Query 044880
Match_columns 91
No_of_seqs 100 out of 266
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 07:39:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044880.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044880hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01780 Ribosomal_L37ae: Ribo 100.0 1.2E-52 2.7E-57 282.5 8.0 90 1-90 1-90 (90)
2 TIGR00280 L37a ribosomal prote 100.0 2.6E-51 5.7E-56 276.6 9.4 90 2-91 2-91 (91)
3 PTZ00255 60S ribosomal protein 100.0 3.2E-51 6.9E-56 275.7 8.8 89 1-89 2-90 (90)
4 PRK03976 rpl37ae 50S ribosomal 100.0 2.9E-50 6.4E-55 271.0 8.8 89 1-89 2-90 (90)
5 KOG0402 60S ribosomal protein 100.0 5.1E-50 1.1E-54 269.1 6.0 91 1-91 2-92 (92)
6 COG1997 RPL43A Ribosomal prote 100.0 7.3E-44 1.6E-48 239.4 7.7 87 3-89 3-89 (89)
7 PF12760 Zn_Tnp_IS1595: Transp 97.3 0.00022 4.8E-09 41.8 2.4 28 35-62 18-46 (46)
8 TIGR03655 anti_R_Lar restricti 97.2 0.0004 8.6E-09 41.8 3.0 39 37-84 3-48 (53)
9 PRK09710 lar restriction allev 96.3 0.0048 1.1E-07 39.6 3.3 34 37-73 8-44 (64)
10 PRK00432 30S ribosomal protein 96.3 0.0024 5.3E-08 38.6 1.7 26 37-63 22-47 (50)
11 COG4888 Uncharacterized Zn rib 96.3 0.0018 3.9E-08 45.0 1.2 46 32-77 19-70 (104)
12 PF14354 Lar_restr_allev: Rest 96.2 0.0082 1.8E-07 36.1 3.7 46 36-85 4-57 (61)
13 PF08271 TF_Zn_Ribbon: TFIIB z 95.9 0.0069 1.5E-07 34.8 2.3 31 36-66 1-32 (43)
14 PHA00626 hypothetical protein 95.9 0.006 1.3E-07 38.7 2.0 33 37-69 2-39 (59)
15 PRK00464 nrdR transcriptional 95.6 0.0079 1.7E-07 43.8 1.9 26 36-65 1-40 (154)
16 PF01807 zf-CHC2: CHC2 zinc fi 95.6 0.0081 1.7E-07 39.9 1.8 52 35-88 33-88 (97)
17 PF05129 Elf1: Transcription e 95.3 0.02 4.4E-07 37.5 3.1 46 30-75 17-68 (81)
18 PF07282 OrfB_Zn_ribbon: Putat 95.1 0.016 3.5E-07 35.6 2.0 27 37-63 30-56 (69)
19 PRK00398 rpoP DNA-directed RNA 95.0 0.02 4.3E-07 33.3 2.1 31 34-64 2-32 (46)
20 smart00661 RPOL9 RNA polymeras 94.7 0.027 5.8E-07 32.7 2.2 32 37-68 2-35 (52)
21 PF08273 Prim_Zn_Ribbon: Zinc- 94.4 0.024 5.1E-07 33.2 1.4 25 37-61 5-34 (40)
22 smart00400 ZnF_CHCC zinc finge 94.4 0.025 5.3E-07 33.8 1.5 32 36-69 3-37 (55)
23 TIGR03831 YgiT_finger YgiT-typ 93.6 0.049 1.1E-06 30.5 1.6 15 50-64 29-43 (46)
24 COG1998 RPS31 Ribosomal protei 93.1 0.048 1E-06 33.7 1.2 30 34-63 18-47 (51)
25 COG0675 Transposase and inacti 92.8 0.07 1.5E-06 39.1 1.9 22 37-63 311-332 (364)
26 smart00778 Prim_Zn_Ribbon Zinc 92.6 0.071 1.5E-06 30.7 1.4 25 37-61 5-33 (37)
27 PF11781 RRN7: RNA polymerase 92.5 0.09 2E-06 29.8 1.7 27 36-63 9-35 (36)
28 PRK00423 tfb transcription ini 92.5 0.085 1.8E-06 41.3 2.1 37 28-64 4-41 (310)
29 PF08646 Rep_fac-A_C: Replicat 92.2 0.097 2.1E-06 36.2 1.9 32 37-69 20-53 (146)
30 PF09986 DUF2225: Uncharacteri 92.2 0.15 3.2E-06 38.2 3.0 37 34-70 4-65 (214)
31 PRK14892 putative transcriptio 91.9 0.049 1.1E-06 37.3 0.1 34 29-63 15-52 (99)
32 PRK05667 dnaG DNA primase; Val 91.5 0.11 2.4E-06 44.3 1.8 48 36-86 37-89 (580)
33 TIGR03830 CxxCG_CxxCG_HTH puta 91.3 0.21 4.6E-06 33.1 2.7 16 50-65 28-43 (127)
34 smart00659 RPOLCX RNA polymera 91.0 0.18 3.8E-06 29.8 1.8 29 35-64 2-30 (44)
35 COG2956 Predicted N-acetylgluc 90.9 0.23 4.9E-06 41.2 3.0 37 20-61 340-376 (389)
36 PF08772 NOB1_Zn_bind: Nin one 90.7 0.15 3.2E-06 33.3 1.4 21 33-53 22-42 (73)
37 TIGR01391 dnaG DNA primase, ca 90.6 0.18 3.8E-06 41.0 2.1 48 36-86 35-87 (415)
38 PHA02942 putative transposase; 90.4 0.16 3.4E-06 41.2 1.7 26 37-63 327-352 (383)
39 PRK14890 putative Zn-ribbon RN 90.4 0.21 4.6E-06 31.6 1.9 29 33-61 23-56 (59)
40 PHA02540 61 DNA primase; Provi 90.4 0.22 4.7E-06 40.3 2.4 28 35-62 27-64 (337)
41 PF13465 zf-H2C2_2: Zinc-finge 90.4 0.18 4E-06 26.1 1.4 15 30-44 9-23 (26)
42 smart00531 TFIIE Transcription 90.0 0.23 4.9E-06 35.0 2.0 42 22-63 81-133 (147)
43 PF02150 RNA_POL_M_15KD: RNA p 89.9 0.32 6.9E-06 27.3 2.2 29 37-65 3-32 (35)
44 PF03604 DNA_RNApol_7kD: DNA d 89.6 0.12 2.7E-06 28.8 0.4 27 36-63 1-27 (32)
45 PRK11823 DNA repair protein Ra 89.5 0.16 3.4E-06 41.8 1.0 24 33-60 5-28 (446)
46 COG1594 RPB9 DNA-directed RNA 89.4 0.31 6.7E-06 33.6 2.3 28 37-64 4-33 (113)
47 PRK12366 replication factor A; 89.3 0.18 3.9E-06 43.4 1.2 24 37-62 534-557 (637)
48 PF03811 Zn_Tnp_IS1: InsA N-te 89.2 0.29 6.3E-06 27.9 1.7 23 37-59 7-35 (36)
49 smart00440 ZnF_C2C2 C2C2 Zinc 88.9 0.37 7.9E-06 27.6 2.0 29 36-64 1-39 (40)
50 TIGR01384 TFS_arch transcripti 88.9 0.22 4.7E-06 32.8 1.2 27 37-65 2-28 (104)
51 PF05605 zf-Di19: Drought indu 88.9 0.19 4.2E-06 29.8 0.8 10 35-44 2-11 (54)
52 TIGR00244 transcriptional regu 88.9 0.24 5.3E-06 36.2 1.5 28 37-64 2-39 (147)
53 TIGR00416 sms DNA repair prote 88.3 0.21 4.5E-06 41.2 1.0 25 32-60 4-28 (454)
54 PF11672 DUF3268: Protein of u 88.3 0.56 1.2E-05 32.3 2.9 52 35-87 2-64 (102)
55 KOG3214 Uncharacterized Zn rib 87.6 0.22 4.8E-06 34.9 0.6 48 30-77 18-71 (109)
56 PF08274 PhnA_Zn_Ribbon: PhnA 87.5 0.5 1.1E-05 26.1 1.9 26 37-63 4-29 (30)
57 COG3677 Transposase and inacti 87.3 0.93 2E-05 31.9 3.7 37 29-65 23-65 (129)
58 PF08792 A2L_zn_ribbon: A2L zi 87.2 0.87 1.9E-05 25.4 2.8 30 35-64 3-32 (33)
59 smart00834 CxxC_CXXC_SSSS Puta 87.1 0.53 1.1E-05 25.8 1.9 27 35-61 5-34 (41)
60 cd04476 RPA1_DBD_C RPA1_DBD_C: 86.9 0.34 7.5E-06 34.0 1.3 26 37-63 36-61 (166)
61 PF07191 zinc-ribbons_6: zinc- 86.6 0.83 1.8E-05 29.7 2.8 33 37-71 3-35 (70)
62 PF09862 DUF2089: Protein of u 86.4 0.77 1.7E-05 32.2 2.8 24 38-66 1-25 (113)
63 COG2888 Predicted Zn-ribbon RN 86.3 0.39 8.5E-06 30.7 1.2 29 33-61 25-58 (61)
64 PRK09678 DNA-binding transcrip 86.0 1 2.2E-05 29.2 3.0 30 36-65 2-41 (72)
65 cd01121 Sms Sms (bacterial rad 86.0 0.38 8.2E-06 38.9 1.2 21 36-60 1-21 (372)
66 PF04606 Ogr_Delta: Ogr/Delta- 85.9 1.7 3.6E-05 25.4 3.7 30 37-66 1-40 (47)
67 PF10571 UPF0547: Uncharacteri 85.3 0.33 7.2E-06 25.8 0.4 24 37-64 2-25 (26)
68 PF01096 TFIIS_C: Transcriptio 85.1 1.8 3.9E-05 24.5 3.5 27 37-63 2-38 (39)
69 COG1405 SUA7 Transcription ini 85.0 0.77 1.7E-05 36.3 2.5 30 36-65 2-32 (285)
70 PF13453 zf-TFIIB: Transcripti 83.9 1.6 3.4E-05 24.7 2.9 24 37-60 1-26 (41)
71 PF14353 CpXC: CpXC protein 83.8 1.2 2.6E-05 30.2 2.7 13 52-64 37-49 (128)
72 COG1571 Predicted DNA-binding 83.8 0.38 8.3E-06 40.3 0.3 30 37-67 352-381 (421)
73 PF03119 DNA_ligase_ZBD: NAD-d 83.6 0.7 1.5E-05 24.8 1.2 21 37-57 1-21 (28)
74 PF06689 zf-C4_ClpX: ClpX C4-t 83.3 0.47 1E-05 27.3 0.5 24 36-59 2-30 (41)
75 PF09538 FYDLN_acid: Protein o 83.1 0.48 1E-05 32.7 0.6 30 34-66 8-39 (108)
76 TIGR02159 PA_CoA_Oxy4 phenylac 83.0 0.36 7.7E-06 34.7 -0.1 28 36-63 106-140 (146)
77 COG1779 C4-type Zn-finger prot 82.4 1.1 2.3E-05 34.4 2.3 31 34-64 13-54 (201)
78 PRK08402 replication factor A; 81.9 0.94 2E-05 36.8 1.9 26 36-61 213-238 (355)
79 PF13240 zinc_ribbon_2: zinc-r 81.8 0.43 9.4E-06 24.6 -0.0 22 37-62 1-22 (23)
80 COG1327 Predicted transcriptio 81.3 0.51 1.1E-05 34.9 0.2 24 37-64 2-39 (156)
81 PF01927 Mut7-C: Mut7-C RNAse 80.9 1.4 2.9E-05 31.0 2.2 31 37-67 93-138 (147)
82 COG1645 Uncharacterized Zn-fin 80.9 1.3 2.8E-05 31.9 2.1 40 23-64 14-55 (131)
83 PF09855 DUF2082: Nucleic-acid 80.7 1.7 3.6E-05 27.6 2.4 10 36-45 1-10 (64)
84 PF14471 DUF4428: Domain of un 80.6 0.29 6.4E-06 29.5 -1.1 32 37-69 1-36 (51)
85 PF14803 Nudix_N_2: Nudix N-te 80.5 1.8 3.8E-05 24.3 2.2 27 37-63 2-32 (34)
86 PF09297 zf-NADH-PPase: NADH p 80.2 2 4.4E-05 23.1 2.3 26 37-62 5-30 (32)
87 cd00729 rubredoxin_SM Rubredox 79.6 1.4 3.1E-05 24.4 1.6 15 53-67 2-16 (34)
88 PF07754 DUF1610: Domain of un 79.0 1.3 2.9E-05 23.4 1.3 10 33-42 14-23 (24)
89 COG1592 Rubrerythrin [Energy p 79.0 1.4 3E-05 32.7 1.8 35 21-60 122-156 (166)
90 TIGR02300 FYDLN_acid conserved 78.8 0.98 2.1E-05 32.5 0.9 27 34-63 8-36 (129)
91 PHA00732 hypothetical protein 78.3 1.2 2.6E-05 28.9 1.2 10 77-86 67-76 (79)
92 PF04981 NMD3: NMD3 family ; 78.1 2.5 5.5E-05 31.8 3.0 21 51-71 33-53 (236)
93 COG2075 RPL24A Ribosomal prote 78.0 1.5 3.1E-05 28.4 1.5 26 36-61 4-38 (66)
94 PRK08173 DNA topoisomerase III 78.0 2.2 4.8E-05 38.2 3.1 26 36-63 625-650 (862)
95 TIGR01384 TFS_arch transcripti 77.2 4.5 9.7E-05 26.5 3.7 34 33-66 60-103 (104)
96 PF09723 Zn-ribbon_8: Zinc rib 76.9 1.6 3.4E-05 25.0 1.3 17 33-49 24-40 (42)
97 TIGR02098 MJ0042_CXXC MJ0042 f 76.7 2 4.4E-05 23.5 1.7 30 35-64 2-36 (38)
98 KOG2593 Transcription initiati 76.3 2.3 4.9E-05 36.0 2.6 41 21-61 112-161 (436)
99 PF08996 zf-DNA_Pol: DNA Polym 76.2 4.2 9E-05 29.8 3.7 27 35-61 18-53 (188)
100 PRK00241 nudC NADH pyrophospha 76.1 2 4.4E-05 33.0 2.1 26 37-62 101-126 (256)
101 PF01396 zf-C4_Topoisom: Topoi 76.0 4 8.6E-05 23.1 2.8 27 37-63 3-34 (39)
102 COG4640 Predicted membrane pro 75.3 1.2 2.6E-05 37.8 0.7 31 37-71 3-33 (465)
103 TIGR00340 zpr1_rel ZPR1-relate 74.7 2.6 5.6E-05 30.9 2.2 33 38-70 1-49 (163)
104 PF03367 zf-ZPR1: ZPR1 zinc-fi 73.8 4.6 0.0001 29.3 3.3 35 37-71 3-52 (161)
105 PF01599 Ribosomal_S27: Riboso 73.7 3.2 6.8E-05 25.1 2.1 28 34-62 17-47 (47)
106 PF04071 zf-like: Cysteine-ric 73.7 7 0.00015 26.2 3.9 12 49-60 45-58 (86)
107 PRK00420 hypothetical protein; 71.8 6.5 0.00014 27.4 3.6 30 34-64 22-51 (112)
108 PHA00616 hypothetical protein 71.6 1.3 2.9E-05 26.4 0.1 10 35-44 1-10 (44)
109 TIGR00617 rpa1 replication fac 71.4 1.8 3.9E-05 37.2 0.8 27 37-64 476-504 (608)
110 cd00350 rubredoxin_like Rubred 71.0 2.6 5.6E-05 23.0 1.1 14 53-66 1-14 (33)
111 PF00096 zf-C2H2: Zinc finger, 70.8 2.9 6.3E-05 20.1 1.2 11 54-64 1-11 (23)
112 PF13248 zf-ribbon_3: zinc-rib 70.7 1.5 3.2E-05 22.8 0.1 23 36-62 3-25 (26)
113 TIGR02605 CxxC_CxxC_SSSS putat 70.1 3.7 7.9E-05 23.7 1.8 27 35-61 5-34 (52)
114 TIGR00311 aIF-2beta translatio 69.9 7.2 0.00016 27.7 3.5 40 22-62 83-127 (133)
115 PF12773 DZR: Double zinc ribb 69.9 1.4 3E-05 25.3 -0.1 30 36-66 13-42 (50)
116 PF13717 zinc_ribbon_4: zinc-r 69.9 3.8 8.3E-05 22.9 1.7 27 36-63 3-35 (36)
117 COG3091 SprT Zn-dependent meta 69.8 3 6.5E-05 30.9 1.6 49 13-63 96-150 (156)
118 PF13894 zf-C2H2_4: C2H2-type 69.8 3.4 7.4E-05 19.3 1.3 11 54-64 1-11 (24)
119 TIGR00382 clpX endopeptidase C 68.8 1.8 3.8E-05 35.8 0.3 25 36-60 8-36 (413)
120 PRK04023 DNA polymerase II lar 68.7 2.3 5.1E-05 39.5 1.0 36 51-87 649-696 (1121)
121 TIGR00686 phnA alkylphosphonat 68.3 3.7 8E-05 28.9 1.8 30 37-67 4-33 (109)
122 KOG2462 C2H2-type Zn-finger pr 67.6 2.4 5.3E-05 33.9 0.8 40 26-65 177-227 (279)
123 PF06676 DUF1178: Protein of u 67.1 6 0.00013 28.8 2.7 23 27-49 23-46 (148)
124 PRK14890 putative Zn-ribbon RN 66.9 3.2 6.9E-05 26.3 1.1 32 31-62 3-34 (59)
125 PF12677 DUF3797: Domain of un 66.9 3.6 7.7E-05 25.3 1.3 12 36-47 13-25 (49)
126 PF09082 DUF1922: Domain of un 66.7 11 0.00023 24.5 3.5 51 36-88 4-56 (68)
127 PRK03988 translation initiatio 66.2 8.7 0.00019 27.5 3.4 40 23-62 89-132 (138)
128 PRK08665 ribonucleotide-diphos 65.1 7.9 0.00017 34.3 3.5 24 37-62 726-749 (752)
129 COG1996 RPC10 DNA-directed RNA 64.2 4.2 9.2E-05 24.8 1.2 29 34-63 5-34 (49)
130 PHA00733 hypothetical protein 64.2 1.9 4.1E-05 30.0 -0.3 36 29-64 67-110 (128)
131 PF13719 zinc_ribbon_5: zinc-r 64.1 5.7 0.00012 22.1 1.7 28 37-64 4-36 (37)
132 COG2158 Uncharacterized protei 64.0 4.9 0.00011 28.4 1.7 14 47-60 54-69 (112)
133 PRK06266 transcription initiat 63.5 9.4 0.0002 28.0 3.2 54 32-88 114-168 (178)
134 TIGR01385 TFSII transcription 61.0 11 0.00023 30.1 3.3 33 31-63 254-296 (299)
135 PRK11788 tetratricopeptide rep 60.9 8.7 0.00019 28.9 2.7 34 22-60 342-375 (389)
136 KOG2462 C2H2-type Zn-finger pr 60.5 1.8 3.8E-05 34.7 -1.2 36 33-68 213-258 (279)
137 COG2051 RPS27A Ribosomal prote 60.5 11 0.00025 24.4 2.8 28 37-64 21-49 (67)
138 KOG1873 Ubiquitin-specific pro 60.3 5.5 0.00012 36.2 1.7 38 34-71 65-111 (877)
139 TIGR00373 conserved hypothetic 60.2 5.4 0.00012 28.6 1.4 27 33-63 107-138 (158)
140 PF01873 eIF-5_eIF-2B: Domain 60.1 11 0.00023 26.5 2.9 40 22-62 79-123 (125)
141 PRK12336 translation initiatio 59.5 13 0.00029 27.7 3.5 47 22-69 84-135 (201)
142 PF11023 DUF2614: Protein of u 59.5 3 6.6E-05 29.5 0.0 26 34-63 68-95 (114)
143 PRK05342 clpX ATP-dependent pr 59.1 3.1 6.7E-05 34.1 0.0 26 34-59 8-37 (412)
144 PRK14715 DNA polymerase II lar 59.0 10 0.00023 36.6 3.3 48 34-87 673-721 (1627)
145 COG4643 Uncharacterized protei 58.1 3.5 7.6E-05 34.2 0.1 29 32-60 29-61 (366)
146 KOG2907 RNA polymerase I trans 58.0 6.8 0.00015 27.8 1.6 30 35-64 74-113 (116)
147 PF14690 zf-ISL3: zinc-finger 57.5 6.1 0.00013 22.1 1.0 14 35-48 2-15 (47)
148 COG1066 Sms Predicted ATP-depe 57.4 4.7 0.0001 34.3 0.8 23 34-60 6-28 (456)
149 PRK07562 ribonucleotide-diphos 57.4 13 0.00027 35.2 3.6 26 36-62 1191-1216(1220)
150 PRK12495 hypothetical protein; 57.4 11 0.00024 29.5 2.8 30 34-65 41-70 (226)
151 PF02945 Endonuclease_7: Recom 57.3 5.2 0.00011 26.2 0.8 29 12-43 2-30 (81)
152 PF04423 Rad50_zn_hook: Rad50 57.1 7.8 0.00017 22.8 1.5 11 35-45 20-30 (54)
153 COG1656 Uncharacterized conser 57.0 6.3 0.00014 29.4 1.3 28 37-64 99-141 (165)
154 PRK04860 hypothetical protein; 56.8 3.8 8.3E-05 29.8 0.2 30 34-64 118-154 (160)
155 PRK05978 hypothetical protein; 56.4 4.9 0.00011 29.2 0.7 39 31-70 29-75 (148)
156 PF09779 Ima1_N: Ima1 N-termin 56.2 5 0.00011 28.0 0.7 24 37-60 2-27 (131)
157 PF13597 NRDD: Anaerobic ribon 55.8 11 0.00023 32.1 2.6 39 19-62 467-513 (546)
158 PRK10220 hypothetical protein; 55.1 8.9 0.00019 27.0 1.8 30 37-67 5-34 (111)
159 PF04216 FdhE: Protein involve 55.0 9.7 0.00021 29.3 2.1 26 35-60 211-245 (290)
160 PF13912 zf-C2H2_6: C2H2-type 55.0 4.9 0.00011 20.0 0.4 9 55-63 3-11 (27)
161 KOG3576 Ovo and related transc 54.3 1.5 3.1E-05 34.7 -2.5 34 32-65 142-185 (267)
162 smart00731 SprT SprT homologue 54.2 10 0.00022 26.4 1.9 30 34-63 111-143 (146)
163 PRK04351 hypothetical protein; 52.9 13 0.00027 26.8 2.3 30 34-63 111-142 (149)
164 PRK07218 replication factor A; 52.6 6.3 0.00014 32.9 0.8 21 36-62 298-318 (423)
165 PF00569 ZZ: Zinc finger, ZZ t 52.6 11 0.00024 21.7 1.7 25 33-60 2-26 (46)
166 PRK03681 hypA hydrogenase nick 52.1 7.3 0.00016 26.6 0.9 27 33-60 68-94 (114)
167 PF10588 NADH-G_4Fe-4S_3: NADH 51.9 13 0.00027 21.2 1.8 22 22-44 1-22 (41)
168 smart00653 eIF2B_5 domain pres 51.9 23 0.0005 24.3 3.4 39 22-61 66-109 (110)
169 TIGR00310 ZPR1_znf ZPR1 zinc f 51.7 15 0.00033 27.5 2.7 35 37-71 2-52 (192)
170 TIGR01206 lysW lysine biosynth 51.3 16 0.00034 22.4 2.2 29 35-63 2-32 (54)
171 COG3809 Uncharacterized protei 51.2 16 0.00034 24.8 2.4 27 37-63 3-31 (88)
172 smart00507 HNHc HNH nucleases. 50.5 13 0.00027 19.9 1.6 13 32-45 8-20 (52)
173 PF04438 zf-HIT: HIT zinc fing 50.3 6.7 0.00014 21.3 0.4 12 33-44 11-22 (30)
174 PF12874 zf-met: Zinc-finger o 50.2 12 0.00025 18.2 1.3 12 54-65 1-12 (25)
175 PRK04023 DNA polymerase II lar 50.1 11 0.00024 35.3 2.0 24 33-62 624-647 (1121)
176 PF14255 Cys_rich_CPXG: Cystei 50.0 8.4 0.00018 23.5 0.9 10 36-45 1-10 (52)
177 smart00355 ZnF_C2H2 zinc finge 50.0 8 0.00017 17.9 0.6 8 56-63 3-10 (26)
178 PF08209 Sgf11: Sgf11 (transcr 49.7 9.7 0.00021 21.3 1.0 18 54-71 5-22 (33)
179 COG3877 Uncharacterized protei 49.5 18 0.0004 25.7 2.6 39 35-78 6-49 (122)
180 PHA02768 hypothetical protein; 49.3 6.8 0.00015 24.3 0.4 29 35-64 5-42 (55)
181 PRK08270 anaerobic ribonucleos 49.2 13 0.00029 32.4 2.3 39 19-62 602-648 (656)
182 PRK14891 50S ribosomal protein 49.0 9.7 0.00021 27.6 1.2 26 35-60 4-38 (131)
183 COG1675 TFA1 Transcription ini 48.9 15 0.00032 27.5 2.2 64 22-88 99-164 (176)
184 cd06956 NR_DBD_RXR DNA-binding 48.8 9.1 0.0002 24.3 0.9 24 36-60 1-24 (77)
185 PF02977 CarbpepA_inh: Carboxy 48.6 3.5 7.6E-05 25.0 -1.0 33 40-72 7-41 (46)
186 TIGR02827 RNR_anaer_Bdell anae 48.3 14 0.0003 32.2 2.2 36 19-61 509-554 (586)
187 PF10058 DUF2296: Predicted in 48.1 5.8 0.00013 24.2 -0.0 29 9-43 24-52 (54)
188 PF01783 Ribosomal_L32p: Ribos 48.0 7.6 0.00017 23.5 0.5 21 35-60 26-46 (56)
189 PF03833 PolC_DP2: DNA polymer 47.6 6.2 0.00013 36.1 0.0 32 35-66 655-693 (900)
190 TIGR00354 polC DNA polymerase, 47.5 9 0.00019 35.8 1.0 47 34-87 624-672 (1095)
191 PF05741 zf-nanos: Nanos RNA b 47.4 7.7 0.00017 24.1 0.4 11 34-44 32-42 (55)
192 PF14311 DUF4379: Domain of un 47.3 12 0.00025 22.1 1.2 11 54-64 29-39 (55)
193 PRK13945 formamidopyrimidine-D 47.3 15 0.00033 28.4 2.1 26 35-60 254-281 (282)
194 PF13909 zf-H2C2_5: C2H2-type 47.1 8.2 0.00018 18.9 0.4 7 36-42 1-7 (24)
195 PRK07220 DNA topoisomerase I; 46.8 18 0.00039 31.8 2.7 27 35-61 635-665 (740)
196 PF10263 SprT-like: SprT-like 46.7 16 0.00035 24.9 2.0 30 34-63 122-153 (157)
197 COG1198 PriA Primosomal protei 46.6 15 0.00032 32.9 2.1 27 36-62 445-471 (730)
198 KOG2463 Predicted RNA-binding 46.2 14 0.00031 30.8 1.9 39 34-75 256-305 (376)
199 KOG4623 Uncharacterized conser 46.1 9 0.0002 33.6 0.8 43 18-60 10-54 (611)
200 PRK00415 rps27e 30S ribosomal 46.0 18 0.0004 22.8 2.0 28 37-64 13-41 (59)
201 KOG3507 DNA-directed RNA polym 46.0 8.2 0.00018 24.7 0.4 30 31-62 16-46 (62)
202 PF00641 zf-RanBP: Zn-finger i 45.7 13 0.00027 19.5 1.0 11 52-62 3-13 (30)
203 PF14447 Prok-RING_4: Prokaryo 45.3 9.7 0.00021 23.8 0.6 8 37-44 41-48 (55)
204 COG4469 CoiA Competence protei 45.3 15 0.00032 30.3 1.8 21 35-55 25-46 (342)
205 smart00290 ZnF_UBP Ubiquitin C 45.2 17 0.00037 20.5 1.6 24 37-66 1-24 (50)
206 PRK06386 replication factor A; 45.2 9.7 0.00021 31.2 0.8 20 36-61 237-256 (358)
207 PF13824 zf-Mss51: Zinc-finger 45.2 10 0.00023 23.5 0.8 13 32-44 11-23 (55)
208 PF06054 CoiA: Competence prot 44.9 14 0.00031 29.8 1.7 52 33-84 28-80 (375)
209 COG1326 Uncharacterized archae 44.6 13 0.00028 28.6 1.4 33 32-64 3-41 (201)
210 PRK00807 50S ribosomal protein 44.4 10 0.00022 22.8 0.6 25 36-60 2-35 (52)
211 KOG4215 Hepatocyte nuclear fac 44.1 9.3 0.0002 32.3 0.5 39 13-61 30-79 (432)
212 CHL00174 accD acetyl-CoA carbo 44.0 4 8.6E-05 32.7 -1.6 29 35-63 38-67 (296)
213 PRK05654 acetyl-CoA carboxylas 44.0 4.9 0.00011 31.8 -1.0 29 35-63 27-56 (292)
214 PRK08271 anaerobic ribonucleos 43.9 18 0.0004 31.6 2.3 38 19-61 543-588 (623)
215 PRK01103 formamidopyrimidine/5 43.9 19 0.00042 27.6 2.2 27 35-61 245-273 (274)
216 TIGR00515 accD acetyl-CoA carb 43.2 4.2 9.1E-05 32.1 -1.5 29 35-63 26-55 (285)
217 cd02341 ZZ_ZZZ3 Zinc finger, Z 43.2 22 0.00048 21.1 1.9 23 36-61 1-23 (48)
218 COG0777 AccD Acetyl-CoA carbox 43.0 7.2 0.00016 31.5 -0.3 29 36-64 29-58 (294)
219 PF00412 LIM: LIM domain; Int 42.9 15 0.00033 20.9 1.2 32 38-69 1-42 (58)
220 PRK11088 rrmA 23S rRNA methylt 42.7 13 0.00029 27.8 1.2 25 36-63 3-27 (272)
221 PF14206 Cys_rich_CPCC: Cystei 42.5 18 0.00039 23.8 1.6 32 35-66 1-33 (78)
222 PF00105 zf-C4: Zinc finger, C 42.5 11 0.00025 23.0 0.6 23 37-60 2-24 (70)
223 TIGR03829 YokU_near_AblA uncha 42.4 29 0.00062 23.4 2.6 9 55-63 37-45 (89)
224 PRK14714 DNA polymerase II lar 42.2 12 0.00026 35.7 1.0 30 36-65 668-704 (1337)
225 PRK14811 formamidopyrimidine-D 42.2 21 0.00045 27.6 2.2 26 36-61 236-263 (269)
226 PF06677 Auto_anti-p27: Sjogre 41.8 24 0.00053 20.4 1.9 23 36-60 18-41 (41)
227 smart00709 Zpr1 Duplicated dom 41.3 25 0.00054 25.5 2.4 35 37-71 2-51 (160)
228 PRK06450 threonine synthase; V 41.3 11 0.00024 29.8 0.6 26 35-63 3-28 (338)
229 PF14319 Zn_Tnp_IS91: Transpos 41.2 16 0.00035 24.8 1.3 30 32-61 39-68 (111)
230 KOG1597 Transcription initiati 41.1 20 0.00043 29.2 2.0 27 37-63 2-31 (308)
231 PRK12286 rpmF 50S ribosomal pr 40.5 18 0.0004 22.2 1.4 23 33-60 25-47 (57)
232 PF08790 zf-LYAR: LYAR-type C2 40.4 28 0.0006 19.0 1.9 19 55-73 2-20 (28)
233 cd06968 NR_DBD_ROR DNA-binding 40.3 15 0.00032 24.5 1.0 24 36-60 6-29 (95)
234 PRK10445 endonuclease VIII; Pr 39.7 24 0.00052 27.1 2.2 28 33-60 233-262 (263)
235 smart00547 ZnF_RBZ Zinc finger 39.7 12 0.00026 18.7 0.3 10 52-61 1-10 (26)
236 cd00085 HNHc HNH nucleases; HN 39.4 22 0.00048 19.3 1.5 10 36-45 12-21 (57)
237 PF09180 ProRS-C_1: Prolyl-tRN 39.4 19 0.0004 22.5 1.3 17 33-49 46-62 (68)
238 PF01155 HypA: Hydrogenase exp 39.3 19 0.00042 24.3 1.4 24 34-60 69-93 (113)
239 cd06960 NR_DBD_HNF4A DNA-bindi 39.3 19 0.0004 22.7 1.3 25 38-63 1-25 (76)
240 TIGR00577 fpg formamidopyrimid 39.0 24 0.00053 27.1 2.1 24 36-59 246-271 (272)
241 TIGR01057 topA_arch DNA topois 38.9 41 0.0009 28.8 3.7 23 36-58 590-614 (618)
242 PRK12380 hydrogenase nickel in 38.9 15 0.00032 25.1 0.8 12 35-46 86-97 (113)
243 PF13397 DUF4109: Domain of un 38.8 18 0.0004 25.2 1.3 31 31-62 24-59 (105)
244 PF05191 ADK_lid: Adenylate ki 38.8 22 0.00049 19.9 1.4 10 54-63 2-11 (36)
245 PHA02998 RNA polymerase subuni 38.7 31 0.00068 26.4 2.6 31 34-64 142-182 (195)
246 PF04032 Rpr2: RNAse P Rpr2/Rp 37.9 24 0.00053 21.8 1.6 48 14-61 22-85 (85)
247 PF01921 tRNA-synt_1f: tRNA sy 37.8 26 0.00057 28.8 2.2 28 37-64 176-210 (360)
248 PF01246 Ribosomal_L24e: Ribos 37.6 14 0.0003 23.9 0.5 23 35-57 3-33 (71)
249 KOG1247 Methionyl-tRNA synthet 37.2 9.7 0.00021 33.0 -0.4 22 37-63 154-175 (567)
250 PRK00564 hypA hydrogenase nick 37.0 18 0.00039 24.8 1.0 11 37-47 90-100 (117)
251 TIGR00100 hypA hydrogenase nic 36.8 16 0.00035 24.9 0.8 12 35-46 86-97 (115)
252 PF02318 FYVE_2: FYVE-type zin 36.3 44 0.00096 22.6 2.8 25 20-44 28-63 (118)
253 PF05899 Cupin_3: Protein of u 36.2 26 0.00056 21.7 1.6 16 49-64 7-22 (74)
254 COG3024 Uncharacterized protei 36.2 16 0.00035 23.6 0.6 15 33-47 5-19 (65)
255 PRK08173 DNA topoisomerase III 36.2 34 0.00074 30.9 2.8 28 34-63 725-759 (862)
256 PF01428 zf-AN1: AN1-like Zinc 35.9 23 0.00049 20.1 1.2 10 55-64 15-24 (43)
257 PRK05582 DNA topoisomerase I; 35.8 53 0.0011 28.4 3.8 28 35-62 571-603 (650)
258 PRK14873 primosome assembly pr 35.7 16 0.00034 32.0 0.6 26 37-62 394-419 (665)
259 cd02249 ZZ Zinc finger, ZZ typ 35.5 25 0.00053 20.1 1.3 21 36-60 1-21 (46)
260 PF00130 C1_1: Phorbol esters/ 35.3 35 0.00076 19.3 1.9 28 33-63 9-38 (53)
261 PRK00762 hypA hydrogenase nick 35.3 18 0.00038 25.0 0.8 12 36-47 93-104 (124)
262 PF02891 zf-MIZ: MIZ/SP-RING z 35.2 17 0.00037 21.4 0.6 10 34-43 40-49 (50)
263 COG1499 NMD3 NMD protein affec 35.1 21 0.00045 29.3 1.2 21 50-70 40-60 (355)
264 cd06963 NR_DBD_GR_like The DNA 35.1 22 0.00047 22.4 1.1 22 38-60 1-22 (73)
265 cd07169 NR_DBD_GCNF_like DNA-b 35.0 19 0.00041 23.7 0.8 27 34-61 5-31 (90)
266 KOG1311 DHHC-type Zn-finger pr 34.8 14 0.00031 28.2 0.2 25 34-62 112-136 (299)
267 PF01363 FYVE: FYVE zinc finge 34.4 27 0.0006 20.9 1.4 27 35-65 9-37 (69)
268 TIGR03844 cysteate_syn cysteat 34.4 17 0.00037 29.6 0.6 23 35-60 2-24 (398)
269 PF03833 PolC_DP2: DNA polymer 34.4 13 0.00029 34.1 0.0 32 55-87 694-725 (900)
270 cd00472 Ribosomal_L24e_L24 Rib 34.3 28 0.00061 21.3 1.5 23 35-57 3-33 (54)
271 PRK14724 DNA topoisomerase III 34.3 23 0.00049 32.5 1.4 26 36-63 644-676 (987)
272 PRK05638 threonine synthase; V 34.2 19 0.00041 29.3 0.9 24 35-62 1-24 (442)
273 PF09151 DUF1936: Domain of un 34.2 18 0.00039 20.7 0.5 13 35-47 1-13 (36)
274 KOG0704 ADP-ribosylation facto 33.9 36 0.00078 28.6 2.4 29 32-60 16-46 (386)
275 PF06397 Desulfoferrod_N: Desu 33.7 29 0.00062 19.8 1.3 12 52-63 5-16 (36)
276 PRK07220 DNA topoisomerase I; 33.7 41 0.0009 29.7 2.9 27 36-62 590-622 (740)
277 COG4332 Uncharacterized protei 33.5 37 0.00079 26.2 2.2 33 37-69 19-65 (203)
278 COG1773 Rubredoxin [Energy pro 33.4 26 0.00056 21.8 1.2 12 53-64 3-14 (55)
279 cd06966 NR_DBD_CAR DNA-binding 33.3 26 0.00055 23.2 1.3 26 37-63 2-27 (94)
280 PF06827 zf-FPG_IleRS: Zinc fi 33.3 45 0.00098 17.3 2.0 24 37-60 3-28 (30)
281 PF09237 GAGA: GAGA factor; I 33.1 17 0.00037 22.7 0.4 13 32-44 21-33 (54)
282 PRK14810 formamidopyrimidine-D 33.1 35 0.00076 26.3 2.1 25 35-60 244-271 (272)
283 PF05876 Terminase_GpA: Phage 33.0 55 0.0012 27.9 3.5 30 52-81 251-286 (557)
284 cd06969 NR_DBD_NGFI-B DNA-bind 32.8 29 0.00062 21.9 1.4 26 37-63 2-27 (75)
285 PF13901 DUF4206: Domain of un 32.8 45 0.00097 24.7 2.6 49 21-69 138-188 (202)
286 PRK06260 threonine synthase; V 32.7 18 0.00039 29.0 0.5 23 36-60 4-26 (397)
287 PRK08197 threonine synthase; V 32.6 19 0.00042 28.8 0.7 23 35-60 7-29 (394)
288 cd07156 NR_DBD_VDR_like The DN 32.4 24 0.00052 22.1 0.9 22 38-60 1-22 (72)
289 PF12171 zf-C2H2_jaz: Zinc-fin 32.4 25 0.00055 17.7 0.9 9 36-44 2-10 (27)
290 PRK14724 DNA topoisomerase III 32.3 37 0.00079 31.2 2.4 21 35-58 755-776 (987)
291 COG2824 PhnA Uncharacterized Z 32.3 35 0.00076 24.1 1.8 29 37-66 5-33 (112)
292 PRK06921 hypothetical protein; 32.3 44 0.00095 25.5 2.5 12 35-46 32-43 (266)
293 cd07157 2DBD_NR_DBD1 The first 32.2 28 0.00061 22.6 1.3 26 37-63 2-27 (86)
294 cd07179 2DBD_NR_DBD2 The secon 32.2 23 0.0005 22.3 0.8 22 38-60 1-22 (74)
295 cd07172 NR_DBD_GR_PR DNA-bindi 32.0 23 0.00049 22.7 0.8 23 37-60 4-26 (78)
296 PRK03824 hypA hydrogenase nick 31.9 33 0.00072 24.0 1.7 15 52-66 69-83 (135)
297 PF05180 zf-DNL: DNL zinc fing 31.9 51 0.0011 21.0 2.4 28 34-61 3-37 (66)
298 PF13913 zf-C2HC_2: zinc-finge 31.9 23 0.0005 18.1 0.7 10 55-64 4-13 (25)
299 PRK02935 hypothetical protein; 31.8 24 0.00052 24.9 0.9 25 34-62 69-95 (110)
300 cd06916 NR_DBD_like DNA-bindin 31.7 30 0.00065 21.5 1.3 25 38-63 1-25 (72)
301 PF06044 DRP: Dam-replacing fa 31.5 40 0.00086 26.8 2.2 41 29-69 25-82 (254)
302 KOG4317 Predicted Zn-finger pr 31.4 20 0.00044 29.8 0.6 14 31-44 15-28 (383)
303 TIGR01051 topA_bact DNA topois 31.2 60 0.0013 27.9 3.4 26 36-61 575-605 (610)
304 TIGR01031 rpmF_bact ribosomal 31.1 32 0.00069 20.9 1.3 22 34-60 25-46 (55)
305 PRK07219 DNA topoisomerase I; 31.1 38 0.00082 30.2 2.3 29 35-63 602-636 (822)
306 TIGR02443 conserved hypothetic 31.1 54 0.0012 20.7 2.4 27 37-63 11-41 (59)
307 PF04475 DUF555: Protein of un 31.1 41 0.00089 23.4 2.0 33 28-63 25-57 (102)
308 cd07162 NR_DBD_PXR DNA-binding 30.9 23 0.00051 23.0 0.7 23 37-60 1-23 (87)
309 PF01412 ArfGap: Putative GTPa 30.8 27 0.00059 23.5 1.1 29 32-60 10-40 (116)
310 cd07163 NR_DBD_TLX DNA-binding 30.7 33 0.00071 22.6 1.4 26 37-63 8-33 (92)
311 COG5189 SFP1 Putative transcri 30.7 19 0.00041 30.2 0.3 12 33-44 396-407 (423)
312 PRK07956 ligA NAD-dependent DN 30.5 40 0.00087 29.6 2.3 24 34-57 403-426 (665)
313 PF01667 Ribosomal_S27e: Ribos 30.4 44 0.00095 20.7 1.9 28 37-64 9-37 (55)
314 PLN03086 PRLI-interacting fact 30.3 26 0.00056 30.6 1.1 28 37-64 435-464 (567)
315 PRK09521 exosome complex RNA-b 30.2 40 0.00087 24.4 1.9 25 37-62 151-175 (189)
316 cd06964 NR_DBD_RAR DNA-binding 30.2 36 0.00079 22.1 1.6 27 36-63 5-31 (85)
317 cd06957 NR_DBD_PNR_like_2 DNA- 30.1 36 0.00077 21.9 1.5 24 38-62 1-24 (82)
318 cd07154 NR_DBD_PNR_like The DN 29.9 35 0.00076 21.3 1.4 24 38-62 1-24 (73)
319 PRK06835 DNA replication prote 29.6 51 0.0011 26.2 2.6 29 19-47 68-110 (329)
320 PRK07111 anaerobic ribonucleos 29.6 23 0.0005 31.4 0.7 37 19-61 657-701 (735)
321 PF03884 DUF329: Domain of unk 29.5 25 0.00055 21.8 0.7 13 35-47 2-14 (57)
322 TIGR00595 priA primosomal prot 29.5 39 0.00085 28.3 2.0 28 37-64 224-251 (505)
323 PRK07591 threonine synthase; V 29.3 21 0.00045 29.1 0.3 26 35-63 18-43 (421)
324 cd07173 NR_DBD_AR DNA-binding 29.2 21 0.00046 23.1 0.3 23 37-60 5-27 (82)
325 TIGR00575 dnlj DNA ligase, NAD 29.2 41 0.0009 29.4 2.1 27 34-60 391-419 (652)
326 PF03107 C1_2: C1 domain; Int 29.1 20 0.00043 18.9 0.1 24 36-62 1-24 (30)
327 cd06955 NR_DBD_VDR DNA-binding 28.8 32 0.0007 23.5 1.2 25 36-61 7-31 (107)
328 smart00746 TRASH metallochaper 28.7 27 0.00059 16.5 0.6 8 38-45 1-8 (39)
329 PF09526 DUF2387: Probable met 28.7 72 0.0016 20.4 2.7 28 37-64 10-41 (71)
330 PRK14559 putative protein seri 28.6 21 0.00045 31.4 0.2 31 37-71 29-59 (645)
331 PRK12496 hypothetical protein; 28.4 24 0.00052 25.5 0.5 28 33-62 125-152 (164)
332 smart00399 ZnF_C4 c4 zinc fing 28.3 27 0.00058 21.5 0.7 24 37-61 1-24 (70)
333 cd06959 NR_DBD_EcR_like The DN 28.3 30 0.00065 21.6 0.9 23 37-60 1-23 (73)
334 COG5319 Uncharacterized protei 28.2 13 0.00029 27.1 -0.8 16 34-49 31-46 (142)
335 PLN00209 ribosomal protein S27 28.1 73 0.0016 21.5 2.8 28 37-64 38-66 (86)
336 KOG2906 RNA polymerase III sub 28.1 75 0.0016 22.2 2.9 29 36-64 2-32 (105)
337 cd07170 NR_DBD_ERR DNA-binding 28.1 30 0.00065 23.2 0.9 25 36-61 5-29 (97)
338 COG3357 Predicted transcriptio 28.0 21 0.00046 24.7 0.1 11 55-65 60-70 (97)
339 PRK08579 anaerobic ribonucleos 28.0 45 0.00098 29.2 2.2 38 19-61 545-590 (625)
340 PF03470 zf-XS: XS zinc finger 27.9 25 0.00054 20.9 0.4 7 38-44 1-7 (43)
341 cd06962 NR_DBD_FXR DNA-binding 27.8 38 0.00081 22.0 1.3 25 37-62 3-27 (84)
342 smart00532 LIGANc Ligase N fam 27.7 53 0.0011 27.5 2.5 24 34-57 398-421 (441)
343 TIGR01374 soxD sarcosine oxida 27.5 27 0.00059 23.3 0.6 7 37-43 3-9 (84)
344 COG0551 TopA Zn-finger domain 27.5 51 0.0011 22.6 2.0 20 35-54 17-37 (140)
345 COG0143 MetG Methionyl-tRNA sy 27.4 19 0.00042 31.1 -0.1 37 28-66 119-155 (558)
346 KOG2879 Predicted E3 ubiquitin 27.2 28 0.0006 28.3 0.7 15 35-49 239-253 (298)
347 COG3816 Uncharacterized protei 26.9 43 0.00092 25.7 1.6 20 36-55 37-56 (205)
348 cd00974 DSRD Desulforedoxin (D 26.9 53 0.0011 17.6 1.6 13 52-64 3-15 (34)
349 KOG0703 Predicted GTPase-activ 26.8 57 0.0012 26.3 2.4 40 20-60 11-52 (287)
350 PF08134 cIII: cIII protein fa 26.7 75 0.0016 19.0 2.3 29 62-90 5-38 (44)
351 COG1110 Reverse gyrase [DNA re 26.6 28 0.0006 33.0 0.7 24 35-59 8-32 (1187)
352 cd06967 NR_DBD_TR2_like DNA-bi 26.5 34 0.00073 22.3 0.9 26 37-63 5-30 (87)
353 cd07160 NR_DBD_LXR DNA-binding 26.5 33 0.00072 23.2 0.9 25 36-61 19-43 (101)
354 PF10601 zf-LITAF-like: LITAF- 26.5 31 0.00067 21.3 0.7 14 31-44 54-67 (73)
355 PF01529 zf-DHHC: DHHC palmito 26.3 27 0.00058 23.9 0.4 31 30-64 43-73 (174)
356 PF01753 zf-MYND: MYND finger; 26.2 51 0.0011 17.7 1.5 19 38-63 1-19 (37)
357 PRK14351 ligA NAD-dependent DN 26.0 51 0.0011 29.2 2.2 22 34-57 422-443 (689)
358 cd07161 NR_DBD_EcR DNA-binding 25.9 34 0.00075 22.5 0.9 23 37-60 3-25 (91)
359 TIGR00319 desulf_FeS4 desulfof 25.9 57 0.0012 17.4 1.6 14 51-64 5-18 (34)
360 smart00714 LITAF Possible memb 25.7 33 0.00072 20.8 0.7 14 31-44 48-61 (67)
361 cd07165 NR_DBD_DmE78_like DNA- 25.6 26 0.00056 22.4 0.2 22 38-60 1-22 (81)
362 PF14951 DUF4503: Domain of un 25.5 31 0.00067 29.0 0.7 28 37-64 276-305 (389)
363 PF12756 zf-C2H2_2: C2H2 type 25.4 34 0.00075 20.8 0.8 11 54-64 51-61 (100)
364 COG1096 Predicted RNA-binding 25.4 58 0.0012 24.8 2.1 24 37-62 151-174 (188)
365 PF12172 DUF35_N: Rubredoxin-l 25.4 28 0.00062 18.8 0.3 8 37-44 27-34 (37)
366 PRK14714 DNA polymerase II lar 25.3 48 0.001 31.9 2.0 53 34-88 691-743 (1337)
367 PRK11032 hypothetical protein; 25.2 39 0.00085 24.9 1.1 14 37-50 144-157 (160)
368 PF00935 Ribosomal_L44: Riboso 25.2 53 0.0011 21.6 1.6 22 33-58 51-72 (77)
369 PF02591 DUF164: Putative zinc 25.1 46 0.00099 19.6 1.3 11 33-43 44-54 (56)
370 PF04267 SoxD: Sarcosine oxida 25.1 22 0.00047 23.8 -0.2 7 37-43 3-9 (84)
371 PF03966 Trm112p: Trm112p-like 24.8 78 0.0017 19.3 2.3 14 50-63 50-63 (68)
372 cd07158 NR_DBD_Ppar_like The D 24.7 30 0.00064 21.6 0.4 22 38-60 1-22 (73)
373 PTZ00083 40S ribosomal protein 24.7 95 0.0021 20.9 2.8 28 37-64 37-65 (85)
374 PF09889 DUF2116: Uncharacteri 24.6 35 0.00076 21.3 0.7 9 37-45 5-13 (59)
375 PF04810 zf-Sec23_Sec24: Sec23 24.6 30 0.00065 19.4 0.4 11 34-44 23-33 (40)
376 PRK14906 DNA-directed RNA poly 24.5 37 0.0008 32.9 1.1 28 34-64 58-85 (1460)
377 COG2093 DNA-directed RNA polym 24.5 35 0.00076 22.0 0.7 11 36-46 19-29 (64)
378 PRK08329 threonine synthase; V 24.5 39 0.00084 26.6 1.1 22 36-61 2-23 (347)
379 COG0333 RpmF Ribosomal protein 24.4 44 0.00095 20.8 1.1 19 37-60 29-47 (57)
380 cd00730 rubredoxin Rubredoxin; 24.4 36 0.00079 20.4 0.7 12 53-64 1-12 (50)
