Query 037152
Match_columns 75
No_of_seqs 110 out of 717
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 09:10:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037152.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037152hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00202 ZnF_GATA Zinc finger D 99.7 3.1E-17 6.8E-22 96.1 3.6 44 9-55 1-44 (54)
2 smart00401 ZnF_GATA zinc finge 99.7 7.3E-17 1.6E-21 93.7 3.5 40 6-45 2-41 (52)
3 PF00320 GATA: GATA zinc finge 99.6 4.1E-17 8.8E-22 88.6 0.6 35 10-44 1-35 (36)
4 KOG1601 GATA-4/5/6 transcripti 99.0 3.6E-10 7.8E-15 76.3 4.4 49 7-55 199-250 (340)
5 COG5641 GAT1 GATA Zn-finger-co 98.5 4E-08 8.7E-13 78.2 2.5 54 6-62 157-215 (498)
6 KOG3554 Histone deacetylase co 91.8 0.13 2.7E-06 42.3 2.3 36 7-42 386-423 (693)
7 PF14803 Nudix_N_2: Nudix N-te 90.9 0.053 1.1E-06 29.0 -0.4 30 8-37 1-30 (34)
8 PF08271 TF_Zn_Ribbon: TFIIB z 84.1 0.32 6.9E-06 26.4 -0.0 30 9-41 2-31 (43)
9 PRK03988 translation initiatio 83.2 0.34 7.3E-06 33.0 -0.2 29 9-38 104-132 (138)
10 COG5641 GAT1 GATA Zn-finger-co 82.9 0.96 2.1E-05 36.6 2.2 37 7-43 297-334 (498)
11 PF01783 Ribosomal_L32p: Ribos 82.5 0.64 1.4E-05 26.9 0.8 23 8-40 27-49 (56)
12 smart00653 eIF2B_5 domain pres 82.3 0.39 8.4E-06 31.5 -0.1 28 9-37 82-109 (110)
13 TIGR00311 aIF-2beta translatio 81.7 0.42 9.1E-06 32.3 -0.1 30 9-39 99-128 (133)
14 COG5347 GTPase-activating prot 80.4 0.69 1.5E-05 35.4 0.6 31 4-36 17-47 (319)
15 PF13248 zf-ribbon_3: zinc-rib 79.3 1.2 2.5E-05 22.0 1.1 23 8-38 3-25 (26)
16 PF07282 OrfB_Zn_ribbon: Putat 78.4 0.78 1.7E-05 26.6 0.3 35 2-40 23-57 (69)
17 PRK12336 translation initiatio 77.8 0.65 1.4E-05 33.0 -0.2 32 9-41 100-131 (201)
18 smart00105 ArfGap Putative GTP 75.4 1.8 3.8E-05 27.8 1.4 33 7-41 3-35 (112)
19 PF01412 ArfGap: Putative GTPa 75.1 2.1 4.5E-05 27.6 1.7 35 5-41 11-45 (116)
20 PF06677 Auto_anti-p27: Sjogre 74.0 1.4 3E-05 24.4 0.5 27 5-36 15-41 (41)
21 PF01873 eIF-5_eIF-2B: Domain 72.9 0.95 2.1E-05 30.2 -0.4 28 9-37 95-122 (125)
22 PRK12286 rpmF 50S ribosomal pr 72.6 1.5 3.3E-05 25.7 0.5 22 8-38 28-49 (57)
23 PF15396 FAM60A: Protein Famil 68.7 2.1 4.5E-05 31.4 0.6 17 29-45 49-65 (213)
24 smart00778 Prim_Zn_Ribbon Zinc 68.5 3.5 7.5E-05 22.3 1.3 30 7-37 3-33 (37)
25 PF01096 TFIIS_C: Transcriptio 68.4 0.68 1.5E-05 25.0 -1.5 32 9-40 2-39 (39)
26 PRK00423 tfb transcription ini 67.6 2.6 5.6E-05 31.4 0.9 36 3-41 7-42 (310)
27 PF04810 zf-Sec23_Sec24: Sec23 65.7 3.1 6.6E-05 22.4 0.7 31 8-38 3-33 (40)
28 PF11781 RRN7: RNA polymerase 64.8 2.8 6.1E-05 22.4 0.5 25 8-37 9-33 (36)
29 PRK00420 hypothetical protein; 64.3 3.2 6.9E-05 27.5 0.8 32 5-41 21-52 (112)
30 PF12773 DZR: Double zinc ribb 63.1 5.4 0.00012 21.6 1.5 30 6-40 11-40 (50)
31 PF09297 zf-NADH-PPase: NADH p 62.4 1.3 2.8E-05 22.6 -1.1 29 7-39 3-31 (32)
32 PRK14892 putative transcriptio 62.0 2.9 6.4E-05 27.1 0.3 33 8-41 22-54 (99)
33 KOG0703 Predicted GTPase-activ 59.8 3.8 8.3E-05 31.2 0.6 27 7-35 25-51 (287)
34 PLN03114 ADP-ribosylation fact 59.1 5.6 0.00012 31.6 1.4 33 6-40 21-53 (395)
35 TIGR01031 rpmF_bact ribosomal 56.5 4.2 9.2E-05 23.5 0.3 20 8-36 27-46 (55)
36 PF04161 Arv1: Arv1-like famil 55.9 5.2 0.00011 28.3 0.7 31 8-38 1-33 (208)
37 PHA00626 hypothetical protein 55.8 4.8 0.0001 24.1 0.4 33 8-41 1-35 (59)
38 PF13240 zinc_ribbon_2: zinc-r 54.6 7.3 0.00016 18.8 0.9 22 9-38 1-22 (23)
39 smart00440 ZnF_C2C2 C2C2 Zinc 54.4 3.3 7.1E-05 22.4 -0.4 32 9-40 2-39 (40)
40 PF02701 zf-Dof: Dof domain, z 54.3 25 0.00055 21.3 3.4 46 6-51 4-52 (63)
41 smart00661 RPOL9 RNA polymeras 53.8 8.8 0.00019 20.8 1.3 30 8-40 1-31 (52)
42 KOG3740 Uncharacterized conser 53.3 5.2 0.00011 33.8 0.4 30 7-36 462-494 (706)
43 PRK08351 DNA-directed RNA poly 51.8 9.4 0.0002 22.8 1.3 16 8-23 16-32 (61)
44 cd07168 NR_DBD_DHR4_like DNA-b 51.7 12 0.00026 23.4 1.8 35 2-41 1-35 (90)
45 COG3529 Predicted nucleic-acid 51.2 2.9 6.3E-05 25.5 -1.0 35 5-40 8-43 (66)
46 COG2816 NPY1 NTP pyrophosphohy 51.1 7.5 0.00016 29.5 0.9 31 6-40 110-140 (279)
47 KOG2907 RNA polymerase I trans 51.0 6.1 0.00013 26.6 0.4 37 4-40 71-113 (116)
48 PF06689 zf-C4_ClpX: ClpX C4-t 50.8 7.3 0.00016 21.1 0.6 30 8-38 2-33 (41)
49 TIGR00244 transcriptional regu 48.7 9.6 0.00021 26.5 1.1 35 8-42 1-41 (147)
50 PRK00241 nudC NADH pyrophospha 48.0 6.9 0.00015 28.6 0.3 31 6-40 98-128 (256)
51 PF09723 Zn-ribbon_8: Zinc rib 46.9 6.4 0.00014 21.2 -0.0 28 9-37 7-34 (42)
52 PRK00085 recO DNA repair prote 46.3 10 0.00022 26.6 0.9 28 8-36 150-177 (247)
