Query 035461
Match_columns 51
No_of_seqs 102 out of 204
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 03:07:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035461.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035461hhsearch_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 4.9E-26 1.1E-30 120.0 5.7 44 8-51 1-44 (44)
2 KOG3507 DNA-directed RNA polym 99.9 1.7E-26 3.8E-31 129.3 -0.2 47 5-51 16-62 (62)
3 COG1996 RPC10 DNA-directed RNA 99.8 1.8E-21 4E-26 105.1 5.0 46 6-51 3-49 (49)
4 PF03604 DNA_RNApol_7kD: DNA d 99.8 8E-21 1.7E-25 94.8 1.8 32 10-41 1-32 (32)
5 PRK00398 rpoP DNA-directed RNA 99.6 9.7E-15 2.1E-19 76.2 5.1 44 8-51 2-46 (46)
6 smart00834 CxxC_CXXC_SSSS Puta 98.1 3.5E-06 7.6E-11 41.8 2.4 28 8-35 4-35 (41)
7 PF09723 Zn-ribbon_8: Zinc rib 98.0 7E-06 1.5E-10 42.1 2.6 28 8-35 4-35 (42)
8 TIGR02605 CxxC_CxxC_SSSS putat 97.9 2.8E-05 6E-10 40.6 3.9 28 8-35 4-35 (52)
9 TIGR02098 MJ0042_CXXC MJ0042 f 97.8 5.7E-05 1.2E-09 37.3 3.9 30 8-37 1-36 (38)
10 PRK03824 hypA hydrogenase nick 97.4 0.00017 3.7E-09 44.7 2.8 32 5-36 66-117 (135)
11 smart00531 TFIIE Transcription 97.4 0.00033 7.1E-09 43.5 4.0 41 4-44 94-141 (147)
12 PF13717 zinc_ribbon_4: zinc-r 97.3 0.00042 9E-09 34.7 3.4 29 8-36 1-35 (36)
13 PF09538 FYDLN_acid: Protein o 97.3 0.00016 3.4E-09 43.9 1.7 36 1-36 1-36 (108)
14 PF13719 zinc_ribbon_5: zinc-r 97.2 0.00078 1.7E-08 33.7 3.5 29 8-36 1-35 (37)
15 PRK00564 hypA hydrogenase nick 97.2 0.00025 5.3E-09 43.0 1.8 33 5-37 67-99 (117)
16 PF13248 zf-ribbon_3: zinc-rib 97.1 0.00012 2.6E-09 34.3 -0.1 25 9-36 2-26 (26)
17 PRK03681 hypA hydrogenase nick 97.0 0.00059 1.3E-08 41.2 2.5 32 5-36 66-97 (114)
18 PF01155 HypA: Hydrogenase exp 97.0 0.00023 4.9E-09 42.8 0.6 32 5-37 66-97 (113)
19 PF10571 UPF0547: Uncharacteri 96.9 0.00039 8.5E-09 32.9 0.9 22 11-35 2-23 (26)
20 cd00729 rubredoxin_SM Rubredox 96.8 0.0013 2.8E-08 32.5 2.4 27 8-35 1-27 (34)
21 PF09297 zf-NADH-PPase: NADH p 96.8 0.0012 2.6E-08 31.9 2.2 25 12-36 6-31 (32)
22 TIGR01206 lysW lysine biosynth 96.8 0.0015 3.3E-08 35.6 2.7 33 8-40 1-36 (54)
23 PF13240 zinc_ribbon_2: zinc-r 96.8 0.00046 1E-08 31.7 0.5 23 11-36 1-23 (23)
24 cd00350 rubredoxin_like Rubred 96.8 0.0014 3E-08 32.0 2.2 25 9-34 1-25 (33)
25 PRK12380 hydrogenase nickel in 96.7 0.0015 3.2E-08 39.4 2.6 30 5-35 66-95 (113)
26 PRK06266 transcription initiat 96.7 0.0012 2.7E-08 42.5 2.1 37 3-39 111-149 (178)
27 COG1579 Zn-ribbon protein, pos 96.6 0.0005 1.1E-08 46.7 -0.0 30 10-40 198-234 (239)
28 TIGR02300 FYDLN_acid conserved 96.6 0.0014 3.1E-08 41.3 1.8 36 1-36 1-36 (129)
29 TIGR00373 conserved hypothetic 96.5 0.0016 3.5E-08 41.1 1.9 37 3-39 103-141 (158)
30 TIGR00100 hypA hydrogenase nic 96.5 0.0028 6.1E-08 38.2 2.6 31 5-36 66-96 (115)
31 PF07295 DUF1451: Protein of u 96.4 0.004 8.6E-08 39.4 3.1 34 5-38 108-142 (146)
32 COG1439 Predicted nucleic acid 96.4 0.0034 7.4E-08 41.2 2.7 32 8-42 138-169 (177)
33 PF07754 DUF1610: Domain of un 96.3 0.0039 8.5E-08 29.2 1.9 23 12-34 1-24 (24)
34 PF08274 PhnA_Zn_Ribbon: PhnA 96.3 0.0022 4.8E-08 31.4 1.1 26 11-36 4-29 (30)
35 PRK00762 hypA hydrogenase nick 96.2 0.0036 7.7E-08 38.3 2.0 31 5-36 66-102 (124)
36 COG2888 Predicted Zn-ribbon RN 96.0 0.0098 2.1E-07 33.4 3.0 27 8-34 26-58 (61)
37 PRK12496 hypothetical protein; 95.9 0.004 8.6E-08 39.6 1.4 31 8-39 126-156 (164)
38 PRK14890 putative Zn-ribbon RN 95.8 0.017 3.6E-07 32.3 3.5 28 10-37 8-36 (59)
39 PF14446 Prok-RING_1: Prokaryo 95.6 0.0082 1.8E-07 32.9 1.6 26 8-34 4-29 (54)
40 COG1096 Predicted RNA-binding 95.6 0.016 3.4E-07 38.5 3.2 31 8-39 148-178 (188)
41 PRK14890 putative Zn-ribbon RN 95.5 0.019 4E-07 32.1 2.7 29 7-35 23-57 (59)
42 PF08271 TF_Zn_Ribbon: TFIIB z 95.4 0.015 3.3E-07 29.4 2.2 27 10-36 1-29 (43)
43 PF09845 DUF2072: Zn-ribbon co 95.1 0.0069 1.5E-07 38.3 0.4 31 10-40 2-33 (131)
44 PF08792 A2L_zn_ribbon: A2L zi 95.0 0.03 6.6E-07 27.6 2.5 26 9-34 3-29 (33)
45 PF12773 DZR: Double zinc ribb 94.9 0.01 2.2E-07 30.4 0.5 25 11-35 14-38 (50)
46 COG0375 HybF Zn finger protein 94.8 0.027 5.9E-07 34.8 2.3 30 5-35 66-95 (115)
47 smart00661 RPOL9 RNA polymeras 94.7 0.031 6.7E-07 28.5 2.1 24 12-35 3-29 (52)
48 PF07282 OrfB_Zn_ribbon: Putat 94.6 0.033 7.3E-07 30.0 2.1 25 11-35 30-55 (69)
49 COG1645 Uncharacterized Zn-fin 94.5 0.048 1E-06 34.4 3.1 31 9-40 28-58 (131)
50 COG2888 Predicted Zn-ribbon RN 94.5 0.045 9.8E-07 30.8 2.6 29 11-39 11-40 (61)
51 PRK00420 hypothetical protein; 94.5 0.043 9.4E-07 33.7 2.7 31 10-40 24-54 (112)
52 PF13451 zf-trcl: Probable zin 94.4 0.017 3.7E-07 31.0 0.8 26 8-33 3-40 (49)
53 COG1592 Rubrerythrin [Energy p 94.4 0.031 6.7E-07 36.3 2.1 25 9-35 134-158 (166)
54 PF02318 FYVE_2: FYVE-type zin 94.3 0.029 6.3E-07 33.6 1.7 29 8-36 53-81 (118)
55 PF14369 zf-RING_3: zinc-finge 94.3 0.065 1.4E-06 26.6 2.7 29 9-37 2-32 (35)
56 PF10263 SprT-like: SprT-like 94.2 0.071 1.5E-06 32.2 3.2 34 6-39 120-156 (157)
57 PF09082 DUF1922: Domain of un 94.1 0.059 1.3E-06 30.8 2.6 33 8-42 2-35 (68)
58 TIGR00686 phnA alkylphosphonat 94.1 0.038 8.1E-07 34.1 1.9 25 11-35 4-28 (109)
59 PRK00432 30S ribosomal protein 94.0 0.049 1.1E-06 28.9 2.1 27 11-37 22-48 (50)
60 PRK06450 threonine synthase; V 94.0 0.046 1E-06 37.8 2.4 29 8-38 2-30 (338)
61 PF06397 Desulfoferrod_N: Desu 94.0 0.061 1.3E-06 27.2 2.2 25 8-34 5-31 (36)
62 PRK07591 threonine synthase; V 93.9 0.063 1.4E-06 38.0 3.0 30 8-39 17-46 (421)
63 COG1571 Predicted DNA-binding 93.8 0.029 6.2E-07 40.9 1.1 32 11-42 352-383 (421)
64 PF09855 DUF2082: Nucleic-acid 93.7 0.068 1.5E-06 29.9 2.4 21 25-45 35-55 (64)
65 PF10122 Mu-like_Com: Mu-like 93.7 0.034 7.4E-07 30.2 1.0 29 9-37 4-35 (51)
66 PHA02768 hypothetical protein; 93.7 0.045 9.8E-07 30.0 1.5 40 8-50 4-52 (55)
67 PF14353 CpXC: CpXC protein 93.5 0.09 2E-06 31.4 2.8 26 11-36 3-48 (128)
68 COG3364 Zn-ribbon containing p 93.5 0.014 3.1E-07 36.0 -0.7 32 8-39 1-34 (112)
69 PRK11032 hypothetical protein; 93.5 0.07 1.5E-06 34.4 2.4 33 6-38 121-154 (160)
70 PRK10220 hypothetical protein; 93.4 0.074 1.6E-06 32.9 2.3 25 11-35 5-29 (111)
71 cd00730 rubredoxin Rubredoxin; 93.0 0.069 1.5E-06 28.5 1.5 26 9-34 1-42 (50)
72 COG3357 Predicted transcriptio 92.8 0.049 1.1E-06 33.0 0.9 25 11-35 60-85 (97)
73 PF05207 zf-CSL: CSL zinc fing 92.8 0.25 5.5E-06 26.5 3.6 35 3-38 12-52 (55)
74 COG2331 Uncharacterized protei 92.8 0.027 5.8E-07 33.2 -0.3 28 8-35 11-42 (82)
75 TIGR01384 TFS_arch transcripti 92.7 0.091 2E-06 30.4 1.9 25 11-36 2-26 (104)
76 PRK06260 threonine synthase; V 92.7 0.13 2.7E-06 36.0 2.9 29 9-38 3-31 (397)
77 PF12172 DUF35_N: Rubredoxin-l 92.6 0.15 3.3E-06 24.8 2.3 26 7-35 9-34 (37)
78 PHA00626 hypothetical protein 92.5 0.14 3E-06 28.6 2.4 26 11-36 2-33 (59)
79 COG2816 NPY1 NTP pyrophosphohy 92.3 0.089 1.9E-06 36.6 1.8 27 11-37 113-140 (279)
80 PF02591 DUF164: Putative zinc 92.2 0.09 2E-06 27.8 1.4 23 11-33 24-53 (56)
81 PF05191 ADK_lid: Adenylate ki 92.2 0.096 2.1E-06 26.2 1.4 28 10-37 2-32 (36)
82 PF00301 Rubredoxin: Rubredoxi 92.0 0.16 3.4E-06 26.8 2.1 27 9-35 1-43 (47)
83 smart00731 SprT SprT homologue 92.0 0.24 5.3E-06 30.3 3.2 32 7-38 110-145 (146)
84 PRK04351 hypothetical protein; 91.9 0.37 8E-06 30.4 4.1 34 6-39 109-145 (149)
85 PRK04136 rpl40e 50S ribosomal 91.9 0.069 1.5E-06 28.8 0.7 27 8-37 13-39 (48)
86 TIGR00416 sms DNA repair prote 91.9 0.14 2.9E-06 36.9 2.3 31 7-40 5-35 (454)
87 COG1326 Uncharacterized archae 91.8 0.2 4.2E-06 33.7 2.9 31 5-35 2-39 (201)
88 PRK14714 DNA polymerase II lar 91.7 0.1 2.2E-06 42.7 1.6 29 9-37 692-720 (1337)
89 PRK11823 DNA repair protein Ra 91.6 0.15 3.3E-06 36.5 2.4 32 7-41 5-36 (446)
90 COG2051 RPS27A Ribosomal prote 91.5 0.44 9.6E-06 27.2 3.7 31 8-38 18-50 (67)
91 PF12760 Zn_Tnp_IS1595: Transp 91.4 0.24 5.2E-06 25.3 2.4 22 21-42 13-34 (46)
92 PRK00415 rps27e 30S ribosomal 91.2 0.36 7.8E-06 26.8 3.1 29 8-36 10-40 (59)
93 COG1379 PHP family phosphoeste 91.2 0.044 9.6E-07 39.7 -0.7 26 11-36 248-275 (403)
94 PRK09521 exosome complex RNA-b 91.0 0.36 7.8E-06 30.8 3.4 30 8-37 148-177 (189)
95 PF11781 RRN7: RNA polymerase 91.0 0.23 5.1E-06 24.7 2.0 25 11-35 10-34 (36)
96 COG5216 Uncharacterized conser 90.6 0.36 7.7E-06 27.4 2.8 31 3-34 16-52 (67)
97 PF13408 Zn_ribbon_recom: Reco 90.3 0.46 9.9E-06 24.2 2.9 20 25-44 4-23 (58)
98 PF10058 DUF2296: Predicted in 90.2 0.43 9.4E-06 25.7 2.8 31 5-35 18-53 (54)
99 cd01121 Sms Sms (bacterial rad 90.2 0.15 3.3E-06 35.9 1.2 29 10-41 1-29 (372)
100 PF14803 Nudix_N_2: Nudix N-te 90.1 0.19 4.2E-06 24.9 1.3 23 12-34 3-30 (34)
101 COG1545 Predicted nucleic-acid 89.8 0.7 1.5E-05 28.7 3.9 30 8-40 28-58 (140)
102 PF07191 zinc-ribbons_6: zinc- 89.8 0.35 7.5E-06 27.7 2.3 25 8-36 16-40 (70)
103 PHA02942 putative transposase; 89.7 0.31 6.7E-06 34.5 2.5 25 11-35 327-351 (383)
104 TIGR03844 cysteate_syn cysteat 89.7 0.26 5.7E-06 34.9 2.1 26 9-36 2-27 (398)
105 PF14311 DUF4379: Domain of un 89.6 0.54 1.2E-05 24.6 2.9 28 5-32 24-55 (55)
106 PF08996 zf-DNA_Pol: DNA Polym 89.1 0.45 9.9E-06 30.5 2.7 30 5-34 14-53 (188)
107 PF02150 RNA_POL_M_15KD: RNA p 89.0 0.38 8.3E-06 23.7 1.9 24 12-35 4-29 (35)
108 COG0675 Transposase and inacti 88.6 0.37 7.9E-06 31.0 2.1 22 10-35 310-331 (364)
109 PF14255 Cys_rich_CPXG: Cystei 88.3 0.21 4.6E-06 26.9 0.6 14 27-40 1-14 (52)
110 PF14599 zinc_ribbon_6: Zinc-r 88.0 0.51 1.1E-05 26.1 2.1 27 8-34 29-56 (61)
111 TIGR01053 LSD1 zinc finger dom 88.0 0.74 1.6E-05 22.4 2.5 24 11-34 3-27 (31)
112 PF02146 SIR2: Sir2 family; I 88.0 0.58 1.2E-05 29.1 2.6 29 8-36 104-139 (178)
113 PF08772 NOB1_Zn_bind: Nin one 88.0 0.61 1.3E-05 26.6 2.5 33 6-40 6-38 (73)
114 PF06677 Auto_anti-p27: Sjogre 87.9 0.65 1.4E-05 23.9 2.3 23 11-33 19-41 (41)
115 PRK08351 DNA-directed RNA poly 87.9 0.25 5.3E-06 27.6 0.8 22 11-37 5-26 (61)
116 TIGR00155 pqiA_fam integral me 87.8 0.47 1E-05 33.9 2.4 26 11-36 15-43 (403)
117 PRK06393 rpoE DNA-directed RNA 87.6 0.26 5.6E-06 27.8 0.8 21 11-36 7-27 (64)
118 PRK15103 paraquat-inducible me 87.5 0.54 1.2E-05 33.8 2.6 27 10-36 11-40 (419)
119 PRK08197 threonine synthase; V 87.0 0.72 1.6E-05 32.2 2.9 29 9-39 7-35 (394)
120 smart00709 Zpr1 Duplicated dom 86.8 0.3 6.5E-06 31.2 0.8 11 25-35 28-38 (160)
121 PRK00464 nrdR transcriptional 86.7 0.44 9.5E-06 30.4 1.6 29 10-38 1-40 (154)
122 smart00647 IBR In Between Ring 86.7 1.1 2.3E-05 23.1 2.8 28 12-39 21-53 (64)
123 PF15616 TerY-C: TerY-C metal 86.7 1 2.2E-05 28.3 3.2 29 11-39 90-118 (131)
124 TIGR00375 conserved hypothetic 86.6 0.24 5.3E-06 35.4 0.4 25 11-36 242-268 (374)
125 PRK08329 threonine synthase; V 86.6 0.58 1.3E-05 32.2 2.2 27 10-39 2-28 (347)
126 COG1552 RPL40A Ribosomal prote 86.5 0.064 1.4E-06 29.1 -2.0 27 9-38 14-40 (50)
127 PRK04860 hypothetical protein; 86.5 1.3 2.7E-05 28.3 3.6 33 7-40 117-157 (160)
128 PF14205 Cys_rich_KTR: Cystein 86.5 0.73 1.6E-05 25.4 2.1 19 27-45 5-23 (55)
129 PF09986 DUF2225: Uncharacteri 86.4 0.59 1.3E-05 30.6 2.1 29 9-37 5-59 (214)
130 TIGR00354 polC DNA polymerase, 86.4 0.54 1.2E-05 37.9 2.2 31 8-39 1011-1041(1095)
131 COG4530 Uncharacterized protei 86.2 0.49 1.1E-05 29.8 1.5 28 8-35 8-35 (129)
132 COG0846 SIR2 NAD-dependent pro 86.2 0.54 1.2E-05 31.9 1.9 28 8-35 121-155 (250)
133 PRK14714 DNA polymerase II lar 86.0 0.58 1.3E-05 38.5 2.2 31 8-39 1252-1282(1337)
134 PF06943 zf-LSD1: LSD1 zinc fi 86.0 1.2 2.6E-05 20.9 2.5 23 12-34 1-24 (25)
135 PF00130 C1_1: Phorbol esters/ 85.8 1.2 2.5E-05 22.6 2.6 27 10-36 12-38 (53)
136 PF03367 zf-ZPR1: ZPR1 zinc-fi 85.8 0.32 7E-06 30.9 0.6 26 11-36 3-40 (161)
137 PRK00241 nudC NADH pyrophospha 85.6 0.84 1.8E-05 30.7 2.5 27 11-37 101-128 (256)
138 PRK14892 putative transcriptio 85.4 1.2 2.6E-05 26.7 2.9 28 7-35 19-51 (99)
139 COG2995 PqiA Uncharacterized p 85.3 0.87 1.9E-05 33.5 2.7 31 7-37 16-49 (418)
140 PF04161 Arv1: Arv1-like famil 85.1 0.44 9.6E-06 31.0 1.0 25 10-34 1-32 (208)
141 COG1066 Sms Predicted ATP-depe 85.0 0.62 1.3E-05 34.6 1.8 25 8-35 6-30 (456)
142 PRK04023 DNA polymerase II lar 85.0 0.68 1.5E-05 37.5 2.1 31 8-39 1036-1066(1121)
143 PF05495 zf-CHY: CHY zinc fing 84.9 0.63 1.4E-05 25.9 1.5 26 9-34 41-69 (71)
144 cd01675 RNR_III Class III ribo 84.9 0.46 1E-05 35.1 1.1 22 11-35 520-541 (555)
145 PF06221 zf-C2HC5: Putative zi 84.9 0.45 9.8E-06 26.1 0.8 31 9-39 18-48 (57)
146 TIGR00310 ZPR1_znf ZPR1 zinc f 84.8 0.58 1.3E-05 30.7 1.4 10 26-35 30-39 (192)
147 PF11023 DUF2614: Protein of u 84.7 0.64 1.4E-05 28.9 1.5 32 5-37 65-96 (114)
148 PF14319 Zn_Tnp_IS91: Transpos 84.6 1.4 3.1E-05 26.3 3.0 30 6-35 39-69 (111)
149 PF09788 Tmemb_55A: Transmembr 84.5 1.2 2.5E-05 30.9 2.9 34 5-38 153-189 (256)
150 PRK05638 threonine synthase; V 84.5 0.71 1.5E-05 32.7 1.9 27 9-38 1-27 (442)
151 PRK11788 tetratricopeptide rep 84.5 0.76 1.7E-05 30.3 1.9 29 10-41 355-383 (389)
152 COG1656 Uncharacterized conser 84.4 0.41 8.8E-06 31.3 0.6 29 6-34 94-138 (165)
153 TIGR00340 zpr1_rel ZPR1-relate 84.4 0.66 1.4E-05 29.8 1.5 11 25-35 27-37 (163)
154 PF09862 DUF2089: Protein of u 84.2 0.81 1.8E-05 28.1 1.8 22 12-36 1-22 (113)
155 COG3091 SprT Zn-dependent meta 84.2 1.2 2.6E-05 28.9 2.7 34 6-40 114-154 (156)
156 KOG2923 Uncharacterized conser 84.1 1.3 2.9E-05 25.2 2.5 31 3-34 16-52 (67)
157 COG1773 Rubredoxin [Energy pro 84.0 0.88 1.9E-05 25.0 1.7 25 9-33 3-43 (55)
158 TIGR03831 YgiT_finger YgiT-typ 84.0 0.9 1.9E-05 22.1 1.7 17 21-37 27-43 (46)
159 PF01667 Ribosomal_S27e: Ribos 83.7 2 4.4E-05 23.4 3.1 29 8-36 6-36 (55)
160 PRK14559 putative protein seri 83.3 0.56 1.2E-05 35.6 1.0 21 12-35 30-50 (645)
161 COG1675 TFA1 Transcription ini 83.3 0.42 9.2E-06 31.2 0.3 34 5-38 109-144 (176)
162 COG4391 Uncharacterized protei 83.2 1.3 2.9E-05 24.9 2.3 16 22-37 44-59 (62)
163 PF00096 zf-C2H2: Zinc finger, 83.2 0.68 1.5E-05 19.8 0.9 12 10-21 1-12 (23)
164 TIGR00155 pqiA_fam integral me 83.1 0.78 1.7E-05 32.8 1.6 26 9-36 215-240 (403)
165 PRK12495 hypothetical protein; 82.9 0.85 1.9E-05 31.1 1.7 29 7-36 40-68 (226)
166 PRK13130 H/ACA RNA-protein com 82.8 1 2.2E-05 24.6 1.7 22 9-35 5-26 (56)
167 COG1997 RPL43A Ribosomal prote 82.5 1 2.2E-05 27.0 1.7 30 7-36 33-63 (89)
168 PF13597 NRDD: Anaerobic ribon 82.4 1.2 2.7E-05 32.9 2.5 29 9-41 491-520 (546)
169 PF11672 DUF3268: Protein of u 82.3 0.83 1.8E-05 27.6 1.3 13 26-38 2-14 (102)
170 COG4031 Predicted metal-bindin 82.3 0.62 1.4E-05 31.7 0.8 20 11-35 2-21 (227)
171 PF13397 DUF4109: Domain of un 82.1 2.2 4.9E-05 26.0 3.1 30 5-35 24-59 (105)
172 PF01485 IBR: IBR domain; Int 81.8 1 2.3E-05 23.0 1.4 26 11-36 20-50 (64)
173 PF10276 zf-CHCC: Zinc-finger 81.6 1.6 3.5E-05 22.3 2.1 12 25-36 28-39 (40)
174 PF04606 Ogr_Delta: Ogr/Delta- 81.5 1.2 2.6E-05 22.9 1.6 13 28-40 1-13 (47)
175 PF01396 zf-C4_Topoisom: Topoi 81.5 1.5 3.3E-05 21.9 1.9 14 27-40 2-15 (39)
176 cd01413 SIR2_Af2 SIR2_Af2: Arc 81.5 0.96 2.1E-05 29.5 1.5 28 8-35 112-145 (222)
177 cd01407 SIR2-fam SIR2 family o 81.3 0.99 2.2E-05 29.1 1.5 28 8-35 108-142 (218)
178 PRK00481 NAD-dependent deacety 81.2 0.96 2.1E-05 29.7 1.4 28 8-35 121-151 (242)
179 COG2824 PhnA Uncharacterized Z 80.8 1.3 2.9E-05 27.4 1.8 24 12-35 6-29 (112)
180 PRK14715 DNA polymerase II lar 80.5 1.3 2.8E-05 37.1 2.1 30 8-39 1541-1570(1627)
181 PF01927 Mut7-C: Mut7-C RNAse 80.4 1.2 2.7E-05 27.4 1.6 17 5-21 87-103 (147)
182 PRK05452 anaerobic nitric oxid 80.4 1.9 4.1E-05 31.3 2.8 31 5-35 421-467 (479)
183 cd00924 Cyt_c_Oxidase_Vb Cytoc 80.0 2.4 5.2E-05 25.3 2.7 21 20-40 73-93 (97)
184 PRK09678 DNA-binding transcrip 79.9 0.94 2E-05 25.8 0.9 9 31-39 34-42 (72)
185 PF04216 FdhE: Protein involve 79.7 1.2 2.5E-05 30.0 1.5 25 8-35 196-220 (290)
186 PF14690 zf-ISL3: zinc-finger 79.5 0.95 2.1E-05 22.5 0.8 14 26-39 2-15 (47)
187 PRK14873 primosome assembly pr 79.5 2.2 4.7E-05 32.5 3.0 25 11-35 394-419 (665)
188 COG4357 Zinc finger domain con 79.4 0.4 8.7E-06 29.4 -0.7 30 7-36 60-90 (105)
189 smart00440 ZnF_C2C2 C2C2 Zinc 79.4 2.3 5.1E-05 21.3 2.2 16 4-19 23-38 (40)
190 TIGR00515 accD acetyl-CoA carb 79.1 0.85 1.9E-05 31.5 0.7 31 5-35 22-54 (285)
191 PF01096 TFIIS_C: Transcriptio 78.8 2.4 5.1E-05 21.1 2.1 16 4-19 23-38 (39)
192 PLN00209 ribosomal protein S27 78.7 3.7 8.1E-05 24.3 3.2 29 8-36 35-65 (86)
193 PRK12775 putative trifunctiona 78.3 1.1 2.4E-05 35.2 1.2 37 7-43 819-855 (1006)
194 PF07503 zf-HYPF: HypF finger; 78.1 0.17 3.7E-06 25.2 -2.2 26 11-36 1-31 (35)
195 PHA00732 hypothetical protein 78.0 0.77 1.7E-05 26.2 0.2 28 10-37 2-38 (79)
196 TIGR00595 priA primosomal prot 78.0 1.9 4.2E-05 31.4 2.2 8 11-18 215-222 (505)
197 COG1503 eRF1 Peptide chain rel 77.8 1.4 3E-05 32.3 1.4 31 6-36 324-358 (411)
198 PRK09710 lar restriction allev 77.6 3.9 8.4E-05 23.1 2.9 21 28-48 8-28 (64)
199 PRK14873 primosome assembly pr 77.5 2.5 5.4E-05 32.2 2.8 22 10-36 411-432 (665)
200 PTZ00083 40S ribosomal protein 77.5 4.4 9.4E-05 24.0 3.3 29 8-36 34-64 (85)
201 PF13894 zf-C2H2_4: C2H2-type 77.5 1.7 3.6E-05 17.9 1.2 11 10-20 1-11 (24)
202 PLN02294 cytochrome c oxidase 77.5 2.9 6.3E-05 27.6 2.8 21 21-41 136-156 (174)
203 COG1110 Reverse gyrase [DNA re 76.9 1 2.3E-05 36.7 0.7 25 11-38 696-720 (1187)
204 PRK08579 anaerobic ribonucleos 76.9 1.4 3E-05 33.4 1.3 23 10-35 569-591 (625)
205 COG1867 TRM1 N2,N2-dimethylgua 76.9 2.3 4.9E-05 31.0 2.3 29 8-36 239-267 (380)
206 PF09567 RE_MamI: MamI restric 76.7 1.2 2.7E-05 31.5 0.9 29 11-42 84-113 (314)
207 COG1594 RPB9 DNA-directed RNA 76.7 2.8 6.1E-05 25.3 2.4 28 12-39 5-35 (113)
208 KOG3134 Predicted membrane pro 76.5 0.94 2E-05 30.9 0.3 25 10-34 1-32 (225)
209 PF14205 Cys_rich_KTR: Cystein 76.5 9.3 0.0002 21.0 4.2 38 10-47 5-49 (55)
210 TIGR00319 desulf_FeS4 desulfof 76.5 2.6 5.6E-05 20.1 1.8 22 8-29 6-29 (34)
211 PF13912 zf-C2H2_6: C2H2-type 76.4 1.5 3.2E-05 19.3 0.9 12 10-21 2-13 (27)
212 cd04476 RPA1_DBD_C RPA1_DBD_C: 76.4 4.8 0.0001 24.7 3.4 30 7-36 32-61 (166)
213 COG1933 Archaeal DNA polymeras 76.1 1.4 3E-05 30.6 1.0 29 8-37 166-194 (253)
214 COG4311 SoxD Sarcosine oxidase 76.1 1.3 2.8E-05 26.9 0.8 10 26-35 3-12 (97)
215 cd00974 DSRD Desulforedoxin (D 76.1 2.7 5.8E-05 20.1 1.8 21 9-29 4-26 (34)
216 cd00029 C1 Protein kinase C co 75.6 1.6 3.5E-05 21.4 1.0 26 11-36 13-38 (50)
217 PF05876 Terminase_GpA: Phage 75.6 2 4.3E-05 31.8 1.8 35 8-42 199-245 (557)
218 PRK15103 paraquat-inducible me 75.5 1.7 3.7E-05 31.3 1.4 23 11-36 223-245 (419)
219 TIGR00320 dfx_rbo desulfoferro 75.5 3.9 8.5E-05 25.1 2.8 25 8-34 6-32 (125)
220 cd00246 RabGEF Nucleotide exch 75.5 1.9 4.1E-05 26.3 1.4 14 26-39 2-15 (103)
221 PF06676 DUF1178: Protein of u 75.4 3.2 7E-05 26.5 2.5 31 9-40 5-46 (148)
222 COG4481 Uncharacterized protei 75.3 2.2 4.8E-05 23.8 1.5 15 25-39 33-47 (60)
223 KOG3623 Homeobox transcription 75.0 0.98 2.1E-05 36.0 0.1 29 8-36 280-319 (1007)
224 PF01780 Ribosomal_L37ae: Ribo 74.6 2.1 4.6E-05 25.5 1.4 30 7-36 33-63 (90)
225 PF09332 Mcm10: Mcm10 replicat 74.6 2.3 5E-05 30.4 1.9 28 8-35 284-312 (344)
226 cd01411 SIR2H SIR2H: Uncharact 74.5 2.5 5.4E-05 27.6 1.9 27 9-35 118-145 (225)
227 CHL00174 accD acetyl-CoA carbo 74.4 1.3 2.8E-05 31.0 0.6 31 5-35 34-66 (296)
228 TIGR02487 NrdD anaerobic ribon 74.3 2.1 4.6E-05 31.9 1.7 23 10-35 525-547 (579)
229 COG2093 DNA-directed RNA polym 74.0 1.6 3.4E-05 24.7 0.8 23 12-37 7-29 (64)
230 COG4888 Uncharacterized Zn rib 73.7 5 0.00011 24.6 2.9 32 6-37 19-57 (104)
231 COG1779 C4-type Zn-finger prot 73.5 1.9 4E-05 29.1 1.1 31 6-36 11-53 (201)
232 cd00065 FYVE FYVE domain; Zinc 73.2 2.5 5.5E-05 21.5 1.4 24 11-35 4-27 (57)
233 PF01363 FYVE: FYVE zinc finge 73.1 3.4 7.5E-05 21.9 2.0 24 10-34 10-33 (69)
234 KOG2907 RNA polymerase I trans 73.1 1.4 3E-05 27.5 0.4 36 11-46 9-45 (116)
235 PF10005 DUF2248: Uncharacteri 73.0 2.6 5.7E-05 30.3 1.8 36 11-49 1-36 (343)
236 smart00109 C1 Protein kinase C 72.8 1.7 3.6E-05 21.0 0.6 24 11-35 13-36 (49)
237 smart00350 MCM minichromosome 72.7 7.3 0.00016 28.3 4.1 30 7-36 35-71 (509)
238 PRK14704 anaerobic ribonucleos 72.6 2.2 4.7E-05 32.3 1.4 23 9-35 559-581 (618)
239 PF09963 DUF2197: Uncharacteri 72.5 1.6 3.5E-05 24.0 0.5 29 9-37 2-42 (56)
240 PF08646 Rep_fac-A_C: Replicat 72.2 4.7 0.0001 24.3 2.6 31 6-36 15-47 (146)
241 PTZ00255 60S ribosomal protein 72.1 3.4 7.4E-05 24.6 1.9 31 6-36 33-64 (90)
242 PRK00423 tfb transcription ini 72.1 2.6 5.6E-05 28.9 1.6 27 8-34 10-38 (310)
243 PF06750 DiS_P_DiS: Bacterial 71.9 2.1 4.6E-05 24.9 1.0 27 10-36 34-68 (92)
244 PRK04023 DNA polymerase II lar 71.7 2.2 4.8E-05 34.7 1.3 22 8-34 625-646 (1121)
245 PHA00616 hypothetical protein 71.4 0.79 1.7E-05 24.0 -0.8 12 10-21 2-13 (44)
246 cd01412 SIRT5_Af1_CobB SIRT5_A 71.4 2.6 5.5E-05 27.2 1.4 28 8-35 108-139 (224)
247 PRK07111 anaerobic ribonucleos 71.3 2.4 5.2E-05 32.7 1.4 22 10-35 681-702 (735)
248 TIGR00280 L37a ribosomal prote 71.2 3.4 7.4E-05 24.6 1.8 31 6-36 32-63 (91)
249 PRK04338 N(2),N(2)-dimethylgua 71.1 5.7 0.00012 28.1 3.1 30 7-36 242-271 (382)
250 PRK14138 NAD-dependent deacety 71.1 3.3 7.2E-05 27.5 1.9 28 8-35 118-152 (244)
251 TIGR00595 priA primosomal prot 71.0 3.8 8.2E-05 29.9 2.3 23 11-37 242-264 (505)
252 PRK09263 anaerobic ribonucleos 70.9 2.6 5.6E-05 32.3 1.5 27 9-35 641-668 (711)
253 PRK05654 acetyl-CoA carboxylas 70.9 1.9 4.1E-05 29.9 0.7 32 5-36 23-56 (292)
254 PF01215 COX5B: Cytochrome c o 70.8 3.4 7.4E-05 26.1 1.8 19 21-39 107-125 (136)
255 PF03119 DNA_ligase_ZBD: NAD-d 70.8 3.8 8.1E-05 19.2 1.6 19 12-30 2-21 (28)
256 COG5254 ARV1 Predicted membran 70.5 1.3 2.9E-05 30.3 -0.1 25 10-34 1-32 (239)
257 PRK04173 glycyl-tRNA synthetas 70.5 3.1 6.8E-05 30.0 1.8 33 8-40 85-148 (456)
258 PRK08271 anaerobic ribonucleos 70.4 2.8 6.1E-05 31.9 1.6 23 10-35 567-589 (623)
259 TIGR00244 transcriptional regu 70.4 1.8 3.8E-05 27.8 0.4 8 27-34 1-8 (147)
260 PRK05580 primosome assembly pr 70.3 3.9 8.5E-05 30.8 2.3 9 28-36 423-431 (679)
261 COG1198 PriA Primosomal protei 70.3 4.7 0.0001 31.3 2.8 9 27-35 476-484 (730)
262 PF05180 zf-DNL: DNL zinc fing 70.3 3.6 7.9E-05 23.1 1.7 30 8-37 3-40 (66)
263 PRK12286 rpmF 50S ribosomal pr 70.2 5.5 0.00012 21.5 2.4 23 7-33 25-47 (57)
264 PRK14559 putative protein seri 69.7 2.3 5.1E-05 32.4 1.0 26 11-36 3-37 (645)
265 COG5257 GCD11 Translation init 69.7 3.9 8.5E-05 30.1 2.1 29 6-36 54-82 (415)
266 cd01408 SIRT1 SIRT1: Eukaryoti 69.6 2.1 4.6E-05 28.2 0.7 28 8-35 115-149 (235)
267 PF10601 zf-LITAF-like: LITAF- 69.4 4.7 0.0001 22.0 2.0 18 25-42 6-23 (73)
268 cd07973 Spt4 Transcription elo 69.4 2.4 5.1E-05 25.4 0.8 23 11-33 5-27 (98)
269 KOG4684 Uncharacterized conser 69.1 3.3 7.1E-05 28.8 1.6 26 8-33 169-196 (275)
270 PF03884 DUF329: Domain of unk 69.0 3.3 7.1E-05 22.7 1.3 14 9-22 2-15 (57)
271 PF09334 tRNA-synt_1g: tRNA sy 68.8 7 0.00015 27.6 3.2 32 11-42 151-182 (391)
272 PF06107 DUF951: Bacterial pro 68.6 4.4 9.5E-05 22.4 1.7 15 25-39 30-44 (57)
273 PF04810 zf-Sec23_Sec24: Sec23 68.5 4.7 0.0001 20.0 1.7 25 11-35 4-33 (40)
274 KOG2462 C2H2-type Zn-finger pr 68.2 4.7 0.0001 28.3 2.2 32 6-37 127-172 (279)
275 KOG2593 Transcription initiati 67.6 2.8 6E-05 31.1 1.0 35 3-37 122-164 (436)
276 TIGR03830 CxxCG_CxxCG_HTH puta 67.4 5.2 0.00011 23.1 2.0 23 15-38 21-43 (127)
277 COG4640 Predicted membrane pro 67.2 2.9 6.2E-05 31.2 1.0 22 12-36 4-25 (465)
278 KOG2846 Predicted membrane pro 67.2 3.2 7E-05 29.7 1.3 34 3-36 214-252 (328)
279 smart00064 FYVE Protein presen 67.1 3.8 8.3E-05 21.7 1.3 25 10-35 11-35 (68)
280 PRK03976 rpl37ae 50S ribosomal 66.8 4.2 9E-05 24.2 1.5 31 6-36 33-64 (90)
281 PF12647 RNHCP: RNHCP domain; 66.6 3 6.6E-05 24.9 0.9 27 9-35 4-33 (92)
282 COG1328 NrdD Oxygen-sensitive 66.5 3.8 8.3E-05 31.8 1.6 23 10-35 642-664 (700)
283 PF04828 GFA: Glutathione-depe 66.3 10 0.00023 20.2 3.0 25 25-49 47-72 (92)
284 PF06054 CoiA: Competence prot 65.9 7.8 0.00017 27.4 3.0 25 24-48 28-52 (375)
285 smart00714 LITAF Possible memb 65.9 7.4 0.00016 20.9 2.3 18 26-43 3-20 (67)
286 KOG0320 Predicted E3 ubiquitin 65.8 1.4 3E-05 29.4 -0.7 14 25-38 166-179 (187)
287 TIGR01562 FdhE formate dehydro 65.7 5.3 0.00012 28.0 2.1 25 8-35 209-233 (305)
288 PRK05580 primosome assembly pr 65.3 5.4 0.00012 30.1 2.2 14 23-36 405-418 (679)
289 KOG0478 DNA replication licens 65.2 3.1 6.8E-05 32.8 0.9 35 8-42 263-305 (804)
290 PLN02569 threonine synthase 65.2 4.6 0.0001 29.6 1.8 29 9-39 49-77 (484)
291 PF05605 zf-Di19: Drought indu 65.1 2.3 4.9E-05 22.1 0.2 27 9-35 2-40 (54)
292 COG1998 RPS31 Ribosomal protei 65.1 5.2 0.00011 21.7 1.5 26 11-36 21-47 (51)
293 COG2260 Predicted Zn-ribbon RN 64.9 4.3 9.2E-05 22.6 1.2 24 8-36 4-27 (59)
294 PF13453 zf-TFIIB: Transcripti 64.8 3.7 8.1E-05 20.3 0.9 27 11-37 1-30 (41)
295 TIGR02443 conserved hypothetic 64.7 5.9 0.00013 22.0 1.8 26 11-36 11-41 (59)
296 COG1241 MCM2 Predicted ATPase 64.6 5.4 0.00012 30.8 2.1 27 6-32 126-157 (682)
297 PRK07218 replication factor A; 64.6 4.4 9.5E-05 29.5 1.5 23 6-33 294-316 (423)
298 PF01020 Ribosomal_L40e: Ribos 64.6 5.3 0.00011 21.7 1.5 24 9-35 17-42 (52)
299 smart00154 ZnF_AN1 AN1-like Zi 64.6 5.7 0.00012 19.8 1.6 27 12-41 1-27 (39)
300 TIGR00308 TRM1 tRNA(guanine-26 64.5 7.4 0.00016 27.6 2.7 30 7-36 231-262 (374)
301 TIGR00354 polC DNA polymerase, 64.0 5.2 0.00011 32.6 2.0 25 7-36 623-647 (1095)
302 KOG2703 C4-type Zn-finger prot 63.8 1.5 3.2E-05 32.6 -1.0 32 4-35 34-77 (460)
303 PF10083 DUF2321: Uncharacteri 63.6 0.83 1.8E-05 29.7 -2.0 20 11-36 30-49 (158)
304 cd01410 SIRT7 SIRT7: Eukaryoti 63.5 3.7 7.9E-05 26.6 0.9 27 9-35 95-129 (206)
305 KOG3352 Cytochrome c oxidase, 63.1 6.5 0.00014 25.5 2.0 18 21-38 128-145 (153)
306 TIGR01374 soxD sarcosine oxida 63.1 3.3 7.1E-05 24.3 0.6 9 27-35 2-10 (84)
307 KOG3854 SPRT-like metalloprote 62.9 4.8 0.00011 30.3 1.5 34 7-40 406-443 (505)
308 PF14569 zf-UDP: Zinc-binding 62.8 3.7 8.1E-05 24.1 0.8 27 10-36 10-38 (80)
309 PF09526 DUF2387: Probable met 62.7 6.4 0.00014 22.2 1.7 25 11-35 10-39 (71)
310 PF13465 zf-H2C2_2: Zinc-finge 62.6 4.8 0.0001 18.1 1.0 12 8-19 13-24 (26)
311 TIGR02827 RNR_anaer_Bdell anae 62.4 6.8 0.00015 29.7 2.3 24 9-35 532-555 (586)
312 PRK11088 rrmA 23S rRNA methylt 62.2 5.6 0.00012 26.1 1.6 26 9-36 2-27 (272)
313 cd01409 SIRT4 SIRT4: Eukaryoti 62.1 7.5 0.00016 26.1 2.2 13 8-20 117-129 (260)
314 smart00238 BIR Baculoviral inh 61.6 6.1 0.00013 21.0 1.5 13 24-36 34-46 (71)
315 PF03107 C1_2: C1 domain; Int 61.6 6 0.00013 18.4 1.3 21 11-33 2-22 (30)
316 PF07649 C1_3: C1-like domain; 61.4 6.7 0.00014 18.1 1.4 21 12-34 3-23 (30)
317 PF05129 Elf1: Transcription e 61.4 4.6 0.0001 23.1 1.0 33 7-39 20-59 (81)
318 PRK08270 anaerobic ribonucleos 61.2 6.7 0.00015 29.9 2.1 22 10-35 627-648 (656)
319 PRK03564 formate dehydrogenase 60.8 7.5 0.00016 27.4 2.1 24 8-34 211-234 (309)
320 PF10533 Plant_zn_clust: Plant 60.6 7 0.00015 20.9 1.5 24 24-50 17-40 (47)
321 PRK14894 glycyl-tRNA synthetas 60.6 5.7 0.00012 30.2 1.6 33 10-43 89-121 (539)
322 PF06524 NOA36: NOA36 protein; 60.6 3.6 7.7E-05 29.3 0.5 15 22-36 205-219 (314)
323 PRK05978 hypothetical protein; 60.3 4.9 0.00011 25.6 1.0 25 11-35 35-61 (148)
324 TIGR02159 PA_CoA_Oxy4 phenylac 60.0 4 8.7E-05 25.6 0.6 10 26-35 105-114 (146)
325 KOG2463 Predicted RNA-binding 59.6 5.5 0.00012 29.0 1.3 31 8-40 241-271 (376)
326 PTZ00408 NAD-dependent deacety 59.5 6.1 0.00013 26.4 1.4 27 8-34 116-145 (242)
327 PHA00733 hypothetical protein 59.2 4.5 9.7E-05 24.7 0.7 29 8-36 72-109 (128)
328 COG0551 TopA Zn-finger domain 58.9 16 0.00034 22.1 3.1 19 25-43 100-118 (140)
329 smart00653 eIF2B_5 domain pres 58.8 8 0.00017 23.3 1.8 25 11-35 82-110 (110)
330 PRK06386 replication factor A; 58.6 8.8 0.00019 27.5 2.2 24 6-34 233-256 (358)
331 PF03833 PolC_DP2: DNA polymer 58.3 3.3 7.1E-05 33.1 0.0 8 28-35 694-701 (900)
332 KOG3993 Transcription factor ( 58.3 5 0.00011 30.1 1.0 15 7-21 293-307 (500)
333 PRK04011 peptide chain release 57.9 9.5 0.00021 27.4 2.3 29 7-35 326-359 (411)
334 COG2401 ABC-type ATPase fused 57.9 7.7 0.00017 29.6 1.9 28 8-38 129-156 (593)
335 PF04267 SoxD: Sarcosine oxida 57.3 3.7 7.9E-05 24.1 0.1 9 27-35 2-10 (84)
336 PRK08402 replication factor A; 57.1 13 0.00029 26.4 2.9 26 8-33 211-237 (355)
337 PF10080 DUF2318: Predicted me 57.0 8.1 0.00017 23.2 1.6 30 8-37 34-63 (102)
338 PTZ00410 NAD-dependent SIR2; P 56.8 8.5 0.00018 27.5 1.9 27 9-35 147-180 (349)
339 PF07967 zf-C3HC: C3HC zinc fi 56.2 10 0.00022 22.8 1.9 28 10-39 29-56 (133)
340 COG3677 Transposase and inacti 56.1 6.2 0.00013 24.3 1.0 14 9-22 53-66 (129)
341 PF00628 PHD: PHD-finger; Int 55.8 21 0.00045 17.6 2.8 22 11-34 1-22 (51)
342 PF02207 zf-UBR: Putative zinc 55.7 7.5 0.00016 21.2 1.2 32 6-42 10-48 (71)
343 PF00653 BIR: Inhibitor of Apo 55.6 7.6 0.00016 20.9 1.2 13 24-36 34-46 (70)
344 PRK12366 replication factor A; 55.2 14 0.00031 27.9 2.9 28 7-35 530-557 (637)
345 PLN02638 cellulose synthase A 55.1 8.3 0.00018 31.5 1.8 26 11-36 19-46 (1079)
346 COG0777 AccD Acetyl-CoA carbox 54.9 6.4 0.00014 27.9 1.0 31 6-36 25-57 (294)
347 PF04438 zf-HIT: HIT zinc fing 54.5 17 0.00037 17.2 2.2 19 11-35 4-22 (30)
348 cd00022 BIR Baculoviral inhibi 54.5 9.5 0.00021 20.1 1.5 14 24-37 32-45 (69)
349 PF08209 Sgf11: Sgf11 (transcr 54.4 11 0.00025 18.4 1.6 12 25-36 3-14 (33)
350 smart00401 ZnF_GATA zinc finge 54.4 6.7 0.00015 20.5 0.8 28 9-36 3-35 (52)
351 TIGR00311 aIF-2beta translatio 54.3 10 0.00023 23.6 1.8 26 10-35 98-127 (133)
352 COG4260 Membrane protease subu 54.3 4.7 0.0001 29.0 0.3 25 11-35 317-343 (345)
353 PHA02998 RNA polymerase subuni 54.0 10 0.00023 25.4 1.8 18 4-21 166-183 (195)
354 PF03811 Zn_Tnp_IS1: InsA N-te 53.5 10 0.00023 18.8 1.4 15 26-40 5-20 (36)
355 PF00641 zf-RanBP: Zn-finger i 53.4 11 0.00023 17.3 1.4 23 9-34 4-26 (30)
356 PF01258 zf-dskA_traR: Prokary 53.2 2.2 4.7E-05 20.6 -1.1 21 12-32 6-30 (36)
357 PRK03988 translation initiatio 53.1 11 0.00025 23.5 1.8 25 11-35 104-132 (138)
358 PRK08665 ribonucleotide-diphos 52.9 7.9 0.00017 30.0 1.3 23 11-34 726-748 (752)
359 PRK05333 NAD-dependent deacety 52.1 13 0.00028 25.1 2.1 13 8-20 127-139 (285)
360 TIGR00622 ssl1 transcription f 52.1 11 0.00024 23.1 1.6 24 10-36 2-25 (112)
361 PRK00418 DNA gyrase inhibitor; 51.9 9 0.0002 21.4 1.1 12 27-38 7-18 (62)
362 PF14354 Lar_restr_allev: Rest 51.5 12 0.00025 19.4 1.5 16 27-42 4-19 (61)
363 PF04502 DUF572: Family of unk 51.5 11 0.00024 26.1 1.7 37 7-43 38-94 (324)
364 COG1327 Predicted transcriptio 51.1 6.3 0.00014 25.6 0.5 7 28-34 2-8 (156)
365 COG0498 ThrC Threonine synthas 50.8 5.6 0.00012 28.9 0.2 28 8-36 4-31 (411)
366 PLN02189 cellulose synthase 49.8 11 0.00024 30.7 1.7 29 8-36 33-63 (1040)
367 PF08790 zf-LYAR: LYAR-type C2 49.7 12 0.00026 17.9 1.2 14 10-23 1-14 (28)
368 PTZ00409 Sir2 (Silent Informat 49.3 11 0.00023 25.7 1.4 26 9-35 137-173 (271)
369 smart00355 ZnF_C2H2 zinc finge 49.0 5.2 0.00011 16.3 -0.1 11 10-20 1-11 (26)
370 PF01873 eIF-5_eIF-2B: Domain 49.0 17 0.00037 22.3 2.1 25 11-35 95-123 (125)
371 PF13913 zf-C2HC_2: zinc-finge 48.8 8.1 0.00018 17.4 0.5 11 26-36 2-12 (25)
372 PF02005 TRM: N2,N2-dimethylgu 48.8 16 0.00035 26.0 2.2 30 7-36 238-269 (377)
373 PRK14715 DNA polymerase II lar 48.5 12 0.00027 31.7 1.8 27 6-37 671-697 (1627)
374 TIGR03826 YvyF flagellar opero 48.5 4.7 0.0001 25.3 -0.4 22 11-34 5-26 (137)
375 COG4307 Uncharacterized protei 47.6 5.3 0.00011 28.7 -0.3 26 9-37 3-28 (349)
376 COG1198 PriA Primosomal protei 47.5 17 0.00036 28.4 2.3 25 11-35 437-471 (730)
377 TIGR01405 polC_Gram_pos DNA po 47.4 10 0.00022 31.1 1.1 26 9-34 683-716 (1213)
378 PF12677 DUF3797: Domain of un 47.0 11 0.00024 20.2 1.0 12 26-37 13-24 (49)
379 PLN02195 cellulose synthase A 47.0 13 0.00028 30.1 1.7 26 11-36 8-35 (977)
380 PTZ00043 cytochrome c oxidase 46.9 12 0.00027 26.1 1.4 16 21-36 176-191 (268)
381 PLN02436 cellulose synthase A 46.6 13 0.00029 30.4 1.7 29 8-36 35-65 (1094)
382 TIGR00627 tfb4 transcription f 46.5 14 0.0003 25.6 1.6 25 8-35 254-278 (279)
383 PLN02915 cellulose synthase A 46.3 13 0.00028 30.3 1.6 29 8-36 14-44 (1044)
384 PLN03158 methionine aminopepti 46.0 11 0.00024 27.0 1.1 28 1-34 1-28 (396)
385 PRK14810 formamidopyrimidine-D 45.7 18 0.00039 24.4 2.0 22 11-32 246-270 (272)
386 PRK00448 polC DNA polymerase I 45.6 11 0.00024 31.4 1.1 27 9-35 908-942 (1437)
387 COG4416 Com Mu-like prophage p 45.3 4.5 9.8E-05 22.5 -0.8 25 10-34 5-32 (60)
388 PF12322 T4_baseplate: T4 bact 45.1 17 0.00038 23.9 1.8 24 6-29 75-99 (205)
389 PRK10445 endonuclease VIII; Pr 45.0 19 0.00042 24.1 2.1 12 27-38 236-247 (263)
390 cd00296 SIR2 SIR2 superfamily 45.0 13 0.00028 23.4 1.2 28 9-36 113-144 (222)
391 TIGR00577 fpg formamidopyrimid 44.6 20 0.00042 24.2 2.0 10 28-37 247-256 (272)
392 COG2956 Predicted N-acetylgluc 44.6 12 0.00025 27.5 1.0 33 7-42 352-384 (389)
393 COG5415 Predicted integral mem 44.5 10 0.00022 26.2 0.7 36 8-43 191-232 (251)
394 PRK14811 formamidopyrimidine-D 43.6 20 0.00043 24.2 2.0 23 11-33 237-262 (269)
395 PRK01103 formamidopyrimidine/5 43.6 21 0.00045 24.0 2.1 21 12-32 248-271 (274)
396 KOG1812 Predicted E3 ubiquitin 43.5 13 0.00029 26.5 1.2 30 11-41 308-338 (384)
397 COG3877 Uncharacterized protei 43.4 14 0.00031 23.1 1.2 27 7-36 4-30 (122)
398 PF01194 RNA_pol_N: RNA polyme 43.3 7 0.00015 21.7 -0.2 11 26-36 4-14 (60)
399 smart00547 ZnF_RBZ Zinc finger 43.2 13 0.00027 16.3 0.7 21 11-34 4-24 (26)
400 PRK13945 formamidopyrimidine-D 43.1 20 0.00044 24.2 2.0 22 11-32 256-280 (282)
401 cd00674 LysRS_core_class_I cat 43.1 22 0.00049 25.2 2.2 35 7-42 167-208 (353)
402 PF13005 zf-IS66: zinc-finger 42.8 13 0.00029 18.3 0.8 11 27-37 3-13 (47)
403 PF11331 DUF3133: Protein of u 42.6 18 0.00039 19.0 1.3 32 10-41 7-46 (46)
404 COG1405 SUA7 Transcription ini 42.1 15 0.00032 25.5 1.2 25 10-34 2-28 (285)
405 PF01921 tRNA-synt_1f: tRNA sy 41.8 20 0.00042 25.9 1.8 36 7-42 172-215 (360)
406 TIGR03829 YokU_near_AblA uncha 41.7 21 0.00045 21.1 1.6 19 19-37 28-46 (89)