381 PF00301 Rubredoxin: Rubredoxi 24.3 57 0.0012 19.3 1.6 14 54-67 2-15 (47)
382 PRK00566 DNA-directed RNA poly 24.3 34 0.00074 32.3 0.8 28 34-64 56-83 (1156)
383 cd07167 NR_DBD_Lrh-1_like The 24.2 30 0.00065 23.0 0.4 22 38-60 1-22 (93)
384 cd07155 NR_DBD_ER_like DNA-bin 24.2 29 0.00062 21.8 0.2 22 38-60 1-22 (75)
385 PRK14873 primosome assembly pr 24.1 53 0.0011 28.9 1.9 22 35-62 410-431 (665)
386 cd02337 ZZ_CBP Zinc finger, ZZ 24.1 45 0.00097 19.0 1.0 20 36-60 1-20 (41)
387 PRK02625 rpoC1 DNA-directed RN 24.0 35 0.00075 30.3 0.8 27 35-64 68-94 (627)
388 TIGR02387 rpoC1_cyan DNA-direc 24.0 35 0.00076 30.2 0.8 27 35-64 61-87 (619)
389 cd07166 NR_DBD_REV_ERB DNA-bin 23.9 30 0.00065 22.6 0.3 25 36-61 4-28 (89)
390 cd03023 DsbA_Com1_like DsbA fa 23.9 26 0.00056 22.7 -0.0 13 32-44 11-23 (154)
391 PF14205 Cys_rich_KTR: Cystein 23.9 45 0.00098 20.9 1.1 27 36-62 5-37 (55)
392 TIGR00155 pqiA_fam integral me 23.9 61 0.0013 26.6 2.1 43 37-79 15-60 (403)
393 PRK05767 rpl44e 50S ribosomal 23.9 28 0.0006 23.7 0.1 42 7-58 45-86 (92)
394 COG4481 Uncharacterized protei 23.9 1E+02 0.0022 19.5 2.7 39 31-70 12-51 (60)
395 PF09706 Cas_CXXC_CXXC: CRISPR 23.8 36 0.00079 21.4 0.7 13 32-44 2-14 (69)
396 cd07168 NR_DBD_DHR4_like DNA-b 23.8 40 0.00087 22.1 0.9 24 37-61 8-31 (90)
397 COG4311 SoxD Sarcosine oxidase 23.7 34 0.00074 23.6 0.6 8 36-43 4-11 (97)
398 COG1601 GCD7 Translation initi 23.7 27 0.00058 25.5 0.0 38 24-61 94-134 (151)
399 PRK14350 ligA NAD-dependent DN 23.6 68 0.0015 28.3 2.5 27 34-62 397-425 (669)
400 COG2260 Predicted Zn-ribbon RN 23.6 52 0.0011 20.9 1.3 36 36-77 6-44 (59)
401 PRK13130 H/ACA RNA-protein com 23.5 51 0.0011 20.4 1.3 35 37-77 7-44 (56)
402 cd06965 NR_DBD_Ppar DNA-bindin 23.5 30 0.00065 22.4 0.2 24 37-61 1-24 (84)
403 cd06958 NR_DBD_COUP_TF DNA-bin 23.4 34 0.00074 21.4 0.5 22 38-60 1-22 (73)
404 cd06961 NR_DBD_TR DNA-binding 23.0 30 0.00065 22.4 0.1 23 37-60 1-23 (85)
405 COG1379 PHP family phosphoeste 22.9 17 0.00036 30.5 -1.3 30 37-66 248-278 (403)
406 PF10122 Mu-like_Com: Mu-like 22.8 35 0.00077 21.0 0.4 31 34-64 3-35 (51)
407 cd07171 NR_DBD_ER DNA-binding 22.7 43 0.00092 21.6 0.8 23 37-60 5-27 (82)
408 cd04718 BAH_plant_2 BAH, or Br 22.6 30 0.00066 25.3 0.1 33 40-72 5-37 (148)
409 cd00674 LysRS_core_class_I cat 22.5 1E+02 0.0022 25.1 3.1 25 37-62 171-201 (353)
410 PF14122 YokU: YokU-like prote 22.5 83 0.0018 21.3 2.2 27 37-63 1-45 (87)
411 PF10080 DUF2318: Predicted me 22.5 98 0.0021 21.1 2.6 27 37-64 37-63 (102)
412 KOG4167 Predicted DNA-binding 22.4 16 0.00035 33.4 -1.5 14 50-63 789-802 (907)
413 PRK15103 paraquat-inducible me 22.3 80 0.0017 26.1 2.5 43 37-79 12-57 (419)
414 PF14634 zf-RING_5: zinc-RING 22.3 59 0.0013 18.1 1.3 11 33-43 34-44 (44)
415 smart00249 PHD PHD zinc finger 22.3 55 0.0012 17.0 1.1 24 37-63 1-24 (47)
416 cd07164 NR_DBD_PNR_like_1 DNA- 22.2 39 0.00084 21.4 0.6 23 38-61 1-23 (78)
417 COG2816 NPY1 NTP pyrophosphohy 22.1 1E+02 0.0022 24.8 3.0 27 36-62 112-138 (279)
418 COG0375 HybF Zn finger protein 22.0 46 0.001 23.4 1.0 13 35-47 86-98 (115)
419 cd03019 DsbA_DsbA DsbA family, 21.9 34 0.00074 23.0 0.3 15 30-44 19-33 (178)
420 PF13695 zf-3CxxC: Zinc-bindin 21.9 77 0.0017 20.8 2.0 26 34-59 4-44 (98)
421 PRK11827 hypothetical protein; 21.7 74 0.0016 19.9 1.8 24 37-61 10-34 (60)
422 PF06839 zf-GRF: GRF zinc fing 21.7 80 0.0017 17.9 1.8 14 37-51 2-15 (45)
423 PF07295 DUF1451: Protein of u 21.5 37 0.00081 24.4 0.4 25 36-60 113-137 (146)
424 PF06107 DUF951: Bacterial pro 21.3 1.2E+02 0.0025 19.1 2.6 28 32-63 10-41 (57)
425 COG4694 Uncharacterized protei 21.3 37 0.00081 30.5 0.4 10 35-44 278-287 (758)
426 cd06970 NR_DBD_PNR DNA-binding 21.2 53 0.0012 21.7 1.1 26 37-63 8-33 (92)
427 PF00097 zf-C3HC4: Zinc finger 21.1 87 0.0019 16.6 1.8 9 33-41 33-41 (41)
428 PRK05452 anaerobic nitric oxid 21.0 44 0.00096 27.8 0.8 13 51-63 423-435 (479)
429 COG0419 SbcC ATPase involved i 21.0 79 0.0017 28.2 2.4 9 35-43 457-465 (908)
430 PF06906 DUF1272: Protein of u 20.8 44 0.00095 21.1 0.6 8 36-43 27-34 (57)
431 PRK14704 anaerobic ribonucleos 20.7 42 0.00092 29.3 0.7 37 19-61 536-580 (618)
432 COG5347 GTPase-activating prot 20.7 1.1E+02 0.0023 24.8 2.9 28 33-60 18-47 (319)
433 PRK07726 DNA topoisomerase III 20.7 1E+02 0.0022 26.8 3.0 23 36-58 611-635 (658)
434 smart00291 ZnF_ZZ Zinc-binding 20.5 68 0.0015 18.1 1.3 24 33-60 2-25 (44)
435 PF02892 zf-BED: BED zinc fing 20.4 59 0.0013 17.8 1.0 17 50-66 13-29 (45)
436 PF15616 TerY-C: TerY-C metal 20.4 78 0.0017 22.7 1.9 8 37-44 79-86 (131)
437 PF07649 C1_3: C1-like domain; 20.4 63 0.0014 16.7 1.1 23 37-62 2-24 (30)
438 PF14446 Prok-RING_1: Prokaryo 20.3 58 0.0013 20.1 1.0 26 35-62 5-30 (54)
439 PF06220 zf-U1: U1 zinc finger 20.2 45 0.00098 18.8 0.5 11 34-44 2-12 (38)
440 PRK08332 ribonucleotide-diphos 20.0 1E+02 0.0023 30.5 3.1 26 37-62 1706-1735(1740)
No 1
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=100.00 E-value=1.2e-52 Score=282.53 Aligned_cols=90 Identities=69% Similarity=1.130 Sum_probs=83.2
Q ss_pred CCcceeeeeccCCccccCchhhHHHHHHHHHhhcccccCCCCceeeEEeeeeeeeeCCCCceEecccccccccHHHHHHH
Q 044880 1 TKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLNTASAVTVRS 80 (91)
Q Consensus 1 ~k~tkkvgi~gk~G~RYG~slRK~v~kie~~q~~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGGAy~~~T~~~~t~~~ 80 (91)
|+||+||||+||||+|||++|||+|++||++||++|+|||||++.|+|+++|||+|++|+++||||||+|+||++.+|++
T Consensus 1 a~rtkkvgi~GkyG~RYG~slRK~vkkie~~q~~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AGGAy~~~T~~~~t~~~ 80 (90)
T PF01780_consen 1 AKRTKKVGIAGKYGTRYGASLRKRVKKIEISQHAKYTCPFCGKTSVKRVATGIWKCKKCGKKFAGGAYTPSTPAAKTVKR 80 (90)
T ss_dssp -S-SSS-TTGGGGTTSSTHHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHH
T ss_pred CCCCceeeecCcCcCCcCHHHHHHHHHHHHHHhCCCcCCCCCCceeEEeeeEEeecCCCCCEEeCCCccccchHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhc
Q 044880 81 TIRRLREQTE 90 (91)
Q Consensus 81 ~i~rl~e~~~ 90 (91)
+|+||+|++|
T Consensus 81 ~i~rl~e~~e 90 (90)
T PF01780_consen 81 AIRRLRELKE 90 (90)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHhcC
Confidence 9999999986
No 2
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=100.00 E-value=2.6e-51 Score=276.58 Aligned_cols=90 Identities=57% Similarity=1.023 Sum_probs=88.2
Q ss_pred CcceeeeeccCCccccCchhhHHHHHHHHHhhcccccCCCCceeeEEeeeeeeeeCCCCceEecccccccccHHHHHHHH
Q 044880 2 KRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLNTASAVTVRST 81 (91)
Q Consensus 2 k~tkkvgi~gk~G~RYG~slRK~v~kie~~q~~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGGAy~~~T~~~~t~~~~ 81 (91)
.||+||||+||||+|||++|||+|++||++||++|+|||||++.|+|+++|||+|++|+++||||||+|+||++.++.++
T Consensus 2 artkkvG~~GrfG~RYG~slRK~v~kie~~q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGAy~p~T~~~~t~~~~ 81 (91)
T TIGR00280 2 KRTKKVGITGRFGPRYGLKLRRQVKKIEIQQKAKYVCPFCGKKTVKRGSTGIWTCRKCGAKFAGGAYTPVTPAGKTVRKT 81 (91)
T ss_pred CCCceeeecCCCcCccCHHHHHHHHHHHHHHhcCccCCCCCCCceEEEeeEEEEcCCCCCEEeCCccccccchhHHHHHH
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhcC
Q 044880 82 IRRLREQTES 91 (91)
Q Consensus 82 i~rl~e~~~~ 91 (91)
|+||+|++|+
T Consensus 82 irrl~e~~~~ 91 (91)
T TIGR00280 82 IRRIVEMKEA 91 (91)
T ss_pred HHHHHHhhcC
Confidence 9999999985
No 3
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=100.00 E-value=3.2e-51 Score=275.70 Aligned_cols=89 Identities=75% Similarity=1.209 Sum_probs=87.1
Q ss_pred CCcceeeeeccCCccccCchhhHHHHHHHHHhhcccccCCCCceeeEEeeeeeeeeCCCCceEecccccccccHHHHHHH
Q 044880 1 TKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLNTASAVTVRS 80 (91)
Q Consensus 1 ~k~tkkvgi~gk~G~RYG~slRK~v~kie~~q~~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGGAy~~~T~~~~t~~~ 80 (91)
++||+||||+||||+|||++|||+|++||++||++|+|||||+++|+|.++|||+|++|+++||||||+|+||++.++.+
T Consensus 2 akrtkkvG~~GrfG~RYG~slRK~v~kie~~q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGAy~~~T~~~~t~~~ 81 (90)
T PTZ00255 2 AKRTKKVGITGKYGTRYGASLRKQIKKIEISQHAKYFCPFCGKHAVKRQAVGIWRCKGCKKTVAGGAWTLSTPAASTVRS 81 (90)
T ss_pred CCcCceeeecCCCcCccCHHHHHHHHHHHHHHhCCccCCCCCCCceeeeeeEEEEcCCCCCEEeCCccccccchhHHHHH
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhh
Q 044880 81 TIRRLREQT 89 (91)
Q Consensus 81 ~i~rl~e~~ 89 (91)
+|+||+|++
T Consensus 82 ~irr~~e~~ 90 (90)
T PTZ00255 82 TIRRLRKLK 90 (90)
T ss_pred HHHHHHhcC
Confidence 999999974
No 4
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=100.00 E-value=2.9e-50 Score=271.00 Aligned_cols=89 Identities=44% Similarity=0.827 Sum_probs=86.4
Q ss_pred CCcceeeeeccCCccccCchhhHHHHHHHHHhhcccccCCCCceeeEEeeeeeeeeCCCCceEecccccccccHHHHHHH
Q 044880 1 TKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLNTASAVTVRS 80 (91)
Q Consensus 1 ~k~tkkvgi~gk~G~RYG~slRK~v~kie~~q~~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGGAy~~~T~~~~t~~~ 80 (91)
++||+||||+||||+|||++|||+|++||++||++|+|||||+++|+|.++|||+|++|+++||||||+|+||++.++.+
T Consensus 2 ~~rtkkvGi~Gr~G~RYG~slRK~v~kie~~q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGAy~~~T~~~~t~~~ 81 (90)
T PRK03976 2 MSRTKKVGSAGRFGARYGRKIRKRVADIEEKMRAKHVCPVCGRPKVKRVGTGIWECRKCGAKFAGGAYTPETPAGKTVTR 81 (90)
T ss_pred CCcCceEeecCCCcCccCHHHHHHHHHHHHHHhcCccCCCCCCCceEEEEEEEEEcCCCCCEEeCCccccccchhhhHHH
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhh
Q 044880 81 TIRRLREQT 89 (91)
Q Consensus 81 ~i~rl~e~~ 89 (91)
+|+||+|.+
T Consensus 82 ~irr~~~~~ 90 (90)
T PRK03976 82 AIRRAVEEK 90 (90)
T ss_pred HHHHHhhcC
Confidence 999999853
No 5
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.1e-50 Score=269.13 Aligned_cols=91 Identities=74% Similarity=1.175 Sum_probs=89.4
Q ss_pred CCcceeeeeccCCccccCchhhHHHHHHHHHhhcccccCCCCceeeEEeeeeeeeeCCCCceEecccccccccHHHHHHH
Q 044880 1 TKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLNTASAVTVRS 80 (91)
Q Consensus 1 ~k~tkkvgi~gk~G~RYG~slRK~v~kie~~q~~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGGAy~~~T~~~~t~~~ 80 (91)
++|||||||+|+||+|||+||||||++||++||++|+|+|||+..|||.++|||.|..|.++||||||+++|++|.++++
T Consensus 2 ~krtKKVgI~gkyGtrYGaSLrk~vKkiei~Qhaky~CsfCGK~~vKR~AvGiW~C~~C~kv~agga~~~~t~aa~t~rs 81 (92)
T KOG0402|consen 2 AKRTKKVGIVGKYGTRYGASLRKMVKKIEIQQHAKYTCSFCGKKTVKRKAVGIWKCGSCKKVVAGGAYTVTTAAAATVRS 81 (92)
T ss_pred CcccceeeeeecccchhhHHHHHHHHHHHHHHhhhhhhhhcchhhhhhhceeEEecCCccceeccceEEeccchhHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhcC
Q 044880 81 TIRRLREQTES 91 (91)
Q Consensus 81 ~i~rl~e~~~~ 91 (91)
+||||+|++|.
T Consensus 82 ~irrlre~~e~ 92 (92)
T KOG0402|consen 82 TIRRLRELVEQ 92 (92)
T ss_pred HHHHHHHHhcC
Confidence 99999999874
No 6
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.3e-44 Score=239.43 Aligned_cols=87 Identities=49% Similarity=0.931 Sum_probs=84.9
Q ss_pred cceeeeeccCCccccCchhhHHHHHHHHHhhcccccCCCCceeeEEeeeeeeeeCCCCceEecccccccccHHHHHHHHH
Q 044880 3 RTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLNTASAVTVRSTI 82 (91)
Q Consensus 3 ~tkkvgi~gk~G~RYG~slRK~v~kie~~q~~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGGAy~~~T~~~~t~~~~i 82 (91)
+||||||+||||+|||++||++|++||+.|+++|.|||||++.|+|+++|||.|.+||.+||||||+|.||++++++++|
T Consensus 3 ~TkkvG~aGrfGpRYG~~~Rrrv~~ie~~~~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGgay~P~t~~~k~~~~~i 82 (89)
T COG1997 3 KTKKVGIAGRFGPRYGSKLRRRVKEIEAQQRAKHVCPFCGRTTVKRIATGIWKCRKCGAKFAGGAYTPVTPAGKAVKRTI 82 (89)
T ss_pred ccceeccCcccccccchHHHHHHHHHHHHHhcCCcCCCCCCcceeeeccCeEEcCCCCCeeccccccccchHHHHHHHHH
Confidence 49999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhh
Q 044880 83 RRLREQT 89 (91)
Q Consensus 83 ~rl~e~~ 89 (91)
+|+.|.+
T Consensus 83 ~r~~e~k 89 (89)
T COG1997 83 RREVEMK 89 (89)
T ss_pred HHHhccC
Confidence 9998863
No 7
>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=97.28 E-value=0.00022 Score=41.79 Aligned_cols=28 Identities=32% Similarity=0.749 Sum_probs=24.1
Q ss_pred ccccCCCCceeeEEeee-eeeeeCCCCce
Q 044880 35 KYFCEFCGKYAVKRKAV-GIWGCKDCGKV 62 (91)
Q Consensus 35 ky~CpfCGk~~VkR~a~-GIW~C~~Cg~~ 62 (91)
-+.||.||...+.+... +.|+|+.|+++
T Consensus 18 g~~CP~Cg~~~~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 18 GFVCPHCGSTKHYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCCeeeEEeCCCCeEECCCCCCc
Confidence 36899999998888777 99999999864
No 8
>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=97.21 E-value=0.0004 Score=41.80 Aligned_cols=39 Identities=26% Similarity=0.517 Sum_probs=26.5
Q ss_pred ccCCCCceee-EE------eeeeeeeeCCCCceEecccccccccHHHHHHHHHHH
Q 044880 37 FCEFCGKYAV-KR------KAVGIWGCKDCGKVKAGGAYTLNTASAVTVRSTIRR 84 (91)
Q Consensus 37 ~CpfCGk~~V-kR------~a~GIW~C~~Cg~~~AGGAy~~~T~~~~t~~~~i~r 84 (91)
.|||||...+ .| ...|+|.|..||... +.+.+...||..
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~---------~~~~~~~~Ai~~ 48 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASG---------PVEEDEAEAIEA 48 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCCCc---------ccccCHHHHHHH
Confidence 5999998765 44 366889999997653 334555555544
No 9
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=96.33 E-value=0.0048 Score=39.64 Aligned_cols=34 Identities=29% Similarity=0.490 Sum_probs=22.3
Q ss_pred ccCCCCceeeEEeee---eeeeeCCCCceEeccccccccc
Q 044880 37 FCEFCGKYAVKRKAV---GIWGCKDCGKVKAGGAYTLNTA 73 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~---GIW~C~~Cg~~~AGGAy~~~T~ 73 (91)
.|||||.+.+.=.+. ..|.|.+|+.. |.|.++-+
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v~C~~CgA~---~~~~~te~ 44 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRAKCNGCESR---TGYGGSEK 44 (64)
T ss_pred CCCCCCCceeEEEecCceEEEEcCCCCcC---cccccCHH
Confidence 599999987554443 34679999873 44444433
No 10
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=96.30 E-value=0.0024 Score=38.64 Aligned_cols=26 Identities=31% Similarity=0.870 Sum_probs=22.3
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
.||.||.. +-....+.|+|.+||.+.
T Consensus 22 fCP~Cg~~-~m~~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSG-FMAEHLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCCCcc-hheccCCcEECCCcCCEE
Confidence 89999997 666667999999999875
No 11
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=96.29 E-value=0.0018 Score=45.04 Aligned_cols=46 Identities=24% Similarity=0.393 Sum_probs=34.2
Q ss_pred hhcccccCCCCcee-----eE-EeeeeeeeeCCCCceEecccccccccHHHH
Q 044880 32 QHSKYFCEFCGKYA-----VK-RKAVGIWGCKDCGKVKAGGAYTLNTASAVT 77 (91)
Q Consensus 32 q~~ky~CpfCGk~~-----Vk-R~a~GIW~C~~Cg~~~AGGAy~~~T~~~~t 77 (91)
....|+|||||..+ |+ -...|.=+|+.||..|.-=.=.+.+|.-..
T Consensus 19 L~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l~~~vDvY 70 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPELSEPVDVY 70 (104)
T ss_pred CCceEecCccCCeeeeEEEEEecCceeEEEcccCcceEEEeccccccchhHH
Confidence 45789999999875 33 336688899999999987766666665443
No 12
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=96.22 E-value=0.0082 Score=36.13 Aligned_cols=46 Identities=28% Similarity=0.489 Sum_probs=26.8
Q ss_pred cccCCCCceeeEEe-eee------ee-eeCCCCceEecccccccccHHHHHHHHHHHH
Q 044880 36 YFCEFCGKYAVKRK-AVG------IW-GCKDCGKVKAGGAYTLNTASAVTVRSTIRRL 85 (91)
Q Consensus 36 y~CpfCGk~~VkR~-a~G------IW-~C~~Cg~~~AGGAy~~~T~~~~t~~~~i~rl 85 (91)
..|||||...+.-. ..+ .+ .|..||. +-....++.......||...
T Consensus 4 kPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga----~~~~~~~~~~~~~~~Ai~~W 57 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA----DDSTSEEPWADDEAEAIEAW 57 (61)
T ss_pred cCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC----ccccccccchHHHHHHHHHH
Confidence 46999997764333 222 11 3999977 33344455555666566544
No 13
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=95.93 E-value=0.0069 Score=34.84 Aligned_cols=31 Identities=29% Similarity=0.513 Sum_probs=23.2
Q ss_pred cccCCCCcee-eEEeeeeeeeeCCCCceEecc
Q 044880 36 YFCEFCGKYA-VKRKAVGIWGCKDCGKVKAGG 66 (91)
Q Consensus 36 y~CpfCGk~~-VkR~a~GIW~C~~Cg~~~AGG 66 (91)
|.||.||... +-=.+.|-..|..||.++.-.
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e~ 32 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVLEEN 32 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBEE-T
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEeecc
Confidence 6899999976 444577999999999887643
No 14
>PHA00626 hypothetical protein
Probab=95.88 E-value=0.006 Score=38.69 Aligned_cols=33 Identities=24% Similarity=0.527 Sum_probs=26.6
Q ss_pred ccCCCCceeeEEe-----eeeeeeeCCCCceEeccccc
Q 044880 37 FCEFCGKYAVKRK-----AVGIWGCKDCGKVKAGGAYT 69 (91)
Q Consensus 37 ~CpfCGk~~VkR~-----a~GIW~C~~Cg~~~AGGAy~ 69 (91)
.||-||...+-|- -.....|+.||+.|+--||-
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~~~ 39 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDAFG 39 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeechhhhh
Confidence 5999999765563 35789999999999887764
No 15
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=95.57 E-value=0.0079 Score=43.78 Aligned_cols=26 Identities=35% Similarity=0.837 Sum_probs=19.9
Q ss_pred cccCCCCcee--------------eEEeeeeeeeeCCCCceEec
Q 044880 36 YFCEFCGKYA--------------VKRKAVGIWGCKDCGKVKAG 65 (91)
Q Consensus 36 y~CpfCGk~~--------------VkR~a~GIW~C~~Cg~~~AG 65 (91)
+.||+||.+. |+|. -+|..||++|.+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~----~~c~~c~~~f~~ 40 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRR----RECLACGKRFTT 40 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeee----eeccccCCcceE
Confidence 4799999643 3333 799999999975
No 16
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 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 CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=95.55 E-value=0.0081 Score=39.87 Aligned_cols=52 Identities=17% Similarity=0.442 Sum_probs=28.1
Q ss_pred ccccCCCCce--eeEE-eeeeeeeeCCCCceEeccccccc-ccHHHHHHHHHHHHHhh
Q 044880 35 KYFCEFCGKY--AVKR-KAVGIWGCKDCGKVKAGGAYTLN-TASAVTVRSTIRRLREQ 88 (91)
Q Consensus 35 ky~CpfCGk~--~VkR-~a~GIW~C~~Cg~~~AGGAy~~~-T~~~~t~~~~i~rl~e~ 88 (91)
.+.||||+.. ++.= ...++|+|..||. .|.+..+- .--+.+++.|++.|.+.
T Consensus 33 ~~~CPfH~d~~pS~~i~~~k~~~~Cf~Cg~--~Gd~i~~v~~~~~~~f~eAv~~l~~~ 88 (97)
T PF01807_consen 33 RCLCPFHDDKTPSFSINPDKNRFKCFGCGK--GGDVIDFVMKYEGCSFKEAVKWLAEE 88 (97)
T ss_dssp EE--SSS--SS--EEEETTTTEEEETTT----EE-HHHHHHHHHT--HHHHHHHHHHH
T ss_pred EEECcCCCCCCCceEEECCCCeEEECCCCC--CCcHHhHHHHHhCCCHHHHHHHHHHH
Confidence 4689999964 2221 2458999999995 56666552 33456777788887663
No 17
>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=95.34 E-value=0.02 Score=37.52 Aligned_cols=46 Identities=24% Similarity=0.536 Sum_probs=21.7
Q ss_pred HHhhcccccCCCC-ceee--E--E-eeeeeeeeCCCCceEecccccccccHH
Q 044880 30 VSQHSKYFCEFCG-KYAV--K--R-KAVGIWGCKDCGKVKAGGAYTLNTASA 75 (91)
Q Consensus 30 ~~q~~ky~CpfCG-k~~V--k--R-~a~GIW~C~~Cg~~~AGGAy~~~T~~~ 75 (91)
......|.||||+ +.+| + + ..+|+=.|..|+..|.=-.-.++.|.=
T Consensus 17 ~~l~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~~L~epiD 68 (81)
T PF05129_consen 17 PKLPKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKINPLSEPID 68 (81)
T ss_dssp ---SS----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE--SS--TTH
T ss_pred CCCCceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccCccCcccc
Confidence 3446789999999 5442 2 2 378999999999888765444455543
No 18
>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=95.10 E-value=0.016 Score=35.56 Aligned_cols=27 Identities=30% Similarity=0.717 Sum_probs=23.8
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
+||.||....++...-+|.|..||..+
T Consensus 30 ~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred CccCcccccccccccceEEcCCCCCEE
Confidence 799999988777788899999999874
No 19
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=94.99 E-value=0.02 Score=33.28 Aligned_cols=31 Identities=23% Similarity=0.370 Sum_probs=23.5
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCceEe
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~A 64 (91)
..|.||-||....--...+.+.|..||..+-
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 3689999999865545555789999997653
No 20
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=94.75 E-value=0.027 Score=32.68 Aligned_cols=32 Identities=22% Similarity=0.594 Sum_probs=25.4
Q ss_pred ccCCCCceeeEEeee--eeeeeCCCCceEecccc
Q 044880 37 FCEFCGKYAVKRKAV--GIWGCKDCGKVKAGGAY 68 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~--GIW~C~~Cg~~~AGGAy 68 (91)
.||.||......... -.|.|..||+.+.-.++
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEECCCc
Confidence 699999977555443 38999999999887776
No 21
>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=94.41 E-value=0.024 Score=33.16 Aligned_cols=25 Identities=32% Similarity=1.001 Sum_probs=13.7
Q ss_pred ccCCCCcee-eE----EeeeeeeeeCCCCc
Q 044880 37 FCEFCGKYA-VK----RKAVGIWGCKDCGK 61 (91)
Q Consensus 37 ~CpfCGk~~-Vk----R~a~GIW~C~~Cg~ 61 (91)
.||.||... .. +...|-|.|..|+.
T Consensus 5 pCP~CGG~DrFri~~d~~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 5 PCPICGGKDRFRIFDDKDGRGTWICRQCGG 34 (40)
T ss_dssp --TTTT-TTTEEEETT----S-EEETTTTB
T ss_pred CCCCCcCccccccCcCcccCCCEECCCCCC
Confidence 699999654 33 23569999999955
No 22
>smart00400 ZnF_CHCC zinc finger.
Probab=94.40 E-value=0.025 Score=33.81 Aligned_cols=32 Identities=22% Similarity=0.573 Sum_probs=21.0
Q ss_pred cccCCCCcee--eE-EeeeeeeeeCCCCceEeccccc
Q 044880 36 YFCEFCGKYA--VK-RKAVGIWGCKDCGKVKAGGAYT 69 (91)
Q Consensus 36 y~CpfCGk~~--Vk-R~a~GIW~C~~Cg~~~AGGAy~ 69 (91)
..|||++... +. ....++|+|-.||+ .|++-.
T Consensus 3 ~~cPfh~d~~pSf~v~~~kn~~~Cf~cg~--gGd~i~ 37 (55)
T smart00400 3 GLCPFHGEKTPSFSVSPDKQFFHCFGCGA--GGNVIS 37 (55)
T ss_pred ccCcCCCCCCCCEEEECCCCEEEEeCCCC--CCCHHH
Confidence 3699999753 22 12458999999984 444433
No 23
>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=93.60 E-value=0.049 Score=30.47 Aligned_cols=15 Identities=27% Similarity=0.503 Sum_probs=12.1
Q ss_pred eeeeeeeCCCCceEe
Q 044880 50 AVGIWGCKDCGKVKA 64 (91)
Q Consensus 50 a~GIW~C~~Cg~~~A 64 (91)
.+-.|.|..||+.+-
T Consensus 29 ~vp~~~C~~CGE~~~ 43 (46)
T TIGR03831 29 NVPALVCPQCGEEYL 43 (46)
T ss_pred CCCccccccCCCEee
Confidence 557799999998764
No 24
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=93.10 E-value=0.048 Score=33.72 Aligned_cols=30 Identities=27% Similarity=0.712 Sum_probs=18.5
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
.+-.||.||.-.+-=.----|.|.+||++-
T Consensus 18 k~~~CPrCG~gvfmA~H~dR~~CGkCgyTe 47 (51)
T COG1998 18 KNRFCPRCGPGVFMADHKDRWACGKCGYTE 47 (51)
T ss_pred ccccCCCCCCcchhhhcCceeEeccccceE
Confidence 445799999532110111149999999873
No 25
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=92.84 E-value=0.07 Score=39.15 Aligned_cols=22 Identities=32% Similarity=0.850 Sum_probs=19.1
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
.||-||. ...+.|.|..||.++
T Consensus 311 ~C~~cg~-----~~~r~~~C~~cg~~~ 332 (364)
T COG0675 311 TCPCCGH-----LSGRLFKCPRCGFVH 332 (364)
T ss_pred cccccCC-----ccceeEECCCCCCee
Confidence 6999999 567889999999864
No 26
>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=92.65 E-value=0.071 Score=30.69 Aligned_cols=25 Identities=32% Similarity=0.834 Sum_probs=18.4
Q ss_pred ccCCCCcee-e---EEeeeeeeeeCCCCc
Q 044880 37 FCEFCGKYA-V---KRKAVGIWGCKDCGK 61 (91)
Q Consensus 37 ~CpfCGk~~-V---kR~a~GIW~C~~Cg~ 61 (91)
.||.||... . .+...|-|.|..|+.
T Consensus 5 pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 5 PCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred CCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 699999654 3 223559999999973
No 27
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=92.54 E-value=0.09 Score=29.84 Aligned_cols=27 Identities=26% Similarity=0.580 Sum_probs=23.0
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
..|+.|+.. .-....|-|.|.+||-+.
T Consensus 9 ~~C~~C~~~-~~~~~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 9 EPCPVCGSR-WFYSDDGFYYCDRCGHQS 35 (36)
T ss_pred CcCCCCCCe-EeEccCCEEEhhhCceEc
Confidence 459999999 777888999999999653
No 28
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=92.50 E-value=0.085 Score=41.29 Aligned_cols=37 Identities=27% Similarity=0.533 Sum_probs=28.9
Q ss_pred HHHHhhcccccCCCCcee-eEEeeeeeeeeCCCCceEe
Q 044880 28 MEVSQHSKYFCEFCGKYA-VKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 28 ie~~q~~ky~CpfCGk~~-VkR~a~GIW~C~~Cg~~~A 64 (91)
.+.+......||.||.+. |.-...|-..|..||.++.
T Consensus 4 ~~~~~~~~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 4 LVLEEEEKLVCPECGSDKLIYDYERGEIVCADCGLVIE 41 (310)
T ss_pred hhhhcccCCcCcCCCCCCeeEECCCCeEeecccCCccc
Confidence 455666778899999844 5556889999999998664
No 29
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=92.25 E-value=0.097 Score=36.19 Aligned_cols=32 Identities=25% Similarity=0.611 Sum_probs=21.8
Q ss_pred ccC--CCCceeeEEeeeeeeeeCCCCceEeccccc
Q 044880 37 FCE--FCGKYAVKRKAVGIWGCKDCGKVKAGGAYT 69 (91)
Q Consensus 37 ~Cp--fCGk~~VkR~a~GIW~C~~Cg~~~AGGAy~ 69 (91)
-|| .|++.... .+.|.|.|.+|+..+.---|.
T Consensus 20 aC~~~~C~kKv~~-~~~~~y~C~~C~~~~~~~~~r 53 (146)
T PF08646_consen 20 ACPNEKCNKKVTE-NGDGSYRCEKCNKTVENPKYR 53 (146)
T ss_dssp E-TSTTTS-B-EE-ETTTEEEETTTTEEESS-EEE
T ss_pred CCCCccCCCEeec-CCCcEEECCCCCCcCCCeeEE
Confidence 699 99986554 477999999999987544443
No 30
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=92.20 E-value=0.15 Score=38.21 Aligned_cols=37 Identities=27% Similarity=0.609 Sum_probs=26.9
Q ss_pred cccccCCCCcee-eEEe------------------------eeeeeeeCCCCceEecccccc
Q 044880 34 SKYFCEFCGKYA-VKRK------------------------AVGIWGCKDCGKVKAGGAYTL 70 (91)
Q Consensus 34 ~ky~CpfCGk~~-VkR~------------------------a~GIW~C~~Cg~~~AGGAy~~ 70 (91)
.+++||+|++.- .+++ =--||.|.+||+.+.-.-+.-
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~F~~ 65 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEEDFEK 65 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccccccc
Confidence 568999999863 2211 125899999999988777663
No 31
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=91.94 E-value=0.049 Score=37.26 Aligned_cols=34 Identities=26% Similarity=0.648 Sum_probs=24.5
Q ss_pred HHHhhcccccCCCCceee----EEeeeeeeeeCCCCceE
Q 044880 29 EVSQHSKYFCEFCGKYAV----KRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 29 e~~q~~ky~CpfCGk~~V----kR~a~GIW~C~~Cg~~~ 63 (91)
-.....-+.|||||...| .| ..+.=.|..||.-+
T Consensus 15 k~klpt~f~CP~Cge~~v~v~~~k-~~~h~~C~~CG~y~ 52 (99)
T PRK14892 15 KPKLPKIFECPRCGKVSISVKIKK-NIAIITCGNCGLYT 52 (99)
T ss_pred ccCCCcEeECCCCCCeEeeeecCC-CcceEECCCCCCcc
Confidence 444467789999997654 23 56677899998654
No 32
>PRK05667 dnaG DNA primase; Validated
Probab=91.48 E-value=0.11 Score=44.25 Aligned_cols=48 Identities=17% Similarity=0.399 Sum_probs=28.9
Q ss_pred cccCCCCcee----eEEeeeeeeeeCCCCceEecccccccccH-HHHHHHHHHHHH
Q 044880 36 YFCEFCGKYA----VKRKAVGIWGCKDCGKVKAGGAYTLNTAS-AVTVRSTIRRLR 86 (91)
Q Consensus 36 y~CpfCGk~~----VkR~a~GIW~C~~Cg~~~AGGAy~~~T~~-~~t~~~~i~rl~ 86 (91)
..||||+... |. ...++|+|..||. .|.+..+-.-. +.++..|++.|-
T Consensus 37 ~~CPfH~ektpSf~V~-~~k~~~~CF~Cg~--~Gd~i~fv~~~~~~sf~eAv~~La 89 (580)
T PRK05667 37 GLCPFHDEKTPSFTVS-PDKQFYHCFGCGA--GGDVIKFLMEYEGLSFVEAVEELA 89 (580)
T ss_pred ecCCCCCCCCCceEEE-CCCCeEEECCCCC--CCCHHHHHHHHhCCCHHHHHHHHH
Confidence 3799999653 43 3579999999997 35554432111 233445555553
No 33
>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=91.31 E-value=0.21 Score=33.07 Aligned_cols=16 Identities=31% Similarity=0.684 Sum_probs=12.9
Q ss_pred eeeeeeeCCCCceEec
Q 044880 50 AVGIWGCKDCGKVKAG 65 (91)
Q Consensus 50 a~GIW~C~~Cg~~~AG 65 (91)
.+..|.|..||..+.-
T Consensus 28 ~~~~~~C~~CGe~~~~ 43 (127)
T TIGR03830 28 GVPGWYCPACGEELLD 43 (127)
T ss_pred eeeeeECCCCCCEEEc
Confidence 5688999999987653
No 34
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=91.02 E-value=0.18 Score=29.77 Aligned_cols=29 Identities=24% Similarity=0.612 Sum_probs=20.8
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCCceEe
Q 044880 35 KYFCEFCGKYAVKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 35 ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~A 64 (91)
.|.|..||.+.--....+| .|+.||..+-
T Consensus 2 ~Y~C~~Cg~~~~~~~~~~i-rC~~CG~rIl 30 (44)
T smart00659 2 IYICGECGRENEIKSKDVV-RCRECGYRIL 30 (44)
T ss_pred EEECCCCCCEeecCCCCce-ECCCCCceEE
Confidence 5899999987533344455 9999997653
No 35
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=90.87 E-value=0.23 Score=41.23 Aligned_cols=37 Identities=27% Similarity=0.677 Sum_probs=27.4
Q ss_pred hhhHHHHHHHHHhhcccccCCCCceeeEEeeeeeeeeCCCCc
Q 044880 20 SLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 20 slRK~v~kie~~q~~ky~CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
.||++|-+ -+.+...|.|..||=.+-. =-|+|++|..
T Consensus 340 ~lr~mvge-~l~~~~~YRC~~CGF~a~~----l~W~CPsC~~ 376 (389)
T COG2956 340 LLRDMVGE-QLRRKPRYRCQNCGFTAHT----LYWHCPSCRA 376 (389)
T ss_pred HHHHHHHH-HHhhcCCceecccCCccee----eeeeCCCccc
Confidence 36777765 5677899999999965422 2499999974
No 36
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=90.67 E-value=0.15 Score=33.26 Aligned_cols=21 Identities=38% Similarity=0.789 Sum_probs=10.4
Q ss_pred hcccccCCCCceeeEEeeeee
Q 044880 33 HSKYFCEFCGKYAVKRKAVGI 53 (91)
Q Consensus 33 ~~ky~CpfCGk~~VkR~a~GI 53 (91)
-.+..||.||...+.|+++.+
T Consensus 22 ~~k~FCp~CGn~TL~rvsvsv 42 (73)
T PF08772_consen 22 MTKQFCPKCGNATLKRVSVSV 42 (73)
T ss_dssp SS--S-SSS--S--EEEE-B-
T ss_pred CCceeCcccCCCcceEEEEEE
Confidence 367899999999999998765
No 37
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=90.63 E-value=0.18 Score=41.02 Aligned_cols=48 Identities=19% Similarity=0.430 Sum_probs=28.3
Q ss_pred cccCCCCcee----eEEeeeeeeeeCCCCceEeccccccccc-HHHHHHHHHHHHH
Q 044880 36 YFCEFCGKYA----VKRKAVGIWGCKDCGKVKAGGAYTLNTA-SAVTVRSTIRRLR 86 (91)
Q Consensus 36 y~CpfCGk~~----VkR~a~GIW~C~~Cg~~~AGGAy~~~T~-~~~t~~~~i~rl~ 86 (91)
..||||+... |. ...++|+|..||. .|.+..+-.- -+.++..|++.|.
T Consensus 35 ~~CPfh~ek~pSf~v~-~~k~~~~Cf~Cg~--~Gd~i~fv~~~~~~sf~eA~~~La 87 (415)
T TIGR01391 35 GLCPFHHEKTPSFSVS-PEKQFYHCFGCGA--GGDAIKFLMEIEGISFVEAVEELA 87 (415)
T ss_pred eeCCCCCCCCCeEEEE-cCCCcEEECCCCC--CCCHHHHHHHHhCCCHHHHHHHHH
Confidence 4799998643 33 3569999999997 4544433211 1223444555543
No 38
>PHA02942 putative transposase; Provisional
Probab=90.44 E-value=0.16 Score=41.22 Aligned_cols=26 Identities=27% Similarity=0.572 Sum_probs=20.6
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
+||.||... ++.+..+|.|..||...
T Consensus 327 ~Cs~CG~~~-~~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 327 SCPKCGHKM-VEIAHRYFHCPSCGYEN 352 (383)
T ss_pred cCCCCCCcc-CcCCCCEEECCCCCCEe
Confidence 699999754 34456689999999875
No 39
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=90.42 E-value=0.21 Score=31.63 Aligned_cols=29 Identities=28% Similarity=0.718 Sum_probs=16.7
Q ss_pred hcccccCCCCceeeEEe-----eeeeeeeCCCCc
Q 044880 33 HSKYFCEFCGKYAVKRK-----AVGIWGCKDCGK 61 (91)
Q Consensus 33 ~~ky~CpfCGk~~VkR~-----a~GIW~C~~Cg~ 61 (91)
...|.||-||...+.|= -.-...|.+||+
T Consensus 23 ~~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCeeEeechhHHhcCCceECCCCCC
Confidence 46788888887654442 223345555543
No 40
>PHA02540 61 DNA primase; Provisional
Probab=90.37 E-value=0.22 Score=40.34 Aligned_cols=28 Identities=29% Similarity=0.865 Sum_probs=18.7
Q ss_pred ccccCCCCcee---------eEEe-eeeeeeeCCCCce
Q 044880 35 KYFCEFCGKYA---------VKRK-AVGIWGCKDCGKV 62 (91)
Q Consensus 35 ky~CpfCGk~~---------VkR~-a~GIW~C~~Cg~~ 62 (91)
...|||||... |-.. .-++|||-.||..