53 cd07169 NR_DBD_GCNF_like DNA-b 46.1 17 0.00037 22.7 1.8 34 3-41 2-35 (90)
54 PF12760 Zn_Tnp_IS1595: Transp 45.8 8.3 0.00018 21.0 0.3 27 8-37 19-45 (46)
55 PRK01110 rpmF 50S ribosomal pr 45.6 8.5 0.00018 22.7 0.4 21 8-38 28-48 (60)
56 smart00659 RPOLCX RNA polymera 45.6 9.7 0.00021 21.1 0.6 26 9-39 4-29 (44)
57 PF09526 DUF2387: Probable met 45.5 6.2 0.00013 24.1 -0.2 36 5-41 6-42 (71)
58 KOG1598 Transcription initiati 45.1 13 0.00028 30.6 1.4 30 8-40 1-30 (521)
59 PRK00432 30S ribosomal protein 45.0 8.6 0.00019 21.8 0.3 29 6-39 19-47 (50)
60 PRK06393 rpoE DNA-directed RNA 44.7 14 0.0003 22.4 1.3 16 7-22 17-33 (64)
61 KOG1597 Transcription initiati 43.4 12 0.00027 28.8 1.1 32 9-41 2-33 (308)
62 PF08273 Prim_Zn_Ribbon: Zinc- 42.8 8.3 0.00018 21.1 0.0 29 8-36 4-33 (40)
63 COG1405 SUA7 Transcription ini 42.7 11 0.00024 28.4 0.7 31 8-41 2-32 (285)
64 PF10083 DUF2321: Uncharacteri 42.6 14 0.0003 26.0 1.1 32 8-39 40-78 (158)
65 PF10058 DUF2296: Predicted in 42.4 10 0.00022 21.9 0.3 35 4-38 19-53 (54)
66 COG3952 Predicted membrane pro 41.8 5.2 0.00011 26.8 -1.0 18 21-40 77-94 (113)
67 PLN03119 putative ADP-ribosyla 41.1 14 0.00031 31.0 1.2 29 6-36 22-50 (648)
68 PF09889 DUF2116: Uncharacteri 39.9 16 0.00035 21.6 1.0 28 7-42 3-31 (59)
69 PF12553 DUF3742: Protein of u 39.5 10 0.00022 22.1 0.1 10 19-28 34-43 (54)
70 PF05191 ADK_lid: Adenylate ki 39.5 13 0.00027 19.8 0.4 29 8-38 2-30 (36)
71 PLN03131 hypothetical protein; 39.4 16 0.00035 31.0 1.2 29 6-36 22-50 (705)
72 KOG0909 Peptide:N-glycanase [P 38.6 18 0.00038 29.6 1.3 34 7-40 161-205 (500)
73 KOG0706 Predicted GTPase-activ 38.4 12 0.00027 30.2 0.4 33 4-38 20-52 (454)
74 TIGR01384 TFS_arch transcripti 37.4 10 0.00022 23.6 -0.2 36 6-41 61-102 (104)
75 TIGR03573 WbuX N-acetyl sugar 37.0 25 0.00055 26.4 1.9 30 8-40 2-32 (343)
76 PHA02998 RNA polymerase subuni 37.0 13 0.00029 26.9 0.3 36 6-41 142-183 (195)
77 PF03604 DNA_RNApol_7kD: DNA d 35.9 22 0.00049 18.5 1.0 26 9-39 2-27 (32)
78 TIGR01385 TFSII transcription 35.4 13 0.00029 28.1 0.2 34 7-40 258-297 (299)
79 PF14122 YokU: YokU-like prote 35.2 12 0.00027 24.0 -0.1 33 9-41 1-47 (87)
80 TIGR02443 conserved hypothetic 34.9 12 0.00025 22.4 -0.2 35 5-40 7-42 (59)
81 PF13717 zinc_ribbon_4: zinc-r 34.8 12 0.00027 19.7 -0.1 31 9-39 4-35 (36)
82 PRK05978 hypothetical protein; 34.4 23 0.0005 24.4 1.2 35 6-43 32-66 (148)
83 TIGR02605 CxxC_CxxC_SSSS putat 34.4 17 0.00037 19.8 0.5 29 8-37 6-34 (52)
84 COG0675 Transposase and inacti 34.4 18 0.00039 25.3 0.7 28 4-40 306-333 (364)
85 TIGR02098 MJ0042_CXXC MJ0042 f 33.6 7.6 0.00017 20.0 -1.0 33 8-40 3-36 (38)
86 PF10080 DUF2318: Predicted me 33.5 8.7 0.00019 24.9 -1.0 16 26-41 49-64 (102)
87 PRK03564 formate dehydrogenase 33.4 17 0.00036 27.8 0.4 35 7-41 226-264 (309)
88 PF10571 UPF0547: Uncharacteri 33.1 18 0.00039 18.0 0.4 24 9-40 2-25 (26)
89 COG1327 Predicted transcriptio 33.1 23 0.00051 24.9 1.1 34 8-41 1-40 (156)
90 cd02337 ZZ_CBP Zinc finger, ZZ 33.0 29 0.00064 18.8 1.3 29 9-37 2-30 (41)
91 PRK12496 hypothetical protein; 31.8 27 0.00058 24.0 1.2 32 6-43 126-157 (164)
92 PF13878 zf-C2H2_3: zinc-finge 31.7 13 0.00029 20.1 -0.3 14 29-42 13-26 (41)
93 COG4260 Membrane protease subu 31.6 27 0.00059 27.2 1.3 29 7-38 315-343 (345)
94 smart00834 CxxC_CXXC_SSSS Puta 31.5 17 0.00036 18.6 0.1 29 9-38 7-35 (41)
95 PRK13130 H/ACA RNA-protein com 31.2 54 0.0012 19.2 2.2 23 7-39 5-27 (56)
96 PF09538 FYDLN_acid: Protein o 30.8 54 0.0012 21.3 2.4 16 26-41 6-21 (108)
97 COG0333 RpmF Ribosomal protein 30.5 22 0.00048 21.0 0.5 8 29-36 40-47 (57)
98 COG2888 Predicted Zn-ribbon RN 30.1 17 0.00036 22.0 -0.1 26 7-36 9-34 (61)
99 PHA02942 putative transposase; 30.1 30 0.00065 26.7 1.3 33 2-39 320-352 (383)
100 COG1601 GCD7 Translation initi 29.3 16 0.00035 25.3 -0.2 31 8-39 106-136 (151)
101 PF02591 DUF164: Putative zinc 29.1 16 0.00034 20.6 -0.3 31 6-38 21-55 (56)
102 PRK05342 clpX ATP-dependent pr 28.8 47 0.001 26.0 2.2 34 4-39 6-41 (412)
103 TIGR00613 reco DNA repair prot 28.3 32 0.0007 23.9 1.1 29 8-37 148-176 (241)
104 PF00130 C1_1: Phorbol esters/ 28.2 20 0.00044 19.3 0.1 31 6-41 10-40 (53)
105 PF07754 DUF1610: Domain of un 27.9 35 0.00075 16.9 0.9 23 10-36 1-23 (24)
106 PF08274 PhnA_Zn_Ribbon: PhnA 27.4 19 0.0004 18.6 -0.2 26 9-39 4-29 (30)
107 TIGR01562 FdhE formate dehydro 27.2 26 0.00057 26.7 0.6 37 7-43 184-224 (305)
108 PF06170 DUF983: Protein of un 27.2 20 0.00043 22.4 -0.1 14 30-43 9-22 (86)