407 COG3809 Uncharacterized protei 41.2 20 0.00042 21.4 1.5 24 11-34 3-29 (88)
408 PF01475 FUR: Ferric uptake re 41.1 19 0.00041 20.7 1.4 15 8-22 79-93 (120)
409 PRK12336 translation initiatio 41.1 21 0.00047 23.2 1.8 26 10-35 99-128 (201)
410 COG3478 Predicted nucleic-acid 41.1 14 0.00029 21.1 0.7 19 25-43 39-57 (68)
411 PF03966 Trm112p: Trm112p-like 41.0 16 0.00035 19.7 1.0 11 25-35 52-62 (68)
412 smart00249 PHD PHD zinc finger 40.9 28 0.00061 16.0 1.8 22 12-35 2-23 (47)
413 cd00202 ZnF_GATA Zinc finger D 40.8 6 0.00013 21.0 -0.7 26 11-36 1-31 (54)
414 PF09158 MotCF: Bacteriophage 40.4 34 0.00074 20.9 2.5 17 34-50 32-48 (103)
415 PF13878 zf-C2H2_3: zinc-finge 40.2 16 0.00036 18.2 0.9 8 26-33 13-20 (41)
416 PF14122 YokU: YokU-like prote 40.2 25 0.00054 20.9 1.8 18 17-34 26-43 (87)
417 TIGR02420 dksA RNA polymerase- 39.9 6.6 0.00014 23.1 -0.7 24 9-32 80-107 (110)
418 smart00290 ZnF_UBP Ubiquitin C 39.9 22 0.00048 17.5 1.4 10 9-18 11-20 (50)
419 KOG2272 Focal adhesion protein 39.6 20 0.00042 25.7 1.5 27 6-32 160-189 (332)
420 COG4049 Uncharacterized protei 39.6 13 0.00028 20.9 0.5 9 26-34 17-25 (65)
421 TIGR03670 rpoB_arch DNA-direct 39.5 36 0.00078 25.9 3.0 32 4-35 533-565 (599)
422 PF14952 zf-tcix: Putative tre 39.3 13 0.00028 19.6 0.4 10 25-34 10-19 (44)
423 cd07153 Fur_like Ferric uptake 39.2 24 0.00051 20.0 1.6 16 8-23 72-87 (116)
424 PRK09462 fur ferric uptake reg 39.0 23 0.0005 21.4 1.6 15 8-22 89-103 (148)
425 PLN02400 cellulose synthase 38.8 22 0.00047 29.2 1.8 28 9-36 36-65 (1085)
426 PRK02935 hypothetical protein; 38.6 33 0.00071 21.2 2.2 28 7-35 68-95 (110)
427 PRK11827 hypothetical protein; 38.6 41 0.00088 18.5 2.4 31 11-43 10-41 (60)
428 TIGR01031 rpmF_bact ribosomal 38.5 23 0.0005 18.9 1.4 23 7-33 24-46 (55)
429 PF14570 zf-RING_4: RING/Ubox 38.2 22 0.00047 18.8 1.2 7 26-32 37-43 (48)
430 PRK00019 rpmE 50S ribosomal pr 38.0 32 0.0007 19.4 2.0 20 3-23 7-26 (72)
431 PRK10996 thioredoxin 2; Provis 37.7 27 0.00059 20.8 1.8 29 9-37 2-33 (139)
432 PF02176 zf-TRAF: TRAF-type zi 37.3 35 0.00076 17.2 1.9 10 26-35 9-19 (60)
433 COG0254 RpmE Ribosomal protein 37.2 30 0.00065 19.9 1.8 18 6-23 11-28 (75)
434 PRK07225 DNA-directed RNA poly 37.1 39 0.00085 25.8 2.8 39 3-41 538-578 (605)
435 COG3024 Uncharacterized protei 37.1 16 0.00034 20.7 0.6 14 25-38 6-19 (65)
436 KOG1829 Uncharacterized conser 37.0 9.4 0.0002 29.2 -0.4 26 9-34 340-366 (580)
437 PRK08332 ribonucleotide-diphos 36.8 23 0.0005 30.4 1.7 24 12-35 1707-1735(1740)
438 PF09889 DUF2116: Uncharacteri 36.7 16 0.00034 20.1 0.5 9 28-36 5-13 (59)
439 PRK13715 conjugal transfer pro 36.5 5.7 0.00012 22.4 -1.3 24 9-32 34-61 (73)
440 KOG2807 RNA polymerase II tran 36.4 28 0.0006 25.5 1.9 26 8-36 275-300 (378)
441 TIGR00108 eRF peptide chain re 36.4 35 0.00076 24.5 2.4 30 7-36 322-356 (409)
442 COG5132 BUD31 Cell cycle contr 36.3 14 0.00031 23.6 0.4 11 25-35 130-140 (146)
443 COG2176 PolC DNA polymerase II 36.2 24 0.00053 29.7 1.7 28 8-35 913-948 (1444)
444 PF13395 HNH_4: HNH endonuclea 36.2 17 0.00036 18.8 0.6 10 29-38 1-10 (54)
445 COG4896 Uncharacterized protei 36.0 12 0.00026 21.3 -0.0 29 11-39 4-44 (68)
446 TIGR00201 comF comF family pro 36.0 16 0.00035 22.9 0.6 22 12-36 1-22 (190)
447 TIGR00398 metG methionyl-tRNA 35.6 17 0.00037 26.1 0.7 33 11-43 151-183 (530)
448 COG1040 ComFC Predicted amidop 35.5 5.9 0.00013 26.1 -1.5 25 11-38 26-50 (225)
449 KOG1105 Transcription elongati 35.4 36 0.00078 24.0 2.3 30 6-35 252-292 (296)
450 PF07150 DUF1390: Protein of u 35.2 57 0.0012 22.3 3.1 32 8-41 6-39 (229)
451 cd02249 ZZ Zinc finger, ZZ typ 35.1 31 0.00067 17.2 1.5 8 10-17 1-8 (46)
452 PF01286 XPA_N: XPA protein N- 35.0 23 0.0005 17.5 0.9 12 11-22 5-16 (34)
453 PF10977 DUF2797: Protein of u 34.9 25 0.00054 23.8 1.4 9 11-19 13-21 (235)
454 KOG2691 RNA polymerase II subu 34.9 20 0.00043 22.3 0.8 20 25-44 72-93 (113)
455 PRK01678 rpmE2 50S ribosomal p 34.5 39 0.00084 19.8 2.0 20 3-22 7-26 (87)
456 smart00778 Prim_Zn_Ribbon Zinc 34.3 20 0.00043 17.9 0.7 8 27-34 4-11 (37)
457 PF15494 SRCR_2: Scavenger rec 34.2 24 0.00052 20.0 1.1 11 25-35 87-97 (98)
458 COG3813 Uncharacterized protei 34.0 15 0.00033 21.6 0.2 17 27-43 42-58 (84)
459 KOG4080 Mitochondrial ribosoma 33.8 17 0.00038 24.1 0.5 10 25-34 92-101 (176)
460 PF14447 Prok-RING_4: Prokaryo 33.8 20 0.00043 19.6 0.6 12 25-36 38-49 (55)
461 cd02335 ZZ_ADA2 Zinc finger, Z 33.6 34 0.00074 17.4 1.5 8 8-15 14-21 (49)
462 PF10825 DUF2752: Protein of u 33.6 15 0.00033 19.2 0.1 12 23-34 6-17 (52)
463 PF14471 DUF4428: Domain of un 33.5 4.7 0.0001 21.2 -1.8 26 11-36 1-30 (51)
464 PF00471 Ribosomal_L33: Riboso 33.5 31 0.00066 18.0 1.3 34 7-40 3-46 (48)
465 PRK00595 rpmG 50S ribosomal pr 33.4 36 0.00079 18.0 1.6 35 6-40 7-51 (53)
466 PF04032 Rpr2: RNAse P Rpr2/Rp 33.4 26 0.00057 19.0 1.1 11 7-17 75-85 (85)
467 smart00746 TRASH metallochaper 33.3 22 0.00049 14.8 0.7 9 29-37 1-9 (39)
468 PF14206 Cys_rich_CPCC: Cystei 33.3 41 0.00088 19.3 1.9 24 10-33 2-27 (78)
469 PF01783 Ribosomal_L32p: Ribos 33.2 27 0.00059 18.4 1.1 22 8-33 25-46 (56)
470 PRK09401 reverse gyrase; Revie 33.0 21 0.00045 29.1 0.9 25 10-37 679-703 (1176)
471 PRK07562 ribonucleotide-diphos 32.4 35 0.00077 28.4 2.1 24 12-35 1193-1216(1220)
472 PF00935 Ribosomal_L44: Riboso 32.1 32 0.00069 19.8 1.4 11 27-37 54-64 (77)
473 COG0735 Fur Fe2+/Zn2+ uptake r 32.1 33 0.00073 21.0 1.5 15 8-22 92-106 (145)
474 COG1631 RPL42A Ribosomal prote 32.0 33 0.00072 20.7 1.4 12 27-38 69-80 (94)
475 KOG1859 Leucine-rich repeat pr 31.9 24 0.00051 28.9 1.0 26 8-33 672-703 (1096)
476 COG0333 RpmF Ribosomal protein 31.7 29 0.00064 18.9 1.1 20 10-33 28-47 (57)
477 PF13901 DUF4206: Domain of un 31.7 32 0.0007 22.3 1.5 24 10-33 153-179 (202)
478 PRK11639 zinc uptake transcrip 31.6 36 0.00077 21.3 1.6 14 9-22 100-113 (169)
479 PF10955 DUF2757: Protein of u 31.3 43 0.00093 19.3 1.8 15 7-21 2-16 (76)
480 PF11789 zf-Nse: Zinc-finger o 31.2 81 0.0018 16.7 2.8 24 10-33 25-55 (57)
481 PRK00807 50S ribosomal protein 30.9 26 0.00057 18.4 0.8 10 28-37 3-12 (52)
482 TIGR01023 rpmG_bact ribosomal 30.9 42 0.00091 17.9 1.6 34 7-40 9-52 (54)
483 PRK00085 recO DNA repair prote 30.8 25 0.00054 22.5 0.8 25 9-33 149-177 (247)
484 COG0266 Nei Formamidopyrimidin 30.6 47 0.001 23.1 2.2 22 11-32 247-271 (273)
485 PF08882 Acetone_carb_G: Aceto 30.6 50 0.0011 20.4 2.1 16 8-23 73-88 (112)
486 PF02892 zf-BED: BED zinc fing 30.5 30 0.00064 16.7 0.9 16 24-39 14-29 (45)
487 PF15135 UPF0515: Uncharacteri 30.5 40 0.00086 23.8 1.8 30 8-37 154-185 (278)
488 PF02748 PyrI_C: Aspartate car 30.5 45 0.00098 17.6 1.7 14 23-36 32-45 (52)
489 PF10609 ParA: ParA/MinD ATPas 30.5 41 0.00089 19.4 1.6 15 8-22 64-78 (81)
490 PF01197 Ribosomal_L31: Riboso 30.5 39 0.00084 18.7 1.5 19 5-23 9-27 (69)
491 PF05280 FlhC: Flagellar trans 30.4 29 0.00063 22.4 1.1 26 8-33 133-161 (175)
492 COG2023 RPR2 RNase P subunit R 30.4 60 0.0013 19.8 2.4 29 10-38 57-94 (105)
493 PHA00080 DksA-like zinc finger 30.4 12 0.00027 20.9 -0.6 26 8-33 30-59 (72)
494 TIGR03676 aRF1/eRF1 peptide ch 30.3 50 0.0011 23.7 2.4 29 7-35 318-351 (403)
495 PF10164 DUF2367: Uncharacteri 30.3 21 0.00045 21.6 0.4 10 9-18 88-97 (98)
496 KOG0477 DNA replication licens 30.0 15 0.00032 29.3 -0.4 32 4-35 287-324 (854)
497 KOG2324 Prolyl-tRNA synthetase 29.8 45 0.00097 25.0 2.1 37 6-42 224-263 (457)
498 PF13575 DUF4135: Domain of un 29.6 30 0.00065 23.9 1.1 14 31-44 68-81 (370)
499 PRK14287 chaperone protein Dna 29.4 78 0.0017 22.2 3.2 21 28-48 197-217 (371)
500 PRK05767 rpl44e 50S ribosomal 29.4 40 0.00087 20.1 1.5 12 27-38 68-79 (92)
No 1
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=99.93 E-value=4.9e-26 Score=120.02 Aligned_cols=44 Identities=66% Similarity=1.334 Sum_probs=42.8
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEEecCceEEEEcC
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R~~~~~~~~Ar 51 (51)
|.|+|++||.+|+++..++|+||+||||||||+||+++++|+||
T Consensus 1 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~rIlyK~R~~~~~~~~Ar 44 (44)
T smart00659 1 MIYICGECGRENEIKSKDVVRCRECGYRILYKKRTKRLVEVKAR 44 (44)
T ss_pred CEEECCCCCCEeecCCCCceECCCCCceEEEEeCCCceEEEEcC
Confidence 68999999999999999999999999999999999999999997
No 2
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=99.91 E-value=1.7e-26 Score=129.28 Aligned_cols=47 Identities=77% Similarity=1.416 Sum_probs=45.5
Q ss_pred CCceEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEEecCceEEEEcC
Q 035461 5 PEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R~~~~~~~~Ar 51 (51)
+++|.|+|++||.+++++.+|.|||++||||||||+|+++++||+||
T Consensus 16 ~~~miYiCgdC~~en~lk~~D~irCReCG~RIlyKkRtkrlvqfear 62 (62)
T KOG3507|consen 16 TATMIYICGDCGQENTLKRGDVIRCRECGYRILYKKRTKRLVQFEAR 62 (62)
T ss_pred cccEEEEeccccccccccCCCcEehhhcchHHHHHHHHhhhheeecC
Confidence 37799999999999999999999999999999999999999999998
No 3
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=99.85 E-value=1.8e-21 Score=105.10 Aligned_cols=46 Identities=37% Similarity=0.647 Sum_probs=42.6
Q ss_pred CceEEEcCCCCCeeecC-CCCeeEcCCCCCcEEEEEecCceEEEEcC
Q 035461 6 EPVSYICGDCGMENTLK-PGDVIQCRECGYRILYKKRTRRIVQYEAR 51 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~-~~~~irC~~CG~RIlyK~R~~~~~~~~Ar 51 (51)
..+.|+|++||+++++. ..+.||||+||||||+|.|++.+++|+||
T Consensus 3 ~~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~K~R~~~~krvkA~ 49 (49)
T COG1996 3 AMMEYKCARCGREVELDQETRGIRCPYCGSRILVKERPKVPKRVKAR 49 (49)
T ss_pred ceEEEEhhhcCCeeehhhccCceeCCCCCcEEEEeccCCccEEEecC
Confidence 45899999999999954 67899999999999999999999999997
No 4
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=99.81 E-value=8e-21 Score=94.85 Aligned_cols=32 Identities=75% Similarity=1.485 Sum_probs=27.7
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCCcEEEEEe
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGYRILYKKR 41 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R 41 (51)
|+|++||++++++.+++|||++||||||||+|
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 5
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=99.56 E-value=9.7e-15 Score=76.17 Aligned_cols=44 Identities=39% Similarity=0.794 Sum_probs=40.8
Q ss_pred eEEEcCCCCCeeecCCCC-eeEcCCCCCcEEEEEecCceEEEEcC
Q 035461 8 VSYICGDCGMENTLKPGD-VIQCRECGYRILYKKRTRRIVQYEAR 51 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~-~irC~~CG~RIlyK~R~~~~~~~~Ar 51 (51)
+.|+|.+||++++++... .++||+||++++||.|++.+..++|+
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~~~~v~~~~~~ 46 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGYRILFKERPPVVKRVKAR 46 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCCeEEEccCCCcceEeecC
Confidence 579999999999998654 89999999999999999999999986
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=98.06 E-value=3.5e-06 Score=41.78 Aligned_cols=28 Identities=32% Similarity=0.730 Sum_probs=23.6
Q ss_pred eEEEcCCCCCeeecCC----CCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENTLKP----GDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~----~~~irC~~CG~R 35 (51)
..|+|.+||..+++.. .+.+.||+||..
T Consensus 4 Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred EEEEcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence 6899999999998642 567999999984
No 7
>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=97.98 E-value=7e-06 Score=42.15 Aligned_cols=28 Identities=36% Similarity=0.838 Sum_probs=23.6
Q ss_pred eEEEcCCCCCeeecC----CCCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENTLK----PGDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~----~~~~irC~~CG~R 35 (51)
..|+|.+||..|+.. ..+.+.||.||..
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSISEDDPVPCPECGST 35 (42)
T ss_pred EEEEeCCCCCEEEEEEEcCCCCCCcCCCCCCC
Confidence 579999999999964 3468999999993
No 8
>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=97.88 E-value=2.8e-05 Score=40.56 Aligned_cols=28 Identities=29% Similarity=0.681 Sum_probs=23.1
Q ss_pred eEEEcCCCCCeeecCC----CCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENTLKP----GDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~----~~~irC~~CG~R 35 (51)
.+|+|.+||.+|++.. .+.+.||.||..
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQKMSDDPLATCPECGGE 35 (52)
T ss_pred EEEEeCCCCCEeEEEEecCCCCCCCCCCCCCC
Confidence 6899999999999752 256889999984
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=97.78 E-value=5.7e-05 Score=37.32 Aligned_cols=30 Identities=20% Similarity=0.561 Sum_probs=24.5
Q ss_pred eEEEcCCCCCeeecCC------CCeeEcCCCCCcEE
Q 035461 8 VSYICGDCGMENTLKP------GDVIQCRECGYRIL 37 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~------~~~irC~~CG~RIl 37 (51)
|.+.|.+||+.+.+.. +..++||+||+.+.
T Consensus 1 M~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 1 MRIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred CEEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 5689999999999862 34599999998764
No 10
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=97.38 E-value=0.00017 Score=44.67 Aligned_cols=32 Identities=34% Similarity=0.708 Sum_probs=25.9
Q ss_pred CCceEEEcCCCCCeeecCC--------------------CCeeEcCCCCCcE
Q 035461 5 PEPVSYICGDCGMENTLKP--------------------GDVIQCRECGYRI 36 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~--------------------~~~irC~~CG~RI 36 (51)
..|..|.|.+||..+++.. ....+||.||+.-
T Consensus 66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRD 117 (135)
T ss_pred ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCC
Confidence 4678999999999998862 3457899999863
No 11
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=97.36 E-value=0.00033 Score=43.45 Aligned_cols=41 Identities=17% Similarity=0.442 Sum_probs=31.7
Q ss_pred CCCceEEEcCCCCCeeecC-------CCCeeEcCCCCCcEEEEEecCc
Q 035461 4 QPEPVSYICGDCGMENTLK-------PGDVIQCRECGYRILYKKRTRR 44 (51)
Q Consensus 4 ~~~~~~Y~C~~Cg~~~~~~-------~~~~irC~~CG~RIlyK~R~~~ 44 (51)
......|+|..||..++.. ..+...||+||..+.....+..
T Consensus 94 e~~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn~~~ 141 (147)
T smart00531 94 ETNNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEEDDNSEP 141 (147)
T ss_pred ccCCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEcCchhh
Confidence 3456899999999999863 2123999999999998766543
No 12
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=97.32 E-value=0.00042 Score=34.67 Aligned_cols=29 Identities=21% Similarity=0.683 Sum_probs=23.9
Q ss_pred eEEEcCCCCCeeecC------CCCeeEcCCCCCcE
Q 035461 8 VSYICGDCGMENTLK------PGDVIQCRECGYRI 36 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~------~~~~irC~~CG~RI 36 (51)
|.-.|.+|++.+++. .+..++|+.||+.+
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 456899999999986 34679999999864
No 13
>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=97.26 E-value=0.00016 Score=43.90 Aligned_cols=36 Identities=25% Similarity=0.433 Sum_probs=29.1
Q ss_pred CCCCCCceEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 1 MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 1 ~~~~~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
|-.+....+-+|.+||+.|---..++|.||+||.-.
T Consensus 1 MakpelGtKR~Cp~CG~kFYDLnk~PivCP~CG~~~ 36 (108)
T PF09538_consen 1 MAKPELGTKRTCPSCGAKFYDLNKDPIVCPKCGTEF 36 (108)
T ss_pred CCccccCCcccCCCCcchhccCCCCCccCCCCCCcc
Confidence 555667788999999999975555999999999643
No 14
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=97.18 E-value=0.00078 Score=33.69 Aligned_cols=29 Identities=21% Similarity=0.611 Sum_probs=23.9
Q ss_pred eEEEcCCCCCeeecC------CCCeeEcCCCCCcE
Q 035461 8 VSYICGDCGMENTLK------PGDVIQCRECGYRI 36 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~------~~~~irC~~CG~RI 36 (51)
|.-.|-+|++.+.+. .+..+||+.||+.+
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 456899999999986 24679999999865
No 15
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=97.16 E-value=0.00025 Score=43.03 Aligned_cols=33 Identities=24% Similarity=0.395 Sum_probs=27.0
Q ss_pred CCceEEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461 5 PEPVSYICGDCGMENTLKPGDVIQCRECGYRIL 37 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl 37 (51)
..|....|.+||..+++......+||.||+.-+
T Consensus 67 ~vp~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~ 99 (117)
T PRK00564 67 DEKVELECKDCSHVFKPNALDYGVCEKCHSKNV 99 (117)
T ss_pred ecCCEEEhhhCCCccccCCccCCcCcCCCCCce
Confidence 457889999999999887666678999998643
No 16
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=97.09 E-value=0.00012 Score=34.26 Aligned_cols=25 Identities=32% Similarity=0.826 Sum_probs=19.2
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
.-.|.+||++++. +.--||+||.++
T Consensus 2 ~~~Cp~Cg~~~~~---~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEIDP---DAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcCCc---ccccChhhCCCC
Confidence 4579999996533 458899999874
No 17
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=97.01 E-value=0.00059 Score=41.21 Aligned_cols=32 Identities=22% Similarity=0.421 Sum_probs=26.4
Q ss_pred CCceEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 5 PEPVSYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
..|....|.+||..+.+......+||.||+.-
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 66 EQEAECWCETCQQYVTLLTQRVRRCPQCHGDM 97 (114)
T ss_pred eeCcEEEcccCCCeeecCCccCCcCcCcCCCC
Confidence 45788999999999988765557899999764
No 18
>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=97.00 E-value=0.00023 Score=42.78 Aligned_cols=32 Identities=31% Similarity=0.580 Sum_probs=22.8
Q ss_pred CCceEEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461 5 PEPVSYICGDCGMENTLKPGDVIQCRECGYRIL 37 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl 37 (51)
..|....|.+||.++++.... ..||.||+.-+
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~-~~CP~Cgs~~~ 97 (113)
T PF01155_consen 66 EVPARARCRDCGHEFEPDEFD-FSCPRCGSPDV 97 (113)
T ss_dssp EE--EEEETTTS-EEECHHCC-HH-SSSSSS-E
T ss_pred ecCCcEECCCCCCEEecCCCC-CCCcCCcCCCc
Confidence 356889999999999998655 78999998743
No 19
>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=96.92 E-value=0.00039 Score=32.93 Aligned_cols=22 Identities=36% Similarity=0.912 Sum_probs=18.1
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
.|-+|++++.+. ...||+|||.
T Consensus 2 ~CP~C~~~V~~~---~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPES---AKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchhh---cCcCCCCCCC
Confidence 488999998654 4899999985
No 20
>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=96.83 E-value=0.0013 Score=32.52 Aligned_cols=27 Identities=22% Similarity=0.540 Sum_probs=21.3
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
+.|+|..||...+.+. .+-.||.||..
T Consensus 1 ~~~~C~~CG~i~~g~~-~p~~CP~Cg~~ 27 (34)
T cd00729 1 KVWVCPVCGYIHEGEE-APEKCPICGAP 27 (34)
T ss_pred CeEECCCCCCEeECCc-CCCcCcCCCCc
Confidence 3699999999877543 45699999973
No 21
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=96.81 E-value=0.0012 Score=31.86 Aligned_cols=25 Identities=36% Similarity=0.876 Sum_probs=16.4
Q ss_pred cCCCCCeeecCC-CCeeEcCCCCCcE
Q 035461 12 CGDCGMENTLKP-GDVIQCRECGYRI 36 (51)
Q Consensus 12 C~~Cg~~~~~~~-~~~irC~~CG~RI 36 (51)
|+.||.+..+.. +-..+||.||+..
T Consensus 6 C~~CG~~t~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 6 CGRCGAPTKPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp -TTT--BEEE-SSSS-EEESSSS-EE
T ss_pred cCcCCccccCCCCcCEeECCCCcCEe
Confidence 899999999875 4789999999864
No 22
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=96.79 E-value=0.0015 Score=35.57 Aligned_cols=33 Identities=33% Similarity=0.827 Sum_probs=26.2
Q ss_pred eEEEcCCCCCeeecCC---CCeeEcCCCCCcEEEEE
Q 035461 8 VSYICGDCGMENTLKP---GDVIQCRECGYRILYKK 40 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~---~~~irC~~CG~RIlyK~ 40 (51)
|.+.|..||.++++.. +..+.||.||..+=.-.
T Consensus 1 ~~~~CP~CG~~iev~~~~~GeiV~Cp~CGaeleVv~ 36 (54)
T TIGR01206 1 MQFECPDCGAEIELENPELGELVICDECGAELEVVS 36 (54)
T ss_pred CccCCCCCCCEEecCCCccCCEEeCCCCCCEEEEEe
Confidence 3578999999999863 57899999997765433
No 23
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=96.78 E-value=0.00046 Score=31.73 Aligned_cols=23 Identities=35% Similarity=0.800 Sum_probs=18.1
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
.|.+||++++. +..-|++||..|
T Consensus 1 ~Cp~CG~~~~~---~~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEIED---DAKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCCCC---cCcchhhhCCcC
Confidence 38899999754 457799999875
No 24
>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=96.77 E-value=0.0014 Score=32.01 Aligned_cols=25 Identities=28% Similarity=0.631 Sum_probs=20.9
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCC
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGY 34 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~ 34 (51)
.|+|..||...+... ++-+||.||.
T Consensus 1 ~~~C~~CGy~y~~~~-~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYDGEE-APWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEECCCc-CCCcCcCCCC
Confidence 489999999987553 6779999997
No 25
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=96.73 E-value=0.0015 Score=39.39 Aligned_cols=30 Identities=27% Similarity=0.521 Sum_probs=24.0
Q ss_pred CCceEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 5 PEPVSYICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
..|....|.+||.++++.... ..||.||+.
T Consensus 66 ~vp~~~~C~~Cg~~~~~~~~~-~~CP~Cgs~ 95 (113)
T PRK12380 66 YKPAQAWCWDCSQVVEIHQHD-AQCPHCHGE 95 (113)
T ss_pred eeCcEEEcccCCCEEecCCcC-ccCcCCCCC
Confidence 356889999999999987533 459999975
No 26
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=96.67 E-value=0.0012 Score=42.49 Aligned_cols=37 Identities=16% Similarity=0.424 Sum_probs=29.7
Q ss_pred CCCCceEEEcCCCCCeeecC--CCCeeEcCCCCCcEEEE
Q 035461 3 PQPEPVSYICGDCGMENTLK--PGDVIQCRECGYRILYK 39 (51)
Q Consensus 3 ~~~~~~~Y~C~~Cg~~~~~~--~~~~irC~~CG~RIlyK 39 (51)
.......|+|..||..++.. ....-.||.||.-..+-
T Consensus 111 ~e~~~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~~ 149 (178)
T PRK06266 111 EEENNMFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEEY 149 (178)
T ss_pred hccCCCEEECCCCCcEEeHHHHhhcCCcCCCCCCCCeec
Confidence 34566899999999999976 34579999999987764
No 27
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=96.61 E-value=0.0005 Score=46.67 Aligned_cols=30 Identities=37% Similarity=0.914 Sum_probs=23.1
Q ss_pred EEcCCCCCeeecC-------CCCeeEcCCCCCcEEEEE
Q 035461 10 YICGDCGMENTLK-------PGDVIQCRECGYRILYKK 40 (51)
Q Consensus 10 Y~C~~Cg~~~~~~-------~~~~irC~~CG~RIlyK~ 40 (51)
-.|+.|+-.+... .++.+.||+|| ||||..
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 4799998887642 56789999998 677753
No 28
>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=96.55 E-value=0.0014 Score=41.28 Aligned_cols=36 Identities=14% Similarity=0.034 Sum_probs=29.0
Q ss_pred CCCCCCceEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 1 MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 1 ~~~~~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
|-.+....+.+|-+||+.|---..++|.||+||.-.
T Consensus 1 m~k~elGtKr~Cp~cg~kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 1 MAKPDLGTKRICPNTGSKFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred CCchhhCccccCCCcCccccccCCCCccCCCcCCcc
Confidence 444556688999999999976666999999999764
No 29
>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=96.52 E-value=0.0016 Score=41.10 Aligned_cols=37 Identities=19% Similarity=0.367 Sum_probs=29.3
Q ss_pred CCCCceEEEcCCCCCeeecC--CCCeeEcCCCCCcEEEE
Q 035461 3 PQPEPVSYICGDCGMENTLK--PGDVIQCRECGYRILYK 39 (51)
Q Consensus 3 ~~~~~~~Y~C~~Cg~~~~~~--~~~~irC~~CG~RIlyK 39 (51)
....+..|.|..||..++.. ....-.||.||....+-
T Consensus 103 ~e~~~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L~~~ 141 (158)
T TIGR00373 103 FETNNMFFICPNMCVRFTFNEAMELNFTCPRCGAMLDYL 141 (158)
T ss_pred hccCCCeEECCCCCcEeeHHHHHHcCCcCCCCCCEeeec
Confidence 34567899999999999876 23568999999986653
No 30
>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=96.46 E-value=0.0028 Score=38.22 Aligned_cols=31 Identities=29% Similarity=0.604 Sum_probs=25.1
Q ss_pred CCceEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 5 PEPVSYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
..|....|.+||.++++... ...||.||+.-
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~-~~~CP~Cgs~~ 96 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEID-LYRCPKCHGIM 96 (115)
T ss_pred eeCcEEEcccCCCEEecCCc-CccCcCCcCCC
Confidence 45788999999999988753 47799999753
No 31
>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=96.40 E-value=0.004 Score=39.45 Aligned_cols=34 Identities=26% Similarity=0.619 Sum_probs=27.9
Q ss_pred CCceEEEcCCCCCeeecCC-CCeeEcCCCCCcEEE
Q 035461 5 PEPVSYICGDCGMENTLKP-GDVIQCRECGYRILY 38 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~-~~~irC~~CG~RIly 38 (51)
+.+-.|+|.+||..+.+.. ..-..||.||+.-+.
T Consensus 108 ~g~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F~ 142 (146)
T PF07295_consen 108 VGPGTLVCENCGHEVELTHPERLPPCPKCGHTEFT 142 (146)
T ss_pred ecCceEecccCCCEEEecCCCcCCCCCCCCCCeee
Confidence 4567899999999999974 455789999997664
No 32
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=96.37 E-value=0.0034 Score=41.24 Aligned_cols=32 Identities=19% Similarity=0.257 Sum_probs=26.1
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEEec
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRILYKKRT 42 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R~ 42 (51)
-.|+|-.|++.|. .+.-.||.||++++-|...
T Consensus 138 w~~rC~GC~~~f~---~~~~~Cp~CG~~~~~~~~~ 169 (177)
T COG1439 138 WRLRCHGCKRIFP---EPKDFCPICGSPLKRKRVK 169 (177)
T ss_pred eeEEEecCceecC---CCCCcCCCCCCceEEeeec
Confidence 6799999999998 4556899999997666544
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=96.27 E-value=0.0039 Score=29.24 Aligned_cols=23 Identities=26% Similarity=0.808 Sum_probs=17.7
Q ss_pred cCCCCCeeecCC-CCeeEcCCCCC
Q 035461 12 CGDCGMENTLKP-GDVIQCRECGY 34 (51)
Q Consensus 12 C~~Cg~~~~~~~-~~~irC~~CG~ 34 (51)
|..||..+.... ...-.||+||.
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 678888877654 56788999984
No 34
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=96.26 E-value=0.0022 Score=31.36 Aligned_cols=26 Identities=38% Similarity=0.856 Sum_probs=16.3
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
.|-.||.+.....+...-||.|||-+
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 68899999999999999999999864
No 35
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=96.19 E-value=0.0036 Score=38.27 Aligned_cols=31 Identities=35% Similarity=0.840 Sum_probs=22.9
Q ss_pred CCceEEEcCCCCCeeecCCCC------eeEcCCCCCcE
Q 035461 5 PEPVSYICGDCGMENTLKPGD------VIQCRECGYRI 36 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~~~------~irC~~CG~RI 36 (51)
..|....| +||.++++...+ ...||.||..-
T Consensus 66 ~vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~ 102 (124)
T PRK00762 66 MIPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKR 102 (124)
T ss_pred ecCeeEEe-eCcCcccccccchhccccCCcCcCCCCCC
Confidence 45788999 999998876321 26799999643
No 36
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=96.00 E-value=0.0098 Score=33.43 Aligned_cols=27 Identities=30% Similarity=0.935 Sum_probs=13.6
Q ss_pred eEEEcCCCCCeeecC------CCCeeEcCCCCC
Q 035461 8 VSYICGDCGMENTLK------PGDVIQCRECGY 34 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~------~~~~irC~~CG~ 34 (51)
+.|.|-+||.+.-.. .+.+-+||+||+
T Consensus 26 v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeehhhhHHHcCCceECCCcCc
Confidence 555555555433221 345556666654
No 37
>PRK12496 hypothetical protein; Provisional
Probab=95.93 E-value=0.004 Score=39.64 Aligned_cols=31 Identities=19% Similarity=0.326 Sum_probs=23.5
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRILYK 39 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK 39 (51)
-.|+|..||+.++... ..-.||.||+.+--|
T Consensus 126 w~~~C~gC~~~~~~~~-~~~~C~~CG~~~~r~ 156 (164)
T PRK12496 126 WRKVCKGCKKKYPEDY-PDDVCEICGSPVKRK 156 (164)
T ss_pred eeEECCCCCccccCCC-CCCcCCCCCChhhhc
Confidence 3599999999997654 225899999987433
No 38
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=95.85 E-value=0.017 Score=32.27 Aligned_cols=28 Identities=29% Similarity=0.650 Sum_probs=13.4
Q ss_pred EEcCCCCCeeecCC-CCeeEcCCCCCcEE
Q 035461 10 YICGDCGMENTLKP-GDVIQCRECGYRIL 37 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~-~~~irC~~CG~RIl 37 (51)
..|..||.++.... ...-.||+||.-++
T Consensus 8 ~~CtSCg~~i~~~~~~~~F~CPnCG~~~I 36 (59)
T PRK14890 8 PKCTSCGIEIAPREKAVKFLCPNCGEVII 36 (59)
T ss_pred ccccCCCCcccCCCccCEeeCCCCCCeeE
Confidence 34555555554332 34455555555433
No 39
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=95.61 E-value=0.0082 Score=32.90 Aligned_cols=26 Identities=31% Similarity=0.671 Sum_probs=21.1
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCC
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGY 34 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~ 34 (51)
...+|..||..|..+ .|.+.||.||-
T Consensus 4 ~~~~C~~Cg~~~~~~-dDiVvCp~Cga 29 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDG-DDIVVCPECGA 29 (54)
T ss_pred cCccChhhCCcccCC-CCEEECCCCCC
Confidence 346899999998655 48899999994
No 40
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=95.61 E-value=0.016 Score=38.53 Aligned_cols=31 Identities=23% Similarity=0.550 Sum_probs=26.2
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRILYK 39 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK 39 (51)
+.=+|++|+.+... .+..++||+||+.-.-|
T Consensus 148 I~A~CsrC~~~L~~-~~~~l~Cp~Cg~tEkRK 178 (188)
T COG1096 148 IYARCSRCRAPLVK-KGNMLKCPNCGNTEKRK 178 (188)
T ss_pred EEEEccCCCcceEE-cCcEEECCCCCCEEeee
Confidence 55689999999988 67999999999876544
No 41
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=95.46 E-value=0.019 Score=32.07 Aligned_cols=29 Identities=28% Similarity=0.840 Sum_probs=23.1
Q ss_pred ceEEEcCCCCCeeec------CCCCeeEcCCCCCc
Q 035461 7 PVSYICGDCGMENTL------KPGDVIQCRECGYR 35 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~------~~~~~irC~~CG~R 35 (51)
.+.|.|-+||.++-. +...+.+||+||+.
T Consensus 23 ~~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CGF~ 57 (59)
T PRK14890 23 AVKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGFE 57 (59)
T ss_pred cCEeeCCCCCCeeEeechhHHhcCCceECCCCCCc
Confidence 589999999998433 25678999999974
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=95.43 E-value=0.015 Score=29.43 Aligned_cols=27 Identities=22% Similarity=0.727 Sum_probs=18.9
Q ss_pred EEcCCCCCeee-cC-CCCeeEcCCCCCcE
Q 035461 10 YICGDCGMENT-LK-PGDVIQCRECGYRI 36 (51)
Q Consensus 10 Y~C~~Cg~~~~-~~-~~~~irC~~CG~RI 36 (51)
|+|..||...- .+ ....+.|++||.=|
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 78999998752 22 45778999998643
No 43
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=95.12 E-value=0.0069 Score=38.25 Aligned_cols=31 Identities=23% Similarity=0.399 Sum_probs=22.0
Q ss_pred EEcCCCCCeeecCCCC-eeEcCCCCCcEEEEE
Q 035461 10 YICGDCGMENTLKPGD-VIQCRECGYRILYKK 40 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~-~irC~~CG~RIlyK~ 40 (51)
.+|.+||+.|+-.... --=||+||.+-+-=.
T Consensus 2 H~Ct~Cg~~f~dgs~eil~GCP~CGg~kF~yv 33 (131)
T PF09845_consen 2 HQCTKCGRVFEDGSKEILSGCPECGGNKFQYV 33 (131)
T ss_pred cccCcCCCCcCCCcHHHHccCcccCCcceEEc
Confidence 4799999999865432 245999997655433
No 44
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=95.04 E-value=0.03 Score=27.60 Aligned_cols=26 Identities=31% Similarity=0.600 Sum_probs=22.0
Q ss_pred EEEcCCCCCeeec-CCCCeeEcCCCCC
Q 035461 9 SYICGDCGMENTL-KPGDVIQCRECGY 34 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~-~~~~~irC~~CG~ 34 (51)
.++|..||.+..+ +..+-..|++||.
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGS 29 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCc
Confidence 3689999999888 6778899999996
No 45
>PF12773 DZR: Double zinc ribbon
Probab=94.85 E-value=0.01 Score=30.36 Aligned_cols=25 Identities=24% Similarity=0.579 Sum_probs=16.2
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
.|..||..+.......+.|+.||..
T Consensus 14 fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 14 FCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred CChhhcCChhhccCCCCCCcCCcCC
Confidence 4666777766444456777777765
No 46
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=94.76 E-value=0.027 Score=34.78 Aligned_cols=30 Identities=40% Similarity=0.733 Sum_probs=25.2
Q ss_pred CCceEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 5 PEPVSYICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
.+|....|.+|+.++++...+.. ||.||+.
T Consensus 66 ~~p~~~~C~~C~~~~~~e~~~~~-CP~C~s~ 95 (115)
T COG0375 66 EEPAECWCLDCGQEVELEELDYR-CPKCGSI 95 (115)
T ss_pred EeccEEEeccCCCeecchhheeE-CCCCCCC
Confidence 35788999999999999876655 9999964
No 47
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=94.71 E-value=0.031 Score=28.55 Aligned_cols=24 Identities=42% Similarity=0.952 Sum_probs=18.5
Q ss_pred cCCCCCeeecCCC---CeeEcCCCCCc
Q 035461 12 CGDCGMENTLKPG---DVIQCRECGYR 35 (51)
Q Consensus 12 C~~Cg~~~~~~~~---~~irC~~CG~R 35 (51)
|.+||..+..+.. .-..||.|||.
T Consensus 3 Cp~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 3 CPKCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCCCCccccccCCCCCEEECCcCCCe
Confidence 8899998877643 36889999974
No 48
>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=94.55 E-value=0.033 Score=30.02 Aligned_cols=25 Identities=36% Similarity=1.024 Sum_probs=18.8
Q ss_pred EcCCCCCeeec-CCCCeeEcCCCCCc
Q 035461 11 ICGDCGMENTL-KPGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~-~~~~~irC~~CG~R 35 (51)
.|..||..... .......||.||+.