T Consensus 27 ~~~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCGa~ 64 (337)
T PHA02540 27 NFRCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCGYH 64 (337)
T ss_pred EecCCCCCCccccCcCCcEEEeccCCceEEEecCCCCC
Confidence 45899999732 2211 1249999999964
No 41
>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=90.36 E-value=0.18 Score=26.10 Aligned_cols=15 Identities=33% Similarity=0.853 Sum_probs=11.6
Q ss_pred HHhhcccccCCCCce
Q 044880 30 VSQHSKYFCEFCGKY 44 (91)
Q Consensus 30 ~~q~~ky~CpfCGk~ 44 (91)
-+...+|.||+|++.
T Consensus 9 H~~~k~~~C~~C~k~ 23 (26)
T PF13465_consen 9 HTGEKPYKCPYCGKS 23 (26)
T ss_dssp HSSSSSEEESSSSEE
T ss_pred cCCCCCCCCCCCcCe
Confidence 445678999999875
No 42
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=90.04 E-value=0.23 Score=35.05 Aligned_cols=42 Identities=24% Similarity=0.472 Sum_probs=25.9
Q ss_pred hHHHHHHHHH-----hhcccccCCCCcee-eE---E--eeeeeeeeCCCCceE
Q 044880 22 RKQIKKMEVS-----QHSKYFCEFCGKYA-VK---R--KAVGIWGCKDCGKVK 63 (91)
Q Consensus 22 RK~v~kie~~-----q~~ky~CpfCGk~~-Vk---R--~a~GIW~C~~Cg~~~ 63 (91)
.++.++++.. .+.-|.||.||..- .. . ...|--.|..||..+
T Consensus 81 ~~~~~~L~~~l~~e~~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 81 DKMRKRLEDKLEDETNNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred HHHHHHHHHHHhcccCCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 3444444443 34578999999653 10 0 124558999999876
No 43
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=89.90 E-value=0.32 Score=27.27 Aligned_cols=29 Identities=24% Similarity=0.613 Sum_probs=18.8
Q ss_pred ccCCCCceeeEEeeeeee-eeCCCCceEec
Q 044880 37 FCEFCGKYAVKRKAVGIW-GCKDCGKVKAG 65 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW-~C~~Cg~~~AG 65 (91)
.||.||...+-+.+..-. .|+.|++..--
T Consensus 3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~~ 32 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRVACRTCGYEEPI 32 (35)
T ss_dssp BETTTTSBEEEEEETTTTEEESSSS-EEE-
T ss_pred eCCCCCccceEcCCCccCcCCCCCCCccCC
Confidence 699999987554432211 69999988643
No 44
>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=89.63 E-value=0.12 Score=28.76 Aligned_cols=27 Identities=30% Similarity=0.691 Sum_probs=17.9
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
|.|..||.+..-.....| .|..||..+
T Consensus 1 Y~C~~Cg~~~~~~~~~~i-rC~~CG~RI 27 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPI-RCPECGHRI 27 (32)
T ss_dssp EBESSSSSSE-BSTSSTS-SBSSSS-SE
T ss_pred CCCCcCCCeeEcCCCCcE-ECCcCCCeE
Confidence 789999987543344456 899998654
No 45
>PRK11823 DNA repair protein RadA; Provisional
Probab=89.49 E-value=0.16 Score=41.75 Aligned_cols=24 Identities=33% Similarity=0.825 Sum_probs=21.6
Q ss_pred hcccccCCCCceeeEEeeeeeeeeCCCC
Q 044880 33 HSKYFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 33 ~~ky~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
+..|.|..||-.+.+.. |+|..|+
T Consensus 5 ~~~y~C~~Cg~~~~~~~----g~Cp~C~ 28 (446)
T PRK11823 5 KTAYVCQECGAESPKWL----GRCPECG 28 (446)
T ss_pred CCeEECCcCCCCCcccC----eeCcCCC
Confidence 56799999999998876 9999997
No 46
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=89.41 E-value=0.31 Score=33.64 Aligned_cols=28 Identities=32% Similarity=0.751 Sum_probs=23.1
Q ss_pred ccCCCCceeeEEe--eeeeeeeCCCCceEe
Q 044880 37 FCEFCGKYAVKRK--AVGIWGCKDCGKVKA 64 (91)
Q Consensus 37 ~CpfCGk~~VkR~--a~GIW~C~~Cg~~~A 64 (91)
.||.||...+-+. ..+.+.|++||+.+-
T Consensus 4 FCp~Cgsll~p~~~~~~~~l~C~kCgye~~ 33 (113)
T COG1594 4 FCPKCGSLLYPKKDDEGGKLVCRKCGYEEE 33 (113)
T ss_pred ccCCccCeeEEeEcCCCcEEECCCCCcchh
Confidence 6999999987776 467999999997653
No 47
>PRK12366 replication factor A; Reviewed
Probab=89.28 E-value=0.18 Score=43.37 Aligned_cols=24 Identities=33% Similarity=0.733 Sum_probs=20.8
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
.||-|.|..+. .-|.|.|.+|+++
T Consensus 534 aCp~CnkKv~~--~~g~~~C~~c~~~ 557 (637)
T PRK12366 534 LCPNCRKRVEE--VDGEYICEFCGEV 557 (637)
T ss_pred cccccCeEeEc--CCCcEECCCCCCC
Confidence 79999887664 6799999999987
No 48
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=89.20 E-value=0.29 Score=27.86 Aligned_cols=23 Identities=35% Similarity=0.810 Sum_probs=18.5
Q ss_pred ccCCCCcee-eEEeee-----eeeeeCCC
Q 044880 37 FCEFCGKYA-VKRKAV-----GIWGCKDC 59 (91)
Q Consensus 37 ~CpfCGk~~-VkR~a~-----GIW~C~~C 59 (91)
.||||+.+. |+|.+- =-|.|+.|
T Consensus 7 ~CP~C~s~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 7 HCPRCQSTEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eCCCCCCCCcceeCCCCCCCCEeEecCcC
Confidence 699999998 998743 35788877
No 49
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=88.92 E-value=0.37 Score=27.62 Aligned_cols=29 Identities=24% Similarity=0.533 Sum_probs=20.7
Q ss_pred cccCCCCceeeE------Ee----eeeeeeeCCCCceEe
Q 044880 36 YFCEFCGKYAVK------RK----AVGIWGCKDCGKVKA 64 (91)
Q Consensus 36 y~CpfCGk~~Vk------R~----a~GIW~C~~Cg~~~A 64 (91)
+.||.||...+- |. .+=++.|.+|+..+.
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~ 39 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWR 39 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeC
Confidence 479999976522 21 356899999998763
No 50
>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=88.89 E-value=0.22 Score=32.80 Aligned_cols=27 Identities=33% Similarity=0.866 Sum_probs=22.1
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceEec
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVKAG 65 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~AG 65 (91)
+||.||...+.. .+.+.|..|++++.-
T Consensus 2 fC~~Cg~~l~~~--~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMTPK--NGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccccC--CCeEECcCCCCcccc
Confidence 699999988664 478999999988654
No 51
>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=88.86 E-value=0.19 Score=29.83 Aligned_cols=10 Identities=40% Similarity=1.212 Sum_probs=8.7
Q ss_pred ccccCCCCce
Q 044880 35 KYFCEFCGKY 44 (91)
Q Consensus 35 ky~CpfCGk~ 44 (91)
.|.|||||+.
T Consensus 2 ~f~CP~C~~~ 11 (54)
T PF05605_consen 2 SFTCPYCGKG 11 (54)
T ss_pred CcCCCCCCCc
Confidence 6899999993
No 52
>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=88.85 E-value=0.24 Score=36.22 Aligned_cols=28 Identities=25% Similarity=0.614 Sum_probs=18.4
Q ss_pred ccCCCCceeeE----Ee---eeee---eeeCCCCceEe
Q 044880 37 FCEFCGKYAVK----RK---AVGI---WGCKDCGKVKA 64 (91)
Q Consensus 37 ~CpfCGk~~Vk----R~---a~GI---W~C~~Cg~~~A 64 (91)
.|||||.+.-+ |. +..| -.|..||+-|+
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFT 39 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccc
Confidence 59999985311 11 2224 57999999887
No 53
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=88.34 E-value=0.21 Score=41.22 Aligned_cols=25 Identities=32% Similarity=0.760 Sum_probs=21.7
Q ss_pred hhcccccCCCCceeeEEeeeeeeeeCCCC
Q 044880 32 QHSKYFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 32 q~~ky~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
.+..|.|..||-.+.+.. |+|..|+
T Consensus 4 ~~~~y~C~~Cg~~~~~~~----g~Cp~C~ 28 (454)
T TIGR00416 4 AKSKFVCQHCGADSPKWQ----GKCPACH 28 (454)
T ss_pred CCCeEECCcCCCCCcccc----EECcCCC
Confidence 356799999999998876 9999996
No 54
>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=88.29 E-value=0.56 Score=32.28 Aligned_cols=52 Identities=17% Similarity=0.360 Sum_probs=30.8
Q ss_pred ccccCCCCceeeEEe----------eee-eeeeCCCCceEecccccccccHHHHHHHHHHHHHh
Q 044880 35 KYFCEFCGKYAVKRK----------AVG-IWGCKDCGKVKAGGAYTLNTASAVTVRSTIRRLRE 87 (91)
Q Consensus 35 ky~CpfCGk~~VkR~----------a~G-IW~C~~Cg~~~AGGAy~~~T~~~~t~~~~i~rl~e 87 (91)
+=.||+||.+.+-+. ... +|.|..|+.=|-==. .-+.|.|..+...+|.+|.
T Consensus 2 p~~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG~H~-~t~~PlGtLAd~~lR~~R~ 64 (102)
T PF11672_consen 2 PIICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTPCDAYVGCHP-GTDIPLGTLADAELRRARK 64 (102)
T ss_pred CcccCCCCCeeEEcccchhcCccCCCCceeEECCCCCceeeeeC-CCCCcCcccCCHHHHHHHH
Confidence 447999999874433 123 499999974332111 1145666666666666554
No 55
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=87.59 E-value=0.22 Score=34.90 Aligned_cols=48 Identities=19% Similarity=0.402 Sum_probs=36.2
Q ss_pred HHhhcccccCCCCcee-----eEEe-eeeeeeeCCCCceEecccccccccHHHH
Q 044880 30 VSQHSKYFCEFCGKYA-----VKRK-AVGIWGCKDCGKVKAGGAYTLNTASAVT 77 (91)
Q Consensus 30 ~~q~~ky~CpfCGk~~-----VkR~-a~GIW~C~~Cg~~~AGGAy~~~T~~~~t 77 (91)
......|+||||...+ |.+. .+|-=.|+-|+..|+--.=.+++|.-+.
T Consensus 18 ~~ldt~FnClfcnHek~v~~~~Dk~~~iG~~sC~iC~esFqt~it~LsepIDVY 71 (109)
T KOG3214|consen 18 EPLDTQFNCLFCNHEKSVSCTLDKKHNIGKASCRICEESFQTTITALSEPIDVY 71 (109)
T ss_pred cchheeeccCccccccceeeeehhhcCcceeeeeehhhhhccchHhhccchHHH
Confidence 3445789999999765 3333 7799999999999988777777776443
No 56
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=87.53 E-value=0.5 Score=26.05 Aligned_cols=26 Identities=23% Similarity=0.557 Sum_probs=15.5
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
.||.|+.+-.- ....++.|..|+..+
T Consensus 4 ~Cp~C~se~~y-~D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCPLCGSEYTY-EDGELLVCPECGHEW 29 (30)
T ss_dssp --TTT-----E-E-SSSEEETTTTEEE
T ss_pred CCCCCCCccee-ccCCEEeCCcccccC
Confidence 59999988665 677899999999875
No 57
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=87.33 E-value=0.93 Score=31.88 Aligned_cols=37 Identities=19% Similarity=0.371 Sum_probs=26.0
Q ss_pred HHHhhcc-cccCCCCceeeEEee-----eeeeeeCCCCceEec
Q 044880 29 EVSQHSK-YFCEFCGKYAVKRKA-----VGIWGCKDCGKVKAG 65 (91)
Q Consensus 29 e~~q~~k-y~CpfCGk~~VkR~a-----~GIW~C~~Cg~~~AG 65 (91)
+..+... =.||+|+...+.+.+ .-=|.|+.|+++|.=
T Consensus 23 ~~~~~~~~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 23 AIRMQITKVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred HHhhhcccCcCCCCCccceeeECCccccccccccCCcCcceee
Confidence 3333333 689999988755553 345999999999863
No 58
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=87.20 E-value=0.87 Score=25.37 Aligned_cols=30 Identities=23% Similarity=0.334 Sum_probs=24.1
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCCceEe
Q 044880 35 KYFCEFCGKYAVKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 35 ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~A 64 (91)
...|+.|+.+.+--..-++-.|..|+.++.
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSSFP 32 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcEee
Confidence 357999999887656778889999998763
No 59
>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=87.14 E-value=0.53 Score=25.81 Aligned_cols=27 Identities=30% Similarity=0.623 Sum_probs=18.5
Q ss_pred ccccCCCCceeeEEee---eeeeeeCCCCc
Q 044880 35 KYFCEFCGKYAVKRKA---VGIWGCKDCGK 61 (91)
Q Consensus 35 ky~CpfCGk~~VkR~a---~GIW~C~~Cg~ 61 (91)
.|.|+.||..--...+ ..+-.|..||.
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 5789999985422222 34778999986
No 60
>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=86.87 E-value=0.34 Score=34.04 Aligned_cols=26 Identities=31% Similarity=0.710 Sum_probs=20.5
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
-||-|.+..+. ...|.|.|.+|+..+
T Consensus 36 aC~~C~kkv~~-~~~~~~~C~~C~~~~ 61 (166)
T cd04476 36 ACPGCNKKVVE-EGNGTYRCEKCNKSV 61 (166)
T ss_pred cccccCcccEe-CCCCcEECCCCCCcC
Confidence 69999987443 334899999999886
No 61
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=86.57 E-value=0.83 Score=29.75 Aligned_cols=33 Identities=21% Similarity=0.516 Sum_probs=20.2
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceEeccccccc
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLN 71 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGGAy~~~ 71 (91)
.||.|..+ +.+.+ |.++|..|..-|.==|+-|+
T Consensus 3 ~CP~C~~~-L~~~~-~~~~C~~C~~~~~~~a~CPd 35 (70)
T PF07191_consen 3 TCPKCQQE-LEWQG-GHYHCEACQKDYKKEAFCPD 35 (70)
T ss_dssp B-SSS-SB-EEEET-TEEEETTT--EEEEEEE-TT
T ss_pred cCCCCCCc-cEEeC-CEEECccccccceecccCCC
Confidence 58999888 55555 88899999887765555553
No 62
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=86.42 E-value=0.77 Score=32.16 Aligned_cols=24 Identities=38% Similarity=0.841 Sum_probs=19.6
Q ss_pred cCCCCcee-eEEeeeeeeeeCCCCceEecc
Q 044880 38 CEFCGKYA-VKRKAVGIWGCKDCGKVKAGG 66 (91)
Q Consensus 38 CpfCGk~~-VkR~a~GIW~C~~Cg~~~AGG 66 (91)
||.||.+. |.|. +|..|+-++-|-
T Consensus 1 CPvCg~~l~vt~l-----~C~~C~t~i~G~ 25 (113)
T PF09862_consen 1 CPVCGGELVVTRL-----KCPSCGTEIEGE 25 (113)
T ss_pred CCCCCCceEEEEE-----EcCCCCCEEEee
Confidence 99999874 5544 799999999884
No 63
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=86.30 E-value=0.39 Score=30.67 Aligned_cols=29 Identities=28% Similarity=0.625 Sum_probs=17.1
Q ss_pred hcccccCCCCceeeEEe-----eeeeeeeCCCCc
Q 044880 33 HSKYFCEFCGKYAVKRK-----AVGIWGCKDCGK 61 (91)
Q Consensus 33 ~~ky~CpfCGk~~VkR~-----a~GIW~C~~Cg~ 61 (91)
...|.||-||+..+.|- -..-+.|.+||+
T Consensus 25 ~v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 25 AVKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eeEeeCCCCCceeeehhhhHHHcCCceECCCcCc
Confidence 45678888886655443 223455666654
No 64
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=86.02 E-value=1 Score=29.24 Aligned_cols=30 Identities=20% Similarity=0.544 Sum_probs=21.9
Q ss_pred cccCCCCceeeEEee--------eeeeeeC--CCCceEec
Q 044880 36 YFCEFCGKYAVKRKA--------VGIWGCK--DCGKVKAG 65 (91)
Q Consensus 36 y~CpfCGk~~VkR~a--------~GIW~C~--~Cg~~~AG 65 (91)
+.||+||....-|.+ -=-++|. .||.+|.-
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFIT 41 (72)
T ss_pred ccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEE
Confidence 579999988744432 2457899 99999864
No 65
>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=86.01 E-value=0.38 Score=38.85 Aligned_cols=21 Identities=38% Similarity=0.888 Sum_probs=19.2
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCC
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
|.|..||-.+.+.. |+|..|+
T Consensus 1 ~~c~~cg~~~~~~~----g~cp~c~ 21 (372)
T cd01121 1 YVCSECGYVSPKWL----GKCPECG 21 (372)
T ss_pred CCCCCCCCCCCCcc----EECcCCC
Confidence 88999999998876 8999997
No 66
>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=85.88 E-value=1.7 Score=25.41 Aligned_cols=30 Identities=27% Similarity=0.546 Sum_probs=22.4
Q ss_pred ccCCCCceeeEEeee--------eeeeeCC--CCceEecc
Q 044880 37 FCEFCGKYAVKRKAV--------GIWGCKD--CGKVKAGG 66 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~--------GIW~C~~--Cg~~~AGG 66 (91)
.||.||.....|.+. =..+|.. ||.+|..-
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFVAN 40 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEEEE
Confidence 599999988766633 4467888 99888654
No 67
>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=85.25 E-value=0.33 Score=25.81 Aligned_cols=24 Identities=25% Similarity=0.423 Sum_probs=16.8
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceEe
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~A 64 (91)
+||.|++.. ....=.|..||+.|.
T Consensus 2 ~CP~C~~~V----~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEV----PESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCc----hhhcCcCCCCCCCCc
Confidence 599998874 223336999998874
No 68
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=85.07 E-value=1.8 Score=24.51 Aligned_cols=27 Identities=22% Similarity=0.465 Sum_probs=17.3
Q ss_pred ccCCCCceee-EEe---------eeeeeeeCCCCceE
Q 044880 37 FCEFCGKYAV-KRK---------AVGIWGCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~~V-kR~---------a~GIW~C~~Cg~~~ 63 (91)
.||.||.... -.+ .+=+..|..|+..|
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCee
Confidence 6999998752 221 36788999999886
No 69
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=84.97 E-value=0.77 Score=36.28 Aligned_cols=30 Identities=30% Similarity=0.543 Sum_probs=24.1
Q ss_pred cccCCCCceeeEE-eeeeeeeeCCCCceEec
Q 044880 36 YFCEFCGKYAVKR-KAVGIWGCKDCGKVKAG 65 (91)
Q Consensus 36 y~CpfCGk~~VkR-~a~GIW~C~~Cg~~~AG 65 (91)
+.||.||.+.+-. ..-|-|.|..||.++-=
T Consensus 2 ~~CpeCg~~~~~~d~~~ge~VC~~CG~Vi~~ 32 (285)
T COG1405 2 MSCPECGSTNIITDYERGEIVCADCGLVLED 32 (285)
T ss_pred CCCCCCCCccceeeccCCeEEeccCCEEecc
Confidence 5799999986554 47799999999977653
No 70
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=83.87 E-value=1.6 Score=24.66 Aligned_cols=24 Identities=38% Similarity=0.679 Sum_probs=17.5
Q ss_pred ccCCCCcee--eEEeeeeeeeeCCCC
Q 044880 37 FCEFCGKYA--VKRKAVGIWGCKDCG 60 (91)
Q Consensus 37 ~CpfCGk~~--VkR~a~GIW~C~~Cg 60 (91)
.||.|+... +.-..+=|+.|.+|+
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~ 26 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCG 26 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCC
Confidence 599999853 222356799999994
No 71
>PF14353 CpXC: CpXC protein
Probab=83.80 E-value=1.2 Score=30.21 Aligned_cols=13 Identities=23% Similarity=0.513 Sum_probs=9.4
Q ss_pred eeeeeCCCCceEe
Q 044880 52 GIWGCKDCGKVKA 64 (91)
Q Consensus 52 GIW~C~~Cg~~~A 64 (91)
-.+.|.+||..+.
T Consensus 37 ~~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 37 FSFTCPSCGHKFR 49 (128)
T ss_pred CEEECCCCCCcee
Confidence 3678888887764
No 72
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=83.76 E-value=0.38 Score=40.28 Aligned_cols=30 Identities=27% Similarity=0.548 Sum_probs=20.5
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceEeccc
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVKAGGA 67 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGGA 67 (91)
.||+||... +=.+-+-|.|++||..+..-.
T Consensus 352 ~Cp~Cg~~m-~S~G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRM-KSAGRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCch-hhcCCCCcccccccccCCccc
Confidence 799999752 212333599999998876533
No 73
>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=83.60 E-value=0.7 Score=24.80 Aligned_cols=21 Identities=24% Similarity=0.495 Sum_probs=12.7
Q ss_pred ccCCCCceeeEEeeeeeeeeC
Q 044880 37 FCEFCGKYAVKRKAVGIWGCK 57 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~ 57 (91)
+||.||...++-..-=+|.|.
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCP 21 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE-
T ss_pred CcCCCCCEeEcCCCCEeEECC
Confidence 599999999976665678875
No 74
>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=83.34 E-value=0.47 Score=27.28 Aligned_cols=24 Identities=38% Similarity=0.920 Sum_probs=13.5
Q ss_pred cccCCCCcee--eEEe--ee-eeeeeCCC
Q 044880 36 YFCEFCGKYA--VKRK--AV-GIWGCKDC 59 (91)
Q Consensus 36 y~CpfCGk~~--VkR~--a~-GIW~C~~C 59 (91)
..|+|||++. +.+. +. |+.-|..|
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~~~IC~~C 30 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNGAYICDEC 30 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-SEEEEHHH
T ss_pred CCccCCCCCHHHHhceecCCCCcEECHHH
Confidence 4799999874 3333 33 67888888
No 75
>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=83.10 E-value=0.48 Score=32.67 Aligned_cols=30 Identities=27% Similarity=0.593 Sum_probs=22.1
Q ss_pred cccccCCCCce--eeEEeeeeeeeeCCCCceEecc
Q 044880 34 SKYFCEFCGKY--AVKRKAVGIWGCKDCGKVKAGG 66 (91)
Q Consensus 34 ~ky~CpfCGk~--~VkR~a~GIW~C~~Cg~~~AGG 66 (91)
.|++||.||+. .+.|.. | .|.+||..|---
T Consensus 8 tKR~Cp~CG~kFYDLnk~P--i-vCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDP--I-VCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhccCCCCC--c-cCCCCCCccCcc
Confidence 57899999986 477643 3 699998776433
No 76
>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=82.95 E-value=0.36 Score=34.69 Aligned_cols=28 Identities=18% Similarity=0.579 Sum_probs=23.0
Q ss_pred cccCCCCceeeEEeee-------eeeeeCCCCceE
Q 044880 36 YFCEFCGKYAVKRKAV-------GIWGCKDCGKVK 63 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~-------GIW~C~~Cg~~~ 63 (91)
-.||.||.....+.+- -+|.|..|.+-|
T Consensus 106 ~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 106 VQCPRCGSADTTITSIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCcH
Confidence 5899999998777732 689999998766
No 77
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=82.40 E-value=1.1 Score=34.42 Aligned_cols=31 Identities=19% Similarity=0.465 Sum_probs=22.1
Q ss_pred cccccCCCCcee-----------eEEeeeeeeeeCCCCceEe
Q 044880 34 SKYFCEFCGKYA-----------VKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 34 ~ky~CpfCGk~~-----------VkR~a~GIW~C~~Cg~~~A 64 (91)
..-.||.||.+- ..++-.--|.|.+||+.++
T Consensus 13 ~~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 13 TRIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred eeecCCcccceeeEEEeeecCCccceEEEEEEEccccCCccc
Confidence 344799999853 3344556789999998654
No 78
>PRK08402 replication factor A; Reviewed
Probab=81.92 E-value=0.94 Score=36.79 Aligned_cols=26 Identities=23% Similarity=0.501 Sum_probs=21.5
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCc
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
..||-|.|.-+.-...|.|.|..|++
T Consensus 213 ~aCp~CnKkv~~~~~~~~~~Ce~~~~ 238 (355)
T PRK08402 213 DACPECRRKVDYDPATDTWICPEHGE 238 (355)
T ss_pred ecCCCCCeEEEEecCCCCEeCCCCCC
Confidence 37999998766456779999999985
No 79
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=81.84 E-value=0.43 Score=24.56 Aligned_cols=22 Identities=27% Similarity=0.696 Sum_probs=13.1
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
.||.||...-.-. =-|..||..
T Consensus 1 ~Cp~CG~~~~~~~----~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDA----KFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcC----cchhhhCCc
Confidence 4788887653311 137777754
No 80
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=81.25 E-value=0.51 Score=34.95 Aligned_cols=24 Identities=33% Similarity=0.942 Sum_probs=17.7
Q ss_pred ccCCCCcee--------------eEEeeeeeeeeCCCCceEe
Q 044880 37 FCEFCGKYA--------------VKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 37 ~CpfCGk~~--------------VkR~a~GIW~C~~Cg~~~A 64 (91)
.||||+... ++|. -.|..|+.-|+
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRR----ReC~~C~~RFT 39 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRR----RECLECGERFT 39 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhh----hcccccccccc
Confidence 599999764 3333 47999998886
No 81
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=80.93 E-value=1.4 Score=31.00 Aligned_cols=31 Identities=32% Similarity=0.772 Sum_probs=22.8
Q ss_pred ccCCCCcee--eEEeee-------------eeeeeCCCCceEeccc
Q 044880 37 FCEFCGKYA--VKRKAV-------------GIWGCKDCGKVKAGGA 67 (91)
Q Consensus 37 ~CpfCGk~~--VkR~a~-------------GIW~C~~Cg~~~AGGA 67 (91)
-||.|+... |....+ =.|.|..||+.+=.|.
T Consensus 93 RC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~Gs 138 (147)
T PF01927_consen 93 RCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGS 138 (147)
T ss_pred ccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccc
Confidence 799999864 322222 3899999999987764
No 82
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=80.91 E-value=1.3 Score=31.91 Aligned_cols=40 Identities=23% Similarity=0.380 Sum_probs=28.2
Q ss_pred HHHHHHHHHhh--cccccCCCCceeeEEeeeeeeeeCCCCceEe
Q 044880 23 KQIKKMEVSQH--SKYFCEFCGKYAVKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 23 K~v~kie~~q~--~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~A 64 (91)
|.++....+.+ ..+.||.||-+.++ -.|==.|.-|++.+-
T Consensus 14 k~iA~lLl~GAkML~~hCp~Cg~PLF~--KdG~v~CPvC~~~~~ 55 (131)
T COG1645 14 KKIAELLLQGAKMLAKHCPKCGTPLFR--KDGEVFCPVCGYREV 55 (131)
T ss_pred HHHHHHHHhhhHHHHhhCcccCCccee--eCCeEECCCCCceEE
Confidence 44444443333 24689999999999 667668999997654
No 83
>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=80.68 E-value=1.7 Score=27.59 Aligned_cols=10 Identities=40% Similarity=0.946 Sum_probs=8.1
Q ss_pred cccCCCCcee
Q 044880 36 YFCEFCGKYA 45 (91)
Q Consensus 36 y~CpfCGk~~ 45 (91)
|.||.||...
T Consensus 1 y~C~KCg~~~ 10 (64)
T PF09855_consen 1 YKCPKCGNEE 10 (64)
T ss_pred CCCCCCCCcc
Confidence 7899999764
No 84
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=80.56 E-value=0.29 Score=29.54 Aligned_cols=32 Identities=41% Similarity=0.632 Sum_probs=23.0
Q ss_pred ccCCCCcee--eEE--eeeeeeeeCCCCceEeccccc
Q 044880 37 FCEFCGKYA--VKR--KAVGIWGCKDCGKVKAGGAYT 69 (91)
Q Consensus 37 ~CpfCGk~~--VkR--~a~GIW~C~~Cg~~~AGGAy~ 69 (91)
.|+.||+.. +.| ..-| |.|+.|-+++.++-..
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl~~~~~~ 36 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKLSGFFSD 36 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHhcCcccc
Confidence 499999874 332 4567 9999999888555433
No 85
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=80.52 E-value=1.8 Score=24.34 Aligned_cols=27 Identities=33% Similarity=0.731 Sum_probs=15.2
Q ss_pred ccCCCCceeeEEeeee----eeeeCCCCceE
Q 044880 37 FCEFCGKYAVKRKAVG----IWGCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~G----IW~C~~Cg~~~ 63 (91)
.||.||.....++..| =+.|..||...
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEEE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCEE
Confidence 5999999876665433 37899998753
No 86
>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=80.18 E-value=2 Score=23.07 Aligned_cols=26 Identities=27% Similarity=0.567 Sum_probs=14.5
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
.||.||...+.-.+--.=.|..|+..
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred ccCcCCccccCCCCcCEeECCCCcCE
Confidence 69999998766444333479999865
No 87
>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=79.62 E-value=1.4 Score=24.39 Aligned_cols=15 Identities=33% Similarity=1.055 Sum_probs=12.7
Q ss_pred eeeeCCCCceEeccc
Q 044880 53 IWGCKDCGKVKAGGA 67 (91)
Q Consensus 53 IW~C~~Cg~~~AGGA 67 (91)
+|.|..||+++.|..
T Consensus 2 ~~~C~~CG~i~~g~~ 16 (34)
T cd00729 2 VWVCPVCGYIHEGEE 16 (34)
T ss_pred eEECCCCCCEeECCc
Confidence 599999999988753
No 88
>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=78.99 E-value=1.3 Score=23.36 Aligned_cols=10 Identities=30% Similarity=0.830 Sum_probs=5.5
Q ss_pred hcccccCCCC
Q 044880 33 HSKYFCEFCG 42 (91)
Q Consensus 33 ~~ky~CpfCG 42 (91)
-..|.||-||
T Consensus 14 ~v~f~CPnCG 23 (24)
T PF07754_consen 14 AVPFPCPNCG 23 (24)
T ss_pred CceEeCCCCC
Confidence 4455555555
No 89
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=78.99 E-value=1.4 Score=32.72 Aligned_cols=35 Identities=23% Similarity=0.521 Sum_probs=16.8
Q ss_pred hhHHHHHHHHHhhcccccCCCCceeeEEeeeeeeeeCCCC
Q 044880 21 LRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 21 lRK~v~kie~~q~~ky~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
+++..+.++..+ -|.||.||-+-.. --.|.|+.||
T Consensus 122 ~~~~Le~~~~~~--~~vC~vCGy~~~g---e~P~~CPiCg 156 (166)
T COG1592 122 FRGLLERLEEGK--VWVCPVCGYTHEG---EAPEVCPICG 156 (166)
T ss_pred HHHHHHhhhcCC--EEEcCCCCCcccC---CCCCcCCCCC
Confidence 444445544444 4555555544322 2335555555
No 90
>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=78.77 E-value=0.98 Score=32.54 Aligned_cols=27 Identities=19% Similarity=0.236 Sum_probs=20.3
Q ss_pred cccccCCCCcee--eEEeeeeeeeeCCCCceE
Q 044880 34 SKYFCEFCGKYA--VKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 34 ~ky~CpfCGk~~--VkR~a~GIW~C~~Cg~~~ 63 (91)
.|+.||.||+.- +.|.. | .|.+||..|
T Consensus 8 tKr~Cp~cg~kFYDLnk~p--~-vcP~cg~~~ 36 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRP--A-VSPYTGEQF 36 (129)
T ss_pred ccccCCCcCccccccCCCC--c-cCCCcCCcc
Confidence 578999999863 65533 2 799998875
No 91
>PHA00732 hypothetical protein
Probab=78.31 E-value=1.2 Score=28.95 Aligned_cols=10 Identities=40% Similarity=0.448 Sum_probs=5.1
Q ss_pred HHHHHHHHHH
Q 044880 77 TVRSTIRRLR 86 (91)
Q Consensus 77 t~~~~i~rl~ 86 (91)
.|+-+|+|--
T Consensus 67 ~~~~~~~~~~ 76 (79)
T PHA00732 67 HVRLAIKRKL 76 (79)
T ss_pred HHHHHHHHHh
Confidence 4555555543
No 92
>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=78.08 E-value=2.5 Score=31.76 Aligned_cols=21 Identities=24% Similarity=0.670 Sum_probs=18.6
Q ss_pred eeeeeeCCCCceEeccccccc
Q 044880 51 VGIWGCKDCGKVKAGGAYTLN 71 (91)
Q Consensus 51 ~GIW~C~~Cg~~~AGGAy~~~ 71 (91)
.-|=.|+.||..+-+|.|...
T Consensus 33 i~v~~C~~Cg~~~~~~~W~~~ 53 (236)
T PF04981_consen 33 IEVTICPKCGRYRIGGRWVDP 53 (236)
T ss_pred cCceECCCCCCEECCCEeeec
Confidence 466789999999999999987
No 93
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=78.04 E-value=1.5 Score=28.44 Aligned_cols=26 Identities=35% Similarity=0.767 Sum_probs=20.6
Q ss_pred cccCCCCcee--------eEEeeeeeeeeC-CCCc
Q 044880 36 YFCEFCGKYA--------VKRKAVGIWGCK-DCGK 61 (91)
Q Consensus 36 y~CpfCGk~~--------VkR~a~GIW~C~-~Cg~ 61 (91)
++|.|||++. |+..+.=.|-|. +|.+
T Consensus 4 ~~CsFcG~~I~PGtG~m~Vr~Dg~v~~FcssKc~k 38 (66)
T COG2075 4 RVCSFCGKKIEPGTGIMYVRNDGKVLRFCSSKCEK 38 (66)
T ss_pred eEecCcCCccCCCceEEEEecCCeEEEEechhHHH
Confidence 5799999875 888888889986 4544
No 94
>PRK08173 DNA topoisomerase III; Validated
Probab=78.00 E-value=2.2 Score=38.21 Aligned_cols=26 Identities=19% Similarity=0.448 Sum_probs=19.4
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
-.||.||...+++ -+.|.|..|+.++
T Consensus 625 ~~CP~Cg~~~~~~--~~~~~Cs~C~f~~ 650 (862)
T PRK08173 625 TPCPNCGGVVKEN--YRRFACTKCDFSI 650 (862)
T ss_pred ccCCccccccccc--CceeEcCCCCccc
Confidence 3699999875432 3459999998775
No 95
>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=77.20 E-value=4.5 Score=26.48 Aligned_cols=34 Identities=24% Similarity=0.532 Sum_probs=25.1
Q ss_pred hcccccCCCCceeeE------Ee----eeeeeeeCCCCceEecc
Q 044880 33 HSKYFCEFCGKYAVK------RK----AVGIWGCKDCGKVKAGG 66 (91)
Q Consensus 33 ~~ky~CpfCGk~~Vk------R~----a~GIW~C~~Cg~~~AGG 66 (91)
.....||.||...+- |. .+=++.|.+|+++|..+
T Consensus 60 ~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~ 103 (104)
T TIGR01384 60 TTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREY 103 (104)
T ss_pred cccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence 345799999987632 21 45689999999998765
No 96
>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=76.86 E-value=1.6 Score=24.98 Aligned_cols=17 Identities=29% Similarity=0.548 Sum_probs=13.4
Q ss_pred hcccccCCCCceeeEEe
Q 044880 33 HSKYFCEFCGKYAVKRK 49 (91)
Q Consensus 33 ~~ky~CpfCGk~~VkR~ 49 (91)
...-.||.||.+.++|+
T Consensus 24 ~~~~~CP~Cg~~~~~r~ 40 (42)
T PF09723_consen 24 DDPVPCPECGSTEVRRV 40 (42)
T ss_pred CCCCcCCCCCCCceEEe
Confidence 45668999999888875
No 97
>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=76.72 E-value=2 Score=23.47 Aligned_cols=30 Identities=27% Similarity=0.418 Sum_probs=18.7
Q ss_pred ccccCCCCcee-eEE--e--eeeeeeeCCCCceEe
Q 044880 35 KYFCEFCGKYA-VKR--K--AVGIWGCKDCGKVKA 64 (91)
Q Consensus 35 ky~CpfCGk~~-VkR--~--a~GIW~C~~Cg~~~A 64 (91)
...||.|+..- +.- . ..+-=.|.+|+..|-
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 36799999853 221 1 112347999998874
No 98
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=76.33 E-value=2.3 Score=35.98 Aligned_cols=41 Identities=24% Similarity=0.601 Sum_probs=26.4
Q ss_pred hhHHHHHHHH--HhhcccccCCCCcee-------eEEeeeeeeeeCCCCc
Q 044880 21 LRKQIKKMEV--SQHSKYFCEFCGKYA-------VKRKAVGIWGCKDCGK 61 (91)
Q Consensus 21 lRK~v~kie~--~q~~ky~CpfCGk~~-------VkR~a~GIW~C~~Cg~ 61 (91)
+||+++.-|. +..+-|.||+|.++- +-=...|-.+|.-|+-
T Consensus 112 m~krled~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 112 MRKRLEDRLRDDTNVAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGG 161 (436)
T ss_pred HHHHHHHHhhhccccccccCCccccchhhhHHHHhhcccCceEEEecCCC
Confidence 3444444332 356789999999872 1112458899999973
No 99
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=76.19 E-value=4.2 Score=29.77 Aligned_cols=27 Identities=22% Similarity=0.418 Sum_probs=15.4
Q ss_pred ccccCCCCceeeE---------EeeeeeeeeCCCCc
Q 044880 35 KYFCEFCGKYAVK---------RKAVGIWGCKDCGK 61 (91)
Q Consensus 35 ky~CpfCGk~~Vk---------R~a~GIW~C~~Cg~ 61 (91)
.+.||.|+....- -.....|.|.+|+.
T Consensus 18 ~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~ 53 (188)
T PF08996_consen 18 KLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCST 53 (188)
T ss_dssp EEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--
T ss_pred EeECCCCCCCccccccccCCccccccCcCcCCCCCC
Confidence 4589999987521 23456899999988
No 100
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=76.10 E-value=2 Score=32.97 Aligned_cols=26 Identities=27% Similarity=0.611 Sum_probs=20.5
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
.||.||.....+.+.-.-.|.+|+..
T Consensus 101 fC~~CG~~~~~~~~~~~~~C~~c~~~ 126 (256)
T PRK00241 101 FCGYCGHPMHPSKTEWAMLCPHCRER 126 (256)
T ss_pred cccccCCCCeecCCceeEECCCCCCE
Confidence 89999998766665566789999854
No 101
>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=76.02 E-value=4 Score=23.13 Aligned_cols=27 Identities=30% Similarity=0.663 Sum_probs=19.4
Q ss_pred ccCCCCceeeEEeee--eeeeeCC---CCceE
Q 044880 37 FCEFCGKYAVKRKAV--GIWGCKD---CGKVK 63 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~--GIW~C~~---Cg~~~ 63 (91)
.||.||.+.+.|.+- =.|-|.. |..+.
T Consensus 3 ~CP~Cg~~lv~r~~k~g~F~~Cs~yP~C~~~~ 34 (39)
T PF01396_consen 3 KCPKCGGPLVLRRGKKGKFLGCSNYPECKYTE 34 (39)
T ss_pred CCCCCCceeEEEECCCCCEEECCCCCCcCCeE
Confidence 699999888777743 3677876 76553
No 102
>COG4640 Predicted membrane protein [Function unknown]
Probab=75.30 E-value=1.2 Score=37.75 Aligned_cols=31 Identities=26% Similarity=0.554 Sum_probs=23.6
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceEeccccccc
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLN 71 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGGAy~~~ 71 (91)
.||-||+.... +--+|..||..|.++-=..+
T Consensus 3 fC~kcG~qk~E----d~~qC~qCG~~~t~~~sqan 33 (465)
T COG4640 3 FCPKCGSQKAE----DDVQCTQCGHKFTSRQSQAN 33 (465)
T ss_pred ccccccccccc----ccccccccCCcCCchhhhhh
Confidence 69999987654 33569999999999865443
No 103
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=74.65 E-value=2.6 Score=30.90 Aligned_cols=33 Identities=21% Similarity=0.471 Sum_probs=21.8
Q ss_pred cCCCCceeeEEe------------eeeeeeeCCCCce----Eecccccc
Q 044880 38 CEFCGKYAVKRK------------AVGIWGCKDCGKV----KAGGAYTL 70 (91)
Q Consensus 38 CpfCGk~~VkR~------------a~GIW~C~~Cg~~----~AGGAy~~ 70 (91)
||.||.+.++.. =.=-+.|.+||+. ..||+..|
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ev~~~~~~~p 49 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYRSTDVYQLEEKEP 49 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCchhheeEcCCcCC
Confidence 999998754442 1223789999964 45666655
No 104
>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=73.76 E-value=4.6 Score=29.26 Aligned_cols=35 Identities=29% Similarity=0.665 Sum_probs=19.8
Q ss_pred ccCCCCceeeEEe-ee----------eeeeeCCCCce----Eeccccccc
Q 044880 37 FCEFCGKYAVKRK-AV----------GIWGCKDCGKV----KAGGAYTLN 71 (91)
Q Consensus 37 ~CpfCGk~~VkR~-a~----------GIW~C~~Cg~~----~AGGAy~~~ 71 (91)
.||.||+..+-|. -+ =-+.|.+||++ ..||+..|.
T Consensus 3 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ev~~~~~~~~~ 52 (161)
T PF03367_consen 3 LCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNNEVKSGGQIQPK 52 (161)
T ss_dssp E-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEEEEEEECSS-SS
T ss_pred cCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEeeeEEECccCCCC
Confidence 6999998864333 22 33899999965 457776664
No 105
>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=73.68 E-value=3.2 Score=25.10 Aligned_cols=28 Identities=21% Similarity=0.428 Sum_probs=17.9
Q ss_pred cccccC--CCCcee-eEEeeeeeeeeCCCCce
Q 044880 34 SKYFCE--FCGKYA-VKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 34 ~ky~Cp--fCGk~~-VkR~a~GIW~C~~Cg~~ 62 (91)
.+-.|| .||.-. |- .-..=|.|.+|+.|
T Consensus 17 ~rk~CP~~~CG~GvFMA-~H~dR~~CGKCg~T 47 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMA-EHKDRHYCGKCGYT 47 (47)
T ss_dssp SSEE-TSTTTTSSSEEE-E-SSEEEETTTSS-
T ss_pred hhhcCCCcccCCceEee-ecCCCccCCCcccC
Confidence 455799 999854 33 22356999999975
No 106
>PF04071 zf-like: Cysteine-rich small domain; InterPro: IPR007212 This is a probable metal-binding domain. It is found in a probable precorrin-3B C17-methyltransferase from Methanobacterium thermoautotrophicum, that catalyses the methylation of C-17 in precorrin-3B to form precorrin-4.
Probab=73.67 E-value=7 Score=26.21 Aligned_cols=12 Identities=42% Similarity=1.337 Sum_probs=9.6
Q ss_pred eeee--eeeeCCCC
Q 044880 49 KAVG--IWGCKDCG 60 (91)
Q Consensus 49 ~a~G--IW~C~~Cg 60 (91)
.+.| ||.|..|.
T Consensus 45 ~~~G~~vw~C~~C~ 58 (86)
T PF04071_consen 45 TKNGSKVWDCSDCT 58 (86)
T ss_pred cCCCCeeeECccCC
Confidence 3556 99999995
No 107
>PRK00420 hypothetical protein; Validated
Probab=71.76 E-value=6.5 Score=27.44 Aligned_cols=30 Identities=27% Similarity=0.329 Sum_probs=21.9
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCceEe
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~A 64 (91)
....||.||-+.++ .-.|-=.|..||..+-
T Consensus 22 l~~~CP~Cg~pLf~-lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 22 LSKHCPVCGLPLFE-LKDGEVVCPVHGKVYI 51 (112)
T ss_pred ccCCCCCCCCccee-cCCCceECCCCCCeee
Confidence 34689999988877 1335567999998654
No 108
>PHA00616 hypothetical protein
Probab=71.62 E-value=1.3 Score=26.38 Aligned_cols=10 Identities=40% Similarity=0.853 Sum_probs=7.7
Q ss_pred ccccCCCCce
Q 044880 35 KYFCEFCGKY 44 (91)
Q Consensus 35 ky~CpfCGk~ 44 (91)
+|.||.||+.
T Consensus 1 pYqC~~CG~~ 10 (44)
T PHA00616 1 MYQCLRCGGI 10 (44)
T ss_pred CCccchhhHH
Confidence 4788888875
No 109
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=71.39 E-value=1.8 Score=37.22 Aligned_cols=27 Identities=33% Similarity=0.685 Sum_probs=20.7
Q ss_pred ccCC--CCceeeEEeeeeeeeeCCCCceEe
Q 044880 37 FCEF--CGKYAVKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 37 ~Cpf--CGk~~VkR~a~GIW~C~~Cg~~~A 64 (91)
-||. |.|..+ -...|.|.|.+|+..+.
T Consensus 476 ACp~~~CnKKV~-~~~~g~~~CekC~~~~~ 504 (608)
T TIGR00617 476 ACPSEDCNKKVV-DQGDGTYRCEKCNKNFA 504 (608)
T ss_pred cCChhhCCCccc-cCCCCCEECCCCCCCCC
Confidence 6876 988654 35569999999997654
No 110
>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=71.00 E-value=2.6 Score=22.95 Aligned_cols=14 Identities=29% Similarity=0.695 Sum_probs=11.1
Q ss_pred eeeeCCCCceEecc
Q 044880 53 IWGCKDCGKVKAGG 66 (91)
Q Consensus 53 IW~C~~Cg~~~AGG 66 (91)
+|.|..||+++.+.
T Consensus 1 ~~~C~~CGy~y~~~ 14 (33)
T cd00350 1 KYVCPVCGYIYDGE 14 (33)
T ss_pred CEECCCCCCEECCC
Confidence 58899999887664
No 111
>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=70.84 E-value=2.9 Score=20.11 Aligned_cols=11 Identities=36% Similarity=0.854 Sum_probs=7.4
Q ss_pred eeeCCCCceEe
Q 044880 54 WGCKDCGKVKA 64 (91)
Q Consensus 54 W~C~~Cg~~~A 64 (91)
|.|..|++.|.
