~~f~ 186 (530)
T TIGR00398 151 HCEVCGRHLEPTELINPRCKICGAKPELRDSEHYFF 186 (530)
T ss_pred hhhhccccCCHHHhcCCccccCCCcceEEecceEEE
Confidence 455566555444444457888888888877665443
No 428
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=23.55 E-value=57 Score=24.30 Aligned_cols=22 Identities=23% Similarity=0.357 Sum_probs=10.4
Q ss_pred EcCcCCcceec---CCCCCeecCCC
Q psy2244 19 YYLECHFENEI---RPRDPIRCREC 40 (73)
Q Consensus 19 iC~~Cg~e~~i---k~~d~IRC~~C 40 (73)
-|..||..+.- ..+...-||.|
T Consensus 256 pC~~Cg~~I~~~~~~gR~t~~CP~C 280 (282)
T PRK13945 256 PCRKCGTPIERIKLAGRSTHWCPNC 280 (282)
T ss_pred CCCcCCCeeEEEEECCCccEECCCC
Confidence 45555555331 13444555555
No 429
>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=23.41 E-value=52 Score=18.67 Aligned_cols=8 Identities=38% Similarity=1.136 Sum_probs=4.4
Q ss_pred ecCCCCCe
Q psy2244 36 RCRECGYR 43 (73)
Q Consensus 36 RC~~CG~R 43 (73)
.|..||..
T Consensus 28 ~C~~Cga~ 35 (53)
T TIGR03655 28 ECSTCGAS 35 (53)
T ss_pred ECCCCCCC
Confidence 46666554
No 430
>KOG3404|consensus
Probab=23.31 E-value=34 Score=24.48 Aligned_cols=15 Identities=27% Similarity=0.753 Sum_probs=11.7
Q ss_pred cCCCCCeecCCCCCe
Q psy2244 29 IRPRDPIRCRECGYR 43 (73)
Q Consensus 29 ik~~d~IRC~~CG~R 43 (73)
++....++|.+||+|
T Consensus 126 ld~~~~~~C~hCGCr 140 (145)
T KOG3404|consen 126 LDVERIVECVHCGCR 140 (145)
T ss_pred cChhheeeeeccCcC
Confidence 444567999999986
No 431
>smart00355 ZnF_C2H2 zinc finger.
Probab=23.20 E-value=29 Score=15.28 Aligned_cols=10 Identities=20% Similarity=-0.041 Sum_probs=4.9
Q ss_pred EEcCcCCcce
Q psy2244 18 KYYLECHFEN 27 (73)
Q Consensus 18 YiC~~Cg~e~ 27 (73)
|.|..|+..+
T Consensus 1 ~~C~~C~~~f 10 (26)
T smart00355 1 YRCPECGKVF 10 (26)
T ss_pred CCCCCCcchh
Confidence 3455555443
No 432
>KOG0482|consensus
Probab=23.15 E-value=46 Score=29.01 Aligned_cols=49 Identities=18% Similarity=0.209 Sum_probs=35.6
Q ss_pred CcceEEEcCcCCcceecC-----CCCCeecC--CC-----CCeEEEeeeCCeeEEEeeccC
Q psy2244 13 PGDIEKYYLECHFENEIR-----PRDPIRCR--EC-----GYRIMYKKRTKRCILYFKPQT 61 (73)
Q Consensus 13 ~~~v~YiC~~Cg~e~~ik-----~~d~IRC~--~C-----G~RILyKkRt~r~vqf~~~~~ 61 (73)
-....|.|-.||.|+--. ..+.+.|| +| |.|...--|-.+.+.|-+-+|
T Consensus 177 m~VatYtCd~CGaE~yQeV~s~~F~pl~~CpS~eC~~n~~~G~L~lqtRgSKFikfQe~km 237 (721)
T KOG0482|consen 177 MVVATYTCDQCGAETYQEVNSRTFTPLSECPSEECRTNKAGGRLYLQTRGSKFIKFQEVKM 237 (721)
T ss_pred eEEEEEecccccHhhhccccCccccchhhCChHHhhhcccCCeEEEEecccccchhhhhhH
Confidence 345789999999995433 34667888 55 458888888888887766554
No 433
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=23.07 E-value=56 Score=18.13 Aligned_cols=20 Identities=20% Similarity=0.413 Sum_probs=11.1
Q ss_pred EEcCcCCcceecCCCCCeecCCCC
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECG 41 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG 41 (73)
|.|..|.... +..++|..|.