T Consensus 30 ~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCcccccccccccceEEcCCCCCE
Confidence 48888888776 35577888888875
No 49
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=94.53 E-value=0.048 Score=34.40 Aligned_cols=31 Identities=26% Similarity=0.558 Sum_probs=24.5
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCCcEEEEE
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGYRILYKK 40 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~ 40 (51)
.+-|..||.+..- ..+.|-||.||++....+
T Consensus 28 ~~hCp~Cg~PLF~-KdG~v~CPvC~~~~~~v~ 58 (131)
T COG1645 28 AKHCPKCGTPLFR-KDGEVFCPVCGYREVVVE 58 (131)
T ss_pred HhhCcccCCccee-eCCeEECCCCCceEEEee
Confidence 4679999999855 557799999999765543
No 50
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=94.49 E-value=0.045 Score=30.76 Aligned_cols=29 Identities=28% Similarity=0.698 Sum_probs=23.5
Q ss_pred EcCCCCCeeecC-CCCeeEcCCCCCcEEEE
Q 035461 11 ICGDCGMENTLK-PGDVIQCRECGYRILYK 39 (51)
Q Consensus 11 ~C~~Cg~~~~~~-~~~~irC~~CG~RIlyK 39 (51)
.|..||.++.+. ....--||+||.-++|.
T Consensus 11 ~CtSCg~~i~p~e~~v~F~CPnCGe~~I~R 40 (61)
T COG2888 11 VCTSCGREIAPGETAVKFPCPNCGEVEIYR 40 (61)
T ss_pred eeccCCCEeccCCceeEeeCCCCCceeeeh
Confidence 799999999655 45678999999877763
No 51
>PRK00420 hypothetical protein; Validated
Probab=94.45 E-value=0.043 Score=33.66 Aligned_cols=31 Identities=19% Similarity=0.286 Sum_probs=24.4
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCCcEEEEE
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGYRILYKK 40 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~ 40 (51)
-.|..||.++.-.....+.||.||.-+..+.
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVYIVKS 54 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCeeeecc
Confidence 4699999988654567899999999776543
No 52
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=94.44 E-value=0.017 Score=31.04 Aligned_cols=26 Identities=27% Similarity=0.713 Sum_probs=21.1
Q ss_pred eEEEcCCCCCeeecC------------CCCeeEcCCCC
Q 035461 8 VSYICGDCGMENTLK------------PGDVIQCRECG 33 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~------------~~~~irC~~CG 33 (51)
..+.|-+||++|.+. .+.+.||+.|-
T Consensus 3 k~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR 40 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCR 40 (49)
T ss_pred eeEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHH
Confidence 468999999999874 24689999885
No 53
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=94.43 E-value=0.031 Score=36.28 Aligned_cols=25 Identities=24% Similarity=0.581 Sum_probs=21.9
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
.|+|..||..+.- ..+-+||.||..
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 577899999964
No 54
>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=94.34 E-value=0.029 Score=33.64 Aligned_cols=29 Identities=21% Similarity=0.390 Sum_probs=23.6
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
....|+.|+.+|.+-.+.+..|.+|+++|
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 45689999999988888889999999887
No 55
>PF14369 zf-RING_3: zinc-finger
Probab=94.34 E-value=0.065 Score=26.60 Aligned_cols=29 Identities=21% Similarity=0.578 Sum_probs=23.1
Q ss_pred EEEcCCCCCeeecCC--CCeeEcCCCCCcEE
Q 035461 9 SYICGDCGMENTLKP--GDVIQCRECGYRIL 37 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~--~~~irC~~CG~RIl 37 (51)
.|=|-.|.+.+.+.. .+.+.||+|+.-.|
T Consensus 2 ~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFv 32 (35)
T PF14369_consen 2 RYWCHQCNRFVRIAPSPDSDVACPRCHGGFV 32 (35)
T ss_pred CEeCccCCCEeEeCcCCCCCcCCcCCCCcEe
Confidence 488999999999853 34456999998776
No 56
>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=94.17 E-value=0.071 Score=32.19 Aligned_cols=34 Identities=24% Similarity=0.531 Sum_probs=25.6
Q ss_pred CceEEEcCCCCCeeecCCC---CeeEcCCCCCcEEEE
Q 035461 6 EPVSYICGDCGMENTLKPG---DVIQCRECGYRILYK 39 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~~~---~~irC~~CG~RIlyK 39 (51)
....|.|..||.++..... ...+|+.||..+...
T Consensus 120 ~~~~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~l~~~ 156 (157)
T PF10263_consen 120 KKYVYRCPSCGREYKRHRRSKRKRYRCGRCGGPLVQV 156 (157)
T ss_pred cceEEEcCCCCCEeeeecccchhhEECCCCCCEEEEc
Confidence 3478999999998876532 457899999776543
No 57
>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=94.10 E-value=0.059 Score=30.77 Aligned_cols=33 Identities=30% Similarity=0.642 Sum_probs=22.8
Q ss_pred eEEEcCCCCCeeecCC-CCeeEcCCCCCcEEEEEec
Q 035461 8 VSYICGDCGMENTLKP-GDVIQCRECGYRILYKKRT 42 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~-~~~irC~~CG~RIlyK~R~ 42 (51)
+.|+| +||+..-.+. ...-+| .||++|=.|+|.
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 47899 7999887664 467899 999999887764
No 58
>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=94.10 E-value=0.038 Score=34.08 Aligned_cols=25 Identities=32% Similarity=0.733 Sum_probs=22.0
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
.|..|+.++.-+.++..-||+|||-
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~E 28 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYE 28 (109)
T ss_pred cCCcCCCcceEecCCeeECcccccc
Confidence 4889999999888889999999985
No 59
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=94.05 E-value=0.049 Score=28.93 Aligned_cols=27 Identities=30% Similarity=0.693 Sum_probs=20.8
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYRIL 37 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~RIl 37 (51)
-|.+||.++.....+...|..||+...
T Consensus 22 fCP~Cg~~~m~~~~~r~~C~~Cgyt~~ 48 (50)
T PRK00432 22 FCPRCGSGFMAEHLDRWHCGKCGYTEF 48 (50)
T ss_pred cCcCCCcchheccCCcEECCCcCCEEe
Confidence 688999875455567899999998654
No 60
>PRK06450 threonine synthase; Validated
Probab=94.00 E-value=0.046 Score=37.78 Aligned_cols=29 Identities=31% Similarity=0.612 Sum_probs=22.3
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcEEE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRILY 38 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIly 38 (51)
+.|+|.+||++... ....+||.||..+..
T Consensus 2 ~~~~C~~Cg~~~~~--~~~~~C~~cg~~l~~ 30 (338)
T PRK06450 2 VKEVCMKCGKERES--IYEIRCKKCGGPFEI 30 (338)
T ss_pred ceeEECCcCCcCCC--cccccCCcCCCEeEE
Confidence 56899999999754 234799999976544
No 61
>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=93.98 E-value=0.061 Score=27.23 Aligned_cols=25 Identities=32% Similarity=0.728 Sum_probs=15.1
Q ss_pred eEEEcCCCCCeeecC--CCCeeEcCCCCC
Q 035461 8 VSYICGDCGMENTLK--PGDVIQCRECGY 34 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~ 34 (51)
-.|+|..||..+++- .+.++-| ||-
T Consensus 5 ~~YkC~~CGniVev~~~g~g~lvC--CGe 31 (36)
T PF06397_consen 5 EFYKCEHCGNIVEVVHDGGGPLVC--CGE 31 (36)
T ss_dssp EEEE-TTT--EEEEEE--SS-EEE--TTE
T ss_pred cEEEccCCCCEEEEEECCCCCEEe--CCc
Confidence 579999999999874 2356777 553
No 62
>PRK07591 threonine synthase; Validated
Probab=93.91 E-value=0.063 Score=38.00 Aligned_cols=30 Identities=33% Similarity=0.597 Sum_probs=23.7
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRILYK 39 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK 39 (51)
..++|.+||+++.+.. . .+||.||.-+-..
T Consensus 17 ~~l~C~~Cg~~~~~~~-~-~~C~~cg~~l~~~ 46 (421)
T PRK07591 17 VALKCRECGAEYPLGP-I-HVCEECFGPLEVA 46 (421)
T ss_pred eEEEeCCCCCcCCCCC-C-ccCCCCCCeEEEE
Confidence 4599999999998764 3 9999999755443
No 63
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=93.76 E-value=0.029 Score=40.94 Aligned_cols=32 Identities=22% Similarity=0.503 Sum_probs=25.3
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCcEEEEEec
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYRILYKKRT 42 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R~ 42 (51)
+|..||...+..-....||+.||+|+=...+.
T Consensus 352 ~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 352 VCPRCGGRMKSAGRNGFRCKKCGTRARETLIK 383 (421)
T ss_pred CCCccCCchhhcCCCCcccccccccCCccccc
Confidence 79999999987743499999999987554443
No 64
>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=93.75 E-value=0.068 Score=29.88 Aligned_cols=21 Identities=33% Similarity=0.823 Sum_probs=17.6
Q ss_pred CeeEcCCCCCcEEEEEecCce
Q 035461 25 DVIQCRECGYRILYKKRTRRI 45 (51)
Q Consensus 25 ~~irC~~CG~RIlyK~R~~~~ 45 (51)
..+-|++|||-=||+..+...
T Consensus 35 ~~v~C~~CGYTE~Y~~~~~~~ 55 (64)
T PF09855_consen 35 TTVSCTNCGYTEFYKAKTSNG 55 (64)
T ss_pred EEEECCCCCCEEEEeecCccc
Confidence 468999999999999877643
No 65
>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=93.68 E-value=0.034 Score=30.24 Aligned_cols=29 Identities=21% Similarity=0.299 Sum_probs=20.6
Q ss_pred EEEcCCCCCeeec-CCC--CeeEcCCCCCcEE
Q 035461 9 SYICGDCGMENTL-KPG--DVIQCRECGYRIL 37 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~-~~~--~~irC~~CG~RIl 37 (51)
+++|+.|++..-. ... -.|+||.||.--.
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~ 35 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINH 35 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccce
Confidence 5789999887654 222 4799999986433
No 66
>PHA02768 hypothetical protein; Provisional
Probab=93.65 E-value=0.045 Score=29.99 Aligned_cols=40 Identities=23% Similarity=0.423 Sum_probs=29.4
Q ss_pred eEEEcCCCCCeeecCCC---------CeeEcCCCCCcEEEEEecCceEEEEc
Q 035461 8 VSYICGDCGMENTLKPG---------DVIQCRECGYRILYKKRTRRIVQYEA 50 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~---------~~irC~~CG~RIlyK~R~~~~~~~~A 50 (51)
.-|.|..||+.|...+. .+-+|.+||- +.. |+...+.++|
T Consensus 4 ~~y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k-~f~--~~s~l~~~~~ 52 (55)
T PHA02768 4 LGYECPICGEIYIKRKSMITHLRKHNTNLKLSNCKR-ISL--RTGEYIEIKA 52 (55)
T ss_pred cccCcchhCCeeccHHHHHHHHHhcCCcccCCcccc-eec--ccceeEEEec
Confidence 35899999999986421 4789999997 333 6666777665
No 67
>PF14353 CpXC: CpXC protein
Probab=93.54 E-value=0.09 Score=31.39 Aligned_cols=26 Identities=27% Similarity=0.667 Sum_probs=19.5
Q ss_pred EcCCCCCeeecC--------------------CCCeeEcCCCCCcE
Q 035461 11 ICGDCGMENTLK--------------------PGDVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~--------------------~~~~irC~~CG~RI 36 (51)
.|..||..++.+ .--...||+||+.+
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKF 48 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCce
Confidence 589999998864 11368999999754
No 68
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=93.52 E-value=0.014 Score=36.01 Aligned_cols=32 Identities=25% Similarity=0.485 Sum_probs=22.2
Q ss_pred eEEEcCCCCCeeecCC-CCeeEcCCCCCcE-EEE
Q 035461 8 VSYICGDCGMENTLKP-GDVIQCRECGYRI-LYK 39 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~-~~~irC~~CG~RI-lyK 39 (51)
|..+|.+||..|+--+ .-.-=||+||.+- +|-
T Consensus 1 MpH~CtrCG~vf~~g~~~il~GCp~CG~nkF~yv 34 (112)
T COG3364 1 MPHQCTRCGEVFDDGSEEILSGCPKCGCNKFLYV 34 (112)
T ss_pred CCceecccccccccccHHHHccCccccchheEec
Confidence 4578999999987632 1224599999764 443
No 69
>PRK11032 hypothetical protein; Provisional
Probab=93.45 E-value=0.07 Score=34.41 Aligned_cols=33 Identities=18% Similarity=0.433 Sum_probs=26.7
Q ss_pred CceEEEcCCCCCeeecC-CCCeeEcCCCCCcEEE
Q 035461 6 EPVSYICGDCGMENTLK-PGDVIQCRECGYRILY 38 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~-~~~~irC~~CG~RIly 38 (51)
.+-...|-+||....+. +..-..||+||+.-+-
T Consensus 121 g~G~LvC~~Cg~~~~~~~p~~i~pCp~C~~~~F~ 154 (160)
T PRK11032 121 GLGNLVCEKCHHHLAFYTPEVLPLCPKCGHDQFQ 154 (160)
T ss_pred ecceEEecCCCCEEEecCCCcCCCCCCCCCCeee
Confidence 44678999999999997 4566789999997653
No 70
>PRK10220 hypothetical protein; Provisional
Probab=93.41 E-value=0.074 Score=32.89 Aligned_cols=25 Identities=28% Similarity=0.638 Sum_probs=21.4
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
.|..|+.++.-+.++..-||+|||.
T Consensus 5 ~CP~C~seytY~d~~~~vCpeC~hE 29 (111)
T PRK10220 5 HCPKCNSEYTYEDNGMYICPECAHE 29 (111)
T ss_pred cCCCCCCcceEcCCCeEECCcccCc
Confidence 4888999988888888999999984
No 71
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=93.02 E-value=0.069 Score=28.50 Aligned_cols=26 Identities=35% Similarity=0.670 Sum_probs=20.1
Q ss_pred EEEcCCCCCeeecCCC----------------CeeEcCCCCC
Q 035461 9 SYICGDCGMENTLKPG----------------DVIQCRECGY 34 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~----------------~~irC~~CG~ 34 (51)
.|+|..||-..+.+.+ +.-+||.||.
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 4899999999886533 3359999995
No 72
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=92.83 E-value=0.049 Score=32.99 Aligned_cols=25 Identities=24% Similarity=0.539 Sum_probs=20.6
Q ss_pred EcCCCCCeeecC-CCCeeEcCCCCCc
Q 035461 11 ICGDCGMENTLK-PGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~~-~~~~irC~~CG~R 35 (51)
.|-+||.+|..+ .+-+-|||.|-+-
T Consensus 60 ~CkkCGfef~~~~ik~pSRCP~CKSE 85 (97)
T COG3357 60 RCKKCGFEFRDDKIKKPSRCPKCKSE 85 (97)
T ss_pred hhcccCccccccccCCcccCCcchhh
Confidence 699999999874 4568999999764
No 73
>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=92.79 E-value=0.25 Score=26.47 Aligned_cols=35 Identities=29% Similarity=0.578 Sum_probs=25.9
Q ss_pred CCCCceEEEcCCCCCeeecCC------CCeeEcCCCCCcEEE
Q 035461 3 PQPEPVSYICGDCGMENTLKP------GDVIQCRECGYRILY 38 (51)
Q Consensus 3 ~~~~~~~Y~C~~Cg~~~~~~~------~~~irC~~CG~RIly 38 (51)
...+...|-| +||..+.+.. ...+-|+.|.-.|-.
T Consensus 12 ~~~~~~~y~C-RCG~~f~i~e~~l~~~~~iv~C~sCSL~I~V 52 (55)
T PF05207_consen 12 EEEGVYSYPC-RCGGEFEISEEDLEEGEVIVQCDSCSLWIRV 52 (55)
T ss_dssp TTTTEEEEEE-TTSSEEEEEHHHHHCT--EEEETTTTEEEEE
T ss_pred CCCCEEEEcC-CCCCEEEEcchhccCcCEEEECCCCccEEEE
Confidence 3445689999 9999999852 245999999977653
No 74
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=92.78 E-value=0.027 Score=33.22 Aligned_cols=28 Identities=36% Similarity=0.816 Sum_probs=23.2
Q ss_pred eEEEcCCCCCeeecC----CCCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENTLK----PGDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~----~~~~irC~~CG~R 35 (51)
..|.|.+||..+++- .....-|++||.+
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 689999999999874 3355899999985
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=92.69 E-value=0.091 Score=30.41 Aligned_cols=25 Identities=40% Similarity=0.842 Sum_probs=19.9
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
-|.+||..+... .+.+.|+.||+..
T Consensus 2 fC~~Cg~~l~~~-~~~~~C~~C~~~~ 26 (104)
T TIGR01384 2 FCPKCGSLMTPK-NGVYVCPSCGYEK 26 (104)
T ss_pred CCcccCcccccC-CCeEECcCCCCcc
Confidence 388999998654 4679999999763
No 76
>PRK06260 threonine synthase; Validated
Probab=92.65 E-value=0.13 Score=35.98 Aligned_cols=29 Identities=28% Similarity=0.512 Sum_probs=22.6
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCCcEEE
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGYRILY 38 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RIly 38 (51)
.++|.+||++..+.. ...+||.||..+..
T Consensus 3 ~~~C~~cg~~~~~~~-~~~~Cp~cg~~l~~ 31 (397)
T PRK06260 3 WLKCIECGKEYDPDE-IIYTCPECGGLLEV 31 (397)
T ss_pred EEEECCCCCCCCCCC-ccccCCCCCCeEEE
Confidence 589999999987664 34789999976443
No 77
>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=92.56 E-value=0.15 Score=24.83 Aligned_cols=26 Identities=27% Similarity=0.552 Sum_probs=15.6
Q ss_pred ceEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 7 PVSYICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
-+.-+|.+||..+-... ..||.||..
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 37789999999865443 789999864
No 78
>PHA00626 hypothetical protein
Probab=92.53 E-value=0.14 Score=28.63 Aligned_cols=26 Identities=38% Similarity=0.758 Sum_probs=17.3
Q ss_pred EcCCCCCeeecC------CCCeeEcCCCCCcE
Q 035461 11 ICGDCGMENTLK------PGDVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~------~~~~irC~~CG~RI 36 (51)
.|.+||...-++ +...-.|+.|||+.
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence 477888743332 24668899999874
No 79
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=92.35 E-value=0.089 Score=36.64 Aligned_cols=27 Identities=30% Similarity=0.759 Sum_probs=22.6
Q ss_pred EcCCCCCeeecCC-CCeeEcCCCCCcEE
Q 035461 11 ICGDCGMENTLKP-GDVIQCRECGYRIL 37 (51)
Q Consensus 11 ~C~~Cg~~~~~~~-~~~irC~~CG~RIl 37 (51)
-|+.||.+..... +....|+.||+...
T Consensus 113 FCg~CG~~~~~~~~g~~~~C~~cg~~~f 140 (279)
T COG2816 113 FCGRCGTKTYPREGGWARVCPKCGHEHF 140 (279)
T ss_pred CCCCCCCcCccccCceeeeCCCCCCccC
Confidence 3999999999875 46799999999753
No 80
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=92.24 E-value=0.09 Score=27.77 Aligned_cols=23 Identities=30% Similarity=0.885 Sum_probs=18.4
Q ss_pred EcCCCCCeeecC------C-CCeeEcCCCC
Q 035461 11 ICGDCGMENTLK------P-GDVIQCRECG 33 (51)
Q Consensus 11 ~C~~Cg~~~~~~------~-~~~irC~~CG 33 (51)
.|+.|+..+... . ...+.||+||
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~Cg 53 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNCG 53 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCCC
Confidence 799999888753 3 3679999998
No 81
>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=92.21 E-value=0.096 Score=26.17 Aligned_cols=28 Identities=25% Similarity=0.526 Sum_probs=22.7
Q ss_pred EEcCCCCCeeecCC---CCeeEcCCCCCcEE
Q 035461 10 YICGDCGMENTLKP---GDVIQCRECGYRIL 37 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~---~~~irC~~CG~RIl 37 (51)
.+|..||+...+.. ...-.|..||..++
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 58999999999874 35689999999553
No 82
>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=92.03 E-value=0.16 Score=26.83 Aligned_cols=27 Identities=33% Similarity=0.676 Sum_probs=19.4
Q ss_pred EEEcCCCCCeeecCCC----------------CeeEcCCCCCc
Q 035461 9 SYICGDCGMENTLKPG----------------DVIQCRECGYR 35 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~----------------~~irC~~CG~R 35 (51)
.|+|..||...+...+ +.-+||.||..
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 5999999988886543 35699999863
No 83
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=91.97 E-value=0.24 Score=30.31 Aligned_cols=32 Identities=22% Similarity=0.622 Sum_probs=24.5
Q ss_pred ceEEEcCCCCCeeecC--C-C-CeeEcCCCCCcEEE
Q 035461 7 PVSYICGDCGMENTLK--P-G-DVIQCRECGYRILY 38 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~--~-~-~~irC~~CG~RIly 38 (51)
...|.|..||....-. . + ...+|..||.++..
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 5799999999876422 1 2 55999999999875
No 84
>PRK04351 hypothetical protein; Provisional
Probab=91.94 E-value=0.37 Score=30.42 Aligned_cols=34 Identities=21% Similarity=0.463 Sum_probs=25.7
Q ss_pred CceEEEcCCCCCeeecC---CCCeeEcCCCCCcEEEE
Q 035461 6 EPVSYICGDCGMENTLK---PGDVIQCRECGYRILYK 39 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~---~~~~irC~~CG~RIlyK 39 (51)
....|.|.+||...--. ....-+|..||.++..+
T Consensus 109 ~~y~Y~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 109 KNYLYECQSCGQQYLRKRRINTKRYRCGKCRGKLKLI 145 (149)
T ss_pred ceEEEECCCCCCEeeeeeecCCCcEEeCCCCcEeeec
Confidence 34889999999866432 12558999999998876
No 85
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=91.91 E-value=0.069 Score=28.75 Aligned_cols=27 Identities=37% Similarity=0.906 Sum_probs=21.7
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRIL 37 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl 37 (51)
...+|-.|++.+...+ .+|..|||.-|
T Consensus 13 ~k~ICrkC~ARnp~~A---~~CRKCg~~~L 39 (48)
T PRK04136 13 NKKICMRCNARNPWRA---TKCRKCGYKNL 39 (48)
T ss_pred cccchhcccCCCCccc---cccccCCCCCc
Confidence 4579999999987664 88999999643
No 86
>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=91.86 E-value=0.14 Score=36.93 Aligned_cols=31 Identities=16% Similarity=0.434 Sum_probs=23.6
Q ss_pred ceEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEE
Q 035461 7 PVSYICGDCGMENTLKPGDVIQCRECGYRILYKK 40 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~ 40 (51)
...|.|.+||.+..- -.-+||.||.+==+++
T Consensus 5 ~~~y~C~~Cg~~~~~---~~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 5 KSKFVCQHCGADSPK---WQGKCPACHAWNTITE 35 (454)
T ss_pred CCeEECCcCCCCCcc---ccEECcCCCCccccch
Confidence 357999999998533 3479999998766555
No 87
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=91.85 E-value=0.2 Score=33.72 Aligned_cols=31 Identities=35% Similarity=0.861 Sum_probs=21.0
Q ss_pred CCceEEEcCCCCCeee----cCC-C--CeeEcCCCCCc
Q 035461 5 PEPVSYICGDCGMENT----LKP-G--DVIQCRECGYR 35 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~----~~~-~--~~irC~~CG~R 35 (51)
.+...+.|..||.+-. ++. + ..+||.+||+=
T Consensus 2 ~~~iy~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V 39 (201)
T COG1326 2 TEEIYIECPSCGSEEVSHEVIKERGREPLVRCEECGTV 39 (201)
T ss_pred cceEEEECCCCCcchhhHHHHHhcCCceEEEccCCCcE
Confidence 3567899999992221 122 2 47999999963
No 88
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=91.68 E-value=0.1 Score=42.69 Aligned_cols=29 Identities=28% Similarity=0.779 Sum_probs=18.0
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGYRIL 37 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl 37 (51)
.|.|.+||.++.........||+||....
T Consensus 692 vy~CPsCGaev~~des~a~~CP~CGtplv 720 (1337)
T PRK14714 692 VYVCPDCGAEVPPDESGRVECPRCDVELT 720 (1337)
T ss_pred ceeCccCCCccCCCccccccCCCCCCccc
Confidence 45677777766554333667777776554
No 89
>PRK11823 DNA repair protein RadA; Provisional
Probab=91.63 E-value=0.15 Score=36.48 Aligned_cols=32 Identities=28% Similarity=0.650 Sum_probs=24.8
Q ss_pred ceEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEEe
Q 035461 7 PVSYICGDCGMENTLKPGDVIQCRECGYRILYKKR 41 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R 41 (51)
...|+|.+||.+..- -.-+||.||.+==+++.
T Consensus 5 ~~~y~C~~Cg~~~~~---~~g~Cp~C~~w~t~~e~ 36 (446)
T PRK11823 5 KTAYVCQECGAESPK---WLGRCPECGAWNTLVEE 36 (446)
T ss_pred CCeEECCcCCCCCcc---cCeeCcCCCCccceeee
Confidence 467999999998643 23799999988777663
No 90
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=91.49 E-value=0.44 Score=27.18 Aligned_cols=31 Identities=29% Similarity=0.650 Sum_probs=24.5
Q ss_pred eEEEcCCCCCeeecC--CCCeeEcCCCCCcEEE
Q 035461 8 VSYICGDCGMENTLK--PGDVIQCRECGYRILY 38 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~RIly 38 (51)
+.-+|.+||.+.-+- +...++|..||--+..
T Consensus 18 l~VkCpdC~N~q~vFshast~V~C~~CG~~l~~ 50 (67)
T COG2051 18 LRVKCPDCGNEQVVFSHASTVVTCLICGTTLAE 50 (67)
T ss_pred EEEECCCCCCEEEEeccCceEEEecccccEEEe
Confidence 667899999987764 5578999999976553
No 91
>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=91.42 E-value=0.24 Score=25.29 Aligned_cols=22 Identities=27% Similarity=0.552 Sum_probs=14.5
Q ss_pred cCCCCeeEcCCCCCcEEEEEec
Q 035461 21 LKPGDVIQCRECGYRILYKKRT 42 (51)
Q Consensus 21 ~~~~~~irC~~CG~RIlyK~R~ 42 (51)
+...+++.||.||+.-.|..++
T Consensus 13 ~RW~~g~~CP~Cg~~~~~~~~~ 34 (46)
T PF12760_consen 13 IRWPDGFVCPHCGSTKHYRLKT 34 (46)
T ss_pred hcCCCCCCCCCCCCeeeEEeCC
Confidence 3445566788888776666665
No 92
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=91.23 E-value=0.36 Score=26.84 Aligned_cols=29 Identities=31% Similarity=0.767 Sum_probs=24.1
Q ss_pred eEEEcCCCCCeeecC--CCCeeEcCCCCCcE
Q 035461 8 VSYICGDCGMENTLK--PGDVIQCRECGYRI 36 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~RI 36 (51)
+.=+|.+|+.+.-+- +...+.|..||.-+
T Consensus 10 ~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L 40 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSHASTVVRCLVCGKTL 40 (59)
T ss_pred EEEECCCCCCeEEEEecCCcEEECcccCCCc
Confidence 777999999998764 56789999999754
No 93
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=91.22 E-value=0.044 Score=39.73 Aligned_cols=26 Identities=27% Similarity=0.638 Sum_probs=21.1
Q ss_pred EcCCCCCeeecCCC--CeeEcCCCCCcE
Q 035461 11 ICGDCGMENTLKPG--DVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~--~~irC~~CG~RI 36 (51)
-|.+|.+.++++.. ...|||.||.+|
T Consensus 248 AC~rC~t~y~le~A~~~~wrCpkCGg~i 275 (403)
T COG1379 248 ACSRCYTRYSLEEAKSLRWRCPKCGGKI 275 (403)
T ss_pred HHHHhhhccCcchhhhhcccCcccccch
Confidence 49999999998853 448999999954
No 94
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=90.99 E-value=0.36 Score=30.76 Aligned_cols=30 Identities=20% Similarity=0.496 Sum_probs=24.4
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRIL 37 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl 37 (51)
+.=+|..||..........+.||+||.+-.
T Consensus 148 v~a~~~~~g~~~~~~~~~~~~c~~~~~~e~ 177 (189)
T PRK09521 148 IYAMCSRCRTPLVKKGENELKCPNCGNIET 177 (189)
T ss_pred EEEEccccCCceEECCCCEEECCCCCCEEe
Confidence 445699999999776668899999997654
No 95
>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=90.97 E-value=0.23 Score=24.75 Aligned_cols=25 Identities=24% Similarity=0.561 Sum_probs=20.0
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
.|+.||..+-........|..||+-
T Consensus 10 ~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 10 PCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred cCCCCCCeEeEccCCEEEhhhCceE
Confidence 4999999966666677889999874
No 96
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=90.64 E-value=0.36 Score=27.41 Aligned_cols=31 Identities=26% Similarity=0.664 Sum_probs=23.8
Q ss_pred CCCCceEEEcCCCCCeeecCC-----C-CeeEcCCCCC
Q 035461 3 PQPEPVSYICGDCGMENTLKP-----G-DVIQCRECGY 34 (51)
Q Consensus 3 ~~~~~~~Y~C~~Cg~~~~~~~-----~-~~irC~~CG~ 34 (51)
+..+...|-|. ||..|++.. + ...|||.|.-
T Consensus 16 ~e~~~ftyPCP-CGDRFeIsLeDl~~GE~VArCPSCSL 52 (67)
T COG5216 16 REEKTFTYPCP-CGDRFEISLEDLRNGEVVARCPSCSL 52 (67)
T ss_pred CCCceEEecCC-CCCEeEEEHHHhhCCceEEEcCCceE
Confidence 44566889998 999999862 2 5689999973
No 97
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=90.34 E-value=0.46 Score=24.20 Aligned_cols=20 Identities=25% Similarity=0.796 Sum_probs=15.8
Q ss_pred CeeEcCCCCCcEEEEEecCc
Q 035461 25 DVIQCRECGYRILYKKRTRR 44 (51)
Q Consensus 25 ~~irC~~CG~RIlyK~R~~~ 44 (51)
+.|+|.+||++...+.++.+
T Consensus 4 g~l~C~~CG~~m~~~~~~~~ 23 (58)
T PF13408_consen 4 GLLRCGHCGSKMTRRKRKGK 23 (58)
T ss_pred CcEEcccCCcEeEEEECCCC
Confidence 56899999999888777643
No 98
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=90.24 E-value=0.43 Score=25.66 Aligned_cols=31 Identities=26% Similarity=0.476 Sum_probs=22.5
Q ss_pred CCceEEEcCCCCCeeecC-----CCCeeEcCCCCCc
Q 035461 5 PEPVSYICGDCGMENTLK-----PGDVIQCRECGYR 35 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~-----~~~~irC~~CG~R 35 (51)
.....-||.+|...+.+- ..-.-+|++||+-
T Consensus 18 ~~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 18 SNRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred cCceeEECcccchhhcccccccCCceEEEcCCCCCc
Confidence 455778999998777654 1235899999973
No 99
>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=90.21 E-value=0.15 Score=35.93 Aligned_cols=29 Identities=28% Similarity=0.665 Sum_probs=22.7
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCCcEEEEEe
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGYRILYKKR 41 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R 41 (51)
|.|.+||.+..- -.-+||.||.+==+++.
T Consensus 1 ~~c~~cg~~~~~---~~g~cp~c~~w~~~~e~ 29 (372)
T cd01121 1 YVCSECGYVSPK---WLGKCPECGEWNTLVEE 29 (372)
T ss_pred CCCCCCCCCCCC---ccEECcCCCCceeeeeh
Confidence 899999998532 34799999988777764
No 100
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=90.12 E-value=0.19 Score=24.90 Aligned_cols=23 Identities=26% Similarity=0.820 Sum_probs=13.4
Q ss_pred cCCCCCeeecC--C---CCeeEcCCCCC
Q 035461 12 CGDCGMENTLK--P---GDVIQCRECGY 34 (51)
Q Consensus 12 C~~Cg~~~~~~--~---~~~irC~~CG~ 34 (51)
|..||..++.. . ..-..|+.||+
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 88999998874 2 23488999985
No 101
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=89.82 E-value=0.7 Score=28.67 Aligned_cols=30 Identities=23% Similarity=0.396 Sum_probs=22.9
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCc-EEEEE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYR-ILYKK 40 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~R-IlyK~ 40 (51)
+-=+|.+||+.+-... ..||+||.+ .|...
T Consensus 28 ~g~kC~~CG~v~~PPr---~~Cp~C~~~~~~E~v 58 (140)
T COG1545 28 LGTKCKKCGRVYFPPR---AYCPKCGSETELEWV 58 (140)
T ss_pred EEEEcCCCCeEEcCCc---ccCCCCCCCCceEEE
Confidence 5568999999986654 789999999 44433
No 102
>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=89.82 E-value=0.35 Score=27.68 Aligned_cols=25 Identities=24% Similarity=0.671 Sum_probs=14.6
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
..|.|..|+.++... ..||+||..+
T Consensus 16 ~~~~C~~C~~~~~~~----a~CPdC~~~L 40 (70)
T PF07191_consen 16 GHYHCEACQKDYKKE----AFCPDCGQPL 40 (70)
T ss_dssp TEEEETTT--EEEEE----EE-TTT-SB-
T ss_pred CEEECccccccceec----ccCCCcccHH
Confidence 468888888887765 5788887653
No 103
>PHA02942 putative transposase; Provisional
Probab=89.73 E-value=0.31 Score=34.50 Aligned_cols=25 Identities=28% Similarity=0.751 Sum_probs=17.0
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
.|..||............|++||+.
T Consensus 327 ~Cs~CG~~~~~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 327 SCPKCGHKMVEIAHRYFHCPSCGYE 351 (383)
T ss_pred cCCCCCCccCcCCCCEEECCCCCCE
Confidence 5888887654223456788888874
No 104
>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=89.73 E-value=0.26 Score=34.92 Aligned_cols=26 Identities=15% Similarity=0.248 Sum_probs=20.4
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
.++|.+||+++. .. ...+||.||..+
T Consensus 2 ~l~C~~Cg~~~~-~~-~~~~C~~c~g~l 27 (398)
T TIGR03844 2 TLRCPGCGEVLP-DH-YTLSCPLDCGLL 27 (398)
T ss_pred EEEeCCCCCccC-Cc-cccCCCCCCCce
Confidence 589999999986 33 468999998543
No 105
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=89.63 E-value=0.54 Score=24.57 Aligned_cols=28 Identities=25% Similarity=0.452 Sum_probs=21.0
Q ss_pred CCceEEEcCCCCCeeecCC----CCeeEcCCC
Q 035461 5 PEPVSYICGDCGMENTLKP----GDVIQCREC 32 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~----~~~irC~~C 32 (51)
...+-.+|..||.+..... ...-.||+|
T Consensus 24 ~~~v~W~C~~Cgh~w~~~v~~R~~~~~~CP~C 55 (55)
T PF14311_consen 24 NKKVWWKCPKCGHEWKASVNDRTRRGKGCPYC 55 (55)
T ss_pred CCEEEEECCCCCCeeEccHhhhccCCCCCCCC
Confidence 3457789999999988652 356788887
No 106
>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=89.13 E-value=0.45 Score=30.50 Aligned_cols=30 Identities=30% Similarity=0.668 Sum_probs=17.8
Q ss_pred CCceEEEcCCCCCeeecCC----------CCeeEcCCCCC
Q 035461 5 PEPVSYICGDCGMENTLKP----------GDVIQCRECGY 34 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~----------~~~irC~~CG~ 34 (51)
-+|....|..||.++.+.. ...+.||+|+.
T Consensus 14 c~~l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~ 53 (188)
T PF08996_consen 14 CEPLKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCST 53 (188)
T ss_dssp ---EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--
T ss_pred CCceEeECCCCCCCccccccccCCccccccCcCcCCCCCC
Confidence 3679999999999998741 24799999998
No 107
>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=89.01 E-value=0.38 Score=23.69 Aligned_cols=24 Identities=38% Similarity=0.904 Sum_probs=15.6
Q ss_pred cCCCCCeeecCCC--CeeEcCCCCCc
Q 035461 12 CGDCGMENTLKPG--DVIQCRECGYR 35 (51)
Q Consensus 12 C~~Cg~~~~~~~~--~~irC~~CG~R 35 (51)
|.+||.-...+.+ ..+.|+.|||-
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 7788888776522 22379999874
No 108
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=88.63 E-value=0.37 Score=30.97 Aligned_cols=22 Identities=32% Similarity=0.937 Sum_probs=15.5
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
=.|..||. .......||.||+.
T Consensus 310 ~~C~~cg~----~~~r~~~C~~cg~~ 331 (364)
T COG0675 310 KTCPCCGH----LSGRLFKCPRCGFV 331 (364)
T ss_pred ccccccCC----ccceeEECCCCCCe
Confidence 35888888 33466888888873
No 109
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=88.26 E-value=0.21 Score=26.90 Aligned_cols=14 Identities=43% Similarity=0.605 Sum_probs=10.7
Q ss_pred eEcCCCCCcEEEEE
Q 035461 27 IQCRECGYRILYKK 40 (51)
Q Consensus 27 irC~~CG~RIlyK~ 40 (51)
|.||+||..|-.-.
T Consensus 1 i~CPyCge~~~~~i 14 (52)
T PF14255_consen 1 IQCPYCGEPIEILI 14 (52)
T ss_pred CCCCCCCCeeEEEE
Confidence 57999999886543
No 110
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=88.02 E-value=0.51 Score=26.13 Aligned_cols=27 Identities=26% Similarity=0.545 Sum_probs=15.5
Q ss_pred eEEEcCCCCCeeecCC-CCeeEcCCCCC
Q 035461 8 VSYICGDCGMENTLKP-GDVIQCRECGY 34 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~-~~~irC~~CG~ 34 (51)
+.-.|.+|++..+... --+.+|.+||+
T Consensus 29 v~IlCNDC~~~s~v~fH~lg~KC~~C~S 56 (61)
T PF14599_consen 29 VWILCNDCNAKSEVPFHFLGHKCSHCGS 56 (61)
T ss_dssp EEEEESSS--EEEEE--TT----TTTS-
T ss_pred EEEECCCCCCccceeeeHhhhcCCCCCC
Confidence 6667999999888764 35799999996
No 111
>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=88.00 E-value=0.74 Score=22.37 Aligned_cols=24 Identities=25% Similarity=0.704 Sum_probs=19.6
Q ss_pred EcCCCCCeeecCCC-CeeEcCCCCC
Q 035461 11 ICGDCGMENTLKPG-DVIQCRECGY 34 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~-~~irC~~CG~ 34 (51)
.|+.|+.......+ ..+||.-|..
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCALCQT 27 (31)
T ss_pred CcCCCCcEeecCCCCCeEECCCCCe
Confidence 58999999988765 6699999963
No 112
>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=87.97 E-value=0.58 Score=29.14 Aligned_cols=29 Identities=24% Similarity=0.607 Sum_probs=22.1
Q ss_pred eEEEcCCCCCeeecC-------CCCeeEcCCCCCcE
Q 035461 8 VSYICGDCGMENTLK-------PGDVIQCRECGYRI 36 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~-------~~~~irC~~CG~RI 36 (51)
....|..|+.++... ....-+||.||..+
T Consensus 104 ~~~~C~~C~~~~~~~~~~~~~~~~~~~~C~~C~~~l 139 (178)
T PF02146_consen 104 FRLRCSKCGKEYDREDIVDSIDEEEPPRCPKCGGLL 139 (178)
T ss_dssp EEEEETTTSBEEEGHHHHHHHHTTSSCBCTTTSCBE
T ss_pred ceeeecCCCccccchhhcccccccccccccccCccC
Confidence 457899999988754 24556999999953
No 113
>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=87.97 E-value=0.61 Score=26.64 Aligned_cols=33 Identities=18% Similarity=0.281 Sum_probs=15.7
Q ss_pred CceEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEE
Q 035461 6 EPVSYICGDCGMENTLKPGDVIQCRECGYRILYKK 40 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~ 40 (51)
....++|..|-+... ..+-.-||.||+.-|.|.
T Consensus 6 k~~vlrC~aCf~~t~--~~~k~FCp~CGn~TL~rv 38 (73)
T PF08772_consen 6 KTWVLRCHACFKITK--DMTKQFCPKCGNATLKRV 38 (73)
T ss_dssp --EEEE-SSS--EES---SS--S-SSS--S--EEE
T ss_pred heeeEEccccccCcC--CCCceeCcccCCCcceEE
Confidence 446789999987764 336689999999988775
No 114
>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=87.87 E-value=0.65 Score=23.87 Aligned_cols=23 Identities=35% Similarity=0.755 Sum_probs=15.1
Q ss_pred EcCCCCCeeecCCCCeeEcCCCC
Q 035461 11 ICGDCGMENTLKPGDVIQCRECG 33 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG 33 (51)
.|..||.+.--..+..+.|+.|+
T Consensus 19 ~Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred ccCCCCCeeEEecCCCEECCCCC
Confidence 47777776655445567777775
No 115
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=87.86 E-value=0.25 Score=27.57 Aligned_cols=22 Identities=36% Similarity=0.747 Sum_probs=16.8
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYRIL 37 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~RIl 37 (51)
-|-+|+..++-+ +||+||+.-|
T Consensus 5 AC~~C~~i~~~~-----~CP~Cgs~~~ 26 (61)
T PRK08351 5 ACRHCHYITTED-----RCPVCGSRDL 26 (61)
T ss_pred hhhhCCcccCCC-----cCCCCcCCcc
Confidence 588999988422 6999998653
No 116
>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=87.76 E-value=0.47 Score=33.89 Aligned_cols=26 Identities=31% Similarity=0.839 Sum_probs=22.0
Q ss_pred EcCCCCCeeecC---CCCeeEcCCCCCcE
Q 035461 11 ICGDCGMENTLK---PGDVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~---~~~~irC~~CG~RI 36 (51)
.|-+|+..++.. .++..+||.||+.+
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTL 43 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCC
Confidence 599999888754 57789999999986
No 117
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=87.61 E-value=0.26 Score=27.79 Aligned_cols=21 Identities=19% Similarity=0.338 Sum_probs=16.0
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
-|-+|+..++- -.||.||+.-
T Consensus 7 AC~~C~~i~~~-----~~Cp~Cgs~~ 27 (64)
T PRK06393 7 ACKKCKRLTPE-----KTCPVHGDEK 27 (64)
T ss_pred hHhhCCcccCC-----CcCCCCCCCc
Confidence 48899988842 2899999853
No 118
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=87.53 E-value=0.54 Score=33.79 Aligned_cols=27 Identities=30% Similarity=0.757 Sum_probs=22.6
Q ss_pred EEcCCCCCeeecC---CCCeeEcCCCCCcE
Q 035461 10 YICGDCGMENTLK---PGDVIQCRECGYRI 36 (51)
Q Consensus 10 Y~C~~Cg~~~~~~---~~~~irC~~CG~RI 36 (51)
-.|-+||..++.. .+..-+||.||+.+
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 40 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTL 40 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCC
Confidence 4599999998765 46778999999987
No 119
>PRK08197 threonine synthase; Validated
Probab=87.03 E-value=0.72 Score=32.20 Aligned_cols=29 Identities=24% Similarity=0.572 Sum_probs=22.2
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGYRILYK 39 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK 39 (51)
.|+|.+||++..++.. ..+| .||.....-
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 5999999999876643 4789 899875543
No 120
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=86.76 E-value=0.3 Score=31.16 Aligned_cols=11 Identities=45% Similarity=1.259 Sum_probs=8.1
Q ss_pred CeeEcCCCCCc
Q 035461 25 DVIQCRECGYR 35 (51)
Q Consensus 25 ~~irC~~CG~R 35 (51)
....|++||||
T Consensus 28 ~sf~C~~CGyk 38 (160)
T smart00709 28 MSFECEHCGYR 38 (160)
T ss_pred EEEECCCCCCc
Confidence 35678888876
No 121
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=86.75 E-value=0.44 Score=30.39 Aligned_cols=29 Identities=31% Similarity=0.729 Sum_probs=18.0
Q ss_pred EEcCCCCCee-e---cC---CCCee----EcCCCCCcEEE
Q 035461 10 YICGDCGMEN-T---LK---PGDVI----QCRECGYRILY 38 (51)
Q Consensus 10 Y~C~~Cg~~~-~---~~---~~~~i----rC~~CG~RIly 38 (51)
++|..||.+. . .. .+..| +|++||++.--
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~ 40 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTT 40 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceE
Confidence 4799999654 2 12 22234 49999988543
No 122
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=86.73 E-value=1.1 Score=23.05 Aligned_cols=28 Identities=21% Similarity=0.787 Sum_probs=21.6
Q ss_pred cC--CCCCeeecC---CCCeeEcCCCCCcEEEE
Q 035461 12 CG--DCGMENTLK---PGDVIQCRECGYRILYK 39 (51)
Q Consensus 12 C~--~Cg~~~~~~---~~~~irC~~CG~RIlyK 39 (51)
|. .|+..+... ....+.|+.||+..-++
T Consensus 21 CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~ 53 (64)
T smart00647 21 CPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFR 53 (64)
T ss_pred CCCCCCcceEEecCCCCCCeeECCCCCCeECCC
Confidence 77 898888876 34679999999876543
No 123
>PF15616 TerY-C: TerY-C metal binding domain
Probab=86.69 E-value=1 Score=28.28 Aligned_cols=29 Identities=17% Similarity=0.353 Sum_probs=24.0
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYRILYK 39 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~RIlyK 39 (51)
.+-.||+.+=+...+.+.||-||..+.|-
T Consensus 90 a~C~CGkl~Ci~g~~~~~CPwCg~~g~~~ 118 (131)
T PF15616_consen 90 AVCGCGKLFCIDGEGEVTCPWCGNEGSFG 118 (131)
T ss_pred EEecCCCEEEeCCCCCEECCCCCCeeeec
Confidence 33379999999888899999999988764
No 124
>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=86.57 E-value=0.24 Score=35.42 Aligned_cols=25 Identities=32% Similarity=0.757 Sum_probs=19.4
Q ss_pred EcCCCCCeeecCCC--CeeEcCCCCCcE
Q 035461 11 ICGDCGMENTLKPG--DVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~--~~irC~~CG~RI 36 (51)
-|.+|+..++.... ...+|| ||++|
T Consensus 242 ~c~~C~~~~~~~~~~~~~~~Cp-CG~~i 268 (374)
T TIGR00375 242 ACEACGEPAVSEDAETACANCP-CGGRI 268 (374)
T ss_pred hhcccCCcCCchhhhhcCCCCC-CCCcc
Confidence 58999998887631 358899 99994
No 125
>PRK08329 threonine synthase; Validated
Probab=86.56 E-value=0.58 Score=32.19 Aligned_cols=27 Identities=30% Similarity=0.701 Sum_probs=21.0
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGYRILYK 39 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK 39 (51)
++|.+||++.... ...+| .||..+...
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 7899999999743 33899 799876554
No 126
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=86.51 E-value=0.064 Score=29.11 Aligned_cols=27 Identities=37% Similarity=0.865 Sum_probs=21.7
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCCcEEE
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGYRILY 38 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RIly 38 (51)
..||-+|++.+.+. +.+|..|||+-|-
T Consensus 14 kkIC~rC~Arnp~~---A~kCRkC~~k~LR 40 (50)
T COG1552 14 KKICRRCYARNPPR---ATKCRKCGYKNLR 40 (50)
T ss_pred HHHHHHhcCCCCcc---hhHHhhccCCCcc
Confidence 46899999987654 4899999998774
No 127
>PRK04860 hypothetical protein; Provisional
Probab=86.50 E-value=1.3 Score=28.35 Aligned_cols=33 Identities=27% Similarity=0.682 Sum_probs=23.8
Q ss_pred ceEEEcCCCCCeeecC-------C-CCeeEcCCCCCcEEEEE
Q 035461 7 PVSYICGDCGMENTLK-------P-GDVIQCRECGYRILYKK 40 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~-------~-~~~irC~~CG~RIlyK~ 40 (51)
...|.|. |+...... . ....+|..|+..+.++.