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 46777777764
No 112
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=70.67 E-value=1.5 Score=22.80 Aligned_cols=23 Identities=30% Similarity=0.730 Sum_probs=15.0
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
..||.||.. + ..+-=-|..||..
T Consensus 3 ~~Cp~Cg~~-~---~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAE-I---DPDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCc-C---CcccccChhhCCC
Confidence 479999984 2 2233468888864
No 113
>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=70.09 E-value=3.7 Score=23.74 Aligned_cols=27 Identities=33% Similarity=0.750 Sum_probs=14.0
Q ss_pred ccccCCCCcee-eEEe-e-eeeeeeCCCCc
Q 044880 35 KYFCEFCGKYA-VKRK-A-VGIWGCKDCGK 61 (91)
Q Consensus 35 ky~CpfCGk~~-VkR~-a-~GIW~C~~Cg~ 61 (91)
.|.|+.||..- +.+. + .....|..||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 46777777632 2211 1 13456777764
No 114
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=69.91 E-value=7.2 Score=27.73 Aligned_cols=40 Identities=18% Similarity=0.415 Sum_probs=25.1
Q ss_pred hHHHHHHHHHhhccc-ccCCCCcee--eEEeeeeee--eeCCCCce
Q 044880 22 RKQIKKMEVSQHSKY-FCEFCGKYA--VKRKAVGIW--GCKDCGKV 62 (91)
Q Consensus 22 RK~v~kie~~q~~ky-~CpfCGk~~--VkR~a~GIW--~C~~Cg~~ 62 (91)
-+.+.++-..=-..| .||.|+.+. +.+. ..+| +|..||..
T Consensus 83 ~~~i~~~L~~yI~~yVlC~~C~sPdT~l~k~-~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 83 HFLLNERIEDYVRKYVICRECNRPDTRIIKE-GRVSLLKCEACGAK 127 (133)
T ss_pred HHHHHHHHHHHHhheEECCCCCCCCcEEEEe-CCeEEEecccCCCC
Confidence 344444444444566 799999864 4433 3455 89999854
No 115
>PF12773 DZR: Double zinc ribbon
Probab=69.90 E-value=1.4 Score=25.32 Aligned_cols=30 Identities=23% Similarity=0.486 Sum_probs=19.1
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCceEecc
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGKVKAGG 66 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGG 66 (91)
-.||.||.... ......+.|..|+..+..+
T Consensus 13 ~fC~~CG~~l~-~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 13 KFCPHCGTPLP-PPDQSKKICPNCGAENPPN 42 (50)
T ss_pred cCChhhcCChh-hccCCCCCCcCCcCCCcCC
Confidence 35888887765 2333456788888765443
No 116
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=69.88 E-value=3.8 Score=22.86 Aligned_cols=27 Identities=22% Similarity=0.411 Sum_probs=17.6
Q ss_pred cccCCCCcee------eEEeeeeeeeeCCCCceE
Q 044880 36 YFCEFCGKYA------VKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 36 y~CpfCGk~~------VkR~a~GIW~C~~Cg~~~ 63 (91)
-.||-|+..- +. .....=+|.+|+.+|
T Consensus 3 i~Cp~C~~~y~i~d~~ip-~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIP-PKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCC-CCCcEEECCCCCCEe
Confidence 3699998753 22 222334899999887
No 117
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=69.82 E-value=3 Score=30.94 Aligned_cols=49 Identities=18% Similarity=0.536 Sum_probs=32.5
Q ss_pred CccccCchhhHHHHHHHHHhhcccccCCCCce--eeEEeeee----eeeeCCCCceE
Q 044880 13 YGTRYGASLRKQIKKMEVSQHSKYFCEFCGKY--AVKRKAVG----IWGCKDCGKVK 63 (91)
Q Consensus 13 ~G~RYG~slRK~v~kie~~q~~ky~CpfCGk~--~VkR~a~G----IW~C~~Cg~~~ 63 (91)
||.||-.++-.-++.+-- ..-.|.|. |+.. +++|...- +..|.+|+-+.
T Consensus 96 ~~l~~~~~h~~~~~~v~~-~~~~Y~C~-C~q~~l~~RRhn~~~~g~~YrC~~C~gkL 150 (156)
T COG3091 96 LGLRFCRTHQFEVQSVRR-TTYPYRCQ-CQQHYLRIRRHNTVRRGEVYRCGKCGGKL 150 (156)
T ss_pred CCCCCCccchHHHhhccc-cceeEEee-cCCccchhhhcccccccceEEeccCCceE
Confidence 677777766655554332 24468999 9986 35555444 59999998653
No 118
>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=69.79 E-value=3.4 Score=19.25 Aligned_cols=11 Identities=36% Similarity=0.791 Sum_probs=5.6
Q ss_pred eeeCCCCceEe
Q 044880 54 WGCKDCGKVKA 64 (91)
Q Consensus 54 W~C~~Cg~~~A 64 (91)
|.|..|+++|.
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 56677766654
No 119
>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.
Probab=68.76 E-value=1.8 Score=35.79 Aligned_cols=25 Identities=36% Similarity=1.040 Sum_probs=18.4
Q ss_pred cccCCCCcee--eEEee--eeeeeeCCCC
Q 044880 36 YFCEFCGKYA--VKRKA--VGIWGCKDCG 60 (91)
Q Consensus 36 y~CpfCGk~~--VkR~a--~GIW~C~~Cg 60 (91)
..|+|||+.. |.+.- .|.+.|..|-
T Consensus 8 ~~c~fc~~~~~~~~~~~~~~~~~ic~~c~ 36 (413)
T TIGR00382 8 LYCSFCGKSQDEVRKLIAGPGVYICDECI 36 (413)
T ss_pred eecCCCCCChhhcccccCCCCCcCCCchH
Confidence 3799999964 55543 3478999994
No 120
>PRK04023 DNA polymerase II large subunit; Validated
Probab=68.65 E-value=2.3 Score=39.51 Aligned_cols=36 Identities=14% Similarity=0.207 Sum_probs=18.7
Q ss_pred eeeeeeCCCCceEe------------cccccccccHHHHHHHHHHHHHh
Q 044880 51 VGIWGCKDCGKVKA------------GGAYTLNTASAVTVRSTIRRLRE 87 (91)
Q Consensus 51 ~GIW~C~~Cg~~~A------------GGAy~~~T~~~~t~~~~i~rl~e 87 (91)
..||.|..|+.... .+.+. .-+....+.+|+.+|.+
T Consensus 649 e~i~fCP~CG~~~~~y~CPKCG~El~~~s~~-~i~l~~~~~~A~~~lg~ 696 (1121)
T PRK04023 649 EPVYRCPRCGIEVEEDECEKCGREPTPYSKR-KIDLKELYDRALENLGE 696 (1121)
T ss_pred CcceeCccccCcCCCCcCCCCCCCCCccceE-EecHHHHHHHHHHHhCC
Confidence 35677777765543 12111 22345566666666654
No 121
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=68.35 E-value=3.7 Score=28.85 Aligned_cols=30 Identities=13% Similarity=0.091 Sum_probs=23.2
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceEeccc
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVKAGGA 67 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGGA 67 (91)
.||.|+..-+.- .-.+|.|..|+.-|+-.+
T Consensus 4 ~CP~C~seytY~-dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 4 PCPKCNSEYTYH-DGTQLICPSCLYEWNENE 33 (109)
T ss_pred cCCcCCCcceEe-cCCeeECccccccccccc
Confidence 599999987773 345899999988776543
No 122
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=67.61 E-value=2.4 Score=33.95 Aligned_cols=40 Identities=35% Similarity=0.671 Sum_probs=27.2
Q ss_pred HHHHHHhhc-ccccCCCCceee--------EEeeee--eeeeCCCCceEec
Q 044880 26 KKMEVSQHS-KYFCEFCGKYAV--------KRKAVG--IWGCKDCGKVKAG 65 (91)
Q Consensus 26 ~kie~~q~~-ky~CpfCGk~~V--------kR~a~G--IW~C~~Cg~~~AG 65 (91)
.++.|.-|. .+.|++|||.-- -|.-+| =..|..|++-||-
T Consensus 177 LkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFAD 227 (279)
T KOG2462|consen 177 LKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFAD 227 (279)
T ss_pred HhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhcc
Confidence 345566666 888999998642 344444 4678888888874
No 123
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=67.07 E-value=6 Score=28.82 Aligned_cols=23 Identities=22% Similarity=0.465 Sum_probs=16.7
Q ss_pred HHHHHhhcc-cccCCCCceeeEEe
Q 044880 27 KMEVSQHSK-YFCEFCGKYAVKRK 49 (91)
Q Consensus 27 kie~~q~~k-y~CpfCGk~~VkR~ 49 (91)
..|.++... -.||+||...|.|.
T Consensus 23 ~fd~Q~~~glv~CP~Cgs~~V~K~ 46 (148)
T PF06676_consen 23 AFDRQQARGLVSCPVCGSTEVSKA 46 (148)
T ss_pred HHHHHHHcCCccCCCCCCCeEeee
Confidence 344444444 48999999999887
No 124
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=66.94 E-value=3.2 Score=26.29 Aligned_cols=32 Identities=25% Similarity=0.489 Sum_probs=20.1
Q ss_pred HhhcccccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 31 SQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 31 ~q~~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
.+..+..|..||....-+.-.-...|..||+.
T Consensus 3 ~~~~~~~CtSCg~~i~~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 3 EMMEPPKCTSCGIEIAPREKAVKFLCPNCGEV 34 (59)
T ss_pred ccccCccccCCCCcccCCCccCEeeCCCCCCe
Confidence 34567789999998876662233444444443
No 125
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=66.86 E-value=3.6 Score=25.26 Aligned_cols=12 Identities=42% Similarity=0.838 Sum_probs=9.7
Q ss_pred c-ccCCCCceeeE
Q 044880 36 Y-FCEFCGKYAVK 47 (91)
Q Consensus 36 y-~CpfCGk~~Vk 47 (91)
| .||.||.+.|-
T Consensus 13 Y~~Cp~CGN~~vG 25 (49)
T PF12677_consen 13 YCKCPKCGNDKVG 25 (49)
T ss_pred hccCcccCCcEee
Confidence 5 89999998753
No 126
>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=66.67 E-value=11 Score=24.51 Aligned_cols=51 Identities=24% Similarity=0.522 Sum_probs=31.1
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCceEecccccc--cccHHHHHHHHHHHHHhh
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTL--NTASAVTVRSTIRRLREQ 88 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGGAy~~--~T~~~~t~~~~i~rl~e~ 88 (91)
|-| -||...+-+..+--=+| -||+++-=.--.+ ....+.-+...+++|.+.
T Consensus 4 frC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~~rIl~~~~~~~eA~eiVrklQ~e 56 (68)
T PF09082_consen 4 FRC-DCGRYLYAKEGAKTKKC-VCGKTLKVKERRILARAENAEEASEIVRKLQEE 56 (68)
T ss_dssp EEE-TTS--EEEETT-SEEEE-TTTEEEE--SSS-BS--SSHHHHHHHHHHHSS-
T ss_pred EEe-cCCCEEEecCCcceeEe-cCCCeeeeeeEEEEEecCCHHHHHHHHHHHHHH
Confidence 468 69999988888888899 9998876543332 445566666677777654
No 127
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=66.19 E-value=8.7 Score=27.46 Aligned_cols=40 Identities=20% Similarity=0.500 Sum_probs=24.3
Q ss_pred HHHHHHHHHhhccc-ccCCCCcee--eEEe-eeeeeeeCCCCce
Q 044880 23 KQIKKMEVSQHSKY-FCEFCGKYA--VKRK-AVGIWGCKDCGKV 62 (91)
Q Consensus 23 K~v~kie~~q~~ky-~CpfCGk~~--VkR~-a~GIW~C~~Cg~~ 62 (91)
+.+..+-..=-..| .||.|+.+. +.+. .+=+=+|..||..
T Consensus 89 ~~i~~~L~~yI~~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 89 RVINEKIDRYVKEYVICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred HHHHHHHHHHHHhcEECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 44444444445556 899999864 3332 2234489999753
No 128
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=65.13 E-value=7.9 Score=34.32 Aligned_cols=24 Identities=29% Similarity=0.754 Sum_probs=18.5
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
.||.||.+ +.++. |=..|+.||+.
T Consensus 726 ~Cp~Cg~~-l~~~~-GC~~C~~CG~s 749 (752)
T PRK08665 726 ACPECGSI-LEHEE-GCVVCHSCGYS 749 (752)
T ss_pred CCCCCCcc-cEECC-CCCcCCCCCCC
Confidence 49999954 55444 88899999974
No 129
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=64.18 E-value=4.2 Score=24.77 Aligned_cols=29 Identities=31% Similarity=0.718 Sum_probs=19.3
Q ss_pred cccccCCCCceee-EEeeeeeeeeCCCCceE
Q 044880 34 SKYFCEFCGKYAV-KRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 34 ~ky~CpfCGk~~V-kR~a~GIW~C~~Cg~~~ 63 (91)
..|.|..||+..- .-...|| .|..||..+
T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~i-rCp~Cg~rI 34 (49)
T COG1996 5 MEYKCARCGREVELDQETRGI-RCPYCGSRI 34 (49)
T ss_pred EEEEhhhcCCeeehhhccCce-eCCCCCcEE
Confidence 4688888888752 2123455 888888765
No 130
>PHA00733 hypothetical protein
Probab=64.16 E-value=1.9 Score=30.05 Aligned_cols=36 Identities=25% Similarity=0.312 Sum_probs=23.5
Q ss_pred HHHhhcccccCCCCceeeE--------EeeeeeeeeCCCCceEe
Q 044880 29 EVSQHSKYFCEFCGKYAVK--------RKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 29 e~~q~~ky~CpfCGk~~Vk--------R~a~GIW~C~~Cg~~~A 64 (91)
......+|.|+.||+.--. +....-..|..|++.|.
T Consensus 67 ~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~ 110 (128)
T PHA00733 67 TSKAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFR 110 (128)
T ss_pred ccCCCCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccC
Confidence 3344668999999986311 11134579999998774
No 131
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=64.07 E-value=5.7 Score=22.13 Aligned_cols=28 Identities=25% Similarity=0.403 Sum_probs=18.7
Q ss_pred ccCCCCcee-eE----EeeeeeeeeCCCCceEe
Q 044880 37 FCEFCGKYA-VK----RKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 37 ~CpfCGk~~-Vk----R~a~GIW~C~~Cg~~~A 64 (91)
+||.|+..- |. +.+.+.=.|.+|+.+|.
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 699999652 21 12344558999998874
No 132
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=64.01 E-value=4.9 Score=28.36 Aligned_cols=14 Identities=36% Similarity=1.137 Sum_probs=10.6
Q ss_pred EEeeee--eeeeCCCC
Q 044880 47 KRKAVG--IWGCKDCG 60 (91)
Q Consensus 47 kR~a~G--IW~C~~Cg 60 (91)
.+...| +|.|..|-
T Consensus 54 i~~~~G~~VwSC~dC~ 69 (112)
T COG2158 54 ISDSNGRKVWSCSDCH 69 (112)
T ss_pred eEcCCCCEEeeccccc
Confidence 444557 99999994
No 133
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=63.54 E-value=9.4 Score=28.02 Aligned_cols=54 Identities=19% Similarity=0.355 Sum_probs=33.2
Q ss_pred hhcccccCCCCcee-eEEeeeeeeeeCCCCceEecccccccccHHHHHHHHHHHHHhh
Q 044880 32 QHSKYFCEFCGKYA-VKRKAVGIWGCKDCGKVKAGGAYTLNTASAVTVRSTIRRLREQ 88 (91)
Q Consensus 32 q~~ky~CpfCGk~~-VkR~a~GIW~C~~Cg~~~AGGAy~~~T~~~~t~~~~i~rl~e~ 88 (91)
.+.-|.||.|+..- ..=.-..-..|..||...- +.=++......+.-|..|.+.
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~---~~dn~~~~~~l~~~I~~l~~~ 168 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLE---EYDNSELIKELKEQIKELEEE 168 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhhcCCcCCCCCCCCe---ecccHHHHHHHHHHHHHHHHH
Confidence 34678999999642 1101113579999987653 234566666666667777654
No 134
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=60.99 E-value=11 Score=30.06 Aligned_cols=33 Identities=18% Similarity=0.450 Sum_probs=23.4
Q ss_pred HhhcccccCCCCceee-E-----Ee----eeeeeeeCCCCceE
Q 044880 31 SQHSKYFCEFCGKYAV-K-----RK----AVGIWGCKDCGKVK 63 (91)
Q Consensus 31 ~q~~ky~CpfCGk~~V-k-----R~----a~GIW~C~~Cg~~~ 63 (91)
.....+.||.||...+ - |. -+-++.|..||..|
T Consensus 254 ~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w 296 (299)
T TIGR01385 254 AVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRW 296 (299)
T ss_pred CCcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCee
Confidence 3445699999998753 1 21 35688999999765
No 135
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=60.91 E-value=8.7 Score=28.89 Aligned_cols=34 Identities=26% Similarity=0.713 Sum_probs=24.8
Q ss_pred hHHHHHHHHHhhcccccCCCCceeeEEeeeeeeeeCCCC
Q 044880 22 RKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 22 RK~v~kie~~q~~ky~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
++++.+ .+.....|.|+.||-..-... |.|..|+
T Consensus 342 ~~~~~~-~~~~~p~~~c~~cg~~~~~~~----~~c~~c~ 375 (389)
T PRK11788 342 RDLVGE-QLKRKPRYRCRNCGFTARTLY----WHCPSCK 375 (389)
T ss_pred HHHHHH-HHhCCCCEECCCCCCCCccce----eECcCCC
Confidence 444433 346666799999998887755 8999996
No 136
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=60.51 E-value=1.8 Score=34.74 Aligned_cols=36 Identities=33% Similarity=0.619 Sum_probs=25.7
Q ss_pred hcccccCCCCceeeEEe----------eeeeeeeCCCCceEecccc
Q 044880 33 HSKYFCEFCGKYAVKRK----------AVGIWGCKDCGKVKAGGAY 68 (91)
Q Consensus 33 ~~ky~CpfCGk~~VkR~----------a~GIW~C~~Cg~~~AGGAy 68 (91)
.++|.||-|+|---.|- .+--.+|..|+++||==.|
T Consensus 213 EKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~Sy 258 (279)
T KOG2462|consen 213 EKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSY 258 (279)
T ss_pred CCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHH
Confidence 57899999998643332 3445789999999874333
No 137
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=60.46 E-value=11 Score=24.38 Aligned_cols=28 Identities=32% Similarity=0.519 Sum_probs=20.7
Q ss_pred ccCCCCcee-eEEeeeeeeeeCCCCceEe
Q 044880 37 FCEFCGKYA-VKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 37 ~CpfCGk~~-VkR~a~GIW~C~~Cg~~~A 64 (91)
.||-||... |-=.+.-.=.|-.||.++|
T Consensus 21 kCpdC~N~q~vFshast~V~C~~CG~~l~ 49 (67)
T COG2051 21 KCPDCGNEQVVFSHASTVVTCLICGTTLA 49 (67)
T ss_pred ECCCCCCEEEEeccCceEEEecccccEEE
Confidence 899999886 3333444449999999886
No 138
>KOG1873 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=60.27 E-value=5.5 Score=36.21 Aligned_cols=38 Identities=21% Similarity=0.405 Sum_probs=30.0
Q ss_pred cccccCCCCceeeEEe---------eeeeeeeCCCCceEeccccccc
Q 044880 34 SKYFCEFCGKYAVKRK---------AVGIWGCKDCGKVKAGGAYTLN 71 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~---------a~GIW~C~~Cg~~~AGGAy~~~ 71 (91)
..|.|..|-.....+. ..-||-|=+||+.+-|+-=.++
T Consensus 65 ~~~~C~eC~e~~~~k~g~s~~~~~~~~~iWLCLkCG~q~CG~~~~~~ 111 (877)
T KOG1873|consen 65 LWIKCSECNEEVKVKDGGSSDQFEFDNAIWLCLKCGYQGCGRNSESQ 111 (877)
T ss_pred HHHHHHHhhhcceeccCCCccccccccceeeecccCCeeeCCCcccc
Confidence 6788999998754434 5689999999999999855543
No 139
>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=60.16 E-value=5.4 Score=28.60 Aligned_cols=27 Identities=15% Similarity=0.343 Sum_probs=19.3
Q ss_pred hcccccCCCCcee-----eEEeeeeeeeeCCCCceE
Q 044880 33 HSKYFCEFCGKYA-----VKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 33 ~~ky~CpfCGk~~-----VkR~a~GIW~C~~Cg~~~ 63 (91)
..-|.||.|+..- +. --..|..||...
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~----~~F~Cp~Cg~~L 138 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME----LNFTCPRCGAML 138 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH----cCCcCCCCCCEe
Confidence 4668999999532 22 247999999774
No 140
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=60.10 E-value=11 Score=26.49 Aligned_cols=40 Identities=28% Similarity=0.562 Sum_probs=24.8
Q ss_pred hHHHHHHHHHhhccc-ccCCCCcee--eEEeeeeee--eeCCCCce
Q 044880 22 RKQIKKMEVSQHSKY-FCEFCGKYA--VKRKAVGIW--GCKDCGKV 62 (91)
Q Consensus 22 RK~v~kie~~q~~ky-~CpfCGk~~--VkR~a~GIW--~C~~Cg~~ 62 (91)
.+.+.++...=-..| .||.|+.+. +.+. .++| +|..||..
T Consensus 79 ~~~i~~~L~~fI~~yVlC~~C~spdT~l~k~-~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 79 SKQIQDLLDKFIKEYVLCPECGSPDTELIKE-GRLIFLKCKACGAS 123 (125)
T ss_dssp CCHHHHHHHHHHCHHSSCTSTSSSSEEEEEE-TTCCEEEETTTSCE
T ss_pred HHHHHHHHHHHHHHEEEcCCCCCCccEEEEc-CCEEEEEecccCCc
Confidence 344555544445566 799999864 3332 3333 79999864
No 141
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=59.52 E-value=13 Score=27.67 Aligned_cols=47 Identities=17% Similarity=0.391 Sum_probs=28.6
Q ss_pred hHHHHHHHHHhhccc-ccCCCCcee--eEEeeeeee--eeCCCCceEeccccc
Q 044880 22 RKQIKKMEVSQHSKY-FCEFCGKYA--VKRKAVGIW--GCKDCGKVKAGGAYT 69 (91)
Q Consensus 22 RK~v~kie~~q~~ky-~CpfCGk~~--VkR~a~GIW--~C~~Cg~~~AGGAy~ 69 (91)
.+.+..+...=-..| .||.|+.+. +.+. ..+| +|..||..-.=.+..
T Consensus 84 ~~~i~~~l~~yi~~yV~C~~C~~pdT~l~k~-~~~~~l~C~aCGa~~~v~~~~ 135 (201)
T PRK12336 84 EEDIQAAIDAYVDEYVICSECGLPDTRLVKE-DRVLMLRCDACGAHRPVKKRK 135 (201)
T ss_pred HHHHHHHHHHHHHheEECCCCCCCCcEEEEc-CCeEEEEcccCCCCccccccc
Confidence 445555554445566 899999864 3332 3444 799998665444443
No 142
>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=59.47 E-value=3 Score=29.49 Aligned_cols=26 Identities=27% Similarity=0.586 Sum_probs=20.2
Q ss_pred cccccCCCCcee--eEEeeeeeeeeCCCCceE
Q 044880 34 SKYFCEFCGKYA--VKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 34 ~ky~CpfCGk~~--VkR~a~GIW~C~~Cg~~~ 63 (91)
....||.|||.. +.|+. .|-.|+...
T Consensus 68 v~V~CP~C~K~TKmLGr~D----~CM~C~~pL 95 (114)
T PF11023_consen 68 VQVECPNCGKQTKMLGRVD----ACMHCKEPL 95 (114)
T ss_pred eeeECCCCCChHhhhchhh----ccCcCCCcC
Confidence 445799999986 78775 699998643
No 143
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=59.10 E-value=3.1 Score=34.13 Aligned_cols=26 Identities=35% Similarity=1.049 Sum_probs=18.9
Q ss_pred cccccCCCCcee--eEEe--eeeeeeeCCC
Q 044880 34 SKYFCEFCGKYA--VKRK--AVGIWGCKDC 59 (91)
Q Consensus 34 ~ky~CpfCGk~~--VkR~--a~GIW~C~~C 59 (91)
....|+|||+.. |.+. +-+.+.|..|
T Consensus 8 ~~~~CSFCGr~~~ev~~li~g~~~~IC~~C 37 (412)
T PRK05342 8 KLLYCSFCGKSQHEVRKLIAGPGVYICDEC 37 (412)
T ss_pred CccccCCCCCChhhccccccCCCCcccchH
Confidence 344899999975 4442 3467899999
No 144
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=59.03 E-value=10 Score=36.58 Aligned_cols=48 Identities=19% Similarity=0.322 Sum_probs=34.4
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCceEecccccc-cccHHHHHHHHHHHHHh
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTL-NTASAVTVRSTIRRLRE 87 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGGAy~~-~T~~~~t~~~~i~rl~e 87 (91)
..+.||.||..... +.|..||..+--..|.- .-+......+|+.+|.+
T Consensus 673 ~~~~Cp~Cg~~~~~------~~Cp~CG~~~~~~~~~~~~i~~~~~~~~A~~~v~~ 721 (1627)
T PRK14715 673 AFFKCPKCGKVGLY------HVCPFCGTRVELKPYARREIPPKDYWYAALENLKI 721 (1627)
T ss_pred EeeeCCCCCCcccc------ccCcccCCcccCCCccceecCHHHHHHHHHHHhCC
Confidence 45689999999888 67999997754444443 34556677777777654
No 145
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.12 E-value=3.5 Score=34.18 Aligned_cols=29 Identities=34% Similarity=0.759 Sum_probs=22.4
Q ss_pred hhcccccCCCCcee----eEEeeeeeeeeCCCC
Q 044880 32 QHSKYFCEFCGKYA----VKRKAVGIWGCKDCG 60 (91)
Q Consensus 32 q~~ky~CpfCGk~~----VkR~a~GIW~C~~Cg 60 (91)
+...|.||.||+.. -.|.+-|-|-|.-|+
T Consensus 29 ~~~~~~cpvcg~k~RFr~dD~kGrGtw~c~y~~ 61 (366)
T COG4643 29 KPGGHPCPVCGGKDRFRFDDRKGRGTWFCNYCG 61 (366)
T ss_pred cCCCCCCCccCCccccccCCccCCccEEEEeec
Confidence 34456999999764 345688999999998
No 146
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=57.99 E-value=6.8 Score=27.83 Aligned_cols=30 Identities=23% Similarity=0.486 Sum_probs=22.6
Q ss_pred ccccCCCCceeeE------Ee----eeeeeeeCCCCceEe
Q 044880 35 KYFCEFCGKYAVK------RK----AVGIWGCKDCGKVKA 64 (91)
Q Consensus 35 ky~CpfCGk~~Vk------R~----a~GIW~C~~Cg~~~A 64 (91)
++.||.||.+.|- |. .+=-+.|.+|+++|.
T Consensus 74 ~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 74 KHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred hccCcccCCchhhhhhhhcccccCCceEEEEcCccceeee
Confidence 6899999987631 22 345689999999885
No 147
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=57.45 E-value=6.1 Score=22.12 Aligned_cols=14 Identities=36% Similarity=0.688 Sum_probs=10.7
Q ss_pred ccccCCCCceeeEE
Q 044880 35 KYFCEFCGKYAVKR 48 (91)
Q Consensus 35 ky~CpfCGk~~VkR 48 (91)
+..||.||...+.+
T Consensus 2 ~~~Cp~Cg~~~~~~ 15 (47)
T PF14690_consen 2 PPRCPHCGSPSVHR 15 (47)
T ss_pred CccCCCcCCCceEC
Confidence 56799999877554
No 148
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=57.43 E-value=4.7 Score=34.33 Aligned_cols=23 Identities=30% Similarity=0.832 Sum_probs=20.6
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCC
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
..|.|..||-.+.|+.+ +|..|+
T Consensus 6 t~f~C~~CG~~s~KW~G----kCp~Cg 28 (456)
T COG1066 6 TAFVCQECGYVSPKWLG----KCPACG 28 (456)
T ss_pred cEEEcccCCCCCccccc----cCCCCC
Confidence 56999999999999776 899997
No 149
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=57.43 E-value=13 Score=35.25 Aligned_cols=26 Identities=27% Similarity=0.765 Sum_probs=22.3
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
-.||.||...|.|.+ +-|+|..||-+
T Consensus 1191 ~~c~~cg~~~~vrng-tc~~c~~cg~t 1216 (1220)
T PRK07562 1191 EACSECGNFTLVRNG-TCLKCDTCGST 1216 (1220)
T ss_pred CcCCCcCCeEEEeCC-eeeeccccCCC
Confidence 369999999999887 57899999865
No 150
>PRK12495 hypothetical protein; Provisional
Probab=57.41 E-value=11 Score=29.46 Aligned_cols=30 Identities=20% Similarity=0.444 Sum_probs=24.6
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCceEec
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAG 65 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~AG 65 (91)
..+.|+.||.+... . -|.=.|-.|...++.
T Consensus 41 sa~hC~~CG~PIpa-~-pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 41 TNAHCDECGDPIFR-H-DGQEFCPTCQQPVTE 70 (226)
T ss_pred chhhcccccCcccC-C-CCeeECCCCCCcccc
Confidence 35699999999983 3 688889999988765
No 151
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=57.29 E-value=5.2 Score=26.23 Aligned_cols=29 Identities=28% Similarity=0.531 Sum_probs=13.7
Q ss_pred CCccccCchhhHHHHHHHHHhhcccccCCCCc
Q 044880 12 KYGTRYGASLRKQIKKMEVSQHSKYFCEFCGK 43 (91)
Q Consensus 12 k~G~RYG~slRK~v~kie~~q~~ky~CpfCGk 43 (91)
+...+||.+....-+-.| .+...||.|+.
T Consensus 2 ~~~~~Ygit~~~~~~l~~---~q~~~C~iC~~ 30 (81)
T PF02945_consen 2 RLKRRYGITPEEYEALLE---EQGGRCAICGK 30 (81)
T ss_dssp -----H-HHHHHHHCCHH---HTTTE-TTT-S
T ss_pred CcccccCCCHHHHHHHHH---HhCCcCcCCCC
Confidence 356789998876653233 33448999998
No 152
>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=57.05 E-value=7.8 Score=22.83 Aligned_cols=11 Identities=36% Similarity=0.845 Sum_probs=5.4
Q ss_pred ccccCCCCcee
Q 044880 35 KYFCEFCGKYA 45 (91)
Q Consensus 35 ky~CpfCGk~~ 45 (91)
.-.||.|+++-
T Consensus 20 ~~~CPlC~r~l 30 (54)
T PF04423_consen 20 KGCCPLCGRPL 30 (54)
T ss_dssp SEE-TTT--EE
T ss_pred CCcCCCCCCCC
Confidence 33899998763
No 153
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=57.01 E-value=6.3 Score=29.39 Aligned_cols=28 Identities=29% Similarity=0.585 Sum_probs=20.6
Q ss_pred ccCCCCcee--eE-------------EeeeeeeeeCCCCceEe
Q 044880 37 FCEFCGKYA--VK-------------RKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 37 ~CpfCGk~~--Vk-------------R~a~GIW~C~~Cg~~~A 64 (91)
-||.|+... |. +...--|.|.+||+.+=
T Consensus 99 RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW 141 (165)
T COG1656 99 RCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYW 141 (165)
T ss_pred cCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccccc
Confidence 699999875 22 33445899999998753
No 154
>PRK04860 hypothetical protein; Provisional
Probab=56.85 E-value=3.8 Score=29.83 Aligned_cols=30 Identities=23% Similarity=0.763 Sum_probs=21.1
Q ss_pred cccccCCCCceee--EEee-----eeeeeeCCCCceEe
Q 044880 34 SKYFCEFCGKYAV--KRKA-----VGIWGCKDCGKVKA 64 (91)
Q Consensus 34 ~ky~CpfCGk~~V--kR~a-----~GIW~C~~Cg~~~A 64 (91)
-+|.|+ |+...+ +|.. .....|+.|+..|.
T Consensus 118 ~~Y~C~-C~~~~~~~rrH~ri~~g~~~YrC~~C~~~l~ 154 (160)
T PRK04860 118 FPYRCK-CQEHQLTVRRHNRVVRGEAVYRCRRCGETLV 154 (160)
T ss_pred EEEEcC-CCCeeCHHHHHHHHhcCCccEECCCCCceeE
Confidence 469998 987543 3333 45689999987763
No 155
>PRK05978 hypothetical protein; Provisional
Probab=56.37 E-value=4.9 Score=29.23 Aligned_cols=39 Identities=23% Similarity=0.276 Sum_probs=24.8
Q ss_pred HhhcccccCCCCceeeEEe--eeeeeeeCCCCceE------ecccccc
Q 044880 31 SQHSKYFCEFCGKYAVKRK--AVGIWGCKDCGKVK------AGGAYTL 70 (91)
Q Consensus 31 ~q~~ky~CpfCGk~~VkR~--a~GIW~C~~Cg~~~------AGGAy~~ 70 (91)
..-.+-.||.||+-.+-+. .+- =+|..||..+ -|+||..
T Consensus 29 ~rGl~grCP~CG~G~LF~g~Lkv~-~~C~~CG~~~~~~~a~DgpAy~~ 75 (148)
T PRK05978 29 WRGFRGRCPACGEGKLFRAFLKPV-DHCAACGEDFTHHRADDLPAYLV 75 (148)
T ss_pred HHHHcCcCCCCCCCcccccccccC-CCccccCCccccCCccccCcchh
Confidence 3455678999999876321 011 1699999655 4677644
No 156
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=56.18 E-value=5 Score=28.03 Aligned_cols=24 Identities=33% Similarity=0.879 Sum_probs=17.2
Q ss_pred ccCCCCcee-eEEeeeee-eeeCCCC
Q 044880 37 FCEFCGKYA-VKRKAVGI-WGCKDCG 60 (91)
Q Consensus 37 ~CpfCGk~~-VkR~a~GI-W~C~~Cg 60 (91)
.|=|||+.+ |......- |.|..|+
T Consensus 2 ~C~fC~~~s~~~~~~~~~~w~C~~C~ 27 (131)
T PF09779_consen 2 NCWFCGQNSKVPYDNRNSNWTCPHCE 27 (131)
T ss_pred eeccCCCCCCCCCCCCCCeeECCCCC
Confidence 588999765 44444343 9999996
No 157
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=55.81 E-value=11 Score=32.12 Aligned_cols=39 Identities=23% Similarity=0.405 Sum_probs=21.5
Q ss_pred chhhHHHHHHHHHhhccc--------ccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 19 ASLRKQIKKMEVSQHSKY--------FCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 19 ~slRK~v~kie~~q~~ky--------~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
..|++.|.++..+..-.| .|+.||.... +-+.|..||..
T Consensus 467 ~al~~lv~~~~~~~~i~Y~~in~~~~~C~~CG~~~~-----~~~~CP~CGs~ 513 (546)
T PF13597_consen 467 EALEKLVRYAMENTGIPYFTINPPIDICPDCGYIGG-----EGDKCPKCGSE 513 (546)
T ss_dssp HHHHHHHHHHHH--H-SEEEEE--EEEETTT---S-------EEE-CCC---
T ss_pred HHHHHHHHHHHHhCCCCeEEEecCcccccCCCcCCC-----CCCCCCCCCCc
Confidence 457788888877666666 7999997543 36899999987
No 158
>PRK10220 hypothetical protein; Provisional
Probab=55.10 E-value=8.9 Score=27.05 Aligned_cols=30 Identities=17% Similarity=0.458 Sum_probs=22.7
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceEeccc
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVKAGGA 67 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGGA 67 (91)
.||.|+..-+. ..-.+|.|..|+.-|.-.+
T Consensus 5 ~CP~C~seytY-~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 5 HCPKCNSEYTY-EDNGMYICPECAHEWNDAE 34 (111)
T ss_pred cCCCCCCcceE-cCCCeEECCcccCcCCccc
Confidence 59999988776 3446899999977665443
No 159
>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=55.04 E-value=9.7 Score=29.29 Aligned_cols=26 Identities=27% Similarity=0.768 Sum_probs=12.5
Q ss_pred ccccCCCCceeeEE---------eeeeeeeeCCCC
Q 044880 35 KYFCEFCGKYAVKR---------KAVGIWGCKDCG 60 (91)
Q Consensus 35 ky~CpfCGk~~VkR---------~a~GIW~C~~Cg 60 (91)
+-.||+||.+.-.. .+.-+=.|.+|+
T Consensus 211 R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~ 245 (290)
T PF04216_consen 211 RIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCG 245 (290)
T ss_dssp TTS-TTT---SS-EEE--------SEEEEEETTTT
T ss_pred CCCCcCCCCCCCcceeeEecCCCCcEEEEECCccc
Confidence 44688888664211 145666788887
No 160
>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=55.03 E-value=4.9 Score=20.01 Aligned_cols=9 Identities=44% Similarity=1.180 Sum_probs=4.5
Q ss_pred eeCCCCceE
Q 044880 55 GCKDCGKVK 63 (91)
Q Consensus 55 ~C~~Cg~~~ 63 (91)
.|..|++.|
T Consensus 3 ~C~~C~~~F 11 (27)
T PF13912_consen 3 ECDECGKTF 11 (27)
T ss_dssp EETTTTEEE
T ss_pred CCCccCCcc
Confidence 455555544
No 161
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=54.33 E-value=1.5 Score=34.69 Aligned_cols=34 Identities=32% Similarity=0.755 Sum_probs=24.5
Q ss_pred hhcccccCCCCce-----eeEEe---eeee--eeeCCCCceEec
Q 044880 32 QHSKYFCEFCGKY-----AVKRK---AVGI--WGCKDCGKVKAG 65 (91)
Q Consensus 32 q~~ky~CpfCGk~-----~VkR~---a~GI--W~C~~Cg~~~AG 65 (91)
+-.+|.|.||||- .+||. -+|| ++|.-|++.|+-
T Consensus 142 ~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftq 185 (267)
T KOG3576|consen 142 DVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQ 185 (267)
T ss_pred HHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHh
Confidence 3467899999984 25553 4454 899999988753
No 162
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=54.18 E-value=10 Score=26.39 Aligned_cols=30 Identities=30% Similarity=0.639 Sum_probs=20.8
Q ss_pred cccccCCCCcee--eEEeee-eeeeeCCCCceE
Q 044880 34 SKYFCEFCGKYA--VKRKAV-GIWGCKDCGKVK 63 (91)
Q Consensus 34 ~ky~CpfCGk~~--VkR~a~-GIW~C~~Cg~~~ 63 (91)
-.|.|.-||... ++|... ..+.|..|+-.+
T Consensus 111 ~~y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~l 143 (146)
T smart00731 111 YPYRCTGCGQRYLRVRRSNNVSRYRCGKCGGKL 143 (146)
T ss_pred EEEECCCCCCCCceEccccCcceEEcCCCCCEE
Confidence 467898898754 444433 678899998654
No 163
>PRK04351 hypothetical protein; Provisional
Probab=52.92 E-value=13 Score=26.78 Aligned_cols=30 Identities=23% Similarity=0.523 Sum_probs=22.6
Q ss_pred cccccCCCCce--eeEEeeeeeeeeCCCCceE
Q 044880 34 SKYFCEFCGKY--AVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 34 ~ky~CpfCGk~--~VkR~a~GIW~C~~Cg~~~ 63 (91)
-.|.|.-||.. ..+|...--..|..|+-.+
T Consensus 111 y~Y~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~L 142 (149)
T PRK04351 111 YLYECQSCGQQYLRKRRINTKRYRCGKCRGKL 142 (149)
T ss_pred EEEECCCCCCEeeeeeecCCCcEEeCCCCcEe
Confidence 45799999974 4667777778999998543
No 164
>PRK07218 replication factor A; Provisional
Probab=52.57 E-value=6.3 Score=32.86 Aligned_cols=21 Identities=33% Similarity=0.632 Sum_probs=17.2
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
..||.|++..-+ |.|+.||++
T Consensus 298 ~rCP~C~r~v~~------~~C~~hG~v 318 (423)
T PRK07218 298 ERCPECGRVIQK------GQCRSHGAV 318 (423)
T ss_pred ecCcCccccccC------CcCCCCCCc
Confidence 579999987644 899999975
No 165
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=52.55 E-value=11 Score=21.67 Aligned_cols=25 Identities=28% Similarity=0.667 Sum_probs=16.5
Q ss_pred hcccccCCCCceeeEEeeeeeeeeCCCC
Q 044880 33 HSKYFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 33 ~~ky~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
|..+.|..|+...+... -|+|..|.
T Consensus 2 h~~~~C~~C~~~~i~g~---Ry~C~~C~ 26 (46)
T PF00569_consen 2 HHGYTCDGCGTDPIIGV---RYHCLVCP 26 (46)
T ss_dssp CSSCE-SSS-SSSEESS---EEEESSSS
T ss_pred CCCeECcCCCCCcCcCC---eEECCCCC
Confidence 67889999998543322 39999995
No 166
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=52.10 E-value=7.3 Score=26.60 Aligned_cols=27 Identities=22% Similarity=0.678 Sum_probs=16.5
Q ss_pred hcccccCCCCceeeEEeeeeeeeeCCCC
Q 044880 33 HSKYFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 33 ~~ky~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
.....|+-||...-. ....++.|+.||
T Consensus 68 p~~~~C~~Cg~~~~~-~~~~~~~CP~Cg 94 (114)
T PRK03681 68 EAECWCETCQQYVTL-LTQRVRRCPQCH 94 (114)
T ss_pred CcEEEcccCCCeeec-CCccCCcCcCcC
Confidence 455678888864322 123457788887
No 167
>PF10588 NADH-G_4Fe-4S_3: NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; InterPro: IPR019574 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the G subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This family does not contain related subunits from formate dehydrogenase complexes. This entry represents the iron-sulphur binding domain of the G subunit.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3.
Probab=51.91 E-value=13 Score=21.25 Aligned_cols=22 Identities=23% Similarity=0.551 Sum_probs=12.4
Q ss_pred hHHHHHHHHHhhcccccCCCCce
Q 044880 22 RKQIKKMEVSQHSKYFCEFCGKY 44 (91)
Q Consensus 22 RK~v~kie~~q~~ky~CpfCGk~ 44 (91)
||.+-+...+.| +..||.|.+.
T Consensus 1 Rr~~lelll~~H-~~dC~~C~~~ 22 (41)
T PF10588_consen 1 RRTVLELLLANH-PLDCPTCDKN 22 (41)
T ss_dssp -HHHHHHHHTT-----TTT-TTG
T ss_pred CHHHHHHHHhCC-CCcCcCCCCC
Confidence 677777777777 6789999863
No 168
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=51.89 E-value=23 Score=24.32 Aligned_cols=39 Identities=21% Similarity=0.610 Sum_probs=24.6
Q ss_pred hHHHHHHHHHhhccc-ccCCCCcee--eEEeeeeee--eeCCCCc
Q 044880 22 RKQIKKMEVSQHSKY-FCEFCGKYA--VKRKAVGIW--GCKDCGK 61 (91)
Q Consensus 22 RK~v~kie~~q~~ky-~CpfCGk~~--VkR~a~GIW--~C~~Cg~ 61 (91)
-+.+.++-..=-..| .||.|+.+. +.+. .++| +|..||.
T Consensus 66 ~~~i~~~l~~yI~~yVlC~~C~spdT~l~k~-~r~~~l~C~aCGa 109 (110)
T smart00653 66 PKKLQDLLRRYIKEYVLCPECGSPDTELIKE-NRLFFLKCEACGA 109 (110)
T ss_pred HHHHHHHHHHHHHhcEECCCCCCCCcEEEEe-CCeEEEEccccCC
Confidence 345555544445566 799999874 4443 3444 6999985
No 169
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=51.71 E-value=15 Score=27.47 Aligned_cols=35 Identities=29% Similarity=0.379 Sum_probs=21.6
Q ss_pred ccCCCCceeeEEe-eee-----------eeeeCCCCce----Eeccccccc
Q 044880 37 FCEFCGKYAVKRK-AVG-----------IWGCKDCGKV----KAGGAYTLN 71 (91)
Q Consensus 37 ~CpfCGk~~VkR~-a~G-----------IW~C~~Cg~~----~AGGAy~~~ 71 (91)
.||.||....-|. -+- -+.|.+||+. ..||+..|.
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ev~~~g~~~p~ 52 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSNDVKTLGAKEPK 52 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccceeEECCCCCCE
Confidence 5999986531111 222 4789999964 466766553
No 170
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=51.29 E-value=16 Score=22.41 Aligned_cols=29 Identities=21% Similarity=0.517 Sum_probs=18.6
Q ss_pred ccccCCCCcee-eEEe-eeeeeeeCCCCceE
Q 044880 35 KYFCEFCGKYA-VKRK-AVGIWGCKDCGKVK 63 (91)
Q Consensus 35 ky~CpfCGk~~-VkR~-a~GIW~C~~Cg~~~ 63 (91)
.++||.||... +.-. .--|=.|..||..+
T Consensus 2 ~~~CP~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 2 QFECPDCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred ccCCCCCCCEEecCCCccCCEEeCCCCCCEE
Confidence 46899999864 2211 12366899998544
No 171
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.18 E-value=16 Score=24.80 Aligned_cols=27 Identities=33% Similarity=0.574 Sum_probs=21.5
Q ss_pred ccCCCCcee--eEEeeeeeeeeCCCCceE
Q 044880 37 FCEFCGKYA--VKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~~--VkR~a~GIW~C~~Cg~~~ 63 (91)
.||.|+-.. +.|.++-|=.|..|+=++
T Consensus 3 lCP~C~v~l~~~~rs~vEiD~CPrCrGVW 31 (88)
T COG3809 3 LCPICGVELVMSVRSGVEIDYCPRCRGVW 31 (88)
T ss_pred ccCcCCceeeeeeecCceeeeCCccccEe
Confidence 599999875 567788899999996443
No 172
>smart00507 HNHc HNH nucleases.
Probab=50.53 E-value=13 Score=19.94 Aligned_cols=13 Identities=38% Similarity=0.912 Sum_probs=10.1
Q ss_pred hhcccccCCCCcee
Q 044880 32 QHSKYFCEFCGKYA 45 (91)
Q Consensus 32 q~~ky~CpfCGk~~ 45 (91)
++. |.|++||...
T Consensus 8 ~r~-~~C~~C~~~~ 20 (52)
T smart00507 8 HRD-GVCAYCGKPA 20 (52)
T ss_pred HHC-CCCcCCcCCC
Confidence 355 8999999764
No 173
>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=50.28 E-value=6.7 Score=21.26 Aligned_cols=12 Identities=42% Similarity=0.874 Sum_probs=6.3
Q ss_pred hcccccCCCCce
Q 044880 33 HSKYFCEFCGKY 44 (91)
Q Consensus 33 ~~ky~CpfCGk~ 44 (91)
.++|.||.|+..