T Consensus 1 y~C~~C~~~~----~~r~~C~~C~ 20 (41)
T cd02337 1 YTCNECKHHV----ETRWHCTVCE 20 (41)
T ss_pred CcCCCCCCcC----CCceECCCCc
Confidence 4566675522 2456666663
No 434
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=22.86 E-value=50 Score=19.40 Aligned_cols=22 Identities=23% Similarity=0.529 Sum_probs=14.3
Q ss_pred EEcCcCCcceecCCCCCeecC--CCCC
Q psy2244 18 KYYLECHFENEIRPRDPIRCR--ECGY 42 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~--~CG~ 42 (73)
=+|.+||..+..+ ..+|. .|+.
T Consensus 12 rkCp~CGt~NG~R---~~~CKN~~C~~ 35 (44)
T PF14952_consen 12 RKCPKCGTYNGTR---GLSCKNKSCPQ 35 (44)
T ss_pred ccCCcCcCccCcc---cccccCCccch
Confidence 4788998888444 36676 4543
No 435
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.82 E-value=1e+02 Score=20.42 Aligned_cols=41 Identities=20% Similarity=0.325 Sum_probs=24.6
Q ss_pred EcCcCCcceecCCC---CCeecCCCCC---------eEEEeeeCCeeEEEeec
Q psy2244 19 YYLECHFENEIRPR---DPIRCRECGY---------RIMYKKRTKRCILYFKP 59 (73)
Q Consensus 19 iC~~Cg~e~~ik~~---d~IRC~~CG~---------RILyKkRt~r~vqf~~~ 59 (73)
.|..|+.+...... ..-.||.|+. +||=+.|-.+...|..|
T Consensus 3 lCP~C~v~l~~~~rs~vEiD~CPrCrGVWLDrGELdKli~r~r~pqpa~ys~~ 55 (88)
T COG3809 3 LCPICGVELVMSVRSGVEIDYCPRCRGVWLDRGELDKLIERSRYPQPAEYSQP 55 (88)
T ss_pred ccCcCCceeeeeeecCceeeeCCccccEeecchhHHHHHHHhcCCCCcccCCc
Confidence 57888887655533 3347888887 45555554444444444
No 436
>smart00078 IlGF Insulin / insulin-like growth factor / relaxin family. Family of proteins including insulin, relaxin, and IGFs. Insulin decreases blood glucose concentration.
Probab=22.58 E-value=6.4 Score=23.83 Aligned_cols=20 Identities=25% Similarity=0.096 Sum_probs=16.5
Q ss_pred ceeccccCCcceEEEcCcCC
Q psy2244 5 QVLVGKCLPGDIEKYYLECH 24 (73)
Q Consensus 5 ~~l~~~~~~~~v~YiC~~Cg 24 (73)
+.|||.+|.....++|++=|
T Consensus 1 ~~lCG~~Lv~al~~vCg~~g 20 (66)
T smart00078 1 QHLCGRHLVRALYLVCGERG 20 (66)
T ss_pred CcccHHHHHHHHHHHccccC
Confidence 46899999999999997744
No 437
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=22.52 E-value=77 Score=19.63 Aligned_cols=25 Identities=28% Similarity=0.568 Sum_probs=16.9
Q ss_pred EcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 19 YYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 19 iC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
+|.-|.+-+-......|.| .||-||
T Consensus 1 iCPVC~~~~L~~~~~~i~C-~Cgl~l 25 (82)
T PF14768_consen 1 ICPVCQKGNLRENSNVISC-SCGLRL 25 (82)
T ss_pred CCCccCCCcccccCCeEEC-CCccEE
Confidence 3666766666667778888 667554
No 438
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=22.50 E-value=52 Score=18.89 Aligned_cols=20 Identities=20% Similarity=0.190 Sum_probs=12.0
Q ss_pred eccccCCcc----eEEEcCcCCcc
Q psy2244 7 LVGKCLPGD----IEKYYLECHFE 26 (73)
Q Consensus 7 l~~~~~~~~----v~YiC~~Cg~e 26 (73)
+||+..++. -.++|.+|-.+
T Consensus 4 iC~~~~~~GI~I~~~fIC~~CE~~ 27 (46)
T PF10764_consen 4 ICGKEKEEGIHIYGKFICSDCEKE 27 (46)
T ss_pred eCCCcCCCCEEEECeEehHHHHHH
Confidence 455555543 35778888555
No 439
>PLN02189 cellulose synthase
Probab=22.47 E-value=62 Score=29.46 Aligned_cols=29 Identities=21% Similarity=0.409 Sum_probs=21.5