T Consensus 117 ~~~Y~C~-C~~~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 117 TFPYRCK-CQEHQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEEcC-CCCeeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 4789998 98733211 2 24599999999998864
No 128
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=86.50 E-value=0.73 Score=25.41 Aligned_cols=19 Identities=32% Similarity=0.618 Sum_probs=11.6
Q ss_pred eEcCCCCCcEEEEEecCce
Q 035461 27 IQCRECGYRILYKKRTRRI 45 (51)
Q Consensus 27 irC~~CG~RIlyK~R~~~~ 45 (51)
+.||-||++-..|.|....
T Consensus 5 i~CP~CgnKTR~kir~DT~ 23 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTV 23 (55)
T ss_pred EECCCCCCccceeeecCce
Confidence 5666666666666665543
No 129
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=86.44 E-value=0.59 Score=30.62 Aligned_cols=29 Identities=34% Similarity=0.661 Sum_probs=21.9
Q ss_pred EEEcCCCCCeeecC--------------------------CCCeeEcCCCCCcEE
Q 035461 9 SYICGDCGMENTLK--------------------------PGDVIQCRECGYRIL 37 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~--------------------------~~~~irC~~CG~RIl 37 (51)
.+.|.-|+.+|..+ ..+.+-||+||+--+
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~ 59 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAF 59 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccc
Confidence 57899999988752 115789999998655
No 130
>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=86.38 E-value=0.54 Score=37.94 Aligned_cols=31 Identities=23% Similarity=0.489 Sum_probs=24.2
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRILYK 39 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK 39 (51)
-.++|..||+...--+. .-+||.||++|+--
T Consensus 1011 Q~fRC~kC~~kYRR~PL-~G~C~kCGg~lilT 1041 (1095)
T TIGR00354 1011 QEVRCTKCNTKYRRIPL-VGKCLKCGNNLTLT 1041 (1095)
T ss_pred cceeecccCCccccCCC-CCcccccCCeEEEE
Confidence 46899999999865443 35899999998754
No 131
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=86.19 E-value=0.49 Score=29.77 Aligned_cols=28 Identities=18% Similarity=-0.012 Sum_probs=23.8
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
.+-+|.+||+.|---..++|.||+||..
T Consensus 8 tKridPetg~KFYDLNrdPiVsPytG~s 35 (129)
T COG4530 8 TKRIDPETGKKFYDLNRDPIVSPYTGKS 35 (129)
T ss_pred ccccCccccchhhccCCCccccCccccc
Confidence 5668999999997667799999999964
No 132
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=86.19 E-value=0.54 Score=31.95 Aligned_cols=28 Identities=25% Similarity=0.565 Sum_probs=20.8
Q ss_pred eEEEcCCCCCeeecC-------CCCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENTLK-------PGDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~-------~~~~irC~~CG~R 35 (51)
-...|..||..+... ....-+||.||..
T Consensus 121 ~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~ 155 (250)
T COG0846 121 KRVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGP 155 (250)
T ss_pred eeeEeCCCcCccchhhhhhhcccCCCCcCccCCCc
Confidence 457899999887632 2245789999996
No 133
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=85.98 E-value=0.58 Score=38.49 Aligned_cols=31 Identities=32% Similarity=0.709 Sum_probs=24.2
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRILYK 39 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK 39 (51)
-.++|..||+...--+. .-+||.||++|+--
T Consensus 1252 Q~~RC~kC~~kyRR~PL-~G~C~kCGg~iilT 1282 (1337)
T PRK14714 1252 QEFRCLKCGTKYRRMPL-AGKCRKCGGRIILT 1282 (1337)
T ss_pred cceeecccCcccccCCC-CCcccccCCeEEEE
Confidence 46899999999865443 25899999999753
No 134
>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=85.98 E-value=1.2 Score=20.87 Aligned_cols=23 Identities=26% Similarity=0.664 Sum_probs=18.5
Q ss_pred cCCCCCeeecCCC-CeeEcCCCCC
Q 035461 12 CGDCGMENTLKPG-DVIQCRECGY 34 (51)
Q Consensus 12 C~~Cg~~~~~~~~-~~irC~~CG~ 34 (51)
|+.|...+....+ ..+||.-|..
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCc
Confidence 7889998887765 5699998864
No 135
>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=85.80 E-value=1.2 Score=22.60 Aligned_cols=27 Identities=22% Similarity=0.295 Sum_probs=19.4
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
-.|..|+..+......+++|..|+..+
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 368899998855566889999998754
No 136
>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=85.76 E-value=0.32 Score=30.89 Aligned_cols=26 Identities=35% Similarity=0.975 Sum_probs=14.6
Q ss_pred EcCCCCCeeecC------C------CCeeEcCCCCCcE
Q 035461 11 ICGDCGMENTLK------P------GDVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~------~------~~~irC~~CG~RI 36 (51)
.|..||...... + -....|++||||-
T Consensus 3 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~ 40 (161)
T PF03367_consen 3 LCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKN 40 (161)
T ss_dssp E-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EE
T ss_pred cCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEe
Confidence 688898875432 1 1467999999974
No 137
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=85.57 E-value=0.84 Score=30.66 Aligned_cols=27 Identities=26% Similarity=0.566 Sum_probs=20.3
Q ss_pred EcCCCCCeeecC-CCCeeEcCCCCCcEE
Q 035461 11 ICGDCGMENTLK-PGDVIQCRECGYRIL 37 (51)
Q Consensus 11 ~C~~Cg~~~~~~-~~~~irC~~CG~RIl 37 (51)
-|+.||..+... .+-...|+.||....
T Consensus 101 fC~~CG~~~~~~~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 101 FCGYCGHPMHPSKTEWAMLCPHCRERYY 128 (256)
T ss_pred cccccCCCCeecCCceeEECCCCCCEEC
Confidence 399999988765 345688999996543
No 138
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=85.44 E-value=1.2 Score=26.68 Aligned_cols=28 Identities=29% Similarity=0.763 Sum_probs=20.2
Q ss_pred ceEEEcCCCCCeeecC-----CCCeeEcCCCCCc
Q 035461 7 PVSYICGDCGMENTLK-----PGDVIQCRECGYR 35 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~-----~~~~irC~~CG~R 35 (51)
+..+.|..||. ..+. ...-+.|+.||+.
T Consensus 19 pt~f~CP~Cge-~~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 19 PKIFECPRCGK-VSISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred CcEeECCCCCC-eEeeeecCCCcceEECCCCCCc
Confidence 46899999993 3332 2256999999975
No 139
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=85.28 E-value=0.87 Score=33.49 Aligned_cols=31 Identities=26% Similarity=0.618 Sum_probs=25.4
Q ss_pred ceEEEcCCCCCeeecC---CCCeeEcCCCCCcEE
Q 035461 7 PVSYICGDCGMENTLK---PGDVIQCRECGYRIL 37 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~---~~~~irC~~CG~RIl 37 (51)
.-.=.|.+|+..+++. .+..-.||.||+.+-
T Consensus 16 ~~~~~C~eCd~~~~~P~l~~~q~A~CPRC~~~l~ 49 (418)
T COG2995 16 GHLILCPECDMLVSLPRLDSGQSAYCPRCGHTLT 49 (418)
T ss_pred cceecCCCCCceeccccCCCCCcccCCCCCCccc
Confidence 3556899999999865 567899999999874
No 140
>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=85.14 E-value=0.44 Score=30.99 Aligned_cols=25 Identities=36% Similarity=0.901 Sum_probs=17.9
Q ss_pred EEcCCCCCeeecC-----CC--CeeEcCCCCC
Q 035461 10 YICGDCGMENTLK-----PG--DVIQCRECGY 34 (51)
Q Consensus 10 Y~C~~Cg~~~~~~-----~~--~~irC~~CG~ 34 (51)
++|-+||.+++-- ++ .--+|++||.
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~ 32 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGK 32 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCC
Confidence 5899999997631 11 3378999994
No 141
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=85.02 E-value=0.62 Score=34.56 Aligned_cols=25 Identities=28% Similarity=0.816 Sum_probs=19.3
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
..|.|.+||.... + -.-+||+||.+
T Consensus 6 t~f~C~~CG~~s~-K--W~GkCp~Cg~W 30 (456)
T COG1066 6 TAFVCQECGYVSP-K--WLGKCPACGAW 30 (456)
T ss_pred cEEEcccCCCCCc-c--ccccCCCCCCc
Confidence 7799999999853 2 33589999943
No 142
>PRK04023 DNA polymerase II large subunit; Validated
Probab=84.99 E-value=0.68 Score=37.49 Aligned_cols=31 Identities=23% Similarity=0.620 Sum_probs=24.2
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRILYK 39 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK 39 (51)
-.++|..||+...--+. .-+||.||++|+.-
T Consensus 1036 Q~fRC~kC~~kYRR~PL-~G~C~kCGg~lilT 1066 (1121)
T PRK04023 1036 QEFRCTKCGAKYRRPPL-SGKCPKCGGNLILT 1066 (1121)
T ss_pred cceeecccCcccccCCC-CCcCccCCCeEEEE
Confidence 36899999999865443 35899999999753
No 143
>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=84.94 E-value=0.63 Score=25.87 Aligned_cols=26 Identities=31% Similarity=0.691 Sum_probs=18.1
Q ss_pred EEEcCCCCCeeecCCC---CeeEcCCCCC
Q 035461 9 SYICGDCGMENTLKPG---DVIQCRECGY 34 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~---~~irC~~CG~ 34 (51)
.=+|+.|+.+..+... ....||.|+.
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 6789999999998754 3479999985
No 144
>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=84.93 E-value=0.46 Score=35.09 Aligned_cols=22 Identities=41% Similarity=1.105 Sum_probs=17.6
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
+|.+||...+ +..-.||.||++
T Consensus 520 ~C~~CG~~~~---~~~~~CP~CGs~ 541 (555)
T cd01675 520 ICNDCGYIGE---GEGFKCPKCGSE 541 (555)
T ss_pred cCCCCCCCCc---CCCCCCcCCCCc
Confidence 9999998653 344789999977
No 145
>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=84.88 E-value=0.45 Score=26.11 Aligned_cols=31 Identities=26% Similarity=0.468 Sum_probs=24.4
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGYRILYK 39 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK 39 (51)
.=.|..||+.+=...+..--|+.||..++-+
T Consensus 18 ~~NCl~CGkIiC~~Eg~~~pC~fCg~~l~~~ 48 (57)
T PF06221_consen 18 APNCLNCGKIICEQEGPLGPCPFCGTPLLSS 48 (57)
T ss_pred cccccccChhhcccccCcCcCCCCCCcccCH
Confidence 5579999999877765467899999877643
No 146
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=84.76 E-value=0.58 Score=30.72 Aligned_cols=10 Identities=50% Similarity=1.311 Sum_probs=7.2
Q ss_pred eeEcCCCCCc
Q 035461 26 VIQCRECGYR 35 (51)
Q Consensus 26 ~irC~~CG~R 35 (51)
...|++||||
T Consensus 30 sf~C~~CGyr 39 (192)
T TIGR00310 30 STICEHCGYR 39 (192)
T ss_pred EEECCCCCCc
Confidence 5677777776
No 147
>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=84.66 E-value=0.64 Score=28.86 Aligned_cols=32 Identities=22% Similarity=0.513 Sum_probs=23.0
Q ss_pred CCceEEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461 5 PEPVSYICGDCGMENTLKPGDVIQCRECGYRIL 37 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl 37 (51)
...+..+|.+||+....-- ..-+|.+|+....
T Consensus 65 tkav~V~CP~C~K~TKmLG-r~D~CM~C~~pLT 96 (114)
T PF11023_consen 65 TKAVQVECPNCGKQTKMLG-RVDACMHCKEPLT 96 (114)
T ss_pred ccceeeECCCCCChHhhhc-hhhccCcCCCcCc
Confidence 3457788999999976442 3349999997543
No 148
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=84.64 E-value=1.4 Score=26.34 Aligned_cols=30 Identities=27% Similarity=0.586 Sum_probs=22.0
Q ss_pred CceEEEcCCCCCeeecCCC-CeeEcCCCCCc
Q 035461 6 EPVSYICGDCGMENTLKPG-DVIQCRECGYR 35 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~~~-~~irC~~CG~R 35 (51)
....|.|.+||.+.-+-.. ..=-||.||.+
T Consensus 39 G~~~~~C~~Cg~~~~~~~SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 39 GFHRYRCEDCGHEKIVYNSCKNRHCPSCQAK 69 (111)
T ss_pred CcceeecCCCCceEEecCcccCcCCCCCCCh
Confidence 4588999999998866421 22379999975
No 149
>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=84.52 E-value=1.2 Score=30.95 Aligned_cols=34 Identities=21% Similarity=0.509 Sum_probs=25.6
Q ss_pred CCceEEEcCCCCCeeecCC---CCeeEcCCCCCcEEE
Q 035461 5 PEPVSYICGDCGMENTLKP---GDVIQCRECGYRILY 38 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~---~~~irC~~CG~RIly 38 (51)
+.....+|+.|...|-... +...|||+|....-.
T Consensus 153 p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSV 189 (256)
T PF09788_consen 153 PGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSV 189 (256)
T ss_pred CCceeEECCCCCCcEeccCCCCCccccCCCCceeccc
Confidence 3458899999999998763 455799999855443
No 150
>PRK05638 threonine synthase; Validated
Probab=84.52 E-value=0.71 Score=32.74 Aligned_cols=27 Identities=26% Similarity=0.416 Sum_probs=20.3
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCCcEEE
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGYRILY 38 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RIly 38 (51)
+++|.+||++.... ...+| .||..+-.
T Consensus 1 ~l~C~~Cg~~~~~~--~~~~C-~c~~~l~~ 27 (442)
T PRK05638 1 KMKCPKCGREYNSY--IPPFC-ICGELLEI 27 (442)
T ss_pred CeEeCCCCCCCCCC--Cceec-CCCCcEEE
Confidence 37899999998743 34899 89976544
No 151
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=84.51 E-value=0.76 Score=30.26 Aligned_cols=29 Identities=24% Similarity=0.496 Sum_probs=20.8
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCCcEEEEEe
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGYRILYKKR 41 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R 41 (51)
|.|.+||...+. -.-.||.||..==++.|
T Consensus 355 ~~c~~cg~~~~~---~~~~c~~c~~~~~~~~~ 383 (389)
T PRK11788 355 YRCRNCGFTART---LYWHCPSCKAWETIKPI 383 (389)
T ss_pred EECCCCCCCCcc---ceeECcCCCCccCcCCc
Confidence 899999987543 34799999975444443
No 152
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=84.39 E-value=0.41 Score=31.27 Aligned_cols=29 Identities=24% Similarity=0.474 Sum_probs=19.9
Q ss_pred CceEEEcCCCCCeeecCCCCe----------------eEcCCCCC
Q 035461 6 EPVSYICGDCGMENTLKPGDV----------------IQCRECGY 34 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~~~~~----------------irC~~CG~ 34 (51)
++..=+|..|+.++..-+.+. -+||.||.
T Consensus 94 ~~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cgk 138 (165)
T COG1656 94 FPEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGK 138 (165)
T ss_pred ccccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcc
Confidence 344568999998887544333 45999984
No 153
>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=84.36 E-value=0.66 Score=29.81 Aligned_cols=11 Identities=45% Similarity=1.259 Sum_probs=8.2
Q ss_pred CeeEcCCCCCc
Q 035461 25 DVIQCRECGYR 35 (51)
Q Consensus 25 ~~irC~~CG~R 35 (51)
....|++||||
T Consensus 27 ~sf~C~~CGyr 37 (163)
T TIGR00340 27 STYICEKCGYR 37 (163)
T ss_pred EEEECCCCCCc
Confidence 45778888886
No 154
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=84.21 E-value=0.81 Score=28.10 Aligned_cols=22 Identities=36% Similarity=0.892 Sum_probs=13.3
Q ss_pred cCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 12 CGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 12 C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
|..||.+..+.. ++|++||-.|
T Consensus 1 CPvCg~~l~vt~---l~C~~C~t~i 22 (113)
T PF09862_consen 1 CPVCGGELVVTR---LKCPSCGTEI 22 (113)
T ss_pred CCCCCCceEEEE---EEcCCCCCEE
Confidence 556666665543 6677776544
No 155
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=84.19 E-value=1.2 Score=28.94 Aligned_cols=34 Identities=26% Similarity=0.696 Sum_probs=25.3
Q ss_pred CceEEEcCCCCCeeecC-------CCCeeEcCCCCCcEEEEE
Q 035461 6 EPVSYICGDCGMENTLK-------PGDVIQCRECGYRILYKK 40 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~-------~~~~irC~~CG~RIlyK~ 40 (51)
....|.|. |+.-..-. .+...||..||.+++++.
T Consensus 114 ~~~~Y~C~-C~q~~l~~RRhn~~~~g~~YrC~~C~gkL~~~~ 154 (156)
T COG3091 114 TTYPYRCQ-CQQHYLRIRRHNTVRRGEVYRCGKCGGKLVFKG 154 (156)
T ss_pred cceeEEee-cCCccchhhhcccccccceEEeccCCceEEecc
Confidence 34789999 98875432 334588999999998863
No 156
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=84.06 E-value=1.3 Score=25.23 Aligned_cols=31 Identities=26% Similarity=0.638 Sum_probs=23.2
Q ss_pred CCCCceEEEcCCCCCeeecC-----C-CCeeEcCCCCC
Q 035461 3 PQPEPVSYICGDCGMENTLK-----P-GDVIQCRECGY 34 (51)
Q Consensus 3 ~~~~~~~Y~C~~Cg~~~~~~-----~-~~~irC~~CG~ 34 (51)
...+...|-|. ||..|++. . .+..+||.|.-
T Consensus 16 ~e~~~y~yPCp-CGDrf~It~edL~~ge~Va~CpsCSL 52 (67)
T KOG2923|consen 16 EENQTYYYPCP-CGDRFQITLEDLENGEDVARCPSCSL 52 (67)
T ss_pred cCCCeEEcCCC-CCCeeeecHHHHhCCCeeecCCCceE
Confidence 44556778886 99999985 2 26789999973
No 157
>COG1773 Rubredoxin [Energy production and conversion]
Probab=84.05 E-value=0.88 Score=24.96 Aligned_cols=25 Identities=36% Similarity=0.810 Sum_probs=19.7
Q ss_pred EEEcCCCCCeeecCCC----------------CeeEcCCCC
Q 035461 9 SYICGDCGMENTLKPG----------------DVIQCRECG 33 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~----------------~~irC~~CG 33 (51)
.|+|.-||-..+.+.+ +.-.||.||
T Consensus 3 ~~~C~~CG~vYd~e~Gdp~~gi~pgT~fedlPd~w~CP~Cg 43 (55)
T COG1773 3 RWRCSVCGYVYDPEKGDPRCGIAPGTPFEDLPDDWVCPECG 43 (55)
T ss_pred ceEecCCceEeccccCCccCCCCCCCchhhCCCccCCCCCC
Confidence 6999999998886532 456899999
No 158
>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=83.99 E-value=0.9 Score=22.15 Aligned_cols=17 Identities=24% Similarity=0.626 Sum_probs=12.5
Q ss_pred cCCCCeeEcCCCCCcEE
Q 035461 21 LKPGDVIQCRECGYRIL 37 (51)
Q Consensus 21 ~~~~~~irC~~CG~RIl 37 (51)
++..+...|+.||-.++
T Consensus 27 i~~vp~~~C~~CGE~~~ 43 (46)
T TIGR03831 27 IENVPALVCPQCGEEYL 43 (46)
T ss_pred EeCCCccccccCCCEee
Confidence 34446778999998775
No 159
>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=83.71 E-value=2 Score=23.43 Aligned_cols=29 Identities=24% Similarity=0.519 Sum_probs=19.3
Q ss_pred eEEEcCCCCCeeecC--CCCeeEcCCCCCcE
Q 035461 8 VSYICGDCGMENTLK--PGDVIQCRECGYRI 36 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~RI 36 (51)
|.=+|.+|+.+..+- +...|.|..||.-+
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 667899999998764 45789999999754
No 160
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=83.29 E-value=0.56 Score=35.65 Aligned_cols=21 Identities=38% Similarity=0.993 Sum_probs=11.2
Q ss_pred cCCCCCeeecCCCCeeEcCCCCCc
Q 035461 12 CGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 12 C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
|.+||+++.. +.--|++||.+
T Consensus 30 Cp~CG~~~~~---~~~fC~~CG~~ 50 (645)
T PRK14559 30 CPQCGTEVPV---DEAHCPNCGAE 50 (645)
T ss_pred CCCCCCCCCc---ccccccccCCc
Confidence 5555555433 23466667665
No 161
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=83.28 E-value=0.42 Score=31.23 Aligned_cols=34 Identities=21% Similarity=0.528 Sum_probs=26.6
Q ss_pred CCceEEEcCCCCCeeecCC--CCeeEcCCCCCcEEE
Q 035461 5 PEPVSYICGDCGMENTLKP--GDVIQCRECGYRILY 38 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~--~~~irC~~CG~RIly 38 (51)
.+.+.|.|..|+-.+++.. ...-.||.||.-+-|
T Consensus 109 ~~~~~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L~~ 144 (176)
T COG1675 109 TENNYYVCPNCHVKYSFDEAMELGFTCPKCGEDLEE 144 (176)
T ss_pred ccCCceeCCCCCCcccHHHHHHhCCCCCCCCchhhh
Confidence 4668999999999998862 345899999986543
No 162
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=83.23 E-value=1.3 Score=24.87 Aligned_cols=16 Identities=19% Similarity=0.353 Sum_probs=12.2
Q ss_pred CCCCeeEcCCCCCcEE
Q 035461 22 KPGDVIQCRECGYRIL 37 (51)
Q Consensus 22 ~~~~~irC~~CG~RIl 37 (51)
.....+.|||||-+.-
T Consensus 44 g~~gev~CPYC~t~y~ 59 (62)
T COG4391 44 GDEGEVVCPYCSTRYR 59 (62)
T ss_pred CCCCcEecCccccEEE
Confidence 3557899999997643
No 163
>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=83.16 E-value=0.68 Score=19.76 Aligned_cols=12 Identities=33% Similarity=0.695 Sum_probs=9.2
Q ss_pred EEcCCCCCeeec
Q 035461 10 YICGDCGMENTL 21 (51)
Q Consensus 10 Y~C~~Cg~~~~~ 21 (51)
|.|..||+.|..
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 788888887753
No 164
>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=83.08 E-value=0.78 Score=32.79 Aligned_cols=26 Identities=19% Similarity=0.466 Sum_probs=20.7
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
.-.|.+|+..+ ..+...+||.||+.+
T Consensus 215 ~~~C~~Cd~~~--~~~~~a~CpRC~~~L 240 (403)
T TIGR00155 215 LRSCSACHTTI--LPAQEPVCPRCSTPL 240 (403)
T ss_pred CCcCCCCCCcc--CCCCCcCCcCCCCcc
Confidence 34599999965 446778999999987
No 165
>PRK12495 hypothetical protein; Provisional
Probab=82.87 E-value=0.85 Score=31.15 Aligned_cols=29 Identities=17% Similarity=0.398 Sum_probs=22.9
Q ss_pred ceEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 7 PVSYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
...+.|..||..+. .....++|+.|+..+
T Consensus 40 msa~hC~~CG~PIp-a~pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 40 MTNAHCDECGDPIF-RHDGQEFCPTCQQPV 68 (226)
T ss_pred cchhhcccccCccc-CCCCeeECCCCCCcc
Confidence 35688999999987 345779999999654
No 166
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=82.78 E-value=1 Score=24.60 Aligned_cols=22 Identities=27% Similarity=0.608 Sum_probs=16.6
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
.-.|.+||.-.- ...||.||..
T Consensus 5 mr~C~~CgvYTL-----k~~CP~CG~~ 26 (56)
T PRK13130 5 IRKCPKCGVYTL-----KEICPVCGGK 26 (56)
T ss_pred ceECCCCCCEEc-----cccCcCCCCC
Confidence 357999998764 4679999964
No 167
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=82.48 E-value=1 Score=26.97 Aligned_cols=30 Identities=23% Similarity=0.690 Sum_probs=22.3
Q ss_pred ceEEEcCCCCCeeecC-CCCeeEcCCCCCcE
Q 035461 7 PVSYICGDCGMENTLK-PGDVIQCRECGYRI 36 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~-~~~~irC~~CG~RI 36 (51)
.-.|.|..||+..-.. ...--.|..||+..
T Consensus 33 ~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 33 RAKHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred hcCCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 3579999999984333 34567999999864
No 168
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=82.36 E-value=1.2 Score=32.87 Aligned_cols=29 Identities=34% Similarity=0.590 Sum_probs=13.9
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCCc-EEEEEe
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGYR-ILYKKR 41 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~R-IlyK~R 41 (51)
.=+|.+||..... .-.||.||.. |-+-.|
T Consensus 491 ~~~C~~CG~~~~~----~~~CP~CGs~~~~~~~R 520 (546)
T PF13597_consen 491 IDICPDCGYIGGE----GDKCPKCGSENIEVYSR 520 (546)
T ss_dssp EEEETTT---S------EEE-CCC----EEEEB-
T ss_pred cccccCCCcCCCC----CCCCCCCCCcccceEEE
Confidence 4589999986542 6789999998 554444
No 169
>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=82.30 E-value=0.83 Score=27.59 Aligned_cols=13 Identities=31% Similarity=0.457 Sum_probs=11.3
Q ss_pred eeEcCCCCCcEEE
Q 035461 26 VIQCRECGYRILY 38 (51)
Q Consensus 26 ~irC~~CG~RIly 38 (51)
+++||+||..+.+
T Consensus 2 p~~CpYCg~~~~l 14 (102)
T PF11672_consen 2 PIICPYCGGPAEL 14 (102)
T ss_pred CcccCCCCCeeEE
Confidence 5899999998876
No 170
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=82.28 E-value=0.62 Score=31.67 Aligned_cols=20 Identities=45% Similarity=0.996 Sum_probs=16.4
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
+| +||.++++. ..|++||-+
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 999997654 789999976
No 171
>PF13397 DUF4109: Domain of unknown function (DUF4109)
Probab=82.07 E-value=2.2 Score=26.04 Aligned_cols=30 Identities=30% Similarity=0.628 Sum_probs=23.5
Q ss_pred CCceEEEcCCCCCeeecCC------CCeeEcCCCCCc
Q 035461 5 PEPVSYICGDCGMENTLKP------GDVIQCRECGYR 35 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~------~~~irC~~CG~R 35 (51)
-+.+.|.|.+ |.+|.+.. -+..-|+.||.-
T Consensus 24 R~~v~Y~C~~-Gh~~~v~Fa~eAevP~~WeC~~cG~~ 59 (105)
T PF13397_consen 24 RQRVSYWCPN-GHETEVPFAAEAEVPATWECPRCGLP 59 (105)
T ss_pred ceEEEEECCC-CCEEeccccccCCCCCceeCCCCCCc
Confidence 3569999999 99988752 256899999964
No 172
>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=81.81 E-value=1 Score=23.00 Aligned_cols=26 Identities=23% Similarity=0.670 Sum_probs=15.0
Q ss_pred EcCC--CCCeeecCCC-Ce--eEcCCCCCcE
Q 035461 11 ICGD--CGMENTLKPG-DV--IQCRECGYRI 36 (51)
Q Consensus 11 ~C~~--Cg~~~~~~~~-~~--irC~~CG~RI 36 (51)
-|.. |+..+..... .. +.|+.||+.+
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 6755 9999888754 33 8999999865
No 173
>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=81.57 E-value=1.6 Score=22.33 Aligned_cols=12 Identities=33% Similarity=0.778 Sum_probs=9.6
Q ss_pred CeeEcCCCCCcE
Q 035461 25 DVIQCRECGYRI 36 (51)
Q Consensus 25 ~~irC~~CG~RI 36 (51)
..+.|||||-+.
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 469999999653
No 174
>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=81.54 E-value=1.2 Score=22.87 Aligned_cols=13 Identities=23% Similarity=0.782 Sum_probs=7.8
Q ss_pred EcCCCCCcEEEEE
Q 035461 28 QCRECGYRILYKK 40 (51)
Q Consensus 28 rC~~CG~RIlyK~ 40 (51)
+||+||.+.....
T Consensus 1 ~CP~Cg~~a~ir~ 13 (47)
T PF04606_consen 1 RCPHCGSKARIRT 13 (47)
T ss_pred CcCCCCCeeEEEE
Confidence 4777777664443
No 175
>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=81.52 E-value=1.5 Score=21.88 Aligned_cols=14 Identities=21% Similarity=0.804 Sum_probs=8.4
Q ss_pred eEcCCCCCcEEEEE
Q 035461 27 IQCRECGYRILYKK 40 (51)
Q Consensus 27 irC~~CG~RIlyK~ 40 (51)
..||.||+.++.|.
T Consensus 2 ~~CP~Cg~~lv~r~ 15 (39)
T PF01396_consen 2 EKCPKCGGPLVLRR 15 (39)
T ss_pred cCCCCCCceeEEEE
Confidence 46888885544443
No 176
>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=81.51 E-value=0.96 Score=29.47 Aligned_cols=28 Identities=29% Similarity=0.663 Sum_probs=20.3
Q ss_pred eEEEcCCCCCeeecC------CCCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENTLK------PGDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~------~~~~irC~~CG~R 35 (51)
....|..|+...... ....-+||.||..
T Consensus 112 ~~~~C~~C~~~~~~~~~~~~~~~~~p~C~~Cgg~ 145 (222)
T cd01413 112 QTAYCVNCGSKYDLEEVKYAKKHEVPRCPKCGGI 145 (222)
T ss_pred CcceECCCCCCcchhHHHHhccCCCCcCCCCCCc
Confidence 456799999887654 1234689999975
No 177
>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=81.26 E-value=0.99 Score=29.10 Aligned_cols=28 Identities=29% Similarity=0.615 Sum_probs=20.4
Q ss_pred eEEEcCCCCCeeecC-------CCCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENTLK-------PGDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~-------~~~~irC~~CG~R 35 (51)
....|..|+..+... ....-+||.||..
T Consensus 108 ~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~ 142 (218)
T cd01407 108 FRVRCTKCGKEYPRDELQADIDREEVPRCPKCGGL 142 (218)
T ss_pred CcceeCCCcCCCcHHHHhHhhccCCCCcCCCCCCc
Confidence 356799999887643 2345689999976
No 178
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=81.22 E-value=0.96 Score=29.66 Aligned_cols=28 Identities=25% Similarity=0.585 Sum_probs=19.6
Q ss_pred eEEEcCCCCCeeecC---CCCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENTLK---PGDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~---~~~~irC~~CG~R 35 (51)
....|..|+...... ..+..+||.||+.
T Consensus 121 ~~~~C~~C~~~~~~~~~~~~~~p~C~~Cgg~ 151 (242)
T PRK00481 121 LRARCTKCGQTYDLDEYLKPEPPRCPKCGGI 151 (242)
T ss_pred CceeeCCCCCCcChhhhccCCCCCCCCCCCc
Confidence 456799998876543 2234569999975
No 179
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=80.80 E-value=1.3 Score=27.42 Aligned_cols=24 Identities=33% Similarity=0.786 Sum_probs=18.1
Q ss_pred cCCCCCeeecCCCCeeEcCCCCCc
Q 035461 12 CGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 12 C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
|..|+.+..-+.+...-||+|+|.
T Consensus 6 cp~c~sEytYed~~~~~cpec~~e 29 (112)
T COG2824 6 CPKCNSEYTYEDGGQLICPECAHE 29 (112)
T ss_pred CCccCCceEEecCceEeCchhccc
Confidence 677777777777777888888764
No 180
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=80.46 E-value=1.3 Score=37.11 Aligned_cols=30 Identities=23% Similarity=0.682 Sum_probs=23.0
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRILYK 39 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK 39 (51)
-.++| .||+...--+. .-+||.||++|+.-
T Consensus 1541 Q~~RC-kC~~kyRR~PL-~G~C~kCGg~~ilT 1570 (1627)
T PRK14715 1541 QEFRC-KCGAKYRRVPL-KGKCPKCGSKLILT 1570 (1627)
T ss_pred cceee-cCCCccccCCC-CCcCcccCCeEEEE
Confidence 46899 99998865443 35899999998753
No 181
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=80.42 E-value=1.2 Score=27.37 Aligned_cols=17 Identities=18% Similarity=0.331 Sum_probs=11.5
Q ss_pred CCceEEEcCCCCCeeec
Q 035461 5 PEPVSYICGDCGMENTL 21 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~ 21 (51)
..+..-+|..|+..+..
T Consensus 87 ~~~~~sRC~~CN~~L~~ 103 (147)
T PF01927_consen 87 LDPIFSRCPKCNGPLRP 103 (147)
T ss_pred cCCCCCccCCCCcEeee
Confidence 34556788888877653
No 182
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=80.40 E-value=1.9 Score=31.25 Aligned_cols=31 Identities=23% Similarity=0.383 Sum_probs=23.8
Q ss_pred CCceEEEcCCCCCeeecCCC----------------CeeEcCCCCCc
Q 035461 5 PEPVSYICGDCGMENTLKPG----------------DVIQCRECGYR 35 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~~----------------~~irC~~CG~R 35 (51)
.....|+|..||..-+...+ +.-+||.||..
T Consensus 421 ~~~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 421 DLGPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred CCCCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 35578999999998887533 35699999954
No 183
>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=80.01 E-value=2.4 Score=25.28 Aligned_cols=21 Identities=29% Similarity=0.502 Sum_probs=15.8
Q ss_pred ecCCCCeeEcCCCCCcEEEEE
Q 035461 20 TLKPGDVIQCRECGYRILYKK 40 (51)
Q Consensus 20 ~~~~~~~irC~~CG~RIlyK~ 40 (51)
.+..+.+-||++||+-...+.
T Consensus 73 ~l~~g~~~rC~eCG~~fkL~~ 93 (97)
T cd00924 73 WLEKGKPKRCPECGHVFKLVD 93 (97)
T ss_pred EEeCCCceeCCCCCcEEEEEE
Confidence 355678999999998766553
No 184
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=79.90 E-value=0.94 Score=25.80 Aligned_cols=9 Identities=11% Similarity=0.379 Sum_probs=4.3
Q ss_pred CCCCcEEEE
Q 035461 31 ECGYRILYK 39 (51)
Q Consensus 31 ~CG~RIlyK 39 (51)
+||++...-
T Consensus 34 eCg~tF~t~ 42 (72)
T PRK09678 34 NCSATFITY 42 (72)
T ss_pred CCCCEEEEE
Confidence 555554433
No 185
>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=79.69 E-value=1.2 Score=30.04 Aligned_cols=25 Identities=32% Similarity=0.646 Sum_probs=13.3
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
-...|+-||.+-.... ++||+||..
T Consensus 196 R~L~Cs~C~t~W~~~R---~~Cp~Cg~~ 220 (290)
T PF04216_consen 196 RYLHCSLCGTEWRFVR---IKCPYCGNT 220 (290)
T ss_dssp EEEEETTT--EEE--T---TS-TTT---
T ss_pred EEEEcCCCCCeeeecC---CCCcCCCCC
Confidence 4567999999887765 679999864
No 186
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=79.54 E-value=0.95 Score=22.46 Aligned_cols=14 Identities=21% Similarity=0.570 Sum_probs=10.9
Q ss_pred eeEcCCCCCcEEEE
Q 035461 26 VIQCRECGYRILYK 39 (51)
Q Consensus 26 ~irC~~CG~RIlyK 39 (51)
+..||.||...+++
T Consensus 2 ~~~Cp~Cg~~~~~~ 15 (47)
T PF14690_consen 2 PPRCPHCGSPSVHR 15 (47)
T ss_pred CccCCCcCCCceEC
Confidence 46899999887554
No 187
>PRK14873 primosome assembly protein PriA; Provisional
Probab=79.53 E-value=2.2 Score=32.50 Aligned_cols=25 Identities=32% Similarity=0.636 Sum_probs=12.1
Q ss_pred EcCCCCCeeecC-CCCeeEcCCCCCc
Q 035461 11 ICGDCGMENTLK-PGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~~-~~~~irC~~CG~R 35 (51)
.|.+|+....+- ....++|.+||+.
T Consensus 394 ~C~~C~~~L~~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 394 RCRHCTGPLGLPSAGGTPRCRWCGRA 419 (665)
T ss_pred ECCCCCCceeEecCCCeeECCCCcCC
Confidence 455554444442 2334566666653
No 188
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=79.45 E-value=0.4 Score=29.36 Aligned_cols=30 Identities=30% Similarity=0.491 Sum_probs=23.2
Q ss_pred ceEEEcCCCCCeeecCC-CCeeEcCCCCCcE
Q 035461 7 PVSYICGDCGMENTLKP-GDVIQCRECGYRI 36 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~-~~~irC~~CG~RI 36 (51)
+-.-+||-|..+..... ++...||+|.++.
T Consensus 60 ~~~iiCGvC~~~LT~~EY~~~~~Cp~C~spF 90 (105)
T COG4357 60 PKAIICGVCRKLLTRAEYGMCGSCPYCQSPF 90 (105)
T ss_pred CccEEhhhhhhhhhHHHHhhcCCCCCcCCCC
Confidence 34468999999888764 4678899998874
No 189
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=79.39 E-value=2.3 Score=21.27 Aligned_cols=16 Identities=38% Similarity=0.904 Sum_probs=11.9
Q ss_pred CCCceEEEcCCCCCee
Q 035461 4 QPEPVSYICGDCGMEN 19 (51)
Q Consensus 4 ~~~~~~Y~C~~Cg~~~ 19 (51)
++....|.|.+||...
T Consensus 23 E~mT~fy~C~~C~~~w 38 (40)
T smart00440 23 EPMTVFYVCTKCGHRW 38 (40)
T ss_pred CCCeEEEEeCCCCCEe
Confidence 4455889999998754
No 190
>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=79.15 E-value=0.85 Score=31.48 Aligned_cols=31 Identities=29% Similarity=0.521 Sum_probs=23.1
Q ss_pred CCceEEEcCCCCCeeecCC--CCeeEcCCCCCc
Q 035461 5 PEPVSYICGDCGMENTLKP--GDVIQCRECGYR 35 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~--~~~irC~~CG~R 35 (51)
++..-.+|.+|+..+-.+. ..---||+|||-
T Consensus 22 ~~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h 54 (285)
T TIGR00515 22 PEGVWTKCPKCGQVLYTKELERNLEVCPKCDHH 54 (285)
T ss_pred CCCCeeECCCCcchhhHHHHHhhCCCCCCCCCc
Confidence 3446789999999887652 234789999985
No 191
>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=78.76 E-value=2.4 Score=21.10 Aligned_cols=16 Identities=31% Similarity=0.887 Sum_probs=11.9
Q ss_pred CCCceEEEcCCCCCee
Q 035461 4 QPEPVSYICGDCGMEN 19 (51)
Q Consensus 4 ~~~~~~Y~C~~Cg~~~ 19 (51)
.+....|.|.+||...
T Consensus 23 E~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 23 EPMTLFYVCCNCGHRW 38 (39)
T ss_dssp SSSEEEEEESSSTEEE
T ss_pred CCCeEEEEeCCCCCee
Confidence 4456889999998754
No 192
>PLN00209 ribosomal protein S27; Provisional
Probab=78.68 E-value=3.7 Score=24.34 Aligned_cols=29 Identities=21% Similarity=0.425 Sum_probs=23.8
Q ss_pred eEEEcCCCCCeeecC--CCCeeEcCCCCCcE
Q 035461 8 VSYICGDCGMENTLK--PGDVIQCRECGYRI 36 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~RI 36 (51)
|.=+|.+|+.+..+- +...|.|..||.-+
T Consensus 35 m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L 65 (86)
T PLN00209 35 MDVKCQGCFNITTVFSHSQTVVVCGSCQTVL 65 (86)
T ss_pred EEEECCCCCCeeEEEecCceEEEccccCCEe
Confidence 677899999988764 55789999999654
No 193
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=78.27 E-value=1.1 Score=35.21 Aligned_cols=37 Identities=22% Similarity=0.426 Sum_probs=27.5
Q ss_pred ceEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEEecC
Q 035461 7 PVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTR 43 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R~~ 43 (51)
..-|+|..||+..+-..-+--+||+||...-.-+|.+
T Consensus 819 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 855 (1006)
T PRK12775 819 ELQWRCDDCGKVSEGFAFPYGMCPACGGKLQALDRRK 855 (1006)
T ss_pred ceeeehhhhccccccccCCcCcCcccccchhhhhccC
Confidence 4678999999987765545579999999865555543
No 194
>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=78.06 E-value=0.17 Score=25.23 Aligned_cols=26 Identities=35% Similarity=0.660 Sum_probs=12.9
Q ss_pred EcCCCCCeeecC-----CCCeeEcCCCCCcE
Q 035461 11 ICGDCGMENTLK-----PGDVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~-----~~~~irC~~CG~RI 36 (51)
+|.+|-+|..-. -...+-|++||=|+
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 366676665322 12689999999654
No 195
>PHA00732 hypothetical protein
Probab=78.01 E-value=0.77 Score=26.21 Aligned_cols=28 Identities=18% Similarity=0.496 Sum_probs=20.0
Q ss_pred EEcCCCCCeeecC--------C-CCeeEcCCCCCcEE
Q 035461 10 YICGDCGMENTLK--------P-GDVIQCRECGYRIL 37 (51)
Q Consensus 10 Y~C~~Cg~~~~~~--------~-~~~irC~~CG~RIl 37 (51)
|.|..||..+... . -.+-+|+.||...-
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 7899999988742 1 12348999998654
No 196
>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=78.00 E-value=1.9 Score=31.41 Aligned_cols=8 Identities=38% Similarity=1.207 Sum_probs=3.9
Q ss_pred EcCCCCCe
Q 035461 11 ICGDCGME 18 (51)
Q Consensus 11 ~C~~Cg~~ 18 (51)
.|.+||..
T Consensus 215 ~C~~Cg~~ 222 (505)
T TIGR00595 215 LCRSCGYI 222 (505)
T ss_pred EhhhCcCc
Confidence 45555444
No 197
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=77.80 E-value=1.4 Score=32.31 Aligned_cols=31 Identities=39% Similarity=0.837 Sum_probs=22.8
Q ss_pred CceEEEcCCCCCeeecCC----CCeeEcCCCCCcE
Q 035461 6 EPVSYICGDCGMENTLKP----GDVIQCRECGYRI 36 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~~----~~~irC~~CG~RI 36 (51)
..+.|.|..||.++.... ....+||+||.-+
T Consensus 324 ~r~~~~c~~~~~e~~~t~~~~~~~~~~~~~~~~e~ 358 (411)
T COG1503 324 ERVTYKCPTCGYENLKSKREFEQKRFRCPECGSEM 358 (411)
T ss_pred cceeecCCCcchhhhhcccccccccccCccccccc
Confidence 458999999999986531 1234999999744
No 198
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=77.56 E-value=3.9 Score=23.08 Aligned_cols=21 Identities=19% Similarity=0.286 Sum_probs=14.5
Q ss_pred EcCCCCCcEEEEEecCceEEE
Q 035461 28 QCRECGYRILYKKRTRRIVQY 48 (51)
Q Consensus 28 rC~~CG~RIlyK~R~~~~~~~ 48 (51)
-||.||..++.-+.+....+|
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v 28 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRA 28 (64)
T ss_pred CCCCCCCceeEEEecCceEEE
Confidence 488888887777766655544
No 199
>PRK14873 primosome assembly protein PriA; Provisional
Probab=77.53 E-value=2.5 Score=32.19 Aligned_cols=22 Identities=27% Similarity=0.554 Sum_probs=13.3
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
-+|--||... .+-+||+||+.-
T Consensus 411 l~Ch~CG~~~-----~p~~Cp~Cgs~~ 432 (665)
T PRK14873 411 PRCRWCGRAA-----PDWRCPRCGSDR 432 (665)
T ss_pred eECCCCcCCC-----cCccCCCCcCCc
Confidence 4577777632 135777777654
No 200
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=77.49 E-value=4.4 Score=24.02 Aligned_cols=29 Identities=21% Similarity=0.539 Sum_probs=23.7
Q ss_pred eEEEcCCCCCeeecC--CCCeeEcCCCCCcE
Q 035461 8 VSYICGDCGMENTLK--PGDVIQCRECGYRI 36 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~RI 36 (51)
|.=+|..|+.+..+- +...|.|..||.-+
T Consensus 34 m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L 64 (85)
T PTZ00083 34 MDVKCPGCSQITTVFSHAQTVVLCGGCSSQL 64 (85)
T ss_pred EEEECCCCCCeeEEEecCceEEEccccCCEe
Confidence 677899999988764 55789999999644
No 201
>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=77.49 E-value=1.7 Score=17.94 Aligned_cols=11 Identities=27% Similarity=0.694 Sum_probs=6.3
Q ss_pred EEcCCCCCeee
Q 035461 10 YICGDCGMENT 20 (51)
Q Consensus 10 Y~C~~Cg~~~~ 20 (51)
|.|..||..+.
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 67777777764
No 202
>PLN02294 cytochrome c oxidase subunit Vb
Probab=77.46 E-value=2.9 Score=27.59 Aligned_cols=21 Identities=19% Similarity=0.393 Sum_probs=16.5
Q ss_pred cCCCCeeEcCCCCCcEEEEEe
Q 035461 21 LKPGDVIQCRECGYRILYKKR 41 (51)
Q Consensus 21 ~~~~~~irC~~CG~RIlyK~R 41 (51)
+..+.+.|||+||+-...|.-
T Consensus 136 L~kGkp~RCpeCG~~fkL~~v 156 (174)
T PLN02294 136 LEKGKSFECPVCTQYFELEVV 156 (174)
T ss_pred ecCCCceeCCCCCCEEEEEEe
Confidence 456788999999997776643
No 203
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=76.92 E-value=1 Score=36.66 Aligned_cols=25 Identities=36% Similarity=0.763 Sum_probs=19.7
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCcEEE
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYRILY 38 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~RIly 38 (51)
+|.+||.-+.-. .+ .||.||++.+-
T Consensus 696 rC~dcg~q~~~~-~~--~cP~Cgs~~v~ 720 (1187)
T COG1110 696 RCRDCGEQFVDS-ED--KCPRCGSRNVE 720 (1187)
T ss_pred HHhhcCceeccc-cc--cCCCCCCcccc
Confidence 699999998665 22 99999997653
No 204
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=76.91 E-value=1.4 Score=33.40 Aligned_cols=23 Identities=30% Similarity=0.881 Sum_probs=17.3
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
=+|.+||.++ .+..-.||.||..
T Consensus 569 ~~C~~CG~~~---~g~~~~CP~CGs~ 591 (625)
T PRK08579 569 TVCNKCGRST---TGLYTRCPRCGSE 591 (625)
T ss_pred ccCCCCCCcc---CCCCCcCcCCCCc
Confidence 4799999954 2335699999964
No 205
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=76.87 E-value=2.3 Score=30.99 Aligned_cols=29 Identities=24% Similarity=0.474 Sum_probs=21.0
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
..|-|.+||..........-+||.||..+
T Consensus 239 ~~~~c~~cg~~~~~~~~~~~~c~~Cg~~~ 267 (380)
T COG1867 239 YIYHCSRCGEIVGSFREVDEKCPHCGGKV 267 (380)
T ss_pred cEEEcccccceecccccccccCCcccccc
Confidence 46999999944444444567999999843
No 206
>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=76.70 E-value=1.2 Score=31.46 Aligned_cols=29 Identities=28% Similarity=0.630 Sum_probs=20.2
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCc-EEEEEec
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYR-ILYKKRT 42 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~R-IlyK~R~ 42 (51)
+|.+||..+..-. ..||+||+- |.-|-++
T Consensus 84 ~C~~CGa~V~~~e---~~Cp~C~StnI~r~DdS 113 (314)
T PF09567_consen 84 KCNNCGANVSRLE---ESCPNCGSTNIKRKDDS 113 (314)
T ss_pred hhccccceeeehh---hcCCCCCcccccccCCc
Confidence 6999999987543 579999964 4444333
No 207
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=76.66 E-value=2.8 Score=25.28 Aligned_cols=28 Identities=36% Similarity=0.741 Sum_probs=21.0
Q ss_pred cCCCCCeeecC---CCCeeEcCCCCCcEEEE
Q 035461 12 CGDCGMENTLK---PGDVIQCRECGYRILYK 39 (51)
Q Consensus 12 C~~Cg~~~~~~---~~~~irC~~CG~RIlyK 39 (51)
|.+||.-+-.. .+..+.|+.|||-.-..