T Consensus 11 ~~kY~Cp~C~~~ 22 (30)
T PF04438_consen 11 PAKYRCPRCGAR 22 (30)
T ss_dssp EESEE-TTT--E
T ss_pred CCEEECCCcCCc
Confidence 467788887754
No 174
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=50.21 E-value=12 Score=18.22 Aligned_cols=12 Identities=25% Similarity=0.559 Sum_probs=9.5
Q ss_pred eeeCCCCceEec
Q 044880 54 WGCKDCGKVKAG 65 (91)
Q Consensus 54 W~C~~Cg~~~AG 65 (91)
|.|.-|+.+|..
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 788888888764
No 175
>PRK04023 DNA polymerase II large subunit; Validated
Probab=50.07 E-value=11 Score=35.30 Aligned_cols=24 Identities=29% Similarity=0.573 Sum_probs=18.4
Q ss_pred hcccccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 33 HSKYFCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 33 ~~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
-....||.||...+. ..|..||..
T Consensus 624 Vg~RfCpsCG~~t~~------frCP~CG~~ 647 (1121)
T PRK04023 624 IGRRKCPSCGKETFY------RRCPFCGTH 647 (1121)
T ss_pred ccCccCCCCCCcCCc------ccCCCCCCC
Confidence 345689999988533 689999876
No 176
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=49.97 E-value=8.4 Score=23.49 Aligned_cols=10 Identities=30% Similarity=0.939 Sum_probs=7.8
Q ss_pred cccCCCCcee
Q 044880 36 YFCEFCGKYA 45 (91)
Q Consensus 36 y~CpfCGk~~ 45 (91)
+.||+||...
T Consensus 1 i~CPyCge~~ 10 (52)
T PF14255_consen 1 IQCPYCGEPI 10 (52)
T ss_pred CCCCCCCCee
Confidence 4799999864
No 177
>smart00355 ZnF_C2H2 zinc finger.
Probab=49.96 E-value=8 Score=17.89 Aligned_cols=8 Identities=63% Similarity=1.456 Sum_probs=3.6
Q ss_pred eCCCCceE
Q 044880 56 CKDCGKVK 63 (91)
Q Consensus 56 C~~Cg~~~ 63 (91)
|..|++.|
T Consensus 3 C~~C~~~f 10 (26)
T smart00355 3 CPECGKVF 10 (26)
T ss_pred CCCCcchh
Confidence 44444444
No 178
>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=49.66 E-value=9.7 Score=21.29 Aligned_cols=18 Identities=22% Similarity=0.636 Sum_probs=13.4
Q ss_pred eeeCCCCceEeccccccc
Q 044880 54 WGCKDCGKVKAGGAYTLN 71 (91)
Q Consensus 54 W~C~~Cg~~~AGGAy~~~ 71 (91)
-.|..|+..|+.+-|.|.
T Consensus 5 ~~C~nC~R~v~a~RfA~H 22 (33)
T PF08209_consen 5 VECPNCGRPVAASRFAPH 22 (33)
T ss_dssp EE-TTTSSEEEGGGHHHH
T ss_pred EECCCCcCCcchhhhHHH
Confidence 368899999998887663
No 179
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.55 E-value=18 Score=25.74 Aligned_cols=39 Identities=21% Similarity=0.519 Sum_probs=26.7
Q ss_pred ccccCCCCcee-eEEeeeeeeeeCCCCceEecc----cccccccHHHHH
Q 044880 35 KYFCEFCGKYA-VKRKAVGIWGCKDCGKVKAGG----AYTLNTASAVTV 78 (91)
Q Consensus 35 ky~CpfCGk~~-VkR~a~GIW~C~~Cg~~~AGG----Ay~~~T~~~~t~ 78 (91)
.-.||.||+.- |-+ -+|+.|+-++-|- -|.+-|+-...+
T Consensus 6 ~~~cPvcg~~~iVTe-----L~c~~~etTVrg~F~~s~F~~Lt~d~LeF 49 (122)
T COG3877 6 INRCPVCGRKLIVTE-----LKCSNCETTVRGNFKMSKFEYLTSDQLEF 49 (122)
T ss_pred CCCCCcccccceeEE-----EecCCCCceEecceecccccccCHhHhHH
Confidence 34799999875 433 4899999999883 455555554433
No 180
>PHA02768 hypothetical protein; Provisional
Probab=49.28 E-value=6.8 Score=24.30 Aligned_cols=29 Identities=21% Similarity=0.633 Sum_probs=20.0
Q ss_pred ccccCCCCceeeE---------EeeeeeeeeCCCCceEe
Q 044880 35 KYFCEFCGKYAVK---------RKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 35 ky~CpfCGk~~Vk---------R~a~GIW~C~~Cg~~~A 64 (91)
-|.||.||+.-.. ....+ -+|..|++.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~k~-~kc~~C~k~f~ 42 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHNTN-LKLSNCKRISL 42 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcCCc-ccCCcccceec
Confidence 4899999997532 22223 38999998775
No 181
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=49.25 E-value=13 Score=32.45 Aligned_cols=39 Identities=23% Similarity=0.363 Sum_probs=28.4
Q ss_pred chhhHHHHHHHHHhhccc--------ccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 19 ASLRKQIKKMEVSQHSKY--------FCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 19 ~slRK~v~kie~~q~~ky--------~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
..|++.|+.+-....-.| .|+.||... .. .|.|..||..
T Consensus 602 ~a~~~lv~~~~~~~~i~Y~~in~~~~~C~~CG~~~-g~----~~~CP~CG~~ 648 (656)
T PRK08270 602 EACKKLVKKALENYRLPYITITPTFSICPKHGYLS-GE----HEFCPKCGEE 648 (656)
T ss_pred HHHHHHHHHHHHhCCCceEEeCCCCcccCCCCCcC-CC----CCCCcCCcCc
Confidence 578888888865545555 799999742 21 4999999864
No 182
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=49.04 E-value=9.7 Score=27.55 Aligned_cols=26 Identities=15% Similarity=0.440 Sum_probs=20.0
Q ss_pred ccccCCCCcee--------eEEeeeeeeeeC-CCC
Q 044880 35 KYFCEFCGKYA--------VKRKAVGIWGCK-DCG 60 (91)
Q Consensus 35 ky~CpfCGk~~--------VkR~a~GIW~C~-~Cg 60 (91)
...|.|||... |++-+.-+|-|. +|.
T Consensus 4 ~e~CsFcG~kIyPG~G~~fVR~DGkvf~FcssKC~ 38 (131)
T PRK14891 4 TRTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCE 38 (131)
T ss_pred eeeecCcCCcccCCCCcEEEecCCCEEEEecHHHH
Confidence 45799998764 888888889886 454
No 183
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=48.88 E-value=15 Score=27.46 Aligned_cols=64 Identities=19% Similarity=0.325 Sum_probs=39.7
Q ss_pred hHHHHHHH-HHhhcccccCCCCce-eeEEeeeeeeeeCCCCceEecccccccccHHHHHHHHHHHHHhh
Q 044880 22 RKQIKKME-VSQHSKYFCEFCGKY-AVKRKAVGIWGCKDCGKVKAGGAYTLNTASAVTVRSTIRRLREQ 88 (91)
Q Consensus 22 RK~v~kie-~~q~~ky~CpfCGk~-~VkR~a~GIW~C~~Cg~~~AGGAy~~~T~~~~t~~~~i~rl~e~ 88 (91)
.+....+| ..++.-|.||-|.-. +...+-.--..|..||..+- |.=+++.-.-..+.|++|.+.
T Consensus 99 e~Lk~~le~~~~~~~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L~---~~d~s~~i~~l~~~i~~l~~~ 164 (176)
T COG1675 99 EKLKRKLEKETENNYYVCPNCHVKYSFDEAMELGFTCPKCGEDLE---EYDSSEEIEELESELDELEEE 164 (176)
T ss_pred HHHHHHHHhhccCCceeCCCCCCcccHHHHHHhCCCCCCCCchhh---hccchHHHHHHHHHHHHHHHH
Confidence 34444455 566777899988843 43332222278999987663 344555556666777777765
No 184
>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear rec
Probab=48.80 E-value=9.1 Score=24.35 Aligned_cols=24 Identities=33% Similarity=0.931 Sum_probs=18.8
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCC
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
|.|..||.++.. .-.|+|.|..|.
T Consensus 1 ~~C~VC~~~~~g-~hygv~sC~aC~ 24 (77)
T cd06956 1 HICAICGDRASG-KHYGVYSCEGCK 24 (77)
T ss_pred CCCcccCCcCcc-eEECceeehhHH
Confidence 469999987654 467899999985
No 185
>PF02977 CarbpepA_inh: Carboxypeptidase A inhibitor; InterPro: IPR004231 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. This family is represented by the well-characterised metallocarboxypeptidase A inhibitor (MCPI) from potatoes, which belongs to the MEROPS inhibitor family I37, clan IE. It inhibits metallopeptidases belonging to MEROPS peptidase family M14, carboxypeptidase A. In Russet Burbank potatoes, it is a mixture of approximately equal amounts of two polypeptide chains containing 38 or 39 amino acid residues. The chains differ in their amino terminal sequence only [] and are resistant to fragmentation by proteases []. The structure of the complex between bovine carboxypeptidase A and the 39-amino-acid carboxypeptidase A inhibitor from potatoes has been determined at 2.5-A resolution []. The potato inhibitor is synthesised as a precursor, having a 29 residue N-terminal signal peptide, a 27 residue pro-peptide, the 39 residue mature inhibitor region and a 7 residue C-terminal extension. The 7 residue C-terminal extension is involved in inhibitor inactivation and may be required for targeting to the vacuole where the mature active inhibitor accumulates []. The N-terminal region and the mature inhibitor are weakly related to other solananaceous proteins found in this entry, from potato, tomato and henbane, which have been incorrectly described as metallocarboxipeptidase inhibitors [].; GO: 0008191 metalloendopeptidase inhibitor activity; PDB: 4CPA_I 1H20_A 2HLG_A.
Probab=48.56 E-value=3.5 Score=25.01 Aligned_cols=33 Identities=30% Similarity=0.525 Sum_probs=19.9
Q ss_pred CCCce-eeEEeeeeeeeeCCC-CceEecccccccc
Q 044880 40 FCGKY-AVKRKAVGIWGCKDC-GKVKAGGAYTLNT 72 (91)
Q Consensus 40 fCGk~-~VkR~a~GIW~C~~C-g~~~AGGAy~~~T 72 (91)
.|++. ...=.-.|||-|.-| ..+..+|-|...+
T Consensus 7 tCn~~C~t~sDC~g~tlC~~C~k~~~t~~g~~~~~ 41 (46)
T PF02977_consen 7 TCNKYCNTNSDCSGITLCQWCWKLKKTCGGYVGSA 41 (46)
T ss_dssp TTT-B-SSSCCCTTSSSS-EE-CCCEBCC--EEEE
T ss_pred ccCCccccCccccceeehHHHHhcccCCCCcccce
Confidence 34444 233335799999999 8888888877654
No 186
>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=48.28 E-value=14 Score=32.16 Aligned_cols=36 Identities=22% Similarity=0.502 Sum_probs=26.2
Q ss_pred chhhHHHHHHHHHhhccc--------ccCCCCceeeEEeeee-e-eeeCCCCc
Q 044880 19 ASLRKQIKKMEVSQHSKY--------FCEFCGKYAVKRKAVG-I-WGCKDCGK 61 (91)
Q Consensus 19 ~slRK~v~kie~~q~~ky--------~CpfCGk~~VkR~a~G-I-W~C~~Cg~ 61 (91)
..+++.|+.+... +-.| .|+.||.. .| + |.|..||.
T Consensus 509 ea~~~lv~~~~~~-~i~Y~tin~~~siC~~CGy~------~g~~~~~CP~CGs 554 (586)
T TIGR02827 509 DGYRKLLRVAADT-GCNYFCFNIKITICNDCHHI------DKRTLHRCPVCGS 554 (586)
T ss_pred HHHHHHHHHHHhc-CCceEEeCCCCeecCCCCCc------CCCcCCcCcCCCC
Confidence 4688888888654 5666 69999972 23 3 99999983
No 187
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=48.07 E-value=5.8 Score=24.16 Aligned_cols=29 Identities=28% Similarity=0.512 Sum_probs=16.9
Q ss_pred eccCCccccCchhhHHHHHHHHHhhcccccCCCCc
Q 044880 9 IVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGK 43 (91)
Q Consensus 9 i~gk~G~RYG~slRK~v~kie~~q~~ky~CpfCGk 43 (91)
|..+=..+-|..+ .|.-..-.|.||+||.
T Consensus 24 IC~~C~~hNGla~------~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 24 ICSKCFSHNGLAP------KEEFEEIQYRCPYCGA 52 (54)
T ss_pred ECcccchhhcccc------cccCCceEEEcCCCCC
Confidence 3444444555444 3444456899999985
No 188
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=48.02 E-value=7.6 Score=23.50 Aligned_cols=21 Identities=29% Similarity=0.760 Sum_probs=14.7
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCC
Q 044880 35 KYFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 35 ky~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
--.||.||...+--. .|..||
T Consensus 26 l~~c~~cg~~~~~H~-----vc~~cG 46 (56)
T PF01783_consen 26 LVKCPNCGEPKLPHR-----VCPSCG 46 (56)
T ss_dssp EEESSSSSSEESTTS-----BCTTTB
T ss_pred eeeeccCCCEecccE-----eeCCCC
Confidence 347999998765433 388886
No 189
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=47.60 E-value=6.2 Score=36.14 Aligned_cols=32 Identities=25% Similarity=0.562 Sum_probs=0.0
Q ss_pred ccccCCCCceeeEEe-------eeeeeeeCCCCceEecc
Q 044880 35 KYFCEFCGKYAVKRK-------AVGIWGCKDCGKVKAGG 66 (91)
Q Consensus 35 ky~CpfCGk~~VkR~-------a~GIW~C~~Cg~~~AGG 66 (91)
.+.||-||..+.... ..=+|.|..|+..+...
T Consensus 655 ~r~Cp~Cg~~t~~~~Cp~CG~~T~~~~~Cp~C~~~~~~~ 693 (900)
T PF03833_consen 655 RRRCPKCGKETFYNRCPECGSHTEPVYVCPDCGIEVEED 693 (900)
T ss_dssp ---------------------------------------
T ss_pred cccCcccCCcchhhcCcccCCccccceeccccccccCcc
Confidence 445777777765543 12367788887776443
No 190
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=47.50 E-value=9 Score=35.75 Aligned_cols=47 Identities=23% Similarity=0.382 Sum_probs=31.4
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCceEecccc--cccccHHHHHHHHHHHHHh
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAY--TLNTASAVTVRSTIRRLRE 87 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGGAy--~~~T~~~~t~~~~i~rl~e 87 (91)
..+.||-||..+.+ +.|..||... --.| ...-+....+.+|+.+|.+
T Consensus 624 ~~RKCPkCG~yTlk------~rCP~CG~~T-e~~~pc~~~i~l~~~~~~A~~~lg~ 672 (1095)
T TIGR00354 624 AIRKCPQCGKESFW------LKCPVCGELT-EQLYYGKRKVDLRELYEEAIANLGE 672 (1095)
T ss_pred EEEECCCCCccccc------ccCCCCCCcc-ccccceeEEecHHHHHHHHHHHhCC
Confidence 34689999999998 7899998652 1111 2244556677777776644
No 191
>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=47.43 E-value=7.7 Score=24.07 Aligned_cols=11 Identities=45% Similarity=1.171 Sum_probs=4.1
Q ss_pred cccccCCCCce
Q 044880 34 SKYFCEFCGKY 44 (91)
Q Consensus 34 ~ky~CpfCGk~ 44 (91)
..|+||.||.+
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 46999999975
No 192
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=47.28 E-value=12 Score=22.11 Aligned_cols=11 Identities=36% Similarity=1.132 Sum_probs=9.1
Q ss_pred eeeCCCCceEe
Q 044880 54 WGCKDCGKVKA 64 (91)
Q Consensus 54 W~C~~Cg~~~A 64 (91)
|.|..||..+-
T Consensus 29 W~C~~Cgh~w~ 39 (55)
T PF14311_consen 29 WKCPKCGHEWK 39 (55)
T ss_pred EECCCCCCeeE
Confidence 99999987664
No 193
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=47.25 E-value=15 Score=28.42 Aligned_cols=26 Identities=23% Similarity=0.445 Sum_probs=18.5
Q ss_pred ccccCCCCceeeEEe--eeeeeeeCCCC
Q 044880 35 KYFCEFCGKYAVKRK--AVGIWGCKDCG 60 (91)
Q Consensus 35 ky~CpfCGk~~VkR~--a~GIW~C~~Cg 60 (91)
.-.||.||.+..+.. +-+.|-|..|-
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCCc
Confidence 347999997654322 34789999994
No 194
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=47.12 E-value=8.2 Score=18.85 Aligned_cols=7 Identities=43% Similarity=1.298 Sum_probs=2.8
Q ss_pred cccCCCC
Q 044880 36 YFCEFCG 42 (91)
Q Consensus 36 y~CpfCG 42 (91)
|.|++|.
T Consensus 1 y~C~~C~ 7 (24)
T PF13909_consen 1 YKCPHCS 7 (24)
T ss_dssp EE-SSSS
T ss_pred CCCCCCC
Confidence 3455554
No 195
>PRK07220 DNA topoisomerase I; Validated
Probab=46.78 E-value=18 Score=31.84 Aligned_cols=27 Identities=26% Similarity=0.484 Sum_probs=18.7
Q ss_pred ccccCCCCceeeEEeeee----eeeeCCCCc
Q 044880 35 KYFCEFCGKYAVKRKAVG----IWGCKDCGK 61 (91)
Q Consensus 35 ky~CpfCGk~~VkR~a~G----IW~C~~Cg~ 61 (91)
...||.||...++....| .|.|..|.+
T Consensus 635 ~~~Cp~Cg~~~~k~~~~g~~~~~~~Cp~C~~ 665 (740)
T PRK07220 635 DKVCEAHGLNHIRIINGGKRPWDLGCPQCNF 665 (740)
T ss_pred CCCCCCCCCceEEEEecCCccceeeCCCCCC
Confidence 468999997544433333 679999985
No 196
>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=46.68 E-value=16 Score=24.86 Aligned_cols=30 Identities=23% Similarity=0.554 Sum_probs=18.9
Q ss_pred cccccCCCCceeeEEe--eeeeeeeCCCCceE
Q 044880 34 SKYFCEFCGKYAVKRK--AVGIWGCKDCGKVK 63 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~--a~GIW~C~~Cg~~~ 63 (91)
-.|.|+-|+....++. ...-..|..|+-.+
T Consensus 122 ~~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 122 YVYRCPSCGREYKRHRRSKRKRYRCGRCGGPL 153 (157)
T ss_pred eEEEcCCCCCEeeeecccchhhEECCCCCCEE
Confidence 3578888986643222 33446888887554
No 197
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=46.60 E-value=15 Score=32.86 Aligned_cols=27 Identities=30% Similarity=0.496 Sum_probs=21.4
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
..||+|+..-+-=...|.=.|..||+.
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~ 471 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCHYCGYQ 471 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeCCCCCC
Confidence 378888887766677788889988876
No 198
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=46.25 E-value=14 Score=30.75 Aligned_cols=39 Identities=31% Similarity=0.470 Sum_probs=26.8
Q ss_pred cccccCCCCceeeEEeeeee-------eeeCCCCceEe----cccccccccHH
Q 044880 34 SKYFCEFCGKYAVKRKAVGI-------WGCKDCGKVKA----GGAYTLNTASA 75 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GI-------W~C~~Cg~~~A----GGAy~~~T~~~ 75 (91)
.+.+||.||...+.+.++.| =||+ .-|. |--|++-+|-|
T Consensus 256 ~k~FCp~CG~~TL~K~aVsv~~dG~~~~h~k---~r~~~n~RG~~YSlp~PkG 305 (376)
T KOG2463|consen 256 PKDFCPSCGHKTLTKCAVSVDEDGNGQTHFK---KRFQWNNRGLQYSLPKPKG 305 (376)
T ss_pred chhcccccCCCeeeEEEEEecCCCceeEEee---cccccccCcceeecCCCCC
Confidence 46799999999999987744 3443 2333 77777777733
No 199
>KOG4623 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.11 E-value=9 Score=33.56 Aligned_cols=43 Identities=26% Similarity=0.539 Sum_probs=34.6
Q ss_pred CchhhHHHHHHHHHhh-cccccCCCCce-eeEEeeeeeeeeCCCC
Q 044880 18 GASLRKQIKKMEVSQH-SKYFCEFCGKY-AVKRKAVGIWGCKDCG 60 (91)
Q Consensus 18 G~slRK~v~kie~~q~-~ky~CpfCGk~-~VkR~a~GIW~C~~Cg 60 (91)
|++|=+.+.-|-.... +.-+|=||.+. .|.++...-|.|.+|.
T Consensus 10 ~a~l~~ly~~Irsr~k~t~VnCwFCnk~t~vpyq~rNswTCpsCE 54 (611)
T KOG4623|consen 10 GAGLGNLYDGIRSRFKDTTVNCWFCNKKTEVPYQGRNSWTCPSCE 54 (611)
T ss_pred hhcchHHHHHHHhhcCCceEEEEEecCcceeccCCCCCCcCCcHH
Confidence 5666666666666666 77799999976 6999999999999995
No 200
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=45.97 E-value=18 Score=22.76 Aligned_cols=28 Identities=36% Similarity=0.567 Sum_probs=20.8
Q ss_pred ccCCCCcee-eEEeeeeeeeeCCCCceEe
Q 044880 37 FCEFCGKYA-VKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 37 ~CpfCGk~~-VkR~a~GIW~C~~Cg~~~A 64 (91)
.||-|++.. |-=.+.-.=.|..||.++|
T Consensus 13 kCp~C~n~q~vFsha~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 13 KCPDCGNEQVVFSHASTVVRCLVCGKTLA 41 (59)
T ss_pred ECCCCCCeEEEEecCCcEEECcccCCCcc
Confidence 799999986 3333555558999998873
No 201
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=45.95 E-value=8.2 Score=24.71 Aligned_cols=30 Identities=30% Similarity=0.772 Sum_probs=22.3
Q ss_pred HhhcccccCCCCce-eeEEeeeeeeeeCCCCce
Q 044880 31 SQHSKYFCEFCGKY-AVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 31 ~q~~ky~CpfCGk~-~VkR~a~GIW~C~~Cg~~ 62 (91)
++-..|.|-.||.. .++|.. .-.|+.||+-
T Consensus 16 ~~~miYiCgdC~~en~lk~~D--~irCReCG~R 46 (62)
T KOG3507|consen 16 TATMIYICGDCGQENTLKRGD--VIRCRECGYR 46 (62)
T ss_pred cccEEEEeccccccccccCCC--cEehhhcchH
Confidence 35567999999976 577543 4589999974
No 202
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=45.68 E-value=13 Score=19.47 Aligned_cols=11 Identities=36% Similarity=1.090 Sum_probs=9.1
Q ss_pred eeeeeCCCCce
Q 044880 52 GIWGCKDCGKV 62 (91)
Q Consensus 52 GIW~C~~Cg~~ 62 (91)
|-|.|..|...
T Consensus 3 g~W~C~~C~~~ 13 (30)
T PF00641_consen 3 GDWKCPSCTFM 13 (30)
T ss_dssp SSEEETTTTEE
T ss_pred cCccCCCCcCC
Confidence 67999999864
No 203
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=45.29 E-value=9.7 Score=23.76 Aligned_cols=8 Identities=50% Similarity=1.161 Sum_probs=6.7
Q ss_pred ccCCCCce
Q 044880 37 FCEFCGKY 44 (91)
Q Consensus 37 ~CpfCGk~ 44 (91)
-|||||..
T Consensus 41 gCPfC~~~ 48 (55)
T PF14447_consen 41 GCPFCGTP 48 (55)
T ss_pred CCCCCCCc
Confidence 59999975
No 204
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=45.27 E-value=15 Score=30.33 Aligned_cols=21 Identities=29% Similarity=0.676 Sum_probs=15.9
Q ss_pred ccccCCCCcee-eEEeeeeeee
Q 044880 35 KYFCEFCGKYA-VKRKAVGIWG 55 (91)
Q Consensus 35 ky~CpfCGk~~-VkR~a~GIW~ 55 (91)
+|.||.||... +|+-..-|||
T Consensus 25 ~ffCPaC~~~l~lK~G~~k~pH 46 (342)
T COG4469 25 RFFCPACGSQLILKQGLIKIPH 46 (342)
T ss_pred ccccCCCCCeeeeecCccccch
Confidence 79999999986 4444556776
No 205
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=45.22 E-value=17 Score=20.48 Aligned_cols=24 Identities=38% Similarity=1.061 Sum_probs=17.4
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceEecc
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVKAGG 66 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGG 66 (91)
.|..|+... .+|.|-.|+..+-|-
T Consensus 1 ~C~~C~~~~------~l~~CL~C~~~~c~~ 24 (50)
T smart00290 1 RCSVCGTIE------NLWLCLTCGQVGCGR 24 (50)
T ss_pred CcccCCCcC------CeEEecCCCCcccCC
Confidence 377887533 499999998777543
No 206
>PRK06386 replication factor A; Reviewed
Probab=45.22 E-value=9.7 Score=31.21 Aligned_cols=20 Identities=30% Similarity=0.476 Sum_probs=16.7
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCc
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
..||.|++..-+ |.|+.||+
T Consensus 237 ~rCP~C~R~l~~------g~C~~HG~ 256 (358)
T PRK06386 237 TKCSVCNKIIED------GVCKDHPD 256 (358)
T ss_pred ecCcCCCeEccC------CcCCCCCC
Confidence 579999987664 79999997
No 207
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=45.17 E-value=10 Score=23.55 Aligned_cols=13 Identities=31% Similarity=0.672 Sum_probs=10.1
Q ss_pred hhcccccCCCCce
Q 044880 32 QHSKYFCEFCGKY 44 (91)
Q Consensus 32 q~~ky~CpfCGk~ 44 (91)
.+..|.||.||=+
T Consensus 11 ~~v~~~Cp~cGip 23 (55)
T PF13824_consen 11 AHVNFECPDCGIP 23 (55)
T ss_pred cccCCcCCCCCCc
Confidence 4678999999854
No 208
>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=44.94 E-value=14 Score=29.80 Aligned_cols=52 Identities=17% Similarity=0.202 Sum_probs=32.2
Q ss_pred hcccccCCCCceeeEEe-eeeeeeeCCCCceEecccccccccHHHHHHHHHHH
Q 044880 33 HSKYFCEFCGKYAVKRK-AVGIWGCKDCGKVKAGGAYTLNTASAVTVRSTIRR 84 (91)
Q Consensus 33 ~~ky~CpfCGk~~VkR~-a~GIW~C~~Cg~~~AGGAy~~~T~~~~t~~~~i~r 84 (91)
...|.||.|+...+-|. ...+||=.+-...---..+.++|......+..|-.
T Consensus 28 ~~~~~CP~C~~~v~lk~G~~k~~HFAH~~~~~c~~~~~~ES~~Hl~~K~~l~~ 80 (375)
T PF06054_consen 28 KGKYFCPGCGEPVILKKGKKKIPHFAHKSKSDCPFFSEGESEEHLQGKELLYQ 80 (375)
T ss_pred CCcEECCCCCCeeEEEEcCcccceeeecCCCCCCcccCCchHHHHHHHHHHHH
Confidence 88999999999875555 44677643332211011345677777777766544
No 209
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=44.62 E-value=13 Score=28.62 Aligned_cols=33 Identities=24% Similarity=0.547 Sum_probs=22.5
Q ss_pred hhcccccCCCCceee----EEeee--eeeeeCCCCceEe
Q 044880 32 QHSKYFCEFCGKYAV----KRKAV--GIWGCKDCGKVKA 64 (91)
Q Consensus 32 q~~ky~CpfCGk~~V----kR~a~--GIW~C~~Cg~~~A 64 (91)
|+--+.||-||...+ -+... =.-+|..||..+.
T Consensus 3 ~~iy~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~~ 41 (201)
T COG1326 3 EEIYIECPSCGSEEVSHEVIKERGREPLVRCEECGTVHP 41 (201)
T ss_pred ceEEEECCCCCcchhhHHHHHhcCCceEEEccCCCcEee
Confidence 455679999995544 22222 3679999998873
No 210
>PRK00807 50S ribosomal protein L24e; Validated
Probab=44.38 E-value=10 Score=22.85 Aligned_cols=25 Identities=36% Similarity=0.837 Sum_probs=15.5
Q ss_pred cccCCCCcee--------eEEeeeeeeeeC-CCC
Q 044880 36 YFCEFCGKYA--------VKRKAVGIWGCK-DCG 60 (91)
Q Consensus 36 y~CpfCGk~~--------VkR~a~GIW~C~-~Cg 60 (91)
+.|.|||... |+..+.=.+-|. +|-
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~Fcs~KC~ 35 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILYFCSSKCE 35 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEEEeCHHHH
Confidence 5799999764 444455555555 553
No 211
>KOG4215 consensus Hepatocyte nuclear factor 4 and similar steroid hormone receptors [Transcription]
Probab=44.15 E-value=9.3 Score=32.28 Aligned_cols=39 Identities=38% Similarity=0.821 Sum_probs=28.8
Q ss_pred CccccCch--------hhHHHHHHHHHhhcccccCC---CCceeeEEeeeeeeeeCCCCc
Q 044880 13 YGTRYGAS--------LRKQIKKMEVSQHSKYFCEF---CGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 13 ~G~RYG~s--------lRK~v~kie~~q~~ky~Cpf---CGk~~VkR~a~GIW~C~~Cg~ 61 (91)
-|.+||++ +|+-|.+ .-.|+|-| |.=++-+|.+ |+.|..
T Consensus 30 TGKHYGA~SCdGCKGFFRRSVrk-----~~~YtCRF~k~C~VDKdkRNa-----CRyCRf 79 (432)
T KOG4215|consen 30 TGKHYGAISCDGCKGFFRRSVRK-----NHQYTCRFNKQCVVDKDKRNA-----CRYCRF 79 (432)
T ss_pred cccccceeecCcchHHHHHHHHh-----cceeeeeccccccccchhhhh-----hhHhhH
Confidence 37789964 6777776 77899988 6666777775 887753
No 212
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=44.01 E-value=4 Score=32.73 Aligned_cols=29 Identities=24% Similarity=0.290 Sum_probs=20.4
Q ss_pred ccccCCCCceee-EEeeeeeeeeCCCCceE
Q 044880 35 KYFCEFCGKYAV-KRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 35 ky~CpfCGk~~V-kR~a~GIW~C~~Cg~~~ 63 (91)
=..||.|+.... +......+.|.+|++.|
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 347999998753 33345668999998744
No 213
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=43.96 E-value=4.9 Score=31.79 Aligned_cols=29 Identities=21% Similarity=0.523 Sum_probs=20.6
Q ss_pred ccccCCCCceeeEEe-eeeeeeeCCCCceE
Q 044880 35 KYFCEFCGKYAVKRK-AVGIWGCKDCGKVK 63 (91)
Q Consensus 35 ky~CpfCGk~~VkR~-a~GIW~C~~Cg~~~ 63 (91)
=..||.|+....++. ....+.|.+|++.|
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 458999998763332 34568999999765
No 214
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=43.94 E-value=18 Score=31.58 Aligned_cols=38 Identities=26% Similarity=0.492 Sum_probs=26.4
Q ss_pred chhhHHHHHHHHHhhccc--------ccCCCCceeeEEeeeeeeeeCCCCc
Q 044880 19 ASLRKQIKKMEVSQHSKY--------FCEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 19 ~slRK~v~kie~~q~~ky--------~CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
..+++.|+.+.. ..-.| .|+.||... ... .|.|..||.
T Consensus 543 eal~~lv~~~~~-~~i~Yf~in~~~~iC~~CG~~~-~g~---~~~CP~CGs 588 (623)
T PRK08271 543 EGYRKLLNIAAK-TGCNYFAFNVKITICNDCHHID-KRT---GKRCPICGS 588 (623)
T ss_pred HHHHHHHHHHHH-cCCceEEeCCCCccCCCCCCcC-CCC---CcCCcCCCC
Confidence 467788888754 44555 799999752 111 499999985
No 215
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=43.85 E-value=19 Score=27.58 Aligned_cols=27 Identities=30% Similarity=0.476 Sum_probs=18.7
Q ss_pred ccccCCCCceeeEEe--eeeeeeeCCCCc
Q 044880 35 KYFCEFCGKYAVKRK--AVGIWGCKDCGK 61 (91)
Q Consensus 35 ky~CpfCGk~~VkR~--a~GIW~C~~Cg~ 61 (91)
.-.||.||.+..+-. +-+.|-|..|-.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCCC
Confidence 346999997743322 347899999954
No 216
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=43.23 E-value=4.2 Score=32.12 Aligned_cols=29 Identities=17% Similarity=0.343 Sum_probs=21.0
Q ss_pred ccccCCCCceeeEE-eeeeeeeeCCCCceE
Q 044880 35 KYFCEFCGKYAVKR-KAVGIWGCKDCGKVK 63 (91)
Q Consensus 35 ky~CpfCGk~~VkR-~a~GIW~C~~Cg~~~ 63 (91)
=..||.|+....+. ..-..+.|.+|++.+
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 35799999876443 344568999999754
No 217
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=43.16 E-value=22 Score=21.10 Aligned_cols=23 Identities=22% Similarity=0.798 Sum_probs=15.8
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCc
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
|.|..|+..-+.-. =|+|..|..
T Consensus 1 y~Cd~C~~~pI~G~---R~~C~~C~~ 23 (48)
T cd02341 1 FKCDSCGIEPIPGT---RYHCSECDD 23 (48)
T ss_pred CCCCCCCCCccccc---eEECCCCCC
Confidence 78999998433211 299999974
No 218
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=43.05 E-value=7.2 Score=31.55 Aligned_cols=29 Identities=21% Similarity=0.551 Sum_probs=21.8
Q ss_pred cccCCCCceeeEEe-eeeeeeeCCCCceEe
Q 044880 36 YFCEFCGKYAVKRK-AVGIWGCKDCGKVKA 64 (91)
Q Consensus 36 y~CpfCGk~~VkR~-a~GIW~C~~Cg~~~A 64 (91)
.+||-|+...-... ....|.|.+|+..+-
T Consensus 29 ~KCp~c~~~~y~~eL~~n~~vcp~c~~h~r 58 (294)
T COG0777 29 TKCPSCGEMLYRKELESNLKVCPKCGHHMR 58 (294)
T ss_pred eECCCccceeeHHHHHhhhhcccccCcccc
Confidence 37999998764433 556899999997654
No 219
>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=42.92 E-value=15 Score=20.86 Aligned_cols=32 Identities=31% Similarity=0.757 Sum_probs=21.4
Q ss_pred cCCCCceee----E-Eeeeeeee-----eCCCCceEeccccc
Q 044880 38 CEFCGKYAV----K-RKAVGIWG-----CKDCGKVKAGGAYT 69 (91)
Q Consensus 38 CpfCGk~~V----k-R~a~GIW~-----C~~Cg~~~AGGAy~ 69 (91)
|+.|++... . +.....|| |..|+..+.++.|.
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~ 42 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFY 42 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEE
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeE
Confidence 677777642 1 23446775 89999998888643
No 220
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=42.71 E-value=13 Score=27.76 Aligned_cols=25 Identities=20% Similarity=0.505 Sum_probs=18.1
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
+.||.|+..-.. ...-|.|.. +..|
T Consensus 3 ~~CP~C~~~l~~--~~~~~~C~~-~h~f 27 (272)
T PRK11088 3 YQCPLCHQPLTL--EENSWICPQ-NHQF 27 (272)
T ss_pred ccCCCCCcchhc--CCCEEEcCC-CCCC
Confidence 689999987633 335699988 6555
No 221
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=42.49 E-value=18 Score=23.75 Aligned_cols=32 Identities=31% Similarity=0.575 Sum_probs=22.6
Q ss_pred ccccCCCCceeeEEeeee-eeeeCCCCceEecc
Q 044880 35 KYFCEFCGKYAVKRKAVG-IWGCKDCGKVKAGG 66 (91)
Q Consensus 35 ky~CpfCGk~~VkR~a~G-IW~C~~Cg~~~AGG 66 (91)
+|.||-||...+...+.| -=.|.-|.=.-.|-
T Consensus 1 K~~CPCCg~~Tl~~~~~~~ydIC~VC~WEdD~~ 33 (78)
T PF14206_consen 1 KYPCPCCGYYTLEERGEGTYDICPVCFWEDDGV 33 (78)
T ss_pred CccCCCCCcEEeccCCCcCceECCCCCcccCCc
Confidence 689999999987655543 22499998555554
No 222
>PF00105 zf-C4: Zinc finger, C4 type (two domains); InterPro: IPR001628 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences, connected via a linker region to a C-terminal ligand-binding domain (IPR000536 from INTERPRO). In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The DNA-binding domain can elicit either an activating or repressing effect by binding to specific regions of the DNA known as hormone-response elements [, ]. These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. The DNA-binding domain is furthermore involved in several other functions including nuclear localisation, and interaction with transcription factors and co-activators []. 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 two C4-type zinc finger modules involved in DNA-binding. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1DSZ_A 1LO1_A 3M9E_F 2EBL_A 1GA5_B 1A6Y_B 1HLZ_B 1HRA_A 1KB6_B 1KB4_B ....
Probab=42.47 E-value=11 Score=22.97 Aligned_cols=23 Identities=30% Similarity=0.769 Sum_probs=18.2
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCC
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
.|..||+.+.. .-.|++.|..|.
T Consensus 2 ~C~VCg~~~~~-~~ygv~sC~~C~ 24 (70)
T PF00105_consen 2 KCKVCGDPASG-YHYGVLSCNACK 24 (70)
T ss_dssp BSTTTSSBESE-EETTEEEEHHHH
T ss_pred CCeECCCccCc-ccccccccccce
Confidence 58999987644 467999999985
No 223
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=42.45 E-value=29 Score=23.44 Aligned_cols=9 Identities=33% Similarity=0.929 Sum_probs=7.2
Q ss_pred eeCCCCceE
Q 044880 55 GCKDCGKVK 63 (91)
Q Consensus 55 ~C~~Cg~~~ 63 (91)
.|..||+.+
T Consensus 37 ~C~~CGe~y 45 (89)
T TIGR03829 37 SCSHCGMEY 45 (89)
T ss_pred cccCCCcEe
Confidence 589998875
No 224
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=42.23 E-value=12 Score=35.68 Aligned_cols=30 Identities=23% Similarity=0.576 Sum_probs=15.4
Q ss_pred cccCCCCceeeEEe-------eeeeeeeCCCCceEec
Q 044880 36 YFCEFCGKYAVKRK-------AVGIWGCKDCGKVKAG 65 (91)
Q Consensus 36 y~CpfCGk~~VkR~-------a~GIW~C~~Cg~~~AG 65 (91)
..||.||.....-. ..-+++|.+||..+..
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~te~vy~CPsCGaev~~ 704 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTHTEPVYVCPDCGAEVPP 704 (1337)
T ss_pred EECCCCCCccccccCcccCCcCCCceeCccCCCccCC
Confidence 56777776432200 0124567777665543
No 225
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=42.16 E-value=21 Score=27.56 Aligned_cols=26 Identities=27% Similarity=0.437 Sum_probs=18.5
Q ss_pred cccCCCCceeeEEe--eeeeeeeCCCCc
Q 044880 36 YFCEFCGKYAVKRK--AVGIWGCKDCGK 61 (91)
Q Consensus 36 y~CpfCGk~~VkR~--a~GIW~C~~Cg~ 61 (91)
-.||.||.+..+.. +-+.|-|..|-.
T Consensus 236 ~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~ 263 (269)
T PRK14811 236 QPCPRCGTPIEKIVVGGRGTHFCPQCQP 263 (269)
T ss_pred CCCCcCCCeeEEEEECCCCcEECCCCcC
Confidence 37999997753322 347899999954
No 226
>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=41.79 E-value=24 Score=20.42 Aligned_cols=23 Identities=30% Similarity=0.756 Sum_probs=16.9
Q ss_pred cccCCCCceeeE-EeeeeeeeeCCCC
Q 044880 36 YFCEFCGKYAVK-RKAVGIWGCKDCG 60 (91)
Q Consensus 36 y~CpfCGk~~Vk-R~a~GIW~C~~Cg 60 (91)
-.||.||-+.++ |. |-=.|-.|+
T Consensus 18 ~~Cp~C~~PL~~~k~--g~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKD--GKIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEEecC--CCEECCCCC
Confidence 479999999888 44 344687774
No 227
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=41.35 E-value=25 Score=25.54 Aligned_cols=35 Identities=31% Similarity=0.645 Sum_probs=21.7
Q ss_pred ccCCCCceeeEEe-----------eeeeeeeCCCCce----Eeccccccc
Q 044880 37 FCEFCGKYAVKRK-----------AVGIWGCKDCGKV----KAGGAYTLN 71 (91)
Q Consensus 37 ~CpfCGk~~VkR~-----------a~GIW~C~~Cg~~----~AGGAy~~~ 71 (91)
.||.||....-|. =.=-..|.+||+. ..||+..|.
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ev~~~~~~~p~ 51 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCGYRNNEVKSGGAIEPK 51 (160)
T ss_pred cCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCCCccceEEECcccCCC
Confidence 4999986542221 2223789999964 456766554
No 228
>PRK06450 threonine synthase; Validated
Probab=41.32 E-value=11 Score=29.82 Aligned_cols=26 Identities=35% Similarity=0.561 Sum_probs=17.9
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 35 KYFCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 35 ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
.+.|+.||+..-. .-.|.|..||-.+
T Consensus 3 ~~~C~~Cg~~~~~---~~~~~C~~cg~~l 28 (338)
T PRK06450 3 KEVCMKCGKERES---IYEIRCKKCGGPF 28 (338)
T ss_pred eeEECCcCCcCCC---cccccCCcCCCEe
Confidence 3789999987521 2358999997433
No 229
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=41.15 E-value=16 Score=24.82 Aligned_cols=30 Identities=23% Similarity=0.537 Sum_probs=22.7
Q ss_pred hhcccccCCCCceeeEEeeeeeeeeCCCCc
Q 044880 32 QHSKYFCEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 32 q~~ky~CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
....|.|+-||...+--.+-+-=+|.+|+.
T Consensus 39 G~~~~~C~~Cg~~~~~~~SCk~R~CP~C~~ 68 (111)
T PF14319_consen 39 GFHRYRCEDCGHEKIVYNSCKNRHCPSCQA 68 (111)
T ss_pred CcceeecCCCCceEEecCcccCcCCCCCCC
Confidence 345679999998887666666668888864
No 230
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=41.10 E-value=20 Score=29.24 Aligned_cols=27 Identities=30% Similarity=0.589 Sum_probs=22.5
Q ss_pred ccCCCCce---eeEEeeeeeeeeCCCCceE
Q 044880 37 FCEFCGKY---AVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~---~VkR~a~GIW~C~~Cg~~~ 63 (91)
+||.|..+ .|.....|.=.|..||.++
T Consensus 2 ~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl 31 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAGDTVCSECGLVL 31 (308)
T ss_pred CCCCCCCCCCCeeeeccCCceecccCCeee
Confidence 47788765 5888899999999999876
No 231
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=40.50 E-value=18 Score=22.20 Aligned_cols=23 Identities=26% Similarity=0.676 Sum_probs=16.2
Q ss_pred hcccccCCCCceeeEEeeeeeeeeCCCC
Q 044880 33 HSKYFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 33 ~~ky~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
.+-..||-||...+.=. .|..||
T Consensus 25 ~~l~~C~~CG~~~~~H~-----vC~~CG 47 (57)
T PRK12286 25 PGLVECPNCGEPKLPHR-----VCPSCG 47 (57)
T ss_pred CcceECCCCCCccCCeE-----ECCCCC
Confidence 44457999998876532 488887
No 232
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=40.41 E-value=28 Score=18.97 Aligned_cols=19 Identities=37% Similarity=0.728 Sum_probs=14.4
Q ss_pred eeCCCCceEeccccccccc
Q 044880 55 GCKDCGKVKAGGAYTLNTA 73 (91)
Q Consensus 55 ~C~~Cg~~~AGGAy~~~T~ 73 (91)
.|=.|++.|.|..|...|.
T Consensus 2 sCiDC~~~F~~~~y~~Ht~ 20 (28)
T PF08790_consen 2 SCIDCSKDFDGDSYKSHTS 20 (28)
T ss_dssp EETTTTEEEEGGGTTT---
T ss_pred eeecCCCCcCcCCcCCCCc
Confidence 5889999999999987764
No 233
>cd06968 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RORS are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum particularly in the regulation of the maturation and survival of Purkinje cells. RORbe
Probab=40.30 E-value=15 Score=24.47 Aligned_cols=24 Identities=25% Similarity=0.704 Sum_probs=19.3
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCC
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
-.|..||..... .-.|.|.|..|.
T Consensus 6 ~~C~VCg~~~~g-~hyGv~sC~aC~ 29 (95)
T cd06968 6 IPCKICGDKSSG-IHYGVITCEGCK 29 (95)
T ss_pred cCCcccCCcCcc-eEECceeehhhH
Confidence 469999987755 358999999997
No 234
>PRK10445 endonuclease VIII; Provisional
Probab=39.71 E-value=24 Score=27.06 Aligned_cols=28 Identities=25% Similarity=0.521 Sum_probs=19.1
Q ss_pred hcccccCCCCceeeEEe--eeeeeeeCCCC
Q 044880 33 HSKYFCEFCGKYAVKRK--AVGIWGCKDCG 60 (91)
Q Consensus 33 ~~ky~CpfCGk~~VkR~--a~GIW~C~~Cg 60 (91)
+..-.||.||....+-. +-+.|-|..|-
T Consensus 233 r~g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 233 RDGEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 33457999997643222 55789999984
No 235
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=39.67 E-value=12 Score=18.72 Aligned_cols=10 Identities=40% Similarity=1.129 Sum_probs=7.9
Q ss_pred eeeeeCCCCc
Q 044880 52 GIWGCKDCGK 61 (91)
Q Consensus 52 GIW~C~~Cg~ 61 (91)
|-|.|..|+.
T Consensus 1 g~W~C~~C~~ 10 (26)
T smart00547 1 GDWECPACTF 10 (26)
T ss_pred CcccCCCCCC
Confidence 5699999964
No 236
>cd00085 HNHc HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.
Probab=39.45 E-value=22 Score=19.31 Aligned_cols=10 Identities=40% Similarity=1.092 Sum_probs=8.3
Q ss_pred cccCCCCcee
Q 044880 36 YFCEFCGKYA 45 (91)
Q Consensus 36 y~CpfCGk~~ 45 (91)
|.|++||...
