Query 035291
Match_columns 68
No_of_seqs 60 out of 62
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 10:43:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035291.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035291hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10601 zf-LITAF-like: LITAF- 97.1 0.00033 7.1E-09 41.9 2.1 52 16-68 2-72 (73)
2 smart00714 LITAF Possible memb 95.9 0.0042 9.2E-08 36.6 1.4 48 19-67 1-65 (67)
3 PRK00464 nrdR transcriptional 93.4 0.076 1.6E-06 36.7 2.7 40 23-67 2-41 (154)
4 PF13240 zinc_ribbon_2: zinc-r 93.2 0.03 6.5E-07 27.8 0.3 9 24-32 2-10 (23)
5 COG3813 Uncharacterized protei 92.7 0.034 7.3E-07 35.7 0.1 19 20-38 40-58 (84)
6 PF14690 zf-ISL3: zinc-finger 92.4 0.23 5E-06 26.7 3.2 39 21-60 2-47 (47)
7 smart00661 RPOL9 RNA polymeras 92.2 0.094 2E-06 28.8 1.4 29 23-64 2-30 (52)
8 PF13248 zf-ribbon_3: zinc-rib 92.2 0.05 1.1E-06 27.3 0.3 9 23-31 4-12 (26)
9 PF13005 zf-IS66: zinc-finger 91.8 0.38 8.2E-06 26.1 3.6 41 21-61 2-47 (47)
10 PF06906 DUF1272: Protein of u 91.3 0.065 1.4E-06 32.4 0.1 14 21-34 41-54 (57)
11 TIGR03830 CxxCG_CxxCG_HTH puta 91.0 0.57 1.2E-05 29.3 4.3 41 24-65 1-42 (127)
12 TIGR03831 YgiT_finger YgiT-typ 89.4 0.75 1.6E-05 24.2 3.4 42 24-65 1-43 (46)
13 PF04216 FdhE: Protein involve 88.9 0.2 4.4E-06 36.4 1.1 43 20-62 171-219 (290)
14 PF02150 RNA_POL_M_15KD: RNA p 88.9 0.52 1.1E-05 25.2 2.5 28 23-64 3-30 (35)
15 PF06827 zf-FPG_IleRS: Zinc fi 87.7 0.7 1.5E-05 23.3 2.4 14 23-36 3-16 (30)
16 PF12760 Zn_Tnp_IS1595: Transp 86.6 0.73 1.6E-05 25.4 2.2 28 22-63 19-46 (46)
17 PRK00420 hypothetical protein; 86.6 0.35 7.6E-06 32.2 1.1 34 16-65 18-51 (112)
18 PF05129 Elf1: Transcription e 83.9 1.8 3.8E-05 27.0 3.3 37 19-65 20-57 (81)
19 PRK00398 rpoP DNA-directed RNA 83.2 1.3 2.8E-05 24.2 2.3 11 21-31 21-31 (46)
20 COG1998 RPS31 Ribosomal protei 83.1 0.62 1.3E-05 27.6 1.0 34 12-63 13-46 (51)
21 PF07282 OrfB_Zn_ribbon: Putat 81.2 1.3 2.7E-05 25.6 1.8 29 20-63 27-55 (69)
22 PF07754 DUF1610: Domain of un 81.0 0.9 2E-05 23.0 1.0 15 14-28 8-23 (24)
23 TIGR00373 conserved hypothetic 80.8 0.36 7.8E-06 32.9 -0.7 35 19-67 107-141 (158)
24 PF11672 DUF3268: Protein of u 80.6 0.94 2E-05 29.7 1.2 39 21-64 2-41 (102)
25 TIGR03655 anti_R_Lar restricti 80.3 1.3 2.9E-05 25.0 1.6 10 23-32 3-12 (53)
26 smart00834 CxxC_CXXC_SSSS Puta 78.4 2 4.3E-05 22.2 1.9 12 19-30 24-35 (41)
27 PRK06266 transcription initiat 78.2 0.44 9.5E-06 33.2 -1.0 35 19-67 115-149 (178)
28 TIGR00622 ssl1 transcription f 77.1 1.1 2.3E-05 30.0 0.7 8 24-31 4-11 (112)
29 PRK00415 rps27e 30S ribosomal 76.8 2.9 6.3E-05 25.2 2.5 30 22-65 12-41 (59)
30 PF08271 TF_Zn_Ribbon: TFIIB z 76.6 2.1 4.5E-05 23.2 1.7 29 23-65 2-30 (43)
31 PRK14892 putative transcriptio 76.6 2.5 5.5E-05 27.5 2.3 33 19-63 19-51 (99)
32 TIGR00244 transcriptional regu 76.5 2 4.4E-05 30.0 2.0 40 23-67 2-41 (147)
33 PF14803 Nudix_N_2: Nudix N-te 76.4 1.8 4E-05 23.2 1.4 29 23-62 2-30 (34)
34 PF14255 Cys_rich_CPXG: Cystei 75.9 2.2 4.7E-05 24.9 1.7 15 23-38 2-16 (52)
35 PF12773 DZR: Double zinc ribb 75.6 0.52 1.1E-05 25.8 -1.0 14 51-64 26-39 (50)
36 COG1933 Archaeal DNA polymeras 75.5 0.43 9.3E-06 36.0 -1.7 20 12-31 145-164 (253)
37 PRK00432 30S ribosomal protein 75.2 1.8 3.9E-05 24.8 1.2 38 6-63 9-46 (50)
38 smart00659 RPOLCX RNA polymera 75.1 2.7 5.8E-05 23.5 1.9 14 18-31 16-29 (44)
39 PRK13945 formamidopyrimidine-D 73.7 3.8 8.2E-05 30.0 2.9 23 13-37 248-270 (282)
40 PF03604 DNA_RNApol_7kD: DNA d 73.6 2 4.4E-05 22.8 1.1 13 19-31 15-27 (32)
41 PF14369 zf-RING_3: zinc-finge 73.0 2.6 5.7E-05 22.5 1.4 27 5-31 5-31 (35)
42 COG2051 RPS27A Ribosomal prote 72.9 5.6 0.00012 24.7 3.1 33 20-66 18-50 (67)
43 PRK10445 endonuclease VIII; Pr 72.4 3.7 8E-05 29.9 2.5 23 13-37 229-251 (263)
44 COG1645 Uncharacterized Zn-fin 72.1 3.6 7.9E-05 28.2 2.3 29 20-65 27-55 (131)
45 TIGR01562 FdhE formate dehydro 72.0 1.4 3.1E-05 33.4 0.3 44 19-62 182-232 (305)
46 COG4391 Uncharacterized protei 72.0 3.1 6.7E-05 25.5 1.8 46 12-66 15-60 (62)
47 PF09723 Zn-ribbon_8: Zinc rib 71.9 5.1 0.00011 21.7 2.5 14 17-30 22-35 (42)
48 PRK14810 formamidopyrimidine-D 71.4 3.7 8.1E-05 30.0 2.4 23 13-37 238-260 (272)
49 cd00729 rubredoxin_SM Rubredox 70.1 5.3 0.00011 21.0 2.2 27 2-31 2-28 (34)
50 PF09297 zf-NADH-PPase: NADH p 70.0 3.3 7.1E-05 21.2 1.4 10 22-31 4-13 (32)
51 PRK03564 formate dehydrogenase 69.6 2.4 5.1E-05 32.4 1.1 43 20-62 186-234 (309)
52 PF09855 DUF2082: Nucleic-acid 68.8 13 0.00028 22.4 4.0 41 23-63 2-45 (64)
53 COG0675 Transposase and inacti 68.6 3.7 8.1E-05 28.2 1.8 22 22-63 310-331 (364)
54 PF14354 Lar_restr_allev: Rest 68.3 6.7 0.00015 22.0 2.6 33 23-62 5-37 (61)
55 PF10263 SprT-like: SprT-like 68.0 5 0.00011 25.9 2.2 36 19-67 121-156 (157)
56 TIGR00100 hypA hydrogenase nic 66.8 4.3 9.4E-05 26.3 1.7 20 12-31 61-80 (115)
57 TIGR02098 MJ0042_CXXC MJ0042 f 66.6 5 0.00011 20.8 1.7 14 20-33 24-37 (38)
58 COG1594 RPB9 DNA-directed RNA 66.2 5.5 0.00012 26.1 2.1 9 23-31 4-12 (113)
59 COG1592 Rubrerythrin [Energy p 66.2 3.5 7.6E-05 29.1 1.3 25 3-31 135-159 (166)
60 PRK03564 formate dehydrogenase 65.9 6.7 0.00015 30.0 2.9 40 21-67 226-265 (309)
61 TIGR01384 TFS_arch transcripti 65.6 3.9 8.4E-05 25.4 1.3 8 24-31 3-10 (104)
62 smart00531 TFIIE Transcription 64.9 3.6 7.8E-05 27.4 1.1 14 22-35 124-137 (147)
63 PRK12775 putative trifunctiona 64.1 2.2 4.7E-05 36.5 -0.1 21 15-35 832-852 (1006)
64 PRK09710 lar restriction allev 63.9 10 0.00023 23.2 2.9 31 21-63 6-36 (64)
65 PF01927 Mut7-C: Mut7-C RNAse 63.9 5.9 0.00013 26.3 2.0 45 18-64 88-134 (147)
66 COG5349 Uncharacterized protei 63.2 2.7 6E-05 28.8 0.3 14 18-31 18-31 (126)
67 smart00709 Zpr1 Duplicated dom 63.0 12 0.00026 25.8 3.5 35 23-64 2-39 (160)
68 PF13453 zf-TFIIB: Transcripti 62.9 9.5 0.00021 20.3 2.4 9 23-31 1-9 (41)
69 PF12677 DUF3797: Domain of un 62.7 3.5 7.5E-05 24.3 0.6 11 21-31 13-23 (49)
70 PRK09401 reverse gyrase; Revie 62.5 3 6.5E-05 36.6 0.5 12 21-32 7-18 (1176)
71 TIGR00577 fpg formamidopyrimid 62.1 7.8 0.00017 28.2 2.5 23 13-37 239-261 (272)
72 PRK01103 formamidopyrimidine/5 61.5 7.7 0.00017 28.2 2.4 22 14-37 240-261 (274)
73 PF07038 DUF1324: Protein of u 61.3 7 0.00015 23.5 1.8 14 39-52 8-21 (59)
74 COG3464 Transposase and inacti 61.0 9 0.00019 29.7 2.8 41 22-64 39-87 (402)
75 PRK09521 exosome complex RNA-b 61.0 8.6 0.00019 26.4 2.5 28 20-63 148-175 (189)
76 COG1110 Reverse gyrase [DNA re 60.7 3.7 7.9E-05 36.7 0.7 18 21-38 8-25 (1187)
77 smart00440 ZnF_C2C2 C2C2 Zinc 60.5 9 0.00019 20.7 2.0 15 23-38 2-16 (40)
78 PF01599 Ribosomal_S27: Riboso 60.1 16 0.00036 21.0 3.2 23 6-31 6-30 (47)
79 TIGR00310 ZPR1_znf ZPR1 zinc f 60.1 18 0.00039 25.7 4.0 38 23-64 2-40 (192)
80 PHA00626 hypothetical protein 59.9 7.4 0.00016 23.7 1.7 32 23-64 2-33 (59)
81 PRK12380 hydrogenase nickel in 59.9 6.7 0.00015 25.4 1.7 20 12-31 61-80 (113)
82 PF14319 Zn_Tnp_IS91: Transpos 59.8 5.7 0.00012 25.7 1.3 30 20-64 41-70 (111)
83 PRK09678 DNA-binding transcrip 59.3 13 0.00029 22.9 2.8 38 23-67 3-42 (72)
84 PF08209 Sgf11: Sgf11 (transcr 59.0 4.7 0.0001 21.6 0.7 13 21-33 4-16 (33)
85 PF13894 zf-C2H2_4: C2H2-type 58.4 5.4 0.00012 17.6 0.8 12 55-66 1-12 (24)
86 PRK14890 putative Zn-ribbon RN 58.4 4.3 9.3E-05 24.6 0.5 33 19-61 23-55 (59)
87 PRK14811 formamidopyrimidine-D 58.3 9.2 0.0002 27.9 2.3 22 14-37 230-251 (269)
88 PF15616 TerY-C: TerY-C metal 58.1 13 0.00027 25.4 2.8 38 22-65 78-116 (131)
89 PF01096 TFIIS_C: Transcriptio 58.0 7.8 0.00017 20.8 1.5 15 23-38 2-16 (39)
90 TIGR00595 priA primosomal prot 57.6 8.4 0.00018 30.4 2.2 28 22-64 223-250 (505)
91 TIGR01054 rgy reverse gyrase. 57.2 4.2 9.2E-05 35.6 0.5 11 21-31 7-17 (1171)
92 PRK03681 hypA hydrogenase nick 57.1 10 0.00022 24.6 2.1 18 12-29 61-78 (114)
93 COG1405 SUA7 Transcription ini 57.1 9.2 0.0002 28.7 2.2 30 22-65 2-31 (285)
94 PF08792 A2L_zn_ribbon: A2L zi 56.8 14 0.00031 19.5 2.4 9 23-31 5-13 (33)
95 PF08273 Prim_Zn_Ribbon: Zinc- 56.3 5.4 0.00012 22.1 0.7 31 21-61 3-33 (40)
96 PF04606 Ogr_Delta: Ogr/Delta- 56.1 8.3 0.00018 21.3 1.4 11 23-33 1-11 (47)
97 COG1656 Uncharacterized conser 55.7 5.4 0.00012 28.3 0.8 44 19-64 95-140 (165)
98 smart00778 Prim_Zn_Ribbon Zinc 55.5 5.5 0.00012 21.8 0.6 11 21-31 3-13 (37)
99 PF14353 CpXC: CpXC protein 55.4 12 0.00025 23.9 2.2 36 12-47 29-70 (128)
100 COG1996 RPC10 DNA-directed RNA 54.9 6.6 0.00014 22.9 0.9 14 18-31 21-34 (49)
101 PRK14873 primosome assembly pr 54.5 11 0.00024 31.2 2.4 11 21-31 392-402 (665)
102 PF06044 DRP: Dam-replacing fa 53.8 12 0.00025 28.4 2.3 33 22-66 32-65 (254)
103 PRK03824 hypA hydrogenase nick 53.5 12 0.00025 25.0 2.0 48 14-63 63-116 (135)
104 PF00412 LIM: LIM domain; Int 53.4 4.8 0.0001 21.8 0.2 36 24-65 1-37 (58)
105 PRK05580 primosome assembly pr 51.9 12 0.00025 30.7 2.2 27 22-63 391-417 (679)
106 PRK04023 DNA polymerase II lar 51.9 6.6 0.00014 35.0 0.8 40 20-67 637-676 (1121)
107 KOG2906 RNA polymerase III sub 51.5 15 0.00033 24.5 2.3 32 9-41 53-84 (105)
108 TIGR00340 zpr1_rel ZPR1-relate 51.2 20 0.00044 24.9 3.0 35 24-63 1-37 (163)
109 PRK05320 rhodanese superfamily 51.2 12 0.00025 27.3 1.9 28 5-32 226-255 (257)
110 COG1096 Predicted RNA-binding 50.8 14 0.0003 26.8 2.2 27 20-63 148-174 (188)
111 PF08063 PADR1: PADR1 (NUC008) 50.7 10 0.00022 22.1 1.2 13 19-31 12-24 (55)
112 PF01667 Ribosomal_S27e: Ribos 50.7 15 0.00032 21.8 2.0 30 22-65 8-37 (55)
113 smart00132 LIM Zinc-binding do 50.2 8.6 0.00019 18.7 0.8 36 23-65 1-38 (39)
114 PRK11827 hypothetical protein; 50.0 15 0.00033 22.0 2.0 27 23-64 10-36 (60)
115 COG1571 Predicted DNA-binding 49.8 8.7 0.00019 30.8 1.1 38 13-66 342-379 (421)
116 PF08772 NOB1_Zn_bind: Nin one 49.3 6.9 0.00015 24.2 0.4 10 22-31 25-34 (73)
117 TIGR02605 CxxC_CxxC_SSSS putat 48.9 16 0.00034 19.9 1.8 12 19-30 24-35 (52)
118 KOG4317 Predicted Zn-finger pr 48.8 7.3 0.00016 30.9 0.6 26 41-66 6-31 (383)
119 PF10164 DUF2367: Uncharacteri 48.8 1.6 3.4E-05 28.9 -2.7 40 20-63 48-97 (98)
120 PF09889 DUF2116: Uncharacteri 48.7 8.3 0.00018 23.0 0.7 10 22-31 4-13 (59)
121 PRK08351 DNA-directed RNA poly 48.1 8.6 0.00019 23.2 0.7 9 23-31 17-25 (61)
122 PLN00209 ribosomal protein S27 48.0 26 0.00056 22.6 2.9 31 21-65 36-66 (86)
123 PF10571 UPF0547: Uncharacteri 47.9 8.5 0.00018 19.4 0.5 11 20-30 13-23 (26)
124 PF13717 zinc_ribbon_4: zinc-r 47.8 7.6 0.00017 20.6 0.4 15 15-29 19-33 (36)
125 TIGR02827 RNR_anaer_Bdell anae 47.7 13 0.00028 30.7 1.8 22 22-47 547-570 (586)
126 PF00096 zf-C2H2: Zinc finger, 47.3 10 0.00022 17.2 0.7 11 55-65 1-11 (23)
127 PF09862 DUF2089: Protein of u 47.3 17 0.00037 24.2 2.1 14 24-37 1-14 (113)
128 PRK14701 reverse gyrase; Provi 47.2 7.6 0.00017 35.4 0.5 13 21-33 6-18 (1638)
129 PF12874 zf-met: Zinc-finger o 47.1 10 0.00022 17.6 0.7 12 55-66 1-12 (25)
130 PRK00564 hypA hydrogenase nick 46.6 15 0.00033 23.8 1.7 19 13-31 63-81 (117)
131 PF04810 zf-Sec23_Sec24: Sec23 46.4 11 0.00025 20.2 0.9 30 21-63 2-33 (40)
132 PF10276 zf-CHCC: Zinc-finger 46.3 9.1 0.0002 21.2 0.6 9 21-29 29-37 (40)
133 COG2888 Predicted Zn-ribbon RN 45.6 11 0.00023 23.1 0.8 12 17-28 46-57 (61)
134 PF14787 zf-CCHC_5: GAG-polypr 45.0 9.3 0.0002 21.2 0.4 10 21-30 2-11 (36)
135 PF12171 zf-C2H2_jaz: Zinc-fin 44.8 5.7 0.00012 19.2 -0.4 13 54-66 1-13 (27)
136 cd00350 rubredoxin_like Rubred 44.2 23 0.00049 18.2 1.9 12 20-31 16-27 (33)
137 PF11793 FANCL_C: FANCL C-term 43.9 13 0.00029 22.1 1.0 15 18-32 52-66 (70)
138 PRK00762 hypA hydrogenase nick 43.9 19 0.00041 23.6 1.9 14 15-29 64-77 (124)
139 PF09845 DUF2072: Zn-ribbon co 43.6 13 0.00028 25.6 1.1 15 17-31 15-29 (131)
140 PTZ00083 40S ribosomal protein 43.6 34 0.00074 22.0 3.0 31 21-65 35-65 (85)
141 PRK04351 hypothetical protein; 43.4 29 0.00062 23.7 2.8 34 20-66 111-144 (149)
142 PF03119 DNA_ligase_ZBD: NAD-d 43.0 17 0.00038 18.4 1.3 20 23-43 1-20 (28)
143 KOG2807 RNA polymerase II tran 42.9 12 0.00026 29.7 1.0 27 21-66 276-302 (378)
144 PF06750 DiS_P_DiS: Bacterial 42.8 2.6 5.7E-05 26.6 -2.3 38 20-65 32-69 (92)
145 COG1885 Uncharacterized protei 42.3 47 0.001 22.5 3.6 33 21-53 49-81 (115)
146 PF06054 CoiA: Competence prot 42.3 38 0.00082 26.0 3.5 15 19-33 28-42 (375)
147 PF10005 DUF2248: Uncharacteri 41.5 12 0.00026 29.3 0.8 9 23-31 1-9 (343)
148 PRK00241 nudC NADH pyrophospha 41.2 20 0.00044 26.0 1.9 9 23-31 101-109 (256)
149 PF06957 COPI_C: Coatomer (COP 40.7 16 0.00035 29.1 1.3 27 39-66 363-392 (422)
150 PRK07111 anaerobic ribonucleos 40.5 13 0.00028 31.2 0.8 18 22-43 694-711 (735)
151 PF09538 FYDLN_acid: Protein o 40.3 14 0.00029 24.2 0.8 15 20-34 25-39 (108)
152 KOG0373 Serine/threonine speci 40.2 23 0.0005 27.3 2.1 25 14-38 253-277 (306)
153 COG1198 PriA Primosomal protei 40.1 14 0.00029 31.4 0.9 13 18-30 472-484 (730)
154 COG1198 PriA Primosomal protei 40.1 22 0.00049 30.1 2.2 16 48-63 456-471 (730)
155 PF04828 GFA: Glutathione-depe 39.5 20 0.00043 20.5 1.3 19 48-66 42-60 (92)
156 PF14392 zf-CCHC_4: Zinc knuck 38.9 16 0.00035 20.2 0.9 18 13-30 23-40 (49)
157 PF13465 zf-H2C2_2: Zinc-finge 38.4 15 0.00032 17.8 0.6 14 51-64 11-24 (26)
158 PF02620 DUF177: Uncharacteriz 38.3 36 0.00078 20.7 2.4 27 19-46 8-34 (119)
159 smart00019 SF_P Pulmonary surf 37.9 15 0.00032 26.6 0.7 22 5-26 101-122 (191)
160 PF05191 ADK_lid: Adenylate ki 37.9 16 0.00035 19.5 0.7 15 18-32 18-32 (36)
161 PF04981 NMD3: NMD3 family ; 37.8 13 0.00029 26.4 0.5 41 24-65 1-46 (236)
162 PF06689 zf-C4_ClpX: ClpX C4-t 37.8 9.9 0.00022 20.7 -0.2 10 55-64 2-11 (41)
163 COG3582 Predicted nucleic acid 37.6 16 0.00035 25.8 0.9 20 15-34 104-123 (162)
164 PF08394 Arc_trans_TRASH: Arch 37.3 36 0.00079 18.6 2.1 9 24-32 1-9 (37)
165 PF01396 zf-C4_Topoisom: Topoi 37.0 24 0.00051 18.9 1.3 10 22-31 2-11 (39)
166 PF05605 zf-Di19: Drought indu 35.8 16 0.00035 20.3 0.5 37 23-64 4-41 (54)
167 smart00731 SprT SprT homologue 35.6 45 0.00098 21.8 2.7 36 19-66 110-145 (146)
168 PF03884 DUF329: Domain of unk 35.6 4.7 0.0001 24.0 -1.8 12 22-33 3-14 (57)
169 TIGR01031 rpmF_bact ribosomal 35.4 30 0.00065 20.0 1.6 16 19-34 24-39 (55)
170 smart00647 IBR In Between Ring 35.0 32 0.00069 18.7 1.7 14 21-34 18-33 (64)
171 PF12653 DUF3785: Protein of u 34.9 30 0.00064 24.2 1.8 12 21-32 120-131 (138)
172 PF09986 DUF2225: Uncharacteri 34.9 40 0.00087 23.8 2.5 40 22-61 6-55 (214)
173 PRK06393 rpoE DNA-directed RNA 34.0 19 0.00042 22.0 0.7 8 23-30 19-26 (64)
174 COG1054 Predicted sulfurtransf 33.9 22 0.00047 27.6 1.1 32 5-36 225-258 (308)
175 PF09947 DUF2180: Uncharacteri 33.4 8.3 0.00018 23.8 -1.0 57 5-64 3-66 (68)
176 PF01155 HypA: Hydrogenase exp 33.3 13 0.00027 23.9 -0.2 18 14-31 63-80 (113)
177 PRK12286 rpmF 50S ribosomal pr 33.1 34 0.00073 20.0 1.6 16 18-33 24-39 (57)
178 PHA00616 hypothetical protein 33.0 13 0.00028 21.1 -0.2 9 22-30 2-10 (44)
179 PHA02942 putative transposase; 32.9 26 0.00056 27.0 1.4 27 22-64 326-352 (383)
180 PRK01343 zinc-binding protein; 32.8 15 0.00032 22.0 -0.0 12 20-31 8-19 (57)
181 PF12172 DUF35_N: Rubredoxin-l 32.6 20 0.00043 18.5 0.5 12 18-29 22-33 (37)
182 COG2093 DNA-directed RNA polym 32.5 22 0.00047 21.9 0.7 10 22-31 19-28 (64)
183 PF13913 zf-C2HC_2: zinc-finge 32.3 21 0.00046 17.5 0.5 9 23-31 4-12 (25)
184 PF05741 zf-nanos: Nanos RNA b 32.3 12 0.00027 22.1 -0.3 11 53-63 32-42 (55)
185 PF06221 zf-C2HC5: Putative zi 32.1 20 0.00044 21.2 0.6 19 13-31 26-45 (57)
186 COG3809 Uncharacterized protei 32.1 25 0.00055 22.8 1.0 8 22-29 22-29 (88)
187 TIGR01053 LSD1 zinc finger dom 32.1 37 0.00079 17.8 1.5 14 50-63 15-28 (31)
188 COG1867 TRM1 N2,N2-dimethylgua 31.5 35 0.00076 27.2 1.9 29 3-31 238-267 (380)
189 PRK14873 primosome assembly pr 31.4 23 0.00049 29.4 0.9 15 16-30 417-431 (665)
190 PF08600 Rsm1: Rsm1-like; Int 31.2 25 0.00055 21.9 0.9 13 54-66 19-31 (91)
191 PF08882 Acetone_carb_G: Aceto 31.1 42 0.0009 22.6 2.0 19 48-66 68-86 (112)
192 PF06677 Auto_anti-p27: Sjogre 30.9 19 0.00042 19.9 0.3 16 16-31 12-27 (41)
193 cd01675 RNR_III Class III ribo 30.6 30 0.00066 27.9 1.4 19 21-43 532-550 (555)
194 PF09334 tRNA-synt_1g: tRNA sy 30.5 33 0.00072 26.2 1.6 21 8-28 123-143 (391)
195 PF13719 zinc_ribbon_5: zinc-r 30.2 35 0.00076 18.0 1.2 16 15-30 19-34 (37)
196 PF11023 DUF2614: Protein of u 30.2 18 0.00039 24.5 0.1 21 8-31 75-95 (114)
197 PRK08270 anaerobic ribonucleos 30.1 29 0.00062 28.8 1.3 9 22-30 640-648 (656)
198 PF07295 DUF1451: Protein of u 30.0 53 0.0012 22.5 2.4 10 21-30 130-139 (146)
199 PF04423 Rad50_zn_hook: Rad50 29.9 24 0.00051 19.7 0.6 9 56-64 22-30 (54)
200 KOG3799 Rab3 effector RIM1 and 29.9 26 0.00057 25.0 0.9 26 23-63 91-116 (169)
201 KOG1598 Transcription initiati 29.4 29 0.00062 28.7 1.1 29 23-65 2-30 (521)
202 COG3024 Uncharacterized protei 29.1 19 0.00042 22.2 0.1 14 19-32 5-18 (65)
203 PF06170 DUF983: Protein of un 28.9 24 0.00052 22.2 0.5 21 16-36 3-23 (86)
204 TIGR02300 FYDLN_acid conserved 28.9 25 0.00055 24.2 0.7 10 21-30 26-35 (129)
205 PF03367 zf-ZPR1: ZPR1 zinc-fi 28.5 93 0.002 21.3 3.4 37 23-64 3-40 (161)
206 PRK05978 hypothetical protein; 28.4 28 0.00061 24.1 0.8 35 18-66 30-64 (148)
207 PRK00423 tfb transcription ini 28.4 44 0.00096 24.7 1.9 31 21-65 11-41 (310)
208 PF03966 Trm112p: Trm112p-like 28.4 66 0.0014 18.6 2.3 14 52-65 51-64 (68)
209 cd04476 RPA1_DBD_C RPA1_DBD_C: 28.1 31 0.00067 22.8 1.0 11 53-63 50-60 (166)
210 PF02591 DUF164: Putative zinc 28.0 28 0.00061 19.5 0.7 13 52-64 44-56 (56)
211 PF05280 FlhC: Flagellar trans 27.9 23 0.00051 24.8 0.4 28 21-61 134-161 (175)
212 TIGR00155 pqiA_fam integral me 27.7 34 0.00073 26.6 1.2 12 54-65 33-44 (403)
213 PF02176 zf-TRAF: TRAF-type zi 27.4 6.8 0.00015 21.6 -2.0 40 19-65 7-53 (60)
214 PF13597 NRDD: Anaerobic ribon 27.3 32 0.00068 27.7 1.0 30 7-43 493-522 (546)
215 PF06397 Desulfoferrod_N: Desu 27.3 49 0.0011 18.0 1.5 15 22-36 7-21 (36)
216 COG1327 Predicted transcriptio 27.2 27 0.00059 24.7 0.6 18 50-67 24-41 (156)
217 PF04879 Molybdop_Fe4S4: Molyb 27.0 59 0.0013 17.7 1.9 20 18-38 2-21 (55)
218 PRK00418 DNA gyrase inhibitor; 26.9 25 0.00054 21.3 0.3 12 20-31 5-16 (62)
219 PF05876 Terminase_GpA: Phage 26.7 46 0.001 26.8 1.9 38 22-64 201-239 (557)
220 PF02701 zf-Dof: Dof domain, z 26.7 26 0.00056 21.5 0.4 36 19-62 3-38 (63)
221 PRK13130 H/ACA RNA-protein com 26.6 32 0.00069 20.3 0.7 11 21-31 17-27 (56)
222 TIGR00354 polC DNA polymerase, 26.4 45 0.00098 29.9 1.9 21 16-36 1023-1043(1095)
223 KOG0372 Serine/threonine speci 25.7 30 0.00064 26.8 0.6 32 12-43 247-280 (303)
224 TIGR02487 NrdD anaerobic ribon 25.7 25 0.00055 28.5 0.2 18 22-43 539-556 (579)
225 PF09082 DUF1922: Domain of un 25.6 79 0.0017 19.5 2.4 6 26-31 7-12 (68)
226 TIGR00308 TRM1 tRNA(guanine-26 25.3 38 0.00082 26.1 1.1 12 18-29 249-260 (374)
227 cd01121 Sms Sms (bacterial rad 24.9 41 0.0009 25.8 1.3 18 18-35 11-28 (372)
228 PF04438 zf-HIT: HIT zinc fing 24.9 36 0.00078 17.5 0.7 14 52-65 11-24 (30)
229 PRK04023 DNA polymerase II lar 24.8 50 0.0011 29.7 1.9 22 16-37 1048-1069(1121)
230 PF04475 DUF555: Protein of un 24.6 1.3E+02 0.0028 20.0 3.4 33 21-53 47-79 (102)
231 PF02005 TRM: N2,N2-dimethylgu 24.4 29 0.00062 26.8 0.3 24 8-31 246-269 (377)
232 COG1439 Predicted nucleic acid 24.1 53 0.0011 23.6 1.6 15 19-33 151-165 (177)
233 COG1675 TFA1 Transcription ini 24.1 27 0.00059 24.8 0.1 14 22-35 133-146 (176)
234 KOG1829 Uncharacterized conser 23.9 10 0.00022 31.5 -2.3 33 23-62 342-374 (580)
235 PF13395 HNH_4: HNH endonuclea 23.6 29 0.00062 19.4 0.1 13 24-36 1-13 (54)
236 PRK14559 putative protein seri 23.5 39 0.00085 28.2 1.0 10 56-65 43-52 (645)