T Consensus 5 Cp~Cgsll~p~~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 5 CPKCGSLLYPKKDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred cCCccCeeEEeEcCCCcEEECCCCCcchhcc
Confidence 78888888774 34579999999865544
No 208
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=76.52 E-value=0.94 Score=30.94 Aligned_cols=25 Identities=36% Similarity=0.882 Sum_probs=18.6
Q ss_pred EEcCCCCCeeecC-----CC--CeeEcCCCCC
Q 035461 10 YICGDCGMENTLK-----PG--DVIQCRECGY 34 (51)
Q Consensus 10 Y~C~~Cg~~~~~~-----~~--~~irC~~CG~ 34 (51)
|+|-+||.++..- .+ .-.+||+|+-
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 6899999998752 11 3468999974
No 209
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=76.49 E-value=9.3 Score=21.01 Aligned_cols=38 Identities=24% Similarity=0.488 Sum_probs=28.4
Q ss_pred EEcCCCCCeeecC-------CCCeeEcCCCCCcEEEEEecCceEE
Q 035461 10 YICGDCGMENTLK-------PGDVIQCRECGYRILYKKRTRRIVQ 47 (51)
Q Consensus 10 Y~C~~Cg~~~~~~-------~~~~irC~~CG~RIlyK~R~~~~~~ 47 (51)
..|.-||....++ .+-++-||.|-...|.-...-.+..
T Consensus 5 i~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI~v~~~~i~v 49 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKNFPLYCPKCKQETLIDVKQLKITV 49 (55)
T ss_pred EECCCCCCccceeeecCceeccccccCCCCCceEEEEeeccEEEE
Confidence 5799999766543 3578999999999988776555443
No 210
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=76.46 E-value=2.6 Score=20.09 Aligned_cols=22 Identities=27% Similarity=0.584 Sum_probs=16.1
Q ss_pred eEEEcCCCCCeeecCC--CCeeEc
Q 035461 8 VSYICGDCGMENTLKP--GDVIQC 29 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~--~~~irC 29 (51)
-.|+|..||..++.-. ..++.|
T Consensus 6 ~~ykC~~Cgniv~v~~~~~~~l~C 29 (34)
T TIGR00319 6 QVYKCEVCGNIVEVLHAGGGQLVC 29 (34)
T ss_pred cEEEcCCCCcEEEEEECCCcceec
Confidence 4799999999998642 234666
No 211
>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=76.44 E-value=1.5 Score=19.35 Aligned_cols=12 Identities=25% Similarity=0.822 Sum_probs=10.2
Q ss_pred EEcCCCCCeeec
Q 035461 10 YICGDCGMENTL 21 (51)
Q Consensus 10 Y~C~~Cg~~~~~ 21 (51)
|.|..|+..|..
T Consensus 2 ~~C~~C~~~F~~ 13 (27)
T PF13912_consen 2 FECDECGKTFSS 13 (27)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCccCCccCC
Confidence 889999998864
No 212
>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=76.40 E-value=4.8 Score=24.72 Aligned_cols=30 Identities=13% Similarity=0.335 Sum_probs=24.0
Q ss_pred ceEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 7 PVSYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
-...-|..|++.+.....+.-+|+.|+..+
T Consensus 32 ~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 32 WWYPACPGCNKKVVEEGNGTYRCEKCNKSV 61 (166)
T ss_pred eEEccccccCcccEeCCCCcEECCCCCCcC
Confidence 355679999999876655789999999875
No 213
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=76.09 E-value=1.4 Score=30.61 Aligned_cols=29 Identities=24% Similarity=0.515 Sum_probs=21.9
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRIL 37 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl 37 (51)
-+++|+.|++.+.--+ -..+|+.||+.+.
T Consensus 166 q~~rc~~c~~k~rr~p-l~g~c~kcg~~~~ 194 (253)
T COG1933 166 QEFRCVKCNTKFRRPP-LDGKCPICGGKIV 194 (253)
T ss_pred heeehHhhhhhhcCCC-ccccccccCCeEE
Confidence 4678999998876544 4479999998654
No 214
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=76.07 E-value=1.3 Score=26.85 Aligned_cols=10 Identities=50% Similarity=1.119 Sum_probs=8.4
Q ss_pred eeEcCCCCCc
Q 035461 26 VIQCRECGYR 35 (51)
Q Consensus 26 ~irC~~CG~R 35 (51)
-|.||+||-|
T Consensus 3 LI~CP~Cg~R 12 (97)
T COG4311 3 LIPCPYCGER 12 (97)
T ss_pred eecCCCCCCC
Confidence 4899999975
No 215
>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=76.05 E-value=2.7 Score=20.09 Aligned_cols=21 Identities=29% Similarity=0.648 Sum_probs=15.6
Q ss_pred EEEcCCCCCeeecCC--CCeeEc
Q 035461 9 SYICGDCGMENTLKP--GDVIQC 29 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~--~~~irC 29 (51)
.|+|..||..++.-. ..++.|
T Consensus 4 ~ykC~~CGniv~v~~~~~~~l~C 26 (34)
T cd00974 4 VYKCEICGNIVEVLNVGGGTLVC 26 (34)
T ss_pred EEEcCCCCcEEEEEECCCcceee
Confidence 699999999998542 334666
No 216
>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=75.63 E-value=1.6 Score=21.35 Aligned_cols=26 Identities=15% Similarity=0.272 Sum_probs=18.3
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
.|.-|+..+......+++|..|+..+
T Consensus 13 ~C~~C~~~i~~~~~~~~~C~~C~~~~ 38 (50)
T cd00029 13 FCDVCRKSIWGLFKQGLRCSWCKVKC 38 (50)
T ss_pred ChhhcchhhhccccceeEcCCCCCch
Confidence 47778777654345789999997643
No 217
>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=75.60 E-value=2 Score=31.80 Aligned_cols=35 Identities=26% Similarity=0.477 Sum_probs=25.0
Q ss_pred eEEEcCCCCCeeecCCC------------CeeEcCCCCCcEEEEEec
Q 035461 8 VSYICGDCGMENTLKPG------------DVIQCRECGYRILYKKRT 42 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~------------~~irC~~CG~RIlyK~R~ 42 (51)
..-.|-+||..+.++.. .-..||.||+.|--..|.
T Consensus 199 ~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~ 245 (557)
T PF05876_consen 199 YYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKR 245 (557)
T ss_pred EEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHh
Confidence 44579999999887511 347899999988655443
No 218
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=75.55 E-value=1.7 Score=31.28 Aligned_cols=23 Identities=26% Similarity=0.515 Sum_probs=18.4
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
.|.+|+..+ .++..+||.||+.+
T Consensus 223 ~C~~Cd~l~---~~~~a~CpRC~~~L 245 (419)
T PRK15103 223 SCSCCTAIL---PADQPVCPRCHTKG 245 (419)
T ss_pred cCCCCCCCC---CCCCCCCCCCCCcC
Confidence 599999975 34556999999987
No 219
>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=75.54 E-value=3.9 Score=25.11 Aligned_cols=25 Identities=24% Similarity=0.495 Sum_probs=17.9
Q ss_pred eEEEcCCCCCeeecC--CCCeeEcCCCCC
Q 035461 8 VSYICGDCGMENTLK--PGDVIQCRECGY 34 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~ 34 (51)
-.|+|..||..++.- .+..+.| ||-
T Consensus 6 ~fYkC~~CGniv~v~~~g~~~l~C--Cge 32 (125)
T TIGR00320 6 QVYKCEVCGNIVEVLNAGIGQLVC--CNQ 32 (125)
T ss_pred cEEECCCCCcEEEEEECCCcceee--CCc
Confidence 489999999999643 2345777 554
No 220
>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=75.48 E-value=1.9 Score=26.28 Aligned_cols=14 Identities=36% Similarity=0.928 Sum_probs=11.9
Q ss_pred eeEcCCCCCcEEEE
Q 035461 26 VIQCRECGYRILYK 39 (51)
Q Consensus 26 ~irC~~CG~RIlyK 39 (51)
.|+|+.||+.||-.
T Consensus 2 ~v~C~~C~S~VL~~ 15 (103)
T cd00246 2 AVLCQRCGSRVLTI 15 (103)
T ss_pred ceECCCCCCEEEec
Confidence 48999999999943
No 221
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=75.42 E-value=3.2 Score=26.48 Aligned_cols=31 Identities=23% Similarity=0.433 Sum_probs=23.3
Q ss_pred EEEcCCCCCeeec--C---------CCCeeEcCCCCCcEEEEE
Q 035461 9 SYICGDCGMENTL--K---------PGDVIQCRECGYRILYKK 40 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~--~---------~~~~irC~~CG~RIlyK~ 40 (51)
...|. +|.+|+- . ....|-||.||+.-+-|.
T Consensus 5 ~L~C~-~gH~FEgWF~ss~~fd~Q~~~glv~CP~Cgs~~V~K~ 46 (148)
T PF06676_consen 5 DLRCE-NGHEFEGWFRSSAAFDRQQARGLVSCPVCGSTEVSKA 46 (148)
T ss_pred EEecC-CCCccceecCCHHHHHHHHHcCCccCCCCCCCeEeee
Confidence 34676 8888884 1 246799999999888775
No 222
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.32 E-value=2.2 Score=23.79 Aligned_cols=15 Identities=27% Similarity=0.747 Sum_probs=12.4
Q ss_pred CeeEcCCCCCcEEEE
Q 035461 25 DVIQCRECGYRILYK 39 (51)
Q Consensus 25 ~~irC~~CG~RIlyK 39 (51)
-.|+|.+|||-||.-
T Consensus 33 IkikC~nC~h~vm~p 47 (60)
T COG4481 33 IKIKCENCGHSVMMP 47 (60)
T ss_pred EEEEecCCCcEEEec
Confidence 358999999999863
No 223
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=74.97 E-value=0.98 Score=35.99 Aligned_cols=29 Identities=28% Similarity=0.770 Sum_probs=23.2
Q ss_pred eEEEcCCCCCeeecC----------CC-CeeEcCCCCCcE
Q 035461 8 VSYICGDCGMENTLK----------PG-DVIQCRECGYRI 36 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~----------~~-~~irC~~CG~RI 36 (51)
-+|+|.+||+-|..+ .+ -+.-|++|+.|.
T Consensus 280 RKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRF 319 (1007)
T KOG3623|consen 280 RKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRF 319 (1007)
T ss_pred ccccccccchhhhhHHHHHhhheeecCCCCcCCccccccc
Confidence 579999999999864 22 468899999874
No 224
>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=74.64 E-value=2.1 Score=25.47 Aligned_cols=30 Identities=23% Similarity=0.744 Sum_probs=21.8
Q ss_pred ceEEEcCCCCCeeecC-CCCeeEcCCCCCcE
Q 035461 7 PVSYICGDCGMENTLK-PGDVIQCRECGYRI 36 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~-~~~~irC~~CG~RI 36 (51)
-..|.|..||+.---. ...--.|..||..+
T Consensus 33 ~~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 33 HAKYTCPFCGKTSVKRVATGIWKCKKCGKKF 63 (90)
T ss_dssp HS-BEESSSSSSEEEEEETTEEEETTTTEEE
T ss_pred hCCCcCCCCCCceeEEeeeEEeecCCCCCEE
Confidence 3579999999987433 34668999999754
No 225
>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=74.60 E-value=2.3 Score=30.37 Aligned_cols=28 Identities=29% Similarity=0.647 Sum_probs=13.3
Q ss_pred eEEEcCCCCCeee-cCCCCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENT-LKPGDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~-~~~~~~irC~~CG~R 35 (51)
-.|.|.+||..+. +...+...|++||.-
T Consensus 284 RFFkC~~C~~Rt~sl~r~P~~~C~~Cg~~ 312 (344)
T PF09332_consen 284 RFFKCKDCGNRTISLERLPKKHCSNCGSS 312 (344)
T ss_dssp EEEE-T-TS-EEEESSSS--S--TTT-S-
T ss_pred eeEECCCCCCeeeecccCCCCCCCcCCcC
Confidence 3588999987644 455677899999964
No 226
>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=74.54 E-value=2.5 Score=27.65 Aligned_cols=27 Identities=19% Similarity=0.279 Sum_probs=19.5
Q ss_pred EEEcCCCCCeeecCC-CCeeEcCCCCCc
Q 035461 9 SYICGDCGMENTLKP-GDVIQCRECGYR 35 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~-~~~irC~~CG~R 35 (51)
...|..|+....... ...-+||.||..
T Consensus 118 ~~~C~~C~~~~~~~~~~~~p~C~~Cgg~ 145 (225)
T cd01411 118 RIYCTVCGKTVDWEEYLKSPYHAKCGGV 145 (225)
T ss_pred eeEeCCCCCccchhhcCCCCCCCCCCCE
Confidence 467999988776443 234689999974
No 227
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=74.38 E-value=1.3 Score=31.01 Aligned_cols=31 Identities=26% Similarity=0.471 Sum_probs=23.1
Q ss_pred CCceEEEcCCCCCeeecCC--CCeeEcCCCCCc
Q 035461 5 PEPVSYICGDCGMENTLKP--GDVIQCRECGYR 35 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~--~~~irC~~CG~R 35 (51)
++..-.+|.+|+..+-.+. ...-.||+|||-
T Consensus 34 p~~lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h 66 (296)
T CHL00174 34 YKHLWVQCENCYGLNYKKFLKSKMNICEQCGYH 66 (296)
T ss_pred CCCCeeECCCccchhhHHHHHHcCCCCCCCCCC
Confidence 3446789999999887653 234689999983
No 228
>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=74.32 E-value=2.1 Score=31.86 Aligned_cols=23 Identities=30% Similarity=0.745 Sum_probs=15.8
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
=+|.+||..-+.. .-.||.||.+
T Consensus 525 ~~C~~CG~~g~~~---~~~CP~Cgs~ 547 (579)
T TIGR02487 525 DVCEDCGYTGEGL---NDKCPKCGSH 547 (579)
T ss_pred ccCCCCCCCCCCC---CCcCcCCCCc
Confidence 3799999732221 2479999976
No 229
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=74.04 E-value=1.6 Score=24.72 Aligned_cols=23 Identities=30% Similarity=0.599 Sum_probs=16.5
Q ss_pred cCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461 12 CGDCGMENTLKPGDVIQCRECGYRIL 37 (51)
Q Consensus 12 C~~Cg~~~~~~~~~~irC~~CG~RIl 37 (51)
|-+|++.++- +.-.||.||+.=|
T Consensus 7 C~~Ck~l~~~---d~e~CP~Cgs~~~ 29 (64)
T COG2093 7 CKNCKRLTPE---DTEICPVCGSTDL 29 (64)
T ss_pred HhhccccCCC---CCccCCCCCCccc
Confidence 7788876543 4467999998743
No 230
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=73.69 E-value=5 Score=24.60 Aligned_cols=32 Identities=25% Similarity=0.603 Sum_probs=24.6
Q ss_pred CceEEEcCCCCCeeecC-------CCCeeEcCCCCCcEE
Q 035461 6 EPVSYICGDCGMENTLK-------PGDVIQCRECGYRIL 37 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~-------~~~~irC~~CG~RIl 37 (51)
=+..|-|..||++.... ....+-|.+||-+.=
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 35789999999998762 236799999997643
No 231
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=73.54 E-value=1.9 Score=29.06 Aligned_cols=31 Identities=26% Similarity=0.405 Sum_probs=22.5
Q ss_pred CceEEEcCCCCCeeecCC------------CCeeEcCCCCCcE
Q 035461 6 EPVSYICGDCGMENTLKP------------GDVIQCRECGYRI 36 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~~------------~~~irC~~CG~RI 36 (51)
+...=.|.-||..+.... -....|.+||||-
T Consensus 11 ~~~~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~ 53 (201)
T COG1779 11 FETRIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRS 53 (201)
T ss_pred eeeeecCCcccceeeEEEeeecCCccceEEEEEEEccccCCcc
Confidence 346678999999766431 1578999999983
No 232
>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=73.22 E-value=2.5 Score=21.51 Aligned_cols=24 Identities=38% Similarity=0.733 Sum_probs=16.1
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
.|..|++.|.+.. ....|..||.-
T Consensus 4 ~C~~C~~~F~~~~-rk~~Cr~Cg~~ 27 (57)
T cd00065 4 SCMGCGKPFTLTR-RRHHCRNCGRI 27 (57)
T ss_pred cCcccCccccCCc-cccccCcCcCC
Confidence 5888998888743 44566666653
No 233
>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=73.15 E-value=3.4 Score=21.90 Aligned_cols=24 Identities=33% Similarity=0.634 Sum_probs=10.1
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCC
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGY 34 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~ 34 (51)
=.|..|++.|.+- ...-.|+.||.
T Consensus 10 ~~C~~C~~~F~~~-~rrhhCr~CG~ 33 (69)
T PF01363_consen 10 SNCMICGKKFSLF-RRRHHCRNCGR 33 (69)
T ss_dssp SB-TTT--B-BSS-S-EEE-TTT--
T ss_pred CcCcCcCCcCCCc-eeeEccCCCCC
Confidence 4588999999764 34455555554
No 234
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=73.06 E-value=1.4 Score=27.49 Aligned_cols=36 Identities=19% Similarity=0.419 Sum_probs=26.3
Q ss_pred EcCCCCCeeecCC-CCeeEcCCCCCcEEEEEecCceE
Q 035461 11 ICGDCGMENTLKP-GDVIQCRECGYRILYKKRTRRIV 46 (51)
Q Consensus 11 ~C~~Cg~~~~~~~-~~~irC~~CG~RIlyK~R~~~~~ 46 (51)
-|+.||..++... .+.+-|..|+..+=-+.+....+
T Consensus 9 FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~~~~~~~v 45 (116)
T KOG2907|consen 9 FCSDCGSLLEEPSAQSTVLCIRCKIEYPVSQFSGLVV 45 (116)
T ss_pred hhhhhhhhcccccccCceEeccccccCCHHHhCCeeE
Confidence 3899999998874 46677999998776655555443
No 235
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=73.03 E-value=2.6 Score=30.25 Aligned_cols=36 Identities=25% Similarity=0.631 Sum_probs=28.6
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCcEEEEEecCceEEEE
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYE 49 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R~~~~~~~~ 49 (51)
.|..||..+-++. ..|-.||+.+=|-.-...++.++
T Consensus 1 ~C~~Cg~~v~FeN---t~C~~Cg~~LGf~p~~~~~~al~ 36 (343)
T PF10005_consen 1 SCPNCGQPVFFEN---TRCLSCGSALGFDPDRREMVALE 36 (343)
T ss_pred CCCCCCCcceeCC---CccccCCccccCCCCCCcEEeec
Confidence 3889999988775 78999999998877766666554
No 236
>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=72.75 E-value=1.7 Score=21.04 Aligned_cols=24 Identities=17% Similarity=0.284 Sum_probs=17.5
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
.|.-|+..+.... .+++|+.|+..
T Consensus 13 ~C~~C~~~i~~~~-~~~~C~~C~~~ 36 (49)
T smart00109 13 KCCVCRKSIWGSF-QGLRCSWCKVK 36 (49)
T ss_pred CccccccccCcCC-CCcCCCCCCch
Confidence 5888888775433 57999999754
No 237
>smart00350 MCM minichromosome maintenance proteins.
Probab=72.68 E-value=7.3 Score=28.28 Aligned_cols=30 Identities=20% Similarity=0.462 Sum_probs=23.1
Q ss_pred ceEEEcCCCCCeeecCC-----CCeeEcCC--CCCcE
Q 035461 7 PVSYICGDCGMENTLKP-----GDVIQCRE--CGYRI 36 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~-----~~~irC~~--CG~RI 36 (51)
...|.|..||.++.... ..+..|+. |+.+-
T Consensus 35 ~~~f~C~~C~~~~~~~~~~~~~~~p~~C~~~~C~~~~ 71 (509)
T smart00350 35 RASFTCEKCGATLGPEIQSGRETEPTVCPPRECQSPT 71 (509)
T ss_pred EEEEEecCCCCEEeEEecCCcccCCCcCCCCcCCCCC
Confidence 37899999999876542 26789998 99764
No 238
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=72.57 E-value=2.2 Score=32.32 Aligned_cols=23 Identities=22% Similarity=0.609 Sum_probs=16.4
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
.=+|.+||..-++. -.||.||.+
T Consensus 559 ~~~C~~CGy~g~~~----~~CP~CG~~ 581 (618)
T PRK14704 559 VDRCKCCSYHGVIG----NECPSCGNE 581 (618)
T ss_pred CeecCCCCCCCCcC----ccCcCCCCC
Confidence 34799999743322 589999974
No 239
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=72.55 E-value=1.6 Score=24.01 Aligned_cols=29 Identities=24% Similarity=0.488 Sum_probs=21.5
Q ss_pred EEEcCCCCCeeecCCC------------CeeEcCCCCCcEE
Q 035461 9 SYICGDCGMENTLKPG------------DVIQCRECGYRIL 37 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~------------~~irC~~CG~RIl 37 (51)
.=+|.-|++.++|..+ ..--|.+|-+||=
T Consensus 2 ~vkC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~RI~ 42 (56)
T PF09963_consen 2 RVKCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKERIR 42 (56)
T ss_pred eeEEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHHHh
Confidence 4578889999888522 4567999988874
No 240
>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=72.17 E-value=4.7 Score=24.30 Aligned_cols=31 Identities=16% Similarity=0.363 Sum_probs=22.0
Q ss_pred CceEEEcC--CCCCeeecCCCCeeEcCCCCCcE
Q 035461 6 EPVSYICG--DCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 6 ~~~~Y~C~--~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
.....-|. .|++.+.....+..+|+.|+.-+
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 44667899 99998887755779999999654
No 241
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=72.09 E-value=3.4 Score=24.58 Aligned_cols=31 Identities=19% Similarity=0.612 Sum_probs=22.3
Q ss_pred CceEEEcCCCCCeeecC-CCCeeEcCCCCCcE
Q 035461 6 EPVSYICGDCGMENTLK-PGDVIQCRECGYRI 36 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~-~~~~irC~~CG~RI 36 (51)
+...|.|..||++.--. ....-.|..||+.+
T Consensus 33 q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 33 QHAKYFCPFCGKHAVKRQAVGIWRCKGCKKTV 64 (90)
T ss_pred HhCCccCCCCCCCceeeeeeEEEEcCCCCCEE
Confidence 34679999999764333 34668999999865
No 242
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=72.07 E-value=2.6 Score=28.88 Aligned_cols=27 Identities=26% Similarity=0.795 Sum_probs=18.8
Q ss_pred eEEEcCCCCCeeec--CCCCeeEcCCCCC
Q 035461 8 VSYICGDCGMENTL--KPGDVIQCRECGY 34 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~--~~~~~irC~~CG~ 34 (51)
-...|.+||...-+ ...+.+-|.+||.
T Consensus 10 ~~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~ 38 (310)
T PRK00423 10 EKLVCPECGSDKLIYDYERGEIVCADCGL 38 (310)
T ss_pred cCCcCcCCCCCCeeEECCCCeEeecccCC
Confidence 34679999973222 2457799999997
No 243
>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=71.93 E-value=2.1 Score=24.89 Aligned_cols=27 Identities=30% Similarity=0.436 Sum_probs=18.4
Q ss_pred EEcCCCCCeeecCCC--------CeeEcCCCCCcE
Q 035461 10 YICGDCGMENTLKPG--------DVIQCRECGYRI 36 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~--------~~irC~~CG~RI 36 (51)
-.|..|++....... -.-||++|+.+|
T Consensus 34 S~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~I 68 (92)
T PF06750_consen 34 SHCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAPI 68 (92)
T ss_pred CcCcCCCCcCcccccchHHHHHHhCCCCcccCCCC
Confidence 468888888765433 234888888776
No 244
>PRK04023 DNA polymerase II large subunit; Validated
Probab=71.66 E-value=2.2 Score=34.73 Aligned_cols=22 Identities=32% Similarity=0.609 Sum_probs=11.4
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCC
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGY 34 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~ 34 (51)
....|.+||... ...+||+||.
T Consensus 625 g~RfCpsCG~~t-----~~frCP~CG~ 646 (1121)
T PRK04023 625 GRRKCPSCGKET-----FYRRCPFCGT 646 (1121)
T ss_pred cCccCCCCCCcC-----CcccCCCCCC
Confidence 345666666663 2245555554
No 245
>PHA00616 hypothetical protein
Probab=71.42 E-value=0.79 Score=24.05 Aligned_cols=12 Identities=33% Similarity=0.534 Sum_probs=9.7
Q ss_pred EEcCCCCCeeec
Q 035461 10 YICGDCGMENTL 21 (51)
Q Consensus 10 Y~C~~Cg~~~~~ 21 (51)
|.|.+||..|.-
T Consensus 2 YqC~~CG~~F~~ 13 (44)
T PHA00616 2 YQCLRCGGIFRK 13 (44)
T ss_pred CccchhhHHHhh
Confidence 789999988763
No 246
>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=71.37 E-value=2.6 Score=27.18 Aligned_cols=28 Identities=21% Similarity=0.580 Sum_probs=19.7
Q ss_pred eEEEcCCCCCeeecC----CCCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENTLK----PGDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~----~~~~irC~~CG~R 35 (51)
....|..|+...... ....-+||.||..
T Consensus 108 ~~~~C~~C~~~~~~~~~~~~~~~p~C~~Cgg~ 139 (224)
T cd01412 108 FRVRCSSCGYVGENNEEIPEEELPRCPKCGGL 139 (224)
T ss_pred CccccCCCCCCCCcchhhhccCCCCCCCCCCc
Confidence 346799999877653 2234689999975
No 247
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=71.29 E-value=2.4 Score=32.66 Aligned_cols=22 Identities=27% Similarity=0.709 Sum_probs=16.6
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
=+|.+||....+. -.||.||..
T Consensus 681 ~~C~~CG~~~~~~----~~CP~CG~~ 702 (735)
T PRK07111 681 DRCPVCGYLGVIE----DKCPKCGST 702 (735)
T ss_pred eecCCCCCCCCcC----ccCcCCCCc
Confidence 4899999755443 689999963
No 248
>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=71.22 E-value=3.4 Score=24.62 Aligned_cols=31 Identities=26% Similarity=0.799 Sum_probs=22.4
Q ss_pred CceEEEcCCCCCeeecC-CCCeeEcCCCCCcE
Q 035461 6 EPVSYICGDCGMENTLK-PGDVIQCRECGYRI 36 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~-~~~~irC~~CG~RI 36 (51)
+...|.|..||+..-.. ....-.|..||+.+
T Consensus 32 q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 32 QKAKYVCPFCGKKTVKRGSTGIWTCRKCGAKF 63 (91)
T ss_pred HhcCccCCCCCCCceEEEeeEEEEcCCCCCEE
Confidence 34679999999765333 34668999999865
No 249
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=71.13 E-value=5.7 Score=28.15 Aligned_cols=30 Identities=20% Similarity=0.466 Sum_probs=21.9
Q ss_pred ceEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 7 PVSYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
...|.|..||..........-.|++||.+.
T Consensus 242 g~~~~C~~c~~~~~~~~~~~~~C~~c~~~~ 271 (382)
T PRK04338 242 GYVYYCPKCLYREEVEGLPPEECPVCGGKF 271 (382)
T ss_pred eeEEECCCCCcEEEecCCCCCCCCCCCCcc
Confidence 357889999987655433345799999864
No 250
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=71.07 E-value=3.3 Score=27.46 Aligned_cols=28 Identities=32% Similarity=0.725 Sum_probs=20.0
Q ss_pred eEEEcCCCCCeeecC-------CCCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENTLK-------PGDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~-------~~~~irC~~CG~R 35 (51)
....|..|+.....+ ..+.-+||.||..
T Consensus 118 ~~~~C~~C~~~~~~~~~~~~~~~~~~p~Cp~Cgg~ 152 (244)
T PRK14138 118 EEYYCVRCGKRYTVEDVIEKLEKSDVPRCDDCSGL 152 (244)
T ss_pred CeeEECCCCCcccHHHHHHHHhcCCCCCCCCCCCe
Confidence 346799999987653 2234689999974
No 251
>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=71.03 E-value=3.8 Score=29.88 Aligned_cols=23 Identities=30% Similarity=0.775 Sum_probs=11.6
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYRIL 37 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~RIl 37 (51)
+|-.||....+ +-+||+||+.-|
T Consensus 242 ~Ch~Cg~~~~~----~~~Cp~C~s~~l 264 (505)
T TIGR00595 242 RCHYCGYQEPI----PKTCPQCGSEDL 264 (505)
T ss_pred EcCCCcCcCCC----CCCCCCCCCCee
Confidence 35555544322 246777776543
No 252
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=70.92 E-value=2.6 Score=32.35 Aligned_cols=27 Identities=22% Similarity=0.650 Sum_probs=18.3
Q ss_pred EEEcCCCCCeeecC-CCCeeEcCCCCCc
Q 035461 9 SYICGDCGMENTLK-PGDVIQCRECGYR 35 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~-~~~~irC~~CG~R 35 (51)
.=+|.+||..=+++ ....-.||.||.+
T Consensus 641 ~~~C~~CG~~Ge~~~~~~~~~CP~CG~~ 668 (711)
T PRK09263 641 IDECYECGFTGEFECTEKGFTCPKCGNH 668 (711)
T ss_pred CcccCCCCCCccccCCCCCCcCcCCCCC
Confidence 35799999854443 2233689999974
No 253
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=70.85 E-value=1.9 Score=29.87 Aligned_cols=32 Identities=28% Similarity=0.587 Sum_probs=23.1
Q ss_pred CCceEEEcCCCCCeeecCC--CCeeEcCCCCCcE
Q 035461 5 PEPVSYICGDCGMENTLKP--GDVIQCRECGYRI 36 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~--~~~irC~~CG~RI 36 (51)
++..--+|.+|+..+-.+. ...--||+|||-.
T Consensus 23 ~~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 23 PEGLWTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred CCCCeeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 3456789999998876552 2346899999854
No 254
>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=70.85 E-value=3.4 Score=26.08 Aligned_cols=19 Identities=37% Similarity=0.695 Sum_probs=14.1
Q ss_pred cCCCCeeEcCCCCCcEEEE
Q 035461 21 LKPGDVIQCRECGYRILYK 39 (51)
Q Consensus 21 ~~~~~~irC~~CG~RIlyK 39 (51)
+..+.+-||++||+-.-.+
T Consensus 107 l~~g~~~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 107 LHKGKPQRCPECGQVFKLK 125 (136)
T ss_dssp EETTSEEEETTTEEEEEEE
T ss_pred EeCCCccCCCCCCeEEEEE
Confidence 4567889999999854443
No 255
>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=70.81 E-value=3.8 Score=19.23 Aligned_cols=19 Identities=32% Similarity=0.655 Sum_probs=6.8
Q ss_pred cCCCCCeeecCCC-CeeEcC
Q 035461 12 CGDCGMENTLKPG-DVIQCR 30 (51)
Q Consensus 12 C~~Cg~~~~~~~~-~~irC~ 30 (51)
|-.||.++.-..+ -.+||+
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 5556665553322 335554
No 256
>COG5254 ARV1 Predicted membrane protein [Function unknown]
Probab=70.50 E-value=1.3 Score=30.31 Aligned_cols=25 Identities=20% Similarity=0.612 Sum_probs=18.4
Q ss_pred EEcCCCCCeeecC----CC---CeeEcCCCCC
Q 035461 10 YICGDCGMENTLK----PG---DVIQCRECGY 34 (51)
Q Consensus 10 Y~C~~Cg~~~~~~----~~---~~irC~~CG~ 34 (51)
|+|-+||++++.- .+ .--+||+|.-
T Consensus 1 mvCIeCg~~vdsLyt~ysts~iqls~Cp~C~~ 32 (239)
T COG5254 1 MVCIECGSRVDSLYTRYSTSAIQLSRCPSCNR 32 (239)
T ss_pred CeeeEcCCccceeeeeccCcceehhcCchHHH
Confidence 5899999999853 22 3468999964
No 257
>PRK04173 glycyl-tRNA synthetase; Provisional
Probab=70.47 E-value=3.1 Score=30.05 Aligned_cols=33 Identities=24% Similarity=0.565 Sum_probs=23.6
Q ss_pred eEEEcCCCCCeeecCC----------------------CCeeEcCCCCCc---------EEEEE
Q 035461 8 VSYICGDCGMENTLKP----------------------GDVIQCRECGYR---------ILYKK 40 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~----------------------~~~irC~~CG~R---------IlyK~ 40 (51)
..|.|..|+..+..+. .-+++||.||+- .||+.
T Consensus 85 ~m~~~~~~~~~~r~d~~~~~~~~~~~~~~~~~~~~~~~~~~m~cp~~~~~~~~~~~~f~l~f~~ 148 (456)
T PRK04173 85 PLVECKKCKKRYRADHLIEELGIDAEGLSNEELKELIRENDIKCPECGGENWTEVRQFNLMFKT 148 (456)
T ss_pred ceeEeCCCCCEeechhhhHHHhhhhccccHHHHHHHHHHhCCCCCCCCCCCCcCccchhhceee
Confidence 4688999997765432 127999999865 77773
No 258
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=70.39 E-value=2.8 Score=31.89 Aligned_cols=23 Identities=30% Similarity=0.667 Sum_probs=17.1
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
=+|.+||... .+..-.||.||+.
T Consensus 567 ~iC~~CG~~~---~g~~~~CP~CGs~ 589 (623)
T PRK08271 567 TICNDCHHID---KRTGKRCPICGSE 589 (623)
T ss_pred ccCCCCCCcC---CCCCcCCcCCCCc
Confidence 4799999862 2345789999975
No 259
>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=70.37 E-value=1.8 Score=27.85 Aligned_cols=8 Identities=25% Similarity=0.779 Sum_probs=5.1
Q ss_pred eEcCCCCC
Q 035461 27 IQCRECGY 34 (51)
Q Consensus 27 irC~~CG~ 34 (51)
++||+||+
T Consensus 1 M~CP~C~~ 8 (147)
T TIGR00244 1 MHCPFCQH 8 (147)
T ss_pred CCCCCCCC
Confidence 36777765
No 260
>PRK05580 primosome assembly protein PriA; Validated
Probab=70.35 E-value=3.9 Score=30.82 Aligned_cols=9 Identities=44% Similarity=0.970 Sum_probs=4.4
Q ss_pred EcCCCCCcE
Q 035461 28 QCRECGYRI 36 (51)
Q Consensus 28 rC~~CG~RI 36 (51)
+||+||+..
T Consensus 423 ~Cp~Cg~~~ 431 (679)
T PRK05580 423 ACPECGSTD 431 (679)
T ss_pred CCCCCcCCe
Confidence 455555443
No 261
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=70.27 E-value=4.7 Score=31.34 Aligned_cols=9 Identities=44% Similarity=1.077 Sum_probs=4.2
Q ss_pred eEcCCCCCc
Q 035461 27 IQCRECGYR 35 (51)
Q Consensus 27 irC~~CG~R 35 (51)
..||+||+.
T Consensus 476 ~~Cp~Cgs~ 484 (730)
T COG1198 476 QSCPECGSE 484 (730)
T ss_pred CCCCCCCCC
Confidence 444444444
No 262
>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=70.26 E-value=3.6 Score=23.14 Aligned_cols=30 Identities=30% Similarity=0.815 Sum_probs=19.5
Q ss_pred eEEEcCCCCCeeecC-------CC-CeeEcCCCCCcEE
Q 035461 8 VSYICGDCGMENTLK-------PG-DVIQCRECGYRIL 37 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~-------~~-~~irC~~CG~RIl 37 (51)
+.|.|..|+....-. .+ --++||.|..+=|
T Consensus 3 l~FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~Hl 40 (66)
T PF05180_consen 3 LTFTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRHL 40 (66)
T ss_dssp EEEEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EEE
T ss_pred EEEEcCCCCCccceeeCHHHHhCCeEEEECCCCcceee
Confidence 679999998876632 22 3489999997755
No 263
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=70.24 E-value=5.5 Score=21.55 Aligned_cols=23 Identities=30% Similarity=0.694 Sum_probs=15.9
Q ss_pred ceEEEcCCCCCeeecCCCCeeEcCCCC
Q 035461 7 PVSYICGDCGMENTLKPGDVIQCRECG 33 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG 33 (51)
+..-.|.+||.... .-.-|++||
T Consensus 25 ~~l~~C~~CG~~~~----~H~vC~~CG 47 (57)
T PRK12286 25 PGLVECPNCGEPKL----PHRVCPSCG 47 (57)
T ss_pred CcceECCCCCCccC----CeEECCCCC
Confidence 45567888887642 347788888
No 264
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=69.71 E-value=2.3 Score=32.38 Aligned_cols=26 Identities=31% Similarity=0.744 Sum_probs=13.7
Q ss_pred EcCCCCCeeecCCC---------CeeEcCCCCCcE
Q 035461 11 ICGDCGMENTLKPG---------DVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~---------~~irC~~CG~RI 36 (51)
+|.+||.++..... ....||+||..+
T Consensus 3 ~Cp~Cg~~n~~~akFC~~CG~~l~~~~Cp~CG~~~ 37 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQKCGTSLTHKPCPQCGTEV 37 (645)
T ss_pred cCCCCCCcCCCCCccccccCCCCCCCcCCCCCCCC
Confidence 56667666543211 123577776653
No 265
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=69.68 E-value=3.9 Score=30.06 Aligned_cols=29 Identities=21% Similarity=0.501 Sum_probs=21.4
Q ss_pred CceEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 6 EPVSYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
....|+|.+|..... ....-.||+||..-
T Consensus 54 d~~i~kC~~c~~~~~--y~~~~~C~~cg~~~ 82 (415)
T COG5257 54 DAKIYKCPECYRPEC--YTTEPKCPNCGAET 82 (415)
T ss_pred cCceEeCCCCCCCcc--cccCCCCCCCCCCc
Confidence 346799999998722 23557899999865
No 266
>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=69.62 E-value=2.1 Score=28.17 Aligned_cols=28 Identities=21% Similarity=0.427 Sum_probs=19.3
Q ss_pred eEEEcCCCCCeeecC-------CCCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENTLK-------PGDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~-------~~~~irC~~CG~R 35 (51)
....|..|+.....+ ..+.-+|+.||..
T Consensus 115 ~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cgg~ 149 (235)
T cd01408 115 ATAHCIKCKHKYPGDWMREDIFNQEVPKCPRCGGL 149 (235)
T ss_pred CccccccCCCcCCHHHHHHHHhCCCCccCCCCCCC
Confidence 356799999876532 1234689999965
No 267
>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=69.45 E-value=4.7 Score=21.96 Aligned_cols=18 Identities=17% Similarity=0.274 Sum_probs=14.0
Q ss_pred CeeEcCCCCCcEEEEEec
Q 035461 25 DVIQCRECGYRILYKKRT 42 (51)
Q Consensus 25 ~~irC~~CG~RIlyK~R~ 42 (51)
..+.||+||..++-..+.
T Consensus 6 ~~~~CP~C~~~~~T~v~~ 23 (73)
T PF10601_consen 6 VRIYCPYCQQQVQTRVEY 23 (73)
T ss_pred eeeECCCCCCEEEEEEEE
Confidence 458999999998876654
No 268
>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=69.37 E-value=2.4 Score=25.38 Aligned_cols=23 Identities=22% Similarity=0.407 Sum_probs=18.2
Q ss_pred EcCCCCCeeecCCCCeeEcCCCC
Q 035461 11 ICGDCGMENTLKPGDVIQCRECG 33 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG 33 (51)
-|..|+...+.+.-..-.||+||
T Consensus 5 AC~~C~~I~~~~qf~~~gCpnC~ 27 (98)
T cd07973 5 ACLLCSLIKTEDQFERDGCPNCE 27 (98)
T ss_pred hhccCCcccccccccCCCCCCCc
Confidence 58899998876655567899996
No 269
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=69.12 E-value=3.3 Score=28.84 Aligned_cols=26 Identities=19% Similarity=0.609 Sum_probs=21.5
Q ss_pred eEEEcCCCCCeeecCC--CCeeEcCCCC
Q 035461 8 VSYICGDCGMENTLKP--GDVIQCRECG 33 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~--~~~irC~~CG 33 (51)
..-+|+.|...|-... +.--|||+|.
T Consensus 169 cRV~CgHC~~tFLfnt~tnaLArCPHCr 196 (275)
T KOG4684|consen 169 CRVKCGHCNETFLFNTLTNALARCPHCR 196 (275)
T ss_pred eEEEecCccceeehhhHHHHHhcCCccc
Confidence 7889999999998763 4568999995
No 270
>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=68.96 E-value=3.3 Score=22.69 Aligned_cols=14 Identities=21% Similarity=0.422 Sum_probs=5.0
Q ss_pred EEEcCCCCCeeecC
Q 035461 9 SYICGDCGMENTLK 22 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~ 22 (51)
...|..||+.++..
T Consensus 2 ~v~CP~C~k~~~~~ 15 (57)
T PF03884_consen 2 TVKCPICGKPVEWS 15 (57)
T ss_dssp EEE-TTT--EEE-S
T ss_pred cccCCCCCCeeccc
Confidence 44555555555543
No 271
>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=68.82 E-value=7 Score=27.63 Aligned_cols=32 Identities=19% Similarity=0.337 Sum_probs=23.9
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCcEEEEEec
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYRILYKKRT 42 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R~ 42 (51)
.|-+||..++......-+|..||.....++.+
T Consensus 151 ~Ce~cG~~~~~~~l~~p~~~~~g~~~~~r~e~ 182 (391)
T PF09334_consen 151 QCENCGRPLEPEELINPVCKICGSPPEVREEE 182 (391)
T ss_dssp EETTTSSBEECCCSECEEETTTS-B-EEEEEE
T ss_pred cccCCCCCcccccccCCccccccccCccccce
Confidence 46689999988877788999999998777543
No 272
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=68.59 E-value=4.4 Score=22.37 Aligned_cols=15 Identities=33% Similarity=0.722 Sum_probs=12.6
Q ss_pred CeeEcCCCCCcEEEE
Q 035461 25 DVIQCRECGYRILYK 39 (51)
Q Consensus 25 ~~irC~~CG~RIlyK 39 (51)
-.++|..||+.||.-
T Consensus 30 ikikC~gCg~~imlp 44 (57)
T PF06107_consen 30 IKIKCLGCGRQIMLP 44 (57)
T ss_pred EEEEECCCCCEEEEe
Confidence 459999999999864
No 273
>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=68.49 E-value=4.7 Score=20.02 Aligned_cols=25 Identities=24% Similarity=0.473 Sum_probs=13.4
Q ss_pred EcCCCCCeeecC-----CCCeeEcCCCCCc
Q 035461 11 ICGDCGMENTLK-----PGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~~-----~~~~irC~~CG~R 35 (51)
+|.+|++-+..- .+..-.|+-|++.
T Consensus 4 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 4 RCRRCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp B-TTT--BS-TTSEEETTTTEEEETTT--E
T ss_pred ccCCCCCEECCcceEcCCCCEEECcCCCCc
Confidence 588888876642 3467899999875
No 274
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=68.21 E-value=4.7 Score=28.32 Aligned_cols=32 Identities=22% Similarity=0.624 Sum_probs=23.3
Q ss_pred CceEEEcCCCCCeeecCC--------------CCeeEcCCCCCcEE
Q 035461 6 EPVSYICGDCGMENTLKP--------------GDVIQCRECGYRIL 37 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~~--------------~~~irC~~CG~RIl 37 (51)
+.-.|+|.+||+...-.. ...-.|++||...+
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~Yv 172 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYV 172 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCceee
Confidence 556899999998765443 35678999996543
No 275
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=67.57 E-value=2.8 Score=31.07 Aligned_cols=35 Identities=20% Similarity=0.580 Sum_probs=26.6
Q ss_pred CCCCceEEEcCCCCCeeecC--------CCCeeEcCCCCCcEE
Q 035461 3 PQPEPVSYICGDCGMENTLK--------PGDVIQCRECGYRIL 37 (51)
Q Consensus 3 ~~~~~~~Y~C~~Cg~~~~~~--------~~~~irC~~CG~RIl 37 (51)
....+-.|.|..|++.++.- ..+..+|..||.-++
T Consensus 122 d~t~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelv 164 (436)
T KOG2593|consen 122 DDTNVAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELV 164 (436)
T ss_pred hccccccccCCccccchhhhHHHHhhcccCceEEEecCCCchh
Confidence 34556789999999997632 136799999998765
No 276
>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=67.42 E-value=5.2 Score=23.09 Aligned_cols=23 Identities=26% Similarity=0.328 Sum_probs=15.5
Q ss_pred CCCeeecCCCCeeEcCCCCCcEEE
Q 035461 15 CGMENTLKPGDVIQCRECGYRILY 38 (51)
Q Consensus 15 Cg~~~~~~~~~~irC~~CG~RIly 38 (51)
+|..+.+ ..+...|+.||..++-
T Consensus 21 ~G~~~~v-~~~~~~C~~CGe~~~~ 43 (127)
T TIGR03830 21 KGESITI-GVPGWYCPACGEELLD 43 (127)
T ss_pred cCEEEEE-eeeeeECCCCCCEEEc
Confidence 4455555 4467889999987653
No 277
>COG4640 Predicted membrane protein [Function unknown]
Probab=67.24 E-value=2.9 Score=31.16 Aligned_cols=22 Identities=36% Similarity=1.054 Sum_probs=15.4
Q ss_pred cCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 12 CGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 12 C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
|..||.... .|.+.|+.||+.+
T Consensus 4 C~kcG~qk~---Ed~~qC~qCG~~~ 25 (465)
T COG4640 4 CPKCGSQKA---EDDVQCTQCGHKF 25 (465)
T ss_pred ccccccccc---cccccccccCCcC
Confidence 788885432 2556699999876
No 278
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=67.24 E-value=3.2 Score=29.70 Aligned_cols=34 Identities=21% Similarity=0.404 Sum_probs=24.1
Q ss_pred CCCCceEEEcCCCCCeeecCC-----CCeeEcCCCCCcE
Q 035461 3 PQPEPVSYICGDCGMENTLKP-----GDVIQCRECGYRI 36 (51)
Q Consensus 3 ~~~~~~~Y~C~~Cg~~~~~~~-----~~~irC~~CG~RI 36 (51)
++.....-||+.|...+.+-. .-.-+|++|++.+
T Consensus 214 sP~~ryALIC~~C~~HNGla~~ee~~yi~F~C~~Cn~LN 252 (328)
T KOG2846|consen 214 SPNNRYALICSQCHHHNGLARKEEYEYITFRCPHCNALN 252 (328)
T ss_pred CCcchhhhcchhhccccCcCChhhcCceEEECccccccC
Confidence 344446679999988887642 3468999999754
No 279
>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 PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=66.80 E-value=4.2 Score=24.20 Aligned_cols=31 Identities=23% Similarity=0.644 Sum_probs=22.6
Q ss_pred CceEEEcCCCCCeeecC-CCCeeEcCCCCCcE
Q 035461 6 EPVSYICGDCGMENTLK-PGDVIQCRECGYRI 36 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~-~~~~irC~~CG~RI 36 (51)
+-..|.|..||+..--. ....-.|..||+.+
T Consensus 33 q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 64 (90)
T PRK03976 33 MRAKHVCPVCGRPKVKRVGTGIWECRKCGAKF 64 (90)
T ss_pred HhcCccCCCCCCCceEEEEEEEEEcCCCCCEE
Confidence 34679999998765444 34668999999865
No 281
>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=66.64 E-value=3 Score=24.94 Aligned_cols=27 Identities=22% Similarity=0.545 Sum_probs=20.1
Q ss_pred EEEcCCCCCeeecCCCC---eeEcCCCCCc
Q 035461 9 SYICGDCGMENTLKPGD---VIQCRECGYR 35 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~---~irC~~CG~R 35 (51)
.|.|..||.++.....+ ---||+|-+-
T Consensus 4 ~F~C~~CG~~V~p~~~g~~~RNHCP~CL~S 33 (92)
T PF12647_consen 4 SFTCVHCGLTVSPLAAGSAHRNHCPSCLSS 33 (92)
T ss_pred ccCccccCCCcccCCCCCCccCcCcccccc
Confidence 58999999999876432 3569988654
No 282
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=66.46 E-value=3.8 Score=31.76 Aligned_cols=23 Identities=26% Similarity=0.736 Sum_probs=17.4
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
=.|.+||...+..... ||.||..