T Consensus 12 ~~C~~c~~~~ 21 (57)
T cd00085 12 GLCPYCGKPG 21 (57)
T ss_pred CcCccCCCcC
Confidence 8999999753
No 237
>PF09180 ProRS-C_1: Prolyl-tRNA synthetase, C-terminal; InterPro: IPR016061 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. Prolyl tRNA synthetase (6.1.1.15 from EC) exists in two forms, which are loosely related. The first form is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota. Prolyl-tRNA synthetase belongs to class IIa. This domain is found at the C-terminal in archaeal and eukaryotic enzymes, as well as in certain bacterial ones.; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1NJ6_A 1NJ2_A 1NJ5_A 1NJ1_A 1H4T_C 1H4S_A 1HC7_C 1H4Q_B 3IAL_B.
Probab=39.39 E-value=19 Score=22.45 Aligned_cols=17 Identities=35% Similarity=0.362 Sum_probs=9.2
Q ss_pred hcccccCCCCceeeEEe
Q 044880 33 HSKYFCEFCGKYAVKRK 49 (91)
Q Consensus 33 ~~ky~CpfCGk~~VkR~ 49 (91)
...=+|++||++...+.
T Consensus 46 ~~~~~Ci~cgk~a~~~~ 62 (68)
T PF09180_consen 46 PEGGKCIVCGKPAKKWV 62 (68)
T ss_dssp BTT-B-TTT-SB-SCEE
T ss_pred CCCCeeecCCChhhEEE
Confidence 34457999999886654
No 238
>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=39.30 E-value=19 Score=24.30 Aligned_cols=24 Identities=25% Similarity=0.663 Sum_probs=10.1
Q ss_pred cccccCCCCcee-eEEeeeeeeeeCCCC
Q 044880 34 SKYFCEFCGKYA-VKRKAVGIWGCKDCG 60 (91)
Q Consensus 34 ~ky~CpfCGk~~-VkR~a~GIW~C~~Cg 60 (91)
....|+.||... +.... ..|+.||
T Consensus 69 ~~~~C~~Cg~~~~~~~~~---~~CP~Cg 93 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDEFD---FSCPRCG 93 (113)
T ss_dssp -EEEETTTS-EEECHHCC---HH-SSSS
T ss_pred CcEECCCCCCEEecCCCC---CCCcCCc
Confidence 344566666553 22111 3466665
No 239
>cd06960 NR_DBD_HNF4A DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is
Probab=39.26 E-value=19 Score=22.67 Aligned_cols=25 Identities=32% Similarity=0.785 Sum_probs=18.2
Q ss_pred cCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 38 CEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 38 CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
|..||.++.. .-.|+|.|..|.-=|
T Consensus 1 C~vCg~~~~~-~hygv~~C~aC~~FF 25 (76)
T cd06960 1 CAVCGDRATG-KHYGVLSCNGCKGFF 25 (76)
T ss_pred CCccCccCcc-cEECcceeeeehhee
Confidence 7788877644 457889999997433
No 240
>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=38.99 E-value=24 Score=27.11 Aligned_cols=24 Identities=33% Similarity=0.562 Sum_probs=17.1
Q ss_pred cccCCCCceeeEEe--eeeeeeeCCC
Q 044880 36 YFCEFCGKYAVKRK--AVGIWGCKDC 59 (91)
Q Consensus 36 y~CpfCGk~~VkR~--a~GIW~C~~C 59 (91)
-.||.||.+..+-. +-+.|-|..|
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 246 EPCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCeeEEEEECCCCCEECCCC
Confidence 47999997753322 3468899988
No 241
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=38.93 E-value=41 Score=28.83 Aligned_cols=23 Identities=30% Similarity=0.626 Sum_probs=16.0
Q ss_pred cccCCCCceeeEE-eeee-eeeeCC
Q 044880 36 YFCEFCGKYAVKR-KAVG-IWGCKD 58 (91)
Q Consensus 36 y~CpfCGk~~VkR-~a~G-IW~C~~ 58 (91)
..||.||+..+.+ ...| -|-|..
T Consensus 590 ~~CPkCg~~l~~~~~k~g~f~gCs~ 614 (618)
T TIGR01057 590 GKCPKCGGKLVSKYAKKGRFVGCSN 614 (618)
T ss_pred CCCCcCCCeeeeeecCCccEEECCC
Confidence 5799999886633 3334 488876
No 242
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=38.89 E-value=15 Score=25.07 Aligned_cols=12 Identities=17% Similarity=0.393 Sum_probs=7.5
Q ss_pred ccccCCCCceee
Q 044880 35 KYFCEFCGKYAV 46 (91)
Q Consensus 35 ky~CpfCGk~~V 46 (91)
.+.||.||...+
T Consensus 86 ~~~CP~Cgs~~~ 97 (113)
T PRK12380 86 DAQCPHCHGERL 97 (113)
T ss_pred CccCcCCCCCCc
Confidence 345777776543
No 243
>PF13397 DUF4109: Domain of unknown function (DUF4109)
Probab=38.82 E-value=18 Score=25.15 Aligned_cols=31 Identities=29% Similarity=0.639 Sum_probs=21.1
Q ss_pred HhhcccccCCCCceeeEEeee-----eeeeeCCCCce
Q 044880 31 SQHSKYFCEFCGKYAVKRKAV-----GIWGCKDCGKV 62 (91)
Q Consensus 31 ~q~~ky~CpfCGk~~VkR~a~-----GIW~C~~Cg~~ 62 (91)
.|...|.||- |....--.+. -.|.|+.||..
T Consensus 24 R~~v~Y~C~~-Gh~~~v~Fa~eAevP~~WeC~~cG~~ 59 (105)
T PF13397_consen 24 RQRVSYWCPN-GHETEVPFAAEAEVPATWECPRCGLP 59 (105)
T ss_pred ceEEEEECCC-CCEEeccccccCCCCCceeCCCCCCc
Confidence 4677899988 5544322332 57999999965
No 244
>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=38.81 E-value=22 Score=19.88 Aligned_cols=10 Identities=30% Similarity=0.903 Sum_probs=7.6
Q ss_pred eeeCCCCceE
Q 044880 54 WGCKDCGKVK 63 (91)
Q Consensus 54 W~C~~Cg~~~ 63 (91)
|.|.+||.++
T Consensus 2 r~C~~Cg~~Y 11 (36)
T PF05191_consen 2 RICPKCGRIY 11 (36)
T ss_dssp EEETTTTEEE
T ss_pred cCcCCCCCcc
Confidence 6788888765
No 245
>PHA02998 RNA polymerase subunit; Provisional
Probab=38.68 E-value=31 Score=26.44 Aligned_cols=31 Identities=23% Similarity=0.394 Sum_probs=21.9
Q ss_pred cccccCCCCceeeE------Ee----eeeeeeeCCCCceEe
Q 044880 34 SKYFCEFCGKYAVK------RK----AVGIWGCKDCGKVKA 64 (91)
Q Consensus 34 ~ky~CpfCGk~~Vk------R~----a~GIW~C~~Cg~~~A 64 (91)
..-.||.||....- |. .+--..|..||+.|.
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccC
Confidence 44579999987522 21 356789999998764
No 246
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=37.85 E-value=24 Score=21.80 Aligned_cols=48 Identities=25% Similarity=0.610 Sum_probs=25.5
Q ss_pred ccccCchhhHHHHHHHHHhh---cccccCCCCcee---------eEE----eeeeeeeeCCCCc
Q 044880 14 GTRYGASLRKQIKKMEVSQH---SKYFCEFCGKYA---------VKR----KAVGIWGCKDCGK 61 (91)
Q Consensus 14 G~RYG~slRK~v~kie~~q~---~ky~CpfCGk~~---------VkR----~a~GIW~C~~Cg~ 61 (91)
..+|...+++...+-++... ..-.|..||... +++ ...=++.|..||.
T Consensus 22 sr~y~~~~~~i~~k~~~~l~~~~kr~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 22 SRHYMKLMRKISKKTRIRLPPEIKRTICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp HHHHHHHHHHHHHHCT---STTCCCTB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTTE
T ss_pred HHHHHHHHHHHHHHhCCCCChHHhcccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccCC
Confidence 34566677777776666543 334899998743 231 3556889999873
No 247
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=37.83 E-value=26 Score=28.85 Aligned_cols=28 Identities=25% Similarity=0.726 Sum_probs=14.8
Q ss_pred ccCCCCc-eeeEEee------eeeeeeCCCCceEe
Q 044880 37 FCEFCGK-YAVKRKA------VGIWGCKDCGKVKA 64 (91)
Q Consensus 37 ~CpfCGk-~~VkR~a------~GIW~C~~Cg~~~A 64 (91)
.|+.||+ +.+.=.. +=-+.|..||....
T Consensus 176 iC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~ 210 (360)
T PF01921_consen 176 ICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGE 210 (360)
T ss_dssp EETTTEE--EEEEEEE--SSSEEEEE--TTS---E
T ss_pred eccccCCcccceeeEeecCCCEEEEEecCCCCEEE
Confidence 7999999 4433222 23689999997643
No 248
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=37.61 E-value=14 Score=23.88 Aligned_cols=23 Identities=22% Similarity=0.413 Sum_probs=12.9
Q ss_pred ccccCCCCcee--------eEEeeeeeeeeC
Q 044880 35 KYFCEFCGKYA--------VKRKAVGIWGCK 57 (91)
Q Consensus 35 ky~CpfCGk~~--------VkR~a~GIW~C~ 57 (91)
...|.|||... |+..+.-+|-|.
T Consensus 3 ~~~C~Fsg~~I~PG~G~~~Vr~DG~v~~F~s 33 (71)
T PF01246_consen 3 TEKCSFSGYKIYPGHGKMYVRNDGKVFYFCS 33 (71)
T ss_dssp SEE-TTT-SEE-SSSSEEEE-TTS-EEEESS
T ss_pred eEEecccCCccCCCCCeEEEecCCCeEEEeC
Confidence 46899999765 555566666664
No 249
>KOG1247 consensus Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=37.22 E-value=9.7 Score=32.97 Aligned_cols=22 Identities=41% Similarity=1.001 Sum_probs=14.1
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
+|||||-+.-+ |- +|.+||+.+
T Consensus 154 ~cp~C~yd~AR----GD-qcd~cG~l~ 175 (567)
T KOG1247|consen 154 KCPFCGYDDAR----GD-QCDKCGKLV 175 (567)
T ss_pred cCCCCCCcccc----ch-hhhhhhhhc
Confidence 67777776644 32 677777654
No 250
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=36.99 E-value=18 Score=24.77 Aligned_cols=11 Identities=36% Similarity=0.637 Sum_probs=7.7
Q ss_pred ccCCCCceeeE
Q 044880 37 FCEFCGKYAVK 47 (91)
Q Consensus 37 ~CpfCGk~~Vk 47 (91)
.||.||...++
T Consensus 90 ~CP~Cgs~~~~ 100 (117)
T PRK00564 90 VCEKCHSKNVI 100 (117)
T ss_pred cCcCCCCCceE
Confidence 48888876644
No 251
>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=36.85 E-value=16 Score=24.86 Aligned_cols=12 Identities=25% Similarity=0.545 Sum_probs=8.3
Q ss_pred ccccCCCCceee
Q 044880 35 KYFCEFCGKYAV 46 (91)
Q Consensus 35 ky~CpfCGk~~V 46 (91)
.+.||.||...+
T Consensus 86 ~~~CP~Cgs~~~ 97 (115)
T TIGR00100 86 LYRCPKCHGIML 97 (115)
T ss_pred CccCcCCcCCCc
Confidence 356888887653
No 252
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=36.30 E-value=44 Score=22.55 Aligned_cols=25 Identities=28% Similarity=0.557 Sum_probs=13.8
Q ss_pred hhhHHHHHH--HHHh-----h----cccccCCCCce
Q 044880 20 SLRKQIKKM--EVSQ-----H----SKYFCEFCGKY 44 (91)
Q Consensus 20 slRK~v~ki--e~~q-----~----~ky~CpfCGk~ 44 (91)
.||++..++ |... . ..+.|..|+++
T Consensus 28 Ri~kLk~~L~~e~~r~~~~~~~~~~~~~~C~~C~~~ 63 (118)
T PF02318_consen 28 RIRKLKQELQKEKMRREALGNSQKYGERHCARCGKP 63 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHCSCSTTHCCSB-TTTS-B
T ss_pred HHHHHHHHHHHHHHHhhccccccccCCcchhhhCCc
Confidence 356666666 3322 2 55689999875
No 253
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=36.25 E-value=26 Score=21.73 Aligned_cols=16 Identities=19% Similarity=0.428 Sum_probs=12.2
Q ss_pred eeeeeeeeCCCCceEe
Q 044880 49 KAVGIWGCKDCGKVKA 64 (91)
Q Consensus 49 ~a~GIW~C~~Cg~~~A 64 (91)
...|+|.|......+.
T Consensus 7 ~~~g~w~~~pg~~~~~ 22 (74)
T PF05899_consen 7 FSAGVWECTPGKFPWP 22 (74)
T ss_dssp EEEEEEEEECEEEEEE
T ss_pred EEEEEEEECCceeEee
Confidence 4789999999765544
No 254
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.25 E-value=16 Score=23.56 Aligned_cols=15 Identities=33% Similarity=0.468 Sum_probs=11.3
Q ss_pred hcccccCCCCceeeE
Q 044880 33 HSKYFCEFCGKYAVK 47 (91)
Q Consensus 33 ~~ky~CpfCGk~~Vk 47 (91)
...-.||.||++.+.
T Consensus 5 ~~~v~CP~Cgkpv~w 19 (65)
T COG3024 5 RITVPCPTCGKPVVW 19 (65)
T ss_pred cccccCCCCCCcccc
Confidence 344579999998764
No 255
>PRK08173 DNA topoisomerase III; Validated
Probab=36.23 E-value=34 Score=30.86 Aligned_cols=28 Identities=18% Similarity=0.331 Sum_probs=20.0
Q ss_pred cccccCCCCceeeEEeeeeeeeeCC-------CCceE
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCKD-------CGKVK 63 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~~-------Cg~~~ 63 (91)
..-.||.||...+. .-..|.|.. |+.++
T Consensus 725 ~~g~CPkCg~~v~e--~~k~y~Cs~~~~~~~~C~f~i 759 (862)
T PRK08173 725 PVGACPKCGGRVFE--HGMSYVCEKSVGPPKTCDFRS 759 (862)
T ss_pred cccCCCCCCCeeEe--eceEEEeCCCcCCCCCCCeee
Confidence 44589999997554 233699986 87665
No 256
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=35.93 E-value=23 Score=20.09 Aligned_cols=10 Identities=50% Similarity=1.049 Sum_probs=4.4
Q ss_pred eeCCCCceEe
Q 044880 55 GCKDCGKVKA 64 (91)
Q Consensus 55 ~C~~Cg~~~A 64 (91)
.|..|+..|=
T Consensus 15 ~C~~C~~~FC 24 (43)
T PF01428_consen 15 KCKHCGKSFC 24 (43)
T ss_dssp E-TTTS-EE-
T ss_pred ECCCCCcccC
Confidence 5666666653
No 257
>PRK05582 DNA topoisomerase I; Validated
Probab=35.77 E-value=53 Score=28.38 Aligned_cols=28 Identities=25% Similarity=0.549 Sum_probs=18.5
Q ss_pred ccccCCCCceeeEEe-eee-eeeeCC---CCce
Q 044880 35 KYFCEFCGKYAVKRK-AVG-IWGCKD---CGKV 62 (91)
Q Consensus 35 ky~CpfCGk~~VkR~-a~G-IW~C~~---Cg~~ 62 (91)
...||.||...+.+. ..| .|.|.. |+..
T Consensus 571 ~~~CP~Cg~~l~~~~~k~gkf~~Cs~~~~C~~~ 603 (650)
T PRK05582 571 GEDCPKCGSPMVIKMGRYGKFIACSNFPDCRNT 603 (650)
T ss_pred CCCCCCCCCEeEEEecCCCceeecCCccccccC
Confidence 367999998766443 233 488876 7644
No 258
>PRK14873 primosome assembly protein PriA; Provisional
Probab=35.72 E-value=16 Score=32.04 Aligned_cols=26 Identities=27% Similarity=0.468 Sum_probs=10.9
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
.||.|+-.-+--...+.=.|..||+.
T Consensus 394 ~C~~C~~~L~~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 394 RCRHCTGPLGLPSAGGTPRCRWCGRA 419 (665)
T ss_pred ECCCCCCceeEecCCCeeECCCCcCC
Confidence 44444443332223334445555443
No 259
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=35.51 E-value=25 Score=20.07 Aligned_cols=21 Identities=33% Similarity=0.586 Sum_probs=15.4
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCC
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
|.|..|+++.+. =.|+|..|.
T Consensus 1 ~~C~~C~~~i~g----~r~~C~~C~ 21 (46)
T cd02249 1 YSCDGCLKPIVG----VRYHCLVCE 21 (46)
T ss_pred CCCcCCCCCCcC----CEEECCCCC
Confidence 679999985432 258999886
No 260
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=35.32 E-value=35 Score=19.33 Aligned_cols=28 Identities=29% Similarity=0.879 Sum_probs=18.1
Q ss_pred hcccccCCCCcee--eEEeeeeeeeeCCCCceE
Q 044880 33 HSKYFCEFCGKYA--VKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 33 ~~ky~CpfCGk~~--VkR~a~GIW~C~~Cg~~~ 63 (91)
..+-.|..|++.. +.+++ ++|..|+..+
T Consensus 9 ~~~~~C~~C~~~i~g~~~~g---~~C~~C~~~~ 38 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGKQG---YRCSWCGLVC 38 (53)
T ss_dssp SSTEB-TTSSSBECSSSSCE---EEETTTT-EE
T ss_pred CCCCCCcccCcccCCCCCCe---EEECCCCChH
Confidence 3455799999887 33333 6999998765
No 261
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=35.27 E-value=18 Score=25.03 Aligned_cols=12 Identities=25% Similarity=0.650 Sum_probs=9.1
Q ss_pred cccCCCCceeeE
Q 044880 36 YFCEFCGKYAVK 47 (91)
Q Consensus 36 y~CpfCGk~~Vk 47 (91)
+.||.||...++
T Consensus 93 ~~CP~Cgs~~~~ 104 (124)
T PRK00762 93 IECPVCGNKRAH 104 (124)
T ss_pred CcCcCCCCCCCE
Confidence 579999976644
No 262
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=35.18 E-value=17 Score=21.44 Aligned_cols=10 Identities=40% Similarity=1.049 Sum_probs=3.2
Q ss_pred cccccCCCCc
Q 044880 34 SKYFCEFCGK 43 (91)
Q Consensus 34 ~ky~CpfCGk 43 (91)
..+.||.|++
T Consensus 40 ~~W~CPiC~~ 49 (50)
T PF02891_consen 40 PKWKCPICNK 49 (50)
T ss_dssp ---B-TTT--
T ss_pred CCeECcCCcC
Confidence 3467888865
No 263
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=35.12 E-value=21 Score=29.30 Aligned_cols=21 Identities=24% Similarity=0.596 Sum_probs=18.5
Q ss_pred eeeeeeeCCCCceEecccccc
Q 044880 50 AVGIWGCKDCGKVKAGGAYTL 70 (91)
Q Consensus 50 a~GIW~C~~Cg~~~AGGAy~~ 70 (91)
.+-|=.|..||..+-+|-|.-
T Consensus 40 ~~~v~~C~~Cga~~~~~~W~~ 60 (355)
T COG1499 40 EVNVEVCRHCGAYRIRGRWVD 60 (355)
T ss_pred ceEEEECCcCCCccCCCccee
Confidence 456778999999999999987
No 264
>cd06963 NR_DBD_GR_like The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family of NRs includes four types of nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). The receptors bind to common DNA elements containing a partial palindrome of the core sequence 5'-TGTTCT-3' with a 3bp spacer. These four receptors regulate some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family have high sequence homology and sha
Probab=35.10 E-value=22 Score=22.42 Aligned_cols=22 Identities=32% Similarity=0.764 Sum_probs=16.4
Q ss_pred cCCCCceeeEEeeeeeeeeCCCC
Q 044880 38 CEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 38 CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
|..||+++.. .-.|.|.|..|.
T Consensus 1 C~VCg~~a~~-~hygv~sC~aCk 22 (73)
T cd06963 1 CLICGDEASG-CHYGVLTCGSCK 22 (73)
T ss_pred CcccCccCcc-eEECceeehhhh
Confidence 6788876543 467889999986
No 265
>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=34.96 E-value=19 Score=23.68 Aligned_cols=27 Identities=30% Similarity=0.652 Sum_probs=21.0
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCc
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
....|..||..+.. .-.|.|.|..|.-
T Consensus 5 ~~~~C~VCg~~a~g-~hyGv~sC~aCk~ 31 (90)
T cd07169 5 EQRTCLICGDRATG-LHYGIISCEGCKG 31 (90)
T ss_pred cCCCCeecCCcCcc-eEECcceehhhHH
Confidence 34569999987755 4579999999973
No 266
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=34.79 E-value=14 Score=28.24 Aligned_cols=25 Identities=24% Similarity=0.619 Sum_probs=21.1
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
.-+.|+.|....-.|. |||+.|+.=
T Consensus 112 ~~~~C~~C~~~rPpRs----~HCsvC~~C 136 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRS----SHCSVCNNC 136 (299)
T ss_pred ceEEcCcCcccCCCCc----ccchhhccc
Confidence 3578999999988887 899999863
No 267
>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=34.45 E-value=27 Score=20.88 Aligned_cols=27 Identities=33% Similarity=0.861 Sum_probs=9.5
Q ss_pred ccccCCCCcee--eEEeeeeeeeeCCCCceEec
Q 044880 35 KYFCEFCGKYA--VKRKAVGIWGCKDCGKVKAG 65 (91)
Q Consensus 35 ky~CpfCGk~~--VkR~a~GIW~C~~Cg~~~AG 65 (91)
.-.|+.|++.- +.|. =+|+.||..|=.
T Consensus 9 ~~~C~~C~~~F~~~~rr----hhCr~CG~~vC~ 37 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRR----HHCRNCGRVVCS 37 (69)
T ss_dssp -SB-TTT--B-BSSS-E----EE-TTT--EEEC
T ss_pred CCcCcCcCCcCCCceee----EccCCCCCEECC
Confidence 34577777652 2333 256666665543
No 268
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=34.41 E-value=17 Score=29.61 Aligned_cols=23 Identities=17% Similarity=0.210 Sum_probs=15.9
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCC
Q 044880 35 KYFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 35 ky~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
.+.|+.||+.-- .. ..|.|..|+
T Consensus 2 ~l~C~~Cg~~~~--~~-~~~~C~~c~ 24 (398)
T TIGR03844 2 TLRCPGCGEVLP--DH-YTLSCPLDC 24 (398)
T ss_pred EEEeCCCCCccC--Cc-cccCCCCCC
Confidence 367999997752 22 368898776
No 269
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=34.37 E-value=13 Score=34.09 Aligned_cols=32 Identities=16% Similarity=0.298 Sum_probs=0.0
Q ss_pred eeCCCCceEecccccccccHHHHHHHHHHHHHh
Q 044880 55 GCKDCGKVKAGGAYTLNTASAVTVRSTIRRLRE 87 (91)
Q Consensus 55 ~C~~Cg~~~AGGAy~~~T~~~~t~~~~i~rl~e 87 (91)
.|.+|+.....-.+ -+-+....+.+|+.+|.+
T Consensus 694 ~C~~C~~~~~~~~~-~~i~l~~~~~~A~e~lg~ 725 (900)
T PF03833_consen 694 ECPKCGRETTSYSK-QKIDLKEEYDRALENLGE 725 (900)
T ss_dssp ---------------------------------
T ss_pred ccccccccCcccce-eecCHHHHHHHHHHhhcc
Confidence 89999977443222 223344455555555543
No 270
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=34.32 E-value=28 Score=21.29 Aligned_cols=23 Identities=26% Similarity=0.495 Sum_probs=16.4
Q ss_pred ccccCCCCcee--------eEEeeeeeeeeC
Q 044880 35 KYFCEFCGKYA--------VKRKAVGIWGCK 57 (91)
Q Consensus 35 ky~CpfCGk~~--------VkR~a~GIW~C~ 57 (91)
...|.|||... |+..+.-.|-|.
T Consensus 3 ~~~C~f~g~~I~PG~G~~~Vr~Dgkv~~F~s 33 (54)
T cd00472 3 TEKCSFCGYKIYPGHGKMYVRNDGKVFRFCS 33 (54)
T ss_pred EEEecCcCCeecCCCccEEEecCCCEEEEEC
Confidence 35799998765 666676777665
No 271
>PRK14724 DNA topoisomerase III; Provisional
Probab=34.27 E-value=23 Score=32.51 Aligned_cols=26 Identities=23% Similarity=0.510 Sum_probs=18.6
Q ss_pred cccCCCCceeeEEeeeeeeeeCC-------CCceE
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKD-------CGKVK 63 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~-------Cg~~~ 63 (91)
-.||.||...+. .-+-|.|.. |+.++
T Consensus 644 ~~CP~Cg~~~~~--~~~~~~Cs~~~~~~~~C~f~~ 676 (987)
T PRK14724 644 TPCPNCGGVVKE--NYRRYACTGANGAGEGCGFSF 676 (987)
T ss_pred ccCCcccccccc--cCceeecCCCcCCCCCCCccc
Confidence 469999987543 234599994 88765
No 272
>PRK05638 threonine synthase; Validated
Probab=34.23 E-value=19 Score=29.32 Aligned_cols=24 Identities=29% Similarity=0.425 Sum_probs=16.2
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 35 KYFCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 35 ky~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
++.|+.||+.-- .. -.|.| .|+-.
T Consensus 1 ~l~C~~Cg~~~~--~~-~~~~C-~c~~~ 24 (442)
T PRK05638 1 KMKCPKCGREYN--SY-IPPFC-ICGEL 24 (442)
T ss_pred CeEeCCCCCCCC--CC-Cceec-CCCCc
Confidence 478999998753 12 23899 89733
No 273
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=34.19 E-value=18 Score=20.66 Aligned_cols=13 Identities=23% Similarity=0.628 Sum_probs=7.3
Q ss_pred ccccCCCCceeeE
Q 044880 35 KYFCEFCGKYAVK 47 (91)
Q Consensus 35 ky~CpfCGk~~Vk 47 (91)
+|.||.||--.+.
T Consensus 1 ~hlcpkcgvgvl~ 13 (36)
T PF09151_consen 1 QHLCPKCGVGVLE 13 (36)
T ss_dssp --B-TTTSSSBEE
T ss_pred CccCCccCceEEE
Confidence 3679999976543
No 274
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=33.91 E-value=36 Score=28.56 Aligned_cols=29 Identities=28% Similarity=0.539 Sum_probs=22.3
Q ss_pred hhcccccCCCCceeeEEe--eeeeeeeCCCC
Q 044880 32 QHSKYFCEFCGKYAVKRK--AVGIWGCKDCG 60 (91)
Q Consensus 32 q~~ky~CpfCGk~~VkR~--a~GIW~C~~Cg 60 (91)
|...-.|=.||..---.+ ..|||.|=.|-
T Consensus 16 ~deNk~CfeC~a~NPQWvSvsyGIfICLECS 46 (386)
T KOG0704|consen 16 QDENKKCFECGAPNPQWVSVSYGIFICLECS 46 (386)
T ss_pred cccCCceeecCCCCCCeEeecccEEEEEecC
Confidence 345668999998765554 56999999995
No 275
>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=33.74 E-value=29 Score=19.79 Aligned_cols=12 Identities=25% Similarity=1.016 Sum_probs=6.7
Q ss_pred eeeeeCCCCceE
Q 044880 52 GIWGCKDCGKVK 63 (91)
Q Consensus 52 GIW~C~~Cg~~~ 63 (91)
.+++|..||..+
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 478888888665
No 276
>PRK07220 DNA topoisomerase I; Validated
Probab=33.71 E-value=41 Score=29.66 Aligned_cols=27 Identities=26% Similarity=0.635 Sum_probs=17.2
Q ss_pred cccCCCCceeeEEee-e-e-eeeeCC---CCce
Q 044880 36 YFCEFCGKYAVKRKA-V-G-IWGCKD---CGKV 62 (91)
Q Consensus 36 y~CpfCGk~~VkR~a-~-G-IW~C~~---Cg~~ 62 (91)
..||.||++.+.|.+ . | -|.|.. |...
T Consensus 590 ~~CP~Cg~~l~~r~~r~g~~f~gCs~yp~C~~~ 622 (740)
T PRK07220 590 GKCPLCGSDLMVRRSKRGSRFIGCEGYPECTFS 622 (740)
T ss_pred cccccCCCeeeEEecCCCceEEEcCCCCCCCce
Confidence 479999988765443 1 2 477753 6543
No 277
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.48 E-value=37 Score=26.21 Aligned_cols=33 Identities=21% Similarity=0.365 Sum_probs=22.7
Q ss_pred ccCCCCcee------eEEe--------eeeeeeeCCCCceEeccccc
Q 044880 37 FCEFCGKYA------VKRK--------AVGIWGCKDCGKVKAGGAYT 69 (91)
Q Consensus 37 ~CpfCGk~~------VkR~--------a~GIW~C~~Cg~~~AGGAy~ 69 (91)
.|+-||... .-|+ .==|++|..|++++-=+-|+
T Consensus 19 ~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWlIYkC~~Cd~tWN~~Ife 65 (203)
T COG4332 19 RCNSCGVKRAFTCSGKFRVNAQGKVLDVWLIYKCTHCDYTWNISIFE 65 (203)
T ss_pred hCcccCCcceeeecCcEEEcCCCcEEEEEEEEEeeccCCccchhhhh
Confidence 599999764 2222 12588999999987665554
No 278
>COG1773 Rubredoxin [Energy production and conversion]
Probab=33.39 E-value=26 Score=21.81 Aligned_cols=12 Identities=42% Similarity=1.013 Sum_probs=9.4
Q ss_pred eeeeCCCCceEe
Q 044880 53 IWGCKDCGKVKA 64 (91)
Q Consensus 53 IW~C~~Cg~~~A 64 (91)
-|+|+-||..+-
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 389999988763
No 279
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian
Probab=33.35 E-value=26 Score=23.25 Aligned_cols=26 Identities=23% Similarity=0.588 Sum_probs=18.4
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
.|..||..+.. .-.|.|.|..|.-=|
T Consensus 2 ~C~VCg~~a~g-~hyGv~sC~aC~~FF 27 (94)
T cd06966 2 ICGVCGDKALG-YNFNAITCESCKAFF 27 (94)
T ss_pred CCeeCCCcCcc-eEECcceeeeehhee
Confidence 38889876544 367889999987433
No 280
>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=33.31 E-value=45 Score=17.25 Aligned_cols=24 Identities=21% Similarity=0.546 Sum_probs=11.4
Q ss_pred ccCCCCcee--eEEeeeeeeeeCCCC
Q 044880 37 FCEFCGKYA--VKRKAVGIWGCKDCG 60 (91)
Q Consensus 37 ~CpfCGk~~--VkR~a~GIW~C~~Cg 60 (91)
.||.|+... +.-.+-.-.-|..|-
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred cCccCCCcceEeEecCCCCeECcCCc
Confidence 588898874 332234556677773
No 281
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=33.12 E-value=17 Score=22.68 Aligned_cols=13 Identities=23% Similarity=0.626 Sum_probs=6.1
Q ss_pred hhcccccCCCCce
Q 044880 32 QHSKYFCEFCGKY 44 (91)
Q Consensus 32 q~~ky~CpfCGk~ 44 (91)
...+.+||.|+..
T Consensus 21 S~~PatCP~C~a~ 33 (54)
T PF09237_consen 21 SEQPATCPICGAV 33 (54)
T ss_dssp TS--EE-TTT--E
T ss_pred cCCCCCCCcchhh
Confidence 3567799999875
No 282
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=33.05 E-value=35 Score=26.30 Aligned_cols=25 Identities=20% Similarity=0.327 Sum_probs=17.6
Q ss_pred ccccCCCCceeeEEe---eeeeeeeCCCC
Q 044880 35 KYFCEFCGKYAVKRK---AVGIWGCKDCG 60 (91)
Q Consensus 35 ky~CpfCGk~~VkR~---a~GIW~C~~Cg 60 (91)
--.||.||... .+. +-+.|-|..|-
T Consensus 244 g~pCprCG~~I-~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPI-RRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCee-EEEEECCCccEECcCCc
Confidence 34899999654 334 34689999984
No 283
>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=32.98 E-value=55 Score=27.85 Aligned_cols=30 Identities=20% Similarity=0.248 Sum_probs=13.3
Q ss_pred eeeeeCCC--CceEec----ccccccccHHHHHHHH
Q 044880 52 GIWGCKDC--GKVKAG----GAYTLNTASAVTVRST 81 (91)
Q Consensus 52 GIW~C~~C--g~~~AG----GAy~~~T~~~~t~~~~ 81 (91)
|.|.+... ....+| +.|.|..+-+..|+.=
T Consensus 251 G~Wv~~~~~~~~~~~gf~i~~l~Sp~~sw~~ia~~~ 286 (557)
T PF05876_consen 251 GRWVATNPDRRPRHVGFHINALYSPFVSWAEIAREF 286 (557)
T ss_pred eEEEeccccCCCCEEEEEeeeeecccCCHHHHHHHH
Confidence 44444444 333333 4444544444444433
No 284
>cd06969 NR_DBD_NGFI-B DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B. DNA-binding domain (DBD) of the orphan nuclear receptor, nerve growth factor-induced-B (NGFI-B) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NGFI-B interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. NGFI-B is a member of the nuclear-steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcrip
Probab=32.81 E-value=29 Score=21.90 Aligned_cols=26 Identities=27% Similarity=0.718 Sum_probs=19.4
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
.|..||.++.. .-.|.|.|..|.-=|
T Consensus 2 ~C~VCg~~~~g-~hyGv~sC~aC~~FF 27 (75)
T cd06969 2 LCAVCGDNAAC-QHYGVRTCEGCKGFF 27 (75)
T ss_pred CCeecCCcCcc-eEECcceeeeeeeee
Confidence 48899987655 357999999997443
No 285
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=32.79 E-value=45 Score=24.71 Aligned_cols=49 Identities=18% Similarity=0.426 Sum_probs=33.8
Q ss_pred hhHHHHHHHHHhhcccccCCCCcee-eEEeee-eeeeeCCCCceEeccccc
Q 044880 21 LRKQIKKMEVSQHSKYFCEFCGKYA-VKRKAV-GIWGCKDCGKVKAGGAYT 69 (91)
Q Consensus 21 lRK~v~kie~~q~~ky~CpfCGk~~-VkR~a~-GIW~C~~Cg~~~AGGAy~ 69 (91)
..+.|...++=+..-|.|.+|..+. +-.-.. ..=.|.+|+..|==.-|.
T Consensus 138 ~~~HV~~C~lC~~kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~ 188 (202)
T PF13901_consen 138 AEKHVYSCELCQQKGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFR 188 (202)
T ss_pred HHHHHHHhHHHHhCCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcC
Confidence 3456777788888899999999754 332233 666899998776444433
No 286
>PRK06260 threonine synthase; Validated
Probab=32.73 E-value=18 Score=28.96 Aligned_cols=23 Identities=35% Similarity=0.674 Sum_probs=12.1
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCC
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
+.|+.||+..-- ..-.|.|..|+
T Consensus 4 ~~C~~cg~~~~~--~~~~~~Cp~cg 26 (397)
T PRK06260 4 LKCIECGKEYDP--DEIIYTCPECG 26 (397)
T ss_pred EEECCCCCCCCC--CCccccCCCCC
Confidence 567777755311 11246676665
No 287
>PRK08197 threonine synthase; Validated
Probab=32.64 E-value=19 Score=28.75 Aligned_cols=23 Identities=26% Similarity=0.462 Sum_probs=16.6
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCC
Q 044880 35 KYFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 35 ky~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
.+.|+.||+..-- ..-+|.| .||
T Consensus 7 ~~~C~~Cg~~~~~--~~~~~~C-~cg 29 (394)
T PRK08197 7 HLECSKCGETYDA--DQVHNLC-KCG 29 (394)
T ss_pred EEEECCCCCCCCC--CCcceec-CCC
Confidence 4899999987521 2236999 896
No 288
>cd07156 NR_DBD_VDR_like The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemi
Probab=32.43 E-value=24 Score=22.06 Aligned_cols=22 Identities=27% Similarity=0.709 Sum_probs=16.4
Q ss_pred cCCCCceeeEEeeeeeeeeCCCC
Q 044880 38 CEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 38 CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
|..||.++.. .-.|.|.|..|.
T Consensus 1 C~VC~~~~~g-~hygv~sC~aC~ 22 (72)
T cd07156 1 CGVCGDRATG-YHFNAMTCEGCK 22 (72)
T ss_pred CCccCccCcc-cEECcceehhhh
Confidence 6778876544 467889999886
No 289
>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=32.35 E-value=25 Score=17.66 Aligned_cols=9 Identities=44% Similarity=1.652 Sum_probs=4.9
Q ss_pred cccCCCCce
Q 044880 36 YFCEFCGKY 44 (91)
Q Consensus 36 y~CpfCGk~ 44 (91)
|.|+.|++.
T Consensus 2 ~~C~~C~k~ 10 (27)
T PF12171_consen 2 FYCDACDKY 10 (27)
T ss_dssp CBBTTTTBB
T ss_pred CCcccCCCC
Confidence 456666543
No 290
>PRK14724 DNA topoisomerase III; Provisional
Probab=32.35 E-value=37 Score=31.20 Aligned_cols=21 Identities=24% Similarity=0.487 Sum_probs=15.9
Q ss_pred ccccCCCCceeeEEeeeee-eeeCC
Q 044880 35 KYFCEFCGKYAVKRKAVGI-WGCKD 58 (91)
Q Consensus 35 ky~CpfCGk~~VkR~a~GI-W~C~~ 58 (91)
--.||.||...+. .|- |.|..
T Consensus 755 ~g~CPkCg~~v~e---~gk~y~Cs~ 776 (987)
T PRK14724 755 LGPCPKCGAPVFE---HGSNYVCEK 776 (987)
T ss_pred ccCCCCCCCceEe---ecceEEcCC
Confidence 3589999988664 344 99985
No 291
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=32.34 E-value=35 Score=24.13 Aligned_cols=29 Identities=14% Similarity=0.232 Sum_probs=24.6
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceEecc
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVKAGG 66 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGG 66 (91)
.||.|...-+.+.+. ...|..|...++..
T Consensus 5 ~cp~c~sEytYed~~-~~~cpec~~ew~~~ 33 (112)
T COG2824 5 PCPKCNSEYTYEDGG-QLICPECAHEWNEN 33 (112)
T ss_pred CCCccCCceEEecCc-eEeCchhccccccc
Confidence 699999999997776 88999999887744
No 292
>PRK06921 hypothetical protein; Provisional
Probab=32.25 E-value=44 Score=25.54 Aligned_cols=12 Identities=25% Similarity=0.733 Sum_probs=9.8
Q ss_pred ccccCCCCceee
Q 044880 35 KYFCEFCGKYAV 46 (91)
Q Consensus 35 ky~CpfCGk~~V 46 (91)
.|.||.|+.+-.
T Consensus 32 ~~~Cp~C~dtG~ 43 (266)
T PRK06921 32 RYDCPKCKDRGI 43 (266)
T ss_pred CCCCCCCCCCEE
Confidence 589999998853
No 293
>cd07157 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers. The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=32.20 E-value=28 Score=22.63 Aligned_cols=26 Identities=31% Similarity=0.667 Sum_probs=19.4
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
.|..||.++.. .-.|.|.|..|.-=|
T Consensus 2 ~C~VCg~~a~g-~hyGv~sC~aCk~FF 27 (86)
T cd07157 2 TCQVCGEPAAG-FHHGAYVCEACKKFF 27 (86)
T ss_pred CCcccCCcCcc-cEECcceeeEeeeEE
Confidence 58999987644 467889999997444
No 294
>cd07179 2DBD_NR_DBD2 The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type zinc fingers. The second DNA-binding domain (DBD) of the 2DBD nuclear receptor (NR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. The proteins contain two DBDs in tandem, probably resulting from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=32.18 E-value=23 Score=22.30 Aligned_cols=22 Identities=27% Similarity=0.744 Sum_probs=16.7
Q ss_pred cCCCCceeeEEeeeeeeeeCCCC
Q 044880 38 CEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 38 CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
|..||.++.. .-.|+|.|..|.
T Consensus 1 C~VCg~~~~g-~hygv~sC~aC~ 22 (74)
T cd07179 1 CRVCGGKSSG-FHFGALTCEGCK 22 (74)
T ss_pred CcccCccCcc-eEECceeehhHH
Confidence 7788877654 457889999886
No 295
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p
Probab=32.02 E-value=23 Score=22.69 Aligned_cols=23 Identities=26% Similarity=0.642 Sum_probs=18.4
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCC
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
.|..||+.+.. .-.|+|.|..|.
T Consensus 4 ~C~VCg~~a~g-~hyGv~sC~aC~ 26 (78)
T cd07172 4 ICLVCSDEASG-CHYGVLTCGSCK 26 (78)
T ss_pred CCeecCCcCcc-eEECceeehhhH
Confidence 49999987644 467999999996
No 296
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.89 E-value=33 Score=24.01 Aligned_cols=15 Identities=20% Similarity=0.607 Sum_probs=12.1
Q ss_pred eeeeeCCCCceEecc
Q 044880 52 GIWGCKDCGKVKAGG 66 (91)
Q Consensus 52 GIW~C~~Cg~~~AGG 66 (91)
..|.|..||..|.-.
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 779999999888654
No 297
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=31.87 E-value=51 Score=21.04 Aligned_cols=28 Identities=29% Similarity=0.584 Sum_probs=19.2
Q ss_pred cccccCCCCceeeEEe-------eeeeeeeCCCCc
Q 044880 34 SKYFCEFCGKYAVKRK-------AVGIWGCKDCGK 61 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~-------a~GIW~C~~Cg~ 61 (91)
-.|+|..|+..+.+.. ++=|=+|..|..
T Consensus 3 l~FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~ 37 (66)
T PF05180_consen 3 LTFTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKN 37 (66)
T ss_dssp EEEEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--
T ss_pred EEEEcCCCCCccceeeCHHHHhCCeEEEECCCCcc
Confidence 4689999998776655 455668999974
No 298
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=31.85 E-value=23 Score=18.13 Aligned_cols=10 Identities=30% Similarity=0.700 Sum_probs=5.9
Q ss_pred eeCCCCceEe
Q 044880 55 GCKDCGKVKA 64 (91)
Q Consensus 55 ~C~~Cg~~~A 64 (91)
.|..||.+|.
T Consensus 4 ~C~~CgR~F~ 13 (25)
T PF13913_consen 4 PCPICGRKFN 13 (25)
T ss_pred cCCCCCCEEC
Confidence 3666666663
No 299
>PRK02935 hypothetical protein; Provisional
Probab=31.79 E-value=24 Score=24.88 Aligned_cols=25 Identities=24% Similarity=0.614 Sum_probs=18.4
Q ss_pred cccccCCCCcee--eEEeeeeeeeeCCCCce
Q 044880 34 SKYFCEFCGKYA--VKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 34 ~ky~CpfCGk~~--VkR~a~GIW~C~~Cg~~ 62 (91)
..-.||.|+|.. +.|+. .|-.|++-
T Consensus 69 vqV~CP~C~K~TKmLGrvD----~CM~C~~P 95 (110)
T PRK02935 69 VQVICPSCEKPTKMLGRVD----ACMHCNQP 95 (110)
T ss_pred eeeECCCCCchhhhcccee----ecCcCCCc
Confidence 344899999975 66665 58888754
No 300
>cd06916 NR_DBD_like DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Most nuclear receptors bind as homodimers or hetero
Probab=31.68 E-value=30 Score=21.53 Aligned_cols=25 Identities=28% Similarity=0.683 Sum_probs=18.1
Q ss_pred cCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 38 CEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 38 CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
|..||.++.. .-.|+|.|..|.-=|
T Consensus 1 C~vC~~~~~~-~hygv~sC~aC~~FF 25 (72)
T cd06916 1 CAVCGDKASG-YHYGVLTCEGCKGFF 25 (72)
T ss_pred CCccCccCcc-cEECcceeeeeeeeE
Confidence 6788876654 457889999997433
No 301
>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=31.53 E-value=40 Score=26.84 Aligned_cols=41 Identities=24% Similarity=0.532 Sum_probs=19.7
Q ss_pred HHHhhcccccCCCCceeeEEe----eeeeeeeCCCCc-------------eEeccccc
Q 044880 29 EVSQHSKYFCEFCGKYAVKRK----AVGIWGCKDCGK-------------VKAGGAYT 69 (91)
Q Consensus 29 e~~q~~ky~CpfCGk~~VkR~----a~GIW~C~~Cg~-------------~~AGGAy~ 69 (91)
|.=-.....||-||...+..- .|.-..|..|++ ++++|||.
T Consensus 25 E~Wv~~n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyELKSk~~~l~~~I~dGAY~ 82 (254)
T PF06044_consen 25 EDWVAENMYCPNCGSKPLSKFENNRPVADFYCPNCNEEYELKSKKKKLSNKINDGAYH 82 (254)
T ss_dssp HHHHHHH---TTT--SS-EE--------EEE-TTT--EEEEEEEESS--SEEEEEEHH
T ss_pred HHHHHHCCcCCCCCChhHhhccCCCccceeECCCCchHHhhhhhccccCCcccCccHH
Confidence 333455678999998855443 456678999974 56888884
No 302
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=31.36 E-value=20 Score=29.81 Aligned_cols=14 Identities=29% Similarity=0.631 Sum_probs=11.2
Q ss_pred HhhcccccCCCCce
Q 044880 31 SQHSKYFCEFCGKY 44 (91)
Q Consensus 31 ~q~~ky~CpfCGk~ 44 (91)
.|...|+||.|+-.
T Consensus 15 vq~~~YtCPRCn~~ 28 (383)
T KOG4317|consen 15 VQKREYTCPRCNLL 28 (383)
T ss_pred cccccccCCCCCcc
Confidence 36677999999865
No 303
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=31.19 E-value=60 Score=27.93 Aligned_cols=26 Identities=27% Similarity=0.648 Sum_probs=17.3
Q ss_pred cccCCCCceeeEEe-eeee-eeeCC---CCc
Q 044880 36 YFCEFCGKYAVKRK-AVGI-WGCKD---CGK 61 (91)
Q Consensus 36 y~CpfCGk~~VkR~-a~GI-W~C~~---Cg~ 61 (91)
-.||.||++.+.|. ..|- |.|.. |+.