237 cd01230 PH_EFA6 EFA6 Pleckstri 23.5 65 0.0014 21.0 1.8 22 46-67 20-41 (117)
238 PRK14714 DNA polymerase II lar 23.5 54 0.0012 30.1 1.8 21 16-36 1264-1284(1337)
239 PF00098 zf-CCHC: Zinc knuckle 23.4 50 0.0011 15.1 0.9 8 23-30 2-9 (18)
240 COG4332 Uncharacterized protei 23.2 95 0.0021 22.9 2.8 47 15-62 11-57 (203)
241 COG3478 Predicted nucleic-acid 23.2 1.3E+02 0.0028 18.7 3.0 40 22-62 5-48 (68)
242 PRK14715 DNA polymerase II lar 23.2 55 0.0012 30.5 1.8 21 16-36 1552-1572(1627)
243 COG4311 SoxD Sarcosine oxidase 22.8 37 0.00081 22.4 0.6 7 23-29 5-11 (97)
244 PRK09263 anaerobic ribonucleos 22.8 52 0.0011 27.6 1.5 23 22-45 660-683 (711)
245 PF14375 Cys_rich_CWC: Cystein 22.7 43 0.00094 18.6 0.8 8 24-31 1-8 (50)
246 PF13912 zf-C2H2_6: C2H2-type 22.5 46 0.00099 15.5 0.7 12 55-66 2-13 (27)
247 TIGR02159 PA_CoA_Oxy4 phenylac 22.5 38 0.00083 23.0 0.6 16 21-38 105-120 (146)
248 PRK08271 anaerobic ribonucleos 22.4 16 0.00034 30.3 -1.5 23 21-47 580-604 (623)
249 PRK08173 DNA topoisomerase III 22.3 68 0.0015 27.5 2.1 14 18-31 723-736 (862)
250 smart00451 ZnF_U1 U1-like zinc 22.1 40 0.00087 16.5 0.5 12 54-65 3-14 (35)
251 TIGR00319 desulf_FeS4 desulfof 21.9 84 0.0018 15.9 1.7 15 21-35 7-21 (34)
252 smart00653 eIF2B_5 domain pres 21.7 1.3E+02 0.0028 19.6 3.0 16 21-38 80-95 (110)
253 PF07503 zf-HYPF: HypF finger; 21.6 36 0.00078 18.2 0.3 14 18-31 18-31 (35)
254 PF13966 zf-RVT: zinc-binding 21.5 45 0.00097 19.7 0.7 13 19-31 57-69 (86)
255 PRK03922 hypothetical protein; 21.5 1.6E+02 0.0034 19.9 3.4 32 21-52 49-80 (113)
256 cd00974 DSRD Desulforedoxin (D 21.4 88 0.0019 15.9 1.7 14 22-35 5-18 (34)
257 PF01363 FYVE: FYVE zinc finge 21.2 55 0.0012 18.5 1.0 14 51-64 22-35 (69)
258 PF15410 PH_9: Pleckstrin homo 21.1 91 0.002 19.7 2.1 23 46-68 20-42 (119)
259 PRK11788 tetratricopeptide rep 21.0 48 0.001 23.4 0.9 14 18-31 365-378 (389)
260 PF12660 zf-TFIIIC: Putative z 20.9 39 0.00085 21.4 0.4 46 19-66 12-67 (99)
261 PF01485 IBR: IBR domain; Int 20.8 11 0.00024 20.5 -1.9 21 18-38 15-37 (64)
262 smart00746 TRASH metallochaper 20.8 1E+02 0.0022 13.6 2.6 9 24-32 1-9 (39)
263 COG0266 Nei Formamidopyrimidin 20.6 71 0.0015 24.1 1.8 24 13-38 239-262 (273)
264 PRK12722 transcriptional activ 20.5 46 0.001 23.9 0.7 15 21-35 134-148 (187)
265 COG0551 TopA Zn-finger domain 20.0 1.5E+02 0.0032 19.2 3.0 48 16-63 12-69 (140)
No 1
>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=97.13 E-value=0.00033 Score=41.92 Aligned_cols=52 Identities=25% Similarity=0.485 Sum_probs=40.4
Q ss_pred eeccCceeCCCCCCceeEEEeeee-----------------eEEEEEeeeecee--eeEEeecccceeeeeC
Q 035291 16 KCKPAAGICSRCGGGASVADMKTA-----------------TRFCHVPFYWKSW--RAIICTFCGAVLKSYQ 68 (68)
Q Consensus 16 g~~~a~g~Cp~CGg~v~a~dv~s~-----------------~rfCflPl~~k~k--r~~~Ct~C~r~L~~~~ 68 (68)
|.+|+.-.||+||..+ -+.++.. |-+|+||++++.- ..+.|+.|++.|-.|+
T Consensus 2 ~~~p~~~~CP~C~~~~-~T~v~~~~g~~t~~~~~~l~~~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg~~~ 72 (73)
T PF10601_consen 2 GPEPVRIYCPYCQQQV-QTRVEYKSGTMTYICAALLCLFGCWPCCCIPFCCDSCKDVYHYCPNCGAFLGTYK 72 (73)
T ss_pred CCCceeeECCCCCCEE-EEEEEEEeChHHHHHHHHHHHHHHHHHhhHhhccccccCceEECCCCCCEeEEEe
Confidence 5688889999999999 5666641 3357889998654 4679999999998764
No 2
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=95.93 E-value=0.0042 Score=36.61 Aligned_cols=48 Identities=31% Similarity=0.652 Sum_probs=35.0
Q ss_pred cCceeCCCCCCceeEEEeeeee---------------EEEEEeeeecee--eeEEeecccceeeee
Q 035291 19 PAAGICSRCGGGASVADMKTAT---------------RFCHVPFYWKSW--RAIICTFCGAVLKSY 67 (68)
Q Consensus 19 ~a~g~Cp~CGg~v~a~dv~s~~---------------rfCflPl~~k~k--r~~~Ct~C~r~L~~~ 67 (68)
|+.-.||+||.-+ .+.||... -+|+||++++.- ..++|+.|++.|-.|
T Consensus 1 p~~i~Cp~C~~~~-~T~v~~~~g~~t~~~~~ll~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg~~ 65 (67)
T smart00714 1 PYQLFCPRCQNNV-TTRVETETGVCAWLICCLLFLLCFCCCLPCCLDSFKDVNHYCPNCGAFLGTY 65 (67)
T ss_pred CcceECCCCCCEE-EEEEEEEeChHHHHHHHHHHHHHHHHHHHHhcccccCccEECCCCCCEeEEe
Confidence 4566899999998 77777521 245679865543 457999999999876
No 3
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=93.43 E-value=0.076 Score=36.73 Aligned_cols=40 Identities=18% Similarity=0.306 Sum_probs=26.3
Q ss_pred eCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceeeee
Q 035291 23 ICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKSY 67 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~~~ 67 (68)
.||+||++. ...++|+. ++=-...+|.+.|..||++...|
T Consensus 2 ~cp~c~~~~-~~~~~s~~----~~~~~~~~~~~~c~~c~~~f~~~ 41 (154)
T PRK00464 2 RCPFCGHPD-TRVIDSRP----AEDGNAIRRRRECLACGKRFTTF 41 (154)
T ss_pred cCCCCCCCC-CEeEeccc----cCCCCceeeeeeccccCCcceEe
Confidence 599999977 23333431 21122456779999999988766
No 4
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=93.21 E-value=0.03 Score=27.77 Aligned_cols=9 Identities=33% Similarity=1.088 Sum_probs=7.1
Q ss_pred CCCCCCcee
Q 035291 24 CSRCGGGAS 32 (68)
Q Consensus 24 Cp~CGg~v~ 32 (68)
||+||..++
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 888888873
No 5
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=92.73 E-value=0.034 Score=35.71 Aligned_cols=19 Identities=26% Similarity=0.796 Sum_probs=15.5
Q ss_pred CceeCCCCCCceeEEEeee
Q 035291 20 AAGICSRCGGGASVADMKT 38 (68)
Q Consensus 20 a~g~Cp~CGg~v~a~dv~s 38 (68)
.-|+||||||..++..++-
T Consensus 40 l~g~CPnCGGelv~RP~RP 58 (84)
T COG3813 40 LHGLCPNCGGELVARPIRP 58 (84)
T ss_pred hcCcCCCCCchhhcCcCCh
Confidence 4689999999998877653
No 6
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=92.45 E-value=0.23 Score=26.74 Aligned_cols=39 Identities=28% Similarity=0.609 Sum_probs=22.0
Q ss_pred ceeCCCCCCceeEE-EeeeeeEEEEE-----eeeece-eeeEEeecc
Q 035291 21 AGICSRCGGGASVA-DMKTATRFCHV-----PFYWKS-WRAIICTFC 60 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~-dv~s~~rfCfl-----Pl~~k~-kr~~~Ct~C 60 (68)
|-.||+||...... +.+ +.++=.+ |+..+. +++|.|..|
T Consensus 2 ~~~Cp~Cg~~~~~~~g~~-~r~i~~l~~~~~~~~L~i~~~R~~C~~C 47 (47)
T PF14690_consen 2 PPRCPHCGSPSVHRHGYK-TRRIRHLPIGGRPVYLRIRKRRYRCKNC 47 (47)
T ss_pred CccCCCcCCCceECCceE-EEEEeecccCCEEEEEEEEeEEEECcCC
Confidence 56899999776221 221 2223344 444443 577888766
No 7
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=92.16 E-value=0.094 Score=28.80 Aligned_cols=29 Identities=28% Similarity=0.597 Sum_probs=16.9
Q ss_pred eCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeeccccee
Q 035291 23 ICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVL 64 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L 64 (68)
-||.||+.+...+. +....+.|+.|+...
T Consensus 2 FCp~Cg~~l~~~~~-------------~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 2 FCPKCGNMLIPKEG-------------KEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCccccccC-------------CCCCEEECCcCCCeE
Confidence 38899987732221 122367788887543
No 8
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=92.15 E-value=0.05 Score=27.27 Aligned_cols=9 Identities=33% Similarity=1.117 Sum_probs=7.1
Q ss_pred eCCCCCCce
Q 035291 23 ICSRCGGGA 31 (68)
Q Consensus 23 ~Cp~CGg~v 31 (68)
.||+||..+
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 589999855
No 9
>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=91.85 E-value=0.38 Score=26.09 Aligned_cols=41 Identities=20% Similarity=0.361 Sum_probs=25.2
Q ss_pred ceeCCCCCCceeEEEee-eeeEEEEEeeeeceee----eEEeeccc
Q 035291 21 AGICSRCGGGASVADMK-TATRFCHVPFYWKSWR----AIICTFCG 61 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~-s~~rfCflPl~~k~kr----~~~Ct~C~ 61 (68)
+.+||.||+.+.-.-.+ ..-.+=++|.-++..+ ++.|+-|+
T Consensus 2 ~~~C~~Cg~~l~~ig~~~~~q~l~~~p~~~~V~e~~~~~y~C~~C~ 47 (47)
T PF13005_consen 2 PRACPDCGGELKEIGEEKVRQVLDLPPAKPEVTEHVRHKYACPCCG 47 (47)
T ss_pred CCcCCCCCceeeECCceeeEEEEeecccceEEEEEEeceEECCCCC
Confidence 46899999988533333 2444556776665433 56677664
No 10
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=91.25 E-value=0.065 Score=32.43 Aligned_cols=14 Identities=36% Similarity=0.968 Sum_probs=11.6
Q ss_pred ceeCCCCCCceeEE
Q 035291 21 AGICSRCGGGASVA 34 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~ 34 (68)
.+.||||||..+..
T Consensus 41 ~~~CPNCgGelv~R 54 (57)
T PF06906_consen 41 NGVCPNCGGELVRR 54 (57)
T ss_pred cCcCcCCCCccccC
Confidence 68999999988543
No 11
>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=90.98 E-value=0.57 Score=29.27 Aligned_cols=41 Identities=27% Similarity=0.505 Sum_probs=31.7
Q ss_pred CCCCCCceeEEEeee-eeEEEEEeeeeceeeeEEeecccceee
Q 035291 24 CSRCGGGASVADMKT-ATRFCHVPFYWKSWRAIICTFCGAVLK 65 (68)
Q Consensus 24 Cp~CGg~v~a~dv~s-~~rfCflPl~~k~kr~~~Ct~C~r~L~ 65 (68)
||.||+.....+++. .+++.-.-+.+ .-..+.|+.||..+.
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v-~~~~~~C~~CGe~~~ 42 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITI-GVPGWYCPACGEELL 42 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEE-eeeeeECCCCCCEEE
Confidence 899997655677776 66788777777 778889999998654
No 12
>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=89.41 E-value=0.75 Score=24.20 Aligned_cols=42 Identities=21% Similarity=0.454 Sum_probs=22.6
Q ss_pred CCCCCCceeEEEeee-eeEEEEEeeeeceeeeEEeecccceee
Q 035291 24 CSRCGGGASVADMKT-ATRFCHVPFYWKSWRAIICTFCGAVLK 65 (68)
Q Consensus 24 Cp~CGg~v~a~dv~s-~~rfCflPl~~k~kr~~~Ct~C~r~L~ 65 (68)
||.|||.....++++ ++..=--=+-.+.-....|+.||..+-
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~~~~~~i~~vp~~~C~~CGE~~~ 43 (46)
T TIGR03831 1 CPICGGEELEGKTTTETYEYGGELIVIENVPALVCPQCGEEYL 43 (46)
T ss_pred CCCCCCceecceEEEEEEEeCCEEEEEeCCCccccccCCCEee
Confidence 788977765555543 222200122333444556888887654
No 13
>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=88.93 E-value=0.2 Score=36.43 Aligned_cols=43 Identities=28% Similarity=0.801 Sum_probs=21.6
Q ss_pred CceeCCCCCCceeEEEeeee----eEEEEEeeeeceee--eEEeecccc
Q 035291 20 AAGICSRCGGGASVADMKTA----TRFCHVPFYWKSWR--AIICTFCGA 62 (68)
Q Consensus 20 a~g~Cp~CGg~v~a~dv~s~----~rfCflPl~~k~kr--~~~Ct~C~r 62 (68)
..|.||-||+.-++..++.. .|+.+=++|.-.|+ ++.|+.||.
T Consensus 171 ~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~ 219 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGN 219 (290)
T ss_dssp T-SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT--
T ss_pred cCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCC
Confidence 35899999999888888874 46666566654443 456666664
No 14
>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=88.85 E-value=0.52 Score=25.20 Aligned_cols=28 Identities=32% Similarity=0.545 Sum_probs=18.8
Q ss_pred eCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeeccccee
Q 035291 23 ICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVL 64 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L 64 (68)
-||.|||.. +|---+..+. .|+.|+..-
T Consensus 3 FCp~C~nlL-------------~p~~~~~~~~-~C~~C~Y~~ 30 (35)
T PF02150_consen 3 FCPECGNLL-------------YPKEDKEKRV-ACRTCGYEE 30 (35)
T ss_dssp BETTTTSBE-------------EEEEETTTTE-EESSSS-EE
T ss_pred eCCCCCccc-------------eEcCCCccCc-CCCCCCCcc
Confidence 389999998 4555555544 788887654
No 15
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=87.70 E-value=0.7 Score=23.32 Aligned_cols=14 Identities=21% Similarity=0.399 Sum_probs=7.3
Q ss_pred eCCCCCCceeEEEe
Q 035291 23 ICSRCGGGASVADM 36 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv 36 (68)
.|++||+.+....+
T Consensus 3 ~C~rC~~~~~~~~~ 16 (30)
T PF06827_consen 3 KCPRCWNYIEDIGI 16 (30)
T ss_dssp B-TTT--BBEEEEE
T ss_pred cCccCCCcceEeEe
Confidence 59999999844433
No 16
>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=86.60 E-value=0.73 Score=25.40 Aligned_cols=28 Identities=25% Similarity=0.513 Sum_probs=18.8
Q ss_pred eeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccce
Q 035291 22 GICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAV 63 (68)
Q Consensus 22 g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~ 63 (68)
-.||+||+.- +.-+++ ...+-|..|+++
T Consensus 19 ~~CP~Cg~~~-~~~~~~-------------~~~~~C~~C~~q 46 (46)
T PF12760_consen 19 FVCPHCGSTK-HYRLKT-------------RGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCee-eEEeCC-------------CCeEECCCCCCc
Confidence 3499999973 444444 556778877753
No 17
>PRK00420 hypothetical protein; Validated
Probab=86.56 E-value=0.35 Score=32.18 Aligned_cols=34 Identities=21% Similarity=0.338 Sum_probs=23.9
Q ss_pred eeccCceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceee
Q 035291 16 KCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLK 65 (68)
Q Consensus 16 g~~~a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~ 65 (68)
|..-....||.||.+. .--...+++|+.||..+.
T Consensus 18 Ga~ml~~~CP~Cg~pL----------------f~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 18 GAKMLSKHCPVCGLPL----------------FELKDGEVVCPVHGKVYI 51 (112)
T ss_pred HHHHccCCCCCCCCcc----------------eecCCCceECCCCCCeee
Confidence 5555678899999776 211456888999988664
No 18
>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=83.89 E-value=1.8 Score=26.96 Aligned_cols=37 Identities=16% Similarity=0.455 Sum_probs=20.0
Q ss_pred cCceeCCCCC-CceeEEEeeeeeEEEEEeeeeceeeeEEeecccceee
Q 035291 19 PAAGICSRCG-GGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLK 65 (68)
Q Consensus 19 ~a~g~Cp~CG-g~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~ 65 (68)
+..=.||.|| ..++..+|+.. ...-.+.|..|+....
T Consensus 20 ~~~F~CPfC~~~~sV~v~idkk----------~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSVKIDKK----------EGIGILSCRVCGESFQ 57 (81)
T ss_dssp SS----TTT--SS-EEEEEETT----------TTEEEEEESSS--EEE
T ss_pred CceEcCCcCCCCCeEEEEEEcc----------CCEEEEEecCCCCeEE
Confidence 3456899999 55656666554 4566788999987654
No 19
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=83.16 E-value=1.3 Score=24.23 Aligned_cols=11 Identities=27% Similarity=0.522 Sum_probs=7.7
Q ss_pred ceeCCCCCCce
Q 035291 21 AGICSRCGGGA 31 (68)
Q Consensus 21 ~g~Cp~CGg~v 31 (68)
...||+||+.+
T Consensus 21 ~~~Cp~CG~~~ 31 (46)
T PRK00398 21 GVRCPYCGYRI 31 (46)
T ss_pred ceECCCCCCeE
Confidence 56777777766
No 20
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=83.11 E-value=0.62 Score=27.65 Aligned_cols=34 Identities=35% Similarity=0.675 Sum_probs=21.0
Q ss_pred eeeeeeccCceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccce
Q 035291 12 RKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAV 63 (68)
Q Consensus 12 ~kv~g~~~a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~ 63 (68)
++|+...+ -|||||.++--+|= +.++.|-.||-.
T Consensus 13 ~kv~rk~~---~CPrCG~gvfmA~H---------------~dR~~CGkCgyT 46 (51)
T COG1998 13 EKVKRKNR---FCPRCGPGVFMADH---------------KDRWACGKCGYT 46 (51)
T ss_pred CcEEEccc---cCCCCCCcchhhhc---------------CceeEeccccce
Confidence 34555443 69999988743332 336777777643
No 21
>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=81.18 E-value=1.3 Score=25.60 Aligned_cols=29 Identities=31% Similarity=0.660 Sum_probs=20.8
Q ss_pred CceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccce
Q 035291 20 AAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAV 63 (68)
Q Consensus 20 a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~ 63 (68)
-.-.||.||..... ..+.|.+.|+.||..
T Consensus 27 TSq~C~~CG~~~~~---------------~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK---------------RRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCccccccc---------------ccccceEEcCCCCCE
Confidence 34569999988733 445778888888865
No 22
>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=80.96 E-value=0.9 Score=23.05 Aligned_cols=15 Identities=20% Similarity=0.532 Sum_probs=11.0
Q ss_pred eeeec-cCceeCCCCC
Q 035291 14 VHKCK-PAAGICSRCG 28 (68)
Q Consensus 14 v~g~~-~a~g~Cp~CG 28 (68)
+.+++ .++=.|||||
T Consensus 8 i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 8 IAPREQAVPFPCPNCG 23 (24)
T ss_pred ccCcccCceEeCCCCC
Confidence 44454 7778899998
No 23
>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=80.85 E-value=0.36 Score=32.91 Aligned_cols=35 Identities=20% Similarity=0.291 Sum_probs=22.8
Q ss_pred cCceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceeeee
Q 035291 19 PAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKSY 67 (68)
Q Consensus 19 ~a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~~~ 67 (68)
+.-=.||+||-..+..|.-+ ..|.|+.||..|+-+
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~--------------~~F~Cp~Cg~~L~~~ 141 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME--------------LNFTCPRCGAMLDYL 141 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH--------------cCCcCCCCCCEeeec
Confidence 34446888886665444433 268888888888754
No 24
>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=80.60 E-value=0.94 Score=29.71 Aligned_cols=39 Identities=28% Similarity=0.525 Sum_probs=22.7
Q ss_pred ceeCCCCCCceeEEEeeeeeEEEEEeeeeceee-eEEeeccccee
Q 035291 21 AGICSRCGGGASVADMKTATRFCHVPFYWKSWR-AIICTFCGAVL 64 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr-~~~Ct~C~r~L 64 (68)
|-.||||||.+.-++= +.. -|-....+. -|.|+-|++-.
T Consensus 2 p~~CpYCg~~~~l~~~-~~i----Yg~~~~~~~~~y~C~~C~AyV 41 (102)
T PF11672_consen 2 PIICPYCGGPAELVDG-SEI----YGHRYDDGPYLYVCTPCDAYV 41 (102)
T ss_pred CcccCCCCCeeEEccc-chh----cCccCCCCceeEECCCCCcee
Confidence 4579999999865552 111 131111122 38999998753
No 25
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=80.35 E-value=1.3 Score=25.02 Aligned_cols=10 Identities=40% Similarity=0.999 Sum_probs=8.1
Q ss_pred eCCCCCCcee
Q 035291 23 ICSRCGGGAS 32 (68)
Q Consensus 23 ~Cp~CGg~v~ 32 (68)
.||.|||...
T Consensus 3 PCPfCGg~~~ 12 (53)
T TIGR03655 3 PCPFCGGADV 12 (53)
T ss_pred CCCCCCCcce
Confidence 4999999774
No 26
>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=78.39 E-value=2 Score=22.25 Aligned_cols=12 Identities=33% Similarity=0.983 Sum_probs=9.6
Q ss_pred cCceeCCCCCCc
Q 035291 19 PAAGICSRCGGG 30 (68)
Q Consensus 19 ~a~g~Cp~CGg~ 30 (68)
...-.||.||+.
T Consensus 24 ~~~~~CP~Cg~~ 35 (41)
T smart00834 24 DPLATCPECGGD 35 (41)
T ss_pred CCCCCCCCCCCc
Confidence 667789999984
No 27
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=78.16 E-value=0.44 Score=33.24 Aligned_cols=35 Identities=20% Similarity=0.452 Sum_probs=24.0
Q ss_pred cCceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceeeee
Q 035291 19 PAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKSY 67 (68)
Q Consensus 19 ~a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~~~ 67 (68)
+.-=.||+||-..+..|.-+ ..|.|+.||..|+-+
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~--------------~~F~Cp~Cg~~L~~~ 149 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME--------------YGFRCPQCGEMLEEY 149 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh--------------cCCcCCCCCCCCeec
Confidence 34556888887776555432 278899999888754
No 28
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=77.12 E-value=1.1 Score=30.00 Aligned_cols=8 Identities=25% Similarity=0.974 Sum_probs=4.6
Q ss_pred CCCCCCce
Q 035291 24 CSRCGGGA 31 (68)
Q Consensus 24 Cp~CGg~v 31 (68)
||+|+.++
T Consensus 4 CPrC~skv 11 (112)
T TIGR00622 4 CPQCRAKV 11 (112)
T ss_pred CCCCCCCc
Confidence 55665555
No 29
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=76.80 E-value=2.9 Score=25.24 Aligned_cols=30 Identities=23% Similarity=0.605 Sum_probs=23.5
Q ss_pred eeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceee
Q 035291 22 GICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLK 65 (68)
Q Consensus 22 g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~ 65 (68)
-.||.|++-- .++.+.-..+.|..||+.|.