109 PF05876 Terminase_GpA: Phage 27.1 29 0.00064 28.0 0.8 36 6-41 199-241 (557)
110 cd06968 NR_DBD_ROR DNA-binding 26.3 52 0.0011 20.7 1.7 32 5-41 3-34 (95)
111 PRK06556 vitamin B12-dependent 26.3 26 0.00056 30.7 0.4 25 7-37 924-948 (953)
112 PF09698 GSu_C4xC__C2xCH: Geob 26.1 41 0.0009 17.6 1.1 17 16-35 19-35 (36)
113 PF04216 FdhE: Protein involve 25.7 9.3 0.0002 28.0 -2.1 36 7-42 172-210 (290)
114 PRK00464 nrdR transcriptional 25.6 34 0.00073 23.6 0.8 34 8-41 1-40 (154)
115 PF02318 FYVE_2: FYVE-type zin 25.5 24 0.00053 22.7 0.1 33 6-38 53-88 (118)
116 TIGR00269 conserved hypothetic 25.4 56 0.0012 20.6 1.7 23 6-38 79-101 (104)
117 COG1997 RPL43A Ribosomal prote 24.6 39 0.00084 21.8 0.9 38 5-46 33-70 (89)
118 TIGR00100 hypA hydrogenase nic 24.6 34 0.00074 22.1 0.7 27 6-38 69-95 (115)
119 PRK09710 lar restriction allev 23.9 25 0.00055 21.3 -0.1 31 7-38 6-36 (64)
120 TIGR03655 anti_R_Lar restricti 23.7 39 0.00085 18.8 0.7 31 8-39 2-36 (53)
121 cd07166 NR_DBD_REV_ERB DNA-bin 23.0 41 0.00088 20.9 0.8 30 7-41 3-32 (89)
122 COG1326 Uncharacterized archae 22.5 18 0.00038 26.5 -1.1 36 5-41 4-42 (201)
123 PLN00162 transport protein sec 22.3 33 0.00072 28.9 0.3 35 6-40 52-86 (761)
124 PF03811 Zn_Tnp_IS1: InsA N-te 21.9 56 0.0012 17.3 1.1 29 6-35 4-35 (36)
125 cd06965 NR_DBD_Ppar DNA-bindin 21.8 41 0.00089 20.6 0.6 27 10-41 2-28 (84)
126 PRK00564 hypA hydrogenase nick 21.5 48 0.001 21.5 0.9 28 6-38 70-97 (117)
127 PRK12380 hydrogenase nickel in 21.4 41 0.00089 21.7 0.6 27 6-38 69-95 (113)
128 PF06869 DUF1258: Protein of u 21.3 32 0.00069 26.0 0.0 19 22-40 11-29 (258)
129 PRK11788 tetratricopeptide rep 21.2 59 0.0013 23.3 1.4 24 7-38 354-377 (389)
130 PF00628 PHD: PHD-finger; Int 21.2 34 0.00075 18.2 0.1 25 10-41 2-26 (51)
131 cd06955 NR_DBD_VDR DNA-binding 21.1 44 0.00095 21.7 0.6 32 5-41 4-35 (107)
132 TIGR00382 clpX endopeptidase C 21.0 80 0.0017 24.9 2.2 31 7-39 7-39 (413)
133 PRK04338 N(2),N(2)-dimethylgua 20.7 27 0.00058 27.0 -0.5 31 6-41 243-273 (382)
134 COG1594 RPB9 DNA-directed RNA 20.2 29 0.00063 22.6 -0.3 32 9-40 74-111 (113)
No 1
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=99.68 E-value=3.1e-17 Score=96.10 Aligned_cols=44 Identities=48% Similarity=0.958 Sum_probs=37.5
Q ss_pred cccccCccCCCCcccCCCCCcccChhhhhhhhhCCCCCCCCCCCCCC
Q 037152 9 KCSHCETRHTPQWRVGPLGPKTLCNACGVRYKSGRLLPEYRPAASPT 55 (75)
Q Consensus 9 ~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~~~~~p~~~~~~~p~ 55 (75)
+|+||++++||+||+||+|..+||||||++|++++ ..+|...+.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~---~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG---VMRPLSKRK 44 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC---CCCCcccCc
Confidence 59999999999999999887899999999999876 455555444
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.66 E-value=7.3e-17 Score=93.67 Aligned_cols=40 Identities=58% Similarity=1.047 Sum_probs=36.3
Q ss_pred cCCcccccCccCCCCcccCCCCCcccChhhhhhhhhCCCC
Q 037152 6 WQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYKSGRLL 45 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~~~~~ 45 (75)
....|+||++++||+||+||.|..+|||||||+|++++.+
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 4678999999999999999999879999999999987654
No 3
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. 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; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=99.63 E-value=4.1e-17 Score=88.57 Aligned_cols=35 Identities=60% Similarity=1.178 Sum_probs=28.0
Q ss_pred ccccCccCCCCcccCCCCCcccChhhhhhhhhCCC
Q 037152 10 CSHCETRHTPQWRVGPLGPKTLCNACGVRYKSGRL 44 (75)
Q Consensus 10 C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~~~~ 44 (75)
|++|++++||+||++|.|..+|||+||++|++++.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~~ 35 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYGK 35 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHSS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhCC
Confidence 89999999999999999987899999999998764
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=99.02 E-value=3.6e-10 Score=76.29 Aligned_cols=49 Identities=67% Similarity=1.316 Sum_probs=42.6
Q ss_pred CCcccccCccCCCCcccCCCCCcccChhhhhhhhhC---CCCCCCCCCCCCC
Q 037152 7 QRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYKSG---RLLPEYRPAASPT 55 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~~---~~~p~~~~~~~p~ 55 (75)
...|.+|+++.||+||+++.|...+|||||++|+++ +.++.+.....+.