T Consensus 642 ~~C~~cg~~~~~~~~~---Cp~CG~~ 664 (700)
T COG1328 642 SVCNRCGYSGEGLRTR---CPKCGSE 664 (700)
T ss_pred eeeccCCccccccccc---CCCCCCc
Confidence 4699999987755433 9999965
No 283
>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=66.35 E-value=10 Score=20.19 Aligned_cols=25 Identities=20% Similarity=0.494 Sum_probs=14.5
Q ss_pred CeeEcCCCCCcEEEE-EecCceEEEE
Q 035461 25 DVIQCRECGYRILYK-KRTRRIVQYE 49 (51)
Q Consensus 25 ~~irC~~CG~RIlyK-~R~~~~~~~~ 49 (51)
.-..|+.||..|++- ...+....+.
T Consensus 47 ~r~FC~~CGs~l~~~~~~~~~~~~V~ 72 (92)
T PF04828_consen 47 ERYFCPTCGSPLFSEDERDPDLVGVN 72 (92)
T ss_dssp EEEEETTT--EEEEEESSTTTEEEEE
T ss_pred cCcccCCCCCeeecccCCCCCEEEEE
Confidence 457899999999964 3344444443
No 284
>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=65.89 E-value=7.8 Score=27.37 Aligned_cols=25 Identities=24% Similarity=0.582 Sum_probs=20.2
Q ss_pred CCeeEcCCCCCcEEEEEecCceEEE
Q 035461 24 GDVIQCRECGYRILYKKRTRRIVQY 48 (51)
Q Consensus 24 ~~~irC~~CG~RIlyK~R~~~~~~~ 48 (51)
.....||.||.+++.|.-..+.-.|
T Consensus 28 ~~~~~CP~C~~~v~lk~G~~k~~HF 52 (375)
T PF06054_consen 28 KGKYFCPGCGEPVILKKGKKKIPHF 52 (375)
T ss_pred CCcEECCCCCCeeEEEEcCccccee
Confidence 5678999999999998877766555
No 285
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=65.88 E-value=7.4 Score=20.88 Aligned_cols=18 Identities=17% Similarity=0.433 Sum_probs=14.6
Q ss_pred eeEcCCCCCcEEEEEecC
Q 035461 26 VIQCRECGYRILYKKRTR 43 (51)
Q Consensus 26 ~irC~~CG~RIlyK~R~~ 43 (51)
.+.||.|+.+++-+.+.+
T Consensus 3 ~i~Cp~C~~~~~T~v~~~ 20 (67)
T smart00714 3 QLFCPRCQNNVTTRVETE 20 (67)
T ss_pred ceECCCCCCEEEEEEEEE
Confidence 489999999998776643
No 286
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.81 E-value=1.4 Score=29.39 Aligned_cols=14 Identities=21% Similarity=0.548 Sum_probs=10.8
Q ss_pred CeeEcCCCCCcEEE
Q 035461 25 DVIQCRECGYRILY 38 (51)
Q Consensus 25 ~~irC~~CG~RIly 38 (51)
.+..||-|+.+|=-
T Consensus 166 ~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 166 NTNKCPTCRKKITH 179 (187)
T ss_pred hCCCCCCcccccch
Confidence 56889999987643
No 287
>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=65.73 E-value=5.3 Score=27.98 Aligned_cols=25 Identities=20% Similarity=0.465 Sum_probs=18.1
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
-...|+-|+.+-.... ++|++||..
T Consensus 209 RyL~CslC~teW~~~R---~~C~~Cg~~ 233 (305)
T TIGR01562 209 RYLSCSLCATEWHYVR---VKCSHCEES 233 (305)
T ss_pred eEEEcCCCCCcccccC---ccCCCCCCC
Confidence 4556888887766554 889999863
No 288
>PRK05580 primosome assembly protein PriA; Validated
Probab=65.32 E-value=5.4 Score=30.11 Aligned_cols=14 Identities=29% Similarity=0.819 Sum_probs=10.1
Q ss_pred CCCeeEcCCCCCcE
Q 035461 23 PGDVIQCRECGYRI 36 (51)
Q Consensus 23 ~~~~irC~~CG~RI 36 (51)
....++|.+||++.
T Consensus 405 ~~~~l~Ch~Cg~~~ 418 (679)
T PRK05580 405 FQRRLRCHHCGYQE 418 (679)
T ss_pred CCCeEECCCCcCCC
Confidence 34668888888764
No 289
>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]
Probab=65.20 E-value=3.1 Score=32.84 Aligned_cols=35 Identities=29% Similarity=0.712 Sum_probs=25.5
Q ss_pred eEEEcCCCCCeeecCC-----CCeeEcCCCCCc---EEEEEec
Q 035461 8 VSYICGDCGMENTLKP-----GDVIQCRECGYR---ILYKKRT 42 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~-----~~~irC~~CG~R---IlyK~R~ 42 (51)
-.|+|..||.+...+. .+++.|++||.+ .|..-|+
T Consensus 263 afFrC~vC~~~~~ve~drg~i~eP~~C~~C~~~~~~~Lihnrs 305 (804)
T KOG0478|consen 263 AFFRCSVCGHEIAVESDRGRIKEPMLCKECGTTNSFQLLHNRS 305 (804)
T ss_pred HhhhhhhcCceEEEEeecCccCCCcccccccCcccceeehhhh
Confidence 5689999999887652 378999999743 3444444
No 290
>PLN02569 threonine synthase
Probab=65.15 E-value=4.6 Score=29.58 Aligned_cols=29 Identities=17% Similarity=0.150 Sum_probs=21.9
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGYRILYK 39 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK 39 (51)
.+.|.+||++..+... ..+| .||..+...
T Consensus 49 ~l~C~~Cg~~y~~~~~-~~~C-~cgg~l~~~ 77 (484)
T PLN02569 49 FLECPLTGEKYSLDEV-VYRS-KSGGLLDVR 77 (484)
T ss_pred ccEeCCCCCcCCCccc-cccC-CCCCeEEEe
Confidence 4789999999887753 4799 798665433
No 291
>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=65.11 E-value=2.3 Score=22.06 Aligned_cols=27 Identities=26% Similarity=0.591 Sum_probs=19.3
Q ss_pred EEEcCCCCCeeecC------------CCCeeEcCCCCCc
Q 035461 9 SYICGDCGMENTLK------------PGDVIQCRECGYR 35 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~------------~~~~irC~~CG~R 35 (51)
.|.|.=||+.++.. ....+.||-|..+
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 47888899866632 2246999999864
No 292
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=65.05 E-value=5.2 Score=21.74 Aligned_cols=26 Identities=31% Similarity=0.682 Sum_probs=17.5
Q ss_pred EcCCCCC-eeecCCCCeeEcCCCCCcE
Q 035461 11 ICGDCGM-ENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~-~~~~~~~~~irC~~CG~RI 36 (51)
.|.+||. .|-..-.+-..|-.|||--
T Consensus 21 ~CPrCG~gvfmA~H~dR~~CGkCgyTe 47 (51)
T COG1998 21 FCPRCGPGVFMADHKDRWACGKCGYTE 47 (51)
T ss_pred cCCCCCCcchhhhcCceeEeccccceE
Confidence 4888886 3333445678888888754
No 293
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=64.86 E-value=4.3 Score=22.64 Aligned_cols=24 Identities=25% Similarity=0.528 Sum_probs=17.2
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
+..+|.+||.-.-. -.||.||...
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 45789998876522 3699999864
No 294
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=64.78 E-value=3.7 Score=20.26 Aligned_cols=27 Identities=26% Similarity=0.501 Sum_probs=16.3
Q ss_pred EcCCCCCeeecCC---CCeeEcCCCCCcEE
Q 035461 11 ICGDCGMENTLKP---GDVIQCRECGYRIL 37 (51)
Q Consensus 11 ~C~~Cg~~~~~~~---~~~irC~~CG~RIl 37 (51)
.|..|+...+... ...-.|+.||.--|
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~G~W~ 30 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCGGIWF 30 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCCeEEc
Confidence 3777877655432 23456888886543
No 295
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=64.71 E-value=5.9 Score=21.99 Aligned_cols=26 Identities=35% Similarity=0.968 Sum_probs=18.2
Q ss_pred EcCCCCCeeecC-----CCCeeEcCCCCCcE
Q 035461 11 ICGDCGMENTLK-----PGDVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~-----~~~~irC~~CG~RI 36 (51)
.|..|+.--.+. ..+.+-|..|||+=
T Consensus 11 ~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 11 VCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred cCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 478887765543 22569999999974
No 296
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=64.60 E-value=5.4 Score=30.84 Aligned_cols=27 Identities=22% Similarity=0.673 Sum_probs=22.0
Q ss_pred CceEEEcCCCCCeeecCCC-----CeeEcCCC
Q 035461 6 EPVSYICGDCGMENTLKPG-----DVIQCREC 32 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~~~-----~~irC~~C 32 (51)
....|.|..||.++..... .+..|++|
T Consensus 126 ~~~~~~C~~Cg~~~~~~~~~~~~~~~~~C~~~ 157 (682)
T COG1241 126 KKAVFECPKCGREVEVEQSEFRVEPPRECENC 157 (682)
T ss_pred EEEEEEcCCCCCEEEEEeccccccCCccCCCc
Confidence 4588999999999987643 55779999
No 297
>PRK07218 replication factor A; Provisional
Probab=64.57 E-value=4.4 Score=29.52 Aligned_cols=23 Identities=30% Similarity=0.517 Sum_probs=18.6
Q ss_pred CceEEEcCCCCCeeecCCCCeeEcCCCC
Q 035461 6 EPVSYICGDCGMENTLKPGDVIQCRECG 33 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~~~~~irC~~CG 33 (51)
....++|.+|++.++. -.||.||
T Consensus 294 sgli~rCP~C~r~v~~-----~~C~~hG 316 (423)
T PRK07218 294 SGLIERCPECGRVIQK-----GQCRSHG 316 (423)
T ss_pred CcceecCcCccccccC-----CcCCCCC
Confidence 4578999999999733 5899999
No 298
>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=64.57 E-value=5.3 Score=21.75 Aligned_cols=24 Identities=29% Similarity=0.737 Sum_probs=15.0
Q ss_pred EEEcCCCCCeeecCCCCeeEcCC--CCCc
Q 035461 9 SYICGDCGMENTLKPGDVIQCRE--CGYR 35 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~--CG~R 35 (51)
.++|-.|.+.+.+.+ +.|.. |||.
T Consensus 17 k~ICrkCyarl~~~A---~nCRKkkCGhs 42 (52)
T PF01020_consen 17 KMICRKCYARLPPRA---TNCRKKKCGHS 42 (52)
T ss_dssp -EEETTT--EE-TTS---SS-TSSSCTS-
T ss_pred ceecccccCcCCCCc---cceecccCCCC
Confidence 579999999987765 78987 9974
No 299
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=64.55 E-value=5.7 Score=19.79 Aligned_cols=27 Identities=30% Similarity=0.605 Sum_probs=15.0
Q ss_pred cCCCCCeeecCCCCeeEcCCCCCcEEEEEe
Q 035461 12 CGDCGMENTLKPGDVIQCRECGYRILYKKR 41 (51)
Q Consensus 12 C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R 41 (51)
|..|++...+. +..|+.|+...=-+=|
T Consensus 1 C~~C~~~~~l~---~f~C~~C~~~FC~~HR 27 (39)
T smart00154 1 CHFCRKKVGLT---GFKCRHCGNLFCGEHR 27 (39)
T ss_pred CcccCCccccc---CeECCccCCccccccC
Confidence 44566554433 5778777765444433
No 300
>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=64.47 E-value=7.4 Score=27.61 Aligned_cols=30 Identities=23% Similarity=0.580 Sum_probs=20.9
Q ss_pred ceEEEcCCCCCeeecC--CCCeeEcCCCCCcE
Q 035461 7 PVSYICGDCGMENTLK--PGDVIQCRECGYRI 36 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~--~~~~irC~~CG~RI 36 (51)
...|.|..|+....+. ....-+|++||.+.
T Consensus 231 g~v~~C~~c~~~~~~~~~~~~~~~C~~c~~~~ 262 (374)
T TIGR00308 231 GYTYHCSRCLHNKPVNGISQRKGRCKECGGEY 262 (374)
T ss_pred eeEEECCCcccccccccccCCCCCCCCCCCcc
Confidence 3577899998765443 22345799999865
No 301
>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=64.05 E-value=5.2 Score=32.61 Aligned_cols=25 Identities=28% Similarity=0.565 Sum_probs=20.0
Q ss_pred ceEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 7 PVSYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
-...+|.+||... -..+||.||.+.
T Consensus 623 v~~RKCPkCG~yT-----lk~rCP~CG~~T 647 (1095)
T TIGR00354 623 IAIRKCPQCGKES-----FWLKCPVCGELT 647 (1095)
T ss_pred EEEEECCCCCccc-----ccccCCCCCCcc
Confidence 3678999999984 346899999874
No 302
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=63.75 E-value=1.5 Score=32.64 Aligned_cols=32 Identities=25% Similarity=0.575 Sum_probs=21.1
Q ss_pred CCCceEEEcCCCCCe-e-ecC----------CCCeeEcCCCCCc
Q 035461 4 QPEPVSYICGDCGME-N-TLK----------PGDVIQCRECGYR 35 (51)
Q Consensus 4 ~~~~~~Y~C~~Cg~~-~-~~~----------~~~~irC~~CG~R 35 (51)
+.+.+.-.|.+||.. . .+. .-.+-.||+||++
T Consensus 34 ~~~EvES~Cm~Cg~nG~TRlllT~IP~fREvVimSF~CpHCG~k 77 (460)
T KOG2703|consen 34 PVQEVESLCMNCGENGTTRLLLTSIPYFREVVIMSFECPHCGHK 77 (460)
T ss_pred chHHHHHhhhhcccCCceeEEEeecchhheeeeEEeecCccCCc
Confidence 345577889999765 1 111 1156789999986
No 303
>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=63.55 E-value=0.83 Score=29.73 Aligned_cols=20 Identities=30% Similarity=0.996 Sum_probs=9.5
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
-|..||.++ -..||+|+..|
T Consensus 30 fC~kCG~~t------I~~Cp~C~~~I 49 (158)
T PF10083_consen 30 FCSKCGAKT------ITSCPNCSTPI 49 (158)
T ss_pred HHHHhhHHH------HHHCcCCCCCC
Confidence 355555543 13455555544
No 304
>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=63.54 E-value=3.7 Score=26.61 Aligned_cols=27 Identities=26% Similarity=0.541 Sum_probs=18.9
Q ss_pred EEEcCCCCCeeecCC--------CCeeEcCCCCCc
Q 035461 9 SYICGDCGMENTLKP--------GDVIQCRECGYR 35 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~--------~~~irC~~CG~R 35 (51)
...|..|+....... ....+|+.||+.
T Consensus 95 ~~~C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cgg~ 129 (206)
T cd01410 95 IEVCKSCGPEYVRDDVVETRGDKETGRRCHACGGI 129 (206)
T ss_pred cccCCCCCCccchHHHHHHhhcCCCCCcCCCCcCc
Confidence 457999998765431 134689999975
No 305
>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]
Probab=63.15 E-value=6.5 Score=25.52 Aligned_cols=18 Identities=33% Similarity=0.754 Sum_probs=13.8
Q ss_pred cCCCCeeEcCCCCCcEEE
Q 035461 21 LKPGDVIQCRECGYRILY 38 (51)
Q Consensus 21 ~~~~~~irC~~CG~RIly 38 (51)
+..+..-|||+||+-.--
T Consensus 128 l~Kge~~rc~eCG~~fkL 145 (153)
T KOG3352|consen 128 LEKGETQRCPECGHYFKL 145 (153)
T ss_pred EEcCCcccCCcccceEEe
Confidence 456788999999986433
No 306
>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=63.06 E-value=3.3 Score=24.35 Aligned_cols=9 Identities=56% Similarity=1.161 Sum_probs=7.6
Q ss_pred eEcCCCCCc
Q 035461 27 IQCRECGYR 35 (51)
Q Consensus 27 irC~~CG~R 35 (51)
|.||.||-|
T Consensus 2 I~CP~CG~R 10 (84)
T TIGR01374 2 IPCPYCGPR 10 (84)
T ss_pred ccCCCCCCc
Confidence 789999965
No 307
>KOG3854 consensus SPRT-like metalloprotease [Function unknown]
Probab=62.88 E-value=4.8 Score=30.34 Aligned_cols=34 Identities=24% Similarity=0.474 Sum_probs=26.9
Q ss_pred ceEEEcCCCCCeeecCCC----CeeEcCCCCCcEEEEE
Q 035461 7 PVSYICGDCGMENTLKPG----DVIQCRECGYRILYKK 40 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~~----~~irC~~CG~RIlyK~ 40 (51)
.+.|.|..|++....... .-++|.+|-++|..+.
T Consensus 406 Kf~Y~C~~C~~~~~~~skSl~t~~~~C~~Ckg~i~l~~ 443 (505)
T KOG3854|consen 406 KFKYTCTKCNKLSGGHSKSLDTSRLRCRYCKGEISLKP 443 (505)
T ss_pred eEEEEecccCcccccccccccHhHHHHHhcccceEEEe
Confidence 488999999998876432 4599999999986553
No 308
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=62.83 E-value=3.7 Score=24.10 Aligned_cols=27 Identities=30% Similarity=0.810 Sum_probs=8.2
Q ss_pred EEcCCCCCeeecCCCC--eeEcCCCCCcE
Q 035461 10 YICGDCGMENTLKPGD--VIQCRECGYRI 36 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~--~irC~~CG~RI 36 (51)
-+|--||.++.+..+. -+-|-+|++.|
T Consensus 10 qiCqiCGD~VGl~~~Ge~FVAC~eC~fPv 38 (80)
T PF14569_consen 10 QICQICGDDVGLTENGEVFVACHECAFPV 38 (80)
T ss_dssp -B-SSS--B--B-SSSSB--S-SSS----
T ss_pred cccccccCccccCCCCCEEEEEcccCCcc
Confidence 4677788777776432 25666666544
No 309
>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=62.72 E-value=6.4 Score=22.21 Aligned_cols=25 Identities=32% Similarity=0.902 Sum_probs=18.2
Q ss_pred EcCCCCCeeecC-----CCCeeEcCCCCCc
Q 035461 11 ICGDCGMENTLK-----PGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~~-----~~~~irC~~CG~R 35 (51)
.|..|+.--.|- ..+-+.|..|||.
T Consensus 10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~ 39 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWRENGVEYVECVECGYT 39 (71)
T ss_pred cCCCCcCccEEEEEEeCCceEEEecCCCCe
Confidence 478887765553 2367999999986
No 310
>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=62.61 E-value=4.8 Score=18.09 Aligned_cols=12 Identities=33% Similarity=0.703 Sum_probs=9.4
Q ss_pred eEEEcCCCCCee
Q 035461 8 VSYICGDCGMEN 19 (51)
Q Consensus 8 ~~Y~C~~Cg~~~ 19 (51)
..|.|..|++.|
T Consensus 13 k~~~C~~C~k~F 24 (26)
T PF13465_consen 13 KPYKCPYCGKSF 24 (26)
T ss_dssp SSEEESSSSEEE
T ss_pred CCCCCCCCcCee
Confidence 348999998876
No 311
>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=62.37 E-value=6.8 Score=29.68 Aligned_cols=24 Identities=29% Similarity=0.657 Sum_probs=16.3
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
.=+|.+||.. .....-.||.||..
T Consensus 532 ~siC~~CGy~---~g~~~~~CP~CGs~ 555 (586)
T TIGR02827 532 ITICNDCHHI---DKRTLHRCPVCGSA 555 (586)
T ss_pred CeecCCCCCc---CCCcCCcCcCCCCc
Confidence 4589999982 11122689999964
No 312
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=62.23 E-value=5.6 Score=26.07 Aligned_cols=26 Identities=27% Similarity=0.479 Sum_probs=20.5
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
.|+|..|+..+.... .+++|.+ ||..
T Consensus 2 ~~~CP~C~~~l~~~~-~~~~C~~-~h~f 27 (272)
T PRK11088 2 SYQCPLCHQPLTLEE-NSWICPQ-NHQF 27 (272)
T ss_pred cccCCCCCcchhcCC-CEEEcCC-CCCC
Confidence 589999999986644 6799977 7764
No 313
>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=62.11 E-value=7.5 Score=26.06 Aligned_cols=13 Identities=23% Similarity=0.720 Sum_probs=9.9
Q ss_pred eEEEcCCCCCeee
Q 035461 8 VSYICGDCGMENT 20 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~ 20 (51)
....|..|+....
T Consensus 117 ~~~~C~~C~~~~~ 129 (260)
T cd01409 117 HRVVCLSCGFRTP 129 (260)
T ss_pred CEEEeCCCcCccC
Confidence 3567999998764
No 314
>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=61.63 E-value=6.1 Score=20.97 Aligned_cols=13 Identities=38% Similarity=0.915 Sum_probs=11.2
Q ss_pred CCeeEcCCCCCcE
Q 035461 24 GDVIQCRECGYRI 36 (51)
Q Consensus 24 ~~~irC~~CG~RI 36 (51)
+|.++|.+||..+
T Consensus 34 ~d~v~C~~C~~~l 46 (71)
T smart00238 34 GDEVKCFFCGGEL 46 (71)
T ss_pred CCEEEeCCCCCCc
Confidence 5789999999875
No 315
>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=61.61 E-value=6 Score=18.44 Aligned_cols=21 Identities=24% Similarity=0.450 Sum_probs=8.9
Q ss_pred EcCCCCCeeecCCCCeeEcCCCC
Q 035461 11 ICGDCGMENTLKPGDVIQCRECG 33 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG 33 (51)
.|.-|+++++... .-+|..|+
T Consensus 2 ~C~~C~~~~~~~~--~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFY--FYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCE--eEEeCCCC
Confidence 3444444433322 34444444
No 316
>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=61.45 E-value=6.7 Score=18.09 Aligned_cols=21 Identities=33% Similarity=0.860 Sum_probs=5.8
Q ss_pred cCCCCCeeecCCCCeeEcCCCCC
Q 035461 12 CGDCGMENTLKPGDVIQCRECGY 34 (51)
Q Consensus 12 C~~Cg~~~~~~~~~~irC~~CG~ 34 (51)
|.-||..... ...-+|+.|.+
T Consensus 3 C~~C~~~~~~--~~~Y~C~~Cdf 23 (30)
T PF07649_consen 3 CDACGKPIDG--GWFYRCSECDF 23 (30)
T ss_dssp -TTTS----S----EEE-TTT--
T ss_pred CCcCCCcCCC--CceEECccCCC
Confidence 4555555433 24455555544
No 317
>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=61.39 E-value=4.6 Score=23.10 Aligned_cols=33 Identities=27% Similarity=0.613 Sum_probs=16.5
Q ss_pred ceEEEcCCCCCeeec----C---CCCeeEcCCCCCcEEEE
Q 035461 7 PVSYICGDCGMENTL----K---PGDVIQCRECGYRILYK 39 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~----~---~~~~irC~~CG~RIlyK 39 (51)
+..|.|.-||.+..+ + ....+.|..||...-++
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 367999999965433 2 23679999999876555
No 318
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=61.22 E-value=6.7 Score=29.91 Aligned_cols=22 Identities=32% Similarity=0.687 Sum_probs=16.8
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
=+|.+||... +..-.||.||+.
T Consensus 627 ~~C~~CG~~~----g~~~~CP~CG~~ 648 (656)
T PRK08270 627 SICPKHGYLS----GEHEFCPKCGEE 648 (656)
T ss_pred cccCCCCCcC----CCCCCCcCCcCc
Confidence 4799999842 345789999976
No 319
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=60.85 E-value=7.5 Score=27.37 Aligned_cols=24 Identities=21% Similarity=0.498 Sum_probs=17.0
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCC
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGY 34 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~ 34 (51)
-...|+-|+.+-.... +.|++||.
T Consensus 211 RyL~CslC~teW~~~R---~~C~~Cg~ 234 (309)
T PRK03564 211 RYLHCNLCESEWHVVR---VKCSNCEQ 234 (309)
T ss_pred eEEEcCCCCCcccccC---ccCCCCCC
Confidence 3456888877766553 78999985
No 320
>PF10533 Plant_zn_clust: Plant zinc cluster domain; InterPro: IPR018872 This zinc binding domain is found associated with the WRKY domain IPR003657 from INTERPRO [].
Probab=60.63 E-value=7 Score=20.87 Aligned_cols=24 Identities=25% Similarity=0.552 Sum_probs=19.7
Q ss_pred CCeeEcCCCCCcEEEEEecCceEEEEc
Q 035461 24 GDVIQCRECGYRILYKKRTRRIVQYEA 50 (51)
Q Consensus 24 ~~~irC~~CG~RIlyK~R~~~~~~~~A 50 (51)
...-+| +|..+ -|.|.++.+.|+|
T Consensus 17 sssgrC-HCsKk--RK~RvKR~irVPA 40 (47)
T PF10533_consen 17 SSSGRC-HCSKK--RKSRVKRTIRVPA 40 (47)
T ss_pred CCCCcc-cCCCc--ccccceeeEEeec
Confidence 356788 99887 6889999999987
No 321
>PRK14894 glycyl-tRNA synthetase; Provisional
Probab=60.62 E-value=5.7 Score=30.16 Aligned_cols=33 Identities=30% Similarity=0.412 Sum_probs=24.9
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCCcEEEEEecC
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGYRILYKKRTR 43 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R~~ 43 (51)
=.|..||..+..+.. .++||.||...|-.+|+-
T Consensus 89 V~CkkCk~ryRaD~L-iikCP~CGs~dLTe~~~F 121 (539)
T PRK14894 89 VDCRDCKMRWRADHI-QGVCPNCGSRDLTEPRPF 121 (539)
T ss_pred eECCCCCccccCccc-eeeCCCCCCcCCCcceec
Confidence 469999998876653 478999997677766653
No 322
>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=60.60 E-value=3.6 Score=29.26 Aligned_cols=15 Identities=40% Similarity=1.048 Sum_probs=12.3
Q ss_pred CCCCeeEcCCCCCcE
Q 035461 22 KPGDVIQCRECGYRI 36 (51)
Q Consensus 22 ~~~~~irC~~CG~RI 36 (51)
+.+.++.||.|||..
T Consensus 205 ~k~k~~PCPKCg~et 219 (314)
T PF06524_consen 205 EKGKPIPCPKCGYET 219 (314)
T ss_pred ccCCCCCCCCCCCcc
Confidence 356889999999965
No 323
>PRK05978 hypothetical protein; Provisional
Probab=60.30 E-value=4.9 Score=25.62 Aligned_cols=25 Identities=28% Similarity=0.659 Sum_probs=10.9
Q ss_pred EcCCCCCeeecC--CCCeeEcCCCCCc
Q 035461 11 ICGDCGMENTLK--PGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~~--~~~~irC~~CG~R 35 (51)
+|-+||.---.+ ..-.-+|+.||-.
T Consensus 35 rCP~CG~G~LF~g~Lkv~~~C~~CG~~ 61 (148)
T PRK05978 35 RCPACGEGKLFRAFLKPVDHCAACGED 61 (148)
T ss_pred cCCCCCCCcccccccccCCCccccCCc
Confidence 455554332222 2233456666543
No 324
>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=60.00 E-value=4 Score=25.64 Aligned_cols=10 Identities=40% Similarity=1.046 Sum_probs=8.9
Q ss_pred eeEcCCCCCc
Q 035461 26 VIQCRECGYR 35 (51)
Q Consensus 26 ~irC~~CG~R 35 (51)
.+.||+||+.
T Consensus 105 ~~~cp~c~s~ 114 (146)
T TIGR02159 105 SVQCPRCGSA 114 (146)
T ss_pred CCcCCCCCCC
Confidence 5999999985
No 325
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=59.58 E-value=5.5 Score=29.02 Aligned_cols=31 Identities=23% Similarity=0.283 Sum_probs=21.5
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRILYKK 40 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~ 40 (51)
..-+|-.|-..+ +...-+-||.||++-|-|.
T Consensus 241 ~iLRCh~Cfsit--~~m~k~FCp~CG~~TL~K~ 271 (376)
T KOG2463|consen 241 YILRCHGCFSIT--SEMPKDFCPSCGHKTLTKC 271 (376)
T ss_pred heeEeeeeeEec--CccchhcccccCCCeeeEE
Confidence 445666665554 2235689999999988774
No 326
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=59.51 E-value=6.1 Score=26.37 Aligned_cols=27 Identities=19% Similarity=0.413 Sum_probs=18.8
Q ss_pred eEEEcCCCCCeeecCC---CCeeEcCCCCC
Q 035461 8 VSYICGDCGMENTLKP---GDVIQCRECGY 34 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~---~~~irC~~CG~ 34 (51)
....|..|+..++... ...-+||.||.
T Consensus 116 ~~~~C~~C~~~~~~~~~~~~~~p~C~~Cg~ 145 (242)
T PTZ00408 116 LKVRCTATGHVFDWTEDVVHGSSRCKCCGC 145 (242)
T ss_pred ceEEECCCCcccCchhhhhcCCCccccCCC
Confidence 3468999998776531 23467999983
No 327
>PHA00733 hypothetical protein
Probab=59.19 E-value=4.5 Score=24.69 Aligned_cols=29 Identities=24% Similarity=0.493 Sum_probs=20.8
Q ss_pred eEEEcCCCCCeeecCC---------CCeeEcCCCCCcE
Q 035461 8 VSYICGDCGMENTLKP---------GDVIQCRECGYRI 36 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~---------~~~irC~~CG~RI 36 (51)
..|.|..||+.|.... ..+..|+.||...
T Consensus 72 kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F 109 (128)
T PHA00733 72 SPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEF 109 (128)
T ss_pred CCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCcc
Confidence 4589999999877431 2356899998753
No 328
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=58.85 E-value=16 Score=22.06 Aligned_cols=19 Identities=32% Similarity=0.723 Sum_probs=13.7
Q ss_pred CeeEcCCCCCcEEEEEecC
Q 035461 25 DVIQCRECGYRILYKKRTR 43 (51)
Q Consensus 25 ~~irC~~CG~RIlyK~R~~ 43 (51)
...+||.||++.|.+++.+
T Consensus 100 ~~~~cp~c~~~~~~~k~~~ 118 (140)
T COG0551 100 KEKKCPKCGSRKLVEKKEK 118 (140)
T ss_pred ccccCCcCCCceeEEEeee
Confidence 4577999999777765543
No 329
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=58.79 E-value=8 Score=23.33 Aligned_cols=25 Identities=32% Similarity=0.824 Sum_probs=16.1
Q ss_pred EcCCCCCeeec---C-CCCeeEcCCCCCc
Q 035461 11 ICGDCGMENTL---K-PGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~---~-~~~~irC~~CG~R 35 (51)
+|.+|+.+-.. + ..-.++|.-||.+
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 68888765332 1 1235889889874
No 330
>PRK06386 replication factor A; Reviewed
Probab=58.57 E-value=8.8 Score=27.49 Aligned_cols=24 Identities=13% Similarity=0.151 Sum_probs=18.8
Q ss_pred CceEEEcCCCCCeeecCCCCeeEcCCCCC
Q 035461 6 EPVSYICGDCGMENTLKPGDVIQCRECGY 34 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~ 34 (51)
....++|.+|++.++- -.||+||-
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 4477899999999872 28999983
No 331
>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=58.33 E-value=3.3 Score=33.13 Aligned_cols=8 Identities=38% Similarity=1.257 Sum_probs=0.0
Q ss_pred EcCCCCCc
Q 035461 28 QCRECGYR 35 (51)
Q Consensus 28 rC~~CG~R 35 (51)
.||.||-.
T Consensus 694 ~C~~C~~~ 701 (900)
T PF03833_consen 694 ECPKCGRE 701 (900)
T ss_dssp --------
T ss_pred cccccccc
Confidence 66666654
No 332
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=58.31 E-value=5 Score=30.14 Aligned_cols=15 Identities=27% Similarity=0.572 Sum_probs=12.9
Q ss_pred ceEEEcCCCCCeeec
Q 035461 7 PVSYICGDCGMENTL 21 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~ 21 (51)
-++|+|.+|++.|+=
T Consensus 293 ~vEYrCPEC~KVFsC 307 (500)
T KOG3993|consen 293 HVEYRCPECDKVFSC 307 (500)
T ss_pred EeeecCCcccccccC
Confidence 389999999999874
No 333
>PRK04011 peptide chain release factor 1; Provisional
Probab=57.91 E-value=9.5 Score=27.36 Aligned_cols=29 Identities=31% Similarity=0.700 Sum_probs=21.9
Q ss_pred ceEEEcCCCCCeeecC-----CCCeeEcCCCCCc
Q 035461 7 PVSYICGDCGMENTLK-----PGDVIQCRECGYR 35 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~-----~~~~irC~~CG~R 35 (51)
.+.|+|.+||.+.... ..+.-.||+||..
T Consensus 326 r~~~~c~~c~~~~~~~~~~~~~~~~~~c~~~~~~ 359 (411)
T PRK04011 326 RVTYKCPNCGYEEEKTVKRREELPEKTCPKCGSE 359 (411)
T ss_pred eEEEEcCCCCcceeeecccccccccccCcccCcc
Confidence 3689999999876542 2356799999976
No 334
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=57.88 E-value=7.7 Score=29.62 Aligned_cols=28 Identities=21% Similarity=0.624 Sum_probs=21.6
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcEEE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRILY 38 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIly 38 (51)
....|.+||..++....+ -| .||.+|-.
T Consensus 129 a~w~c~~cg~~iean~kp--~c-~cg~~~~~ 156 (593)
T COG2401 129 ALWRCEKCGTIIEANTKP--EC-KCGSHVHI 156 (593)
T ss_pred EEEecchhchhhhhcCCc--cc-CCCCceEE
Confidence 678999999987766544 78 99987643
No 335
>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=57.31 E-value=3.7 Score=24.09 Aligned_cols=9 Identities=56% Similarity=1.276 Sum_probs=7.6
Q ss_pred eEcCCCCCc
Q 035461 27 IQCRECGYR 35 (51)
Q Consensus 27 irC~~CG~R 35 (51)
|.||.||-|
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 336
>PRK08402 replication factor A; Reviewed
Probab=57.14 E-value=13 Score=26.42 Aligned_cols=26 Identities=27% Similarity=0.494 Sum_probs=21.1
Q ss_pred eEEEcCCCCCeeecC-CCCeeEcCCCC
Q 035461 8 VSYICGDCGMENTLK-PGDVIQCRECG 33 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~-~~~~irC~~CG 33 (51)
....|..|++.+..+ ..+.-+|+.||
T Consensus 211 ~y~aCp~CnKkv~~~~~~~~~~Ce~~~ 237 (355)
T PRK08402 211 VYDACPECRRKVDYDPATDTWICPEHG 237 (355)
T ss_pred eEecCCCCCeEEEEecCCCCEeCCCCC
Confidence 567899999999854 34678999998
No 337
>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=57.01 E-value=8.1 Score=23.16 Aligned_cols=30 Identities=30% Similarity=0.699 Sum_probs=21.6
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRIL 37 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl 37 (51)
..=.|.-||..=-...++.|-|..||-|+-
T Consensus 34 a~daCeiC~~~GY~q~g~~lvC~~C~~~~~ 63 (102)
T PF10080_consen 34 AFDACEICGPKGYYQEGDQLVCKNCGVRFN 63 (102)
T ss_pred EEEeccccCCCceEEECCEEEEecCCCEEe
Confidence 444677786555456678999999998763
No 338
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=56.81 E-value=8.5 Score=27.48 Aligned_cols=27 Identities=26% Similarity=0.628 Sum_probs=18.9
Q ss_pred EEEcCCCCCeeecC-------CCCeeEcCCCCCc
Q 035461 9 SYICGDCGMENTLK-------PGDVIQCRECGYR 35 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~-------~~~~irC~~CG~R 35 (51)
...|..|+....+. ....-+|+.||..
T Consensus 147 ~~~C~~C~~~~~~~~~~~~~~~~~vP~C~~CgG~ 180 (349)
T PTZ00410 147 AASCIECHTPYDIEQAYLEARSGKVPHCSTCGGI 180 (349)
T ss_pred eeEeCCCCCCcchhHHHHHhhcCCCCCCCCCCCc
Confidence 46799999877643 1234589999974
No 339
>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=56.16 E-value=10 Score=22.81 Aligned_cols=28 Identities=29% Similarity=0.642 Sum_probs=20.6
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGYRILYK 39 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK 39 (51)
..|+.-|=... ..+.++|..||.++.++
T Consensus 29 l~cA~~GW~~~--~~d~l~C~~C~~~l~~~ 56 (133)
T PF07967_consen 29 LECARRGWICV--SKDMLKCESCGARLCVK 56 (133)
T ss_pred HHHHHcCCCcC--CCCEEEeCCCCCEEEEe
Confidence 34555555542 25899999999999998
No 340
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=56.08 E-value=6.2 Score=24.27 Aligned_cols=14 Identities=36% Similarity=0.843 Sum_probs=7.0
Q ss_pred EEEcCCCCCeeecC
Q 035461 9 SYICGDCGMENTLK 22 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~ 22 (51)
.|+|..|+..|..+
T Consensus 53 RyrC~~C~~tf~~~ 66 (129)
T COG3677 53 RYKCKSCGSTFTVE 66 (129)
T ss_pred ccccCCcCcceeee
Confidence 35555555555444
No 341
>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=55.83 E-value=21 Score=17.59 Aligned_cols=22 Identities=41% Similarity=0.936 Sum_probs=15.8
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCC
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGY 34 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~ 34 (51)
.|.-||. ....++.|.|-.|+.
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 4677887 344568899998884
No 342
>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=55.70 E-value=7.5 Score=21.22 Aligned_cols=32 Identities=28% Similarity=0.752 Sum_probs=21.0
Q ss_pred CceEEEcCCCCCeeecCCCCeeEcCCC-------CCcEEEEEec
Q 035461 6 EPVSYICGDCGMENTLKPGDVIQCREC-------GYRILYKKRT 42 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~~~~~irC~~C-------G~RIlyK~R~ 42 (51)
....|.|..|+.. ...+-|.+| ||++.+..-+
T Consensus 10 ~q~~y~C~tC~~~-----~~~~iC~~CF~~~~H~gH~~~~~~~~ 48 (71)
T PF02207_consen 10 GQIFYRCLTCSLD-----ESSGICEECFANSCHEGHRVVYYRSS 48 (71)
T ss_dssp T-EEEEETTTBSS-----TT-BBEHHHHCTSGGGGSSEEEEE--
T ss_pred CCEEEECccCCCC-----CCEEEchhhCCCCCcCCCcEEEEEeC
Confidence 3578999999872 245778888 8888776543
No 343
>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=55.60 E-value=7.6 Score=20.86 Aligned_cols=13 Identities=38% Similarity=1.045 Sum_probs=11.5
Q ss_pred CCeeEcCCCCCcE
Q 035461 24 GDVIQCRECGYRI 36 (51)
Q Consensus 24 ~~~irC~~CG~RI 36 (51)
.+.++|.+||..|
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 5899999999877
No 344
>PRK12366 replication factor A; Reviewed
Probab=55.21 E-value=14 Score=27.91 Aligned_cols=28 Identities=21% Similarity=0.487 Sum_probs=21.9
Q ss_pred ceEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 7 PVSYICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
.....|..|++.+.. ..+.-+|+.||.-
T Consensus 530 ~~y~aCp~CnkKv~~-~~g~~~C~~c~~~ 557 (637)
T PRK12366 530 IILYLCPNCRKRVEE-VDGEYICEFCGEV 557 (637)
T ss_pred EEEecccccCeEeEc-CCCcEECCCCCCC
Confidence 366789999999864 4567899999953
No 345
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=55.14 E-value=8.3 Score=31.47 Aligned_cols=26 Identities=19% Similarity=0.657 Sum_probs=20.5
Q ss_pred EcCCCCCeeecCCC-Ce-eEcCCCCCcE
Q 035461 11 ICGDCGMENTLKPG-DV-IQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~-~~-irC~~CG~RI 36 (51)
+|--||.++.+... +. |-|.+||+.|
T Consensus 19 iCqICGD~vg~~~~Ge~FVAC~eC~FPV 46 (1079)
T PLN02638 19 VCQICGDNVGKTVDGEPFVACDVCAFPV 46 (1079)
T ss_pred eeeecccccCcCCCCCEEEEeccCCCcc
Confidence 89999999998754 33 8899998765
No 346
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=54.87 E-value=6.4 Score=27.89 Aligned_cols=31 Identities=26% Similarity=0.519 Sum_probs=21.9
Q ss_pred CceEEEcCCCCCeeecCC--CCeeEcCCCCCcE
Q 035461 6 EPVSYICGDCGMENTLKP--GDVIQCRECGYRI 36 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~~--~~~irC~~CG~RI 36 (51)
+..--+|.+||..+--+. ...-.||.|||-.
T Consensus 25 e~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKELESNLKVCPKCGHHM 57 (294)
T ss_pred CCceeECCCccceeeHHHHHhhhhcccccCccc
Confidence 446678999998775442 2457899999743
No 347
>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=54.55 E-value=17 Score=17.22 Aligned_cols=19 Identities=37% Similarity=1.010 Sum_probs=8.8
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
.|.-||.. ...+||.||-+
T Consensus 4 ~C~vC~~~------~kY~Cp~C~~~ 22 (30)
T PF04438_consen 4 LCSVCGNP------AKYRCPRCGAR 22 (30)
T ss_dssp EETSSSSE------ESEE-TTT--E
T ss_pred CCccCcCC------CEEECCCcCCc
Confidence 45666651 23667777654
No 348
>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=54.48 E-value=9.5 Score=20.08 Aligned_cols=14 Identities=36% Similarity=0.895 Sum_probs=11.4
Q ss_pred CCeeEcCCCCCcEE
Q 035461 24 GDVIQCRECGYRIL 37 (51)
Q Consensus 24 ~~~irC~~CG~RIl 37 (51)
.+.++|.+||..+-
T Consensus 32 ~d~v~C~~C~~~~~ 45 (69)
T cd00022 32 GDEVKCFFCGLELK 45 (69)
T ss_pred CCEEEeCCCCCCcc
Confidence 47899999998763
No 349
>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=54.37 E-value=11 Score=18.41 Aligned_cols=12 Identities=25% Similarity=0.916 Sum_probs=6.2
Q ss_pred CeeEcCCCCCcE
Q 035461 25 DVIQCRECGYRI 36 (51)
Q Consensus 25 ~~irC~~CG~RI 36 (51)
..+.||+||-.|
T Consensus 3 ~~~~C~nC~R~v 14 (33)
T PF08209_consen 3 PYVECPNCGRPV 14 (33)
T ss_dssp -EEE-TTTSSEE
T ss_pred CeEECCCCcCCc
Confidence 346677777544
No 350
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=54.36 E-value=6.7 Score=20.54 Aligned_cols=28 Identities=29% Similarity=0.650 Sum_probs=20.3
Q ss_pred EEEcCCCCCeeecCC-----CCeeEcCCCCCcE
Q 035461 9 SYICGDCGMENTLKP-----GDVIQCRECGYRI 36 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~-----~~~irC~~CG~RI 36 (51)
.+.|..||....... +..+-|..||-+.
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~ 35 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYY 35 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHH
Confidence 367999998887652 2348899999554
No 351
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=54.31 E-value=10 Score=23.55 Aligned_cols=26 Identities=35% Similarity=0.957 Sum_probs=16.8
Q ss_pred EEcCCCCCeeec--CCC--CeeEcCCCCCc
Q 035461 10 YICGDCGMENTL--KPG--DVIQCRECGYR 35 (51)
Q Consensus 10 Y~C~~Cg~~~~~--~~~--~~irC~~CG~R 35 (51)
=+|..||.+-.. +.+ -.++|..||++
T Consensus 98 VlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred EECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 369999775432 112 34799999975
No 352
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=54.26 E-value=4.7 Score=29.00 Aligned_cols=25 Identities=32% Similarity=0.814 Sum_probs=14.8
Q ss_pred EcCCCC--CeeecCCCCeeEcCCCCCc
Q 035461 11 ICGDCG--MENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg--~~~~~~~~~~irC~~CG~R 35 (51)
-|.+|| +..++..+.+--||+||..
T Consensus 317 fc~ncG~~~t~~~~ng~a~fcp~cgq~ 343 (345)
T COG4260 317 FCLNCGCGTTADFDNGKAKFCPECGQG 343 (345)
T ss_pred cccccCcccccCCccchhhhChhhcCC
Confidence 355555 3333444567789999864
No 353
>PHA02998 RNA polymerase subunit; Provisional
Probab=54.03 E-value=10 Score=25.44 Aligned_cols=18 Identities=28% Similarity=0.482 Sum_probs=10.7
Q ss_pred CCCceEEEcCCCCCeeec
Q 035461 4 QPEPVSYICGDCGMENTL 21 (51)
Q Consensus 4 ~~~~~~Y~C~~Cg~~~~~ 21 (51)
+++...|.|.+||..+..
T Consensus 166 EPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 166 EPPLVRHACRDCKKHFKP 183 (195)
T ss_pred CCceEEEEcCCCCCccCC
Confidence 344566666666666554
No 354
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=53.55 E-value=10 Score=18.76 Aligned_cols=15 Identities=20% Similarity=0.485 Sum_probs=11.7
Q ss_pred eeEcCCCCCcE-EEEE
Q 035461 26 VIQCRECGYRI-LYKK 40 (51)
Q Consensus 26 ~irC~~CG~RI-lyK~ 40 (51)
.|.||.|+.-- ++|-
T Consensus 5 ~v~CP~C~s~~~v~k~ 20 (36)
T PF03811_consen 5 DVHCPRCQSTEGVKKN 20 (36)
T ss_pred eeeCCCCCCCCcceeC
Confidence 58999999877 6653
No 355
>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=53.43 E-value=11 Score=17.33 Aligned_cols=23 Identities=26% Similarity=0.723 Sum_probs=14.8
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCC
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGY 34 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~ 34 (51)
.-.|..|+..+.... ..|..||.
T Consensus 4 ~W~C~~C~~~N~~~~---~~C~~C~~ 26 (30)
T PF00641_consen 4 DWKCPSCTFMNPASR---SKCVACGA 26 (30)
T ss_dssp SEEETTTTEEEESSS---SB-TTT--
T ss_pred CccCCCCcCCchHHh---hhhhCcCC
Confidence 357889998877654 67888874
No 356
>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=53.25 E-value=2.2 Score=20.62 Aligned_cols=21 Identities=33% Similarity=0.729 Sum_probs=11.8
Q ss_pred cCCCCCeeecC----CCCeeEcCCC
Q 035461 12 CGDCGMENTLK----PGDVIQCREC 32 (51)
Q Consensus 12 C~~Cg~~~~~~----~~~~irC~~C 32 (51)
|.+||..+... ......|..|
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C 30 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVEC 30 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHH
Confidence 88888888764 2244555544
No 357
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=53.10 E-value=11 Score=23.53 Aligned_cols=25 Identities=36% Similarity=0.816 Sum_probs=16.7
Q ss_pred EcCCCCCeeec---CC-CCeeEcCCCCCc
Q 035461 11 ICGDCGMENTL---KP-GDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~~---~~-~~~irC~~CG~R 35 (51)
+|.+||..... +. .-.++|.-||++
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 68999775432 21 246899999975
No 358
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=52.92 E-value=7.9 Score=29.96 Aligned_cols=23 Identities=30% Similarity=0.885 Sum_probs=16.0
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCC
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGY 34 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~ 34 (51)
.|.+||..+... ..=..|+.|||
T Consensus 726 ~Cp~Cg~~l~~~-~GC~~C~~CG~ 748 (752)
T PRK08665 726 ACPECGSILEHE-EGCVVCHSCGY 748 (752)
T ss_pred CCCCCCcccEEC-CCCCcCCCCCC
Confidence 499998654333 35578999987
No 359
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=52.13 E-value=13 Score=25.13 Aligned_cols=13 Identities=23% Similarity=0.544 Sum_probs=9.5
Q ss_pred eEEEcCCCCCeee
Q 035461 8 VSYICGDCGMENT 20 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~ 20 (51)
....|..|+....