T Consensus 12 VkCp~C~n~q--------------~vFsha~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 12 VKCPDCGNEQ--------------VVFSHASTVVRCLVCGKTLA 41 (59)
T ss_pred EECCCCCCeE--------------EEEecCCcEEECcccCCCcc
Confidence 4688888865 35667788899999999885
No 30
>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=76.64 E-value=2.1 Score=23.16 Aligned_cols=29 Identities=34% Similarity=0.786 Sum_probs=18.5
Q ss_pred eCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceee
Q 035291 23 ICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLK 65 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~ 65 (68)
.||+||......| ...-.++|+.||..|.
T Consensus 2 ~Cp~Cg~~~~~~D--------------~~~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 2 KCPNCGSKEIVFD--------------PERGELVCPNCGLVLE 30 (43)
T ss_dssp SBTTTSSSEEEEE--------------TTTTEEEETTT-BBEE
T ss_pred CCcCCcCCceEEc--------------CCCCeEECCCCCCEee
Confidence 4888888763333 2345678888887765
No 31
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=76.63 E-value=2.5 Score=27.45 Aligned_cols=33 Identities=30% Similarity=0.583 Sum_probs=21.9
Q ss_pred cCceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccce
Q 035291 19 PAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAV 63 (68)
Q Consensus 19 ~a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~ 63 (68)
+..-.||+||.......+.. .+-.+.|..||-.
T Consensus 19 pt~f~CP~Cge~~v~v~~~k------------~~~h~~C~~CG~y 51 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKK------------NIAIITCGNCGLY 51 (99)
T ss_pred CcEeECCCCCCeEeeeecCC------------CcceEECCCCCCc
Confidence 45568999997653333332 4667889999853
No 32
>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=76.49 E-value=2 Score=29.96 Aligned_cols=40 Identities=13% Similarity=0.155 Sum_probs=27.5
Q ss_pred eCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceeeee
Q 035291 23 ICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKSY 67 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~~~ 67 (68)
.||+||+.= -.+++|... -=-..+.|+=.|..|++|..+|
T Consensus 2 ~CP~C~~~d-tkViDSR~~----~dg~~IRRRReC~~C~~RFTTy 41 (147)
T TIGR00244 2 HCPFCQHHN-TRVLDSRLV----EDGQSIRRRRECLECHERFTTF 41 (147)
T ss_pred CCCCCCCCC-CEeeecccc----CCCCeeeecccCCccCCcccee
Confidence 599999965 455555221 1122467888999999998887
No 33
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=76.39 E-value=1.8 Score=23.21 Aligned_cols=29 Identities=24% Similarity=0.575 Sum_probs=13.1
Q ss_pred eCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccc
Q 035291 23 ICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGA 62 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r 62 (68)
-||.||+.++-.-. - --...+.+|+.||.
T Consensus 2 fC~~CG~~l~~~ip----------~-gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 2 FCPQCGGPLERRIP----------E-GDDRERLVCPACGF 30 (34)
T ss_dssp B-TTT--B-EEE------------T-T-SS-EEEETTTTE
T ss_pred ccccccChhhhhcC----------C-CCCccceECCCCCC
Confidence 39999999854433 1 12345667777774
No 34
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=75.91 E-value=2.2 Score=24.91 Aligned_cols=15 Identities=20% Similarity=0.434 Sum_probs=11.8
Q ss_pred eCCCCCCceeEEEeee
Q 035291 23 ICSRCGGGASVADMKT 38 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s 38 (68)
+|||||-.. .+.++.
T Consensus 2 ~CPyCge~~-~~~iD~ 16 (52)
T PF14255_consen 2 QCPYCGEPI-EILIDP 16 (52)
T ss_pred CCCCCCCee-EEEEec
Confidence 699999998 556664
No 35
>PF12773 DZR: Double zinc ribbon
Probab=75.62 E-value=0.52 Score=25.77 Aligned_cols=14 Identities=36% Similarity=0.553 Sum_probs=7.6
Q ss_pred eeeeEEeeccccee
Q 035291 51 SWRAIICTFCGAVL 64 (68)
Q Consensus 51 ~kr~~~Ct~C~r~L 64 (68)
....+.|+.|++.+
T Consensus 26 ~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 26 DQSKKICPNCGAEN 39 (50)
T ss_pred cCCCCCCcCCcCCC
Confidence 34445566666554
No 36
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=75.49 E-value=0.43 Score=35.98 Aligned_cols=20 Identities=5% Similarity=-0.056 Sum_probs=18.1
Q ss_pred eeeeeeccCceeCCCCCCce
Q 035291 12 RKVHKCKPAAGICSRCGGGA 31 (68)
Q Consensus 12 ~kv~g~~~a~g~Cp~CGg~v 31 (68)
++|+.+...|+.|+|||+.+
T Consensus 145 ~~v~~~hfLpd~~gn~r~f~ 164 (253)
T COG1933 145 ERVLNSHFIPDLRGNLRSFT 164 (253)
T ss_pred HHhhccCCCcchhhhhhhhh
Confidence 78899999999999999887
No 37
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=75.16 E-value=1.8 Score=24.80 Aligned_cols=38 Identities=32% Similarity=0.627 Sum_probs=22.1
Q ss_pred EEeCCceeeeeeccCceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccce
Q 035291 6 FLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAV 63 (68)
Q Consensus 6 fvcde~~kv~g~~~a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~ 63 (68)
|-.|.+ +|.... -.||+||+...+. ...++.|..|+..
T Consensus 9 y~v~~~-~v~~~~---~fCP~Cg~~~m~~----------------~~~r~~C~~Cgyt 46 (50)
T PRK00432 9 YEVDGG-KVKRKN---KFCPRCGSGFMAE----------------HLDRWHCGKCGYT 46 (50)
T ss_pred EEECCC-EEEEcc---CcCcCCCcchhec----------------cCCcEECCCcCCE
Confidence 344543 555333 3899999842121 1257788888864
No 38
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=75.13 E-value=2.7 Score=23.54 Aligned_cols=14 Identities=21% Similarity=0.420 Sum_probs=11.5
Q ss_pred ccCceeCCCCCCce
Q 035291 18 KPAAGICSRCGGGA 31 (68)
Q Consensus 18 ~~a~g~Cp~CGg~v 31 (68)
...+-.||+||..+
T Consensus 16 ~~~~irC~~CG~rI 29 (44)
T smart00659 16 SKDVVRCRECGYRI 29 (44)
T ss_pred CCCceECCCCCceE
Confidence 56778899999887
No 39
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=73.66 E-value=3.8 Score=30.03 Aligned_cols=23 Identities=17% Similarity=0.319 Sum_probs=15.3
Q ss_pred eeeeeccCceeCCCCCCceeEEEee
Q 035291 13 KVHKCKPAAGICSRCGGGASVADMK 37 (68)
Q Consensus 13 kv~g~~~a~g~Cp~CGg~v~a~dv~ 37 (68)
+|-|+++ -.||+||+.+.-..+.
T Consensus 248 ~Vy~R~g--~pC~~Cg~~I~~~~~~ 270 (282)
T PRK13945 248 WVYRRTG--KPCRKCGTPIERIKLA 270 (282)
T ss_pred EEeCCCc--CCCCcCCCeeEEEEEC
Confidence 4555544 3599999999655553
No 40
>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=73.56 E-value=2 Score=22.78 Aligned_cols=13 Identities=23% Similarity=0.480 Sum_probs=8.9
Q ss_pred cCceeCCCCCCce
Q 035291 19 PAAGICSRCGGGA 31 (68)
Q Consensus 19 ~a~g~Cp~CGg~v 31 (68)
..+-+|++||..+
T Consensus 15 ~~~irC~~CG~RI 27 (32)
T PF03604_consen 15 GDPIRCPECGHRI 27 (32)
T ss_dssp SSTSSBSSSS-SE
T ss_pred CCcEECCcCCCeE
Confidence 3455899999876
No 41
>PF14369 zf-RING_3: zinc-finger
Probab=73.02 E-value=2.6 Score=22.52 Aligned_cols=27 Identities=22% Similarity=0.578 Sum_probs=14.9
Q ss_pred EEEeCCceeeeeeccCceeCCCCCCce
Q 035291 5 CFLVDQTRKVHKCKPAAGICSRCGGGA 31 (68)
Q Consensus 5 ~fvcde~~kv~g~~~a~g~Cp~CGg~v 31 (68)
+.-|+..=.+.......-+||+|+|+-
T Consensus 5 Ch~C~~~V~~~~~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 5 CHQCNRFVRIAPSPDSDVACPRCHGGF 31 (35)
T ss_pred CccCCCEeEeCcCCCCCcCCcCCCCcE
Confidence 344544433322333444799999976
No 42
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=72.86 E-value=5.6 Score=24.69 Aligned_cols=33 Identities=21% Similarity=0.579 Sum_probs=24.1
Q ss_pred CceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceeee
Q 035291 20 AAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKS 66 (68)
Q Consensus 20 a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~~ 66 (68)
..-.||.|||--. ++.+.-..+.|.+||+.|..
T Consensus 18 l~VkCpdC~N~q~--------------vFshast~V~C~~CG~~l~~ 50 (67)
T COG2051 18 LRVKCPDCGNEQV--------------VFSHASTVVTCLICGTTLAE 50 (67)
T ss_pred EEEECCCCCCEEE--------------EeccCceEEEecccccEEEe
Confidence 3457999999651 23455678999999999864
No 43
>PRK10445 endonuclease VIII; Provisional
Probab=72.40 E-value=3.7 Score=29.85 Aligned_cols=23 Identities=30% Similarity=0.611 Sum_probs=15.4
Q ss_pred eeeeeccCceeCCCCCCceeEEEee
Q 035291 13 KVHKCKPAAGICSRCGGGASVADMK 37 (68)
Q Consensus 13 kv~g~~~a~g~Cp~CGg~v~a~dv~ 37 (68)
+|-|++ -..||+||+.+.-..+-
T Consensus 229 ~Vy~r~--g~~Cp~Cg~~I~~~~~~ 251 (263)
T PRK10445 229 KVFHRD--GEACERCGGIIEKTTLS 251 (263)
T ss_pred EEeCCC--CCCCCCCCCEeEEEEEC
Confidence 445543 34599999999666554
No 44
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=72.08 E-value=3.6 Score=28.22 Aligned_cols=29 Identities=24% Similarity=0.567 Sum_probs=20.6
Q ss_pred CceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceee
Q 035291 20 AAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLK 65 (68)
Q Consensus 20 a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~ 65 (68)
..-.||.||-+. +- .--+++|++|+.+-+
T Consensus 27 L~~hCp~Cg~PL----------------F~-KdG~v~CPvC~~~~~ 55 (131)
T COG1645 27 LAKHCPKCGTPL----------------FR-KDGEVFCPVCGYREV 55 (131)
T ss_pred HHhhCcccCCcc----------------ee-eCCeEECCCCCceEE
Confidence 345789988655 44 567899999996543
No 45
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=72.01 E-value=1.4 Score=33.42 Aligned_cols=44 Identities=16% Similarity=0.560 Sum_probs=29.0
Q ss_pred cCceeCCCCCCceeEEEeee-----eeEEEEEeeeecee--eeEEeecccc
Q 035291 19 PAAGICSRCGGGASVADMKT-----ATRFCHVPFYWKSW--RAIICTFCGA 62 (68)
Q Consensus 19 ~a~g~Cp~CGg~v~a~dv~s-----~~rfCflPl~~k~k--r~~~Ct~C~r 62 (68)
...|.||-||+.-.+..+.. -.|+..=++|.--| ++..|+.|+.
T Consensus 182 ~~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 182 ESRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEE 232 (305)
T ss_pred CCCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 44678999999876665532 35666556665444 4677888875
No 46
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.97 E-value=3.1 Score=25.51 Aligned_cols=46 Identities=9% Similarity=0.252 Sum_probs=34.0
Q ss_pred eeeeeeccCceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceeee
Q 035291 12 RKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKS 66 (68)
Q Consensus 12 ~kv~g~~~a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~~ 66 (68)
...+.....+-+|+-=+++ -..-|. |||+ +....+.|+-|++++++
T Consensus 15 ~~~I~~~~~~l~C~g~~~p------~~HPrV-~L~m--g~~gev~CPYC~t~y~l 60 (62)
T COG4391 15 HETIEIGDLPLMCPGPEPP------NDHPRV-FLDM--GDEGEVVCPYCSTRYRL 60 (62)
T ss_pred ceEEEeCCeeEEcCCCCCC------CCCCEE-EEEc--CCCCcEecCccccEEEe
Confidence 5667777888888755554 233343 6888 88899999999999886
No 47
>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=71.86 E-value=5.1 Score=21.75 Aligned_cols=14 Identities=21% Similarity=0.582 Sum_probs=11.1
Q ss_pred eccCceeCCCCCCc
Q 035291 17 CKPAAGICSRCGGG 30 (68)
Q Consensus 17 ~~~a~g~Cp~CGg~ 30 (68)
.+..+-.||.||+.
T Consensus 22 ~~~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 22 SEDDPVPCPECGST 35 (42)
T ss_pred CCCCCCcCCCCCCC
Confidence 34688899999993
No 48
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=71.36 E-value=3.7 Score=29.97 Aligned_cols=23 Identities=13% Similarity=0.174 Sum_probs=15.4
Q ss_pred eeeeeccCceeCCCCCCceeEEEee
Q 035291 13 KVHKCKPAAGICSRCGGGASVADMK 37 (68)
Q Consensus 13 kv~g~~~a~g~Cp~CGg~v~a~dv~ 37 (68)
+|-|+++- .||+||+.+.-..+-
T Consensus 238 ~Vy~R~g~--pCprCG~~I~~~~~~ 260 (272)
T PRK14810 238 RVYQRTGE--PCLNCKTPIRRVVVA 260 (272)
T ss_pred eecCCCCC--cCCCCCCeeEEEEEC
Confidence 45555544 499999999555554
No 49
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=70.05 E-value=5.3 Score=21.04 Aligned_cols=27 Identities=26% Similarity=0.514 Sum_probs=17.0
Q ss_pred eEEEEEeCCceeeeeeccCceeCCCCCCce
Q 035291 2 VCFCFLVDQTRKVHKCKPAAGICSRCGGGA 31 (68)
Q Consensus 2 M~~~fvcde~~kv~g~~~a~g~Cp~CGg~v 31 (68)
.+.+-+||.. ...+.+|..||-||.+.
T Consensus 2 ~~~C~~CG~i---~~g~~~p~~CP~Cg~~~ 28 (34)
T cd00729 2 VWVCPVCGYI---HEGEEAPEKCPICGAPK 28 (34)
T ss_pred eEECCCCCCE---eECCcCCCcCcCCCCch
Confidence 3455566643 12244788999999865
No 50
>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=70.00 E-value=3.3 Score=21.17 Aligned_cols=10 Identities=40% Similarity=1.139 Sum_probs=5.3
Q ss_pred eeCCCCCCce
Q 035291 22 GICSRCGGGA 31 (68)
Q Consensus 22 g~Cp~CGg~v 31 (68)
.-|++||++.
T Consensus 4 rfC~~CG~~t 13 (32)
T PF09297_consen 4 RFCGRCGAPT 13 (32)
T ss_dssp SB-TTT--BE
T ss_pred cccCcCCccc
Confidence 3589999988
No 51
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=69.59 E-value=2.4 Score=32.39 Aligned_cols=43 Identities=19% Similarity=0.519 Sum_probs=27.9
Q ss_pred CceeCCCCCCceeEEEee----eeeEEEEEeeeecee--eeEEeecccc
Q 035291 20 AAGICSRCGGGASVADMK----TATRFCHVPFYWKSW--RAIICTFCGA 62 (68)
Q Consensus 20 a~g~Cp~CGg~v~a~dv~----s~~rfCflPl~~k~k--r~~~Ct~C~r 62 (68)
..+.||-||+.-.+..++ .-.|+..=++|.--| ++..|+.|+.
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 568899999986555442 245666556665444 4677777774
No 52
>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=68.82 E-value=13 Score=22.44 Aligned_cols=41 Identities=20% Similarity=0.493 Sum_probs=23.8
Q ss_pred eCCCCCCceeEEE-eeee-eEEE-EEeeeeceeeeEEeecccce
Q 035291 23 ICSRCGGGASVAD-MKTA-TRFC-HVPFYWKSWRAIICTFCGAV 63 (68)
Q Consensus 23 ~Cp~CGg~v~a~d-v~s~-~rfC-flPl~~k~kr~~~Ct~C~r~ 63 (68)
.||.||+.--..+ +... -.|= ...+-.|.+.-++|+.||-.
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYT 45 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCE
Confidence 4888888542111 1111 1111 24667778888999999854
No 53
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=68.57 E-value=3.7 Score=28.23 Aligned_cols=22 Identities=41% Similarity=0.769 Sum_probs=17.1
Q ss_pred eeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccce
Q 035291 22 GICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAV 63 (68)
Q Consensus 22 g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~ 63 (68)
-.||.||. ...|.+.|+.||..
T Consensus 310 ~~C~~cg~--------------------~~~r~~~C~~cg~~ 331 (364)
T COG0675 310 KTCPCCGH--------------------LSGRLFKCPRCGFV 331 (364)
T ss_pred ccccccCC--------------------ccceeEECCCCCCe
Confidence 57999998 33678899999854
No 54
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=68.35 E-value=6.7 Score=22.01 Aligned_cols=33 Identities=24% Similarity=0.546 Sum_probs=16.9
Q ss_pred eCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccc
Q 035291 23 ICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGA 62 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r 62 (68)
-||-||......+-+..+. ...+-.+.|+.|+.
T Consensus 5 PCPFCG~~~~~~~~~~~~~-------~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFD-------YGMYYYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeecccCCC-------CCCEEEEEcCCCCC
Confidence 3899976663333322110 00004467888887
No 55
>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=68.05 E-value=5 Score=25.91 Aligned_cols=36 Identities=19% Similarity=0.353 Sum_probs=23.1
Q ss_pred cCceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceeeee
Q 035291 19 PAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKSY 67 (68)
Q Consensus 19 ~a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~~~ 67 (68)
.-.-.|+.||..+... -+ ....++.|..|+..|+..
T Consensus 121 ~~~~~C~~C~~~~~r~-~~------------~~~~~~~C~~C~~~l~~~ 156 (157)
T PF10263_consen 121 KYVYRCPSCGREYKRH-RR------------SKRKRYRCGRCGGPLVQV 156 (157)
T ss_pred ceEEEcCCCCCEeeee-cc------------cchhhEECCCCCCEEEEc
Confidence 3456788888776211 11 123458999999999753
No 56
>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=66.77 E-value=4.3 Score=26.31 Aligned_cols=20 Identities=15% Similarity=0.338 Sum_probs=13.6
Q ss_pred eeeeeeccCceeCCCCCCce
Q 035291 12 RKVHKCKPAAGICSRCGGGA 31 (68)
Q Consensus 12 ~kv~g~~~a~g~Cp~CGg~v 31 (68)
+=.+-..|+.+.|++||...
T Consensus 61 ~L~I~~~p~~~~C~~Cg~~~ 80 (115)
T TIGR00100 61 KLNIEDEPVECECEDCSEEV 80 (115)
T ss_pred EEEEEeeCcEEEcccCCCEE
Confidence 33455677888888888554
No 57
>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=66.56 E-value=5 Score=20.77 Aligned_cols=14 Identities=21% Similarity=0.406 Sum_probs=10.2
Q ss_pred CceeCCCCCCceeE
Q 035291 20 AAGICSRCGGGASV 33 (68)
Q Consensus 20 a~g~Cp~CGg~v~a 33 (68)
..-.||+||....|
T Consensus 24 ~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 24 GKVRCGKCGHVWYA 37 (38)
T ss_pred CEEECCCCCCEEEe
Confidence 35689999987744
No 58
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=66.18 E-value=5.5 Score=26.07 Aligned_cols=9 Identities=33% Similarity=1.054 Sum_probs=6.4
Q ss_pred eCCCCCCce
Q 035291 23 ICSRCGGGA 31 (68)
Q Consensus 23 ~Cp~CGg~v 31 (68)
-||.||+..
T Consensus 4 FCp~Cgsll 12 (113)
T COG1594 4 FCPKCGSLL 12 (113)
T ss_pred ccCCccCee
Confidence 377777776
No 59
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=66.18 E-value=3.5 Score=29.07 Aligned_cols=25 Identities=20% Similarity=0.467 Sum_probs=16.3
Q ss_pred EEEEEeCCceeeeeeccCceeCCCCCCce
Q 035291 3 CFCFLVDQTRKVHKCKPAAGICSRCGGGA 31 (68)
Q Consensus 3 ~~~fvcde~~kv~g~~~a~g~Cp~CGg~v 31 (68)
|.|-+||- .+.| .+|+.||-||.+-
T Consensus 135 ~vC~vCGy--~~~g--e~P~~CPiCga~k 159 (166)
T COG1592 135 WVCPVCGY--THEG--EAPEVCPICGAPK 159 (166)
T ss_pred EEcCCCCC--cccC--CCCCcCCCCCChH
Confidence 44455552 2334 8999999999753
No 60
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=65.94 E-value=6.7 Score=29.95 Aligned_cols=40 Identities=23% Similarity=0.350 Sum_probs=26.2
Q ss_pred ceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceeeee
Q 035291 21 AGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKSY 67 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~~~ 67 (68)
...||+||+.- ...+.-++--....|..+|..|+.=|+++
T Consensus 226 R~~C~~Cg~~~-------~l~y~~~~~~~~~~r~e~C~~C~~YlK~~ 265 (309)
T PRK03564 226 RVKCSNCEQSG-------KLHYWSLDSEQAAVKAESCGDCGTYLKIL 265 (309)
T ss_pred CccCCCCCCCC-------ceeeeeecCCCcceEeeecccccccceec
Confidence 46799999731 22222233222467999999999988864
No 61
>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=65.62 E-value=3.9 Score=25.35 Aligned_cols=8 Identities=38% Similarity=1.165 Sum_probs=5.7
Q ss_pred CCCCCCce
Q 035291 24 CSRCGGGA 31 (68)
Q Consensus 24 Cp~CGg~v 31 (68)
||+||+.+
T Consensus 3 C~~Cg~~l 10 (104)
T TIGR01384 3 CPKCGSLM 10 (104)
T ss_pred CcccCccc
Confidence 77777766
No 62
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=64.90 E-value=3.6 Score=27.40 Aligned_cols=14 Identities=36% Similarity=0.686 Sum_probs=11.3
Q ss_pred eeCCCCCCceeEEE
Q 035291 22 GICSRCGGGASVAD 35 (68)
Q Consensus 22 g~Cp~CGg~v~a~d 35 (68)
-.||+||+.+.-.|
T Consensus 124 f~Cp~Cg~~l~~~d 137 (147)
T smart00531 124 FTCPRCGEELEEDD 137 (147)
T ss_pred EECCCCCCEEEEcC
Confidence 78999999985544
No 63
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=64.14 E-value=2.2 Score=36.50 Aligned_cols=21 Identities=29% Similarity=0.619 Sum_probs=15.1
Q ss_pred eeeccCceeCCCCCCceeEEE
Q 035291 15 HKCKPAAGICSRCGGGASVAD 35 (68)
Q Consensus 15 ~g~~~a~g~Cp~CGg~v~a~d 35 (68)
.|.---.|.||+|||.+++.|
T Consensus 832 ~~~~~~~~~~~~~~~~~~~~~ 852 (1006)
T PRK12775 832 EGFAFPYGMCPACGGKLQALD 852 (1006)
T ss_pred ccccCCcCcCcccccchhhhh
Confidence 344434499999999987654
No 64
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=63.94 E-value=10 Score=23.24 Aligned_cols=31 Identities=19% Similarity=0.433 Sum_probs=20.3
Q ss_pred ceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccce
Q 035291 21 AGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAV 63 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~ 63 (68)
.-.||.||..+. +|+.. ..|-.+.|.-|++.
T Consensus 6 lKPCPFCG~~~~--~v~~~----------~g~~~v~C~~CgA~ 36 (64)
T PRK09710 6 VKPCPFCGCPSV--TVKAI----------SGYYRAKCNGCESR 36 (64)
T ss_pred ccCCCCCCCcee--EEEec----------CceEEEEcCCCCcC
Confidence 346999999873 34431 23446788888875
No 65
>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=63.86 E-value=5.9 Score=26.31 Aligned_cols=45 Identities=22% Similarity=0.406 Sum_probs=27.8
Q ss_pred ccCceeCCCCCCceeEEEeeeeeEEEEEeeeece--eeeEEeeccccee
Q 035291 18 KPAAGICSRCGGGASVADMKTATRFCHVPFYWKS--WRAIICTFCGAVL 64 (68)
Q Consensus 18 ~~a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~--kr~~~Ct~C~r~L 64 (68)
.+....|+.|+|.+..++-+.-..- ||-.... -+=+.|+.|++.+
T Consensus 88 ~~~~sRC~~CN~~L~~v~~~~v~~~--vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 88 DPIFSRCPKCNGPLRPVSKEEVKDR--VPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CCCCCccCCCCcEeeechhhccccc--cCccccccCCeEEECCCCCCEe
Confidence 3345899999998866654432111 5444332 2356799999864
No 66
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.23 E-value=2.7 Score=28.85 Aligned_cols=14 Identities=43% Similarity=1.032 Sum_probs=11.2
Q ss_pred ccCceeCCCCCCce
Q 035291 18 KPAAGICSRCGGGA 31 (68)
Q Consensus 18 ~~a~g~Cp~CGg~v 31 (68)
.+..|.|||||.+=
T Consensus 18 ~Gl~grCP~CGeGr 31 (126)
T COG5349 18 RGLRGRCPRCGEGR 31 (126)
T ss_pred HHhcCCCCCCCCch
Confidence 46789999999763
No 67
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=63.02 E-value=12 Score=25.79 Aligned_cols=35 Identities=29% Similarity=0.743 Sum_probs=22.3
Q ss_pred eCCCCCCceeEEEeeeeeEEEE--Eeeeecee-eeEEeeccccee
Q 035291 23 ICSRCGGGASVADMKTATRFCH--VPFYWKSW-RAIICTFCGAVL 64 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfCf--lPl~~k~k-r~~~Ct~C~r~L 64 (68)
.||+||+... ++++. ||..-+.= -.+.|..||-+-
T Consensus 2 ~Cp~C~~~~~-------~~~~~~~IP~F~evii~sf~C~~CGyk~ 39 (160)
T smart00709 2 DCPSCGGNGT-------TRMLLTSIPYFREVIIMSFECEHCGYRN 39 (160)
T ss_pred cCCCCCCCCE-------EEEEEecCCCcceEEEEEEECCCCCCcc
Confidence 5999997752 34443 47654443 377899898653
No 68
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=62.90 E-value=9.5 Score=20.33 Aligned_cols=9 Identities=44% Similarity=1.091 Sum_probs=5.3
Q ss_pred eCCCCCCce
Q 035291 23 ICSRCGGGA 31 (68)
Q Consensus 23 ~Cp~CGg~v 31 (68)
.||.|+...