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~~~~~~ 250 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRPASSPR 250 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcCccccccccCcccccc
Confidence 578999999999999999999889999999999998 6667766666555
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.54 E-value=4e-08 Score=78.17 Aligned_cols=54 Identities=33% Similarity=0.608 Sum_probs=44.5
Q ss_pred cCCcccccCccCCCCcccCCC-----CCcccChhhhhhhhhCCCCCCCCCCCCCCCcccccc
Q 037152 6 WQRKCSHCETRHTPQWRVGPL-----GPKTLCNACGVRYKSGRLLPEYRPAASPTFDVHIHS 62 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~-----G~~~LCNaCGl~~~~~~~~p~~~~~~~p~~~~~~~s 62 (75)
...+|.||.++.||+|||++. | -+|||||||+|+.++..-. |.+.+.+.+.+++
T Consensus 157 ~~~vc~Nc~t~stPlwrR~~~~~s~~~-n~lcnaCgl~~klhg~~r~--P~t~ks~~~ks~~ 215 (498)
T COG5641 157 QPHVCSNCKTTSTPLWRRASSESSLPG-NNLCNACGLYLKLHGSPRA--PISLKSDSIKSRS 215 (498)
T ss_pred ccchhccccccCCccccccccccccCC-ccccccccccccccCCcCC--Ccccccccccccc
Confidence 344899999999999999999 6 6899999999998775443 7777777776666
No 6
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=91.80 E-value=0.13 Score=42.28 Aligned_cols=36 Identities=33% Similarity=0.680 Sum_probs=29.4
Q ss_pred CCcccccCccCCCCc-ccCC-CCCcccChhhhhhhhhC
Q 037152 7 QRKCSHCETRHTPQW-RVGP-LGPKTLCNACGVRYKSG 42 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~W-R~gp-~G~~~LCNaCGl~~~~~ 42 (75)
.+.|.+|+|+++-+| ..|| +-...||..|-++|++.
T Consensus 386 g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKy 423 (693)
T KOG3554|consen 386 GRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKY 423 (693)
T ss_pred CCcccccccccccceeccCCCCccchhhHHHHHHHHHh
Confidence 568999999999999 3455 44457999999999983
No 7
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=90.92 E-value=0.053 Score=29.02 Aligned_cols=30 Identities=23% Similarity=0.556 Sum_probs=15.2
Q ss_pred CcccccCccCCCCcccCCCCCcccChhhhh
Q 037152 8 RKCSHCETRHTPQWRVGPLGPKTLCNACGV 37 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl 37 (75)
+.|.+||..-+-.--.|++-.+.+|.+||.
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCC
Confidence 479999987433333555655679999984
No 8
>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=84.12 E-value=0.32 Score=26.42 Aligned_cols=30 Identities=23% Similarity=0.607 Sum_probs=19.7
Q ss_pred cccccCccCCCCcccCCCCCcccChhhhhhhhh
Q 037152 9 KCSHCETRHTPQWRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 9 ~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~ 41 (75)
.|.+|++.. .--+...| ..+|..||+-+..
T Consensus 2 ~Cp~Cg~~~--~~~D~~~g-~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKE--IVFDPERG-ELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSSE--EEEETTTT-EEEETTT-BBEE-
T ss_pred CCcCCcCCc--eEEcCCCC-eEECCCCCCEeec
Confidence 699999976 23334445 6799999987664
No 9
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=83.17 E-value=0.34 Score=32.98 Aligned_cols=29 Identities=28% Similarity=0.621 Sum_probs=21.2
Q ss_pred cccccCccCCCCcccCCCCCcccChhhhhh
Q 037152 9 KCSHCETRHTPQWRVGPLGPKTLCNACGVR 38 (75)
Q Consensus 9 ~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~ 38 (75)
.|..|+.++|-+=+++-.- -..|+|||-.
T Consensus 104 lC~~C~spdT~l~k~~r~~-~l~C~ACGa~ 132 (138)
T PRK03988 104 ICPECGSPDTKLIKEGRIW-VLKCEACGAE 132 (138)
T ss_pred ECCCCCCCCcEEEEcCCeE-EEEcccCCCC
Confidence 5999999999987653211 2359999964
No 10
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=82.87 E-value=0.96 Score=36.65 Aligned_cols=37 Identities=32% Similarity=0.416 Sum_probs=28.7
Q ss_pred CCcccccCc-cCCCCcccCCCCCcccChhhhhhhhhCC
Q 037152 7 QRKCSHCET-RHTPQWRVGPLGPKTLCNACGVRYKSGR 43 (75)
Q Consensus 7 ~~~C~~C~t-~~Tp~WR~gp~G~~~LCNaCGl~~~~~~ 43 (75)
+..+.+|.+ +.||.||+...-.-++||+||++.+..+
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~~ 334 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKPPG 334 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccCCcc
Confidence 455777776 6788888877655789999999998644
No 11
>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=82.46 E-value=0.64 Score=26.89 Aligned_cols=23 Identities=39% Similarity=1.044 Sum_probs=15.4
Q ss_pred CcccccCccCCCCcccCCCCCcccChhhhhhhh
Q 037152 8 RKCSHCETRHTPQWRVGPLGPKTLCNACGVRYK 40 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~ 40 (75)
..|.+||...-| +.+|.+|| +|+
T Consensus 27 ~~c~~cg~~~~~---------H~vc~~cG-~y~ 49 (56)
T PF01783_consen 27 VKCPNCGEPKLP---------HRVCPSCG-YYK 49 (56)
T ss_dssp EESSSSSSEEST---------TSBCTTTB-BSS
T ss_pred eeeccCCCEecc---------cEeeCCCC-eEC
Confidence 467788754332 68999999 444
No 12
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=82.27 E-value=0.39 Score=31.50 Aligned_cols=28 Identities=29% Similarity=0.547 Sum_probs=20.7
Q ss_pred cccccCccCCCCcccCCCCCcccChhhhh
Q 037152 9 KCSHCETRHTPQWRVGPLGPKTLCNACGV 37 (75)
Q Consensus 9 ~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl 37 (75)
.|..|+.++|-+=+.+..- -.-|+|||-
T Consensus 82 lC~~C~spdT~l~k~~r~~-~l~C~aCGa 109 (110)
T smart00653 82 LCPECGSPDTELIKENRLF-FLKCEACGA 109 (110)
T ss_pred ECCCCCCCCcEEEEeCCeE-EEEccccCC
Confidence 5999999999988873211 234999995
No 13
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=81.72 E-value=0.42 Score=32.34 Aligned_cols=30 Identities=27% Similarity=0.622 Sum_probs=21.5
Q ss_pred cccccCccCCCCcccCCCCCcccChhhhhhh
Q 037152 9 KCSHCETRHTPQWRVGPLGPKTLCNACGVRY 39 (75)
Q Consensus 9 ~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~ 39 (75)
.|..|+.++|-+=+.+-.- -.-|+|||-..