T Consensus 575 ~~CP~Cg~~~~~~~~~~gkf~gCs~y~~C~~ 605 (610)
T TIGR01051 575 QDCPLCGRPMVVKLGKYGPFLACSNFPECKY 605 (610)
T ss_pred CCCCCCCCeeEEEecCCCceeeCCCCCCCCC
Confidence 46999998765433 2343 99977 653
No 304
>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=31.10 E-value=32 Score=20.92 Aligned_cols=22 Identities=27% Similarity=0.924 Sum_probs=14.4
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCC
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
+--.||.||...+-=. .|..||
T Consensus 25 ~l~~C~~cG~~~~~H~-----vc~~cG 46 (55)
T TIGR01031 25 TLVVCPNCGEFKLPHR-----VCPSCG 46 (55)
T ss_pred cceECCCCCCcccCee-----ECCccC
Confidence 3346999998765422 377777
No 305
>PRK07219 DNA topoisomerase I; Validated
Probab=31.09 E-value=38 Score=30.18 Aligned_cols=29 Identities=24% Similarity=0.476 Sum_probs=20.0
Q ss_pred ccccCCCCceeeEEe-eee--eeeeCC---CCceE
Q 044880 35 KYFCEFCGKYAVKRK-AVG--IWGCKD---CGKVK 63 (91)
Q Consensus 35 ky~CpfCGk~~VkR~-a~G--IW~C~~---Cg~~~ 63 (91)
...||.||++.+.|. ..| -|.|.. |..+.
T Consensus 602 ~~~CP~Cg~~l~~r~~~~g~~F~gCs~yp~C~~t~ 636 (822)
T PRK07219 602 IGKCPECGGDLIIIRTDKGSRFVGCSGYPDCRNTF 636 (822)
T ss_pred cCcCCCCCCcceeeeccCCceeeecCCCcCCCCee
Confidence 357999998765443 333 589977 88663
No 306
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=31.08 E-value=54 Score=20.70 Aligned_cols=27 Identities=19% Similarity=0.617 Sum_probs=17.8
Q ss_pred ccCCCCcee---eEEe-eeeeeeeCCCCceE
Q 044880 37 FCEFCGKYA---VKRK-AVGIWGCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~~---VkR~-a~GIW~C~~Cg~~~ 63 (91)
.||.|+... +.+. .+-.=.|-.||++-
T Consensus 11 ~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 11 VCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred cCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 799999753 2222 23346899999875
No 307
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=31.05 E-value=41 Score=23.43 Aligned_cols=33 Identities=24% Similarity=0.311 Sum_probs=20.5
Q ss_pred HHHHhhcccccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 28 MEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 28 ie~~q~~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
|-+++-.+-.-| +.+.|. +.+|.+.|.+||+-+
T Consensus 25 iAIseaGkrLn~--~~~~Ve-IevG~~~cP~Cge~~ 57 (102)
T PF04475_consen 25 IAISEAGKRLNP--DLDYVE-IEVGDTICPKCGEEL 57 (102)
T ss_pred HHHHHHHHhhCC--CCCeEE-EecCcccCCCCCCcc
Confidence 334444444555 444454 788888999998654
No 308
>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers. DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding
Probab=30.92 E-value=23 Score=22.98 Aligned_cols=23 Identities=26% Similarity=0.710 Sum_probs=17.3
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCC
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
.|..||..... .-.|.|.|..|.
T Consensus 1 ~C~VCg~~~~g-~hygv~sC~aC~ 23 (87)
T cd07162 1 ICRVCGDRATG-YHFNAMTCEGCK 23 (87)
T ss_pred CCcccCCcCcc-eEECcceehhhH
Confidence 38889887654 357889998886
No 309
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=30.78 E-value=27 Score=23.49 Aligned_cols=29 Identities=24% Similarity=0.588 Sum_probs=18.4
Q ss_pred hhcccccCCCCceeeEEee--eeeeeeCCCC
Q 044880 32 QHSKYFCEFCGKYAVKRKA--VGIWGCKDCG 60 (91)
Q Consensus 32 q~~ky~CpfCGk~~VkR~a--~GIW~C~~Cg 60 (91)
....-.|--||.......+ .||..|-.|.
T Consensus 10 ~~~N~~CaDCg~~~p~w~s~~~GiflC~~Ca 40 (116)
T PF01412_consen 10 KPGNKVCADCGAPNPTWASLNYGIFLCLECA 40 (116)
T ss_dssp STTCTB-TTT-SBS--EEETTTTEEE-HHHH
T ss_pred CcCcCcCCCCCCCCCCEEEeecChhhhHHHH
Confidence 4556789999988776664 4899999984
No 310
>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=30.66 E-value=33 Score=22.60 Aligned_cols=26 Identities=31% Similarity=0.782 Sum_probs=20.4
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
.|..||..+.. .-.|+|.|..|.-=|
T Consensus 8 ~C~VCg~~a~g-~hyGv~sC~aCk~FF 33 (92)
T cd07163 8 PCKVCGDRSSG-KHYGIYACDGCSGFF 33 (92)
T ss_pred CCcccCCcCcc-cEECceeeeeeeeEE
Confidence 69999987655 467999999998433
No 311
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=30.66 E-value=19 Score=30.19 Aligned_cols=12 Identities=42% Similarity=0.908 Sum_probs=10.5
Q ss_pred hcccccCCCCce
Q 044880 33 HSKYFCEFCGKY 44 (91)
Q Consensus 33 ~~ky~CpfCGk~ 44 (91)
.++|.|+||+|.
T Consensus 396 ~KPYrCevC~KR 407 (423)
T COG5189 396 DKPYRCEVCDKR 407 (423)
T ss_pred CCceeccccchh
Confidence 589999999985
No 312
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=30.54 E-value=40 Score=29.57 Aligned_cols=24 Identities=21% Similarity=0.540 Sum_probs=18.7
Q ss_pred cccccCCCCceeeEEeeeeeeeeC
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCK 57 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~ 57 (91)
.+..||.||.+.++....-.|.|.
T Consensus 403 ~P~~CP~Cgs~l~~~~~~~~~~C~ 426 (665)
T PRK07956 403 MPTHCPVCGSELVRVEGEAVLRCT 426 (665)
T ss_pred CCCCCCCCCCEeEecCCCeEEECC
Confidence 466999999998875555578886
No 313
>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=30.42 E-value=44 Score=20.67 Aligned_cols=28 Identities=29% Similarity=0.418 Sum_probs=16.2
Q ss_pred ccCCCCceee-EEeeeeeeeeCCCCceEe
Q 044880 37 FCEFCGKYAV-KRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 37 ~CpfCGk~~V-kR~a~GIW~C~~Cg~~~A 64 (91)
.||-|++..+ -=.+.-.=.|..|+.+++
T Consensus 9 kCp~C~~~q~vFSha~t~V~C~~Cg~~L~ 37 (55)
T PF01667_consen 9 KCPGCYNIQTVFSHAQTVVKCVVCGTVLA 37 (55)
T ss_dssp E-TTT-SEEEEETT-SS-EE-SSSTSEEE
T ss_pred ECCCCCCeeEEEecCCeEEEcccCCCEec
Confidence 7999998863 223444458999998874
No 314
>PLN03086 PRLI-interacting factor K; Provisional
Probab=30.27 E-value=26 Score=30.57 Aligned_cols=28 Identities=25% Similarity=0.559 Sum_probs=22.2
Q ss_pred ccCC--CCceeeEEeeeeeeeeCCCCceEe
Q 044880 37 FCEF--CGKYAVKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 37 ~Cpf--CGk~~VkR~a~GIW~C~~Cg~~~A 64 (91)
.||. ||..-.++.----|+|..|++.|.
T Consensus 435 ~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~ 464 (567)
T PLN03086 435 VCPHDGCGIVLRVEEAKNHVHCEKCGQAFQ 464 (567)
T ss_pred eCCcccccceeeccccccCccCCCCCCccc
Confidence 4664 888877777778899999998873
No 315
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=30.22 E-value=40 Score=24.39 Aligned_cols=25 Identities=28% Similarity=0.732 Sum_probs=18.3
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
.|+.||...+.+.-.. =.|..|+..
T Consensus 151 ~~~~~g~~~~~~~~~~-~~c~~~~~~ 175 (189)
T PRK09521 151 MCSRCRTPLVKKGENE-LKCPNCGNI 175 (189)
T ss_pred EccccCCceEECCCCE-EECCCCCCE
Confidence 5999999887755333 489999854
No 316
>cd06964 NR_DBD_RAR DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RARs mediate the biological effect of retinoids, including both natural dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RAR function as a heterodimer with retinoic X receptor by binding to specific RAR response elements (RAREs), which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair and found in the promoter reg
Probab=30.22 E-value=36 Score=22.07 Aligned_cols=27 Identities=19% Similarity=0.390 Sum_probs=20.6
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
-.|..||..... .-.|+|.|..|.-=|
T Consensus 5 ~~C~VCg~~~~g-~hyGv~sC~aC~~FF 31 (85)
T cd06964 5 KPCFVCQDKSSG-YHYGVSACEGCKGFF 31 (85)
T ss_pred CCCcccCCcCcc-cEECcceeeeeeeEE
Confidence 469999987655 458999999997443
No 317
>cd06957 NR_DBD_PNR_like_2 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like is composed of two C4-type zinc fingers. The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members
Probab=30.12 E-value=36 Score=21.87 Aligned_cols=24 Identities=29% Similarity=0.869 Sum_probs=17.2
Q ss_pred cCCCCceeeEEeeeeeeeeCCCCce
Q 044880 38 CEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 38 CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
|..||..+.. .-.|.|.|..|.-=
T Consensus 1 C~VCg~~~~g-~hyGv~sC~aCk~F 24 (82)
T cd06957 1 CKVCGDKSYG-KHYGVYCCDGCSCF 24 (82)
T ss_pred CCccCccCcc-eEECcceEeeeeeE
Confidence 6778876654 36788889988743
No 318
>cd07154 NR_DBD_PNR_like The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family. The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear
Probab=29.93 E-value=35 Score=21.30 Aligned_cols=24 Identities=29% Similarity=0.933 Sum_probs=17.7
Q ss_pred cCCCCceeeEEeeeeeeeeCCCCce
Q 044880 38 CEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 38 CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
|..||.+... .-.|.|.|..|.-=
T Consensus 1 C~vCg~~~~~-~hyGv~sC~aC~~F 24 (73)
T cd07154 1 CKVCGDRSSG-KHYGVYACDGCSGF 24 (73)
T ss_pred CcccCccCcc-eEECcceeeeeeeE
Confidence 6788876644 46788999999743
No 319
>PRK06835 DNA replication protein DnaC; Validated
Probab=29.64 E-value=51 Score=26.23 Aligned_cols=29 Identities=24% Similarity=0.518 Sum_probs=19.9
Q ss_pred chhhHHHHHHHHHh--------------hcccccCCCCceeeE
Q 044880 19 ASLRKQIKKMEVSQ--------------HSKYFCEFCGKYAVK 47 (91)
Q Consensus 19 ~slRK~v~kie~~q--------------~~ky~CpfCGk~~Vk 47 (91)
..|+..+.++.... ...|.||.|+.+-.-
T Consensus 68 ~~l~~~~~~l~~~~~~lL~~~g~~~dyl~~~y~Cp~C~dtG~i 110 (329)
T PRK06835 68 KELKEKITDLRVKKAELLVSNGYPPDYLEMKYTCPKCKDTGFI 110 (329)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCChhhcCCCCCCCCCCCCCCc
Confidence 35666666665554 456899999988643
No 320
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=29.61 E-value=23 Score=31.43 Aligned_cols=37 Identities=27% Similarity=0.579 Sum_probs=23.6
Q ss_pred chhhHHHHHHHHHhhccc--------ccCCCCceeeEEeeeeeeeeCCCCc
Q 044880 19 ASLRKQIKKMEVSQHSKY--------FCEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 19 ~slRK~v~kie~~q~~ky--------~CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
..+.+.|+.++ ...-.| .|+.||-.... -|.|..||.
T Consensus 657 eal~~lvk~~~-~~~i~Y~sin~~~~~C~~CG~~~~~-----~~~CP~CG~ 701 (735)
T PRK07111 657 EAFEIIVKAMK-NTNIGYGSINHPVDRCPVCGYLGVI-----EDKCPKCGS 701 (735)
T ss_pred HHHHHHHHHHH-hCCCceEEeCCCCeecCCCCCCCCc-----CccCcCCCC
Confidence 35666666543 334455 79999954432 199999984
No 321
>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=29.53 E-value=25 Score=21.82 Aligned_cols=13 Identities=31% Similarity=0.529 Sum_probs=6.7
Q ss_pred ccccCCCCceeeE
Q 044880 35 KYFCEFCGKYAVK 47 (91)
Q Consensus 35 ky~CpfCGk~~Vk 47 (91)
+..||.||+....
T Consensus 2 ~v~CP~C~k~~~~ 14 (57)
T PF03884_consen 2 TVKCPICGKPVEW 14 (57)
T ss_dssp EEE-TTT--EEE-
T ss_pred cccCCCCCCeecc
Confidence 3579999988765
No 322
>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=29.47 E-value=39 Score=28.30 Aligned_cols=28 Identities=25% Similarity=0.494 Sum_probs=16.7
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceEe
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~A 64 (91)
.||.|+-.-+--...+.=.|..||++..
T Consensus 224 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 224 CCPNCDVSLTYHKKEGKLRCHYCGYQEP 251 (505)
T ss_pred CCCCCCCceEEecCCCeEEcCCCcCcCC
Confidence 4888876554333445556666666654
No 323
>PRK07591 threonine synthase; Validated
Probab=29.32 E-value=21 Score=29.05 Aligned_cols=26 Identities=23% Similarity=0.369 Sum_probs=18.1
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 35 KYFCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 35 ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
.+.|+.||+.--- . ..|.|..||-.+
T Consensus 18 ~l~C~~Cg~~~~~--~-~~~~C~~cg~~l 43 (421)
T PRK07591 18 ALKCRECGAEYPL--G-PIHVCEECFGPL 43 (421)
T ss_pred EEEeCCCCCcCCC--C-CCccCCCCCCeE
Confidence 5789999987532 1 239999997433
No 324
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=29.25 E-value=21 Score=23.12 Aligned_cols=23 Identities=30% Similarity=0.642 Sum_probs=18.6
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCC
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
.|..||..+.. .-.|+|.|..|.
T Consensus 5 ~C~VCg~~a~g-~hyGv~sC~aCk 27 (82)
T cd07173 5 TCLICGDEASG-CHYGALTCGSCK 27 (82)
T ss_pred CCeecCCcCcc-eEECcchhhhHH
Confidence 59999987755 457999999996
No 325
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=29.15 E-value=41 Score=29.37 Aligned_cols=27 Identities=26% Similarity=0.544 Sum_probs=20.2
Q ss_pred cccccCCCCceeeEEeeeeeeeeC--CCC
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCK--DCG 60 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~--~Cg 60 (91)
.+-.||.||.+.++...--.|.|. .|-
T Consensus 391 ~P~~CP~C~s~l~~~~~~~~~~C~n~~C~ 419 (652)
T TIGR00575 391 FPTHCPSCGSPLVKIEEEAVIRCPNLNCP 419 (652)
T ss_pred CCCCCCCCCCEeEecCCcEEEEECCCCCH
Confidence 356999999998876555578885 464
No 326
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=29.05 E-value=20 Score=18.94 Aligned_cols=24 Identities=17% Similarity=0.670 Sum_probs=14.2
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
|.|..|++..-.-. ..+|..|+.+
T Consensus 1 ~~C~~C~~~~~~~~---~Y~C~~c~f~ 24 (30)
T PF03107_consen 1 FWCDVCRRKIDGFY---FYHCSECCFT 24 (30)
T ss_pred CCCCCCCCCcCCCE---eEEeCCCCCe
Confidence 45777766543311 5778777744
No 327
>cd06955 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of core
Probab=28.80 E-value=32 Score=23.48 Aligned_cols=25 Identities=24% Similarity=0.583 Sum_probs=19.2
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCc
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
-.|..||..+.. .-.|+|.|..|.-
T Consensus 7 ~~C~VCg~~a~g-~hyGv~sC~aCk~ 31 (107)
T cd06955 7 RICGVCGDRATG-FHFNAMTCEGCKG 31 (107)
T ss_pred CCCeecCCcCcc-cEECcceeeeecc
Confidence 459999987654 4678899999974
No 328
>smart00746 TRASH metallochaperone-like domain.
Probab=28.72 E-value=27 Score=16.54 Aligned_cols=8 Identities=63% Similarity=1.514 Sum_probs=5.9
Q ss_pred cCCCCcee
Q 044880 38 CEFCGKYA 45 (91)
Q Consensus 38 CpfCGk~~ 45 (91)
||+||...
T Consensus 1 c~~C~~~~ 8 (39)
T smart00746 1 CSFCGKDI 8 (39)
T ss_pred CCCCCCCc
Confidence 78888765
No 329
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=28.70 E-value=72 Score=20.41 Aligned_cols=28 Identities=25% Similarity=0.590 Sum_probs=19.1
Q ss_pred ccCCCCcee---eEEe-eeeeeeeCCCCceEe
Q 044880 37 FCEFCGKYA---VKRK-AVGIWGCKDCGKVKA 64 (91)
Q Consensus 37 ~CpfCGk~~---VkR~-a~GIW~C~~Cg~~~A 64 (91)
.||.|+... +.+. .+-.=.|-+||++..
T Consensus 10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~ 41 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWRENGVEYVECVECGYTER 41 (71)
T ss_pred cCCCCcCccEEEEEEeCCceEEEecCCCCeec
Confidence 799999754 2222 344558999998764
No 330
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=28.65 E-value=21 Score=31.38 Aligned_cols=31 Identities=23% Similarity=0.423 Sum_probs=17.2
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceEeccccccc
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLN 71 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGGAy~~~ 71 (91)
.||.||...- .|-=.|..||....-=.|.+-
T Consensus 29 ~Cp~CG~~~~----~~~~fC~~CG~~~~~~~~~~~ 59 (645)
T PRK14559 29 PCPQCGTEVP----VDEAHCPNCGAETGTIWWAII 59 (645)
T ss_pred cCCCCCCCCC----cccccccccCCcccchhhhhc
Confidence 4777776632 233367777766554444433
No 331
>PRK12496 hypothetical protein; Provisional
Probab=28.39 E-value=24 Score=25.50 Aligned_cols=28 Identities=21% Similarity=0.374 Sum_probs=15.2
Q ss_pred hcccccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 33 HSKYFCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 33 ~~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
.=+|.|+-||+.--.-.... .|.-||..
T Consensus 125 ~w~~~C~gC~~~~~~~~~~~--~C~~CG~~ 152 (164)
T PRK12496 125 KWRKVCKGCKKKYPEDYPDD--VCEICGSP 152 (164)
T ss_pred eeeEECCCCCccccCCCCCC--cCCCCCCh
Confidence 34577888886542111111 38888743
No 332
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=28.31 E-value=27 Score=21.49 Aligned_cols=24 Identities=29% Similarity=0.782 Sum_probs=17.3
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCc
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
.|..||.++.. .-.|+|.|..|.-
T Consensus 1 ~C~vC~~~~~~-~hygv~~C~aC~~ 24 (70)
T smart00399 1 LCCVCGDHASG-FHFGVCSCRACKA 24 (70)
T ss_pred CCeEeCCcCcc-cEeCCcEechhhh
Confidence 37888876544 3678899998863
No 333
>cd06959 NR_DBD_EcR_like The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: Ecdysone receptor (EcR), Liver X receptor (LXR) and Farnesoid X receptor (FXR). The DNA binding activity is regulated by their corresponding ligands. The ligands for EcR are ecdysteroids; LXR is regulated by oxidized cholesterol derivatives or oxysterols; and bile acids control FXR's activities. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcR-like receptors have a central well conserved DNA binding domai
Probab=28.28 E-value=30 Score=21.64 Aligned_cols=23 Identities=30% Similarity=0.736 Sum_probs=17.3
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCC
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
.|..||..+.. .-.|+|.|..|.
T Consensus 1 ~C~vCg~~~~~-~hygv~sC~aC~ 23 (73)
T cd06959 1 NCVVCGDKASG-FHYGVLSCEGCK 23 (73)
T ss_pred CCceeCCcCcc-eEECceeehhhH
Confidence 37889876544 467889999986
No 334
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.21 E-value=13 Score=27.12 Aligned_cols=16 Identities=25% Similarity=0.553 Sum_probs=12.5
Q ss_pred cccccCCCCceeeEEe
Q 044880 34 SKYFCEFCGKYAVKRK 49 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~ 49 (91)
.--+||.||.+.|.+.
T Consensus 31 gLv~CPvCgs~~VsK~ 46 (142)
T COG5319 31 GLVTCPVCGSTEVSKL 46 (142)
T ss_pred CceeCCCCCcHHHHHH
Confidence 3458999999988765
No 335
>PLN00209 ribosomal protein S27; Provisional
Probab=28.13 E-value=73 Score=21.52 Aligned_cols=28 Identities=21% Similarity=0.373 Sum_probs=21.5
Q ss_pred ccCCCCcee-eEEeeeeeeeeCCCCceEe
Q 044880 37 FCEFCGKYA-VKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 37 ~CpfCGk~~-VkR~a~GIW~C~~Cg~~~A 64 (91)
.||-|++.. |-=.+.-.=.|..||.+++
T Consensus 38 kCp~C~n~q~VFShA~t~V~C~~Cg~~L~ 66 (86)
T PLN00209 38 KCQGCFNITTVFSHSQTVVVCGSCQTVLC 66 (86)
T ss_pred ECCCCCCeeEEEecCceEEEccccCCEee
Confidence 799999975 4444555668999999884
No 336
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=28.11 E-value=75 Score=22.23 Aligned_cols=29 Identities=24% Similarity=0.665 Sum_probs=19.9
Q ss_pred cccCCCCceeeE-Eee-eeeeeeCCCCceEe
Q 044880 36 YFCEFCGKYAVK-RKA-VGIWGCKDCGKVKA 64 (91)
Q Consensus 36 y~CpfCGk~~Vk-R~a-~GIW~C~~Cg~~~A 64 (91)
..||.||...+- -.+ ..-..|+-|.+.+.
T Consensus 2 ~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESGESCNRFSCRTCPYVFP 32 (105)
T ss_pred cccCCCCCEEEEecCCeEeeEEcCCCCceee
Confidence 369999987633 222 24578999998764
No 337
>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription
Probab=28.08 E-value=30 Score=23.16 Aligned_cols=25 Identities=28% Similarity=0.695 Sum_probs=19.7
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCc
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
-.|..||..+.. .-.|+|.|..|.-
T Consensus 5 ~~C~VCg~~a~g-~hyGv~sC~aCk~ 29 (97)
T cd07170 5 RLCLVCGDIASG-YHYGVASCEACKA 29 (97)
T ss_pred CCCeecCCcCcc-eEECceeehhhhH
Confidence 359999987755 4589999999963
No 338
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=28.04 E-value=21 Score=24.65 Aligned_cols=11 Identities=36% Similarity=0.706 Sum_probs=9.1
Q ss_pred eeCCCCceEec
Q 044880 55 GCKDCGKVKAG 65 (91)
Q Consensus 55 ~C~~Cg~~~AG 65 (91)
.|++||+.|--
T Consensus 60 ~CkkCGfef~~ 70 (97)
T COG3357 60 RCKKCGFEFRD 70 (97)
T ss_pred hhcccCccccc
Confidence 69999998854
No 339
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=28.01 E-value=45 Score=29.17 Aligned_cols=38 Identities=26% Similarity=0.664 Sum_probs=26.7
Q ss_pred chhhHHHHHHHHHhhccc--------ccCCCCceeeEEeeeeeeeeCCCCc
Q 044880 19 ASLRKQIKKMEVSQHSKY--------FCEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 19 ~slRK~v~kie~~q~~ky--------~CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
..|.+.|+.| ....-.| .|+.||... .+. .|.|..||.
T Consensus 545 ~al~~lv~~~-~~~~i~Y~~inp~~~~C~~CG~~~---~g~-~~~CP~CGs 590 (625)
T PRK08579 545 EALAKLTKRI-MNTKLVYWSYTPAITVCNKCGRST---TGL-YTRCPRCGS 590 (625)
T ss_pred HHHHHHHHHH-HhcCCceEEeCCCCccCCCCCCcc---CCC-CCcCcCCCC
Confidence 5678888888 3444555 799999843 111 489999986
No 340
>PF03470 zf-XS: XS zinc finger domain; InterPro: IPR005381 This domain is a putative nucleic acid binding zinc finger and is found at the N terminus of proteins that also contain an adjacent XS domain IPR005380 from INTERPRO and in some proteins a C-terminal XH domain IPR005379 from INTERPRO.
Probab=27.94 E-value=25 Score=20.92 Aligned_cols=7 Identities=43% Similarity=1.175 Sum_probs=5.0
Q ss_pred cCCCCce
Q 044880 38 CEFCGKY 44 (91)
Q Consensus 38 CpfCGk~ 44 (91)
||||-..
T Consensus 1 CP~C~~k 7 (43)
T PF03470_consen 1 CPFCPGK 7 (43)
T ss_pred CCCCCCC
Confidence 8888643
No 341
>cd06962 NR_DBD_FXR DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. FXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. FXR is a member of the nuclear receptor family of ligand activated transcription factors. Bile acids are endogenous ligands for FXRs. Upon binding of a ligand, FXR binds to FXR response element (FXRE), which is an inverted repeat of TGACCT spaced by one nucleotide, either as a monomer or as a heterodimer with retinoid X receptor (RXR), to regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, FXR has a central well conserved
Probab=27.84 E-value=38 Score=21.99 Aligned_cols=25 Identities=24% Similarity=0.594 Sum_probs=18.7
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
.|..||.++.. .-.|+|.|..|.-=
T Consensus 3 ~C~VCg~~a~g-~hyGv~sC~aCk~F 27 (84)
T cd06962 3 LCVVCGDKASG-YHYNALTCEGCKGF 27 (84)
T ss_pred CCeecCCcCcc-eEECcceeecceee
Confidence 48899987654 46788999999743
No 342
>smart00532 LIGANc Ligase N family.
Probab=27.69 E-value=53 Score=27.46 Aligned_cols=24 Identities=21% Similarity=0.360 Sum_probs=19.2
Q ss_pred cccccCCCCceeeEEeeeeeeeeC
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCK 57 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~ 57 (91)
.+-.||.||...++....-.|.|.
T Consensus 398 ~P~~CP~C~s~l~~~~~~~~~~C~ 421 (441)
T smart00532 398 MPTHCPSCGSELVREEGEVDIRCP 421 (441)
T ss_pred CCCCCCCCCCEeEecCCceEEEeC
Confidence 467999999998876655678896
No 343
>TIGR01374 soxD sarcosine oxidase, delta subunit family, heterotetrameric form. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) form
Probab=27.52 E-value=27 Score=23.34 Aligned_cols=7 Identities=43% Similarity=1.416 Sum_probs=5.6
Q ss_pred ccCCCCc
Q 044880 37 FCEFCGK 43 (91)
Q Consensus 37 ~CpfCGk 43 (91)
.||+||.
T Consensus 3 ~CP~CG~ 9 (84)
T TIGR01374 3 PCPYCGP 9 (84)
T ss_pred cCCCCCC
Confidence 6999993
No 344
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=27.51 E-value=51 Score=22.58 Aligned_cols=20 Identities=40% Similarity=0.735 Sum_probs=15.2
Q ss_pred ccccCCCCceeeEEeee-eee
Q 044880 35 KYFCEFCGKYAVKRKAV-GIW 54 (91)
Q Consensus 35 ky~CpfCGk~~VkR~a~-GIW 54 (91)
.-.||.||...+.+..- |+|
T Consensus 17 ~~~Cp~Cg~~m~~~~~~~g~f 37 (140)
T COG0551 17 GQICPKCGKNMVKKFGKYGIF 37 (140)
T ss_pred CccCCcCCCeeEEEEccCCeE
Confidence 45799999998877754 544
No 345
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=27.42 E-value=19 Score=31.07 Aligned_cols=37 Identities=24% Similarity=0.628 Sum_probs=29.1
Q ss_pred HHHHhhcccccCCCCceeeEEeeeeeeeeCCCCceEecc
Q 044880 28 MEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGG 66 (91)
Q Consensus 28 ie~~q~~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGG 66 (91)
|+.....-+-|+.|+..-..|.-.|. |..||...|+|
T Consensus 119 I~~~~~~~~Yc~~~e~fl~dr~v~g~--cp~cg~~~arG 155 (558)
T COG0143 119 IYLREYEGLYCVSCERFLPDRYVEGT--CPKCGGEDARG 155 (558)
T ss_pred EeccceeeeEcccccccccchheecc--CCCcCccccCc
Confidence 45556667789999999888888887 99998777763
No 346
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.24 E-value=28 Score=28.30 Aligned_cols=15 Identities=20% Similarity=0.443 Sum_probs=10.6
Q ss_pred ccccCCCCceeeEEe
Q 044880 35 KYFCEFCGKYAVKRK 49 (91)
Q Consensus 35 ky~CpfCGk~~VkR~ 49 (91)
.=+||+||.+-+-..
T Consensus 239 ~~~C~~Cg~~PtiP~ 253 (298)
T KOG2879|consen 239 DTECPVCGEPPTIPH 253 (298)
T ss_pred CceeeccCCCCCCCe
Confidence 348999998764433
No 347
>COG3816 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.94 E-value=43 Score=25.67 Aligned_cols=20 Identities=30% Similarity=0.660 Sum_probs=17.4
Q ss_pred cccCCCCceeeEEeeeeeee
Q 044880 36 YFCEFCGKYAVKRKAVGIWG 55 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~ 55 (91)
.+=||||...|+=.+-|.|-
T Consensus 37 WNPpfCGdiDmeIr~DGtWF 56 (205)
T COG3816 37 WNPPFCGDIDMEIRADGTWF 56 (205)
T ss_pred cCCCCccceeeEEecCceEE
Confidence 46799999999888999996
No 348
>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=26.85 E-value=53 Score=17.59 Aligned_cols=13 Identities=23% Similarity=0.884 Sum_probs=10.1
Q ss_pred eeeeeCCCCceEe
Q 044880 52 GIWGCKDCGKVKA 64 (91)
Q Consensus 52 GIW~C~~Cg~~~A 64 (91)
.+++|..||..+.
T Consensus 3 ~~ykC~~CGniv~ 15 (34)
T cd00974 3 EVYKCEICGNIVE 15 (34)
T ss_pred cEEEcCCCCcEEE
Confidence 4788999997774
No 349
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=26.78 E-value=57 Score=26.27 Aligned_cols=40 Identities=15% Similarity=0.503 Sum_probs=28.0
Q ss_pred hhhHHHHHHHHHhhcccccCCCCceeeEEe--eeeeeeeCCCC
Q 044880 20 SLRKQIKKMEVSQHSKYFCEFCGKYAVKRK--AVGIWGCKDCG 60 (91)
Q Consensus 20 slRK~v~kie~~q~~ky~CpfCGk~~VkR~--a~GIW~C~~Cg 60 (91)
..+++++++.-+ -..-.|.-||....++. ..||..|-+|-
T Consensus 11 ~~~~~l~~Ll~~-~~N~~CADC~a~~P~WaSwnlGvFiC~~C~ 52 (287)
T KOG0703|consen 11 RNKRRLRELLRE-PDNKVCADCGAKGPRWASWNLGVFICLRCA 52 (287)
T ss_pred hHHHHHHHHHcC-cccCcccccCCCCCCeEEeecCeEEEeecc
Confidence 344555554333 33557999999988887 45999999994
No 350
>PF08134 cIII: cIII protein family; InterPro: IPR012995 This family consists of the CIII family of regulatory proteins. The lambda CIII protein has 54 amino acids and it forms an amphipathic helix within its amino acid sequence. Lambda CIII stabilises the lambda CII protein and the host sigma factor 32, responsible for transcribing genes of the heat shock regulon [].
Probab=26.73 E-value=75 Score=18.97 Aligned_cols=29 Identities=34% Similarity=0.442 Sum_probs=18.6
Q ss_pred eEecc----c-ccccccHHHHHHHHHHHHHhhhc
Q 044880 62 VKAGG----A-YTLNTASAVTVRSTIRRLREQTE 90 (91)
Q Consensus 62 ~~AGG----A-y~~~T~~~~t~~~~i~rl~e~~~ 90 (91)
.+||| | |.++....+-+++-||..+..-|
T Consensus 5 ~laG~gvmSAyYP~ESELskr~rrLIRaa~k~le 38 (44)
T PF08134_consen 5 QLAGSGVMSAYYPTESELSKRIRRLIRAARKQLE 38 (44)
T ss_pred EecCceeeeeecCcHHHHHHHHHHHHHHHHHHHH
Confidence 46665 3 44466777778888877665433
No 351
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=26.57 E-value=28 Score=32.98 Aligned_cols=24 Identities=29% Similarity=0.697 Sum_probs=20.7
Q ss_pred ccccCCCCce-eeEEeeeeeeeeCCC
Q 044880 35 KYFCEFCGKY-AVKRKAVGIWGCKDC 59 (91)
Q Consensus 35 ky~CpfCGk~-~VkR~a~GIW~C~~C 59 (91)
.+-||-||-+ +-.|...|+ -|.+|
T Consensus 8 ~~~CpNCGG~isseRL~~gl-pCe~C 32 (1187)
T COG1110 8 GSSCPNCGGDISSERLEKGL-PCERC 32 (1187)
T ss_pred hccCCCCCCcCcHHHHhcCC-Cchhc
Confidence 4679999977 688899998 59999
No 352
>cd06967 NR_DBD_TR2_like DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. It has been shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or
Probab=26.53 E-value=34 Score=22.30 Aligned_cols=26 Identities=27% Similarity=0.664 Sum_probs=19.8
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
.|..||..... .-.|.|.|..|.-=|
T Consensus 5 ~C~VCg~~~~g-~hyGv~sC~aC~~FF 30 (87)
T cd06967 5 LCVVCGDKASG-RHYGAVSCEGCKGFF 30 (87)
T ss_pred CCeecCCcCCc-CEeCcceEeeeeeEe
Confidence 49999987655 357899999997443
No 353
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=26.52 E-value=33 Score=23.17 Aligned_cols=25 Identities=24% Similarity=0.615 Sum_probs=19.9
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCc
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
-.|..||..+.. .-.|+|.|..|.-
T Consensus 19 ~~C~VCg~~a~g-~hyGv~sC~aCk~ 43 (101)
T cd07160 19 EVCSVCGDKASG-FHYNVLSCEGCKG 43 (101)
T ss_pred CCCeecCCcCcc-eEECcceehhhhh
Confidence 369999987654 4779999999973
No 354
>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=26.50 E-value=31 Score=21.28 Aligned_cols=14 Identities=21% Similarity=0.774 Sum_probs=10.9
Q ss_pred HhhcccccCCCCce
Q 044880 31 SQHSKYFCEFCGKY 44 (91)
Q Consensus 31 ~q~~ky~CpfCGk~ 44 (91)
-+...|.||.|+..
T Consensus 54 ~kd~~H~Cp~C~~~ 67 (73)
T PF10601_consen 54 CKDVYHYCPNCGAF 67 (73)
T ss_pred ccCceEECCCCCCE
Confidence 35678899999875
No 355
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=26.26 E-value=27 Score=23.92 Aligned_cols=31 Identities=16% Similarity=0.405 Sum_probs=23.5
Q ss_pred HHhhcccccCCCCceeeEEeeeeeeeeCCCCceEe
Q 044880 30 VSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 30 ~~q~~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~A 64 (91)
........|+.|...+..|. .||+.|++-+.
T Consensus 43 ~~~~~~~~C~~C~~~kp~Rs----~HC~~C~~CV~ 73 (174)
T PF01529_consen 43 DENGELKYCSTCKIIKPPRS----HHCRVCNRCVL 73 (174)
T ss_pred ccCCCCEECcccCCcCCCcc----eeccccccccc
Confidence 34455668999998887775 79999987654
No 356
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 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 MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=26.20 E-value=51 Score=17.72 Aligned_cols=19 Identities=47% Similarity=1.039 Sum_probs=11.5
Q ss_pred cCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 38 CEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 38 CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
|..|+++.+. .|..|..++
T Consensus 1 C~~C~~~~~~-------~C~~C~~~~ 19 (37)
T PF01753_consen 1 CAVCGKPALK-------RCSRCKSVY 19 (37)
T ss_dssp -TTTSSCSSE-------EETTTSSSE
T ss_pred CcCCCCCcCC-------cCCCCCCEE
Confidence 6677774333 688886553
No 357
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=25.99 E-value=51 Score=29.17 Aligned_cols=22 Identities=14% Similarity=0.339 Sum_probs=16.5
Q ss_pred cccccCCCCceeeEEeeeeeeeeC
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCK 57 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~ 57 (91)
-+-.||.||.+.++ .++-+| |.
T Consensus 422 ~P~~CP~C~~~l~~-~~~~~~-C~ 443 (689)
T PRK14351 422 FPDTCPVCDSAVER-DGPLAF-CT 443 (689)
T ss_pred CCCCCCCCCCEeee-CCceEE-cC
Confidence 45689999999886 555565 75
No 358
>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers. DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs h
Probab=25.94 E-value=34 Score=22.53 Aligned_cols=23 Identities=26% Similarity=0.651 Sum_probs=17.5
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCC
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
.|..||.++.. .-.|+|.|..|.
T Consensus 3 ~C~VCg~~a~g-~hyGv~sC~aCk 25 (91)
T cd07161 3 LCLVCGDRASG-YHYNALTCEGCK 25 (91)
T ss_pred CCeeCCCcCcc-eEECceeehhhH
Confidence 48899977654 467888999886
No 359
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=25.86 E-value=57 Score=17.40 Aligned_cols=14 Identities=21% Similarity=0.759 Sum_probs=10.7
Q ss_pred eeeeeeCCCCceEe
Q 044880 51 VGIWGCKDCGKVKA 64 (91)
Q Consensus 51 ~GIW~C~~Cg~~~A 64 (91)
..+++|..||..+.
T Consensus 5 ~~~ykC~~Cgniv~ 18 (34)
T TIGR00319 5 GQVYKCEVCGNIVE 18 (34)
T ss_pred CcEEEcCCCCcEEE
Confidence 35788999997774
No 360
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=25.73 E-value=33 Score=20.83 Aligned_cols=14 Identities=21% Similarity=0.774 Sum_probs=10.6
Q ss_pred HhhcccccCCCCce
Q 044880 31 SQHSKYFCEFCGKY 44 (91)
Q Consensus 31 ~q~~ky~CpfCGk~ 44 (91)
-+...|.||.||..
T Consensus 48 ~kd~~H~Cp~C~~~ 61 (67)
T smart00714 48 FKDVNHYCPNCGAF 61 (67)
T ss_pred ccCccEECCCCCCE
Confidence 35677889999875
No 361
>cd07165 NR_DBD_DmE78_like DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers. DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. The SmE78 may be involved in transduction of an ecdysone signal in S. mansoni,
Probab=25.59 E-value=26 Score=22.41 Aligned_cols=22 Identities=32% Similarity=0.839 Sum_probs=15.6
Q ss_pred cCCCCceeeEEeeeeeeeeCCCC
Q 044880 38 CEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 38 CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
|..||..+.. .-.|+|.|..|.
T Consensus 1 C~VCg~~~~g-~hyG~~sC~aC~ 22 (81)
T cd07165 1 CKVCGDKASG-YHYGVTSCEGCK 22 (81)
T ss_pred CCccCccCcc-eEECchhhhhHH
Confidence 6778876544 366888888885
No 362
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=25.50 E-value=31 Score=28.99 Aligned_cols=28 Identities=29% Similarity=0.827 Sum_probs=23.7
Q ss_pred ccCCCCceeeEEe--eeeeeeeCCCCceEe
Q 044880 37 FCEFCGKYAVKRK--AVGIWGCKDCGKVKA 64 (91)
Q Consensus 37 ~CpfCGk~~VkR~--a~GIW~C~~Cg~~~A 64 (91)
.|..||...+.+. .-|..+|..|...++
T Consensus 276 vCd~CGn~rLe~~pe~rg~~~C~~Cs~~V~ 305 (389)
T PF14951_consen 276 VCDRCGNGRLEQSPEDRGAFSCGDCSRVVT 305 (389)
T ss_pred cccccCCccceeCccCCCceeccchhhhcc
Confidence 7999999988765 478899999998776
No 363
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=25.44 E-value=34 Score=20.77 Aligned_cols=11 Identities=27% Similarity=0.664 Sum_probs=6.0
Q ss_pred eeeCCCCceEe
Q 044880 54 WGCKDCGKVKA 64 (91)
Q Consensus 54 W~C~~Cg~~~A 64 (91)
|.|.-|++.|.
T Consensus 51 ~~C~~C~~~f~ 61 (100)
T PF12756_consen 51 FRCPYCNKTFR 61 (100)
T ss_dssp EEBSSSS-EES
T ss_pred CCCCccCCCCc
Confidence 66666666653
No 364
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=25.41 E-value=58 Score=24.82 Aligned_cols=24 Identities=33% Similarity=0.757 Sum_probs=15.2
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
.|+.|+...++ .. -.-.|..||.+
T Consensus 151 ~CsrC~~~L~~-~~-~~l~Cp~Cg~t 174 (188)
T COG1096 151 RCSRCRAPLVK-KG-NMLKCPNCGNT 174 (188)
T ss_pred EccCCCcceEE-cC-cEEECCCCCCE
Confidence 47777777766 22 33477777754
No 365
>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=25.35 E-value=28 Score=18.84 Aligned_cols=8 Identities=38% Similarity=1.099 Sum_probs=2.9
Q ss_pred ccCCCCce
Q 044880 37 FCEFCGKY 44 (91)
Q Consensus 37 ~CpfCGk~ 44 (91)
.||.||..
T Consensus 27 ~Cp~C~s~ 34 (37)
T PF12172_consen 27 VCPHCGSD 34 (37)
T ss_dssp EETTTT--
T ss_pred CCCCcCcc
Confidence 44454443
No 366
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=25.32 E-value=48 Score=31.89 Aligned_cols=53 Identities=19% Similarity=0.302 Sum_probs=31.4
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCceEecccccccccHHHHHHHHHHHHHhh
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLNTASAVTVRSTIRRLREQ 88 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~AGGAy~~~T~~~~t~~~~i~rl~e~ 88 (91)
..|.||-||....--. ++-=.|..|+...-.-.+. .-+....+.+|+.+|.+-
T Consensus 691 ~vy~CPsCGaev~~de-s~a~~CP~CGtplv~~~~~-~i~~~~~~~~A~~~~g~~ 743 (1337)
T PRK14714 691 PVYVCPDCGAEVPPDE-SGRVECPRCDVELTPYQRR-TINVKEEYRSALENVGER 743 (1337)
T ss_pred CceeCccCCCccCCCc-cccccCCCCCCcccccceE-EecHHHHHHHHHHHhCcc
Confidence 3567777777533211 2233799999655443332 345567777888877653
No 367
>PRK11032 hypothetical protein; Provisional
Probab=25.23 E-value=39 Score=24.86 Aligned_cols=14 Identities=29% Similarity=0.826 Sum_probs=11.9
Q ss_pred ccCCCCceeeEEee
Q 044880 37 FCEFCGKYAVKRKA 50 (91)
Q Consensus 37 ~CpfCGk~~VkR~a 50 (91)
.||-||.+...|++
T Consensus 144 pCp~C~~~~F~R~~ 157 (160)
T PRK11032 144 LCPKCGHDQFQRRP 157 (160)
T ss_pred CCCCCCCCeeeeCC
Confidence 69999999888875
No 368
>PF00935 Ribosomal_L44: Ribosomal protein L44; InterPro: IPR000552 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of mammalian [], Trypanosoma brucei, Caenorhabditis elegans and fungal L44, and Haloarcula marismortui LA [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_r 1S1I_Z 3O5H_f 3O58_f 3IZR_r 1M1K_4 3CCQ_3 3CCL_3 3CME_3 1K73_4 ....
Probab=25.16 E-value=53 Score=21.58 Aligned_cols=22 Identities=27% Similarity=0.457 Sum_probs=14.8
Q ss_pred hcccccCCCCceeeEEeeeeeeeeCC
Q 044880 33 HSKYFCEFCGKYAVKRKAVGIWGCKD 58 (91)
Q Consensus 33 ~~ky~CpfCGk~~VkR~a~GIW~C~~ 58 (91)
..+|.|..|++..++. +|.|++
T Consensus 51 ~Lrl~C~~C~~~~~~~----~~R~kk 72 (77)
T PF00935_consen 51 VLRLECTECGKAHMRP----GKRCKK 72 (77)
T ss_dssp EEEEEETTTS-EEEEE-----BBESS
T ss_pred EEEEEeCCCCcccccc----cceeEE
Confidence 4678999999887763 266654
No 369
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=25.12 E-value=46 Score=19.60 Aligned_cols=11 Identities=36% Similarity=1.002 Sum_probs=8.0
Q ss_pred hcccccCCCCc
Q 044880 33 HSKYFCEFCGK 43 (91)
Q Consensus 33 ~~ky~CpfCGk 43 (91)
..-..||.||+
T Consensus 44 ~~i~~Cp~CgR 54 (56)
T PF02591_consen 44 DEIVFCPNCGR 54 (56)
T ss_pred CCeEECcCCCc
Confidence 45678888875
No 370
>PF04267 SoxD: Sarcosine oxidase, delta subunit family ; InterPro: IPR006279 These sequences represent the delta subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Rhizobium loti (Mesorhizobium loti) and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate []. Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the heterotetrameric form.; GO: 0008115 sarcosine oxidase activity, 0046653 tetrahydrofolate metabolic process; PDB: 3AD7_D 1X31_D 1VRQ_D 3AD8_D 3ADA_D 3AD9_D 2GAG_D 2GAH_D.
Probab=25.09 E-value=22 Score=23.76 Aligned_cols=7 Identities=43% Similarity=1.170 Sum_probs=5.7
Q ss_pred ccCCCCc
Q 044880 37 FCEFCGK 43 (91)
Q Consensus 37 ~CpfCGk 43 (91)
.||+||.
T Consensus 3 ~CP~CG~ 9 (84)
T PF04267_consen 3 PCPHCGP 9 (84)
T ss_dssp EETTTEE
T ss_pred cCCCCCc
Confidence 5899986
No 371
>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=24.81 E-value=78 Score=19.30 Aligned_cols=14 Identities=29% Similarity=0.650 Sum_probs=10.4
Q ss_pred eeeeeeeCCCCceE
Q 044880 50 AVGIWGCKDCGKVK 63 (91)
Q Consensus 50 a~GIW~C~~Cg~~~ 63 (91)
-.|.=.|..|+..|
T Consensus 50 ~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 50 VEGELICPECGREY 63 (68)
T ss_dssp TTTEEEETTTTEEE
T ss_pred cCCEEEcCCCCCEE
Confidence 44777888888765
No 372
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=24.74 E-value=30 Score=21.58 Aligned_cols=22 Identities=32% Similarity=0.862 Sum_probs=15.8
Q ss_pred cCCCCceeeEEeeeeeeeeCCCC
Q 044880 38 CEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 38 CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
|..||.++.. .-.|+|.|..|.