T Consensus 1 ~CP~C~~~l 9 (41)
T PF13453_consen 1 KCPRCGTEL 9 (41)
T ss_pred CcCCCCccc
Confidence 366776644
No 69
>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=62.68 E-value=3.5 Score=24.26 Aligned_cols=11 Identities=27% Similarity=0.803 Sum_probs=9.3
Q ss_pred ceeCCCCCCce
Q 035291 21 AGICSRCGGGA 31 (68)
Q Consensus 21 ~g~Cp~CGg~v 31 (68)
.+.||.|||--
T Consensus 13 Y~~Cp~CGN~~ 23 (49)
T PF12677_consen 13 YCKCPKCGNDK 23 (49)
T ss_pred hccCcccCCcE
Confidence 78999999854
No 70
>PRK09401 reverse gyrase; Reviewed
Probab=62.52 E-value=3 Score=36.57 Aligned_cols=12 Identities=42% Similarity=1.016 Sum_probs=10.1
Q ss_pred ceeCCCCCCcee
Q 035291 21 AGICSRCGGGAS 32 (68)
Q Consensus 21 ~g~Cp~CGg~v~ 32 (68)
.++||||||.++
T Consensus 7 ~~~cpnc~g~i~ 18 (1176)
T PRK09401 7 KNSCPNCGGDIS 18 (1176)
T ss_pred cccCCCCCCcCc
Confidence 368999999985
No 71
>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=62.15 E-value=7.8 Score=28.23 Aligned_cols=23 Identities=26% Similarity=0.391 Sum_probs=14.9
Q ss_pred eeeeeccCceeCCCCCCceeEEEee
Q 035291 13 KVHKCKPAAGICSRCGGGASVADMK 37 (68)
Q Consensus 13 kv~g~~~a~g~Cp~CGg~v~a~dv~ 37 (68)
+|-|+++ -.||+||+.+.-..+-
T Consensus 239 ~Vy~r~g--~pC~~Cg~~I~~~~~~ 261 (272)
T TIGR00577 239 QVYGRKG--EPCRRCGTPIEKIKVG 261 (272)
T ss_pred EEeCCCC--CCCCCCCCeeEEEEEC
Confidence 4445444 3599999999555444
No 72
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=61.53 E-value=7.7 Score=28.19 Aligned_cols=22 Identities=23% Similarity=0.317 Sum_probs=14.1
Q ss_pred eeeeccCceeCCCCCCceeEEEee
Q 035291 14 VHKCKPAAGICSRCGGGASVADMK 37 (68)
Q Consensus 14 v~g~~~a~g~Cp~CGg~v~a~dv~ 37 (68)
|-|+++ -.||+||+.+.-..+-
T Consensus 240 Vy~R~g--~pC~~Cg~~I~~~~~~ 261 (274)
T PRK01103 240 VYGREG--EPCRRCGTPIEKIKQG 261 (274)
T ss_pred EcCCCC--CCCCCCCCeeEEEEEC
Confidence 444433 3599999999554443
No 73
>PF07038 DUF1324: Protein of unknown function (DUF1324); InterPro: IPR009757 This family consists of several Circovirus proteins of around 60 residues in length. The function of this family is unknown.
Probab=61.25 E-value=7 Score=23.46 Aligned_cols=14 Identities=43% Similarity=0.852 Sum_probs=12.1
Q ss_pred eeEEEEEeeeecee
Q 035291 39 ATRFCHVPFYWKSW 52 (68)
Q Consensus 39 ~~rfCflPl~~k~k 52 (68)
+.|||..|+.+|+-
T Consensus 8 qsrfcifpltfkss 21 (59)
T PF07038_consen 8 QSRFCIFPLTFKSS 21 (59)
T ss_pred eeeeEEEEeeeccC
Confidence 77999999999863
No 74
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=61.02 E-value=9 Score=29.65 Aligned_cols=41 Identities=20% Similarity=0.465 Sum_probs=29.3
Q ss_pred eeCCCCCCceeEEEee--eeeEEEEEeeeec------eeeeEEeeccccee
Q 035291 22 GICSRCGGGASVADMK--TATRFCHVPFYWK------SWRAIICTFCGAVL 64 (68)
Q Consensus 22 g~Cp~CGg~v~a~dv~--s~~rfCflPl~~k------~kr~~~Ct~C~r~L 64 (68)
..||.||++. .+.- .....++||+.-+ .+++|.|+.|+..-
T Consensus 39 ~~CP~Cg~~~--~~~~~~~~~~I~~L~~~~~~~~L~~r~rR~~c~~c~~~~ 87 (402)
T COG3464 39 HRCPECGQRT--IRRHGWRIRKIQDLPLFEVPVYLFLRKRRYKCCRCGKRF 87 (402)
T ss_pred CCCCCCCCcc--eeccccceeeeeecccCCeeEEEEeccceeecccCCCCc
Confidence 8999999998 2221 2677788854432 36889999998763
No 75
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=60.99 E-value=8.6 Score=26.40 Aligned_cols=28 Identities=29% Similarity=0.555 Sum_probs=21.2
Q ss_pred CceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccce
Q 035291 20 AAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAV 63 (68)
Q Consensus 20 a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~ 63 (68)
.-..|+.||+.. +|.+ |....|+.|+.+
T Consensus 148 v~a~~~~~g~~~-------------~~~~---~~~~~c~~~~~~ 175 (189)
T PRK09521 148 IYAMCSRCRTPL-------------VKKG---ENELKCPNCGNI 175 (189)
T ss_pred EEEEccccCCce-------------EECC---CCEEECCCCCCE
Confidence 345788898877 7755 467999999965
No 76
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=60.72 E-value=3.7 Score=36.65 Aligned_cols=18 Identities=28% Similarity=0.746 Sum_probs=12.8
Q ss_pred ceeCCCCCCceeEEEeee
Q 035291 21 AGICSRCGGGASVADMKT 38 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~s 38 (68)
.++||||||..+.--.++
T Consensus 8 ~~~CpNCGG~isseRL~~ 25 (1187)
T COG1110 8 GSSCPNCGGDISSERLEK 25 (1187)
T ss_pred hccCCCCCCcCcHHHHhc
Confidence 368999999986544443
No 77
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=60.51 E-value=9 Score=20.74 Aligned_cols=15 Identities=20% Similarity=0.612 Sum_probs=10.3
Q ss_pred eCCCCCCceeEEEeee
Q 035291 23 ICSRCGGGASVADMKT 38 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s 38 (68)
.||+||+.- |.=.+.
T Consensus 2 ~Cp~C~~~~-a~~~q~ 16 (40)
T smart00440 2 PCPKCGNRE-ATFFQL 16 (40)
T ss_pred cCCCCCCCe-EEEEEE
Confidence 599999876 544443
No 78
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=60.14 E-value=16 Score=20.99 Aligned_cols=23 Identities=39% Similarity=0.848 Sum_probs=15.4
Q ss_pred EEeCCceeeeeeccCceeCC--CCCCce
Q 035291 6 FLVDQTRKVHKCKPAAGICS--RCGGGA 31 (68)
Q Consensus 6 fvcde~~kv~g~~~a~g~Cp--~CGg~v 31 (68)
+-+|++.||.. ..-.|| +||.++
T Consensus 6 Ykvd~~Gkv~r---~rk~CP~~~CG~Gv 30 (47)
T PF01599_consen 6 YKVDENGKVKR---LRKECPSPRCGAGV 30 (47)
T ss_dssp CEEETTTEEEE---SSEE-TSTTTTSSS
T ss_pred EEECCCCcEEE---hhhcCCCcccCCce
Confidence 34566667654 456899 999988
No 79
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=60.07 E-value=18 Score=25.72 Aligned_cols=38 Identities=24% Similarity=0.630 Sum_probs=21.2
Q ss_pred eCCCCCCceeEEEeeeeeEEEEEeeeecee-eeEEeeccccee
Q 035291 23 ICSRCGGGASVADMKTATRFCHVPFYWKSW-RAIICTFCGAVL 64 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~k-r~~~Ct~C~r~L 64 (68)
-||+||+......+...- ||..-+.= -.+.|..||-+-
T Consensus 2 ~Cp~C~~~~~~~~~~~~~----IP~F~evii~sf~C~~CGyr~ 40 (192)
T TIGR00310 2 DCPSCGGECETVMKTVND----IPYFGEVLETSTICEHCGYRS 40 (192)
T ss_pred cCCCCCCCCEEEEEEEcC----CCCcceEEEEEEECCCCCCcc
Confidence 399999765333333330 45433322 367788888653
No 80
>PHA00626 hypothetical protein
Probab=59.94 E-value=7.4 Score=23.69 Aligned_cols=32 Identities=25% Similarity=0.458 Sum_probs=20.2
Q ss_pred eCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeeccccee
Q 035291 23 ICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVL 64 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L 64 (68)
.||+||..-. +++ ..+.+...+|.|..||-..
T Consensus 2 ~CP~CGS~~I---vrc-------g~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNI---AKE-------KTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCcee---eee-------ceecccCcceEcCCCCCee
Confidence 5999998531 121 3344556788898888543
No 81
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=59.87 E-value=6.7 Score=25.38 Aligned_cols=20 Identities=25% Similarity=0.310 Sum_probs=12.3
Q ss_pred eeeeeeccCceeCCCCCCce
Q 035291 12 RKVHKCKPAAGICSRCGGGA 31 (68)
Q Consensus 12 ~kv~g~~~a~g~Cp~CGg~v 31 (68)
+=++-..|+.+.|+.||...
T Consensus 61 ~L~I~~vp~~~~C~~Cg~~~ 80 (113)
T PRK12380 61 DLHIVYKPAQAWCWDCSQVV 80 (113)
T ss_pred EEEEEeeCcEEEcccCCCEE
Confidence 33455567777777777443
No 82
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=59.75 E-value=5.7 Score=25.71 Aligned_cols=30 Identities=27% Similarity=0.338 Sum_probs=21.5
Q ss_pred CceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeeccccee
Q 035291 20 AAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVL 64 (68)
Q Consensus 20 a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L 64 (68)
..-.|++||.-- ++|.|-|+. .|+.|+.+.
T Consensus 41 ~~~~C~~Cg~~~------------~~~~SCk~R---~CP~C~~~~ 70 (111)
T PF14319_consen 41 HRYRCEDCGHEK------------IVYNSCKNR---HCPSCQAKA 70 (111)
T ss_pred ceeecCCCCceE------------EecCcccCc---CCCCCCChH
Confidence 345688888655 578888865 888888753
No 83
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=59.32 E-value=13 Score=22.90 Aligned_cols=38 Identities=21% Similarity=0.309 Sum_probs=23.5
Q ss_pred eCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEee--cccceeeee
Q 035291 23 ICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICT--FCGAVLKSY 67 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct--~C~r~L~~~ 67 (68)
.||.||..+. ..+|.+-= +. -..+.+.|+ -||.+.+++
T Consensus 3 ~CP~Cg~~a~--irtSr~~s---~~--~~~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 3 HCPLCQHAAH--ARTSRYIT---DT--TKERYHQCQNVNCSATFITY 42 (72)
T ss_pred cCCCCCCccE--EEEChhcC---hh--hheeeeecCCCCCCCEEEEE
Confidence 4999999873 33332100 22 235667888 899888765
No 84
>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=59.05 E-value=4.7 Score=21.61 Aligned_cols=13 Identities=23% Similarity=0.534 Sum_probs=9.5
Q ss_pred ceeCCCCCCceeE
Q 035291 21 AGICSRCGGGASV 33 (68)
Q Consensus 21 ~g~Cp~CGg~v~a 33 (68)
.-.|||||-.++|
T Consensus 4 ~~~C~nC~R~v~a 16 (33)
T PF08209_consen 4 YVECPNCGRPVAA 16 (33)
T ss_dssp EEE-TTTSSEEEG
T ss_pred eEECCCCcCCcch
Confidence 4579999998865
No 85
>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=58.42 E-value=5.4 Score=17.59 Aligned_cols=12 Identities=33% Similarity=0.980 Sum_probs=6.7
Q ss_pred EEeecccceeee
Q 035291 55 IICTFCGAVLKS 66 (68)
Q Consensus 55 ~~Ct~C~r~L~~ 66 (68)
|.|++|++...+
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 568888877654
No 86
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=58.37 E-value=4.3 Score=24.58 Aligned_cols=33 Identities=21% Similarity=0.399 Sum_probs=19.4
Q ss_pred cCceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeeccc
Q 035291 19 PAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCG 61 (68)
Q Consensus 19 ~a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~ 61 (68)
.+.=.|||||..+-.. =+-|.|--..|.|+-||
T Consensus 23 ~~~F~CPnCG~~~I~R----------C~~CRk~~~~Y~CP~CG 55 (59)
T PRK14890 23 AVKFLCPNCGEVIIYR----------CEKCRKQSNPYTCPKCG 55 (59)
T ss_pred cCEeeCCCCCCeeEee----------chhHHhcCCceECCCCC
Confidence 5666799998763121 13344455566676665
No 87
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=58.34 E-value=9.2 Score=27.94 Aligned_cols=22 Identities=23% Similarity=0.311 Sum_probs=14.0
Q ss_pred eeeeccCceeCCCCCCceeEEEee
Q 035291 14 VHKCKPAAGICSRCGGGASVADMK 37 (68)
Q Consensus 14 v~g~~~a~g~Cp~CGg~v~a~dv~ 37 (68)
|-|+++ -.||+||..+.-..+-
T Consensus 230 Vy~R~g--~pC~~Cg~~I~~~~~~ 251 (269)
T PRK14811 230 VYGREG--QPCPRCGTPIEKIVVG 251 (269)
T ss_pred ecCCCc--CCCCcCCCeeEEEEEC
Confidence 444433 3599999999554443
No 88
>PF15616 TerY-C: TerY-C metal binding domain
Probab=58.06 E-value=13 Score=25.42 Aligned_cols=38 Identities=18% Similarity=0.394 Sum_probs=24.3
Q ss_pred eeCCCCCCceeEEEeee-eeEEEEEeeeeceeeeEEeecccceee
Q 035291 22 GICSRCGGGASVADMKT-ATRFCHVPFYWKSWRAIICTFCGAVLK 65 (68)
Q Consensus 22 g~Cp~CGg~v~a~dv~s-~~rfCflPl~~k~kr~~~Ct~C~r~L~ 65 (68)
.-||+||+.. |.-+=+ -= =+|+..-..+.|+-|++...
T Consensus 78 PgCP~CGn~~-~fa~C~CGk-----l~Ci~g~~~~~CPwCg~~g~ 116 (131)
T PF15616_consen 78 PGCPHCGNQY-AFAVCGCGK-----LFCIDGEGEVTCPWCGNEGS 116 (131)
T ss_pred CCCCCCcChh-cEEEecCCC-----EEEeCCCCCEECCCCCCeee
Confidence 4599999995 222222 22 24455566889999988653
No 89
>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=58.02 E-value=7.8 Score=20.82 Aligned_cols=15 Identities=20% Similarity=0.618 Sum_probs=7.9
Q ss_pred eCCCCCCceeEEEeee
Q 035291 23 ICSRCGGGASVADMKT 38 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s 38 (68)
.||+||+.- |.=++.
T Consensus 2 ~Cp~Cg~~~-a~~~~~ 16 (39)
T PF01096_consen 2 KCPKCGHNE-AVFFQI 16 (39)
T ss_dssp --SSS-SSE-EEEEEE
T ss_pred CCcCCCCCe-EEEEEe
Confidence 599999987 444433
No 90
>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=57.59 E-value=8.4 Score=30.45 Aligned_cols=28 Identities=25% Similarity=0.579 Sum_probs=16.7
Q ss_pred eeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeeccccee
Q 035291 22 GICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVL 64 (68)
Q Consensus 22 g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L 64 (68)
..||+|++... ++|..+...|+.||...
T Consensus 223 ~~C~~C~~~l~---------------~h~~~~~l~Ch~Cg~~~ 250 (505)
T TIGR00595 223 LCCPNCDVSLT---------------YHKKEGKLRCHYCGYQE 250 (505)
T ss_pred cCCCCCCCceE---------------EecCCCeEEcCCCcCcC
Confidence 34777766652 33556666777776553
No 91
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=57.16 E-value=4.2 Score=35.61 Aligned_cols=11 Identities=36% Similarity=1.198 Sum_probs=9.8
Q ss_pred ceeCCCCCCce
Q 035291 21 AGICSRCGGGA 31 (68)
Q Consensus 21 ~g~Cp~CGg~v 31 (68)
.+.||||||.+
T Consensus 7 ~~~CPnCgg~i 17 (1171)
T TIGR01054 7 SNLCPNCGGEI 17 (1171)
T ss_pred cCCCCCCCCcc
Confidence 47899999998
No 92
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=57.15 E-value=10 Score=24.61 Aligned_cols=18 Identities=17% Similarity=0.289 Sum_probs=13.2
Q ss_pred eeeeeeccCceeCCCCCC
Q 035291 12 RKVHKCKPAAGICSRCGG 29 (68)
Q Consensus 12 ~kv~g~~~a~g~Cp~CGg 29 (68)
+=.+-..|+.+.|+.||.
T Consensus 61 ~L~i~~~p~~~~C~~Cg~ 78 (114)
T PRK03681 61 KLHLEEQEAECWCETCQQ 78 (114)
T ss_pred EEEEEeeCcEEEcccCCC
Confidence 345566788888888885
No 93
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=57.06 E-value=9.2 Score=28.72 Aligned_cols=30 Identities=33% Similarity=0.770 Sum_probs=20.6
Q ss_pred eeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceee
Q 035291 22 GICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLK 65 (68)
Q Consensus 22 g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~ 65 (68)
..||+||+.--..|.+ .-++.|.-||-.+.
T Consensus 2 ~~CpeCg~~~~~~d~~--------------~ge~VC~~CG~Vi~ 31 (285)
T COG1405 2 MSCPECGSTNIITDYE--------------RGEIVCADCGLVLE 31 (285)
T ss_pred CCCCCCCCccceeecc--------------CCeEEeccCCEEec
Confidence 4799999985455544 45677777776553
No 94
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=56.82 E-value=14 Score=19.47 Aligned_cols=9 Identities=56% Similarity=1.475 Sum_probs=6.5
Q ss_pred eCCCCCCce
Q 035291 23 ICSRCGGGA 31 (68)
Q Consensus 23 ~Cp~CGg~v 31 (68)
.|+.||+..
T Consensus 5 ~C~~C~~~~ 13 (33)
T PF08792_consen 5 KCSKCGGNG 13 (33)
T ss_pred EcCCCCCCe
Confidence 577777776
No 95
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=56.35 E-value=5.4 Score=22.10 Aligned_cols=31 Identities=35% Similarity=0.692 Sum_probs=13.0
Q ss_pred ceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeeccc
Q 035291 21 AGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCG 61 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~ 61 (68)
.+.||.|||.= ||-..+ -.+..-.++|..|+
T Consensus 3 h~pCP~CGG~D---------rFri~~-d~~~~G~~~C~~C~ 33 (40)
T PF08273_consen 3 HGPCPICGGKD---------RFRIFD-DKDGRGTWICRQCG 33 (40)
T ss_dssp EE--TTTT-TT---------TEEEET-T----S-EEETTTT
T ss_pred CCCCCCCcCcc---------ccccCc-CcccCCCEECCCCC
Confidence 36799999954 333111 11233566777773
No 96
>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=56.14 E-value=8.3 Score=21.32 Aligned_cols=11 Identities=36% Similarity=0.993 Sum_probs=8.6
Q ss_pred eCCCCCCceeE
Q 035291 23 ICSRCGGGASV 33 (68)
Q Consensus 23 ~Cp~CGg~v~a 33 (68)
-||.||..+..
T Consensus 1 ~CP~Cg~~a~i 11 (47)
T PF04606_consen 1 RCPHCGSKARI 11 (47)
T ss_pred CcCCCCCeeEE
Confidence 39999998743
No 97
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=55.69 E-value=5.4 Score=28.33 Aligned_cols=44 Identities=20% Similarity=0.581 Sum_probs=25.4
Q ss_pred cCceeCCCCCCceeEEEeeeeeEEEEEe-eeeceeeeEE-eeccccee
Q 035291 19 PAAGICSRCGGGASVADMKTATRFCHVP-FYWKSWRAII-CTFCGAVL 64 (68)
Q Consensus 19 ~a~g~Cp~CGg~v~a~dv~s~~rfCflP-l~~k~kr~~~-Ct~C~r~L 64 (68)
+--..||.|+|.+....=|-.- ==|| -......++. |+.|++.+
T Consensus 95 ~e~~RCp~CN~~L~~vs~eev~--~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 95 PEFSRCPECNGELEKVSREEVK--EKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred cccccCcccCCEeccCcHHHHh--hccchhhhhcccceeECCCCcccc
Confidence 4467899999988433222100 0022 2345566666 99999864
No 98
>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=55.55 E-value=5.5 Score=21.77 Aligned_cols=11 Identities=45% Similarity=1.217 Sum_probs=8.5
Q ss_pred ceeCCCCCCce
Q 035291 21 AGICSRCGGGA 31 (68)
Q Consensus 21 ~g~Cp~CGg~v 31 (68)
.+.||.|||.=
T Consensus 3 ~~pCP~CGG~D 13 (37)
T smart00778 3 HGPCPNCGGSD 13 (37)
T ss_pred ccCCCCCCCcc
Confidence 46799999954
No 99
>PF14353 CpXC: CpXC protein
Probab=55.43 E-value=12 Score=23.94 Aligned_cols=36 Identities=17% Similarity=0.167 Sum_probs=24.2
Q ss_pred eeeeeeccCceeCCCCCCcee------EEEeeeeeEEEEEee
Q 035291 12 RKVHKCKPAAGICSRCGGGAS------VADMKTATRFCHVPF 47 (68)
Q Consensus 12 ~kv~g~~~a~g~Cp~CGg~v~------a~dv~s~~rfCflPl 47 (68)
++++.-+=-.-.||+||.... -+|.+-.+.+-+.|-
T Consensus 29 e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~~~~~~i~~~P~ 70 (128)
T PF14353_consen 29 EKILDGSLFSFTCPSCGHKFRLEYPLLYHDPEKKFMIYYFPD 70 (128)
T ss_pred HHHHcCCcCEEECCCCCCceecCCCEEEEcCCCCEEEEEcCC
Confidence 455555566789999998873 245555666666665
No 100
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=54.88 E-value=6.6 Score=22.87 Aligned_cols=14 Identities=21% Similarity=0.503 Sum_probs=10.8
Q ss_pred ccCceeCCCCCCce
Q 035291 18 KPAAGICSRCGGGA 31 (68)
Q Consensus 18 ~~a~g~Cp~CGg~v 31 (68)
..-.-.|||||..+
T Consensus 21 ~~~~irCp~Cg~rI 34 (49)
T COG1996 21 ETRGIRCPYCGSRI 34 (49)
T ss_pred ccCceeCCCCCcEE
Confidence 34456899999988
No 101
>PRK14873 primosome assembly protein PriA; Provisional
Probab=54.53 E-value=11 Score=31.23 Aligned_cols=11 Identities=27% Similarity=0.742 Sum_probs=7.1
Q ss_pred ceeCCCCCCce
Q 035291 21 AGICSRCGGGA 31 (68)
Q Consensus 21 ~g~Cp~CGg~v 31 (68)
+-.||+|++..
T Consensus 392 ~~~C~~C~~~L 402 (665)
T PRK14873 392 PARCRHCTGPL 402 (665)
T ss_pred eeECCCCCCce
Confidence 34677777666
No 102
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=53.76 E-value=12 Score=28.44 Aligned_cols=33 Identities=18% Similarity=0.424 Sum_probs=12.0
Q ss_pred eeCCCCCCc-eeEEEeeeeeEEEEEeeeeceeeeEEeecccceeee
Q 035291 22 GICSRCGGG-ASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKS 66 (68)
Q Consensus 22 g~Cp~CGg~-v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~~ 66 (68)
.-|||||.. .+. .+. .+.-.+|.|.-|+-.+++
T Consensus 32 ~yCP~Cg~~~L~~--f~N----------N~PVaDF~C~~C~eeyEL 65 (254)
T PF06044_consen 32 MYCPNCGSKPLSK--FEN----------NRPVADFYCPNCNEEYEL 65 (254)
T ss_dssp ---TTT--SS-EE--------------------EEE-TTT--EEEE
T ss_pred CcCCCCCChhHhh--ccC----------CCccceeECCCCchHHhh
Confidence 579999998 422 122 223458899999877654
No 103
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=53.45 E-value=12 Score=24.99 Aligned_cols=48 Identities=19% Similarity=0.400 Sum_probs=28.9
Q ss_pred eeeeccCceeCCCCCCceeEEEe------eeeeEEEEEeeeeceeeeEEeecccce
Q 035291 14 VHKCKPAAGICSRCGGGASVADM------KTATRFCHVPFYWKSWRAIICTFCGAV 63 (68)
Q Consensus 14 v~g~~~a~g~Cp~CGg~v~a~dv------~s~~rfCflPl~~k~kr~~~Ct~C~r~ 63 (68)
.+-..++...|++||.-....|. +...-+=|+|--.. ..+.|+.||..
T Consensus 63 ~i~~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~CP~Cgs~ 116 (135)
T PRK03824 63 IFEEEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVH--AFLKCPKCGSR 116 (135)
T ss_pred EEEecceEEECCCCCCEEecccccccccccccccccccccccc--cCcCCcCCCCC
Confidence 34478899999999966543321 22334445664322 22569999864
No 104
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=53.39 E-value=4.8 Score=21.80 Aligned_cols=36 Identities=28% Similarity=0.580 Sum_probs=17.6
Q ss_pred CCCCCCceeEEEee-eeeEEEEEeeeeceeeeEEeecccceee
Q 035291 24 CSRCGGGASVADMK-TATRFCHVPFYWKSWRAIICTFCGAVLK 65 (68)
Q Consensus 24 Cp~CGg~v~a~dv~-s~~rfCflPl~~k~kr~~~Ct~C~r~L~ 65 (68)
|+.|+..+...++. +...--|=| .=+.|+.|++.|.
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~------~Cf~C~~C~~~l~ 37 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHP------ECFKCSKCGKPLN 37 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEET------TTSBETTTTCBTT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEc------cccccCCCCCccC
Confidence 67777777544443 111111112 2345777777664
No 105
>PRK05580 primosome assembly protein PriA; Validated
Probab=51.93 E-value=12 Score=30.71 Aligned_cols=27 Identities=22% Similarity=0.612 Sum_probs=16.7
Q ss_pred eeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccce
Q 035291 22 GICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAV 63 (68)
Q Consensus 22 g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~ 63 (68)
..||+|++... ++|..+...|+.||..