T Consensus 99 lC~~C~sPdT~l~k~~r~~-~l~C~ACGa~~ 128 (133)
T TIGR00311 99 ICRECNRPDTRIIKEGRVS-LLKCEACGAKA 128 (133)
T ss_pred ECCCCCCCCcEEEEeCCeE-EEecccCCCCC
Confidence 5999999999987753211 23599999643
No 14
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=80.35 E-value=0.69 Score=35.39 Aligned_cols=31 Identities=32% Similarity=0.813 Sum_probs=27.5
Q ss_pred cccCCcccccCccCCCCcccCCCCCcccChhhh
Q 037152 4 ELWQRKCSHCETRHTPQWRVGPLGPKTLCNACG 36 (75)
Q Consensus 4 ~~~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCG 36 (75)
......|..|++.. |+|-.-.-| ..||-.|.
T Consensus 17 ~~~Nk~CaDCga~~-P~W~S~nlG-vfiCi~Ca 47 (319)
T COG5347 17 DSSNKKCADCGAPN-PTWASVNLG-VFLCIDCA 47 (319)
T ss_pred ccccCccccCCCCC-CceEecccC-eEEEeecc
Confidence 34578999999999 999999999 79999993
No 15
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=79.33 E-value=1.2 Score=21.97 Aligned_cols=23 Identities=26% Similarity=0.855 Sum_probs=15.9
Q ss_pred CcccccCccCCCCcccCCCCCcccChhhhhh
Q 037152 8 RKCSHCETRHTPQWRVGPLGPKTLCNACGVR 38 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~ 38 (75)
+.|.+||....+. ...|..||..
T Consensus 3 ~~Cp~Cg~~~~~~--------~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPD--------AKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcc--------cccChhhCCC
Confidence 5789999855333 3588888854
No 16
>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=78.41 E-value=0.78 Score=26.62 Aligned_cols=35 Identities=23% Similarity=0.554 Sum_probs=24.7
Q ss_pred cccccCCcccccCccCCCCcccCCCCCcccChhhhhhhh
Q 037152 2 NEELWQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYK 40 (75)
Q Consensus 2 ~~~~~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~ 40 (75)
++..--..|..||..... ...+....|..||..+.
T Consensus 23 ~~~~TSq~C~~CG~~~~~----~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 23 DEAYTSQTCPRCGHRNKK----RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CCCCCccCccCccccccc----ccccceEEcCCCCCEEC
Confidence 455567789999987655 33444578999998654
No 17
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=77.78 E-value=0.65 Score=33.03 Aligned_cols=32 Identities=25% Similarity=0.442 Sum_probs=23.2
Q ss_pred cccccCccCCCCcccCCCCCcccChhhhhhhhh
Q 037152 9 KCSHCETRHTPQWRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 9 ~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~ 41 (75)
.|..|+..+|-+=+.+..- ..-|+|||-..-.
T Consensus 100 ~C~~C~~pdT~l~k~~~~~-~l~C~aCGa~~~v 131 (201)
T PRK12336 100 ICSECGLPDTRLVKEDRVL-MLRCDACGAHRPV 131 (201)
T ss_pred ECCCCCCCCcEEEEcCCeE-EEEcccCCCCccc
Confidence 5999999999987763211 2359999977653
No 18
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=75.44 E-value=1.8 Score=27.82 Aligned_cols=33 Identities=33% Similarity=0.714 Sum_probs=27.4
Q ss_pred CCcccccCccCCCCcccCCCCCcccChhhhhhhhh
Q 037152 7 QRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~ 41 (75)
...|++|+. ..|.|-.-..| ..||-.|.-..+.
T Consensus 3 N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~ 35 (112)
T smart00105 3 NKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRS 35 (112)
T ss_pred CCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHh
Confidence 578999998 56999999889 7899999765554
No 19
>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=75.10 E-value=2.1 Score=27.59 Aligned_cols=35 Identities=26% Similarity=0.560 Sum_probs=23.8
Q ss_pred ccCCcccccCccCCCCcccCCCCCcccChhhhhhhhh
Q 037152 5 LWQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 5 ~~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~ 41 (75)
.....|+.|++.. |.|-.-..| ..||-.|.-..+.