T Consensus 1 C~VCg~~~~g-~hyGv~~C~aC~ 22 (73)
T cd07158 1 CKVCGDKASG-FHYGVHSCEGCK 22 (73)
T ss_pred CcccCccCcc-eEECcchhhHHH
Confidence 6778876544 357888888886
No 373
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=24.72 E-value=95 Score=20.94 Aligned_cols=28 Identities=21% Similarity=0.377 Sum_probs=21.5
Q ss_pred ccCCCCcee-eEEeeeeeeeeCCCCceEe
Q 044880 37 FCEFCGKYA-VKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 37 ~CpfCGk~~-VkR~a~GIW~C~~Cg~~~A 64 (91)
.||-|++.. |-=.|.-.=.|..|+.+++
T Consensus 37 kCp~C~n~q~VFShA~t~V~C~~Cg~~L~ 65 (85)
T PTZ00083 37 KCPGCSQITTVFSHAQTVVLCGGCSSQLC 65 (85)
T ss_pred ECCCCCCeeEEEecCceEEEccccCCEee
Confidence 799999875 4444555668999999884
No 374
>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=24.65 E-value=35 Score=21.31 Aligned_cols=9 Identities=44% Similarity=1.051 Sum_probs=7.3
Q ss_pred ccCCCCcee
Q 044880 37 FCEFCGKYA 45 (91)
Q Consensus 37 ~CpfCGk~~ 45 (91)
.||+||+..
T Consensus 5 HC~~CG~~I 13 (59)
T PF09889_consen 5 HCPVCGKPI 13 (59)
T ss_pred cCCcCCCcC
Confidence 699999764
No 375
>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=24.64 E-value=30 Score=19.40 Aligned_cols=11 Identities=36% Similarity=1.235 Sum_probs=5.4
Q ss_pred cccccCCCCce
Q 044880 34 SKYFCEFCGKY 44 (91)
Q Consensus 34 ~ky~CpfCGk~ 44 (91)
....|+||+..
T Consensus 23 ~~w~C~~C~~~ 33 (40)
T PF04810_consen 23 KTWICNFCGTK 33 (40)
T ss_dssp TEEEETTT--E
T ss_pred CEEECcCCCCc
Confidence 35567777653
No 376
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=24.55 E-value=37 Score=32.88 Aligned_cols=28 Identities=39% Similarity=0.802 Sum_probs=18.9
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCceEe
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~A 64 (91)
..|.| .|||.+-.|. -|+ .|.+||--++
T Consensus 58 kd~eC-~CGKyk~~~~-~g~-~C~~CGVEvt 85 (1460)
T PRK14906 58 KDWEC-ACGKYKRIRF-KGI-VCERCGVEVT 85 (1460)
T ss_pred cCcEE-eCccccccCc-CCe-EcCCCCcEec
Confidence 35788 7997654332 266 7999987664
No 377
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=24.54 E-value=35 Score=21.95 Aligned_cols=11 Identities=27% Similarity=0.824 Sum_probs=8.5
Q ss_pred cccCCCCceee
Q 044880 36 YFCEFCGKYAV 46 (91)
Q Consensus 36 y~CpfCGk~~V 46 (91)
-.||.||.+++
T Consensus 19 e~CP~Cgs~~~ 29 (64)
T COG2093 19 EICPVCGSTDL 29 (64)
T ss_pred ccCCCCCCccc
Confidence 35999998853
No 378
>PRK08329 threonine synthase; Validated
Probab=24.49 E-value=39 Score=26.62 Aligned_cols=22 Identities=32% Similarity=0.773 Sum_probs=15.5
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCc
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
+.|+.||..--. ..- |.| .|+-
T Consensus 2 l~C~~Cg~~~~~--~~~-~~C-~c~~ 23 (347)
T PRK08329 2 LRCTKCGRTYEE--KFK-LRC-DCGG 23 (347)
T ss_pred cCcCCCCCCcCC--CCc-eec-CCCC
Confidence 689999987532 223 899 7964
No 379
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=24.42 E-value=44 Score=20.84 Aligned_cols=19 Identities=37% Similarity=1.120 Sum_probs=13.5
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCC
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
.||.||...+-=. .|..||
T Consensus 29 ~c~~cG~~~l~Hr-----vc~~cg 47 (57)
T COG0333 29 VCPNCGEYKLPHR-----VCLKCG 47 (57)
T ss_pred eccCCCCcccCce-----EcCCCC
Confidence 7999998765422 377777
No 380
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=24.40 E-value=36 Score=20.38 Aligned_cols=12 Identities=25% Similarity=0.786 Sum_probs=9.8
Q ss_pred eeeeCCCCceEe
Q 044880 53 IWGCKDCGKVKA 64 (91)
Q Consensus 53 IW~C~~Cg~~~A 64 (91)
.|.|..||+.+-
T Consensus 1 ~y~C~~CgyiYd 12 (50)
T cd00730 1 KYECRICGYIYD 12 (50)
T ss_pred CcCCCCCCeEEC
Confidence 488999998875
No 381
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=24.33 E-value=57 Score=19.31 Aligned_cols=14 Identities=29% Similarity=0.603 Sum_probs=10.3
Q ss_pred eeeCCCCceEeccc
Q 044880 54 WGCKDCGKVKAGGA 67 (91)
Q Consensus 54 W~C~~Cg~~~AGGA 67 (91)
|+|..||+..---.
T Consensus 2 y~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 2 YQCPVCGYVYDPEK 15 (47)
T ss_dssp EEETTTSBEEETTT
T ss_pred cCCCCCCEEEcCCc
Confidence 78999988765433
No 382
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=24.26 E-value=34 Score=32.26 Aligned_cols=28 Identities=43% Similarity=0.917 Sum_probs=18.1
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCceEe
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~A 64 (91)
..|.| .|||.+-.+.. |+ .|.+||-.++
T Consensus 56 kd~eC-~Cgkyk~~~~~-~~-~C~~cgve~~ 83 (1156)
T PRK00566 56 KDYEC-LCGKYKRVRYK-GI-ICERCGVEVT 83 (1156)
T ss_pred cCcEE-eCccccccCcC-Cc-CCCCCCceee
Confidence 45788 88876533322 55 7888886654
No 383
>cd07167 NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which is required at several stages of development. Particularly, FTZ-F1 regulated genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development; SF-1 is an essential regu
Probab=24.20 E-value=30 Score=22.99 Aligned_cols=22 Identities=27% Similarity=0.800 Sum_probs=15.8
Q ss_pred cCCCCceeeEEeeeeeeeeCCCC
Q 044880 38 CEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 38 CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
|..||.++.. .-.|.|.|..|.
T Consensus 1 C~VCg~~a~g-~hyGv~sC~aCk 22 (93)
T cd07167 1 CPVCGDKVSG-YHYGLLTCESCK 22 (93)
T ss_pred CcccCccCcc-eEECchhhhhHH
Confidence 6778876554 466888888885
No 384
>cd07155 NR_DBD_ER_like DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. E
Probab=24.15 E-value=29 Score=21.85 Aligned_cols=22 Identities=32% Similarity=0.792 Sum_probs=15.5
Q ss_pred cCCCCceeeEEeeeeeeeeCCCC
Q 044880 38 CEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 38 CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
|..||.++.. .-.|.|.|..|.
T Consensus 1 C~VC~~~~~g-~hygv~sC~aCk 22 (75)
T cd07155 1 CLVCGDIASG-YHYGVASCEACK 22 (75)
T ss_pred CcccCccCcc-eEEChhhhhhhH
Confidence 6778876544 466888888885
No 385
>PRK14873 primosome assembly protein PriA; Provisional
Probab=24.14 E-value=53 Score=28.85 Aligned_cols=22 Identities=36% Similarity=0.966 Sum_probs=16.7
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 35 KYFCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 35 ky~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
.-.|..||.... -|.|.+||..
T Consensus 410 ~l~Ch~CG~~~~------p~~Cp~Cgs~ 431 (665)
T PRK14873 410 TPRCRWCGRAAP------DWRCPRCGSD 431 (665)
T ss_pred eeECCCCcCCCc------CccCCCCcCC
Confidence 467999997531 4999999754
No 386
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=24.08 E-value=45 Score=19.03 Aligned_cols=20 Identities=35% Similarity=0.936 Sum_probs=14.2
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCC
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
|+|..|... +. --|+|..|.
T Consensus 1 y~C~~C~~~-~~----~r~~C~~C~ 20 (41)
T cd02337 1 YTCNECKHH-VE----TRWHCTVCE 20 (41)
T ss_pred CcCCCCCCc-CC----CceECCCCc
Confidence 689999773 21 348999985
No 387
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=24.05 E-value=35 Score=30.27 Aligned_cols=27 Identities=41% Similarity=0.907 Sum_probs=14.9
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCCceEe
Q 044880 35 KYFCEFCGKYAVKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 35 ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~A 64 (91)
.|.| .|||.+-.+. -|+ .|..||-.++
T Consensus 68 ~~eC-~CGkyk~~~~-~~~-~C~~CgvE~t 94 (627)
T PRK02625 68 DWEC-HCGKYKRVRH-RGI-VCERCGVEVT 94 (627)
T ss_pred CcEE-eCCCccccCc-CCc-CCCCCCcEec
Confidence 4666 6776543332 244 5777775443
No 388
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit. The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Probab=24.00 E-value=35 Score=30.20 Aligned_cols=27 Identities=41% Similarity=0.907 Sum_probs=15.0
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCCceEe
Q 044880 35 KYFCEFCGKYAVKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 35 ky~CpfCGk~~VkR~a~GIW~C~~Cg~~~A 64 (91)
.|.| .|||.+-.+. -|+ .|..||-.++
T Consensus 61 ~~eC-~CGkyk~~~~-~~~-~C~~CgvE~t 87 (619)
T TIGR02387 61 DWEC-HCGKYKRVRH-RGI-VCERCGVEVT 87 (619)
T ss_pred CcEE-eCCCccccCc-CCc-CCCCCCCEEc
Confidence 4666 6776543332 244 5777775443
No 389
>cd07166 NR_DBD_REV_ERB DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers. DNA-binding domain of REV-ERB receptor- like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. REV-ERB receptors are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. REV-ERB receptors bind as a monomer to a (A/G)GGTCA half-site with a 5' AT-rich extension or as a homodimer to a direct repeat 2 element (AGGTCA sequence with a 2-bp spacer), indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target genes. The porphyr
Probab=23.94 E-value=30 Score=22.64 Aligned_cols=25 Identities=28% Similarity=0.757 Sum_probs=19.3
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCc
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
..|..||..+.. .-.|+|.|..|.-
T Consensus 4 ~~C~VCg~~a~g-~hyGv~sC~aCk~ 28 (89)
T cd07166 4 VLCKVCGDKASG-FHYGVHACEGCKG 28 (89)
T ss_pred CCCcccCccCcc-eEEChhhhhhHhh
Confidence 359999987644 4578999999974
No 390
>cd03023 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
Probab=23.92 E-value=26 Score=22.66 Aligned_cols=13 Identities=31% Similarity=0.856 Sum_probs=9.8
Q ss_pred hhcccccCCCCce
Q 044880 32 QHSKYFCEFCGKY 44 (91)
Q Consensus 32 q~~ky~CpfCGk~ 44 (91)
.-..|.||+|.+.
T Consensus 11 ~f~D~~Cp~C~~~ 23 (154)
T cd03023 11 EFFDYNCGYCKKL 23 (154)
T ss_pred EEECCCChhHHHh
Confidence 3456899999875
No 391
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=23.90 E-value=45 Score=20.85 Aligned_cols=27 Identities=26% Similarity=0.620 Sum_probs=15.3
Q ss_pred cccCCCCcee-eE-Eeee----eeeeeCCCCce
Q 044880 36 YFCEFCGKYA-VK-RKAV----GIWGCKDCGKV 62 (91)
Q Consensus 36 y~CpfCGk~~-Vk-R~a~----GIW~C~~Cg~~ 62 (91)
..||.||... ++ |..+ =.=.|.+|...
T Consensus 5 i~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~E 37 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKNFPLYCPKCKQE 37 (55)
T ss_pred EECCCCCCccceeeecCceeccccccCCCCCce
Confidence 3699999543 32 1211 12368888753
No 392
>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=23.88 E-value=61 Score=26.63 Aligned_cols=43 Identities=19% Similarity=0.397 Sum_probs=26.7
Q ss_pred ccCCCCcee-eEEe-eeeeeeeCCCCceEec-ccccccccHHHHHH
Q 044880 37 FCEFCGKYA-VKRK-AVGIWGCKDCGKVKAG-GAYTLNTASAVTVR 79 (91)
Q Consensus 37 ~CpfCGk~~-VkR~-a~GIW~C~~Cg~~~AG-GAy~~~T~~~~t~~ 79 (91)
.||.||--. +.+. ....-+|..||.+..- ..+.++.+.+-.+.
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~~~~~~~~~~lAl~it 60 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTLTVGWDWSLQRPAAYALA 60 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCCcCCCCCCHHHHHHHHHH
Confidence 499999653 3322 3345789999988854 34555555554443
No 393
>PRK05767 rpl44e 50S ribosomal protein L44e; Validated
Probab=23.87 E-value=28 Score=23.73 Aligned_cols=42 Identities=31% Similarity=0.450 Sum_probs=24.2
Q ss_pred eeeccCCccccCchhhHHHHHHHHHhhcccccCCCCceeeEEeeeeeeeeCC
Q 044880 7 AGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKD 58 (91)
Q Consensus 7 vgi~gk~G~RYG~slRK~v~kie~~q~~ky~CpfCGk~~VkR~a~GIW~C~~ 58 (91)
.|.-|.+-+-++ --|--++ ...+|.|+.|++..+. -||.|++
T Consensus 45 ~GygGq~kpv~~--~aK~TKK----i~Lr~~C~~C~~~~~~----~~~R~k~ 86 (92)
T PRK05767 45 IGYGGKFSPVPG--GAKPTKK----VDLRYRCTECGKAHTR----EGFRAKK 86 (92)
T ss_pred cccCCcCCcccC--CCcccee----EEEEEEecccChhhcc----ccceeee
Confidence 455555555554 2222333 3568999999988765 2366653
No 394
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.86 E-value=1e+02 Score=19.53 Aligned_cols=39 Identities=18% Similarity=0.430 Sum_probs=26.2
Q ss_pred HhhcccccCCCCceeeEEeeeee-eeeCCCCceEecccccc
Q 044880 31 SQHSKYFCEFCGKYAVKRKAVGI-WGCKDCGKVKAGGAYTL 70 (91)
Q Consensus 31 ~q~~ky~CpfCGk~~VkR~a~GI-W~C~~Cg~~~AGGAy~~ 70 (91)
.|..+|.|-. .+-.+-|.+.-| =+|..|+..+-=+-|..
T Consensus 12 EMKK~H~Cg~-NrwkIiRvGaDIkikC~nC~h~vm~pR~~F 51 (60)
T COG4481 12 EMKKPHACGT-NRWKIIRVGADIKIKCENCGHSVMMPRYDF 51 (60)
T ss_pred eecCCCcccc-ceEEEEEecCcEEEEecCCCcEEEecHHHH
Confidence 4667777755 444677776654 38999999886555543
No 395
>PF09706 Cas_CXXC_CXXC: CRISPR-associated protein (Cas_CXXC_CXXC); InterPro: IPR019121 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved domain of about 65 amino acids found in otherwise highly divergent proteins encoded in CRISPR-associated regions. This domain features two CXXC motifs.
Probab=23.76 E-value=36 Score=21.36 Aligned_cols=13 Identities=46% Similarity=1.078 Sum_probs=10.5
Q ss_pred hhcccccCCCCce
Q 044880 32 QHSKYFCEFCGKY 44 (91)
Q Consensus 32 q~~ky~CpfCGk~ 44 (91)
+..+|.|.+||..
T Consensus 2 ~k~~~~C~~Cg~r 14 (69)
T PF09706_consen 2 SKKKYNCIFCGER 14 (69)
T ss_pred CCCCCcCcCCCCc
Confidence 5678999999943
No 396
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=23.76 E-value=40 Score=22.08 Aligned_cols=24 Identities=29% Similarity=0.707 Sum_probs=19.2
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCc
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
.|..||..+.. .-.|.|.|..|.-
T Consensus 8 ~C~VCg~~~~g-~hyGv~sC~aCk~ 31 (90)
T cd07168 8 LCSICEDKATG-LHYGIITCEGCKG 31 (90)
T ss_pred CCcccCCcCcc-eEECceehhhhhH
Confidence 59999987654 4679999999963
No 397
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=23.70 E-value=34 Score=23.62 Aligned_cols=8 Identities=38% Similarity=1.285 Sum_probs=6.4
Q ss_pred cccCCCCc
Q 044880 36 YFCEFCGK 43 (91)
Q Consensus 36 y~CpfCGk 43 (91)
-.||+||.
T Consensus 4 I~CP~Cg~ 11 (97)
T COG4311 4 IPCPYCGE 11 (97)
T ss_pred ecCCCCCC
Confidence 36999996
No 398
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=23.69 E-value=27 Score=25.53 Aligned_cols=38 Identities=21% Similarity=0.475 Sum_probs=21.1
Q ss_pred HHHHHHHHhhcccccCCCCcee---eEEeeeeeeeeCCCCc
Q 044880 24 QIKKMEVSQHSKYFCEFCGKYA---VKRKAVGIWGCKDCGK 61 (91)
Q Consensus 24 ~v~kie~~q~~ky~CpfCGk~~---VkR~a~GIW~C~~Cg~ 61 (91)
.+.+|+.-...-=.|+.||+.. ++..-.=.=+|..||.
T Consensus 94 i~~~i~~yi~~yv~C~~c~s~dt~l~~~~R~~~l~c~acGa 134 (151)
T COG1601 94 IVNEIERYIAEYVKCKECGSPDTELIKEERLLFLKCEACGA 134 (151)
T ss_pred HHHHHHHHHHheeEeccCCCCchhhhhhhhhHhhHHHHhCC
Confidence 3334443333333899999874 3333333347888864
No 399
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=23.65 E-value=68 Score=28.32 Aligned_cols=27 Identities=22% Similarity=0.384 Sum_probs=19.8
Q ss_pred cccccCCCCceeeEEeeeeeeeeC--CCCce
Q 044880 34 SKYFCEFCGKYAVKRKAVGIWGCK--DCGKV 62 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR~a~GIW~C~--~Cg~~ 62 (91)
.+..||.||.+.++ .+ -.|.|. .|-.+
T Consensus 397 ~P~~CP~C~s~l~~-~~-~~~~C~n~~C~aq 425 (669)
T PRK14350 397 IPDNCPSCKTALIK-EG-AHLFCVNNHCPSV 425 (669)
T ss_pred CCCCCCCCCCEeee-CC-EEEEECCCCCHHH
Confidence 37799999999886 23 478995 48543
No 400
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=23.58 E-value=52 Score=20.87 Aligned_cols=36 Identities=22% Similarity=0.492 Sum_probs=23.5
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCceEec---ccccccccHHHH
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGKVKAG---GAYTLNTASAVT 77 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~~~AG---GAy~~~T~~~~t 77 (91)
..||.||...++ + .|..||....- --|+|+-+-++.
T Consensus 6 rkC~~cg~YTLk-e-----~Cp~CG~~t~~~~PprFSPeD~y~kY 44 (59)
T COG2260 6 RKCPKCGRYTLK-E-----KCPVCGGDTKVPHPPRFSPEDKYGKY 44 (59)
T ss_pred hcCcCCCceeec-c-----cCCCCCCccccCCCCCCCccchHHHH
Confidence 369999999888 2 59999855432 235555555443
No 401
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=23.52 E-value=51 Score=20.40 Aligned_cols=35 Identities=23% Similarity=0.443 Sum_probs=22.7
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceEec---ccccccccHHHH
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVKAG---GAYTLNTASAVT 77 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~AG---GAy~~~T~~~~t 77 (91)
+||-||...++ =.|..||...-- --|+|+-.-++.
T Consensus 7 ~C~~CgvYTLk------~~CP~CG~~t~~~~P~rfSp~D~y~~y 44 (56)
T PRK13130 7 KCPKCGVYTLK------EICPVCGGKTKNPHPPRFSPEDKYGKY 44 (56)
T ss_pred ECCCCCCEEcc------ccCcCCCCCCCCCCCCCCCCCCccHHH
Confidence 69999999885 258999865322 335555555443
No 402
>cd06965 NR_DBD_Ppar DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive gene
Probab=23.46 E-value=30 Score=22.35 Aligned_cols=24 Identities=29% Similarity=0.711 Sum_probs=17.7
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCc
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
.|..||..+.. .-.|.|.|..|.-
T Consensus 1 ~C~VCg~~~~g-~hyGv~sC~aCk~ 24 (84)
T cd06965 1 ECRVCGDKASG-FHYGVHACEGCKG 24 (84)
T ss_pred CCcccCccCcc-eEEChhhhhhhhh
Confidence 38888876644 3578899998873
No 403
>cd06958 NR_DBD_COUP_TF DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. COUP-TFs homodimerize or heterodimerize with retinoid X receptor (RXR) and a few other nuclear receptors and bind to a variety of response elements that are composed of imperfect AGGTCA direct or inverted repeats with various spacings. COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone recept
Probab=23.45 E-value=34 Score=21.39 Aligned_cols=22 Identities=32% Similarity=0.862 Sum_probs=15.5
Q ss_pred cCCCCceeeEEeeeeeeeeCCCC
Q 044880 38 CEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 38 CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
|..||.++.. .-.|.|.|..|.
T Consensus 1 C~VCg~~~~g-~hygv~sC~aC~ 22 (73)
T cd06958 1 CVVCGDKSSG-KHYGQFTCEGCK 22 (73)
T ss_pred CCccCccCcc-eEEChhhhhhhh
Confidence 6678776544 456888888886
No 404
>cd06961 NR_DBD_TR DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the he
Probab=22.97 E-value=30 Score=22.42 Aligned_cols=23 Identities=26% Similarity=0.550 Sum_probs=17.0
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCC
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
.|..||..+.. .-.|+|.|..|.
T Consensus 1 ~C~VCg~~~~g-~hygv~sC~aC~ 23 (85)
T cd06961 1 PCVVCGDKATG-YHYRCITCEGCK 23 (85)
T ss_pred CCceeCCcCcc-eEEChhhhhhhh
Confidence 37888876654 357888898886
No 405
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=22.88 E-value=17 Score=30.51 Aligned_cols=30 Identities=23% Similarity=0.565 Sum_probs=20.2
Q ss_pred ccCCCCce-eeEEeeeeeeeeCCCCceEecc
Q 044880 37 FCEFCGKY-AVKRKAVGIWGCKDCGKVKAGG 66 (91)
Q Consensus 37 ~CpfCGk~-~VkR~a~GIW~C~~Cg~~~AGG 66 (91)
.|..|... ++.-.-.+-|.|.+||-+|-=|
T Consensus 248 AC~rC~t~y~le~A~~~~wrCpkCGg~ikKG 278 (403)
T COG1379 248 ACSRCYTRYSLEEAKSLRWRCPKCGGKIKKG 278 (403)
T ss_pred HHHHhhhccCcchhhhhcccCcccccchhhh
Confidence 69999832 3433334569999999776544
No 406
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=22.80 E-value=35 Score=20.99 Aligned_cols=31 Identities=19% Similarity=0.371 Sum_probs=19.3
Q ss_pred cccccCCCCceeeEE--eeeeeeeeCCCCceEe
Q 044880 34 SKYFCEFCGKYAVKR--KAVGIWGCKDCGKVKA 64 (91)
Q Consensus 34 ~ky~CpfCGk~~VkR--~a~GIW~C~~Cg~~~A 64 (91)
..+-|+.|++...+= ....-=+|..|+...-
T Consensus 3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~ 35 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTINH 35 (51)
T ss_pred cceeccchhHHHhhhcCccEEEEECCCCCccce
Confidence 456789998876541 2222338999986543
No 407
>cd07171 NR_DBD_ER DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well-conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserv
Probab=22.70 E-value=43 Score=21.63 Aligned_cols=23 Identities=39% Similarity=1.196 Sum_probs=18.5
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCC
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
.|..||..+.. .-.|.|.|..|.
T Consensus 5 ~C~VCg~~~~g-~hyGv~sC~aC~ 27 (82)
T cd07171 5 FCAVCSDYASG-YHYGVWSCEGCK 27 (82)
T ss_pred CCeecCCcCcc-eEECceeehhhH
Confidence 59999987654 467899999996
No 408
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=22.61 E-value=30 Score=25.29 Aligned_cols=33 Identities=24% Similarity=0.401 Sum_probs=27.1
Q ss_pred CCCceeeEEeeeeeeeeCCCCceEecccccccc
Q 044880 40 FCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLNT 72 (91)
Q Consensus 40 fCGk~~VkR~a~GIW~C~~Cg~~~AGGAy~~~T 72 (91)
.|=++-+..+..|-|.|..|-..-+|.......
T Consensus 5 ~CL~Ppl~~~P~g~W~Cp~C~~~~~~~~~~~~~ 37 (148)
T cd04718 5 CCLRPPLKEVPEGDWICPFCEVEKSGQSAMPQL 37 (148)
T ss_pred ccCCCCCCCCCCCCcCCCCCcCCCCCCcccccC
Confidence 466777888888999999999988888877653
No 409
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=22.54 E-value=1e+02 Score=25.05 Aligned_cols=25 Identities=36% Similarity=0.903 Sum_probs=16.2
Q ss_pred ccCCCCceeeEEee------eeeeeeCCCCce
Q 044880 37 FCEFCGKYAVKRKA------VGIWGCKDCGKV 62 (91)
Q Consensus 37 ~CpfCGk~~VkR~a------~GIW~C~~Cg~~ 62 (91)
.||.||+..+.-.+ +=-|.| +||..
T Consensus 171 ~c~~cg~~~~~v~~~d~~~~~v~y~c-~cG~~ 201 (353)
T cd00674 171 YCEKCGKDTTTVEAYDAKAGTVTYKC-ECGHE 201 (353)
T ss_pred ecCCcCcceeEEEEEeCCCCeEEEEc-CCCCE
Confidence 79999976533222 235888 58865
No 410
>PF14122 YokU: YokU-like protein
Probab=22.48 E-value=83 Score=21.33 Aligned_cols=27 Identities=37% Similarity=0.902 Sum_probs=17.9
Q ss_pred ccCCCCce-eeEEeeeeee-----------------eeCCCCceE
Q 044880 37 FCEFCGKY-AVKRKAVGIW-----------------GCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~-~VkR~a~GIW-----------------~C~~Cg~~~ 63 (91)
+|..||.. .+.+.++=-| .|.+||.++
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvY 45 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVY 45 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEE
Confidence 48888875 4444444445 688998764
No 411
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=22.48 E-value=98 Score=21.08 Aligned_cols=27 Identities=30% Similarity=0.655 Sum_probs=19.2
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceEe
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVKA 64 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~A 64 (91)
.|..|+...-.=.+-.| .|..|+-.|.
T Consensus 37 aCeiC~~~GY~q~g~~l-vC~~C~~~~~ 63 (102)
T PF10080_consen 37 ACEICGPKGYYQEGDQL-VCKNCGVRFN 63 (102)
T ss_pred eccccCCCceEEECCEE-EEecCCCEEe
Confidence 59999887655334344 8999997764
No 412
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=22.45 E-value=16 Score=33.37 Aligned_cols=14 Identities=50% Similarity=1.217 Sum_probs=12.8
Q ss_pred eeeeeeeCCCCceE
Q 044880 50 AVGIWGCKDCGKVK 63 (91)
Q Consensus 50 a~GIW~C~~Cg~~~ 63 (91)
+.||.+|+.|++.|
T Consensus 789 ~~giFpCreC~kvF 802 (907)
T KOG4167|consen 789 PTGIFPCRECGKVF 802 (907)
T ss_pred CCceeehHHHHHHH
Confidence 58999999999987
No 413
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=22.33 E-value=80 Score=26.13 Aligned_cols=43 Identities=16% Similarity=0.270 Sum_probs=26.3
Q ss_pred ccCCCCcee-eEEe-eeeeeeeCCCCceEeccc-ccccccHHHHHH
Q 044880 37 FCEFCGKYA-VKRK-AVGIWGCKDCGKVKAGGA-YTLNTASAVTVR 79 (91)
Q Consensus 37 ~CpfCGk~~-VkR~-a~GIW~C~~Cg~~~AGGA-y~~~T~~~~t~~ 79 (91)
.||.||.-. +.+. .-..-+|..||....-.. ..++.+.|-++.
T Consensus 12 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~~~~~~~~~~lAl~it 57 (419)
T PRK15103 12 LCPQCDMLVALPRLEHGQKAACPRCGTTLTVRWDEPRQRPTAYALS 57 (419)
T ss_pred cCCCCCceeecCCCCCCCeeECCCCCCCCcCCCCCcHHHHHHHHHH
Confidence 499999753 3332 233578999999885433 344545444443
No 414
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=22.33 E-value=59 Score=18.06 Aligned_cols=11 Identities=27% Similarity=0.609 Sum_probs=8.2
Q ss_pred hcccccCCCCc
Q 044880 33 HSKYFCEFCGK 43 (91)
Q Consensus 33 ~~ky~CpfCGk 43 (91)
.....||+|++
T Consensus 34 ~~~~~CP~C~k 44 (44)
T PF14634_consen 34 GKSVKCPICRK 44 (44)
T ss_pred CCCCCCcCCCC
Confidence 45678999975
No 415
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the cd07164 NR_DBD_PNR_like_1 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-t
Probab=22.20 E-value=39 Score=21.40 Aligned_cols=23 Identities=35% Similarity=0.826 Sum_probs=16.0
Q ss_pred cCCCCceeeEEeeeeeeeeCCCCc
Q 044880 38 CEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 38 CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
|..||....- .-.|+|.|..|.-
T Consensus 1 C~VCg~~~~g-~hyG~~~C~~C~~ 23 (78)
T cd07164 1 CRVCGDRASG-KHYGVPSCDGCRG 23 (78)
T ss_pred CcccCccCcc-eEECcchhhhhhh
Confidence 6778876544 3668888888863
No 417
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=22.12 E-value=1e+02 Score=24.76 Aligned_cols=27 Identities=30% Similarity=0.609 Sum_probs=18.0
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
-.|+.||.+..-+.+-=-=.|.+||..
T Consensus 112 RFCg~CG~~~~~~~~g~~~~C~~cg~~ 138 (279)
T COG2816 112 RFCGRCGTKTYPREGGWARVCPKCGHE 138 (279)
T ss_pred cCCCCCCCcCccccCceeeeCCCCCCc
Confidence 389999987644333223379999864
No 418
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=21.95 E-value=46 Score=23.36 Aligned_cols=13 Identities=31% Similarity=0.884 Sum_probs=8.8
Q ss_pred ccccCCCCceeeE
Q 044880 35 KYFCEFCGKYAVK 47 (91)
Q Consensus 35 ky~CpfCGk~~Vk 47 (91)
.|.||.||...++
T Consensus 86 ~~~CP~C~s~~~~ 98 (115)
T COG0375 86 DYRCPKCGSINLR 98 (115)
T ss_pred eeECCCCCCCceE
Confidence 3459999976544
No 419
>cd03019 DsbA_DsbA DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol oxidant known, due to the unusual stability of the thiolate anion form of the first cysteine in the CXXC motif. The highly unstable oxidized form of DsbA directly donates disulfide bonds to reduced proteins secreted into the bacterial periplasm. This rapid and unidirectional process helps to catalyze the folding of newly-synthesized polypeptides. To regain catalytic activity, reduced DsbA is then reoxidized by the membrane protein DsbB, which generates its disulfides from oxidized quinones, which in turn are reoxidized by the electron transport chain.
Probab=21.95 E-value=34 Score=22.99 Aligned_cols=15 Identities=27% Similarity=0.609 Sum_probs=10.4
Q ss_pred HHhhcccccCCCCce
Q 044880 30 VSQHSKYFCEFCGKY 44 (91)
Q Consensus 30 ~~q~~ky~CpfCGk~ 44 (91)
+.--..|.||+|...
T Consensus 19 i~~f~D~~Cp~C~~~ 33 (178)
T cd03019 19 VIEFFSYGCPHCYNF 33 (178)
T ss_pred EEEEECCCCcchhhh
Confidence 333456899999864
No 420
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=21.87 E-value=77 Score=20.80 Aligned_cols=26 Identities=19% Similarity=0.588 Sum_probs=18.5
Q ss_pred cccccCCCCce-eeEEeeeeee--------------eeCCC
Q 044880 34 SKYFCEFCGKY-AVKRKAVGIW--------------GCKDC 59 (91)
Q Consensus 34 ~ky~CpfCGk~-~VkR~a~GIW--------------~C~~C 59 (91)
.+|.|+-|++. .-.++.+-|| .|++|
T Consensus 4 grF~C~~C~~~W~S~~v~i~f~~~~~g~v~~rv~~Q~C~~C 44 (98)
T PF13695_consen 4 GRFQCSKCSRGWTSAKVWILFHMYRGGQVNMRVFGQRCKKC 44 (98)
T ss_pred EEEECCCCCCCCccCEEEEEEEEcCCCeEEEEEECCCCCCC
Confidence 47899999765 3444566665 78999
No 421
>PRK11827 hypothetical protein; Provisional
Probab=21.73 E-value=74 Score=19.92 Aligned_cols=24 Identities=17% Similarity=0.203 Sum_probs=15.4
Q ss_pred ccCCCCceeeEE-eeeeeeeeCCCCc
Q 044880 37 FCEFCGKYAVKR-KAVGIWGCKDCGK 61 (91)
Q Consensus 37 ~CpfCGk~~VkR-~a~GIW~C~~Cg~ 61 (91)
.||.|..+..-- ....+ .|+.|+.
T Consensus 10 aCP~ckg~L~~~~~~~~L-ic~~~~l 34 (60)
T PRK11827 10 ACPVCNGKLWYNQEKQEL-ICKLDNL 34 (60)
T ss_pred ECCCCCCcCeEcCCCCeE-ECCccCe
Confidence 599998765332 23345 4998864
No 422
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=21.66 E-value=80 Score=17.88 Aligned_cols=14 Identities=43% Similarity=0.871 Sum_probs=10.8
Q ss_pred ccCCCCceeeEEeee
Q 044880 37 FCEFCGKYAVKRKAV 51 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~ 51 (91)
.|+ ||...+.+++.
T Consensus 2 ~C~-Cg~~~~~~~s~ 15 (45)
T PF06839_consen 2 KCP-CGEPAVRRTSK 15 (45)
T ss_pred CCC-CCCEeEEEEEe
Confidence 488 99888777764
No 423
>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=21.48 E-value=37 Score=24.43 Aligned_cols=25 Identities=28% Similarity=0.636 Sum_probs=10.9
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCC
Q 044880 36 YFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 36 y~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
|.|.-||....--.+.=|=.|.+|+
T Consensus 113 l~C~~Cg~~~~~~~~~~l~~Cp~C~ 137 (146)
T PF07295_consen 113 LVCENCGHEVELTHPERLPPCPKCG 137 (146)
T ss_pred EecccCCCEEEecCCCcCCCCCCCC
Confidence 4555555443221233344555554
No 424
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=21.28 E-value=1.2e+02 Score=19.05 Aligned_cols=28 Identities=25% Similarity=0.508 Sum_probs=19.2
Q ss_pred hhcccccCCCCce--eeEEeee--eeeeeCCCCceE
Q 044880 32 QHSKYFCEFCGKY--AVKRKAV--GIWGCKDCGKVK 63 (91)
Q Consensus 32 q~~ky~CpfCGk~--~VkR~a~--GIW~C~~Cg~~~ 63 (91)
+..+|.| |.. .|-|.+. .| +|..||..+
T Consensus 10 mKK~HPC---G~~~Wei~R~GaDiki-kC~gCg~~i 41 (57)
T PF06107_consen 10 MKKPHPC---GSNEWEIIRIGADIKI-KCLGCGRQI 41 (57)
T ss_pred EcCCCCC---CCCEEEEEEccCcEEE-EECCCCCEE
Confidence 4566665 555 3777754 55 799999876
No 425
>COG4694 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.28 E-value=37 Score=30.47 Aligned_cols=10 Identities=50% Similarity=1.221 Sum_probs=7.6
Q ss_pred ccccCCCCce
Q 044880 35 KYFCEFCGKY 44 (91)
Q Consensus 35 ky~CpfCGk~ 44 (91)
.--|||||+.
T Consensus 278 ~q~CpFCg~e 287 (758)
T COG4694 278 NQICPFCGKE 287 (758)
T ss_pred CCCCCccchH
Confidence 4469999964
No 426
>cd06970 NR_DBD_PNR DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of the nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hing
Probab=21.15 E-value=53 Score=21.71 Aligned_cols=26 Identities=31% Similarity=0.848 Sum_probs=19.9
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCceE
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKVK 63 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~~ 63 (91)
.|..||++..- .-.|.|.|..|.-=|
T Consensus 8 ~C~VCg~~a~g-~hyGv~sC~aCk~FF 33 (92)
T cd06970 8 LCRVCGDTSSG-KHYGIYACNGCSGFF 33 (92)
T ss_pred CCeecCCcCcc-cEECccEEeeeeeEe
Confidence 59999987655 367899999997433
No 427
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=21.09 E-value=87 Score=16.59 Aligned_cols=9 Identities=22% Similarity=0.755 Sum_probs=7.1
Q ss_pred hcccccCCC
Q 044880 33 HSKYFCEFC 41 (91)
Q Consensus 33 ~~ky~CpfC 41 (91)
...+.||.|
T Consensus 33 ~~~~~CP~C 41 (41)
T PF00097_consen 33 SGSVKCPLC 41 (41)
T ss_dssp TSSSBTTTT
T ss_pred cCCccCCcC
Confidence 667789987
No 428
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=21.04 E-value=44 Score=27.79 Aligned_cols=13 Identities=15% Similarity=0.192 Sum_probs=6.8
Q ss_pred eeeeeeCCCCceE
Q 044880 51 VGIWGCKDCGKVK 63 (91)
Q Consensus 51 ~GIW~C~~Cg~~~ 63 (91)
...|+|..||+..
T Consensus 423 ~~~~~c~~c~~~y 435 (479)
T PRK05452 423 GPRMQCSVCQWIY 435 (479)
T ss_pred CCeEEECCCCeEE
Confidence 3455555555543
No 429
>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=20.96 E-value=79 Score=28.16 Aligned_cols=9 Identities=33% Similarity=0.874 Sum_probs=7.1
Q ss_pred ccccCCCCc
Q 044880 35 KYFCEFCGK 43 (91)
Q Consensus 35 ky~CpfCGk 43 (91)
.-.||.||.
T Consensus 457 ~~~CPvCg~ 465 (908)
T COG0419 457 GEKCPVCGQ 465 (908)
T ss_pred CCCCCCCCC
Confidence 457999994
No 430
>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=20.83 E-value=44 Score=21.07 Aligned_cols=8 Identities=38% Similarity=1.335 Sum_probs=3.7
Q ss_pred cccCCCCc
Q 044880 36 YFCEFCGK 43 (91)
Q Consensus 36 y~CpfCGk 43 (91)
|.|.||..
T Consensus 27 fECTFC~~ 34 (57)
T PF06906_consen 27 FECTFCAD 34 (57)
T ss_pred EeCcccHH
Confidence 44455443
No 431
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.73 E-value=42 Score=29.26 Aligned_cols=37 Identities=24% Similarity=0.529 Sum_probs=23.5
Q ss_pred chhhHHHHHHHHHhhccc--------ccCCCCceeeEEeeeeeeeeCCCCc
Q 044880 19 ASLRKQIKKMEVSQHSKY--------FCEFCGKYAVKRKAVGIWGCKDCGK 61 (91)
Q Consensus 19 ~slRK~v~kie~~q~~ky--------~CpfCGk~~VkR~a~GIW~C~~Cg~ 61 (91)
..|...|+.+.. ..-.| .|+.||-...- .|.|..||.
T Consensus 536 ~Al~~lvk~~~~-~~i~Y~sin~~~~~C~~CGy~g~~-----~~~CP~CG~ 580 (618)
T PRK14704 536 KALKQIVQAMAE-HGVGYGSINHPVDRCKCCSYHGVI-----GNECPSCGN 580 (618)
T ss_pred HHHHHHHHHHHh-cCCceEEeCCCCeecCCCCCCCCc-----CccCcCCCC
Confidence 456666666543 33444 79999963221 199999985
No 432
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=20.67 E-value=1.1e+02 Score=24.84 Aligned_cols=28 Identities=32% Similarity=0.649 Sum_probs=23.1
Q ss_pred hcccccCCCCceeeEEeee--eeeeeCCCC
Q 044880 33 HSKYFCEFCGKYAVKRKAV--GIWGCKDCG 60 (91)
Q Consensus 33 ~~ky~CpfCGk~~VkR~a~--GIW~C~~Cg 60 (91)
...=.|--||.+.+.+.++ ||--|-.|-
T Consensus 18 ~~Nk~CaDCga~~P~W~S~nlGvfiCi~Ca 47 (319)
T COG5347 18 SSNKKCADCGAPNPTWASVNLGVFLCIDCA 47 (319)
T ss_pred cccCccccCCCCCCceEecccCeEEEeecc
Confidence 3444799999999888865 999999994
No 433
>PRK07726 DNA topoisomerase III; Provisional
Probab=20.66 E-value=1e+02 Score=26.77 Aligned_cols=23 Identities=39% Similarity=0.638 Sum_probs=16.1
Q ss_pred cccCCCCceeeEEe-eee-eeeeCC
Q 044880 36 YFCEFCGKYAVKRK-AVG-IWGCKD 58 (91)
Q Consensus 36 y~CpfCGk~~VkR~-a~G-IW~C~~ 58 (91)
..||.||+..+.+. ..| .|.|..
T Consensus 611 ~~CP~C~~~~~~~~~~~~~f~~Cs~ 635 (658)
T PRK07726 611 PKCPDCGKPMLKVKGKNGKMLVCQD 635 (658)
T ss_pred ccccccCccceeecccCCeeEecCC
Confidence 56999998766432 224 499988
No 434
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=20.46 E-value=68 Score=18.10 Aligned_cols=24 Identities=38% Similarity=0.778 Sum_probs=16.0
Q ss_pred hcccccCCCCceeeEEeeeeeeeeCCCC
Q 044880 33 HSKYFCEFCGKYAVKRKAVGIWGCKDCG 60 (91)
Q Consensus 33 ~~ky~CpfCGk~~VkR~a~GIW~C~~Cg 60 (91)
+..+.|..|+.+.+. --|+|..|.
T Consensus 2 ~~~~~C~~C~~~i~g----~ry~C~~C~ 25 (44)
T smart00291 2 HHSYSCDTCGKPIVG----VRYHCLVCP 25 (44)
T ss_pred CCCcCCCCCCCCCcC----CEEECCCCC
Confidence 346789999984322 237888884
No 435
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=20.45 E-value=59 Score=17.81 Aligned_cols=17 Identities=35% Similarity=0.405 Sum_probs=9.9
Q ss_pred eeeeeeeCCCCceEecc
Q 044880 50 AVGIWGCKDCGKVKAGG 66 (91)
Q Consensus 50 a~GIW~C~~Cg~~~AGG 66 (91)
......|+.|++.+.++
T Consensus 13 ~~~~a~C~~C~~~~~~~ 29 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYS 29 (45)
T ss_dssp CSS-EEETTTTEE----
T ss_pred CcCeEEeCCCCeEEeeC
Confidence 34567899999999987
No 436
>PF15616 TerY-C: TerY-C metal binding domain
Probab=20.40 E-value=78 Score=22.66 Aligned_cols=8 Identities=38% Similarity=0.953 Sum_probs=7.0
Q ss_pred ccCCCCce
Q 044880 37 FCEFCGKY 44 (91)
Q Consensus 37 ~CpfCGk~ 44 (91)
.||.||..
T Consensus 79 gCP~CGn~ 86 (131)
T PF15616_consen 79 GCPHCGNQ 86 (131)
T ss_pred CCCCCcCh
Confidence 79999986
No 437
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=20.35 E-value=63 Score=16.75 Aligned_cols=23 Identities=26% Similarity=0.560 Sum_probs=7.0
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 37 FCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 37 ~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
.|..|+++... .-...|..|++.
T Consensus 2 ~C~~C~~~~~~---~~~Y~C~~Cdf~ 24 (30)
T PF07649_consen 2 RCDACGKPIDG---GWFYRCSECDFD 24 (30)
T ss_dssp --TTTS----S-----EEE-TTT---
T ss_pred cCCcCCCcCCC---CceEECccCCCc
Confidence 46666655432 124677777654
No 438
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=20.30 E-value=58 Score=20.13 Aligned_cols=26 Identities=31% Similarity=0.606 Sum_probs=16.9
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCCce
Q 044880 35 KYFCEFCGKYAVKRKAVGIWGCKDCGKV 62 (91)
Q Consensus 35 ky~CpfCGk~~VkR~a~GIW~C~~Cg~~ 62 (91)
...|++||++... .--|=.|..|+..
T Consensus 5 ~~~C~~Cg~~~~~--~dDiVvCp~Cgap 30 (54)
T PF14446_consen 5 GCKCPVCGKKFKD--GDDIVVCPECGAP 30 (54)
T ss_pred CccChhhCCcccC--CCCEEECCCCCCc
Confidence 4579999987532 2334468888754
No 439
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=20.17 E-value=45 Score=18.76 Aligned_cols=11 Identities=45% Similarity=1.715 Sum_probs=4.4
Q ss_pred cccccCCCCce
Q 044880 34 SKYFCEFCGKY 44 (91)
Q Consensus 34 ~ky~CpfCGk~ 44 (91)
.+|.|.+|...
T Consensus 2 ~ryyCdyC~~~ 12 (38)
T PF06220_consen 2 PRYYCDYCKKY 12 (38)
T ss_dssp -S-B-TTT--B
T ss_pred cCeecccccce
Confidence 36888888653
No 440
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=20.02 E-value=1e+02 Score=30.46 Aligned_cols=26 Identities=31% Similarity=0.626 Sum_probs=18.9
Q ss_pred ccCCCCcee---e-EEeeeeeeeeCCCCce
Q 044880 37 FCEFCGKYA---V-KRKAVGIWGCKDCGKV 62 (91)
Q Consensus 37 ~CpfCGk~~---V-kR~a~GIW~C~~Cg~~ 62 (91)
.||.||... | -+...|==.|..||..
T Consensus 1706 ~cp~c~~~~~~~~~~~~~~gc~~c~~cg~s 1735 (1740)
T PRK08332 1706 YCPVCYEKEGKLVELRMESGCATCPVCGWS 1735 (1740)
T ss_pred CCCCCCCCCCcceeeEecCCceeCCCCCCc
Confidence 399999873 1 1345677789999965
Done!