T Consensus 391 ~~C~~C~~~l~---------------~h~~~~~l~Ch~Cg~~ 417 (679)
T PRK05580 391 AECPHCDASLT---------------LHRFQRRLRCHHCGYQ 417 (679)
T ss_pred cCCCCCCCcee---------------EECCCCeEECCCCcCC
Confidence 46777777662 2355566667777654
No 106
>PRK04023 DNA polymerase II large subunit; Validated
Probab=51.90 E-value=6.6 Score=34.96 Aligned_cols=40 Identities=23% Similarity=0.357 Sum_probs=21.4
Q ss_pred CceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceeeee
Q 035291 20 AAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKSY 67 (68)
Q Consensus 20 a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~~~ 67 (68)
..-.||+||... ..-+|| |=|-+.-..+.|..|++.+..+
T Consensus 637 ~~frCP~CG~~T------e~i~fC--P~CG~~~~~y~CPKCG~El~~~ 676 (1121)
T PRK04023 637 FYRRCPFCGTHT------EPVYRC--PRCGIEVEEDECEKCGREPTPY 676 (1121)
T ss_pred CcccCCCCCCCC------CcceeC--ccccCcCCCCcCCCCCCCCCcc
Confidence 445666666651 122344 5554444446677777766543
No 107
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=51.48 E-value=15 Score=24.54 Aligned_cols=32 Identities=19% Similarity=0.318 Sum_probs=20.3
Q ss_pred CCceeeeeeccCceeCCCCCCceeEEEeeeeeE
Q 035291 9 DQTRKVHKCKPAAGICSRCGGGASVADMKTATR 41 (68)
Q Consensus 9 de~~kv~g~~~a~g~Cp~CGg~v~a~dv~s~~r 41 (68)
|+++....-++....||.||+.- |-=|+-|+|
T Consensus 53 gg~~a~~nv~~t~~~Cp~Cgh~r-ayF~qlQtR 84 (105)
T KOG2906|consen 53 GGDEAWENVDQTEATCPTCGHER-AYFMQLQTR 84 (105)
T ss_pred CCcccccchhhccCcCCCCCCCc-eEEEEeeec
Confidence 33344444566778999999987 555544443
No 108
>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=51.22 E-value=20 Score=24.90 Aligned_cols=35 Identities=26% Similarity=0.651 Sum_probs=18.4
Q ss_pred CCCCCCc-eeEEEeeeeeEEEEEeeeecee-eeEEeecccce
Q 035291 24 CSRCGGG-ASVADMKTATRFCHVPFYWKSW-RAIICTFCGAV 63 (68)
Q Consensus 24 Cp~CGg~-v~a~dv~s~~rfCflPl~~k~k-r~~~Ct~C~r~ 63 (68)
||.||+. .......+ =||..-+.= -.+.|..||-+
T Consensus 1 CP~Cg~~~~~~~~~~~-----~IP~F~evii~sf~C~~CGyr 37 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDY-----DIPYFGKIMLSTYICEKCGYR 37 (163)
T ss_pred CCCCCCcceEeeeEec-----cCCCcceEEEEEEECCCCCCc
Confidence 8999986 32222111 134333322 35678888754
No 109
>PRK05320 rhodanese superfamily protein; Provisional
Probab=51.21 E-value=12 Score=27.29 Aligned_cols=28 Identities=18% Similarity=0.419 Sum_probs=19.5
Q ss_pred EEEeCCceeeee--eccCceeCCCCCCcee
Q 035291 5 CFLVDQTRKVHK--CKPAAGICSRCGGGAS 32 (68)
Q Consensus 5 ~fvcde~~kv~g--~~~a~g~Cp~CGg~v~ 32 (68)
+||+|++--|.- ...+...|+.||-+++
T Consensus 226 ~fVFD~R~~~~~~~~~~~~~~c~~c~~~~~ 255 (257)
T PRK05320 226 CFVFDYRTALDPQLAPLVDVTCFACRAVVT 255 (257)
T ss_pred eeeecCeeecCCCCccCccceecCCCCcCC
Confidence 689998843322 2345678999998874
No 110
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=50.77 E-value=14 Score=26.78 Aligned_cols=27 Identities=33% Similarity=0.630 Sum_probs=19.2
Q ss_pred CceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccce
Q 035291 20 AAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAV 63 (68)
Q Consensus 20 a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~ 63 (68)
+-..|+|||+.. + +.++...|+.|++.
T Consensus 148 I~A~CsrC~~~L-------------~----~~~~~l~Cp~Cg~t 174 (188)
T COG1096 148 IYARCSRCRAPL-------------V----KKGNMLKCPNCGNT 174 (188)
T ss_pred EEEEccCCCcce-------------E----EcCcEEECCCCCCE
Confidence 446799999877 1 24667788888864
No 111
>PF08063 PADR1: PADR1 (NUC008) domain; InterPro: IPR012982 This domain is found in poly(ADP-ribose)-synthetases []. The function of this domain is unknown.; GO: 0003950 NAD+ ADP-ribosyltransferase activity, 0005634 nucleus; PDB: 2JVN_A 4DQY_E 2RIQ_A.
Probab=50.74 E-value=10 Score=22.07 Aligned_cols=13 Identities=38% Similarity=0.877 Sum_probs=7.5
Q ss_pred cCceeCCCCCCce
Q 035291 19 PAAGICSRCGGGA 31 (68)
Q Consensus 19 ~a~g~Cp~CGg~v 31 (68)
+|...||.|+|..
T Consensus 12 Gal~~Cp~C~~~~ 24 (55)
T PF08063_consen 12 GALEPCPKCKGGQ 24 (55)
T ss_dssp TEE---SSSSE-E
T ss_pred cCCCCCCCCCCCe
Confidence 5788999999965
No 112
>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=50.66 E-value=15 Score=21.76 Aligned_cols=30 Identities=23% Similarity=0.533 Sum_probs=17.6
Q ss_pred eeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceee
Q 035291 22 GICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLK 65 (68)
Q Consensus 22 g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~ 65 (68)
-.||.|++-- -++.+.-..+.|..|+..|.
T Consensus 8 VkCp~C~~~q--------------~vFSha~t~V~C~~Cg~~L~ 37 (55)
T PF01667_consen 8 VKCPGCYNIQ--------------TVFSHAQTVVKCVVCGTVLA 37 (55)
T ss_dssp EE-TTT-SEE--------------EEETT-SS-EE-SSSTSEEE
T ss_pred EECCCCCCee--------------EEEecCCeEEEcccCCCEec
Confidence 3577777754 24566778888999988885
No 113
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=50.18 E-value=8.6 Score=18.73 Aligned_cols=36 Identities=25% Similarity=0.595 Sum_probs=19.6
Q ss_pred eCCCCCCceeEEEeeeeeEEEEEeeeecee--eeEEeecccceee
Q 035291 23 ICSRCGGGASVADMKTATRFCHVPFYWKSW--RAIICTFCGAVLK 65 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~k--r~~~Ct~C~r~L~ 65 (68)
.|+.|+..+...+.. +..-.+.| .=|.|+.|++.|.
T Consensus 1 ~C~~C~~~i~~~~~~-------~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELV-------LRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEE-------EEeCCccccccCCCCcccCCcCc
Confidence 377787776443111 11112223 3377999998875
No 114
>PRK11827 hypothetical protein; Provisional
Probab=50.01 E-value=15 Score=22.00 Aligned_cols=27 Identities=19% Similarity=0.466 Sum_probs=17.4
Q ss_pred eCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeeccccee
Q 035291 23 ICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVL 64 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L 64 (68)
.||.|.|.+. -|- ......|+.|+..+
T Consensus 10 aCP~ckg~L~-~~~--------------~~~~Lic~~~~laY 36 (60)
T PRK11827 10 ACPVCNGKLW-YNQ--------------EKQELICKLDNLAF 36 (60)
T ss_pred ECCCCCCcCe-EcC--------------CCCeEECCccCeec
Confidence 6999999883 332 23356677776554
No 115
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=49.80 E-value=8.7 Score=30.77 Aligned_cols=38 Identities=26% Similarity=0.632 Sum_probs=27.5
Q ss_pred eeeeeccCceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceeee
Q 035291 13 KVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKS 66 (68)
Q Consensus 13 kv~g~~~a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~~ 66 (68)
++..++...-.||+||+-. | .+++..|-|..|+++..+
T Consensus 342 ~l~~~~~~~p~Cp~Cg~~m-----~-----------S~G~~g~rC~kCg~~~~~ 379 (421)
T COG1571 342 KLARYERVNPVCPRCGGRM-----K-----------SAGRNGFRCKKCGTRARE 379 (421)
T ss_pred EeeeeEEcCCCCCccCCch-----h-----------hcCCCCcccccccccCCc
Confidence 4445777778999999865 2 244457899999988754
No 116
>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=49.28 E-value=6.9 Score=24.22 Aligned_cols=10 Identities=30% Similarity=1.139 Sum_probs=4.4
Q ss_pred eeCCCCCCce
Q 035291 22 GICSRCGGGA 31 (68)
Q Consensus 22 g~Cp~CGg~v 31 (68)
--||+|||..
T Consensus 25 ~FCp~CGn~T 34 (73)
T PF08772_consen 25 QFCPKCGNAT 34 (73)
T ss_dssp -S-SSS--S-
T ss_pred eeCcccCCCc
Confidence 3699999974
No 117
>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=48.89 E-value=16 Score=19.93 Aligned_cols=12 Identities=33% Similarity=0.958 Sum_probs=9.1
Q ss_pred cCceeCCCCCCc
Q 035291 19 PAAGICSRCGGG 30 (68)
Q Consensus 19 ~a~g~Cp~CGg~ 30 (68)
..+-.||.||..
T Consensus 24 ~~~~~CP~Cg~~ 35 (52)
T TIGR02605 24 DPLATCPECGGE 35 (52)
T ss_pred CCCCCCCCCCCC
Confidence 355679999984
No 118
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=48.80 E-value=7.3 Score=30.89 Aligned_cols=26 Identities=19% Similarity=0.234 Sum_probs=21.0
Q ss_pred EEEEEeeeeceeeeEEeecccceeee
Q 035291 41 RFCHVPFYWKSWRAIICTFCGAVLKS 66 (68)
Q Consensus 41 rfCflPl~~k~kr~~~Ct~C~r~L~~ 66 (68)
.|-|-|+|-+-+++|.|++|+.++=|
T Consensus 6 ~~~~C~ic~vq~~~YtCPRCn~~YCs 31 (383)
T KOG4317|consen 6 SFLACGICGVQKREYTCPRCNLLYCS 31 (383)
T ss_pred ceeeccccccccccccCCCCCcccee
Confidence 34445889999999999999988755
No 119
>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=48.76 E-value=1.6 Score=28.86 Aligned_cols=40 Identities=28% Similarity=0.650 Sum_probs=26.3
Q ss_pred CceeCCCCCCceeEEEeeeeeEEEEE-------ee---eeceeeeEEeecccce
Q 035291 20 AAGICSRCGGGASVADMKTATRFCHV-------PF---YWKSWRAIICTFCGAV 63 (68)
Q Consensus 20 a~g~Cp~CGg~v~a~dv~s~~rfCfl-------Pl---~~k~kr~~~Ct~C~r~ 63 (68)
+.|.||.|+-++ +|+.++.|-| |+ +.=.-|+..|+.||+.
T Consensus 48 vvggCp~CrvG~----le~~ft~~Gi~~AI~fFPiGilcc~~~r~~rC~nCG~~ 97 (98)
T PF10164_consen 48 VVGGCPACRVGV----LEDSFTCCGILCAIFFFPIGILCCLAMRERRCSNCGAT 97 (98)
T ss_pred EecCCCCCceee----ecccccHHHHHHHHHHHhhHHHHhhhcCccccCCCCcc
Confidence 458899999888 4555554422 54 2223467779999875
No 120
>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=48.71 E-value=8.3 Score=23.04 Aligned_cols=10 Identities=30% Similarity=0.707 Sum_probs=8.3
Q ss_pred eeCCCCCCce
Q 035291 22 GICSRCGGGA 31 (68)
Q Consensus 22 g~Cp~CGg~v 31 (68)
.-||+||.++
T Consensus 4 kHC~~CG~~I 13 (59)
T PF09889_consen 4 KHCPVCGKPI 13 (59)
T ss_pred CcCCcCCCcC
Confidence 3599999887
No 121
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=48.11 E-value=8.6 Score=23.22 Aligned_cols=9 Identities=33% Similarity=0.914 Sum_probs=7.4
Q ss_pred eCCCCCCce
Q 035291 23 ICSRCGGGA 31 (68)
Q Consensus 23 ~Cp~CGg~v 31 (68)
+||+||+..
T Consensus 17 ~CP~Cgs~~ 25 (61)
T PRK08351 17 RCPVCGSRD 25 (61)
T ss_pred cCCCCcCCc
Confidence 699999844
No 122
>PLN00209 ribosomal protein S27; Provisional
Probab=48.02 E-value=26 Score=22.65 Aligned_cols=31 Identities=23% Similarity=0.424 Sum_probs=23.6
Q ss_pred ceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceee
Q 035291 21 AGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLK 65 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~ 65 (68)
--.||.|++-- .++.+.-..+.|..||..|.
T Consensus 36 ~VkCp~C~n~q--------------~VFShA~t~V~C~~Cg~~L~ 66 (86)
T PLN00209 36 DVKCQGCFNIT--------------TVFSHSQTVVVCGSCQTVLC 66 (86)
T ss_pred EEECCCCCCee--------------EEEecCceEEEccccCCEee
Confidence 45688888865 35566778899999999885
No 123
>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=47.87 E-value=8.5 Score=19.43 Aligned_cols=11 Identities=36% Similarity=0.912 Sum_probs=8.1
Q ss_pred CceeCCCCCCc
Q 035291 20 AAGICSRCGGG 30 (68)
Q Consensus 20 a~g~Cp~CGg~ 30 (68)
+.-.||+||--
T Consensus 13 ~~~~Cp~CG~~ 23 (26)
T PF10571_consen 13 SAKFCPHCGYD 23 (26)
T ss_pred hcCcCCCCCCC
Confidence 45679999964
No 124
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=47.75 E-value=7.6 Score=20.62 Aligned_cols=15 Identities=33% Similarity=0.492 Sum_probs=12.0
Q ss_pred eeeccCceeCCCCCC
Q 035291 15 HKCKPAAGICSRCGG 29 (68)
Q Consensus 15 ~g~~~a~g~Cp~CGg 29 (68)
+.-+++..+|++||.
T Consensus 19 ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 19 IPPKGRKVRCSKCGH 33 (36)
T ss_pred CCCCCcEEECCCCCC
Confidence 556777889999986
No 125
>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=47.67 E-value=13 Score=30.68 Aligned_cols=22 Identities=27% Similarity=0.543 Sum_probs=17.1
Q ss_pred eeCCCCCCceeEEEeeeeeEEE-EE-ee
Q 035291 22 GICSRCGGGASVADMKTATRFC-HV-PF 47 (68)
Q Consensus 22 g~Cp~CGg~v~a~dv~s~~rfC-fl-Pl 47 (68)
-.||.||+ .|++.+.|.| ++ |+
T Consensus 547 ~~CP~CGs----~~~ev~sRv~GYl~~v 570 (586)
T TIGR02827 547 HRCPVCGS----ANIDYGTRVIGYLKRV 570 (586)
T ss_pred CcCcCCCC----ccceEEEeecceecCc
Confidence 58999997 3688888988 34 65
No 126
>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=47.30 E-value=10 Score=17.22 Aligned_cols=11 Identities=27% Similarity=0.866 Sum_probs=7.4
Q ss_pred EEeecccceee
Q 035291 55 IICTFCGAVLK 65 (68)
Q Consensus 55 ~~Ct~C~r~L~ 65 (68)
|.|..|++...
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 56777777654
No 127
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=47.27 E-value=17 Score=24.22 Aligned_cols=14 Identities=43% Similarity=0.983 Sum_probs=9.0
Q ss_pred CCCCCCceeEEEee
Q 035291 24 CSRCGGGASVADMK 37 (68)
Q Consensus 24 Cp~CGg~v~a~dv~ 37 (68)
||-||+...++-++
T Consensus 1 CPvCg~~l~vt~l~ 14 (113)
T PF09862_consen 1 CPVCGGELVVTRLK 14 (113)
T ss_pred CCCCCCceEEEEEE
Confidence 77777777655443
No 128
>PRK14701 reverse gyrase; Provisional
Probab=47.22 E-value=7.6 Score=35.42 Aligned_cols=13 Identities=31% Similarity=0.925 Sum_probs=10.2
Q ss_pred ceeCCCCCCceeE
Q 035291 21 AGICSRCGGGASV 33 (68)
Q Consensus 21 ~g~Cp~CGg~v~a 33 (68)
.++||||||.++.
T Consensus 6 ~~~cpnc~g~~~~ 18 (1638)
T PRK14701 6 KEMCPNCGGDITD 18 (1638)
T ss_pred cccCCCCCCccch
Confidence 3689999999843
No 129
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=47.12 E-value=10 Score=17.57 Aligned_cols=12 Identities=25% Similarity=0.766 Sum_probs=9.3
Q ss_pred EEeecccceeee
Q 035291 55 IICTFCGAVLKS 66 (68)
Q Consensus 55 ~~Ct~C~r~L~~ 66 (68)
|.|.+|++...+
T Consensus 1 ~~C~~C~~~f~s 12 (25)
T PF12874_consen 1 FYCDICNKSFSS 12 (25)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCCcCC
Confidence 579999987654
No 130
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.61 E-value=15 Score=23.85 Aligned_cols=19 Identities=11% Similarity=-0.038 Sum_probs=12.0
Q ss_pred eeeeeccCceeCCCCCCce
Q 035291 13 KVHKCKPAAGICSRCGGGA 31 (68)
Q Consensus 13 kv~g~~~a~g~Cp~CGg~v 31 (68)
=.+-..|+.+.|..||...
T Consensus 63 L~Ie~vp~~~~C~~Cg~~~ 81 (117)
T PRK00564 63 LDIVDEKVELECKDCSHVF 81 (117)
T ss_pred EEEEecCCEEEhhhCCCcc
Confidence 3445567777777777544
No 131
>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=46.37 E-value=11 Score=20.19 Aligned_cols=30 Identities=33% Similarity=0.703 Sum_probs=14.3
Q ss_pred ceeCCCCCCceeEEEeeeeeEEEEEeeeec--eeeeEEeecccce
Q 035291 21 AGICSRCGGGASVADMKTATRFCHVPFYWK--SWRAIICTFCGAV 63 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k--~kr~~~Ct~C~r~ 63 (68)
|-.|.+|++.++ |++.= .-+...|.+|+..
T Consensus 2 p~rC~~C~aylN-------------p~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 2 PVRCRRCRAYLN-------------PFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp S-B-TTT--BS--------------TTSEEETTTTEEEETTT--E
T ss_pred ccccCCCCCEEC-------------CcceEcCCCCEEECcCCCCc
Confidence 457889998873 22222 2346789998864
No 132
>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=46.32 E-value=9.1 Score=21.23 Aligned_cols=9 Identities=33% Similarity=1.006 Sum_probs=7.4
Q ss_pred ceeCCCCCC
Q 035291 21 AGICSRCGG 29 (68)
Q Consensus 21 ~g~Cp~CGg 29 (68)
+..|||||.
T Consensus 29 ~~~CpYCg~ 37 (40)
T PF10276_consen 29 PVVCPYCGT 37 (40)
T ss_dssp EEEETTTTE
T ss_pred eEECCCCCC
Confidence 578999985
No 133
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=45.58 E-value=11 Score=23.14 Aligned_cols=12 Identities=25% Similarity=0.551 Sum_probs=8.2
Q ss_pred eccCceeCCCCC
Q 035291 17 CKPAAGICSRCG 28 (68)
Q Consensus 17 ~~~a~g~Cp~CG 28 (68)
.+.++-.||+||
T Consensus 46 k~g~~Y~Cp~CG 57 (61)
T COG2888 46 KLGNPYRCPKCG 57 (61)
T ss_pred HcCCceECCCcC
Confidence 356677777776
No 134
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=44.96 E-value=9.3 Score=21.16 Aligned_cols=10 Identities=60% Similarity=1.660 Sum_probs=5.8
Q ss_pred ceeCCCCCCc
Q 035291 21 AGICSRCGGG 30 (68)
Q Consensus 21 ~g~Cp~CGg~ 30 (68)
++.||+||-+
T Consensus 2 ~~~CprC~kg 11 (36)
T PF14787_consen 2 PGLCPRCGKG 11 (36)
T ss_dssp --C-TTTSSS
T ss_pred CccCcccCCC
Confidence 6789999865
No 135
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=44.85 E-value=5.7 Score=19.22 Aligned_cols=13 Identities=23% Similarity=0.608 Sum_probs=9.4
Q ss_pred eEEeecccceeee
Q 035291 54 AIICTFCGAVLKS 66 (68)
Q Consensus 54 ~~~Ct~C~r~L~~ 66 (68)
.|.|..|++.+.+
T Consensus 1 q~~C~~C~k~f~~ 13 (27)
T PF12171_consen 1 QFYCDACDKYFSS 13 (27)
T ss_dssp -CBBTTTTBBBSS
T ss_pred CCCcccCCCCcCC
Confidence 3679999987653
No 136
>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=44.22 E-value=23 Score=18.21 Aligned_cols=12 Identities=33% Similarity=0.786 Sum_probs=9.4
Q ss_pred CceeCCCCCCce
Q 035291 20 AAGICSRCGGGA 31 (68)
Q Consensus 20 a~g~Cp~CGg~v 31 (68)
++-.||.||...
T Consensus 16 ~~~~CP~Cg~~~ 27 (33)
T cd00350 16 APWVCPVCGAPK 27 (33)
T ss_pred CCCcCcCCCCcH
Confidence 777888888754
No 137
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=43.93 E-value=13 Score=22.08 Aligned_cols=15 Identities=33% Similarity=0.634 Sum_probs=9.0
Q ss_pred ccCceeCCCCCCcee
Q 035291 18 KPAAGICSRCGGGAS 32 (68)
Q Consensus 18 ~~a~g~Cp~CGg~v~ 32 (68)
.++-|.||+|...++
T Consensus 52 ~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 52 IPIFGECPYCSSPIS 66 (70)
T ss_dssp T--EEE-TTT-SEEE
T ss_pred cccccCCcCCCCeee
Confidence 467799999998874
No 138
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=43.89 E-value=19 Score=23.64 Aligned_cols=14 Identities=29% Similarity=0.541 Sum_probs=7.0
Q ss_pred eeeccCceeCCCCCC
Q 035291 15 HKCKPAAGICSRCGG 29 (68)
Q Consensus 15 ~g~~~a~g~Cp~CGg 29 (68)
+-..|+.+.| .||.
T Consensus 64 I~~vp~~~~C-~Cg~ 77 (124)
T PRK00762 64 VEMIPVEIEC-ECGY 77 (124)
T ss_pred EEecCeeEEe-eCcC
Confidence 3344555555 5553
No 139
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=43.63 E-value=13 Score=25.59 Aligned_cols=15 Identities=33% Similarity=0.749 Sum_probs=10.0
Q ss_pred eccCceeCCCCCCce
Q 035291 17 CKPAAGICSRCGGGA 31 (68)
Q Consensus 17 ~~~a~g~Cp~CGg~v 31 (68)
+...--=||.|||.-
T Consensus 15 s~eil~GCP~CGg~k 29 (131)
T PF09845_consen 15 SKEILSGCPECGGNK 29 (131)
T ss_pred cHHHHccCcccCCcc
Confidence 333445599999875
No 140
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=43.55 E-value=34 Score=22.04 Aligned_cols=31 Identities=16% Similarity=0.398 Sum_probs=23.3
Q ss_pred ceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceee
Q 035291 21 AGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLK 65 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~ 65 (68)
--.||.|++-- .++.+.-..+.|..||..|.
T Consensus 35 ~VkCp~C~n~q--------------~VFShA~t~V~C~~Cg~~L~ 65 (85)
T PTZ00083 35 DVKCPGCSQIT--------------TVFSHAQTVVLCGGCSSQLC 65 (85)
T ss_pred EEECCCCCCee--------------EEEecCceEEEccccCCEee
Confidence 35688888755 34566778899999998885
No 141
>PRK04351 hypothetical protein; Provisional
Probab=43.40 E-value=29 Score=23.68 Aligned_cols=34 Identities=24% Similarity=0.388 Sum_probs=23.0
Q ss_pred CceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceeee
Q 035291 20 AAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKS 66 (68)
Q Consensus 20 a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~~ 66 (68)
-.=+|.+||.-. .. ..++ +.++|.|..|+.+|+.
T Consensus 111 y~Y~C~~Cg~~~-~r----~Rr~--------n~~~yrCg~C~g~L~~ 144 (149)
T PRK04351 111 YLYECQSCGQQY-LR----KRRI--------NTKRYRCGKCRGKLKL 144 (149)
T ss_pred EEEECCCCCCEe-ee----eeec--------CCCcEEeCCCCcEeee
Confidence 346788898543 22 1221 3589999999999975
No 142
>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=42.97 E-value=17 Score=18.39 Aligned_cols=20 Identities=20% Similarity=0.491 Sum_probs=9.0
Q ss_pred eCCCCCCceeEEEeeeeeEEE
Q 035291 23 ICSRCGGGASVADMKTATRFC 43 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfC 43 (68)
.||-||..+. .+-+....+|
T Consensus 1 ~CP~C~s~l~-~~~~ev~~~C 20 (28)
T PF03119_consen 1 TCPVCGSKLV-REEGEVDIRC 20 (28)
T ss_dssp B-TTT--BEE-E-CCTTCEEE
T ss_pred CcCCCCCEeE-cCCCCEeEEC
Confidence 4899999984 3333334444
No 143
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=42.86 E-value=12 Score=29.72 Aligned_cols=27 Identities=30% Similarity=0.834 Sum_probs=20.3
Q ss_pred ceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceeee
Q 035291 21 AGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKS 66 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~~ 66 (68)
.-.||+|+.++ |=||. .|++|+-.|++
T Consensus 276 Gy~CP~Ckakv-----------CsLP~--------eCpiC~ltLVs 302 (378)
T KOG2807|consen 276 GYFCPQCKAKV-----------CSLPI--------ECPICSLTLVS 302 (378)
T ss_pred ceeCCcccCee-----------ecCCc--------cCCccceeEec
Confidence 34688888776 77775 58888888876
No 144
>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=42.83 E-value=2.6 Score=26.56 Aligned_cols=38 Identities=26% Similarity=0.517 Sum_probs=27.7
Q ss_pred CceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceee
Q 035291 20 AAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLK 65 (68)
Q Consensus 20 a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~ 65 (68)
.+..|++||..+...|. ||+-.=-.-+-.|.-|++++-
T Consensus 32 ~rS~C~~C~~~L~~~~l--------IPi~S~l~lrGrCr~C~~~I~ 69 (92)
T PF06750_consen 32 PRSHCPHCGHPLSWWDL--------IPILSYLLLRGRCRYCGAPIP 69 (92)
T ss_pred CCCcCcCCCCcCccccc--------chHHHHHHhCCCCcccCCCCC
Confidence 35789999999966654 677666666667888887764
No 145
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=42.35 E-value=47 Score=22.51 Aligned_cols=33 Identities=18% Similarity=0.309 Sum_probs=23.8
Q ss_pred ceeCCCCCCceeEEEeeeeeEEEEEeeeeceee
Q 035291 21 AGICSRCGGGASVADMKTATRFCHVPFYWKSWR 53 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr 53 (68)
..+||.||....++=|-...-+=-|=|+.|...
T Consensus 49 ~t~CP~Cg~~~e~~fvva~~aLVgl~l~mkVFN 81 (115)
T COG1885 49 STSCPKCGEPFESAFVVANTALVGLILSMKVFN 81 (115)
T ss_pred cccCCCCCCccceeEEEecceeEEEEEEEEEec
Confidence 357999999998777766666666666666543
No 146
>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=42.27 E-value=38 Score=25.95 Aligned_cols=15 Identities=20% Similarity=0.516 Sum_probs=12.3
Q ss_pred cCceeCCCCCCceeE
Q 035291 19 PAAGICSRCGGGASV 33 (68)
Q Consensus 19 ~a~g~Cp~CGg~v~a 33 (68)
.-.-.||.||+.|..