Q ss_pred eEEEcCcCCcceecCCCC--CeecCCCCCeE
Q psy2244 16 IEKYYLECHFENEIRPRD--PIRCRECGYRI 44 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d--~IRC~~CG~RI 44 (73)
...+|--||.++.++... =|-|.+||+-|
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpv 63 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPV 63 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCcc
Confidence 456899999998887543 27888887743
No 440
>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=22.24 E-value=53 Score=19.97 Aligned_cols=18 Identities=33% Similarity=0.495 Sum_probs=13.2
Q ss_pred CCeecCCCCCeEEEeeeC
Q psy2244 33 DPIRCRECGYRIMYKKRT 50 (73)
Q Consensus 33 d~IRC~~CG~RILyKkRt 50 (73)
+.-.|..||.|+..+.+.
T Consensus 4 ~~~~C~~Cg~r~~~~~k~ 21 (69)
T PF09706_consen 4 KKYNCIFCGERPSKKKKG 21 (69)
T ss_pred CCCcCcCCCCcccccccc
Confidence 456788888887777665
No 441
>PF15494 SRCR_2: Scavenger receptor cysteine-rich domain
Probab=22.16 E-value=45 Score=20.73 Aligned_cols=25 Identities=20% Similarity=0.517 Sum_probs=15.7
Q ss_pred ceEEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 15 DIEKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 15 ~v~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
...+.-..|....-+ .++|..||.|
T Consensus 73 ~~~~~~~~C~S~~vV----sL~C~~CG~r 97 (98)
T PF15494_consen 73 QSLSPSSSCSSGSVV----SLQCSDCGKR 97 (98)
T ss_pred EEEecCCCCCCCCEE----EEECcccCCc
Confidence 445566677333222 3789999987
No 442
>PRK08173 DNA topoisomerase III; Validated
Probab=22.14 E-value=58 Score=28.39 Aligned_cols=26 Identities=15% Similarity=0.305 Sum_probs=18.4
Q ss_pred EEcCcCCcceecCCCCCeecCCCCCeE
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
=.|..||..+ ........|.+|++.|
T Consensus 625 ~~CP~Cg~~~-~~~~~~~~Cs~C~f~~ 650 (862)
T PRK08173 625 TPCPNCGGVV-KENYRRFACTKCDFSI 650 (862)
T ss_pred ccCCcccccc-cccCceeEcCCCCccc
Confidence 3699998865 3333448899998876
No 443
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=22.13 E-value=52 Score=15.35 Aligned_cols=9 Identities=33% Similarity=1.206 Sum_probs=4.7
Q ss_pred ecCCCCCeE
Q psy2244 36 RCRECGYRI 44 (73)
Q Consensus 36 RC~~CG~RI 44 (73)
+|+.|.+.-
T Consensus 2 ~C~~C~y~t 10 (24)
T PF13909_consen 2 KCPHCSYST 10 (24)
T ss_dssp E-SSSS-EE
T ss_pred CCCCCCCcC
Confidence 677777654
No 444
>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=21.85 E-value=84 Score=21.30 Aligned_cols=18 Identities=39% Similarity=0.455 Sum_probs=15.3
Q ss_pred CeEEEeeeCCeeEEEeec
Q psy2244 42 YRIMYKKRTKRCILYFKP 59 (73)
Q Consensus 42 ~RILyKkRt~r~vqf~~~ 59 (73)
+-|+++||++..-||+=-
T Consensus 32 ~~i~f~KRt~GirqfEi~ 49 (103)
T PF09158_consen 32 YEIRFKKRTKGIRQFEIR 49 (103)
T ss_dssp EEEEEEEEETTEEEEEEE
T ss_pred eEEeeecccCceeEEEEe
Confidence 578999999999999753
No 445
>PLN02195 cellulose synthase A
Probab=21.83 E-value=61 Score=29.32 Aligned_cols=25 Identities=24% Similarity=0.583 Sum_probs=15.3
Q ss_pred EcCcCCcceecCCC-C-CeecCCCCCe
Q psy2244 19 YYLECHFENEIRPR-D-PIRCRECGYR 43 (73)
Q Consensus 19 iC~~Cg~e~~ik~~-d-~IRC~~CG~R 43 (73)
+|.-||.++.++.. + =|-|.+||+.