T Consensus 127 ~~~~C~~C~~~~~ 139 (285)
T PRK05333 127 DGVRCMGCGARHP 139 (285)
T ss_pred CEEEECCCCCcCC
Confidence 4578999996643
No 360
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=52.11 E-value=11 Score=23.13 Aligned_cols=24 Identities=25% Similarity=0.758 Sum_probs=18.3
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
|.|.+|+..+--- ++.||-||=.+
T Consensus 2 Y~CPrC~skvC~L---P~~CpiCgLtL 25 (112)
T TIGR00622 2 YFCPQCRAKVCEL---PVECPICGLTL 25 (112)
T ss_pred ccCCCCCCCccCC---CCcCCcCCCEE
Confidence 8899999887543 37899998654
No 361
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=51.94 E-value=9 Score=21.35 Aligned_cols=12 Identities=25% Similarity=0.938 Sum_probs=6.2
Q ss_pred eEcCCCCCcEEE
Q 035461 27 IQCRECGYRILY 38 (51)
Q Consensus 27 irC~~CG~RIly 38 (51)
++||.||..+.+
T Consensus 7 v~CP~C~k~~~w 18 (62)
T PRK00418 7 VNCPTCGKPVEW 18 (62)
T ss_pred ccCCCCCCcccc
Confidence 455555555443
No 362
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=51.55 E-value=12 Score=19.40 Aligned_cols=16 Identities=19% Similarity=0.420 Sum_probs=11.3
Q ss_pred eEcCCCCCcEEEEEec
Q 035461 27 IQCRECGYRILYKKRT 42 (51)
Q Consensus 27 irC~~CG~RIlyK~R~ 42 (51)
.-||.||...+.....
T Consensus 4 kPCPFCG~~~~~~~~~ 19 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQD 19 (61)
T ss_pred cCCCCCCCcceEeecc
Confidence 3599999777665543
No 363
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=51.52 E-value=11 Score=26.14 Aligned_cols=37 Identities=27% Similarity=0.625 Sum_probs=24.9
Q ss_pred ceEEEcCCCCCee------ecC---CC-----------CeeEcCCCCCcEEEEEecC
Q 035461 7 PVSYICGDCGMEN------TLK---PG-----------DVIQCRECGYRILYKKRTR 43 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~------~~~---~~-----------~~irC~~CG~RIlyK~R~~ 43 (51)
|+.-.|..||.-+ ..+ .+ --|+|+.|++.|-+|-=++
T Consensus 38 Pf~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i~~kTDPk 94 (324)
T PF04502_consen 38 PFNIWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKCPRCSNEIEFKTDPK 94 (324)
T ss_pred CccCcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEcCCCCCEEeeecCCC
Confidence 4556899996543 221 11 3589999999999885443
No 364
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=51.08 E-value=6.3 Score=25.65 Aligned_cols=7 Identities=43% Similarity=1.146 Sum_probs=3.7
Q ss_pred EcCCCCC
Q 035461 28 QCRECGY 34 (51)
Q Consensus 28 rC~~CG~ 34 (51)
+||.|||
T Consensus 2 ~CPfC~~ 8 (156)
T COG1327 2 KCPFCGH 8 (156)
T ss_pred CCCCCCC
Confidence 4555554
No 365
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=50.83 E-value=5.6 Score=28.85 Aligned_cols=28 Identities=32% Similarity=0.528 Sum_probs=20.4
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
+.-+|.+||.+++... -..+||+||.-+
T Consensus 4 ~~~rc~~cg~~f~~a~-~~~~c~~cGl~l 31 (411)
T COG0498 4 VSLRCLKCGREFSQAL-LQGLCPDCGLFL 31 (411)
T ss_pred eEeecCCCCcchhhHH-hhCcCCcCCccc
Confidence 4568999998775332 368999999744
No 366
>PLN02189 cellulose synthase
Probab=49.81 E-value=11 Score=30.66 Aligned_cols=29 Identities=31% Similarity=0.788 Sum_probs=20.9
Q ss_pred eEEEcCCCCCeeecCCCC-e-eEcCCCCCcE
Q 035461 8 VSYICGDCGMENTLKPGD-V-IQCRECGYRI 36 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~-~-irC~~CG~RI 36 (51)
...+|--||.++.+...+ . +-|.+||+.|
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpv 63 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPV 63 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCcc
Confidence 345888899988876532 2 7888888765
No 367
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=49.74 E-value=12 Score=17.93 Aligned_cols=14 Identities=21% Similarity=0.515 Sum_probs=11.4
Q ss_pred EEcCCCCCeeecCC
Q 035461 10 YICGDCGMENTLKP 23 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~ 23 (51)
|.|.+|+..|....
T Consensus 1 ~sCiDC~~~F~~~~ 14 (28)
T PF08790_consen 1 FSCIDCSKDFDGDS 14 (28)
T ss_dssp EEETTTTEEEEGGG
T ss_pred CeeecCCCCcCcCC
Confidence 67999999997653
No 368
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=49.29 E-value=11 Score=25.71 Aligned_cols=26 Identities=23% Similarity=0.387 Sum_probs=17.1
Q ss_pred EEEcCCCCCeeecCC-----------CCeeEcCCCCCc
Q 035461 9 SYICGDCGMENTLKP-----------GDVIQCRECGYR 35 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~-----------~~~irC~~CG~R 35 (51)
...|..|+..+.... ...-+|+ ||..
T Consensus 137 ~~~C~~C~~~~~~~~~~~~~~~~~~~~~~P~C~-Cgg~ 173 (271)
T PTZ00409 137 EARCCTCRKTIQLNKIMLQKTSHFMHQLPPECP-CGGI 173 (271)
T ss_pred cceeCCCCCCcccCHHHHhhhhhhccCCCCCCC-CCCc
Confidence 567999998776421 1124798 9964
No 369
>smart00355 ZnF_C2H2 zinc finger.
Probab=49.02 E-value=5.2 Score=16.33 Aligned_cols=11 Identities=36% Similarity=0.902 Sum_probs=6.6
Q ss_pred EEcCCCCCeee
Q 035461 10 YICGDCGMENT 20 (51)
Q Consensus 10 Y~C~~Cg~~~~ 20 (51)
|.|..|+..+.
T Consensus 1 ~~C~~C~~~f~ 11 (26)
T smart00355 1 YRCPECGKVFK 11 (26)
T ss_pred CCCCCCcchhC
Confidence 45666766553
No 370
>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=48.97 E-value=17 Score=22.29 Aligned_cols=25 Identities=32% Similarity=0.889 Sum_probs=17.0
Q ss_pred EcCCCCCeee-c--C-CCCeeEcCCCCCc
Q 035461 11 ICGDCGMENT-L--K-PGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~-~--~-~~~~irC~~CG~R 35 (51)
+|..|+..-. + + ..-.++|..||.+
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 5888976533 2 1 3356999999975
No 371
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=48.83 E-value=8.1 Score=17.44 Aligned_cols=11 Identities=27% Similarity=0.987 Sum_probs=8.3
Q ss_pred eeEcCCCCCcE
Q 035461 26 VIQCRECGYRI 36 (51)
Q Consensus 26 ~irC~~CG~RI 36 (51)
.+.||.||-+.
T Consensus 2 l~~C~~CgR~F 12 (25)
T PF13913_consen 2 LVPCPICGRKF 12 (25)
T ss_pred CCcCCCCCCEE
Confidence 46799999654
No 372
>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=48.82 E-value=16 Score=25.98 Aligned_cols=30 Identities=30% Similarity=0.687 Sum_probs=17.6
Q ss_pred ceEEEcCCCCCeeecCCC--CeeEcCCCCCcE
Q 035461 7 PVSYICGDCGMENTLKPG--DVIQCRECGYRI 36 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~~--~~irC~~CG~RI 36 (51)
...|.|..|+........ ....|++||.+.
T Consensus 238 G~v~~C~~C~~~~~~~~~~~~~~~c~~cg~~~ 269 (377)
T PF02005_consen 238 GYVYYCPSCGYREEVKGLQKLKSKCPECGSKL 269 (377)
T ss_dssp EEEEEETTT--EECCT-GCC--CEETTT-SCC
T ss_pred eEEEECCCccccccccCccccCCcCCCCCCcc
Confidence 467999999864333321 238999999875
No 373
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=48.50 E-value=12 Score=31.69 Aligned_cols=27 Identities=30% Similarity=0.568 Sum_probs=21.0
Q ss_pred CceEEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461 6 EPVSYICGDCGMENTLKPGDVIQCRECGYRIL 37 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl 37 (51)
+-..++|..||... ...+||.||.++-
T Consensus 671 ei~~~~Cp~Cg~~~-----~~~~Cp~CG~~~~ 697 (1627)
T PRK14715 671 EIAFFKCPKCGKVG-----LYHVCPFCGTRVE 697 (1627)
T ss_pred EEEeeeCCCCCCcc-----ccccCcccCCccc
Confidence 34678999999873 4579999998843
No 374
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=48.47 E-value=4.7 Score=25.35 Aligned_cols=22 Identities=27% Similarity=0.496 Sum_probs=16.2
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCC
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGY 34 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~ 34 (51)
.|..||+.|.- .+. -.||.|..
T Consensus 5 nC~~CgklF~~-~~~-~iCp~C~~ 26 (137)
T TIGR03826 5 NCPKCGRLFVK-TGR-DVCPSCYE 26 (137)
T ss_pred cccccchhhhh-cCC-ccCHHHhH
Confidence 58899998876 333 45999974
No 375
>COG4307 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.63 E-value=5.3 Score=28.66 Aligned_cols=26 Identities=23% Similarity=0.708 Sum_probs=20.8
Q ss_pred EEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461 9 SYICGDCGMENTLKPGDVIQCRECGYRIL 37 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl 37 (51)
.|-|.+||..+-++. .+|-.||+++=
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 477999999987764 78999998754
No 376
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=47.51 E-value=17 Score=28.43 Aligned_cols=25 Identities=36% Similarity=1.016 Sum_probs=15.3
Q ss_pred EcCCCCCeee---------cC-CCCeeEcCCCCCc
Q 035461 11 ICGDCGMENT---------LK-PGDVIQCRECGYR 35 (51)
Q Consensus 11 ~C~~Cg~~~~---------~~-~~~~irC~~CG~R 35 (51)
.|.+||..++ +- ....++|.+||+.
T Consensus 437 ~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~ 471 (730)
T COG1198 437 LCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQ 471 (730)
T ss_pred ecccCCCcccCCCCCcceEEecCCCeeEeCCCCCC
Confidence 4777766643 21 3356777777775
No 377
>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=47.41 E-value=10 Score=31.07 Aligned_cols=26 Identities=23% Similarity=0.671 Sum_probs=18.2
Q ss_pred EEEcCCCCCeeecCC--------CCeeEcCCCCC
Q 035461 9 SYICGDCGMENTLKP--------GDVIQCRECGY 34 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~--------~~~irC~~CG~ 34 (51)
-|+|.+|....-++. .+.-.||.||.
T Consensus 683 hy~c~~c~~~ef~~~~~~~sg~dlp~k~cp~c~~ 716 (1213)
T TIGR01405 683 HYLCPNCKYSEFITDGSVGSGFDLPDKDCPKCGA 716 (1213)
T ss_pred cccCcccccccccccccccccccCccccCccccc
Confidence 499999966433331 25678999985
No 378
>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=46.97 E-value=11 Score=20.25 Aligned_cols=12 Identities=25% Similarity=0.755 Sum_probs=8.9
Q ss_pred eeEcCCCCCcEE
Q 035461 26 VIQCRECGYRIL 37 (51)
Q Consensus 26 ~irC~~CG~RIl 37 (51)
-..||.||.-.+
T Consensus 13 Y~~Cp~CGN~~v 24 (49)
T PF12677_consen 13 YCKCPKCGNDKV 24 (49)
T ss_pred hccCcccCCcEe
Confidence 367999997654
No 379
>PLN02195 cellulose synthase A
Probab=46.95 E-value=13 Score=30.11 Aligned_cols=26 Identities=35% Similarity=1.006 Sum_probs=17.4
Q ss_pred EcCCCCCeeecCCC-Ce-eEcCCCCCcE
Q 035461 11 ICGDCGMENTLKPG-DV-IQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~-~~-irC~~CG~RI 36 (51)
+|.-||.++.+..+ ++ |-|.+||+.|
T Consensus 8 ~c~~cgd~~~~~~~g~~fvaC~eC~~pv 35 (977)
T PLN02195 8 ICATCGEEVGVDSNGEAFVACHECSYPL 35 (977)
T ss_pred cceecccccCcCCCCCeEEEeccCCCcc
Confidence 57777777777643 22 7777777654
No 380
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=46.90 E-value=12 Score=26.10 Aligned_cols=16 Identities=25% Similarity=0.584 Sum_probs=12.7
Q ss_pred cCCCCeeEcCCCCCcE
Q 035461 21 LKPGDVIQCRECGYRI 36 (51)
Q Consensus 21 ~~~~~~irC~~CG~RI 36 (51)
+..+.+-||++||+-.
T Consensus 176 LrEGkpqRCpECGqVF 191 (268)
T PTZ00043 176 CREGFLYRCGECDQIF 191 (268)
T ss_pred ecCCCCccCCCCCcEE
Confidence 4567889999999744
No 381
>PLN02436 cellulose synthase A
Probab=46.58 E-value=13 Score=30.40 Aligned_cols=29 Identities=28% Similarity=0.696 Sum_probs=21.9
Q ss_pred eEEEcCCCCCeeecCCC-Ce-eEcCCCCCcE
Q 035461 8 VSYICGDCGMENTLKPG-DV-IQCRECGYRI 36 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~-~~-irC~~CG~RI 36 (51)
...+|--||.++.+... +. +-|.+||+.|
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpv 65 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPV 65 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCcc
Confidence 34589999999988753 33 8899998765
No 382
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=46.53 E-value=14 Score=25.55 Aligned_cols=25 Identities=16% Similarity=0.466 Sum_probs=19.8
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
+-|.|..|...+-..+ ..|+-||.+
T Consensus 254 ~GyvCs~Clsi~C~~p---~~C~~Cgt~ 278 (279)
T TIGR00627 254 IGFVCSVCLSVLCQYT---PICKTCKTA 278 (279)
T ss_pred ceEECCCccCCcCCCC---CCCCCCCCC
Confidence 5599999998875443 599999975
No 383
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=46.28 E-value=13 Score=30.33 Aligned_cols=29 Identities=28% Similarity=0.698 Sum_probs=22.7
Q ss_pred eEEEcCCCCCeeecCCC-Ce-eEcCCCCCcE
Q 035461 8 VSYICGDCGMENTLKPG-DV-IQCRECGYRI 36 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~-~~-irC~~CG~RI 36 (51)
...+|--||.++.+..+ ++ |-|.+||+.|
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpv 44 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPFVACHVCGFPV 44 (1044)
T ss_pred CcchhhccccccCcCCCCCEEEEeccCCCcc
Confidence 56789999999998754 33 8899998765
No 384
>PLN03158 methionine aminopeptidase; Provisional
Probab=45.99 E-value=11 Score=26.99 Aligned_cols=28 Identities=21% Similarity=0.521 Sum_probs=19.5
Q ss_pred CCCCCCceEEEcCCCCCeeecCCCCeeEcCCCCC
Q 035461 1 MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGY 34 (51)
Q Consensus 1 ~~~~~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~ 34 (51)
|+....+..-+|..||++ ..++||.|-.
T Consensus 1 ~~~~~~~~~~~c~~c~~~------a~l~Cp~C~k 28 (396)
T PLN03158 1 MEEALTTSPLACARCSKP------AHLQCPKCLE 28 (396)
T ss_pred CCcccCCCcccccCCCCc------ccccCccchh
Confidence 444555666679999985 2388998853
No 385
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=45.67 E-value=18 Score=24.40 Aligned_cols=22 Identities=18% Similarity=0.374 Sum_probs=10.0
Q ss_pred EcCCCCCeeecC---CCCeeEcCCC
Q 035461 11 ICGDCGMENTLK---PGDVIQCREC 32 (51)
Q Consensus 11 ~C~~Cg~~~~~~---~~~~irC~~C 32 (51)
-|..||..+.-. .....-||.|
T Consensus 246 pCprCG~~I~~~~~~gR~t~~CP~C 270 (272)
T PRK14810 246 PCLNCKTPIRRVVVAGRSSHYCPHC 270 (272)
T ss_pred cCCCCCCeeEEEEECCCccEECcCC
Confidence 355555554422 2344555555
No 386
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=45.64 E-value=11 Score=31.42 Aligned_cols=27 Identities=22% Similarity=0.677 Sum_probs=18.7
Q ss_pred EEEcCCCCCeeecCC--------CCeeEcCCCCCc
Q 035461 9 SYICGDCGMENTLKP--------GDVIQCRECGYR 35 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~--------~~~irC~~CG~R 35 (51)
-|+|.+|....-+.. .+.-.||.||..
T Consensus 908 hy~C~~C~~~ef~~~~~~~sG~Dlpdk~Cp~Cg~~ 942 (1437)
T PRK00448 908 HYVCPNCKYSEFFTDGSVGSGFDLPDKDCPKCGTK 942 (1437)
T ss_pred cccCcccccccccccccccccccCccccCcccccc
Confidence 599999965443332 256789999864
No 387
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=45.32 E-value=4.5 Score=22.53 Aligned_cols=25 Identities=16% Similarity=0.268 Sum_probs=15.2
Q ss_pred EEcCCCCCeeecC---CCCeeEcCCCCC
Q 035461 10 YICGDCGMENTLK---PGDVIQCRECGY 34 (51)
Q Consensus 10 Y~C~~Cg~~~~~~---~~~~irC~~CG~ 34 (51)
-+|..|++..--- ..-.++||.|--
T Consensus 5 iRC~~CnKlLa~a~~~~yle~KCPrCK~ 32 (60)
T COG4416 5 IRCAKCNKLLAEAEGQAYLEKKCPRCKE 32 (60)
T ss_pred eehHHHhHHHHhcccceeeeecCCccce
Confidence 4678887654322 234588888853
No 388
>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=45.11 E-value=17 Score=23.92 Aligned_cols=24 Identities=42% Similarity=0.706 Sum_probs=17.3
Q ss_pred CceEEEcCCCCCeeecCC-CCeeEc
Q 035461 6 EPVSYICGDCGMENTLKP-GDVIQC 29 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~~-~~~irC 29 (51)
-++.|.|..||.++.... .+.+.+
T Consensus 75 v~~~~~C~~cg~~~~~~i~l~~~~l 99 (205)
T PF12322_consen 75 VPVNYTCPDCGEEVKVPINLDQIKL 99 (205)
T ss_pred ceEEEECCCCCcEEEEEecchhccc
Confidence 468999999999888763 244444
No 389
>PRK10445 endonuclease VIII; Provisional
Probab=45.00 E-value=19 Score=24.12 Aligned_cols=12 Identities=33% Similarity=0.562 Sum_probs=6.3
Q ss_pred eEcCCCCCcEEE
Q 035461 27 IQCRECGYRILY 38 (51)
Q Consensus 27 irC~~CG~RIly 38 (51)
-.||.||..|.-
T Consensus 236 ~~Cp~Cg~~I~~ 247 (263)
T PRK10445 236 EACERCGGIIEK 247 (263)
T ss_pred CCCCCCCCEeEE
Confidence 346666655543
No 390
>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=44.97 E-value=13 Score=23.43 Aligned_cols=28 Identities=25% Similarity=0.564 Sum_probs=18.4
Q ss_pred EEEcCCCCCeeecCC----CCeeEcCCCCCcE
Q 035461 9 SYICGDCGMENTLKP----GDVIQCRECGYRI 36 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~----~~~irC~~CG~RI 36 (51)
...|..|+....... ...-+||.||..+
T Consensus 113 ~~~C~~C~~~~~~~~~~~~~~~p~C~~C~~~l 144 (222)
T cd00296 113 RVRCTSCGKEYPRDEVLEREKPPRCPKCGGLL 144 (222)
T ss_pred ccEECCCCCCcchhhhhhccCCCCCCCCCCcc
Confidence 356888986654432 2456799999753
No 391
>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=44.56 E-value=20 Score=24.18 Aligned_cols=10 Identities=50% Similarity=1.095 Sum_probs=4.6
Q ss_pred EcCCCCCcEE
Q 035461 28 QCRECGYRIL 37 (51)
Q Consensus 28 rC~~CG~RIl 37 (51)
-||.||..|.
T Consensus 247 pC~~Cg~~I~ 256 (272)
T TIGR00577 247 PCRRCGTPIE 256 (272)
T ss_pred CCCCCCCeeE
Confidence 3444444443
No 392
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=44.55 E-value=12 Score=27.53 Aligned_cols=33 Identities=21% Similarity=0.427 Sum_probs=24.7
Q ss_pred ceEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEEec
Q 035461 7 PVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRT 42 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R~ 42 (51)
...|+|-+||...-.- --.||.|...=-+|++.
T Consensus 352 ~~~YRC~~CGF~a~~l---~W~CPsC~~W~TikPir 384 (389)
T COG2956 352 KPRYRCQNCGFTAHTL---YWHCPSCRAWETIKPIR 384 (389)
T ss_pred cCCceecccCCcceee---eeeCCCcccccccCCcc
Confidence 4679999999765433 36899999887777654
No 393
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=44.50 E-value=10 Score=26.23 Aligned_cols=36 Identities=28% Similarity=0.463 Sum_probs=26.0
Q ss_pred eEEEcCCCCCeeecC-----CCCeeEcCCCCCcE-EEEEecC
Q 035461 8 VSYICGDCGMENTLK-----PGDVIQCRECGYRI-LYKKRTR 43 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~-----~~~~irC~~CG~RI-lyK~R~~ 43 (51)
-.-||..|...+.+- +.+.-.|++|.+.+ +-+.|..
T Consensus 191 ~alIC~~C~hhngl~~~~ek~~~efiC~~Cn~~n~~~~~~~d 232 (251)
T COG5415 191 KALICPQCHHHNGLYRLAEKPIIEFICPHCNHKNDEVKERED 232 (251)
T ss_pred hhhccccccccccccccccccchheecccchhhcCccccccc
Confidence 346899998887763 23457899999998 6666543
No 394
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=43.63 E-value=20 Score=24.17 Aligned_cols=23 Identities=22% Similarity=0.471 Sum_probs=15.5
Q ss_pred EcCCCCCeeecC---CCCeeEcCCCC
Q 035461 11 ICGDCGMENTLK---PGDVIQCRECG 33 (51)
Q Consensus 11 ~C~~Cg~~~~~~---~~~~irC~~CG 33 (51)
.|..||..+... .....-||.|-
T Consensus 237 pC~~Cg~~I~~~~~~gR~ty~Cp~CQ 262 (269)
T PRK14811 237 PCPRCGTPIEKIVVGGRGTHFCPQCQ 262 (269)
T ss_pred CCCcCCCeeEEEEECCCCcEECCCCc
Confidence 588888777643 34667788774
No 395
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=43.59 E-value=21 Score=23.99 Aligned_cols=21 Identities=24% Similarity=0.618 Sum_probs=10.0
Q ss_pred cCCCCCeeecC---CCCeeEcCCC
Q 035461 12 CGDCGMENTLK---PGDVIQCREC 32 (51)
Q Consensus 12 C~~Cg~~~~~~---~~~~irC~~C 32 (51)
|..||..+... .....-||.|
T Consensus 248 C~~Cg~~I~~~~~~gR~t~~CP~C 271 (274)
T PRK01103 248 CRRCGTPIEKIKQGGRSTFFCPRC 271 (274)
T ss_pred CCCCCCeeEEEEECCCCcEECcCC
Confidence 55555554422 2244555555
No 396
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.48 E-value=13 Score=26.49 Aligned_cols=30 Identities=30% Similarity=0.713 Sum_probs=23.5
Q ss_pred EcCCCCCeeecCCC-CeeEcCCCCCcEEEEEe
Q 035461 11 ICGDCGMENTLKPG-DVIQCRECGYRILYKKR 41 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~-~~irC~~CG~RIlyK~R 41 (51)
.|..|+..+++..+ .-+.|+ |||.+-|.-.
T Consensus 308 ~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~ 338 (384)
T KOG1812|consen 308 QCPKCKFMIELSEGCNHMTCR-CGHQFCYMCG 338 (384)
T ss_pred cCcccceeeeecCCcceEEee-ccccchhhcC
Confidence 58889988888766 668998 9988777544
No 397
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.43 E-value=14 Score=23.09 Aligned_cols=27 Identities=22% Similarity=0.572 Sum_probs=18.7
Q ss_pred ceEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 7 PVSYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
++.-.|..||+..-+ ..++|++|+-.|
T Consensus 4 ~~~~~cPvcg~~~iV---TeL~c~~~etTV 30 (122)
T COG3877 4 KVINRCPVCGRKLIV---TELKCSNCETTV 30 (122)
T ss_pred CCCCCCCccccccee---EEEecCCCCceE
Confidence 455678888887654 348888888654
No 398
>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=43.33 E-value=7 Score=21.70 Aligned_cols=11 Identities=36% Similarity=0.878 Sum_probs=7.8
Q ss_pred eeEcCCCCCcE
Q 035461 26 VIQCRECGYRI 36 (51)
Q Consensus 26 ~irC~~CG~RI 36 (51)
+|||.-||.-|
T Consensus 4 PVRCFTCGkvi 14 (60)
T PF01194_consen 4 PVRCFTCGKVI 14 (60)
T ss_dssp SSS-STTTSBT
T ss_pred ceecCCCCCCh
Confidence 68999999754
No 399
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=43.24 E-value=13 Score=16.31 Aligned_cols=21 Identities=29% Similarity=0.629 Sum_probs=13.9
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCC
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGY 34 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~ 34 (51)
.|..|+..+.... ..|-.||.
T Consensus 4 ~C~~C~~~N~~~~---~~C~~C~~ 24 (26)
T smart00547 4 ECPACTFLNFASR---SKCFACGA 24 (26)
T ss_pred cCCCCCCcChhhh---ccccccCC
Confidence 5778887665544 56777764
No 400
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=43.10 E-value=20 Score=24.22 Aligned_cols=22 Identities=23% Similarity=0.519 Sum_probs=12.6
Q ss_pred EcCCCCCeeecC---CCCeeEcCCC
Q 035461 11 ICGDCGMENTLK---PGDVIQCREC 32 (51)
Q Consensus 11 ~C~~Cg~~~~~~---~~~~irC~~C 32 (51)
-|..||..+... .....-||.|
T Consensus 256 pC~~Cg~~I~~~~~~gR~t~~CP~C 280 (282)
T PRK13945 256 PCRKCGTPIERIKLAGRSTHWCPNC 280 (282)
T ss_pred CCCcCCCeeEEEEECCCccEECCCC
Confidence 566666665532 2355666666
No 401
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=43.06 E-value=22 Score=25.18 Aligned_cols=35 Identities=34% Similarity=0.698 Sum_probs=21.0
Q ss_pred ceEEEcCCCCCeee----cCC--C-CeeEcCCCCCcEEEEEec
Q 035461 7 PVSYICGDCGMENT----LKP--G-DVIQCRECGYRILYKKRT 42 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~----~~~--~-~~irC~~CG~RIlyK~R~ 42 (51)
|..=+|.+||.... ... + -.-+| +|||..-...+.
T Consensus 167 P~~p~c~~cg~~~~~v~~~d~~~~~v~y~c-~cG~~g~~~~~~ 208 (353)
T cd00674 167 PFMPYCEKCGKDTTTVEAYDAKAGTVTYKC-ECGHEETVDIRT 208 (353)
T ss_pred eeeeecCCcCcceeEEEEEeCCCCeEEEEc-CCCCEEEEeecC
Confidence 45668999985321 222 2 23577 689887666654
No 402
>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=42.77 E-value=13 Score=18.29 Aligned_cols=11 Identities=27% Similarity=0.785 Sum_probs=8.2
Q ss_pred eEcCCCCCcEE
Q 035461 27 IQCRECGYRIL 37 (51)
Q Consensus 27 irC~~CG~RIl 37 (51)
-.|+.||..+-
T Consensus 3 ~~C~~Cg~~l~ 13 (47)
T PF13005_consen 3 RACPDCGGELK 13 (47)
T ss_pred CcCCCCCceee
Confidence 46999998654
No 403
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=42.64 E-value=18 Score=18.99 Aligned_cols=32 Identities=16% Similarity=0.415 Sum_probs=22.3
Q ss_pred EEcCCCCCeeecCC--------CCeeEcCCCCCcEEEEEe
Q 035461 10 YICGDCGMENTLKP--------GDVIQCRECGYRILYKKR 41 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~--------~~~irC~~CG~RIlyK~R 41 (51)
-.|.+|...+.+.. ...+||-.|..=|-|+.|
T Consensus 7 v~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~s~~ 46 (46)
T PF11331_consen 7 VVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSFSLP 46 (46)
T ss_pred eECccHHHHHcCCCccCCCccceeEEeCCCCceeEEEecC
Confidence 36888866666531 246899999988887754
No 404
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=42.12 E-value=15 Score=25.47 Aligned_cols=25 Identities=32% Similarity=0.856 Sum_probs=14.4
Q ss_pred EEcCCCCCeeecC--CCCeeEcCCCCC
Q 035461 10 YICGDCGMENTLK--PGDVIQCRECGY 34 (51)
Q Consensus 10 Y~C~~Cg~~~~~~--~~~~irC~~CG~ 34 (51)
+.|.+||.+.-.. ....+-|..||.
T Consensus 2 ~~CpeCg~~~~~~d~~~ge~VC~~CG~ 28 (285)
T COG1405 2 MSCPECGSTNIITDYERGEIVCADCGL 28 (285)
T ss_pred CCCCCCCCccceeeccCCeEEeccCCE
Confidence 3577777663222 235677777774
No 405
>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=41.82 E-value=20 Score=25.88 Aligned_cols=36 Identities=28% Similarity=0.571 Sum_probs=18.3
Q ss_pred ceEEEcCCCCCe--eec---C-CCC--eeEcCCCCCcEEEEEec
Q 035461 7 PVSYICGDCGME--NTL---K-PGD--VIQCRECGYRILYKKRT 42 (51)
Q Consensus 7 ~~~Y~C~~Cg~~--~~~---~-~~~--~irC~~CG~RIlyK~R~ 42 (51)
|+.=+|.+||+. +.+ + ... .-+|+.|||..-...+.
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 566789999983 222 1 112 36899999887665554
No 406
>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=41.71 E-value=21 Score=21.14 Aligned_cols=19 Identities=26% Similarity=0.557 Sum_probs=13.3
Q ss_pred eecCCCCeeEcCCCCCcEE
Q 035461 19 NTLKPGDVIQCRECGYRIL 37 (51)
Q Consensus 19 ~~~~~~~~irC~~CG~RIl 37 (51)
+.++..+.+.|++||--.+
T Consensus 28 IvIknVPa~~C~~CGe~y~ 46 (89)
T TIGR03829 28 IEIKETPSISCSHCGMEYQ 46 (89)
T ss_pred EEEecCCcccccCCCcEee
Confidence 3445557899999996543
No 407
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.22 E-value=20 Score=21.35 Aligned_cols=24 Identities=25% Similarity=0.654 Sum_probs=17.3
Q ss_pred EcCCCCCeeecCCC---CeeEcCCCCC
Q 035461 11 ICGDCGMENTLKPG---DVIQCRECGY 34 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~---~~irC~~CG~ 34 (51)
.|..|+.+...... .--.||.|+.
T Consensus 3 lCP~C~v~l~~~~rs~vEiD~CPrCrG 29 (88)
T COG3809 3 LCPICGVELVMSVRSGVEIDYCPRCRG 29 (88)
T ss_pred ccCcCCceeeeeeecCceeeeCCcccc
Confidence 58889988776533 3347999986
No 408
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=41.10 E-value=19 Score=20.73 Aligned_cols=15 Identities=33% Similarity=0.771 Sum_probs=11.2
Q ss_pred eEEEcCCCCCeeecC
Q 035461 8 VSYICGDCGMENTLK 22 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~ 22 (51)
.-.+|..||+.+++.
T Consensus 79 ~h~iC~~Cg~v~~~~ 93 (120)
T PF01475_consen 79 HHFICTQCGKVIDLD 93 (120)
T ss_dssp EEEEETTTS-EEEE-
T ss_pred eEEEECCCCCEEEec
Confidence 567999999999876
No 409
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=41.06 E-value=21 Score=23.25 Aligned_cols=26 Identities=35% Similarity=0.940 Sum_probs=16.8
Q ss_pred EEcCCCCCeee-c--CC-CCeeEcCCCCCc
Q 035461 10 YICGDCGMENT-L--KP-GDVIQCRECGYR 35 (51)
Q Consensus 10 Y~C~~Cg~~~~-~--~~-~~~irC~~CG~R 35 (51)
=+|..||..-. + +. .-.++|.-||..
T Consensus 99 V~C~~C~~pdT~l~k~~~~~~l~C~aCGa~ 128 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRVLMLRCDACGAH 128 (201)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 37999976543 2 11 235799999965
No 410
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=41.06 E-value=14 Score=21.15 Aligned_cols=19 Identities=37% Similarity=0.931 Sum_probs=16.0
Q ss_pred CeeEcCCCCCcEEEEEecC
Q 035461 25 DVIQCRECGYRILYKKRTR 43 (51)
Q Consensus 25 ~~irC~~CG~RIlyK~R~~ 43 (51)
-.|-|.+|||.=+|+.-+.
T Consensus 39 ~~itCk~CgYtEfY~a~~s 57 (68)
T COG3478 39 IVITCKNCGYTEFYSAKIS 57 (68)
T ss_pred EEEEeccCCchhheecccc
Confidence 3689999999999987654
No 411
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=41.04 E-value=16 Score=19.67 Aligned_cols=11 Identities=36% Similarity=0.908 Sum_probs=7.3
Q ss_pred CeeEcCCCCCc
Q 035461 25 DVIQCRECGYR 35 (51)
Q Consensus 25 ~~irC~~CG~R 35 (51)
..+.||+||..
T Consensus 52 g~L~Cp~c~r~ 62 (68)
T PF03966_consen 52 GELICPECGRE 62 (68)
T ss_dssp TEEEETTTTEE
T ss_pred CEEEcCCCCCE
Confidence 56777777743
No 412
>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 cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=40.85 E-value=6 Score=21.00 Aligned_cols=26 Identities=31% Similarity=0.694 Sum_probs=18.6
Q ss_pred EcCCCCCeeecCC-----CCeeEcCCCCCcE
Q 035461 11 ICGDCGMENTLKP-----GDVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~~-----~~~irC~~CG~RI 36 (51)
+|..||....... +...-|..||-+.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~ 31 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYW 31 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHH
Confidence 4899999877642 4567799998443
No 414
>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=40.45 E-value=34 Score=20.88 Aligned_cols=17 Identities=53% Similarity=0.843 Sum_probs=15.0
Q ss_pred CcEEEEEecCceEEEEc
Q 035461 34 YRILYKKRTRRIVQYEA 50 (51)
Q Consensus 34 ~RIlyK~R~~~~~~~~A 50 (51)
+-|++++|+..+.|||-
T Consensus 32 ~~i~f~KRt~GirqfEi 48 (103)
T PF09158_consen 32 YEIRFKKRTKGIRQFEI 48 (103)
T ss_dssp EEEEEEEEETTEEEEEE
T ss_pred eEEeeecccCceeEEEE
Confidence 66899999999999984
No 415
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=40.25 E-value=16 Score=18.23 Aligned_cols=8 Identities=38% Similarity=1.169 Sum_probs=7.0
Q ss_pred eeEcCCCC
Q 035461 26 VIQCRECG 33 (51)
Q Consensus 26 ~irC~~CG 33 (51)
.+.|+.||
T Consensus 13 ~~~C~~Cg 20 (41)
T PF13878_consen 13 ATTCPTCG 20 (41)
T ss_pred CcCCCCCC
Confidence 58999998
No 416
>PF14122 YokU: YokU-like protein
Probab=40.21 E-value=25 Score=20.93 Aligned_cols=18 Identities=22% Similarity=0.521 Sum_probs=13.2
Q ss_pred CeeecCCCCeeEcCCCCC
Q 035461 17 MENTLKPGDVIQCRECGY 34 (51)
Q Consensus 17 ~~~~~~~~~~irC~~CG~ 34 (51)
+.+++...+.+-|.+||-
T Consensus 26 raIeI~~tP~i~C~~Cgm 43 (87)
T PF14122_consen 26 RAIEITDTPAIICSNCGM 43 (87)
T ss_pred eEEEecCCceeeecCCCc
Confidence 355666678899999984
No 417
>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=39.89 E-value=6.6 Score=23.13 Aligned_cols=24 Identities=29% Similarity=0.692 Sum_probs=16.5
Q ss_pred EEEcCCCCCeeecC---CC-CeeEcCCC
Q 035461 9 SYICGDCGMENTLK---PG-DVIQCREC 32 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~---~~-~~irC~~C 32 (51)
.=+|-+||.++... .. ...+|..|
T Consensus 80 yG~C~~Cge~I~~~RL~a~P~a~~Cv~C 107 (110)
T TIGR02420 80 YGYCEECGEEIGLRRLEARPTATLCIDC 107 (110)
T ss_pred CCchhccCCcccHHHHhhCCCccccHHh
Confidence 34799999998865 22 44667666
No 418
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=39.85 E-value=22 Score=17.53 Aligned_cols=10 Identities=30% Similarity=0.903 Sum_probs=5.5
Q ss_pred EEEcCCCCCe
Q 035461 9 SYICGDCGME 18 (51)
Q Consensus 9 ~Y~C~~Cg~~ 18 (51)
.|+|..|+..
T Consensus 11 l~~CL~C~~~ 20 (50)
T smart00290 11 LWLCLTCGQV 20 (50)
T ss_pred eEEecCCCCc
Confidence 5566666543
No 419
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=39.65 E-value=20 Score=25.66 Aligned_cols=27 Identities=30% Similarity=0.716 Sum_probs=17.6
Q ss_pred CceEEEcCCCCCeeecCC---CCeeEcCCC
Q 035461 6 EPVSYICGDCGMENTLKP---GDVIQCREC 32 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~~---~~~irC~~C 32 (51)
-|.-++|..||++.+..+ .+.+-|+.|
T Consensus 160 H~yHFkCt~C~keL~sdaRevk~eLyClrC 189 (332)
T KOG2272|consen 160 HPYHFKCTTCGKELTSDAREVKGELYCLRC 189 (332)
T ss_pred Cccceecccccccccchhhhhccceecccc
Confidence 345678999999888753 244555444
No 420
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=39.57 E-value=13 Score=20.93 Aligned_cols=9 Identities=33% Similarity=1.232 Sum_probs=7.5
Q ss_pred eeEcCCCCC
Q 035461 26 VIQCRECGY 34 (51)
Q Consensus 26 ~irC~~CG~ 34 (51)
-+|||.||-
T Consensus 17 ~lrCPRC~~ 25 (65)
T COG4049 17 FLRCPRCGM 25 (65)
T ss_pred eeeCCchhH
Confidence 489999984
No 421
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Probab=39.48 E-value=36 Score=25.92 Aligned_cols=32 Identities=25% Similarity=0.538 Sum_probs=23.1
Q ss_pred CCCceEEEcCCCCCeeecCC-CCeeEcCCCCCc
Q 035461 4 QPEPVSYICGDCGMENTLKP-GDVIQCRECGYR 35 (51)
Q Consensus 4 ~~~~~~Y~C~~Cg~~~~~~~-~~~irC~~CG~R 35 (51)
+..-..|+|..||....... .....|+.|+..
T Consensus 533 SD~~~~~vC~~CG~~~~~~~~~~~~~C~~c~~~ 565 (599)
T TIGR03670 533 SDKYVVYVCENCGHIAWEDKRKGTAYCPVCGET 565 (599)
T ss_pred CcceeEEeecccCceeehhcccCceeccccCCC
Confidence 34446799999999875433 345779999874
No 422
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=39.34 E-value=13 Score=19.61 Aligned_cols=10 Identities=30% Similarity=1.009 Sum_probs=6.8
Q ss_pred CeeEcCCCCC
Q 035461 25 DVIQCRECGY 34 (51)
Q Consensus 25 ~~irC~~CG~ 34 (51)
..-+||.||-
T Consensus 10 GirkCp~CGt 19 (44)
T PF14952_consen 10 GIRKCPKCGT 19 (44)
T ss_pred ccccCCcCcC
Confidence 3457998883
No 423
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=39.23 E-value=24 Score=20.00 Aligned_cols=16 Identities=25% Similarity=0.567 Sum_probs=13.0
Q ss_pred eEEEcCCCCCeeecCC
Q 035461 8 VSYICGDCGMENTLKP 23 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~ 23 (51)
.-.+|.+||+.+++..
T Consensus 72 ~H~~C~~Cg~i~~~~~ 87 (116)
T cd07153 72 HHLICTKCGKVIDFED 87 (116)
T ss_pred CceEeCCCCCEEEecC
Confidence 4578999999998863
No 424
>PRK09462 fur ferric uptake regulator; Provisional
Probab=38.96 E-value=23 Score=21.38 Aligned_cols=15 Identities=33% Similarity=0.594 Sum_probs=12.5
Q ss_pred eEEEcCCCCCeeecC
Q 035461 8 VSYICGDCGMENTLK 22 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~ 22 (51)
.-.+|.+||+.+++.
T Consensus 89 ~H~iC~~Cg~i~~i~ 103 (148)
T PRK09462 89 DHLICLDCGKVIEFS 103 (148)
T ss_pred CceEECCCCCEEEeC
Confidence 357899999999875
No 425
>PLN02400 cellulose synthase
Probab=38.78 E-value=22 Score=29.21 Aligned_cols=28 Identities=32% Similarity=0.832 Sum_probs=20.4
Q ss_pred EEEcCCCCCeeecCCC-Ce-eEcCCCCCcE
Q 035461 9 SYICGDCGMENTLKPG-DV-IQCRECGYRI 36 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~~-~~-irC~~CG~RI 36 (51)
.-+|--||.++.+..+ +. |-|.+||+.|
T Consensus 36 gqiCqICGD~VG~t~dGe~FVAC~eCaFPV 65 (1085)
T PLN02400 36 GQICQICGDDVGVTETGDVFVACNECAFPV 65 (1085)
T ss_pred CceeeecccccCcCCCCCEEEEEccCCCcc
Confidence 3488889999888754 22 7888887754
No 426
>PRK02935 hypothetical protein; Provisional
Probab=38.65 E-value=33 Score=21.22 Aligned_cols=28 Identities=29% Similarity=0.625 Sum_probs=19.1
Q ss_pred ceEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461 7 PVSYICGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
.+.-.|.+|+++...- +..-.|.+|+-.
T Consensus 68 avqV~CP~C~K~TKmL-GrvD~CM~C~~P 95 (110)
T PRK02935 68 AVQVICPSCEKPTKML-GRVDACMHCNQP 95 (110)
T ss_pred ceeeECCCCCchhhhc-cceeecCcCCCc
Confidence 3555788888886543 355688888753
No 427
>PRK11827 hypothetical protein; Provisional
Probab=38.57 E-value=41 Score=18.48 Aligned_cols=31 Identities=13% Similarity=0.270 Sum_probs=21.3
Q ss_pred EcCCCCCeeecCC-CCeeEcCCCCCcEEEEEecC
Q 035461 11 ICGDCGMENTLKP-GDVIQCRECGYRILYKKRTR 43 (51)
Q Consensus 11 ~C~~Cg~~~~~~~-~~~irC~~CG~RIlyK~R~~ 43 (51)
.|-.|+.++.... ...+.|+.|| +.|-.|..
T Consensus 10 aCP~ckg~L~~~~~~~~Lic~~~~--laYPI~dg 41 (60)
T PRK11827 10 ACPVCNGKLWYNQEKQELICKLDN--LAFPLRDG 41 (60)
T ss_pred ECCCCCCcCeEcCCCCeEECCccC--eeccccCC
Confidence 5888888877753 4678899886 44555543
No 428
>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=38.50 E-value=23 Score=18.86 Aligned_cols=23 Identities=30% Similarity=0.732 Sum_probs=14.4
Q ss_pred ceEEEcCCCCCeeecCCCCeeEcCCCC
Q 035461 7 PVSYICGDCGMENTLKPGDVIQCRECG 33 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG 33 (51)
+..-.|.+||... ..---|+.||
T Consensus 24 p~l~~C~~cG~~~----~~H~vc~~cG 46 (55)
T TIGR01031 24 PTLVVCPNCGEFK----LPHRVCPSCG 46 (55)
T ss_pred CcceECCCCCCcc----cCeeECCccC
Confidence 4445677787643 2346688888
No 429
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=38.19 E-value=22 Score=18.82 Aligned_cols=7 Identities=29% Similarity=0.714 Sum_probs=2.6
Q ss_pred eeEcCCC
Q 035461 26 VIQCREC 32 (51)
Q Consensus 26 ~irC~~C 32 (51)
.-+||.|
T Consensus 37 ~g~CPgC 43 (48)
T PF14570_consen 37 GGRCPGC 43 (48)
T ss_dssp -SB-TTT
T ss_pred CCCCCCC
Confidence 4455555
No 430
>PRK00019 rpmE 50S ribosomal protein L31; Reviewed
Probab=38.04 E-value=32 Score=19.42 Aligned_cols=20 Identities=30% Similarity=0.614 Sum_probs=15.5
Q ss_pred CCCCceEEEcCCCCCeeecCC
Q 035461 3 PQPEPVSYICGDCGMENTLKP 23 (51)
Q Consensus 3 ~~~~~~~Y~C~~Cg~~~~~~~ 23 (51)
|.-.++.+.|+ ||.++...+
T Consensus 7 P~y~~v~~~c~-~g~~f~~~S 26 (72)
T PRK00019 7 PKYEEVTVTCS-CGNVFETRS 26 (72)
T ss_pred CCCEEEEEEEC-CCCEEEEee
Confidence 33456888999 999999764
No 431
>PRK10996 thioredoxin 2; Provisional
Probab=37.74 E-value=27 Score=20.79 Aligned_cols=29 Identities=28% Similarity=0.717 Sum_probs=22.6
Q ss_pred EEEcCCCCCeeecCC---CCeeEcCCCCCcEE
Q 035461 9 SYICGDCGMENTLKP---GDVIQCRECGYRIL 37 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~~---~~~irC~~CG~RIl 37 (51)
.-.|..|..++++.. .+.-.|+-||..++
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 33 (139)
T PRK10996 2 NTVCTSCQAINRLPDERIEDAAKCGRCGHDLF 33 (139)
T ss_pred eEECCCCCCcCCCCCccccCCCcCCCCCCccC
Confidence 346899999888763 36788999998776
No 432
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=37.28 E-value=35 Score=17.22 Aligned_cols=10 Identities=20% Similarity=0.704 Sum_probs=3.5
Q ss_pred eeEcCC-CCCc
Q 035461 26 VIQCRE-CGYR 35 (51)
Q Consensus 26 ~irC~~-CG~R 35 (51)
.|.||+ |+..