T Consensus 28 ~~~~~CP~C~~~v~l 42 (375)
T PF06054_consen 28 KGKYFCPGCGEPVIL 42 (375)
T ss_pred CCcEECCCCCCeeEE
Confidence 557789999999954
No 147
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=41.52 E-value=12 Score=29.26 Aligned_cols=9 Identities=33% Similarity=0.962 Sum_probs=6.1
Q ss_pred eCCCCCCce
Q 035291 23 ICSRCGGGA 31 (68)
Q Consensus 23 ~Cp~CGg~v 31 (68)
+|++||+.+
T Consensus 1 ~C~~Cg~~v 9 (343)
T PF10005_consen 1 SCPNCGQPV 9 (343)
T ss_pred CCCCCCCcc
Confidence 477777766
No 148
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=41.19 E-value=20 Score=25.99 Aligned_cols=9 Identities=33% Similarity=0.944 Sum_probs=5.1
Q ss_pred eCCCCCCce
Q 035291 23 ICSRCGGGA 31 (68)
Q Consensus 23 ~Cp~CGg~v 31 (68)
-||+||...
T Consensus 101 fC~~CG~~~ 109 (256)
T PRK00241 101 FCGYCGHPM 109 (256)
T ss_pred cccccCCCC
Confidence 466666554
No 149
>PF06957 COPI_C: Coatomer (COPI) alpha subunit C-terminus; InterPro: IPR010714 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit [, ]. This domain is found along with the IPR006692 from INTERPRO domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat; PDB: 3MKR_B 3MV2_E 3MKQ_B 3MV3_A.
Probab=40.69 E-value=16 Score=29.10 Aligned_cols=27 Identities=26% Similarity=0.765 Sum_probs=16.7
Q ss_pred eeEEE---EEeeeeceeeeEEeecccceeee
Q 035291 39 ATRFC---HVPFYWKSWRAIICTFCGAVLKS 66 (68)
Q Consensus 39 ~~rfC---flPl~~k~kr~~~Ct~C~r~L~~ 66 (68)
.|.+| |.|+| |+...+.|+.|++++..
T Consensus 363 pF~ICa~s~tPIY-~G~~~v~CP~cgA~y~~ 392 (422)
T PF06957_consen 363 PFDICAASYTPIY-RGSPSVKCPYCGAKYHP 392 (422)
T ss_dssp -EEEBTTT--EEE-TTS-EEE-TTT--EEEG
T ss_pred Cceeeeccccccc-CCCCCeeCCCCCCccCh
Confidence 67778 45998 78889999999998763
No 150
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=40.51 E-value=13 Score=31.21 Aligned_cols=18 Identities=22% Similarity=0.776 Sum_probs=14.5
Q ss_pred eeCCCCCCceeEEEeeeeeEEE
Q 035291 22 GICSRCGGGASVADMKTATRFC 43 (68)
Q Consensus 22 g~Cp~CGg~v~a~dv~s~~rfC 43 (68)
-.||+||+ .+++.+.|.|
T Consensus 694 ~~CP~CG~----~~~~~~~Ri~ 711 (735)
T PRK07111 694 DKCPKCGS----TNIQRIRRIT 711 (735)
T ss_pred ccCcCCCC----ccceeeehhh
Confidence 68999998 4677788887
No 151
>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=40.26 E-value=14 Score=24.23 Aligned_cols=15 Identities=20% Similarity=0.572 Sum_probs=10.9
Q ss_pred CceeCCCCCCceeEE
Q 035291 20 AAGICSRCGGGASVA 34 (68)
Q Consensus 20 a~g~Cp~CGg~v~a~ 34 (68)
-|-.||+||.-....
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 456799999877443
No 152
>KOG0373 consensus Serine/threonine specific protein phosphatase involved in cell cycle control, PP2A-related [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=40.16 E-value=23 Score=27.27 Aligned_cols=25 Identities=28% Similarity=0.512 Sum_probs=21.6
Q ss_pred eeeeccCceeCCCCCCceeEEEeee
Q 035291 14 VHKCKPAAGICSRCGGGASVADMKT 38 (68)
Q Consensus 14 v~g~~~a~g~Cp~CGg~v~a~dv~s 38 (68)
++--=.||--|.+|||-++.+.++.
T Consensus 253 lvTVWSAPNYCYRCGNvAsi~~~d~ 277 (306)
T KOG0373|consen 253 LVTVWSAPNYCYRCGNVASIMSFDD 277 (306)
T ss_pred EEEEecCCchhhhccCeeeEEEecc
Confidence 6667789999999999998888775
No 153
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=40.14 E-value=14 Score=31.37 Aligned_cols=13 Identities=31% Similarity=0.910 Sum_probs=11.6
Q ss_pred ccCceeCCCCCCc
Q 035291 18 KPAAGICSRCGGG 30 (68)
Q Consensus 18 ~~a~g~Cp~CGg~ 30 (68)
++.|-+||+||+.
T Consensus 472 ~~~p~~Cp~Cgs~ 484 (730)
T COG1198 472 EPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCC
Confidence 4889999999997
No 154
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=40.12 E-value=22 Score=30.12 Aligned_cols=16 Identities=25% Similarity=0.623 Sum_probs=11.0
Q ss_pred eeceeeeEEeecccce
Q 035291 48 YWKSWRAIICTFCGAV 63 (68)
Q Consensus 48 ~~k~kr~~~Ct~C~r~ 63 (68)
++|..+...|+.||++
T Consensus 456 ~H~~~~~L~CH~Cg~~ 471 (730)
T COG1198 456 LHKATGQLRCHYCGYQ 471 (730)
T ss_pred EecCCCeeEeCCCCCC
Confidence 3555677778887776
No 155
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=39.54 E-value=20 Score=20.55 Aligned_cols=19 Identities=32% Similarity=0.438 Sum_probs=13.0
Q ss_pred eeceeeeEEeecccceeee
Q 035291 48 YWKSWRAIICTFCGAVLKS 66 (68)
Q Consensus 48 ~~k~kr~~~Ct~C~r~L~~ 66 (68)
+-+..++++|..||..|-.
T Consensus 42 s~~~~~r~FC~~CGs~l~~ 60 (92)
T PF04828_consen 42 SGKGVERYFCPTCGSPLFS 60 (92)
T ss_dssp TTSSCEEEEETTT--EEEE
T ss_pred CCCcCcCcccCCCCCeeec
Confidence 4556678999999988864
No 156
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=38.93 E-value=16 Score=20.18 Aligned_cols=18 Identities=22% Similarity=0.346 Sum_probs=14.8
Q ss_pred eeeeeccCceeCCCCCCc
Q 035291 13 KVHKCKPAAGICSRCGGG 30 (68)
Q Consensus 13 kv~g~~~a~g~Cp~CGg~ 30 (68)
--+.||..|-.|.+||-.
T Consensus 23 ~~v~YE~lp~~C~~C~~~ 40 (49)
T PF14392_consen 23 VKVKYERLPRFCFHCGRI 40 (49)
T ss_pred EEEEECCcChhhcCCCCc
Confidence 446789999999999953
No 157
>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=38.45 E-value=15 Score=17.83 Aligned_cols=14 Identities=21% Similarity=0.755 Sum_probs=9.8
Q ss_pred eeeeEEeeccccee
Q 035291 51 SWRAIICTFCGAVL 64 (68)
Q Consensus 51 ~kr~~~Ct~C~r~L 64 (68)
+.+.|.|..|++..
T Consensus 11 ~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 11 GEKPYKCPYCGKSF 24 (26)
T ss_dssp SSSSEEESSSSEEE
T ss_pred CCCCCCCCCCcCee
Confidence 34668888888764
No 158
>PF02620 DUF177: Uncharacterized ACR, COG1399; InterPro: IPR003772 This entry describes proteins of unknown function.
Probab=38.27 E-value=36 Score=20.70 Aligned_cols=27 Identities=19% Similarity=0.186 Sum_probs=22.6
Q ss_pred cCceeCCCCCCceeEEEeeeeeEEEEEe
Q 035291 19 PAAGICSRCGGGASVADMKTATRFCHVP 46 (68)
Q Consensus 19 ~a~g~Cp~CGg~v~a~dv~s~~rfCflP 46 (68)
.+...|.+|...+ ..+++..+..-|+|
T Consensus 8 ~v~~~C~RCL~~~-~~~i~~~~~~~~~~ 34 (119)
T PF02620_consen 8 TVTLPCDRCLEPF-DYPIDEDFEEVFVP 34 (119)
T ss_pred EEEEEEcccCccc-CceEEEEEEEEEEc
Confidence 3567899999999 88888888888875
No 159
>smart00019 SF_P Pulmonary surfactant proteins. Pulmonary surfactant associated proteins promote alveolar stability by lowering the surface tension at the air-liquid interface in the peripheral air spaces. SP-C, a component of surfactant, is a highly hydrophobic peptide of 35 amino acid residues which is processed from a larger precursor protein. SP-C is post-translationally modified by the covalent attachment of two palmitoyl groups on two adjacent cysteines
Probab=37.95 E-value=15 Score=26.57 Aligned_cols=22 Identities=32% Similarity=0.505 Sum_probs=18.6
Q ss_pred EEEeCCceeeeeeccCceeCCC
Q 035291 5 CFLVDQTRKVHKCKPAAGICSR 26 (68)
Q Consensus 5 ~fvcde~~kv~g~~~a~g~Cp~ 26 (68)
..|+|-++-+++++||||.|-|
T Consensus 101 ~VvyDYqrLLiaykPaPGtcCY 122 (191)
T smart00019 101 IVVYDYQRLLIAYKPAPGTCCY 122 (191)
T ss_pred EEEEEhhhhheeccCCCCceEE
Confidence 3578888999999999999854
No 160
>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=37.87 E-value=16 Score=19.55 Aligned_cols=15 Identities=33% Similarity=0.946 Sum_probs=11.4
Q ss_pred ccCceeCCCCCCcee
Q 035291 18 KPAAGICSRCGGGAS 32 (68)
Q Consensus 18 ~~a~g~Cp~CGg~v~ 32 (68)
-+.+|.|.+||+.+.
T Consensus 18 P~~~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 18 PKVEGVCDNCGGELV 32 (36)
T ss_dssp -SSTTBCTTTTEBEB
T ss_pred CCCCCccCCCCCeeE
Confidence 356799999999763
No 161
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=37.81 E-value=13 Score=26.37 Aligned_cols=41 Identities=22% Similarity=0.429 Sum_probs=21.0
Q ss_pred CCCCCCceeEEEeeeeeEEEEE---eeee--ceeeeEEeecccceee
Q 035291 24 CSRCGGGASVADMKTATRFCHV---PFYW--KSWRAIICTFCGAVLK 65 (68)
Q Consensus 24 Cp~CGg~v~a~dv~s~~rfCfl---Pl~~--k~kr~~~Ct~C~r~L~ 65 (68)
||.||.... ..++.-=.=||+ |+.. +.-.=..|+.|||.+.
T Consensus 1 C~~CG~~~~-~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~ 46 (236)
T PF04981_consen 1 CPRCGREIE-PLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRI 46 (236)
T ss_pred CCCCCCCCC-CcccccChHHhcccCCeeecCCccCceECCCCCCEEC
Confidence 777777552 222221111233 4444 2225578899988764
No 162
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=37.76 E-value=9.9 Score=20.67 Aligned_cols=10 Identities=40% Similarity=0.946 Sum_probs=4.5
Q ss_pred EEeeccccee
Q 035291 55 IICTFCGAVL 64 (68)
Q Consensus 55 ~~Ct~C~r~L 64 (68)
-.|++|||..
T Consensus 2 ~~CSFCgr~~ 11 (41)
T PF06689_consen 2 KRCSFCGRPE 11 (41)
T ss_dssp -B-TTT--BT
T ss_pred CCccCCCCCH
Confidence 4699999864
No 163
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=37.57 E-value=16 Score=25.75 Aligned_cols=20 Identities=30% Similarity=0.454 Sum_probs=15.8
Q ss_pred eeeccCceeCCCCCCceeEE
Q 035291 15 HKCKPAAGICSRCGGGASVA 34 (68)
Q Consensus 15 ~g~~~a~g~Cp~CGg~v~a~ 34 (68)
.+..+++++|++|||.--+.
T Consensus 104 g~~s~l~~~c~~c~g~fc~~ 123 (162)
T COG3582 104 GKGSTLAGKCNYCTGYFCAE 123 (162)
T ss_pred cCCccccccccCCCCcceec
Confidence 35678999999999987543
No 164
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=37.26 E-value=36 Score=18.64 Aligned_cols=9 Identities=44% Similarity=1.287 Sum_probs=7.4
Q ss_pred CCCCCCcee
Q 035291 24 CSRCGGGAS 32 (68)
Q Consensus 24 Cp~CGg~v~ 32 (68)
|.+|||.+.
T Consensus 1 Cd~CG~~I~ 9 (37)
T PF08394_consen 1 CDYCGGEIT 9 (37)
T ss_pred CCccCCccc
Confidence 789999883
No 165
>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=37.02 E-value=24 Score=18.95 Aligned_cols=10 Identities=40% Similarity=1.119 Sum_probs=8.0
Q ss_pred eeCCCCCCce
Q 035291 22 GICSRCGGGA 31 (68)
Q Consensus 22 g~Cp~CGg~v 31 (68)
..||.||+..
T Consensus 2 ~~CP~Cg~~l 11 (39)
T PF01396_consen 2 EKCPKCGGPL 11 (39)
T ss_pred cCCCCCCcee
Confidence 4699999766
No 166
>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=35.82 E-value=16 Score=20.33 Aligned_cols=37 Identities=19% Similarity=0.500 Sum_probs=19.9
Q ss_pred eCCCCCCceeEEEeeeeeEEEEEeeee-ceeeeEEeeccccee
Q 035291 23 ICSRCGGGASVADMKTATRFCHVPFYW-KSWRAIICTFCGAVL 64 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~-k~kr~~~Ct~C~r~L 64 (68)
.||+||-..+..++... +--.. ...+.+.|++|.+++
T Consensus 4 ~CP~C~~~~~~~~L~~H-----~~~~H~~~~~~v~CPiC~~~~ 41 (54)
T PF05605_consen 4 TCPYCGKGFSESSLVEH-----CEDEHRSESKNVVCPICSSRV 41 (54)
T ss_pred CCCCCCCccCHHHHHHH-----HHhHCcCCCCCccCCCchhhh
Confidence 69999985532222111 11111 123468999998754
No 167
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=35.58 E-value=45 Score=21.84 Aligned_cols=36 Identities=19% Similarity=0.334 Sum_probs=23.6
Q ss_pred cCceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceeee
Q 035291 19 PAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKS 66 (68)
Q Consensus 19 ~a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~~ 66 (68)
.-.-.|..||... ...-++.-. +++.|..|+..|+.
T Consensus 110 ~~~y~C~~C~~~~-~~~rr~~~~-----------~~y~C~~C~g~l~~ 145 (146)
T smart00731 110 KYPYRCTGCGQRY-LRVRRSNNV-----------SRYRCGKCGGKLIL 145 (146)
T ss_pred eEEEECCCCCCCC-ceEccccCc-----------ceEEcCCCCCEEEe
Confidence 4567888899766 222221111 77999999999875
No 168
>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=35.57 E-value=4.7 Score=24.00 Aligned_cols=12 Identities=25% Similarity=0.479 Sum_probs=6.2
Q ss_pred eeCCCCCCceeE
Q 035291 22 GICSRCGGGASV 33 (68)
Q Consensus 22 g~Cp~CGg~v~a 33 (68)
-.||.||..+..
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 469999998844
No 169
>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=35.42 E-value=30 Score=20.03 Aligned_cols=16 Identities=25% Similarity=0.542 Sum_probs=12.0
Q ss_pred cCceeCCCCCCceeEE
Q 035291 19 PAAGICSRCGGGASVA 34 (68)
Q Consensus 19 ~a~g~Cp~CGg~v~a~ 34 (68)
++...||+||.+...+
T Consensus 24 p~l~~C~~cG~~~~~H 39 (55)
T TIGR01031 24 PTLVVCPNCGEFKLPH 39 (55)
T ss_pred CcceECCCCCCcccCe
Confidence 5667799999987443
No 170
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=35.03 E-value=32 Score=18.67 Aligned_cols=14 Identities=21% Similarity=0.520 Sum_probs=9.8
Q ss_pred ceeCC--CCCCceeEE
Q 035291 21 AGICS--RCGGGASVA 34 (68)
Q Consensus 21 ~g~Cp--~CGg~v~a~ 34 (68)
.--|| .|+..+...
T Consensus 18 ~~~CP~~~C~~~~~~~ 33 (64)
T smart00647 18 LKWCPAPDCSAAIIVT 33 (64)
T ss_pred ccCCCCCCCcceEEec
Confidence 34588 998887554
No 171
>PF12653 DUF3785: Protein of unknown function (DUF3785); InterPro: IPR024210 This family of proteins is functionally uncharacterised. Proteins in this family are approximately 140 amino acids in length and share two CXXC motifs suggesting these are zinc binding proteins. In clostridia proteins are found in an operon with three signalling proteins, suggesting that they are involved in DNA-binding transcription regulator downstream of an as yet unknown signalling pathway.
Probab=34.91 E-value=30 Score=24.16 Aligned_cols=12 Identities=25% Similarity=0.661 Sum_probs=9.6
Q ss_pred ceeCCCCCCcee
Q 035291 21 AGICSRCGGGAS 32 (68)
Q Consensus 21 ~g~Cp~CGg~v~ 32 (68)
.-.|||||..+.
T Consensus 120 i~VC~nCG~y~i 131 (138)
T PF12653_consen 120 IIVCPNCGNYSI 131 (138)
T ss_pred EEECCCCCceEE
Confidence 357999999883
No 172
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=34.86 E-value=40 Score=23.84 Aligned_cols=40 Identities=23% Similarity=0.555 Sum_probs=26.2
Q ss_pred eeCCCCCCceeEEEeee-eeE-------EEEE--eeeeceeeeEEeeccc
Q 035291 22 GICSRCGGGASVADMKT-ATR-------FCHV--PFYWKSWRAIICTFCG 61 (68)
Q Consensus 22 g~Cp~CGg~v~a~dv~s-~~r-------fCfl--Pl~~k~kr~~~Ct~C~ 61 (68)
-.||.||..-...-|+| ..| ||=. .+.-=.|.-.+|+.||
T Consensus 6 ~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~Cg 55 (214)
T PF09986_consen 6 ITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCG 55 (214)
T ss_pred eECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCC
Confidence 47999999988888877 333 3422 2222236667899987
No 173
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=33.98 E-value=19 Score=21.95 Aligned_cols=8 Identities=25% Similarity=0.580 Sum_probs=7.2
Q ss_pred eCCCCCCc
Q 035291 23 ICSRCGGG 30 (68)
Q Consensus 23 ~Cp~CGg~ 30 (68)
.||+||+.
T Consensus 19 ~Cp~Cgs~ 26 (64)
T PRK06393 19 TCPVHGDE 26 (64)
T ss_pred cCCCCCCC
Confidence 89999985
No 174
>COG1054 Predicted sulfurtransferase [General function prediction only]
Probab=33.87 E-value=22 Score=27.62 Aligned_cols=32 Identities=19% Similarity=0.351 Sum_probs=21.6
Q ss_pred EEEeCCceee--eeeccCceeCCCCCCceeEEEe
Q 035291 5 CFLVDQTRKV--HKCKPAAGICSRCGGGASVADM 36 (68)
Q Consensus 5 ~fvcde~~kv--~g~~~a~g~Cp~CGg~v~a~dv 36 (68)
+||+|++--| -=..+....|.||++++...+.
T Consensus 225 cFVFDeRvav~~~l~~~~~~~C~~C~~p~~~~~~ 258 (308)
T COG1054 225 CFVFDERVAVPIGLVEGDHTPCDNCRNPLCNLLF 258 (308)
T ss_pred eeEecceecccCcccCCCcchhhhcCCCCCHHHh
Confidence 6899988222 2234555889999999855443
No 175
>PF09947 DUF2180: Uncharacterized protein conserved in archaea (DUF2180); InterPro: IPR017211 This group represents a predicted zinc finger protein, AF1427 type.
Probab=33.44 E-value=8.3 Score=23.82 Aligned_cols=57 Identities=28% Similarity=0.501 Sum_probs=34.3
Q ss_pred EEEeCCceeeeeeccCceeCCCCCCceeEEEeeeeeEEE---EEeee----eceeeeEEeeccccee
Q 035291 5 CFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFC---HVPFY----WKSWRAIICTFCGAVL 64 (68)
Q Consensus 5 ~fvcde~~kv~g~~~a~g~Cp~CGg~v~a~dv~s~~rfC---flPl~----~k~kr~~~Ct~C~r~L 64 (68)
+|.|.++++. ..|.|.|-.||-++=..-+...-..- =-|+. .+.-+++.|+-|...+
T Consensus 3 CY~Ca~~gkd---t~AVavCivCG~GlC~~H~~~e~~~~~~g~yp~~~~~~~~~l~RilC~~C~~a~ 66 (68)
T PF09947_consen 3 CYDCAEEGKD---TDAVAVCIVCGAGLCMDHSKREEIPVWEGGYPFPSKKLKKPLPRILCPECHAAL 66 (68)
T ss_pred chhhhhcCCC---ccceehHHhcCchhhHHHHhhhheeeeccCCCCccccccCCCCeeecHHHHHHh
Confidence 3556666553 38999999999988222121111111 12544 4566899999987655
No 176
>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=33.25 E-value=13 Score=23.94 Aligned_cols=18 Identities=28% Similarity=0.455 Sum_probs=8.1
Q ss_pred eeeeccCceeCCCCCCce
Q 035291 14 VHKCKPAAGICSRCGGGA 31 (68)
Q Consensus 14 v~g~~~a~g~Cp~CGg~v 31 (68)
.+-..|+.+.|..||.-.
T Consensus 63 ~Ie~~p~~~~C~~Cg~~~ 80 (113)
T PF01155_consen 63 EIEEVPARARCRDCGHEF 80 (113)
T ss_dssp EEEEE--EEEETTTS-EE
T ss_pred EEEecCCcEECCCCCCEE
Confidence 344455556666666544
No 177
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=33.11 E-value=34 Score=20.03 Aligned_cols=16 Identities=25% Similarity=0.503 Sum_probs=11.8
Q ss_pred ccCceeCCCCCCceeE
Q 035291 18 KPAAGICSRCGGGASV 33 (68)
Q Consensus 18 ~~a~g~Cp~CGg~v~a 33 (68)
.++...||+||.....
T Consensus 24 ~~~l~~C~~CG~~~~~ 39 (57)
T PRK12286 24 APGLVECPNCGEPKLP 39 (57)
T ss_pred CCcceECCCCCCccCC
Confidence 4566679999988744
No 178
>PHA00616 hypothetical protein
Probab=33.00 E-value=13 Score=21.12 Aligned_cols=9 Identities=56% Similarity=1.051 Sum_probs=6.4
Q ss_pred eeCCCCCCc
Q 035291 22 GICSRCGGG 30 (68)
Q Consensus 22 g~Cp~CGg~ 30 (68)
-+||.||..
T Consensus 2 YqC~~CG~~ 10 (44)
T PHA00616 2 YQCLRCGGI 10 (44)
T ss_pred CccchhhHH
Confidence 468888864
No 179
>PHA02942 putative transposase; Provisional
Probab=32.94 E-value=26 Score=26.97 Aligned_cols=27 Identities=26% Similarity=0.560 Sum_probs=18.6
Q ss_pred eeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeeccccee
Q 035291 22 GICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVL 64 (68)
Q Consensus 22 g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L 64 (68)
-.||+||.... ++ +.|.|.|..||-..
T Consensus 326 q~Cs~CG~~~~-------------~l---~~r~f~C~~CG~~~ 352 (383)
T PHA02942 326 VSCPKCGHKMV-------------EI---AHRYFHCPSCGYEN 352 (383)
T ss_pred ccCCCCCCccC-------------cC---CCCEEECCCCCCEe
Confidence 45999998651 12 34679999998643
No 180
>PRK01343 zinc-binding protein; Provisional
Probab=32.75 E-value=15 Score=22.03 Aligned_cols=12 Identities=25% Similarity=0.725 Sum_probs=9.7
Q ss_pred CceeCCCCCCce
Q 035291 20 AAGICSRCGGGA 31 (68)
Q Consensus 20 a~g~Cp~CGg~v 31 (68)
..-.||.||..+
T Consensus 8 p~~~CP~C~k~~ 19 (57)
T PRK01343 8 PTRPCPECGKPS 19 (57)
T ss_pred CCCcCCCCCCcC
Confidence 346799999987
No 181
>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=32.59 E-value=20 Score=18.53 Aligned_cols=12 Identities=33% Similarity=1.013 Sum_probs=7.1
Q ss_pred ccCceeCCCCCC
Q 035291 18 KPAAGICSRCGG 29 (68)
Q Consensus 18 ~~a~g~Cp~CGg 29 (68)
-+....||+||+
T Consensus 22 ~pPr~~Cp~C~s 33 (37)
T PF12172_consen 22 FPPRPVCPHCGS 33 (37)
T ss_dssp ES--SEETTTT-
T ss_pred cCCCcCCCCcCc
Confidence 345578999974
No 182
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=32.45 E-value=22 Score=21.94 Aligned_cols=10 Identities=40% Similarity=1.006 Sum_probs=7.8
Q ss_pred eeCCCCCCce
Q 035291 22 GICSRCGGGA 31 (68)
Q Consensus 22 g~Cp~CGg~v 31 (68)
-+||+||...
T Consensus 19 e~CP~Cgs~~ 28 (64)
T COG2093 19 EICPVCGSTD 28 (64)
T ss_pred ccCCCCCCcc
Confidence 3699999763
No 183
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=32.26 E-value=21 Score=17.45 Aligned_cols=9 Identities=33% Similarity=0.763 Sum_probs=6.0
Q ss_pred eCCCCCCce
Q 035291 23 ICSRCGGGA 31 (68)
Q Consensus 23 ~Cp~CGg~v 31 (68)
.||.||..-
T Consensus 4 ~C~~CgR~F 12 (25)
T PF13913_consen 4 PCPICGRKF 12 (25)
T ss_pred cCCCCCCEE
Confidence 577777654
No 184
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=32.26 E-value=12 Score=22.08 Aligned_cols=11 Identities=45% Similarity=1.204 Sum_probs=3.7
Q ss_pred eeEEeecccce
Q 035291 53 RAIICTFCGAV 63 (68)
Q Consensus 53 r~~~Ct~C~r~ 63 (68)
|+|.|.+|++.
T Consensus 32 r~y~Cp~CgAt 42 (55)
T PF05741_consen 32 RKYVCPICGAT 42 (55)
T ss_dssp GG---TTT---
T ss_pred hcCcCCCCcCc
Confidence 56788888763
No 185
>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=32.10 E-value=20 Score=21.24 Aligned_cols=19 Identities=26% Similarity=0.448 Sum_probs=10.9
Q ss_pred eeeeeccC-ceeCCCCCCce
Q 035291 13 KVHKCKPA-AGICSRCGGGA 31 (68)
Q Consensus 13 kv~g~~~a-~g~Cp~CGg~v 31 (68)
+++=.+.. -|.|+.||..+
T Consensus 26 kIiC~~Eg~~~pC~fCg~~l 45 (57)
T PF06221_consen 26 KIICEQEGPLGPCPFCGTPL 45 (57)
T ss_pred hhhcccccCcCcCCCCCCcc
Confidence 33444444 47777777665
No 186
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.06 E-value=25 Score=22.81 Aligned_cols=8 Identities=50% Similarity=1.377 Sum_probs=3.8
Q ss_pred eeCCCCCC
Q 035291 22 GICSRCGG 29 (68)
Q Consensus 22 g~Cp~CGg 29 (68)
-.||+|+|
T Consensus 22 D~CPrCrG 29 (88)
T COG3809 22 DYCPRCRG 29 (88)
T ss_pred eeCCcccc
Confidence 44555544
No 187
>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=32.05 E-value=37 Score=17.75 Aligned_cols=14 Identities=21% Similarity=0.707 Sum_probs=10.1
Q ss_pred ceeeeEEeecccce
Q 035291 50 KSWRAIICTFCGAV 63 (68)
Q Consensus 50 k~kr~~~Ct~C~r~ 63 (68)
.+-+.+-|+.|+..