T Consensus 8 ~c~~cgd~~~~~~~g~~fvaC~eC~~p 34 (977)
T PLN02195 8 ICATCGEEVGVDSNGEAFVACHECSYP 34 (977)
T ss_pred cceecccccCcCCCCCeEEEeccCCCc
Confidence 56677777766643 2 2667777653
No 446
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=21.79 E-value=42 Score=20.32 Aligned_cols=16 Identities=19% Similarity=0.372 Sum_probs=9.9
Q ss_pred cCCcceEEEcCcCCcc
Q psy2244 11 CLPGDIEKYYLECHFE 26 (73)
Q Consensus 11 ~~~~~v~YiC~~Cg~e 26 (73)
.++..+.|-|.+||-.
T Consensus 8 ~~~~~v~~~Cp~cGip 23 (55)
T PF13824_consen 8 DLPAHVNFECPDCGIP 23 (55)
T ss_pred ccccccCCcCCCCCCc
Confidence 3455666777777654
No 447
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=21.55 E-value=48 Score=15.92 Aligned_cols=22 Identities=27% Similarity=0.448 Sum_probs=13.7
Q ss_pred EEcCcCCcceecCCCCCeecCCCCC
Q psy2244 18 KYYLECHFENEIRPRDPIRCRECGY 42 (73)
Q Consensus 18 YiC~~Cg~e~~ik~~d~IRC~~CG~ 42 (73)
-.|..|+..|.... ..|-.|+.
T Consensus 3 W~C~~C~~~N~~~~---~~C~~C~~ 24 (26)
T smart00547 3 WECPACTFLNFASR---SKCFACGA 24 (26)
T ss_pred ccCCCCCCcChhhh---ccccccCC
Confidence 35777876665543 56766664
No 448
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=21.52 E-value=34 Score=21.77 Aligned_cols=19 Identities=32% Similarity=0.835 Sum_probs=15.9
Q ss_pred CCeecCCCCCeEEEeeeCC
Q psy2244 33 DPIRCRECGYRIMYKKRTK 51 (73)
Q Consensus 33 d~IRC~~CG~RILyKkRt~ 51 (73)
-.|.|.+|||-=+|+..+.
T Consensus 39 ~~itCk~CgYtEfY~a~~s 57 (68)
T COG3478 39 IVITCKNCGYTEFYSAKIS 57 (68)
T ss_pred EEEEeccCCchhheecccc
Confidence 4689999999999987654
No 449
>PRK02935 hypothetical protein; Provisional
Probab=21.38 E-value=63 Score=22.26 Aligned_cols=27 Identities=11% Similarity=0.265 Sum_probs=18.3
Q ss_pred eEEEcCcCCcceecCCCCCeecCCCCCe
Q psy2244 16 IEKYYLECHFENEIRPRDPIRCRECGYR 43 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~R 43 (73)
+.-.|.+|+++...-. ..-+|.+|+-.
T Consensus 69 vqV~CP~C~K~TKmLG-rvD~CM~C~~P 95 (110)
T PRK02935 69 VQVICPSCEKPTKMLG-RVDACMHCNQP 95 (110)
T ss_pred eeeECCCCCchhhhcc-ceeecCcCCCc
Confidence 4557889988876442 33488888753
No 450
>KOG0480|consensus
Probab=21.34 E-value=1.2e+02 Score=27.00 Aligned_cols=45 Identities=11% Similarity=0.270 Sum_probs=30.1
Q ss_pred CCcceEEEcCcCCccee-----cCCCCCeecCC--CCCeEEEeeeCCeeEEEe
Q psy2244 12 LPGDIEKYYLECHFENE-----IRPRDPIRCRE--CGYRIMYKKRTKRCILYF 57 (73)
Q Consensus 12 ~~~~v~YiC~~Cg~e~~-----ik~~d~IRC~~--CG~RILyKkRt~r~vqf~ 57 (73)
..-.+.+.|.+||..+. .+-..|-.||+ |..|=.|+.=... .+|.