T Consensus 11 ~~N~~CaDCg~~~-p~w~s~~~G-iflC~~Cag~HR~ 45 (116)
T PF01412_consen 11 PGNKVCADCGAPN-PTWASLNYG-IFLCLECAGIHRS 45 (116)
T ss_dssp TTCTB-TTT-SBS---EEETTTT-EEE-HHHHHHHHH
T ss_pred cCcCcCCCCCCCC-CCEEEeecC-hhhhHHHHHHHHH
Confidence 4568999999554 699999999 7899999866654
No 20
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=74.04 E-value=1.4 Score=24.38 Aligned_cols=27 Identities=37% Similarity=0.886 Sum_probs=20.2
Q ss_pred ccCCcccccCccCCCCcccCCCCCcccChhhh
Q 037152 5 LWQRKCSHCETRHTPQWRVGPLGPKTLCNACG 36 (75)
Q Consensus 5 ~~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCG 36 (75)
.++..|..| .+|+.| ..+| ..+|-+|+
T Consensus 15 ML~~~Cp~C---~~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 15 MLDEHCPDC---GTPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred HhcCccCCC---CCeeEE-ecCC-CEECCCCC
Confidence 467789999 489998 3355 67999885
No 21
>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=72.88 E-value=0.95 Score=30.24 Aligned_cols=28 Identities=32% Similarity=0.628 Sum_probs=21.1
Q ss_pred cccccCccCCCCcccCCCCCcccChhhhh
Q 037152 9 KCSHCETRHTPQWRVGPLGPKTLCNACGV 37 (75)
Q Consensus 9 ~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl 37 (75)
.|..|+.++|-+=.++..- ..-|+|||-
T Consensus 95 lC~~C~spdT~l~k~~r~~-~l~C~aCGa 122 (125)
T PF01873_consen 95 LCPECGSPDTELIKEGRLI-FLKCKACGA 122 (125)
T ss_dssp SCTSTSSSSEEEEEETTCC-EEEETTTSC
T ss_pred EcCCCCCCccEEEEcCCEE-EEEecccCC
Confidence 5999999999888773322 245999994
No 22
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=72.65 E-value=1.5 Score=25.66 Aligned_cols=22 Identities=27% Similarity=0.878 Sum_probs=16.2
Q ss_pred CcccccCccCCCCcccCCCCCcccChhhhhh
Q 037152 8 RKCSHCETRHTPQWRVGPLGPKTLCNACGVR 38 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~ 38 (75)
-.|.+||...-| +.+|..||.|
T Consensus 28 ~~C~~CG~~~~~---------H~vC~~CG~Y 49 (57)
T PRK12286 28 VECPNCGEPKLP---------HRVCPSCGYY 49 (57)
T ss_pred eECCCCCCccCC---------eEECCCCCcC
Confidence 458888876655 6799999944
No 23
>PF15396 FAM60A: Protein Family FAM60A
Probab=68.66 E-value=2.1 Score=31.45 Aligned_cols=17 Identities=35% Similarity=0.581 Sum_probs=12.9
Q ss_pred cccChhhhhhhhhCCCC
Q 037152 29 KTLCNACGVRYKSGRLL 45 (75)
Q Consensus 29 ~~LCNaCGl~~~~~~~~ 45 (75)
+.+||||-|++++-+.|
T Consensus 49 GeICNACVLLVKRwKKL 65 (213)
T PF15396_consen 49 GEICNACVLLVKRWKKL 65 (213)
T ss_pred chhhHHHHHHHHHHhhC
Confidence 47999999999874333
No 24
>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=68.49 E-value=3.5 Score=22.34 Aligned_cols=30 Identities=20% Similarity=0.582 Sum_probs=21.6
Q ss_pred CCcccccCccCCCCcccCC-CCCcccChhhhh
Q 037152 7 QRKCSHCETRHTPQWRVGP-LGPKTLCNACGV 37 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~WR~gp-~G~~~LCNaCGl 37 (75)
...|-.|+....=.|.+.. .| ..+|+.||.
T Consensus 3 ~~pCP~CGG~DrFr~~d~~g~G-~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFRFDDKDGRG-TWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCccccccccCCCCc-CEEeCCCCC
Confidence 3579999998776675533 34 679999973
No 25
>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=68.38 E-value=0.68 Score=24.97 Aligned_cols=32 Identities=25% Similarity=0.555 Sum_probs=19.9
Q ss_pred cccccCccCCCC----cccCCCCCc--ccChhhhhhhh
Q 037152 9 KCSHCETRHTPQ----WRVGPLGPK--TLCNACGVRYK 40 (75)
Q Consensus 9 ~C~~C~t~~Tp~----WR~gp~G~~--~LCNaCGl~~~ 40 (75)
.|.+|+..+.-- =|.++++.. +.|..||-.|+
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence 588899876543 367777732 36999997763
No 26
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=67.63 E-value=2.6 Score=31.42 Aligned_cols=36 Identities=22% Similarity=0.421 Sum_probs=23.3
Q ss_pred ccccCCcccccCccCCCCcccCCCCCcccChhhhhhhhh
Q 037152 3 EELWQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 3 ~~~~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~ 41 (75)
++.....|.+|+. +..--+-..| .++|..||+=+..
T Consensus 7 ~~~~~~~Cp~Cg~--~~iv~d~~~G-e~vC~~CG~Vl~e 42 (310)
T PRK00423 7 EEEEKLVCPECGS--DKLIYDYERG-EIVCADCGLVIEE 42 (310)
T ss_pred hcccCCcCcCCCC--CCeeEECCCC-eEeecccCCcccc
Confidence 3445567999996 3333334566 6889999986543
No 27
>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=65.66 E-value=3.1 Score=22.38 Aligned_cols=31 Identities=26% Similarity=0.664 Sum_probs=19.4
Q ss_pred CcccccCccCCCCcccCCCCCcccChhhhhh
Q 037152 8 RKCSHCETRHTPQWRVGPLGPKTLCNACGVR 38 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~ 38 (75)
.+|.+|++--.|--.=...|....||-|+..
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEEEETTT--E
T ss_pred cccCCCCCEECCcceEcCCCCEEECcCCCCc
Confidence 5799999988887766667767899999864
No 28
>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=64.81 E-value=2.8 Score=22.39 Aligned_cols=25 Identities=32% Similarity=0.837 Sum_probs=19.1
Q ss_pred CcccccCccCCCCcccCCCCCcccChhhhh
Q 037152 8 RKCSHCETRHTPQWRVGPLGPKTLCNACGV 37 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl 37 (75)
..|..|+.. |-...+| .+.|..||-
T Consensus 9 ~~C~~C~~~----~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEccCC-EEEhhhCce
Confidence 458888876 6666777 688999984
No 29
>PRK00420 hypothetical protein; Validated
Probab=64.28 E-value=3.2 Score=27.51 Aligned_cols=32 Identities=22% Similarity=0.612 Sum_probs=23.7
Q ss_pred ccCCcccccCccCCCCcccCCCCCcccChhhhhhhhh
Q 037152 5 LWQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 5 ~~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~ 41 (75)
++...|..|| +|..+- ..| ..+|-+||..+..