T Consensus 15 ~gA~~vrCs~C~~v 28 (31)
T TIGR01053 15 RGASSVRCALCQTV 28 (31)
T ss_pred CCCCeEECCCCCeE
Confidence 55667888888753
No 188
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=31.54 E-value=35 Score=27.15 Aligned_cols=29 Identities=17% Similarity=0.479 Sum_probs=20.6
Q ss_pred EEEEEeCCc-eeeeeeccCceeCCCCCCce
Q 035291 3 CFCFLVDQT-RKVHKCKPAAGICSRCGGGA 31 (68)
Q Consensus 3 ~~~fvcde~-~kv~g~~~a~g~Cp~CGg~v 31 (68)
..++.|.+. +.+.+.++.-.-||+||+.+
T Consensus 238 g~~~~c~~cg~~~~~~~~~~~~c~~Cg~~~ 267 (380)
T COG1867 238 GYIYHCSRCGEIVGSFREVDEKCPHCGGKV 267 (380)
T ss_pred CcEEEcccccceecccccccccCCcccccc
Confidence 345666666 45666678888899999744
No 189
>PRK14873 primosome assembly protein PriA; Provisional
Probab=31.44 E-value=23 Score=29.42 Aligned_cols=15 Identities=27% Similarity=0.565 Sum_probs=8.7
Q ss_pred eeccCceeCCCCCCc
Q 035291 16 KCKPAAGICSRCGGG 30 (68)
Q Consensus 16 g~~~a~g~Cp~CGg~ 30 (68)
|++..|-+||+||+.
T Consensus 417 G~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 417 GRAAPDWRCPRCGSD 431 (665)
T ss_pred cCCCcCccCCCCcCC
Confidence 344456667777664
No 190
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=31.21 E-value=25 Score=21.89 Aligned_cols=13 Identities=23% Similarity=0.575 Sum_probs=11.0
Q ss_pred eEEeecccceeee
Q 035291 54 AIICTFCGAVLKS 66 (68)
Q Consensus 54 ~~~Ct~C~r~L~~ 66 (68)
-+.|+.|.|+|-+
T Consensus 19 ~~~C~~C~Rr~GL 31 (91)
T PF08600_consen 19 LLSCSYCFRRLGL 31 (91)
T ss_pred eEEccccCcEeee
Confidence 6889999999854
No 191
>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=31.11 E-value=42 Score=22.64 Aligned_cols=19 Identities=32% Similarity=0.725 Sum_probs=16.0
Q ss_pred eeceeeeEEeecccceeee
Q 035291 48 YWKSWRAIICTFCGAVLKS 66 (68)
Q Consensus 48 ~~k~kr~~~Ct~C~r~L~~ 66 (68)
.|...|.|.|+-||..|..
T Consensus 68 ~w~~irEyyCP~Cgt~lev 86 (112)
T PF08882_consen 68 EWQVIREYYCPGCGTQLEV 86 (112)
T ss_pred CcEEEEEEECCCCcceeEE
Confidence 4667899999999998864
No 192
>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=30.93 E-value=19 Score=19.92 Aligned_cols=16 Identities=19% Similarity=0.353 Sum_probs=10.6
Q ss_pred eeccCceeCCCCCCce
Q 035291 16 KCKPAAGICSRCGGGA 31 (68)
Q Consensus 16 g~~~a~g~Cp~CGg~v 31 (68)
|+.=....||.||.+.
T Consensus 12 G~~ML~~~Cp~C~~PL 27 (41)
T PF06677_consen 12 GWTMLDEHCPDCGTPL 27 (41)
T ss_pred hHhHhcCccCCCCCee
Confidence 4444556799997666
No 193
>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=30.59 E-value=30 Score=27.86 Aligned_cols=19 Identities=26% Similarity=0.683 Sum_probs=14.8
Q ss_pred ceeCCCCCCceeEEEeeeeeEEE
Q 035291 21 AGICSRCGGGASVADMKTATRFC 43 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~s~~rfC 43 (68)
--.||.||+. |++.+.|.|
T Consensus 532 ~~~CP~CGs~----~~~~~~Rv~ 550 (555)
T cd01675 532 GFKCPKCGSE----DVEVISRIT 550 (555)
T ss_pred CCCCcCCCCc----CceEEEeee
Confidence 3689999974 577788877
No 194
>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=30.53 E-value=33 Score=26.25 Aligned_cols=21 Identities=19% Similarity=0.434 Sum_probs=10.9
Q ss_pred eCCceeeeeeccCceeCCCCC
Q 035291 8 VDQTRKVHKCKPAAGICSRCG 28 (68)
Q Consensus 8 cde~~kv~g~~~a~g~Cp~CG 28 (68)
|-+.++-+.-..+.|.||+||
T Consensus 123 c~~~e~fl~e~~v~g~CP~C~ 143 (391)
T PF09334_consen 123 CPSCERFLPESFVEGTCPYCG 143 (391)
T ss_dssp ETTTTEEE-GGGETCEETTT-
T ss_pred ecCcCcccccceeeccccCcC
Confidence 344445555555667777655
No 195
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=30.23 E-value=35 Score=17.96 Aligned_cols=16 Identities=19% Similarity=0.347 Sum_probs=11.9
Q ss_pred eeeccCceeCCCCCCc
Q 035291 15 HKCKPAAGICSRCGGG 30 (68)
Q Consensus 15 ~g~~~a~g~Cp~CGg~ 30 (68)
++..+..-.||+||.-
T Consensus 19 l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 19 LPAGGRKVRCPKCGHV 34 (37)
T ss_pred cccCCcEEECCCCCcE
Confidence 4456778889999864
No 196
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=30.18 E-value=18 Score=24.48 Aligned_cols=21 Identities=14% Similarity=0.245 Sum_probs=9.9
Q ss_pred eCCceeeeeeccCceeCCCCCCce
Q 035291 8 VDQTRKVHKCKPAAGICSRCGGGA 31 (68)
Q Consensus 8 cde~~kv~g~~~a~g~Cp~CGg~v 31 (68)
||.+-|++|++. +|.+|+-++
T Consensus 75 C~K~TKmLGr~D---~CM~C~~pL 95 (114)
T PF11023_consen 75 CGKQTKMLGRVD---ACMHCKEPL 95 (114)
T ss_pred CCChHhhhchhh---ccCcCCCcC
Confidence 333344455543 455555544
No 197
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=30.10 E-value=29 Score=28.84 Aligned_cols=9 Identities=33% Similarity=1.158 Sum_probs=4.6
Q ss_pred eeCCCCCCc
Q 035291 22 GICSRCGGG 30 (68)
Q Consensus 22 g~Cp~CGg~ 30 (68)
-.||+||+.
T Consensus 640 ~~CP~CG~~ 648 (656)
T PRK08270 640 EFCPKCGEE 648 (656)
T ss_pred CCCcCCcCc
Confidence 355555543
No 198
>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=30.04 E-value=53 Score=22.46 Aligned_cols=10 Identities=30% Similarity=0.826 Sum_probs=5.6
Q ss_pred ceeCCCCCCc
Q 035291 21 AGICSRCGGG 30 (68)
Q Consensus 21 ~g~Cp~CGg~ 30 (68)
--.||.|||-
T Consensus 130 l~~Cp~C~~~ 139 (146)
T PF07295_consen 130 LPPCPKCGHT 139 (146)
T ss_pred CCCCCCCCCC
Confidence 3456666654
No 199
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=29.94 E-value=24 Score=19.68 Aligned_cols=9 Identities=44% Similarity=1.191 Sum_probs=2.9
Q ss_pred Eeeccccee
Q 035291 56 ICTFCGAVL 64 (68)
Q Consensus 56 ~Ct~C~r~L 64 (68)
.|+.|+|.|
T Consensus 22 ~CPlC~r~l 30 (54)
T PF04423_consen 22 CCPLCGRPL 30 (54)
T ss_dssp E-TTT--EE
T ss_pred cCCCCCCCC
Confidence 455555544
No 200
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.94 E-value=26 Score=24.96 Aligned_cols=26 Identities=31% Similarity=0.823 Sum_probs=16.3
Q ss_pred eCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccce
Q 035291 23 ICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAV 63 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~ 63 (68)
.|-+|||.|+-. .+|-...|+.|..+
T Consensus 91 ~CARCGGrv~lr---------------sNKv~wvcnlc~k~ 116 (169)
T KOG3799|consen 91 FCARCGGRVSLR---------------SNKVMWVCNLCRKQ 116 (169)
T ss_pred HHHhcCCeeeec---------------cCceEEeccCCcHH
Confidence 467788888321 25666677777654
No 201
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=29.42 E-value=29 Score=28.71 Aligned_cols=29 Identities=38% Similarity=0.857 Sum_probs=20.9
Q ss_pred eCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceee
Q 035291 23 ICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLK 65 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~ 65 (68)
.|+||||-.-..|- .--+.+|+.||..|+
T Consensus 2 ~C~~C~~s~fe~d~--------------a~g~~~C~~CG~v~E 30 (521)
T KOG1598|consen 2 VCKNCGGSNFERDE--------------ATGNLYCTACGTVLE 30 (521)
T ss_pred cCCCCCCCCccccc--------------ccCCceeccccceee
Confidence 58999988755443 235678899988875
No 202
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.11 E-value=19 Score=22.22 Aligned_cols=14 Identities=21% Similarity=0.458 Sum_probs=10.8
Q ss_pred cCceeCCCCCCcee
Q 035291 19 PAAGICSRCGGGAS 32 (68)
Q Consensus 19 ~a~g~Cp~CGg~v~ 32 (68)
.+.--||-||-.|.
T Consensus 5 ~~~v~CP~Cgkpv~ 18 (65)
T COG3024 5 RITVPCPTCGKPVV 18 (65)
T ss_pred cccccCCCCCCccc
Confidence 44567999999983
No 203
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=28.91 E-value=24 Score=22.15 Aligned_cols=21 Identities=29% Similarity=0.317 Sum_probs=15.9
Q ss_pred eeccCceeCCCCCCceeEEEe
Q 035291 16 KCKPAAGICSRCGGGASVADM 36 (68)
Q Consensus 16 g~~~a~g~Cp~CGg~v~a~dv 36 (68)
|+-+..-.|++||-.-+..|-
T Consensus 3 g~Lk~~~~C~~CG~d~~~~~a 23 (86)
T PF06170_consen 3 GYLKVAPRCPHCGLDYSHARA 23 (86)
T ss_pred ccccCCCcccccCCccccCCc
Confidence 566788899999987655554
No 204
>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=28.87 E-value=25 Score=24.16 Aligned_cols=10 Identities=10% Similarity=0.232 Sum_probs=5.1
Q ss_pred ceeCCCCCCc
Q 035291 21 AGICSRCGGG 30 (68)
Q Consensus 21 ~g~Cp~CGg~ 30 (68)
|-.||+||.-
T Consensus 26 p~vcP~cg~~ 35 (129)
T TIGR02300 26 PAVSPYTGEQ 35 (129)
T ss_pred CccCCCcCCc
Confidence 4455555544
No 205
>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=28.53 E-value=93 Score=21.31 Aligned_cols=37 Identities=19% Similarity=0.660 Sum_probs=18.5
Q ss_pred eCCCCCCceeEEEeeeeeEEEEEeeeece-eeeEEeeccccee
Q 035291 23 ICSRCGGGASVADMKTATRFCHVPFYWKS-WRAIICTFCGAVL 64 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~-kr~~~Ct~C~r~L 64 (68)
.||+||.... +.+ ..==||..-+. --.+.|..||-+-
T Consensus 3 ~Cp~C~~~~~-~~~----~~~~IP~F~evii~sf~C~~CGyk~ 40 (161)
T PF03367_consen 3 LCPNCGENGT-TRI----LLTDIPYFKEVIIMSFECEHCGYKN 40 (161)
T ss_dssp E-TTTSSCCE-EEE----EEEEETTTEEEEEEEEE-TTT--EE
T ss_pred cCCCCCCCcE-EEE----EEEcCCCCceEEEEEeECCCCCCEe
Confidence 6999998862 111 11124655443 3456888888654
No 206
>PRK05978 hypothetical protein; Provisional
Probab=28.44 E-value=28 Score=24.07 Aligned_cols=35 Identities=23% Similarity=0.434 Sum_probs=22.1
Q ss_pred ccCceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceeee
Q 035291 18 KPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKS 66 (68)
Q Consensus 18 ~~a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~~ 66 (68)
.+..|.||+||.+--= + .--|-.-.|+.||..+..
T Consensus 30 rGl~grCP~CG~G~LF---~-----------g~Lkv~~~C~~CG~~~~~ 64 (148)
T PRK05978 30 RGFRGRCPACGEGKLF---R-----------AFLKPVDHCAACGEDFTH 64 (148)
T ss_pred HHHcCcCCCCCCCccc---c-----------cccccCCCccccCCcccc
Confidence 4567899999987611 0 111344568888877654
No 207
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=28.41 E-value=44 Score=24.73 Aligned_cols=31 Identities=29% Similarity=0.739 Sum_probs=20.2
Q ss_pred ceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceee
Q 035291 21 AGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLK 65 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~ 65 (68)
.-.||+||+.....|- .--+++|+-||..|.
T Consensus 11 ~~~Cp~Cg~~~iv~d~--------------~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 11 KLVCPECGSDKLIYDY--------------ERGEIVCADCGLVIE 41 (310)
T ss_pred CCcCcCCCCCCeeEEC--------------CCCeEeecccCCccc
Confidence 3479999985434442 245677788887653
No 208
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=28.37 E-value=66 Score=18.64 Aligned_cols=14 Identities=29% Similarity=0.577 Sum_probs=8.9
Q ss_pred eeeEEeecccceee
Q 035291 52 WRAIICTFCGAVLK 65 (68)
Q Consensus 52 kr~~~Ct~C~r~L~ 65 (68)
.-...|+.|+|.+.
T Consensus 51 eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 51 EGELICPECGREYP 64 (68)
T ss_dssp TTEEEETTTTEEEE
T ss_pred CCEEEcCCCCCEEe
Confidence 44567777777654
No 209
>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=28.14 E-value=31 Score=22.75 Aligned_cols=11 Identities=18% Similarity=0.458 Sum_probs=6.8
Q ss_pred eeEEeecccce
Q 035291 53 RAIICTFCGAV 63 (68)
Q Consensus 53 r~~~Ct~C~r~ 63 (68)
..+.|..|+..
T Consensus 50 ~~~~C~~C~~~ 60 (166)
T cd04476 50 GTYRCEKCNKS 60 (166)
T ss_pred CcEECCCCCCc
Confidence 45667777654
No 210
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=28.03 E-value=28 Score=19.51 Aligned_cols=13 Identities=31% Similarity=0.810 Sum_probs=8.8
Q ss_pred eeeEEeeccccee
Q 035291 52 WRAIICTFCGAVL 64 (68)
Q Consensus 52 kr~~~Ct~C~r~L 64 (68)
..-++|+-|||.|
T Consensus 44 ~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 44 DEIVFCPNCGRIL 56 (56)
T ss_pred CCeEECcCCCccC
Confidence 3457777777765
No 211
>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=27.91 E-value=23 Score=24.81 Aligned_cols=28 Identities=29% Similarity=0.768 Sum_probs=10.8
Q ss_pred ceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeeccc
Q 035291 21 AGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCG 61 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~ 61 (68)
--.|..|||.-.+..-+ ....|.|++|+
T Consensus 134 l~~C~~C~~~fv~~~~~-------------~~~~~~Cp~C~ 161 (175)
T PF05280_consen 134 LAPCRRCGGHFVTHAHD-------------PRHSFVCPFCQ 161 (175)
T ss_dssp EEE-TTT--EEEEESS---------------SS----TT--
T ss_pred ccCCCCCCCCeECcCCC-------------CCcCcCCCCCC
Confidence 35799999987554322 34566777776
No 212
>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=27.71 E-value=34 Score=26.62 Aligned_cols=12 Identities=33% Similarity=0.811 Sum_probs=7.5
Q ss_pred eEEeecccceee
Q 035291 54 AIICTFCGAVLK 65 (68)
Q Consensus 54 ~~~Ct~C~r~L~ 65 (68)
+-.|++||..|.
T Consensus 33 ~a~CpRCg~~L~ 44 (403)
T TIGR00155 33 KAACPRCGTTLT 44 (403)
T ss_pred eeECCCCCCCCc
Confidence 455777776664
No 213
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=27.44 E-value=6.8 Score=21.60 Aligned_cols=40 Identities=15% Similarity=0.378 Sum_probs=21.3
Q ss_pred cCceeCCC-CC-CceeEEEeeeeeE-EEEEeeeeceeeeEEeec----ccceee
Q 035291 19 PAAGICSR-CG-GGASVADMKTATR-FCHVPFYWKSWRAIICTF----CGAVLK 65 (68)
Q Consensus 19 ~a~g~Cp~-CG-g~v~a~dv~s~~r-fCflPl~~k~kr~~~Ct~----C~r~L~ 65 (68)
.++-.||+ || ..+...+++.... -| .++.+.|+. |+.+..
T Consensus 7 ~~~v~C~~~cc~~~i~r~~l~~H~~~~C-------~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 7 FRPVPCPNGCCNEMIPRKELDDHLENEC-------PKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp TSEEE-TT--S-BEEECCCHHHHHHTTS-------TTSEEE-SS----S--EEE
T ss_pred CCEeeCCCCCcccceeHHHHHHHHHccC-------CCCcEECCCCCCCCCCccc
Confidence 46678998 44 4466666665443 33 456778887 776653
No 214
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=27.31 E-value=32 Score=27.75 Aligned_cols=30 Identities=13% Similarity=0.388 Sum_probs=12.2
Q ss_pred EeCCceeeeeeccCceeCCCCCCceeEEEeeeeeEEE
Q 035291 7 LVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFC 43 (68)
Q Consensus 7 vcde~~kv~g~~~a~g~Cp~CGg~v~a~dv~s~~rfC 43 (68)
+|.+.+...+. .-.||.||+.- ++.+.|.|
T Consensus 493 ~C~~CG~~~~~---~~~CP~CGs~~----~~~~~Rv~ 522 (546)
T PF13597_consen 493 ICPDCGYIGGE---GDKCPKCGSEN----IEVYSRVT 522 (546)
T ss_dssp EETTT---S-----EEE-CCC--------EEEEB-SS
T ss_pred cccCCCcCCCC---CCCCCCCCCcc----cceEEEee
Confidence 45555443332 56799998764 66677766
No 215
>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=27.29 E-value=49 Score=17.99 Aligned_cols=15 Identities=27% Similarity=0.476 Sum_probs=7.9
Q ss_pred eeCCCCCCceeEEEe
Q 035291 22 GICSRCGGGASVADM 36 (68)
Q Consensus 22 g~Cp~CGg~v~a~dv 36 (68)
-.|..|||-+...+-
T Consensus 7 YkC~~CGniVev~~~ 21 (36)
T PF06397_consen 7 YKCEHCGNIVEVVHD 21 (36)
T ss_dssp EE-TTT--EEEEEE-
T ss_pred EEccCCCCEEEEEEC
Confidence 369999999865543
No 216
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=27.18 E-value=27 Score=24.74 Aligned_cols=18 Identities=22% Similarity=0.488 Sum_probs=9.7
Q ss_pred ceeeeEEeecccceeeee
Q 035291 50 KSWRAIICTFCGAVLKSY 67 (68)
Q Consensus 50 k~kr~~~Ct~C~r~L~~~ 67 (68)
.+.|+=.|.-|+.|..+|
T Consensus 24 aIRRRReC~~C~~RFTTf 41 (156)
T COG1327 24 AIRRRRECLECGERFTTF 41 (156)
T ss_pred hhhhhhcccccccccchh
Confidence 345555566666555443
No 217
>PF04879 Molybdop_Fe4S4: Molybdopterin oxidoreductase Fe4S4 domain; InterPro: IPR006963 The molybdopterin oxidoreductase Fe4S4 domain is found in a number of reductase/dehydrogenase families, which include the periplasmic nitrate reductase precursor and the formate dehydrogenase alpha chain [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 2VPZ_A 2VPY_A 2VPW_A 2VPX_A 2NYA_A 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 ....
Probab=27.03 E-value=59 Score=17.72 Aligned_cols=20 Identities=25% Similarity=0.589 Sum_probs=11.8
Q ss_pred ccCceeCCCCCCceeEEEeee
Q 035291 18 KPAAGICSRCGGGASVADMKT 38 (68)
Q Consensus 18 ~~a~g~Cp~CGg~v~a~dv~s 38 (68)
+.++..|++|+..= ..+++.
T Consensus 2 k~~~t~C~~C~~gC-~i~~~v 21 (55)
T PF04879_consen 2 KTVPTVCPYCSSGC-GIDVYV 21 (55)
T ss_dssp EEEEEE-SSCTT---EEEEEE
T ss_pred eEEeeECcCCcCCC-cEEEEE
Confidence 45678999999876 555443
No 218
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=26.86 E-value=25 Score=21.32 Aligned_cols=12 Identities=25% Similarity=0.581 Sum_probs=9.8
Q ss_pred CceeCCCCCCce
Q 035291 20 AAGICSRCGGGA 31 (68)
Q Consensus 20 a~g~Cp~CGg~v 31 (68)
..-.||.||..+
T Consensus 5 ~~v~CP~C~k~~ 16 (62)
T PRK00418 5 ITVNCPTCGKPV 16 (62)
T ss_pred ccccCCCCCCcc
Confidence 456799999987
No 219
>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=26.73 E-value=46 Score=26.79 Aligned_cols=38 Identities=18% Similarity=0.441 Sum_probs=21.9
Q ss_pred eeCCCCCCceeEEEeeeeeEEEEEeee-eceeeeEEeeccccee
Q 035291 22 GICSRCGGGASVADMKTATRFCHVPFY-WKSWRAIICTFCGAVL 64 (68)
Q Consensus 22 g~Cp~CGg~v~a~dv~s~~rfCflPl~-~k~kr~~~Ct~C~r~L 64 (68)
-.||+||..- ..+.+. +++ |-- ....-.|.|..||...
T Consensus 201 vpCPhCg~~~-~l~~~~-l~w---~~~~~~~~a~y~C~~Cg~~i 239 (557)
T PF05876_consen 201 VPCPHCGEEQ-VLEWEN-LKW---DKGEAPETARYVCPHCGCEI 239 (557)
T ss_pred ccCCCCCCCc-cccccc-eee---cCCCCccceEEECCCCcCCC
Confidence 3589999887 333332 111 211 3345678888888654
No 220
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=26.67 E-value=26 Score=21.53 Aligned_cols=36 Identities=28% Similarity=0.513 Sum_probs=25.5
Q ss_pred cCceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccc
Q 035291 19 PAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGA 62 (68)
Q Consensus 19 ~a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r 62 (68)
+.+-.||+|+.. .+.||+-==+..+--+++|.-|.|
T Consensus 3 ~~~~~CPRC~S~--------nTKFcYyNNy~~~QPR~~Ck~C~r 38 (63)
T PF02701_consen 3 EQPLPCPRCDST--------NTKFCYYNNYNLSQPRYFCKSCRR 38 (63)
T ss_pred ccCCCCCCcCCC--------CCEEEeecCCCCCCcchhhHHHHH
Confidence 345679999843 489998855555566788877765
No 221
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=26.63 E-value=32 Score=20.34 Aligned_cols=11 Identities=45% Similarity=1.117 Sum_probs=9.0
Q ss_pred ceeCCCCCCce
Q 035291 21 AGICSRCGGGA 31 (68)
Q Consensus 21 ~g~Cp~CGg~v 31 (68)
-.+||.||+..
T Consensus 17 k~~CP~CG~~t 27 (56)
T PRK13130 17 KEICPVCGGKT 27 (56)
T ss_pred cccCcCCCCCC
Confidence 56899999875
No 222
>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=26.39 E-value=45 Score=29.92 Aligned_cols=21 Identities=24% Similarity=0.616 Sum_probs=16.7
Q ss_pred eeccCceeCCCCCCceeEEEe
Q 035291 16 KCKPAAGICSRCGGGASVADM 36 (68)
Q Consensus 16 g~~~a~g~Cp~CGg~v~a~dv 36 (68)
++-|..|.||.|||.+.-+.=
T Consensus 1023 RR~PL~G~C~kCGg~lilTV~ 1043 (1095)
T TIGR00354 1023 RRIPLVGKCLKCGNNLTLTVS 1043 (1095)
T ss_pred ccCCCCCcccccCCeEEEEEe
Confidence 456889999999999865543
No 223
>KOG0372 consensus Serine/threonine specific protein phosphatase involved in glycogen accumulation, PP2A-related [Carbohydrate transport and metabolism; Signal transduction mechanisms]
Probab=25.73 E-value=30 Score=26.85 Aligned_cols=32 Identities=28% Similarity=0.516 Sum_probs=25.7
Q ss_pred eeeeeeccCceeCCCCCCceeEEEeee--eeEEE
Q 035291 12 RKVHKCKPAAGICSRCGGGASVADMKT--ATRFC 43 (68)
Q Consensus 12 ~kv~g~~~a~g~Cp~CGg~v~a~dv~s--~~rfC 43 (68)
++|+--=.||--|.+|||.++...+.. ..-|+
T Consensus 247 ~~v~TVWSAPNYCYrCGN~AsIl~lde~~~~~F~ 280 (303)
T KOG0372|consen 247 EKVVTVWSAPNYCYRCGNVAAILELDEDLDKDFR 280 (303)
T ss_pred CceEEEecCCchhhhcCChHHheeeccccCcceE
Confidence 677888889999999999998887776 34444
No 224
>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=25.68 E-value=25 Score=28.50 Aligned_cols=18 Identities=28% Similarity=0.815 Sum_probs=14.4
Q ss_pred eeCCCCCCceeEEEeeeeeEEE
Q 035291 22 GICSRCGGGASVADMKTATRFC 43 (68)
Q Consensus 22 g~Cp~CGg~v~a~dv~s~~rfC 43 (68)
-.||.||+. |++.+.|.|
T Consensus 539 ~~CP~Cgs~----~~~~~~Rv~ 556 (579)
T TIGR02487 539 DKCPKCGSH----DIEVISRIT 556 (579)
T ss_pred CcCcCCCCc----cceehhhhh
Confidence 579999984 577788887
No 225
>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=25.65 E-value=79 Score=19.53 Aligned_cols=6 Identities=33% Similarity=0.645 Sum_probs=1.9
Q ss_pred CCCCce
Q 035291 26 RCGGGA 31 (68)
Q Consensus 26 ~CGg~v 31 (68)
.||..+
T Consensus 7 ~Cgr~l 12 (68)
T PF09082_consen 7 DCGRYL 12 (68)
T ss_dssp TTS--E
T ss_pred cCCCEE
Confidence 355544
No 226
>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=25.26 E-value=38 Score=26.09 Aligned_cols=12 Identities=42% Similarity=1.104 Sum_probs=5.9
Q ss_pred ccCceeCCCCCC
Q 035291 18 KPAAGICSRCGG 29 (68)
Q Consensus 18 ~~a~g~Cp~CGg 29 (68)
++..+.||+||+
T Consensus 249 ~~~~~~C~~c~~ 260 (374)
T TIGR00308 249 SQRKGRCKECGG 260 (374)
T ss_pred cCCCCCCCCCCC
Confidence 334445555554
No 227
>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=24.91 E-value=41 Score=25.77 Aligned_cols=18 Identities=22% Similarity=0.554 Sum_probs=14.0
Q ss_pred ccCceeCCCCCCceeEEE
Q 035291 18 KPAAGICSRCGGGASVAD 35 (68)
Q Consensus 18 ~~a~g~Cp~CGg~v~a~d 35 (68)
.+--|+||.||.|-+-..