T Consensus 152 elt~~~F~C~~C~t~i~~v~q~fkYt~Pt~C~np~C~nrr~f~l~~~~-s~f~ 203 (764)
T KOG0480|consen 152 ELTKMTFLCEKCGTVIRNVEQQFKYTEPTKCPNPVCSNRRSFTLDRSS-SRFL 203 (764)
T ss_pred eeeeeEEEHhhCCCeeccchhcCccCCCccCCCccccCCceeeeeccc-ceee
Confidence 34458899999999865 34568999995 6665566554333 4443
No 451
>KOG0402|consensus
Probab=21.21 E-value=21 Score=23.88 Aligned_cols=31 Identities=13% Similarity=0.173 Sum_probs=21.1
Q ss_pred cCCcceEEEcCcCCcceecC-CCCCeecCCCC
Q psy2244 11 CLPGDIEKYYLECHFENEIR-PRDPIRCRECG 41 (73)
Q Consensus 11 ~~~~~v~YiC~~Cg~e~~ik-~~d~IRC~~CG 41 (73)
++.+-..|.|.-||+..--+ ....-.|..|.
T Consensus 30 ei~Qhaky~CsfCGK~~vKR~AvGiW~C~~C~ 61 (92)
T KOG0402|consen 30 EIQQHAKYTCSFCGKKTVKRKAVGIWKCGSCK 61 (92)
T ss_pred HHHHhhhhhhhhcchhhhhhhceeEEecCCcc
Confidence 34566789999999885444 44555677664
No 452
>TIGR00201 comF comF family protein. This protein is found in species that do (Bacillus subtilis, Haemophilus influenzae) or do not (E. coli, Borrelia burgdorferi) have described systems for natural transformation with exogenous DNA. It is involved in competence for transformation in Bacillus subtilis.
Probab=21.19 E-value=44 Score=22.97 Aligned_cols=22 Identities=23% Similarity=0.344 Sum_probs=10.8
Q ss_pred cCcCCcceecCCCCCeecCCCCCeE
Q psy2244 20 YLECHFENEIRPRDPIRCRECGYRI 44 (73)
Q Consensus 20 C~~Cg~e~~ik~~d~IRC~~CG~RI 44 (73)
|..||+.+.. +...|+.|...+
T Consensus 1 C~~C~~~~~~---~~~~C~~C~~~~ 22 (190)
T TIGR00201 1 CSLCGRPYQS---VHALCRQCGSWR 22 (190)
T ss_pred CCcccccccc---ccCCchhhCCcc
Confidence 5556654322 124566665543
No 453
>KOG4684|consensus
Probab=21.09 E-value=52 Score=25.62 Aligned_cols=31 Identities=16% Similarity=0.234 Sum_probs=22.6
Q ss_pred CCcceEEEcCcCCcceecCC--CCCeecCCCCC
Q psy2244 12 LPGDIEKYYLECHFENEIRP--RDPIRCRECGY 42 (73)
Q Consensus 12 ~~~~v~YiC~~Cg~e~~ik~--~d~IRC~~CG~ 42 (73)
.|.-..-+|+.|...+-... ....|||+|..
T Consensus 165 ~P~gcRV~CgHC~~tFLfnt~tnaLArCPHCrK 197 (275)
T KOG4684|consen 165 APTGCRVKCGHCNETFLFNTLTNALARCPHCRK 197 (275)
T ss_pred CCcceEEEecCccceeehhhHHHHHhcCCcccc
Confidence 34456789999988876652 36689999964
No 454
>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=20.80 E-value=88 Score=16.11 Aligned_cols=10 Identities=30% Similarity=0.394 Sum_probs=6.0
Q ss_pred eecCCCCCeE
Q psy2244 35 IRCRECGYRI 44 (73)
Q Consensus 35 IRC~~CG~RI 44 (73)
-+|..||.++
T Consensus 12 ~~C~~c~~~~ 21 (57)
T cd00085 12 GLCPYCGKPG 21 (57)
T ss_pred CcCccCCCcC
Confidence 3566666655
No 455
>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=20.56 E-value=62 Score=16.88 Aligned_cols=26 Identities=19% Similarity=0.294 Sum_probs=9.8
Q ss_pred cCCCCCeEEEeeeCCeeEEEeeccCCCC
Q psy2244 37 CRECGYRIMYKKRTKRCILYFKPQTGGF 64 (73)
Q Consensus 37 C~~CG~RILyKkRt~r~vqf~~~~~~~~ 64 (73)
|+.||..+-.. ..-.+....|...|.