T Consensus 21 ml~~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~v 52 (112)
T PRK00420 21 MLSKHCPVCG---LPLFEL-KDG-EVVCPVHGKVYIV 52 (112)
T ss_pred HccCCCCCCC---Ccceec-CCC-ceECCCCCCeeee
Confidence 3667888888 577764 445 6899999987763
No 30
>PF12773 DZR: Double zinc ribbon
Probab=63.12 E-value=5.4 Score=21.64 Aligned_cols=30 Identities=30% Similarity=0.632 Sum_probs=20.6
Q ss_pred cCCcccccCccCCCCcccCCCCCcccChhhhhhhh
Q 037152 6 WQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYK 40 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~ 40 (75)
....|.+||+.-. ........|..||..+.
T Consensus 11 ~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 11 DAKFCPHCGTPLP-----PPDQSKKICPNCGAENP 40 (50)
T ss_pred cccCChhhcCChh-----hccCCCCCCcCCcCCCc
Confidence 4678899998777 33333467888887654
No 31
>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=62.40 E-value=1.3 Score=22.60 Aligned_cols=29 Identities=31% Similarity=0.698 Sum_probs=15.3
Q ss_pred CCcccccCccCCCCcccCCCCCcccChhhhhhh
Q 037152 7 QRKCSHCETRHTPQWRVGPLGPKTLCNACGVRY 39 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~ 39 (75)
.+.|..||+...+. +.|-...|.+||..+
T Consensus 3 ~rfC~~CG~~t~~~----~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 3 HRFCGRCGAPTKPA----PGGWARRCPSCGHEH 31 (32)
T ss_dssp TSB-TTT--BEEE-----SSSS-EEESSSS-EE
T ss_pred CcccCcCCccccCC----CCcCEeECCCCcCEe
Confidence 46799999876543 224456899998653
No 32
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=61.97 E-value=2.9 Score=27.06 Aligned_cols=33 Identities=15% Similarity=0.241 Sum_probs=20.7
Q ss_pred CcccccCccCCCCcccCCCCCcccChhhhhhhhh
Q 037152 8 RKCSHCETRHTPQWRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~ 41 (75)
-.|.+|+...-+.=... ...+..|..||.++..
T Consensus 22 f~CP~Cge~~v~v~~~k-~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 22 FECPRCGKVSISVKIKK-NIAIITCGNCGLYTEF 54 (99)
T ss_pred eECCCCCCeEeeeecCC-CcceEECCCCCCccCE
Confidence 36999995332221111 2336789999999864
No 33
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=59.80 E-value=3.8 Score=31.19 Aligned_cols=27 Identities=30% Similarity=0.904 Sum_probs=24.9
Q ss_pred CCcccccCccCCCCcccCCCCCcccChhh
Q 037152 7 QRKCSHCETRHTPQWRVGPLGPKTLCNAC 35 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~WR~gp~G~~~LCNaC 35 (75)
.+.|+.|++. .|.|-.-..| ..+|-.|
T Consensus 25 N~~CADC~a~-~P~WaSwnlG-vFiC~~C 51 (287)
T KOG0703|consen 25 NKVCADCGAK-GPRWASWNLG-VFICLRC 51 (287)
T ss_pred cCcccccCCC-CCCeEEeecC-eEEEeec
Confidence 7899999999 9999998888 7899999
No 34
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=59.06 E-value=5.6 Score=31.60 Aligned_cols=33 Identities=24% Similarity=0.643 Sum_probs=26.8
Q ss_pred cCCcccccCccCCCCcccCCCCCcccChhhhhhhh
Q 037152 6 WQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYK 40 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~ 40 (75)
....|..|+.. .|.|-.-..| ..||..|.=..+
T Consensus 21 gNk~CaDCga~-nPtWASvn~G-IFLCl~CSGVHR 53 (395)
T PLN03114 21 DNKICFDCNAK-NPTWASVTYG-IFLCIDCSAVHR 53 (395)
T ss_pred CCCcCccCCCC-CCCceeeccc-eeehhhhhHhhc
Confidence 56889999986 4999999999 789999954333
No 35
>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=56.52 E-value=4.2 Score=23.54 Aligned_cols=20 Identities=30% Similarity=0.928 Sum_probs=12.6
Q ss_pred CcccccCccCCCCcccCCCCCcccChhhh
Q 037152 8 RKCSHCETRHTPQWRVGPLGPKTLCNACG 36 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~gp~G~~~LCNaCG 36 (75)
-.|.+||...-| +.+|-.||
T Consensus 27 ~~C~~cG~~~~~---------H~vc~~cG 46 (55)
T TIGR01031 27 VVCPNCGEFKLP---------HRVCPSCG 46 (55)
T ss_pred eECCCCCCcccC---------eeECCccC
Confidence 347777664332 56788888
No 36
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=55.89 E-value=5.2 Score=28.27 Aligned_cols=31 Identities=26% Similarity=0.461 Sum_probs=23.3
Q ss_pred CcccccCccCCCCcccCCCCCc--ccChhhhhh
Q 037152 8 RKCSHCETRHTPQWRVGPLGPK--TLCNACGVR 38 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~gp~G~~--~LCNaCGl~ 38 (75)
.+|.+||......++.=..|.- +.|..||..
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~v 33 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKV 33 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCCc
Confidence 4799999998888888544432 569999843
No 37
>PHA00626 hypothetical protein
Probab=55.84 E-value=4.8 Score=24.13 Aligned_cols=33 Identities=18% Similarity=0.419 Sum_probs=21.7
Q ss_pred CcccccCccCCCC--cccCCCCCcccChhhhhhhhh
Q 037152 8 RKCSHCETRHTPQ--WRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 8 ~~C~~C~t~~Tp~--WR~gp~G~~~LCNaCGl~~~~ 41 (75)
+.|.+||+.+--. -=+++.. .+.|..||..|.+
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~sn-rYkCkdCGY~ft~ 35 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSD-DYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCCceeeeeceecccCc-ceEcCCCCCeech
Confidence 3588999853221 1123344 6899999999976
No 38
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=54.60 E-value=7.3 Score=18.78 Aligned_cols=22 Identities=23% Similarity=0.742 Sum_probs=12.7
Q ss_pred cccccCccCCCCcccCCCCCcccChhhhhh
Q 037152 9 KCSHCETRHTPQWRVGPLGPKTLCNACGVR 38 (75)
Q Consensus 9 ~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~ 38 (75)
.|.+||..... + ...|..||..