T Consensus 11 ~~~~g~cp~c~~w~~~~e 28 (372)
T cd01121 11 PKWLGKCPECGEWNTLVE 28 (372)
T ss_pred CCccEECcCCCCceeeee
Confidence 456799999999975554
No 228
>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=24.90 E-value=36 Score=17.51 Aligned_cols=14 Identities=29% Similarity=0.358 Sum_probs=7.8
Q ss_pred eeeEEeecccceee
Q 035291 52 WRAIICTFCGAVLK 65 (68)
Q Consensus 52 kr~~~Ct~C~r~L~ 65 (68)
+.+|.|+.|+.++=
T Consensus 11 ~~kY~Cp~C~~~~C 24 (30)
T PF04438_consen 11 PAKYRCPRCGARYC 24 (30)
T ss_dssp EESEE-TTT--EES
T ss_pred CCEEECCCcCCcee
Confidence 66788888877653
No 229
>PRK04023 DNA polymerase II large subunit; Validated
Probab=24.83 E-value=50 Score=29.72 Aligned_cols=22 Identities=32% Similarity=0.757 Sum_probs=17.1
Q ss_pred eeccCceeCCCCCCceeEEEee
Q 035291 16 KCKPAAGICSRCGGGASVADMK 37 (68)
Q Consensus 16 g~~~a~g~Cp~CGg~v~a~dv~ 37 (68)
++-|..|.||.|||.+.-+.=|
T Consensus 1048 RR~PL~G~C~kCGg~lilTVh~ 1069 (1121)
T PRK04023 1048 RRPPLSGKCPKCGGNLILTVHK 1069 (1121)
T ss_pred ccCCCCCcCccCCCeEEEEEec
Confidence 4568899999999999655433
No 230
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=24.63 E-value=1.3e+02 Score=20.02 Aligned_cols=33 Identities=21% Similarity=0.367 Sum_probs=22.9
Q ss_pred ceeCCCCCCceeEEEeeeeeEEEEEeeeeceee
Q 035291 21 AGICSRCGGGASVADMKTATRFCHVPFYWKSWR 53 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr 53 (68)
.-.||.||.....+=+-..+-+=-|=|..|.++
T Consensus 47 ~~~cP~Cge~~~~a~vva~taLVgL~l~mkVfn 79 (102)
T PF04475_consen 47 DTICPKCGEELDSAFVVADTALVGLILEMKVFN 79 (102)
T ss_pred cccCCCCCCccCceEEEeccceEEEEEEEEEee
Confidence 357999999987776666666655666666553
No 231
>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=24.43 E-value=29 Score=26.78 Aligned_cols=24 Identities=17% Similarity=0.380 Sum_probs=11.5
Q ss_pred eCCceeeeeeccCceeCCCCCCce
Q 035291 8 VDQTRKVHKCKPAAGICSRCGGGA 31 (68)
Q Consensus 8 cde~~kv~g~~~a~g~Cp~CGg~v 31 (68)
|+.++.+.|.++....||.||+..
T Consensus 246 C~~~~~~~~~~~~~~~c~~cg~~~ 269 (377)
T PF02005_consen 246 CGYREEVKGLQKLKSKCPECGSKL 269 (377)
T ss_dssp T--EECCT-GCC--CEETTT-SCC
T ss_pred ccccccccCccccCCcCCCCCCcc
Confidence 334455666666667777777655
No 232
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=24.15 E-value=53 Score=23.55 Aligned_cols=15 Identities=20% Similarity=0.530 Sum_probs=11.3
Q ss_pred cCceeCCCCCCceeE
Q 035291 19 PAAGICSRCGGGASV 33 (68)
Q Consensus 19 ~a~g~Cp~CGg~v~a 33 (68)
.--+.||.||+.+.-
T Consensus 151 ~~~~~Cp~CG~~~~~ 165 (177)
T COG1439 151 EPKDFCPICGSPLKR 165 (177)
T ss_pred CCCCcCCCCCCceEE
Confidence 345789999999743
No 233
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=24.14 E-value=27 Score=24.78 Aligned_cols=14 Identities=29% Similarity=0.615 Sum_probs=11.6
Q ss_pred eeCCCCCCceeEEE
Q 035291 22 GICSRCGGGASVAD 35 (68)
Q Consensus 22 g~Cp~CGg~v~a~d 35 (68)
..||.||+.++..|
T Consensus 133 F~Cp~Cg~~L~~~d 146 (176)
T COG1675 133 FTCPKCGEDLEEYD 146 (176)
T ss_pred CCCCCCCchhhhcc
Confidence 68999999986655
No 234
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=23.90 E-value=10 Score=31.51 Aligned_cols=33 Identities=24% Similarity=0.677 Sum_probs=25.0
Q ss_pred eCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccc
Q 035291 23 ICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGA 62 (68)
Q Consensus 23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r 62 (68)
.|--||-.+ ..+...++|+| ...-+|+|+.|+.
T Consensus 342 ~CAgC~~~i-~~~~~~~~R~C------~y~G~y~C~~Ch~ 374 (580)
T KOG1829|consen 342 RCAGCGHTI-GPDLEQRPRLC------RYLGKYFCDCCHQ 374 (580)
T ss_pred eecccCCCc-ccccccchhHh------hhhhhhhCchhcc
Confidence 599999999 66888999999 2345566666654
No 235
>PF13395 HNH_4: HNH endonuclease
Probab=23.58 E-value=29 Score=19.43 Aligned_cols=13 Identities=31% Similarity=0.897 Sum_probs=10.6
Q ss_pred CCCCCCceeEEEe
Q 035291 24 CSRCGGGASVADM 36 (68)
Q Consensus 24 Cp~CGg~v~a~dv 36 (68)
|+|||-.+...++
T Consensus 1 C~Y~g~~i~~~~l 13 (54)
T PF13395_consen 1 CPYCGKPISIENL 13 (54)
T ss_pred CCCCCCCCChhhc
Confidence 8999999876654
No 236
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=23.53 E-value=39 Score=28.16 Aligned_cols=10 Identities=40% Similarity=0.750 Sum_probs=6.3
Q ss_pred Eeecccceee
Q 035291 56 ICTFCGAVLK 65 (68)
Q Consensus 56 ~Ct~C~r~L~ 65 (68)
+|+.||..+.
T Consensus 43 fC~~CG~~~~ 52 (645)
T PRK14559 43 HCPNCGAETG 52 (645)
T ss_pred cccccCCccc
Confidence 6667766653
No 237
>cd01230 PH_EFA6 EFA6 Pleckstrin Homology (PH) domain. EFA6 Pleckstrin Homology (PH) domain. EFA6 is an guanine nucleotide exchange factor for ARF6, which is involved in membrane recycling. It consists of a SEC7 domain followed by a PH domain. The EFA6 PH domain regulates its association with the plasma membrane. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=23.52 E-value=65 Score=21.01 Aligned_cols=22 Identities=32% Similarity=0.495 Sum_probs=18.9
Q ss_pred eeeeceeeeEEeecccceeeee
Q 035291 46 PFYWKSWRAIICTFCGAVLKSY 67 (68)
Q Consensus 46 Pl~~k~kr~~~Ct~C~r~L~~~ 67 (68)
|+..++|+++.|.+.+..|..|
T Consensus 20 ~~~~R~Wk~~y~vL~g~~L~~y 41 (117)
T cd01230 20 PFGKRSWKMFYGILRGLVLYLQ 41 (117)
T ss_pred CCCCCcceEEEEEEECCEEEEE
Confidence 5667899999999999998876
No 238
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=23.50 E-value=54 Score=30.06 Aligned_cols=21 Identities=33% Similarity=0.725 Sum_probs=16.7
Q ss_pred eeccCceeCCCCCCceeEEEe
Q 035291 16 KCKPAAGICSRCGGGASVADM 36 (68)
Q Consensus 16 g~~~a~g~Cp~CGg~v~a~dv 36 (68)
++-|..|.||.|||.+.-+.=
T Consensus 1264 RR~PL~G~C~kCGg~iilTv~ 1284 (1337)
T PRK14714 1264 RRMPLAGKCRKCGGRIILTVH 1284 (1337)
T ss_pred ccCCCCCcccccCCeEEEEEe
Confidence 456899999999999865543
No 239
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=23.39 E-value=50 Score=15.07 Aligned_cols=8 Identities=38% Similarity=0.941 Sum_probs=5.8
Q ss_pred eCCCCCCc
Q 035291 23 ICSRCGGG 30 (68)
Q Consensus 23 ~Cp~CGg~ 30 (68)
.|.+||..
T Consensus 2 ~C~~C~~~ 9 (18)
T PF00098_consen 2 KCFNCGEP 9 (18)
T ss_dssp BCTTTSCS
T ss_pred cCcCCCCc
Confidence 58888864
No 240
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.23 E-value=95 Score=22.92 Aligned_cols=47 Identities=19% Similarity=0.282 Sum_probs=27.7
Q ss_pred eeeccCceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccc
Q 035291 15 HKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGA 62 (68)
Q Consensus 15 ~g~~~a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r 62 (68)
++.++..-.|+.||+.- |---.-.||+=-=-=..-.|--|-|+.|+.
T Consensus 11 ~~~pq~~k~C~~Cg~kr-~f~cSg~fRvNAq~K~LDvWlIYkC~~Cd~ 57 (203)
T COG4332 11 VGAPQPAKRCNSCGVKR-AFTCSGKFRVNAQGKVLDVWLIYKCTHCDY 57 (203)
T ss_pred ccCChhhhhCcccCCcc-eeeecCcEEEcCCCcEEEEEEEEEeeccCC
Confidence 57788888999999875 211111333221122334466788888875
No 241
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=23.21 E-value=1.3e+02 Score=18.71 Aligned_cols=40 Identities=20% Similarity=0.435 Sum_probs=23.7
Q ss_pred eeCCCCCCceeEEEeeeeeE---EE-EEeeeeceeeeEEeecccc
Q 035291 22 GICSRCGGGASVADMKTATR---FC-HVPFYWKSWRAIICTFCGA 62 (68)
Q Consensus 22 g~Cp~CGg~v~a~dv~s~~r---fC-flPl~~k~kr~~~Ct~C~r 62 (68)
.+||-||+-- .-.=|...+ += ++-+-.+.+-.+.|..||-
T Consensus 5 ~kCpKCgn~~-~~ekei~~tg~~lskifdvq~n~f~~itCk~CgY 48 (68)
T COG3478 5 FKCPKCGNTN-YEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGY 48 (68)
T ss_pred ccCCCcCCcc-hhhceeeccCCCcceeEEecccEEEEEEeccCCc
Confidence 4599999865 222222111 11 3466677778888988873
No 242
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=23.20 E-value=55 Score=30.55 Aligned_cols=21 Identities=24% Similarity=0.578 Sum_probs=16.8
Q ss_pred eeccCceeCCCCCCceeEEEe
Q 035291 16 KCKPAAGICSRCGGGASVADM 36 (68)
Q Consensus 16 g~~~a~g~Cp~CGg~v~a~dv 36 (68)
++-|..|.||.|||.+.-+.=
T Consensus 1552 RR~PL~G~C~kCGg~~ilTV~ 1572 (1627)
T PRK14715 1552 RRVPLKGKCPKCGSKLILTVS 1572 (1627)
T ss_pred ccCCCCCcCcccCCeEEEEEe
Confidence 456899999999999965543
No 243
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=22.84 E-value=37 Score=22.41 Aligned_cols=7 Identities=43% Similarity=1.179 Sum_probs=5.7
Q ss_pred eCCCCCC
Q 035291 23 ICSRCGG 29 (68)
Q Consensus 23 ~Cp~CGg 29 (68)
.||+||-
T Consensus 5 ~CP~Cg~ 11 (97)
T COG4311 5 PCPYCGE 11 (97)
T ss_pred cCCCCCC
Confidence 5999984
No 244
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.76 E-value=52 Score=27.60 Aligned_cols=23 Identities=22% Similarity=0.567 Sum_probs=16.8
Q ss_pred eeCCCCCCceeEEEeeeeeEEE-EE
Q 035291 22 GICSRCGGGASVADMKTATRFC-HV 45 (68)
Q Consensus 22 g~Cp~CGg~v~a~dv~s~~rfC-fl 45 (68)
-.||+||+.- ...++.+.|.| ++
T Consensus 660 ~~CP~CG~~~-~~~~~v~~Ri~GYl 683 (711)
T PRK09263 660 FTCPKCGNHD-PKTVSVTRRTCGYL 683 (711)
T ss_pred CcCcCCCCCC-CcceeEEEeecccc
Confidence 5899999852 23377889998 45
No 245
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=22.69 E-value=43 Score=18.63 Aligned_cols=8 Identities=50% Similarity=1.302 Sum_probs=5.9
Q ss_pred CCCCCCce
Q 035291 24 CSRCGGGA 31 (68)
Q Consensus 24 Cp~CGg~v 31 (68)
||+||+.-
T Consensus 1 CP~Cg~~f 8 (50)
T PF14375_consen 1 CPRCGAPF 8 (50)
T ss_pred CCCCCCcC
Confidence 78888765
No 246
>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=22.50 E-value=46 Score=15.49 Aligned_cols=12 Identities=33% Similarity=0.775 Sum_probs=8.5
Q ss_pred EEeecccceeee
Q 035291 55 IICTFCGAVLKS 66 (68)
Q Consensus 55 ~~Ct~C~r~L~~ 66 (68)
+.|..|++...+
T Consensus 2 ~~C~~C~~~F~~ 13 (27)
T PF13912_consen 2 FECDECGKTFSS 13 (27)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCccCCccCC
Confidence 568888877654
No 247
>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=22.46 E-value=38 Score=23.00 Aligned_cols=16 Identities=25% Similarity=0.748 Sum_probs=11.0
Q ss_pred ceeCCCCCCceeEEEeee
Q 035291 21 AGICSRCGGGASVADMKT 38 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~s 38 (68)
+-.||+||..- +.+.|
T Consensus 105 ~~~cp~c~s~~--t~~~s 120 (146)
T TIGR02159 105 SVQCPRCGSAD--TTITS 120 (146)
T ss_pred CCcCCCCCCCC--cEeec
Confidence 46999999753 44444
No 248
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.44 E-value=16 Score=30.34 Aligned_cols=23 Identities=22% Similarity=0.452 Sum_probs=17.1
Q ss_pred ceeCCCCCCceeEEEeeeeeEEE-EE-ee
Q 035291 21 AGICSRCGGGASVADMKTATRFC-HV-PF 47 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~s~~rfC-fl-Pl 47 (68)
--.||.||+ .|++.+.|.| ++ |+
T Consensus 580 ~~~CP~CGs----~~~ev~~RV~GYl~~v 604 (623)
T PRK08271 580 GKRCPICGS----ENIDYYTRVIGYLKRV 604 (623)
T ss_pred CcCCcCCCC----cchhHHHHHhhhhcCc
Confidence 368999998 4677788888 33 65
No 249
>PRK08173 DNA topoisomerase III; Validated
Probab=22.26 E-value=68 Score=27.49 Aligned_cols=14 Identities=36% Similarity=1.085 Sum_probs=11.5
Q ss_pred ccCceeCCCCCCce
Q 035291 18 KPAAGICSRCGGGA 31 (68)
Q Consensus 18 ~~a~g~Cp~CGg~v 31 (68)
+...|.||.||+.+
T Consensus 723 ~~~~g~CPkCg~~v 736 (862)
T PRK08173 723 QEPVGACPKCGGRV 736 (862)
T ss_pred cccccCCCCCCCee
Confidence 56679999999965
No 250
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=22.06 E-value=40 Score=16.46 Aligned_cols=12 Identities=17% Similarity=0.791 Sum_probs=9.5
Q ss_pred eEEeecccceee
Q 035291 54 AIICTFCGAVLK 65 (68)
Q Consensus 54 ~~~Ct~C~r~L~ 65 (68)
.+.|.+|+..+.
T Consensus 3 ~~~C~~C~~~~~ 14 (35)
T smart00451 3 GFYCKLCNVTFT 14 (35)
T ss_pred CeEccccCCccC
Confidence 578999988765
No 251
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=21.94 E-value=84 Score=15.91 Aligned_cols=15 Identities=27% Similarity=0.459 Sum_probs=11.6
Q ss_pred ceeCCCCCCceeEEE
Q 035291 21 AGICSRCGGGASVAD 35 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~d 35 (68)
--.|..||+-+.+.+
T Consensus 7 ~ykC~~Cgniv~v~~ 21 (34)
T TIGR00319 7 VYKCEVCGNIVEVLH 21 (34)
T ss_pred EEEcCCCCcEEEEEE
Confidence 457999999996654
No 252
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=21.72 E-value=1.3e+02 Score=19.60 Aligned_cols=16 Identities=19% Similarity=0.632 Sum_probs=11.3
Q ss_pred ceeCCCCCCceeEEEeee
Q 035291 21 AGICSRCGGGASVADMKT 38 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~s 38 (68)
--.||.||++= +++..
T Consensus 80 yVlC~~C~spd--T~l~k 95 (110)
T smart00653 80 YVLCPECGSPD--TELIK 95 (110)
T ss_pred cEECCCCCCCC--cEEEE
Confidence 36899999984 45443
No 253
>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=21.57 E-value=36 Score=18.20 Aligned_cols=14 Identities=21% Similarity=0.365 Sum_probs=6.5
Q ss_pred ccCceeCCCCCCce
Q 035291 18 KPAAGICSRCGGGA 31 (68)
Q Consensus 18 ~~a~g~Cp~CGg~v 31 (68)
.-.+-+|++||-..
T Consensus 18 ~~~~isC~~CGPr~ 31 (35)
T PF07503_consen 18 HYQFISCTNCGPRY 31 (35)
T ss_dssp T-TT--BTTCC-SC
T ss_pred cCcCccCCCCCCCE
Confidence 34456778887655
No 254
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=21.51 E-value=45 Score=19.75 Aligned_cols=13 Identities=31% Similarity=0.754 Sum_probs=10.8
Q ss_pred cCceeCCCCCCce
Q 035291 19 PAAGICSRCGGGA 31 (68)
Q Consensus 19 ~a~g~Cp~CGg~v 31 (68)
..+..|+.||+..
T Consensus 57 ~~~~~C~~C~~~~ 69 (86)
T PF13966_consen 57 QVDPICPLCGNEE 69 (86)
T ss_pred ccCCccccCCCcc
Confidence 5678999999865
No 255
>PRK03922 hypothetical protein; Provisional
Probab=21.47 E-value=1.6e+02 Score=19.94 Aligned_cols=32 Identities=22% Similarity=0.349 Sum_probs=22.3
Q ss_pred ceeCCCCCCceeEEEeeeeeEEEEEeeeecee
Q 035291 21 AGICSRCGGGASVADMKTATRFCHVPFYWKSW 52 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~k 52 (68)
.-+||.||.....+=+-..+-+=-|=|..|..
T Consensus 49 ~~~cP~cge~~~~afvvA~taLVgL~lemkVF 80 (113)
T PRK03922 49 LTICPKCGEPFDSAFVVADTALVGLLLEMKVF 80 (113)
T ss_pred cccCCCCCCcCCcEEEEeccceEEEEEEEEEe
Confidence 45799999998776666666665566666554
No 256
>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=21.37 E-value=88 Score=15.89 Aligned_cols=14 Identities=29% Similarity=0.522 Sum_probs=10.7
Q ss_pred eeCCCCCCceeEEE
Q 035291 22 GICSRCGGGASVAD 35 (68)
Q Consensus 22 g~Cp~CGg~v~a~d 35 (68)
-.|..||+-+.+.+
T Consensus 5 ykC~~CGniv~v~~ 18 (34)
T cd00974 5 YKCEICGNIVEVLN 18 (34)
T ss_pred EEcCCCCcEEEEEE
Confidence 46889999996554
No 257
>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=21.21 E-value=55 Score=18.51 Aligned_cols=14 Identities=36% Similarity=0.624 Sum_probs=7.8
Q ss_pred eeeeEEeeccccee
Q 035291 51 SWRAIICTFCGAVL 64 (68)
Q Consensus 51 ~kr~~~Ct~C~r~L 64 (68)
..|++.|..||+..
T Consensus 22 ~~rrhhCr~CG~~v 35 (69)
T PF01363_consen 22 FRRRHHCRNCGRVV 35 (69)
T ss_dssp SS-EEE-TTT--EE
T ss_pred ceeeEccCCCCCEE
Confidence 38899999998754
No 258
>PF15410 PH_9: Pleckstrin homology domain; PDB: 1WJM_A 1BTN_A 1MPH_A.
Probab=21.09 E-value=91 Score=19.73 Aligned_cols=23 Identities=22% Similarity=0.434 Sum_probs=15.9
Q ss_pred eeeeceeeeEEeecccceeeeeC
Q 035291 46 PFYWKSWRAIICTFCGAVLKSYQ 68 (68)
Q Consensus 46 Pl~~k~kr~~~Ct~C~r~L~~~~ 68 (68)
|...++|+.+.+.+.|..|-.|.
T Consensus 20 ~~~~R~Wk~~y~vL~g~~L~~~k 42 (119)
T PF15410_consen 20 SRSKRSWKQVYAVLQGGQLYFYK 42 (119)
T ss_dssp --S---EEEEEEEEETTEEEEES
T ss_pred CCCCCCccEEeEEEECCEEEEEc
Confidence 56788999999999999998773
No 259
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=21.03 E-value=48 Score=23.43 Aligned_cols=14 Identities=14% Similarity=0.282 Sum_probs=9.9
Q ss_pred ccCceeCCCCCCce
Q 035291 18 KPAAGICSRCGGGA 31 (68)
Q Consensus 18 ~~a~g~Cp~CGg~v 31 (68)
+.-.-.||+||++=
T Consensus 365 ~~~~~~c~~c~~~~ 378 (389)
T PRK11788 365 RTLYWHCPSCKAWE 378 (389)
T ss_pred ccceeECcCCCCcc
Confidence 44556799998864
No 260
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=20.94 E-value=39 Score=21.39 Aligned_cols=46 Identities=22% Similarity=0.480 Sum_probs=14.6
Q ss_pred cCceeCCCCCCceeEEEeee-------eeEEEE---EeeeeceeeeEEeecccceeee
Q 035291 19 PAAGICSRCGGGASVADMKT-------ATRFCH---VPFYWKSWRAIICTFCGAVLKS 66 (68)
Q Consensus 19 ~a~g~Cp~CGg~v~a~dv~s-------~~rfCf---lPl~~k~kr~~~Ct~C~r~L~~ 66 (68)
++.-.|+-|+..+...|.+. .|.=|. +|+.--.. -.|..|+++.-.
T Consensus 12 ~i~E~C~~C~~~i~~~~~~~~~C~~GH~w~RC~lT~l~i~~~~~--r~C~~C~~~~l~ 67 (99)
T PF12660_consen 12 PIFEKCPICGAPIPFDDLDEAQCENGHVWPRCALTFLPIQTPGV--RVCPVCGRRALD 67 (99)
T ss_dssp -----------------SSEEE-TTS-EEEB-SSS-SBS-SS-E--EE-TTT--EEE-
T ss_pred cccccccccccccccCCcCEeECCCCCEEeeeeeeeeeeccCCe--eEcCCCCCEEec
Confidence 44478999999987777553 566674 58777666 679999987643
No 261
>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=20.81 E-value=11 Score=20.47 Aligned_cols=21 Identities=19% Similarity=0.238 Sum_probs=7.3
Q ss_pred ccCceeCCC--CCCceeEEEeee
Q 035291 18 KPAAGICSR--CGGGASVADMKT 38 (68)
Q Consensus 18 ~~a~g~Cp~--CGg~v~a~dv~s 38 (68)
.+..-.||+ |++.+...+-..
T Consensus 15 ~~~~~~Cp~~~C~~~~~~~~~~~ 37 (64)
T PF01485_consen 15 DPNIRWCPNPDCEYIIEKDDGCN 37 (64)
T ss_dssp ---CC--TTSST---ECS-SSTT
T ss_pred CCCccCCCCCCCcccEEecCCCC
Confidence 333348988 999886555443
No 262
>smart00746 TRASH metallochaperone-like domain.
Probab=20.78 E-value=1e+02 Score=13.56 Aligned_cols=9 Identities=44% Similarity=0.922 Sum_probs=6.3
Q ss_pred CCCCCCcee
Q 035291 24 CSRCGGGAS 32 (68)
Q Consensus 24 Cp~CGg~v~ 32 (68)
|+.||-.+.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 677877663
No 263
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=20.64 E-value=71 Score=24.15 Aligned_cols=24 Identities=25% Similarity=0.350 Sum_probs=15.0
Q ss_pred eeeeeccCceeCCCCCCceeEEEeee
Q 035291 13 KVHKCKPAAGICSRCGGGASVADMKT 38 (68)
Q Consensus 13 kv~g~~~a~g~Cp~CGg~v~a~dv~s 38 (68)
+|=|+++ --|+.||+.+.-..+..
T Consensus 239 ~VYgR~G--epC~~CGt~I~k~~~~g 262 (273)
T COG0266 239 KVYGRAG--EPCRRCGTPIEKIKLGG 262 (273)
T ss_pred EEecCCC--CCCCccCCEeEEEEEcC
Confidence 3444444 35889999995555443
No 264
>PRK12722 transcriptional activator FlhC; Provisional
Probab=20.48 E-value=46 Score=23.89 Aligned_cols=15 Identities=27% Similarity=0.589 Sum_probs=10.5
Q ss_pred ceeCCCCCCceeEEE
Q 035291 21 AGICSRCGGGASVAD 35 (68)
Q Consensus 21 ~g~Cp~CGg~v~a~d 35 (68)
.-.|..|||.-.++.
T Consensus 134 l~~C~~Cgg~fv~~~ 148 (187)
T PRK12722 134 LSSCNCCGGHFVTHA 148 (187)
T ss_pred eccCCCCCCCeeccc
Confidence 346999999864433
No 265
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=20.05 E-value=1.5e+02 Score=19.18 Aligned_cols=48 Identities=25% Similarity=0.323 Sum_probs=29.5
Q ss_pred eeccCceeCCCCCCceeEEEeee-eeEEEEE-eeee-----ceee---eEEeecccce
Q 035291 16 KCKPAAGICSRCGGGASVADMKT-ATRFCHV-PFYW-----KSWR---AIICTFCGAV 63 (68)
Q Consensus 16 g~~~a~g~Cp~CGg~v~a~dv~s-~~rfCfl-Pl~~-----k~kr---~~~Ct~C~r~ 63 (68)
....+-+.||-||+.....--+. +|--|.. |-+. +... .+.|.-|+..
T Consensus 12 ~~~~~~~~Cp~Cg~~m~~~~~~~g~f~gCs~yP~C~~~~~~~~~~~~~~~~Cp~C~~~ 69 (140)
T COG0551 12 KDLKTGQICPKCGKNMVKKFGKYGIFLGCSNYPKCDYYEPEKAIAEKTGVKCPKCGKG 69 (140)
T ss_pred cccccCccCCcCCCeeEEEEccCCeEEEeCCCCCCCCCcccccccccCceeCCCCCCC
Confidence 44567888999998774433332 4555543 6666 3333 3888888853
Done!