T Consensus 1 C~~C~~~~~~~--~~~~v~Hi~~~~~gg 26 (47)
T PF01844_consen 1 CQYCGKPGSDN--ESLHVHHIIPRSKGG 26 (47)
T ss_dssp -TTT--B--GG---GEEEEESS-TTTT-
T ss_pred CCCCCCcCccC--cceEeECcCchhcCC
Confidence 56666655444 344555556655443
No 456
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.54 E-value=42 Score=23.60 Aligned_cols=17 Identities=24% Similarity=0.530 Sum_probs=11.1
Q ss_pred CCCCCeecCCCCCeEEE
Q psy2244 30 RPRDPIRCRECGYRIMY 46 (73)
Q Consensus 30 k~~d~IRC~~CG~RILy 46 (73)
+.+-.-|||+||.-=||
T Consensus 17 ~~Gl~grCP~CGeGrLF 33 (126)
T COG5349 17 KRGLRGRCPRCGEGRLF 33 (126)
T ss_pred HHHhcCCCCCCCCchhh
Confidence 34445689999974443
No 457
>KOG2767|consensus
Probab=20.53 E-value=34 Score=28.04 Aligned_cols=33 Identities=24% Similarity=0.488 Sum_probs=23.8
Q ss_pred EcCcCCcc---eecCC--CCCeecCCCCCeEEEeeeCC
Q psy2244 19 YYLECHFE---NEIRP--RDPIRCRECGYRIMYKKRTK 51 (73)
Q Consensus 19 iC~~Cg~e---~~ik~--~d~IRC~~CG~RILyKkRt~ 51 (73)
.|..|+.. .-+.. .=...|.-||+|-...-|.+
T Consensus 98 lC~~C~NPETel~itk~q~i~~~CkACG~r~~~d~rhK 135 (400)
T KOG2767|consen 98 LCPSCENPETELIITKKQTISLKCKACGFRSDMDLRHK 135 (400)
T ss_pred eCcCCCCCceeEEecccchhhhHHHHcCCcccccchhh
Confidence 68899765 22332 34478999999999888876
No 458
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=20.47 E-value=55 Score=25.61 Aligned_cols=24 Identities=21% Similarity=0.337 Sum_probs=17.6
Q ss_pred EEcCcCCcceecC----CCCCeecCCCCC
Q psy2244 18 KYYLECHFENEIR----PRDPIRCRECGY 42 (73)
Q Consensus 18 YiC~~Cg~e~~ik----~~d~IRC~~CG~ 42 (73)
=+|++||+.+ .. .....-|-+|..
T Consensus 21 k~CaDCga~~-P~W~S~nlGvfiCi~Cag 48 (319)
T COG5347 21 KKCADCGAPN-PTWASVNLGVFLCIDCAG 48 (319)
T ss_pred CccccCCCCC-CceEecccCeEEEeecch
Confidence 3699999887 44 346788888863
No 459
>PF14996 RMP: Retinal Maintenance
Probab=20.43 E-value=63 Score=23.00 Aligned_cols=15 Identities=33% Similarity=1.019 Sum_probs=13.1
Q ss_pred CCCeecCCCCCeEEE
Q psy2244 32 RDPIRCRECGYRIMY 46 (73)
Q Consensus 32 ~d~IRC~~CG~RILy 46 (73)
=+.+||..|.++|+.