T Consensus 9 ~v~C~~~cc~~ 19 (60)
T PF02176_consen 9 PVPCPNGCCNE 19 (60)
T ss_dssp EEE-TT--S-B
T ss_pred EeeCCCCCccc
Confidence 455654 4444
No 433
>COG0254 RpmE Ribosomal protein L31 [Translation, ribosomal structure and biogenesis]
Probab=37.23 E-value=30 Score=19.87 Aligned_cols=18 Identities=39% Similarity=0.957 Sum_probs=15.8
Q ss_pred CceEEEcCCCCCeeecCC
Q 035461 6 EPVSYICGDCGMENTLKP 23 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~~ 23 (51)
+++.+.|+.||..|.+.+
T Consensus 11 ~~v~~~~~s~g~~f~~~S 28 (75)
T COG0254 11 RPVVFVCSSCGNEFTTRS 28 (75)
T ss_pred ceEEEEeCCCCCEEEEEe
Confidence 569999999999999864
No 434
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=37.12 E-value=39 Score=25.75 Aligned_cols=39 Identities=23% Similarity=0.515 Sum_probs=25.0
Q ss_pred CCCCceEEEcCCCCCeeecCC-CCeeEcCCCCC-cEEEEEe
Q 035461 3 PQPEPVSYICGDCGMENTLKP-GDVIQCRECGY-RILYKKR 41 (51)
Q Consensus 3 ~~~~~~~Y~C~~Cg~~~~~~~-~~~irC~~CG~-RIlyK~R 41 (51)
.+..-..|+|..||....... .....|+.|+. .-+.+.+
T Consensus 538 ~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~i~~v~ 578 (605)
T PRK07225 538 ESDKVEIYVCAKCGMIAIYDKKRNRKYCPICGEETDIYPVE 578 (605)
T ss_pred cCcceeEEeecCcCcceehhcccCceeecccCCCCceeecc
Confidence 344456799999999765433 24567999975 2344443
No 435
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.10 E-value=16 Score=20.72 Aligned_cols=14 Identities=21% Similarity=0.802 Sum_probs=8.8
Q ss_pred CeeEcCCCCCcEEE
Q 035461 25 DVIQCRECGYRILY 38 (51)
Q Consensus 25 ~~irC~~CG~RIly 38 (51)
..+.||.||.-+..
T Consensus 6 ~~v~CP~Cgkpv~w 19 (65)
T COG3024 6 ITVPCPTCGKPVVW 19 (65)
T ss_pred ccccCCCCCCcccc
Confidence 34667777766655
No 436
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=36.99 E-value=9.4 Score=29.17 Aligned_cols=26 Identities=23% Similarity=0.457 Sum_probs=17.6
Q ss_pred EEEcCCCCCeeecC-CCCeeEcCCCCC
Q 035461 9 SYICGDCGMENTLK-PGDVIQCRECGY 34 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~-~~~~irC~~CG~ 34 (51)
-|+|+.||..+... ....-.|.++|.
T Consensus 340 ~~~CAgC~~~i~~~~~~~~R~C~y~G~ 366 (580)
T KOG1829|consen 340 NFRCAGCGHTIGPDLEQRPRLCRYLGK 366 (580)
T ss_pred CceecccCCCcccccccchhHhhhhhh
Confidence 48999999999843 334455555553
No 437
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=36.77 E-value=23 Score=30.38 Aligned_cols=24 Identities=25% Similarity=0.641 Sum_probs=17.1
Q ss_pred cCCCCCe----eecCC-CCeeEcCCCCCc
Q 035461 12 CGDCGME----NTLKP-GDVIQCRECGYR 35 (51)
Q Consensus 12 C~~Cg~~----~~~~~-~~~irC~~CG~R 35 (51)
|..||.. +++.. .+=..||.||+-
T Consensus 1707 cp~c~~~~~~~~~~~~~~gc~~c~~cg~s 1735 (1740)
T PRK08332 1707 CPVCYEKEGKLVELRMESGCATCPVCGWS 1735 (1740)
T ss_pred CCCCCCCCCcceeeEecCCceeCCCCCCc
Confidence 9999877 44442 355899999973
No 438
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=36.67 E-value=16 Score=20.07 Aligned_cols=9 Identities=44% Similarity=1.073 Sum_probs=6.9
Q ss_pred EcCCCCCcE
Q 035461 28 QCRECGYRI 36 (51)
Q Consensus 28 rC~~CG~RI 36 (51)
-|++||..|
T Consensus 5 HC~~CG~~I 13 (59)
T PF09889_consen 5 HCPVCGKPI 13 (59)
T ss_pred cCCcCCCcC
Confidence 488898765
No 439
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=36.48 E-value=5.7 Score=22.40 Aligned_cols=24 Identities=33% Similarity=0.661 Sum_probs=17.2
Q ss_pred EEEcCCCCCeeecC---CC-CeeEcCCC
Q 035461 9 SYICGDCGMENTLK---PG-DVIQCREC 32 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~---~~-~~irC~~C 32 (51)
.+.|-+||.++... .. ...+|..|
T Consensus 34 ~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~C 61 (73)
T PRK13715 34 VYLCEACGNPIPEARRKIFPGVTLCVEC 61 (73)
T ss_pred cccHhhcCCcCCHHHHhcCCCcCCCHHH
Confidence 45899999998865 22 45677776
No 440
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=36.42 E-value=28 Score=25.50 Aligned_cols=26 Identities=27% Similarity=0.723 Sum_probs=18.5
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
--|.|..|++.+-.-+ +-||-||--.
T Consensus 275 ~Gy~CP~CkakvCsLP---~eCpiC~ltL 300 (378)
T KOG2807|consen 275 GGYFCPQCKAKVCSLP---IECPICSLTL 300 (378)
T ss_pred CceeCCcccCeeecCC---ccCCccceeE
Confidence 4588888888776543 7788887543
No 441
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=36.38 E-value=35 Score=24.49 Aligned_cols=30 Identities=27% Similarity=0.651 Sum_probs=19.9
Q ss_pred ceEEEcCCCCCeeecCC-----CCeeEcCCCCCcE
Q 035461 7 PVSYICGDCGMENTLKP-----GDVIQCRECGYRI 36 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~-----~~~irC~~CG~RI 36 (51)
...|+|..||.+..+.. .....||+||...
T Consensus 322 r~~~r~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~ 356 (409)
T TIGR00108 322 RVTYKCAECGEVIEKTVRELKDKKFAICPACGQEM 356 (409)
T ss_pred eEEEEcCCCCceeecccccccccccccCcccCccc
Confidence 36799999997533221 1235799999764
No 442
>COG5132 BUD31 Cell cycle control protein, G10 family [Transcription / Cell division and chromosome partitioning]
Probab=36.34 E-value=14 Score=23.62 Aligned_cols=11 Identities=36% Similarity=1.123 Sum_probs=8.9
Q ss_pred CeeEcCCCCCc
Q 035461 25 DVIQCRECGYR 35 (51)
Q Consensus 25 ~~irC~~CG~R 35 (51)
..++|.+||.|
T Consensus 130 qr~kC~hCGCr 140 (146)
T COG5132 130 QRLKCDHCGCR 140 (146)
T ss_pred HhccccccCCC
Confidence 45889999986
No 443
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=36.24 E-value=24 Score=29.75 Aligned_cols=28 Identities=21% Similarity=0.605 Sum_probs=19.9
Q ss_pred eEEEcCCCCCeeecC--------CCCeeEcCCCCCc
Q 035461 8 VSYICGDCGMENTLK--------PGDVIQCRECGYR 35 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~--------~~~~irC~~CG~R 35 (51)
--|+|.+|..---++ ..+.--||.||..
T Consensus 913 PHY~Cp~Cky~Ef~~d~svgsGfDLpdK~CPkCg~p 948 (1444)
T COG2176 913 PHYLCPECKYSEFIDDGSVGSGFDLPDKDCPKCGTP 948 (1444)
T ss_pred ccccCCCCceeeeecCCCcCCCCCCCCCCCCcCCCc
Confidence 469999996543333 1255789999987
No 444
>PF13395 HNH_4: HNH endonuclease
Probab=36.24 E-value=17 Score=18.83 Aligned_cols=10 Identities=40% Similarity=0.806 Sum_probs=7.4
Q ss_pred cCCCCCcEEE
Q 035461 29 CRECGYRILY 38 (51)
Q Consensus 29 C~~CG~RIly 38 (51)
|+|||-.|=.
T Consensus 1 C~Y~g~~i~~ 10 (54)
T PF13395_consen 1 CPYCGKPISI 10 (54)
T ss_pred CCCCCCCCCh
Confidence 8889887643
No 445
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.02 E-value=12 Score=21.32 Aligned_cols=29 Identities=24% Similarity=0.504 Sum_probs=20.3
Q ss_pred EcCCCCCeeecCC---------C---CeeEcCCCCCcEEEE
Q 035461 11 ICGDCGMENTLKP---------G---DVIQCRECGYRILYK 39 (51)
Q Consensus 11 ~C~~Cg~~~~~~~---------~---~~irC~~CG~RIlyK 39 (51)
+|.-|.+..+++. + ...-|++|-+||-.|
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 5777777777641 2 345699999998776
No 446
>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=35.98 E-value=16 Score=22.91 Aligned_cols=22 Identities=32% Similarity=0.653 Sum_probs=13.9
Q ss_pred cCCCCCeeecCCCCeeEcCCCCCcE
Q 035461 12 CGDCGMENTLKPGDVIQCRECGYRI 36 (51)
Q Consensus 12 C~~Cg~~~~~~~~~~irC~~CG~RI 36 (51)
|..||+.+.. ....|+.|+..+
T Consensus 1 C~~C~~~~~~---~~~~C~~C~~~~ 22 (190)
T TIGR00201 1 CSLCGRPYQS---VHALCRQCGSWR 22 (190)
T ss_pred CCcccccccc---ccCCchhhCCcc
Confidence 6778876533 235688887654
No 447
>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=35.59 E-value=17 Score=26.14 Aligned_cols=33 Identities=18% Similarity=0.338 Sum_probs=19.6
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCcEEEEEecC
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYRILYKKRTR 43 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R~~ 43 (51)
.|..||..++......-+|..||..+.+++...
T Consensus 151 ~ce~cg~~~~~~~l~~p~~~~~~~~~e~~~~~~ 183 (530)
T TIGR00398 151 HCEVCGRHLEPTELINPRCKICGAKPELRDSEH 183 (530)
T ss_pred hhhhccccCCHHHhcCCccccCCCcceEEecce
Confidence 455566655544334456777888777765543
No 448
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=35.49 E-value=5.9 Score=26.12 Aligned_cols=25 Identities=24% Similarity=0.631 Sum_probs=15.5
Q ss_pred EcCCCCCeeecCCCCeeEcCCCCCcEEE
Q 035461 11 ICGDCGMENTLKPGDVIQCRECGYRILY 38 (51)
Q Consensus 11 ~C~~Cg~~~~~~~~~~irC~~CG~RIly 38 (51)
.|..|++.++...+ .|+.||..+..
T Consensus 26 ~C~~C~~~~~~~~~---~C~~C~~~l~~ 50 (225)
T COG1040 26 LCSGCQADLPLIGN---LCPLCGLPLSS 50 (225)
T ss_pred cChhhhhchhHHHh---hhHhhhChhcc
Confidence 57777777665433 67777665544
No 449
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=35.39 E-value=36 Score=24.03 Aligned_cols=30 Identities=30% Similarity=0.775 Sum_probs=21.8
Q ss_pred CceEEEcCCCCCeeec------C-----CCCeeEcCCCCCc
Q 035461 6 EPVSYICGDCGMENTL------K-----PGDVIQCRECGYR 35 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~------~-----~~~~irC~~CG~R 35 (51)
+.-.++|+.|+..+-. . ...-+-|.+||.|
T Consensus 252 ~td~fkcgkckk~~cty~q~Qtrs~DePmtTfv~C~ecgnr 292 (296)
T KOG1105|consen 252 QTDLFKCGKCKKKNCTYTQLQTRSADEPMTTFVTCNECGNR 292 (296)
T ss_pred cccceeeccccccceeEEeeccCCCCCCcceeeeecccCCc
Confidence 3357999999986654 1 1245899999987
No 450
>PF07150 DUF1390: Protein of unknown function (DUF1390); InterPro: IPR009820 This entry is represented by Paramecium bursaria Chlorella virus 1, A79R; it is a family of uncharacterised viral proteins.
Probab=35.22 E-value=57 Score=22.28 Aligned_cols=32 Identities=25% Similarity=0.567 Sum_probs=22.0
Q ss_pred eEEEcCCCCCeeecCCCCe--eEcCCCCCcEEEEEe
Q 035461 8 VSYICGDCGMENTLKPGDV--IQCRECGYRILYKKR 41 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~--irC~~CG~RIlyK~R 41 (51)
..|.| .||-......+.. -+= .|||+++-..+
T Consensus 6 ~lY~C-~CGYkT~~~gnAsKHkKt-sC~hem~~~~~ 39 (229)
T PF07150_consen 6 TLYTC-GCGYKTTNKGNASKHKKT-SCGHEMKSETK 39 (229)
T ss_pred EEEEe-cCCceecCCccccccCCC-cCCCeeeeeee
Confidence 57999 5999987764321 111 78999877665
No 451
>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=35.12 E-value=31 Score=17.20 Aligned_cols=8 Identities=38% Similarity=0.974 Sum_probs=4.1
Q ss_pred EEcCCCCC
Q 035461 10 YICGDCGM 17 (51)
Q Consensus 10 Y~C~~Cg~ 17 (51)
|.|..|+.
T Consensus 1 ~~C~~C~~ 8 (46)
T cd02249 1 YSCDGCLK 8 (46)
T ss_pred CCCcCCCC
Confidence 34555555
No 452
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=35.05 E-value=23 Score=17.51 Aligned_cols=12 Identities=25% Similarity=0.578 Sum_probs=6.8
Q ss_pred EcCCCCCeeecC
Q 035461 11 ICGDCGMENTLK 22 (51)
Q Consensus 11 ~C~~Cg~~~~~~ 22 (51)
+|.+||++|.-+
T Consensus 5 ~C~eC~~~f~dS 16 (34)
T PF01286_consen 5 KCDECGKPFMDS 16 (34)
T ss_dssp E-TTT--EES-S
T ss_pred hHhHhCCHHHHH
Confidence 699999999765
No 453
>PF10977 DUF2797: Protein of unknown function (DUF2797); InterPro: IPR021246 This family of proteins has no known function.
Probab=34.89 E-value=25 Score=23.79 Aligned_cols=9 Identities=33% Similarity=0.944 Sum_probs=4.8
Q ss_pred EcCCCCCee
Q 035461 11 ICGDCGMEN 19 (51)
Q Consensus 11 ~C~~Cg~~~ 19 (51)
.|.+||+..
T Consensus 13 ~c~~cG~~~ 21 (235)
T PF10977_consen 13 QCLNCGRKT 21 (235)
T ss_pred EEecCCccc
Confidence 455565554
No 454
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=34.86 E-value=20 Score=22.28 Aligned_cols=20 Identities=35% Similarity=0.896 Sum_probs=14.4
Q ss_pred CeeEcCCCCCc--EEEEEecCc
Q 035461 25 DVIQCRECGYR--ILYKKRTRR 44 (51)
Q Consensus 25 ~~irC~~CG~R--IlyK~R~~~ 44 (51)
....||.||++ ++|-.++.+
T Consensus 72 s~~~C~~C~~~eavffQ~~~~r 93 (113)
T KOG2691|consen 72 SDKHCPKCGHREAVFFQAQTRR 93 (113)
T ss_pred ccccCCccCCcceEEEeccccc
Confidence 45789999986 666666554
No 455
>PRK01678 rpmE2 50S ribosomal protein L31 type B; Reviewed
Probab=34.55 E-value=39 Score=19.83 Aligned_cols=20 Identities=20% Similarity=0.298 Sum_probs=16.1
Q ss_pred CCCCceEEEcCCCCCeeecC
Q 035461 3 PQPEPVSYICGDCGMENTLK 22 (51)
Q Consensus 3 ~~~~~~~Y~C~~Cg~~~~~~ 22 (51)
|.-.++.+.|..||..|...
T Consensus 7 P~y~~v~~~~~t~g~~f~~~ 26 (87)
T PRK01678 7 PEYRPVVFHDTSTGFKFLTG 26 (87)
T ss_pred CCCEEEEEEECCCCCEEEEe
Confidence 34467999999999999865
No 456
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=34.26 E-value=20 Score=17.91 Aligned_cols=8 Identities=38% Similarity=0.870 Sum_probs=6.6
Q ss_pred eEcCCCCC
Q 035461 27 IQCRECGY 34 (51)
Q Consensus 27 irC~~CG~ 34 (51)
.-||.||.
T Consensus 4 ~pCP~CGG 11 (37)
T smart00778 4 GPCPNCGG 11 (37)
T ss_pred cCCCCCCC
Confidence 56999996
No 457
>PF15494 SRCR_2: Scavenger receptor cysteine-rich domain
Probab=34.22 E-value=24 Score=20.02 Aligned_cols=11 Identities=45% Similarity=1.099 Sum_probs=8.7
Q ss_pred CeeEcCCCCCc
Q 035461 25 DVIQCRECGYR 35 (51)
Q Consensus 25 ~~irC~~CG~R 35 (51)
-.++|..||.|
T Consensus 87 VsL~C~~CG~r 97 (98)
T PF15494_consen 87 VSLQCSDCGKR 97 (98)
T ss_pred EEEECcccCCc
Confidence 35889999976
No 458
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.96 E-value=15 Score=21.60 Aligned_cols=17 Identities=18% Similarity=0.411 Sum_probs=12.4
Q ss_pred eEcCCCCCcEEEEEecC
Q 035461 27 IQCRECGYRILYKKRTR 43 (51)
Q Consensus 27 irC~~CG~RIlyK~R~~ 43 (51)
--||+||..++-..+-+
T Consensus 42 g~CPnCGGelv~RP~RP 58 (84)
T COG3813 42 GLCPNCGGELVARPIRP 58 (84)
T ss_pred CcCCCCCchhhcCcCCh
Confidence 36999999887655443
No 459
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=33.85 E-value=17 Score=24.06 Aligned_cols=10 Identities=30% Similarity=0.923 Sum_probs=8.3
Q ss_pred CeeEcCCCCC
Q 035461 25 DVIQCRECGY 34 (51)
Q Consensus 25 ~~irC~~CG~ 34 (51)
.-.+||.|||
T Consensus 92 nl~~CP~CGh 101 (176)
T KOG4080|consen 92 NLNTCPACGH 101 (176)
T ss_pred ccccCcccCc
Confidence 3578999998
No 460
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=33.78 E-value=20 Score=19.63 Aligned_cols=12 Identities=25% Similarity=0.495 Sum_probs=9.3
Q ss_pred CeeEcCCCCCcE
Q 035461 25 DVIQCRECGYRI 36 (51)
Q Consensus 25 ~~irC~~CG~RI 36 (51)
+---||.||.|+
T Consensus 38 rYngCPfC~~~~ 49 (55)
T PF14447_consen 38 RYNGCPFCGTPF 49 (55)
T ss_pred hccCCCCCCCcc
Confidence 345699999886
No 461
>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=33.58 E-value=34 Score=17.40 Aligned_cols=8 Identities=25% Similarity=1.094 Sum_probs=4.4
Q ss_pred eEEEcCCC
Q 035461 8 VSYICGDC 15 (51)
Q Consensus 8 ~~Y~C~~C 15 (51)
..|+|.+|
T Consensus 14 ~r~~C~~C 21 (49)
T cd02335 14 IRIKCAEC 21 (49)
T ss_pred cEEECCCC
Confidence 45555555
No 462
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=33.55 E-value=15 Score=19.20 Aligned_cols=12 Identities=33% Similarity=0.670 Sum_probs=8.9
Q ss_pred CCCeeEcCCCCC
Q 035461 23 PGDVIQCRECGY 34 (51)
Q Consensus 23 ~~~~irC~~CG~ 34 (51)
...++.||-||-
T Consensus 6 ~ltG~~CPgCG~ 17 (52)
T PF10825_consen 6 ALTGIPCPGCGM 17 (52)
T ss_pred hhhCCCCCCCcH
Confidence 345688999994
No 463
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=33.55 E-value=4.7 Score=21.25 Aligned_cols=26 Identities=27% Similarity=0.556 Sum_probs=19.5
Q ss_pred EcCCCCCeeecC----CCCeeEcCCCCCcE
Q 035461 11 ICGDCGMENTLK----PGDVIQCRECGYRI 36 (51)
Q Consensus 11 ~C~~Cg~~~~~~----~~~~irC~~CG~RI 36 (51)
+|+-||.++.+- ..|..-|..|-.++
T Consensus 1 ~C~iCg~kigl~~~~k~~DG~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDGYICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCccchHHHHHHh
Confidence 478888887754 34678899998776
No 464
>PF00471 Ribosomal_L33: Ribosomal protein L33; InterPro: IPR001705 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L33 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L33 has been shown to be on the surface of 50S subunit. L33 belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , ], groups: Eubacterial L33. Algal and plant chloroplast L33. Cyanelle L33. L33 is a small protein of 49 to 66 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3PIO_1 3PIP_1 3PYT_3 3MS1_3 3F1F_6 3F1H_6 3MRZ_3 3PYO_3 3D5B_6 3D5D_6 ....
Probab=33.51 E-value=31 Score=18.00 Aligned_cols=34 Identities=24% Similarity=0.495 Sum_probs=23.9
Q ss_pred ceEEEcCCCCCeeecC----CC------CeeEcCCCCCcEEEEE
Q 035461 7 PVSYICGDCGMENTLK----PG------DVIQCRECGYRILYKK 40 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~----~~------~~irC~~CG~RIlyK~ 40 (51)
.+.-.|.+|+..+=.. .+ ----||.|+-..|+++
T Consensus 3 ~i~L~c~~c~~~nY~t~kn~~~~~~rL~lkKycp~~~khtlhkE 46 (48)
T PF00471_consen 3 KIKLVCTECGGRNYTTTKNKKNTPERLELKKYCPRCRKHTLHKE 46 (48)
T ss_dssp CEEEEEEESSSSEEEEEEETTTSSSSSEEEEEETSSSSEEEEEC
T ss_pred EEEEEEcCCCCeeEEEecCCCCCCceeeEeccCCCCCCEecEEE
Confidence 3567888998776542 11 1246999999999986
No 465
>PRK00595 rpmG 50S ribosomal protein L33; Validated
Probab=33.44 E-value=36 Score=18.03 Aligned_cols=35 Identities=6% Similarity=-0.172 Sum_probs=24.5
Q ss_pred CceEEEcCCCCCeeecCC----CC------eeEcCCCCCcEEEEE
Q 035461 6 EPVSYICGDCGMENTLKP----GD------VIQCRECGYRILYKK 40 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~~----~~------~irC~~CG~RIlyK~ 40 (51)
..+.-.|.+|+..+-... +. ---||.|+-.+|+|+
T Consensus 7 ~~i~L~ct~c~~~nY~t~Kn~k~~~~rL~lkKycp~~~khtlhkE 51 (53)
T PRK00595 7 VKIKLESTEGTGRFYTTTKNKRNTPEKLELKKYDPVLRKHVLHKE 51 (53)
T ss_pred eEEEEEecCCCCEEEEEccCCCCCCCceEEECcCCCCCCEEeEEe
Confidence 347789999986554321 11 245999999999986
No 466
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=33.36 E-value=26 Score=18.97 Aligned_cols=11 Identities=36% Similarity=0.917 Sum_probs=8.6
Q ss_pred ceEEEcCCCCC
Q 035461 7 PVSYICGDCGM 17 (51)
Q Consensus 7 ~~~Y~C~~Cg~ 17 (51)
-+.|.|..||.
T Consensus 75 ~l~~~C~~C~~ 85 (85)
T PF04032_consen 75 FLVYTCLNCGH 85 (85)
T ss_dssp EEEEEETTTTE
T ss_pred EEEEEccccCC
Confidence 47888888874
No 467
>smart00746 TRASH metallochaperone-like domain.
Probab=33.34 E-value=22 Score=14.77 Aligned_cols=9 Identities=44% Similarity=1.003 Sum_probs=6.6
Q ss_pred cCCCCCcEE
Q 035461 29 CRECGYRIL 37 (51)
Q Consensus 29 C~~CG~RIl 37 (51)
|+.||..|.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 677887774
No 468
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=33.32 E-value=41 Score=19.34 Aligned_cols=24 Identities=29% Similarity=0.574 Sum_probs=12.0
Q ss_pred EEcCCCCCeeecCCCC--eeEcCCCC
Q 035461 10 YICGDCGMENTLKPGD--VIQCRECG 33 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~--~irC~~CG 33 (51)
|.|.=||..+-....+ --.||.|+
T Consensus 2 ~~CPCCg~~Tl~~~~~~~ydIC~VC~ 27 (78)
T PF14206_consen 2 YPCPCCGYYTLEERGEGTYDICPVCF 27 (78)
T ss_pred ccCCCCCcEEeccCCCcCceECCCCC
Confidence 4555566555433322 34566554
No 469
>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=33.15 E-value=27 Score=18.43 Aligned_cols=22 Identities=27% Similarity=0.637 Sum_probs=13.9
Q ss_pred eEEEcCCCCCeeecCCCCeeEcCCCC
Q 035461 8 VSYICGDCGMENTLKPGDVIQCRECG 33 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG 33 (51)
..-.|..||.... .---|++||
T Consensus 25 ~l~~c~~cg~~~~----~H~vc~~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPKL----PHRVCPSCG 46 (56)
T ss_dssp SEEESSSSSSEES----TTSBCTTTB
T ss_pred ceeeeccCCCEec----ccEeeCCCC
Confidence 4467888884432 225688887
No 470
>PRK09401 reverse gyrase; Reviewed
Probab=32.95 E-value=21 Score=29.09 Aligned_cols=25 Identities=32% Similarity=0.694 Sum_probs=18.8
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461 10 YICGDCGMENTLKPGDVIQCRECGYRIL 37 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG~RIl 37 (51)
-.|..||..|.... -+||.||.+..
T Consensus 679 k~c~~~g~~f~~~~---~~~~~c~~~~~ 703 (1176)
T PRK09401 679 KRCRDCGYQFTDES---DKCPRCGSTNI 703 (1176)
T ss_pred cccccccccccccc---ccccccccccC
Confidence 35999999887653 29999997753
No 471
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=32.44 E-value=35 Score=28.38 Aligned_cols=24 Identities=29% Similarity=0.935 Sum_probs=20.4
Q ss_pred cCCCCCeeecCCCCeeEcCCCCCc
Q 035461 12 CGDCGMENTLKPGDVIQCRECGYR 35 (51)
Q Consensus 12 C~~Cg~~~~~~~~~~irC~~CG~R 35 (51)
|.+||.-.-...+.-++|-.||..
T Consensus 1193 c~~cg~~~~vrngtc~~c~~cg~t 1216 (1220)
T PRK07562 1193 CSECGNFTLVRNGTCLKCDTCGST 1216 (1220)
T ss_pred CCCcCCeEEEeCCeeeeccccCCC
Confidence 999998887788888999999963
No 472
>PF00935 Ribosomal_L44: Ribosomal protein L44; InterPro: IPR000552 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of mammalian [], Trypanosoma brucei, Caenorhabditis elegans and fungal L44, and Haloarcula marismortui LA [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_r 1S1I_Z 3O5H_f 3O58_f 3IZR_r 1M1K_4 3CCQ_3 3CCL_3 3CME_3 1K73_4 ....
Probab=32.13 E-value=32 Score=19.82 Aligned_cols=11 Identities=36% Similarity=1.072 Sum_probs=5.3
Q ss_pred eEcCCCCCcEE
Q 035461 27 IQCRECGYRIL 37 (51)
Q Consensus 27 irC~~CG~RIl 37 (51)
++|.+||+..+
T Consensus 54 l~C~~C~~~~~ 64 (77)
T PF00935_consen 54 LECTECGKAHM 64 (77)
T ss_dssp EEETTTS-EEE
T ss_pred EEeCCCCcccc
Confidence 45555555444
No 473
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=32.10 E-value=33 Score=21.02 Aligned_cols=15 Identities=33% Similarity=0.638 Sum_probs=12.6
Q ss_pred eEEEcCCCCCeeecC
Q 035461 8 VSYICGDCGMENTLK 22 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~ 22 (51)
--.+|.+||+.+++.
T Consensus 92 ~HliC~~CG~v~e~~ 106 (145)
T COG0735 92 HHLICLDCGKVIEFE 106 (145)
T ss_pred cEEEecCCCCEEEec
Confidence 356999999999986
No 474
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=31.96 E-value=33 Score=20.67 Aligned_cols=12 Identities=33% Similarity=0.805 Sum_probs=7.9
Q ss_pred eEcCCCCCcEEE
Q 035461 27 IQCRECGYRILY 38 (51)
Q Consensus 27 irC~~CG~RIly 38 (51)
++|.+||+.+.-
T Consensus 69 ~~Ct~Cgkah~~ 80 (94)
T COG1631 69 LRCTECGKAHQR 80 (94)
T ss_pred EEehhhcccccc
Confidence 567777766654
No 475
>KOG1859 consensus Leucine-rich repeat proteins [General function prediction only]
Probab=31.90 E-value=24 Score=28.86 Aligned_cols=26 Identities=19% Similarity=0.581 Sum_probs=19.1
Q ss_pred eEEEcCCCCCeeecCCC------CeeEcCCCC
Q 035461 8 VSYICGDCGMENTLKPG------DVIQCRECG 33 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~------~~irC~~CG 33 (51)
..|.|..||..|.++.- ...|||.|-
T Consensus 672 ~i~~C~~cgt~F~~eqp~kg~~~kelr~pd~~ 703 (1096)
T KOG1859|consen 672 SIYRCVNCGTQFLIEQPEKGSKIKELRCPDSR 703 (1096)
T ss_pred ceeeeccccccccccCcccccchhhhcCcchh
Confidence 47999999999987621 346777663
No 476
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=31.71 E-value=29 Score=18.95 Aligned_cols=20 Identities=30% Similarity=0.752 Sum_probs=9.8
Q ss_pred EEcCCCCCeeecCCCCeeEcCCCC
Q 035461 10 YICGDCGMENTLKPGDVIQCRECG 33 (51)
Q Consensus 10 Y~C~~Cg~~~~~~~~~~irC~~CG 33 (51)
=.|.+||.-. ..---|++||
T Consensus 28 ~~c~~cG~~~----l~Hrvc~~cg 47 (57)
T COG0333 28 SVCPNCGEYK----LPHRVCLKCG 47 (57)
T ss_pred eeccCCCCcc----cCceEcCCCC
Confidence 4555555432 1234566666
No 477
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=31.66 E-value=32 Score=22.26 Aligned_cols=24 Identities=21% Similarity=0.825 Sum_probs=13.5
Q ss_pred EEcCCCCCeeec---CCCCeeEcCCCC
Q 035461 10 YICGDCGMENTL---KPGDVIQCRECG 33 (51)
Q Consensus 10 Y~C~~Cg~~~~~---~~~~~irC~~CG 33 (51)
|+|.-|+..--| .....++|+.|+
T Consensus 153 fiCe~C~~~~~IfPF~~~~~~~C~~C~ 179 (202)
T PF13901_consen 153 FICEICNSDDIIFPFQIDTTVRCPKCK 179 (202)
T ss_pred CCCccCCCCCCCCCCCCCCeeeCCcCc
Confidence 567777654222 233567777776
No 478
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=31.56 E-value=36 Score=21.33 Aligned_cols=14 Identities=29% Similarity=0.705 Sum_probs=12.2
Q ss_pred EEEcCCCCCeeecC
Q 035461 9 SYICGDCGMENTLK 22 (51)
Q Consensus 9 ~Y~C~~Cg~~~~~~ 22 (51)
-.+|.+||+.+++.
T Consensus 100 H~iC~~CGki~~i~ 113 (169)
T PRK11639 100 MFICDRCGAVKEEC 113 (169)
T ss_pred eEEeCCCCCEEEec
Confidence 47999999999975
No 479
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=31.26 E-value=43 Score=19.29 Aligned_cols=15 Identities=27% Similarity=0.771 Sum_probs=12.0
Q ss_pred ceEEEcCCCCCeeec
Q 035461 7 PVSYICGDCGMENTL 21 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~ 21 (51)
.+.|.|-.||..+..
T Consensus 2 ai~Y~CRHCg~~IG~ 16 (76)
T PF10955_consen 2 AIHYYCRHCGTKIGT 16 (76)
T ss_pred ceEEEecCCCCEEEE
Confidence 468999999988763
No 480
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=31.18 E-value=81 Score=16.69 Aligned_cols=24 Identities=17% Similarity=0.317 Sum_probs=12.0
Q ss_pred EEcCCCCCeeecC-------CCCeeEcCCCC
Q 035461 10 YICGDCGMENTLK-------PGDVIQCRECG 33 (51)
Q Consensus 10 Y~C~~Cg~~~~~~-------~~~~irC~~CG 33 (51)
++...||..|+-+ .+..++||.-|
T Consensus 25 V~s~~C~H~fek~aI~~~i~~~~~~~CPv~G 55 (57)
T PF11789_consen 25 VKSKKCGHTFEKEAILQYIQRNGSKRCPVAG 55 (57)
T ss_dssp EEESSS--EEEHHHHHHHCTTTS-EE-SCCC
T ss_pred cCcCCCCCeecHHHHHHHHHhcCCCCCCCCC
Confidence 3445777777743 35677887744
No 481
>PRK00807 50S ribosomal protein L24e; Validated
Probab=30.94 E-value=26 Score=18.43 Aligned_cols=10 Identities=40% Similarity=0.833 Sum_probs=7.0
Q ss_pred EcCCCCCcEE
Q 035461 28 QCRECGYRIL 37 (51)
Q Consensus 28 rC~~CG~RIl 37 (51)
.|-+||+.|-
T Consensus 3 ~C~fcG~~I~ 12 (52)
T PRK00807 3 TCSFCGKEIE 12 (52)
T ss_pred ccCCCCCeEc
Confidence 4777877775
No 482
>TIGR01023 rpmG_bact ribosomal protein L33, bacterial type. This model describes bacterial ribosomal protein L33 and its chloroplast and mitochondrial equivalents.
Probab=30.89 E-value=42 Score=17.91 Aligned_cols=34 Identities=21% Similarity=0.402 Sum_probs=24.1
Q ss_pred ceEEEcCCCCCeeecCC----CC------eeEcCCCCCcEEEEE
Q 035461 7 PVSYICGDCGMENTLKP----GD------VIQCRECGYRILYKK 40 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~----~~------~irC~~CG~RIlyK~ 40 (51)
.+.-.|.+|+..+-... +. ---||.|+..+|+|+
T Consensus 9 ~i~L~ct~c~~~nY~t~Kn~~~~~~kL~lkKycp~~~khtlhkE 52 (54)
T TIGR01023 9 LIRLVCTACTGINYTTTKNRRNKPEKLELRKYCPVCRKHVLHKE 52 (54)
T ss_pred EEEEEecCCCCCCEEEcCCCCCCCCceEEECcCCCCCCeEeEEe
Confidence 47889999976654321 11 235999999999986
No 483
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=30.76 E-value=25 Score=22.54 Aligned_cols=25 Identities=28% Similarity=0.634 Sum_probs=18.0
Q ss_pred EEEcCCCCCeee---cC-CCCeeEcCCCC
Q 035461 9 SYICGDCGMENT---LK-PGDVIQCRECG 33 (51)
Q Consensus 9 ~Y~C~~Cg~~~~---~~-~~~~irC~~CG 33 (51)
.-.|+.||.... .. ..+++.|..|+
T Consensus 149 l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 149 LDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred hhhHhcCCCCCCceEEecccCCccccccc
Confidence 346999998754 22 34779999996
No 484
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=30.63 E-value=47 Score=23.12 Aligned_cols=22 Identities=23% Similarity=0.529 Sum_probs=14.2
Q ss_pred EcCCCCCeeecC---CCCeeEcCCC
Q 035461 11 ICGDCGMENTLK---PGDVIQCREC 32 (51)
Q Consensus 11 ~C~~Cg~~~~~~---~~~~irC~~C 32 (51)
-|-.||..++-. ....--||.|
T Consensus 247 pC~~CGt~I~k~~~~gR~t~~CP~C 271 (273)
T COG0266 247 PCRRCGTPIEKIKLGGRSTFYCPVC 271 (273)
T ss_pred CCCccCCEeEEEEEcCCcCEeCCCC
Confidence 367777776643 3466777777
No 485
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=30.58 E-value=50 Score=20.44 Aligned_cols=16 Identities=25% Similarity=0.723 Sum_probs=14.1
Q ss_pred eEEEcCCCCCeeecCC
Q 035461 8 VSYICGDCGMENTLKP 23 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~ 23 (51)
-+|.|-.||.-++.+.
T Consensus 73 rEyyCP~Cgt~levE~ 88 (112)
T PF08882_consen 73 REYYCPGCGTQLEVEA 88 (112)
T ss_pred EEEECCCCcceeEEcc
Confidence 6899999999998874
No 486
>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=30.54 E-value=30 Score=16.71 Aligned_cols=16 Identities=31% Similarity=0.702 Sum_probs=8.8
Q ss_pred CCeeEcCCCCCcEEEE
Q 035461 24 GDVIQCRECGYRILYK 39 (51)
Q Consensus 24 ~~~irC~~CG~RIlyK 39 (51)
...++|.+|+..+-+.
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 4668899998776554
No 487
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=30.54 E-value=40 Score=23.81 Aligned_cols=30 Identities=20% Similarity=0.423 Sum_probs=21.0
Q ss_pred eEEEcCCCCCeeecC--CCCeeEcCCCCCcEE
Q 035461 8 VSYICGDCGMENTLK--PGDVIQCRECGYRIL 37 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~RIl 37 (51)
-+|.|..|+..|.-- .+.+--|=.||+.++
T Consensus 154 aef~C~~C~h~F~G~~qm~v~sPCy~C~~~v~ 185 (278)
T PF15135_consen 154 AEFHCPKCRHNFRGFAQMGVPSPCYGCGNPVY 185 (278)
T ss_pred eeeecccccccchhhhhcCCCCCccCCCCccC
Confidence 678888888888743 345556778887654
No 488
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=30.50 E-value=45 Score=17.59 Aligned_cols=14 Identities=21% Similarity=0.396 Sum_probs=9.4
Q ss_pred CCCeeEcCCCCCcE
Q 035461 23 PGDVIQCRECGYRI 36 (51)
Q Consensus 23 ~~~~irC~~CG~RI 36 (51)
....+||-||+..+
T Consensus 32 ~~~~~rC~YCe~~~ 45 (52)
T PF02748_consen 32 EPIKLRCHYCERII 45 (52)
T ss_dssp TTCEEEETTT--EE
T ss_pred CCCEEEeeCCCCEe
Confidence 45779999998765
No 489
>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=30.49 E-value=41 Score=19.36 Aligned_cols=15 Identities=20% Similarity=0.598 Sum_probs=7.8
Q ss_pred eEEEcCCCCCeeecC
Q 035461 8 VSYICGDCGMENTLK 22 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~ 22 (51)
..|.|..||....+-
T Consensus 64 s~~~Cp~Cg~~~~iF 78 (81)
T PF10609_consen 64 SYFVCPHCGERIYIF 78 (81)
T ss_dssp -EEE-TTT--EEETT
T ss_pred CccCCCCCCCeecCC
Confidence 457888888877653
No 490
>PF01197 Ribosomal_L31: Ribosomal protein L31; InterPro: IPR002150 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L31 is one of the proteins from the large ribosomal subunit. L31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3D5D_4 3PYO_1 3D5B_4 3PYV_1 3PYT_1 3MRZ_1 3MS1_1 3PYR_1 3F1F_4 3F1H_4 ....
Probab=30.46 E-value=39 Score=18.66 Aligned_cols=19 Identities=21% Similarity=0.447 Sum_probs=15.0
Q ss_pred CCceEEEcCCCCCeeecCC
Q 035461 5 PEPVSYICGDCGMENTLKP 23 (51)
Q Consensus 5 ~~~~~Y~C~~Cg~~~~~~~ 23 (51)
-.++.+.|..||.++...+
T Consensus 9 y~~v~v~c~s~g~~~~~~S 27 (69)
T PF01197_consen 9 YREVKVTCSSCGNTFETRS 27 (69)
T ss_dssp HCEEEEEES-SSSCECECS
T ss_pred CEEEEEEEcCCCCEEEEEE
Confidence 3568999999999998874
No 491
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=30.44 E-value=29 Score=22.44 Aligned_cols=26 Identities=23% Similarity=0.415 Sum_probs=11.5
Q ss_pred eEEEcCCCCCeeecCCCC---eeEcCCCC
Q 035461 8 VSYICGDCGMENTLKPGD---VIQCRECG 33 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~~~~---~irC~~CG 33 (51)
..=.|..||..+-....+ ...||.|.
T Consensus 133 ~l~~C~~C~~~fv~~~~~~~~~~~Cp~C~ 161 (175)
T PF05280_consen 133 QLAPCRRCGGHFVTHAHDPRHSFVCPFCQ 161 (175)
T ss_dssp EEEE-TTT--EEEEESS--SS----TT--
T ss_pred cccCCCCCCCCeECcCCCCCcCcCCCCCC
Confidence 456799999988765443 58888887
No 492
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=30.41 E-value=60 Score=19.81 Aligned_cols=29 Identities=38% Similarity=0.717 Sum_probs=18.4
Q ss_pred EEcCCCCCee--------ecCCC-CeeEcCCCCCcEEE
Q 035461 10 YICGDCGMEN--------TLKPG-DVIQCRECGYRILY 38 (51)
Q Consensus 10 Y~C~~Cg~~~--------~~~~~-~~irC~~CG~RIly 38 (51)
-.|-.|.... .+..+ -.+.|.+||+-.-|
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~ 94 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRY 94 (105)
T ss_pred HhccccCcccccCcceEEEEcCCeEEEEecCCCcEEEe
Confidence 3588886642 23333 45899999975544
No 493
>PHA00080 DksA-like zinc finger domain containing protein
Probab=30.36 E-value=12 Score=20.89 Aligned_cols=26 Identities=19% Similarity=0.424 Sum_probs=17.3
Q ss_pred eEEEcCCCCCeeecC---CC-CeeEcCCCC
Q 035461 8 VSYICGDCGMENTLK---PG-DVIQCRECG 33 (51)
Q Consensus 8 ~~Y~C~~Cg~~~~~~---~~-~~irC~~CG 33 (51)
..-.|.+||.++... .. ...+|..|-
T Consensus 30 ~~~~C~~Cg~~Ip~~Rl~a~P~~~~Cv~Cq 59 (72)
T PHA00080 30 SATHCEECGDPIPEARREAVPGCRTCVSCQ 59 (72)
T ss_pred CCCEecCCCCcCcHHHHHhCCCccCcHHHH
Confidence 344799999998764 22 456677773
No 494
>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=30.35 E-value=50 Score=23.75 Aligned_cols=29 Identities=28% Similarity=0.710 Sum_probs=19.8
Q ss_pred ceEEEcCCCCCeeecCC--C---CeeEcCCCCCc
Q 035461 7 PVSYICGDCGMENTLKP--G---DVIQCRECGYR 35 (51)
Q Consensus 7 ~~~Y~C~~Cg~~~~~~~--~---~~irC~~CG~R 35 (51)
...|+|..||.+..... . +.-.||+||..
T Consensus 318 r~~~rc~~c~~~~~~~~~~~~~~~~~~~~~~~~~ 351 (403)
T TIGR03676 318 RVTFKCPNCGYEEEKTVKPEEGDKSEACPKCGSE 351 (403)
T ss_pred eEEEEcCCCCcceeeecccccccccccCcccCcc
Confidence 36799999998765321 1 12458999976
No 495
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=30.30 E-value=21 Score=21.64 Aligned_cols=10 Identities=30% Similarity=0.913 Sum_probs=5.7
Q ss_pred EEEcCCCCCe
Q 035461 9 SYICGDCGME 18 (51)
Q Consensus 9 ~Y~C~~Cg~~ 18 (51)
+++|.+||..
T Consensus 88 ~~rC~nCG~~ 97 (98)
T PF10164_consen 88 ERRCSNCGAT 97 (98)
T ss_pred ccccCCCCcc
Confidence 3556666654
No 496
>KOG0477 consensus DNA replication licensing factor, MCM2 component [Replication, recombination and repair]
Probab=29.96 E-value=15 Score=29.33 Aligned_cols=32 Identities=28% Similarity=0.446 Sum_probs=22.0
Q ss_pred CCCceEEEcCCCCCeeecC---CC---CeeEcCCCCCc
Q 035461 4 QPEPVSYICGDCGMENTLK---PG---DVIQCRECGYR 35 (51)
Q Consensus 4 ~~~~~~Y~C~~Cg~~~~~~---~~---~~irC~~CG~R 35 (51)
+...+.|.|..||..+..- .+ -+--||+|-++
T Consensus 287 ql~~vky~C~KC~~vlgPF~qs~n~evkp~~C~~cqSk 324 (854)
T KOG0477|consen 287 QLSVVKYDCLKCGFVLGPFVQSSNSEVKPGSCPECQSK 324 (854)
T ss_pred hhHHHhhhHHhhCCccCceeeccCceeCCCCCccccCC
Confidence 4456899999999765542 33 33569999765
No 497
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=29.77 E-value=45 Score=24.98 Aligned_cols=37 Identities=22% Similarity=0.505 Sum_probs=25.8
Q ss_pred CceEEEcCCCCCeeecC---CCCeeEcCCCCCcEEEEEec
Q 035461 6 EPVSYICGDCGMENTLK---PGDVIQCRECGYRILYKKRT 42 (51)
Q Consensus 6 ~~~~Y~C~~Cg~~~~~~---~~~~irC~~CG~RIlyK~R~ 42 (51)
+-..+.|.+||..-+.+ ....+.||.|...-|-|.++
T Consensus 224 ED~l~~C~~C~~s~n~e~~~~sk~~~Cp~C~~~~L~~~~~ 263 (457)
T KOG2324|consen 224 EDTLMSCPSCGYSKNSEDLDLSKIASCPKCNEGRLTKTKS 263 (457)
T ss_pred ccceeecCcCCccCchhhhcCCccccCCcccCCCcccccc
Confidence 45889999997655444 23448999999865555543
No 498
>PF13575 DUF4135: Domain of unknown function (DUF4135)
Probab=29.56 E-value=30 Score=23.92 Aligned_cols=14 Identities=36% Similarity=0.655 Sum_probs=10.9
Q ss_pred CCCCcEEEEEecCc
Q 035461 31 ECGYRILYKKRTRR 44 (51)
Q Consensus 31 ~CG~RIlyK~R~~~ 44 (51)
.-|.+|+||+|+-.
T Consensus 68 ~~g~kivYKPRsl~ 81 (370)
T PF13575_consen 68 SSGKKIVYKPRSLS 81 (370)
T ss_pred CCCCEEEEeCcccH
Confidence 35679999999753
No 499
>PRK14287 chaperone protein DnaJ; Provisional
Probab=29.45 E-value=78 Score=22.25 Aligned_cols=21 Identities=29% Similarity=0.531 Sum_probs=13.1
Q ss_pred EcCCCCCcEEEEEecCceEEE
Q 035461 28 QCRECGYRILYKKRTRRIVQY 48 (51)
Q Consensus 28 rC~~CG~RIlyK~R~~~~~~~ 48 (51)
.|+.|+.+...+......+.+
T Consensus 197 ~C~~C~G~g~v~~~~~l~V~I 217 (371)
T PRK14287 197 KCATCGGKGKVRKRKKINVKV 217 (371)
T ss_pred cCCCCCCeeEEeeeEEEEEEE
Confidence 488888877776544333443
No 500
>PRK05767 rpl44e 50S ribosomal protein L44e; Validated
Probab=29.39 E-value=40 Score=20.10 Aligned_cols=12 Identities=33% Similarity=0.717 Sum_probs=7.1
Q ss_pred eEcCCCCCcEEE
Q 035461 27 IQCRECGYRILY 38 (51)
Q Consensus 27 irC~~CG~RIly 38 (51)
++|.+||+..+.
T Consensus 68 ~~C~~C~~~~~~ 79 (92)
T PRK05767 68 YRCTECGKAHTR 79 (92)
T ss_pred EEecccChhhcc
Confidence 566666655443
Done!