T Consensus 66 C~~LrC~~CDf~V~~ 80 (146)
T PF14996_consen 66 CDNLRCTKCDFRVVR 80 (146)
T ss_pred CCCCEEecCCcEEEE
Confidence 388999999999874
No 460
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=20.33 E-value=72 Score=18.87 Aligned_cols=15 Identities=13% Similarity=0.005 Sum_probs=7.0
Q ss_pred eEEEcCcCCcceecC
Q psy2244 16 IEKYYLECHFENEIR 30 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik 30 (73)
..|.|.+|+..+=++
T Consensus 20 ~~y~C~~C~~~FC~d 34 (51)
T PF07975_consen 20 SRYRCPKCKNHFCID 34 (51)
T ss_dssp EEE--TTTT--B-HH
T ss_pred CeEECCCCCCccccC
Confidence 678888887765433
No 461
>PRK07220 DNA topoisomerase I; Validated
Probab=20.26 E-value=1.1e+02 Score=26.04 Aligned_cols=12 Identities=8% Similarity=-0.017 Sum_probs=7.0
Q ss_pred EEcCcCCcceec
Q psy2244 18 KYYLECHFENEI 29 (73)
Q Consensus 18 YiC~~Cg~e~~i 29 (73)
-.|..||....+
T Consensus 590 ~~CP~Cg~~l~~ 601 (740)
T PRK07220 590 GKCPLCGSDLMV 601 (740)
T ss_pred cccccCCCeeeE
Confidence 367777665444
No 462
>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=20.18 E-value=51 Score=22.57 Aligned_cols=21 Identities=29% Similarity=0.793 Sum_probs=12.2
Q ss_pred CCeecCCCCCeEEEeeeCCeeEEE
Q psy2244 33 DPIRCRECGYRIMYKKRTKRCILY 56 (73)
Q Consensus 33 d~IRC~~CG~RILyKkRt~r~vqf 56 (73)
.+|+|.+||..+ ++.+.+..|
T Consensus 19 ~~V~C~nCgr~v---PKDKAIkrf 39 (113)
T PF01283_consen 19 QPVRCDNCGRCV---PKDKAIKRF 39 (113)
T ss_dssp -EEE-TTTB-EE---ECCCSEEEE
T ss_pred cCEeeCcccccC---cCCceEEEE
Confidence 679999999866 444444444
No 463
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.16 E-value=63 Score=21.84 Aligned_cols=9 Identities=33% Similarity=1.172 Sum_probs=5.3
Q ss_pred CeecCCCCC
Q psy2244 34 PIRCRECGY 42 (73)
Q Consensus 34 ~IRC~~CG~ 42 (73)
--+|+.|+.
T Consensus 53 RyrC~~C~~ 61 (129)
T COG3677 53 RYKCKSCGS 61 (129)
T ss_pred ccccCCcCc
Confidence 345666665
No 464
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=20.12 E-value=93 Score=27.04 Aligned_cols=12 Identities=25% Similarity=0.631 Sum_probs=6.4
Q ss_pred CeecCCCCCeEE
Q psy2244 34 PIRCRECGYRIM 45 (73)
Q Consensus 34 ~IRC~~CG~RIL 45 (73)
...||.||..-|
T Consensus 592 ~~~CP~Cg~~~L 603 (860)
T PRK06319 592 EIDCPKCHKGKL 603 (860)
T ss_pred CcccCCCCCcce
Confidence 356666654333
No 465
>PLN02436 cellulose synthase A
Probab=20.08 E-value=74 Score=29.18 Aligned_cols=29 Identities=21% Similarity=0.417 Sum_probs=22.0
Q ss_pred eEEEcCcCCcceecCCCC--CeecCCCCCeE
Q psy2244 16 IEKYYLECHFENEIRPRD--PIRCRECGYRI 44 (73)
Q Consensus 16 v~YiC~~Cg~e~~ik~~d--~IRC~~CG~RI 44 (73)
..-+|--||.++.+.... =|-|.+||+-|
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpv 65 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPV 65 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCcc
Confidence 456999999999887442 28899998744
No 466
>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=20.03 E-value=63 Score=17.11 Aligned_cols=16 Identities=31% Similarity=0.843 Sum_probs=9.6
Q ss_pred CCCeecCCCCCeEEEe
Q psy2244 32 RDPIRCRECGYRIMYK 47 (73)
Q Consensus 32 ~d~IRC~~CG~RILyK 47 (73)
...++|.+|+..+-+.
T Consensus 14 ~~~a~C~~C~~~~~~~ 29 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYS 29 (45)
T ss_dssp SS-EEETTTTEE----
T ss_pred cCeEEeCCCCeEEeeC
Confidence 5679999999877665
Done!