T Consensus 1 ~Cp~CG~~~~~-------~-~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIED-------D-AKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCC-------c-CcchhhhCCc
Confidence 36777765432 2 3467777753
No 39
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=54.43 E-value=3.3 Score=22.39 Aligned_cols=32 Identities=25% Similarity=0.686 Sum_probs=21.8
Q ss_pred cccccCccCCCCc----ccCCCCCc--ccChhhhhhhh
Q 037152 9 KCSHCETRHTPQW----RVGPLGPK--TLCNACGVRYK 40 (75)
Q Consensus 9 ~C~~C~t~~Tp~W----R~gp~G~~--~LCNaCGl~~~ 40 (75)
.|.+|+-.+.--| |.++++.. +.|..||-.|+
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~ 39 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWR 39 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeC
Confidence 5888986654433 66777632 36999997765
No 40
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=54.26 E-value=25 Score=21.29 Aligned_cols=46 Identities=17% Similarity=0.432 Sum_probs=32.6
Q ss_pred cCCcccccCccCCCC--ccc-CCCCCcccChhhhhhhhhCCCCCCCCCC
Q 037152 6 WQRKCSHCETRHTPQ--WRV-GPLGPKTLCNACGVRYKSGRLLPEYRPA 51 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~--WR~-gp~G~~~LCNaCGl~~~~~~~~p~~~~~ 51 (75)
....|..|.+..|-- .-. ...-+.+.|-+|-.+|..++.+-..+..
T Consensus 4 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvg 52 (63)
T PF02701_consen 4 QPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVG 52 (63)
T ss_pred cCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccC
Confidence 456799999888753 222 2234568999999999998877666443
No 41
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=53.76 E-value=8.8 Score=20.77 Aligned_cols=30 Identities=20% Similarity=0.553 Sum_probs=19.1
Q ss_pred CcccccCccCCCC-cccCCCCCcccChhhhhhhh
Q 037152 8 RKCSHCETRHTPQ-WRVGPLGPKTLCNACGVRYK 40 (75)
Q Consensus 8 ~~C~~C~t~~Tp~-WR~gp~G~~~LCNaCGl~~~ 40 (75)
..|..||..-.+. +. ......|..||..+.
T Consensus 1 ~FCp~Cg~~l~~~~~~---~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 1 KFCPKCGNMLIPKEGK---EKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCCccccccCC---CCCEEECCcCCCeEE
Confidence 3689998854433 22 123678999996554
No 42
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=53.31 E-value=5.2 Score=33.77 Aligned_cols=30 Identities=27% Similarity=0.751 Sum_probs=25.1
Q ss_pred CCcccccCccCCCCcccCCCCC---cccChhhh
Q 037152 7 QRKCSHCETRHTPQWRVGPLGP---KTLCNACG 36 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~WR~gp~G~---~~LCNaCG 36 (75)
.-.|..|.+.-||.|+.-+.+. ..+|.+|-
T Consensus 462 P~~caqcktdftp~wk~ekstq~d~~i~cE~cv 494 (706)
T KOG3740|consen 462 PYACAQCKTDFTPAWKKEKSTQADAAIVCENCV 494 (706)
T ss_pred chhhhhcccccccccccccccCcchHHHHHhhh
Confidence 4579999999999999887763 46899994
No 43
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=51.75 E-value=9.4 Score=22.84 Aligned_cols=16 Identities=25% Similarity=0.837 Sum_probs=12.7
Q ss_pred CcccccCccC-CCCccc
Q 037152 8 RKCSHCETRH-TPQWRV 23 (75)
Q Consensus 8 ~~C~~C~t~~-Tp~WR~ 23 (75)
..|.+|+++. |..|.-
T Consensus 16 ~~CP~Cgs~~~T~~W~G 32 (61)
T PRK08351 16 DRCPVCGSRDLSDEWFD 32 (61)
T ss_pred CcCCCCcCCcccccccc
Confidence 3699999888 888864
No 44
>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=51.69 E-value=12 Score=23.36 Aligned_cols=35 Identities=29% Similarity=0.549 Sum_probs=25.3
Q ss_pred cccccCCcccccCccCCCCcccCCCCCcccChhhhhhhhh
Q 037152 2 NEELWQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 2 ~~~~~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~ 41 (75)
||+.....|.-|+...+-. .= | ...|+||..+|++
T Consensus 1 ~~~~~~~~C~VCg~~~~g~-hy---G-v~sC~aCk~FFRR 35 (90)
T cd07168 1 DEDESPKLCSICEDKATGL-HY---G-IITCEGCKGFFKR 35 (90)
T ss_pred CccccCCCCcccCCcCcce-EE---C-ceehhhhhHhhhh
Confidence 4667778899999755432 22 3 4679999999986
No 45
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=51.20 E-value=2.9 Score=25.50 Aligned_cols=35 Identities=23% Similarity=0.597 Sum_probs=26.3
Q ss_pred ccCCcccccCccCCC-CcccCCCCCcccChhhhhhhh
Q 037152 5 LWQRKCSHCETRHTP-QWRVGPLGPKTLCNACGVRYK 40 (75)
Q Consensus 5 ~~~~~C~~C~t~~Tp-~WR~gp~G~~~LCNaCGl~~~ 40 (75)
+....|..|.+..|= +||...-. ..-|-+||..-+
T Consensus 8 IAGA~CP~C~~~Dtl~mW~En~ve-~vECV~CG~~~~ 43 (66)
T COG3529 8 IAGAVCPACQAQDTLAMWRENNVE-IVECVKCGHHMR 43 (66)
T ss_pred hccCCCcccchhhHHHHHHhcCCc-eEehhhcchHhh
Confidence 456789999999884 56665444 567999998765
No 46
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=51.10 E-value=7.5 Score=29.50 Aligned_cols=31 Identities=29% Similarity=0.563 Sum_probs=22.7
Q ss_pred cCCcccccCccCCCCcccCCCCCcccChhhhhhhh
Q 037152 6 WQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYK 40 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~ 40 (75)
..+.|..||+...+. . .|-..+|+.||..+.
T Consensus 110 ~~RFCg~CG~~~~~~--~--~g~~~~C~~cg~~~f 140 (279)
T COG2816 110 SHRFCGRCGTKTYPR--E--GGWARVCPKCGHEHF 140 (279)
T ss_pred hCcCCCCCCCcCccc--c--CceeeeCCCCCCccC
Confidence 457899999887663 2 233579999998764
No 47
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=51.01 E-value=6.1 Score=26.58 Aligned_cols=37 Identities=24% Similarity=0.565 Sum_probs=28.7
Q ss_pred cccCCcccccCccC----CCCcccCCCCCc--ccChhhhhhhh
Q 037152 4 ELWQRKCSHCETRH----TPQWRVGPLGPK--TLCNACGVRYK 40 (75)
Q Consensus 4 ~~~~~~C~~C~t~~----Tp~WR~gp~G~~--~LCNaCGl~~~ 40 (75)
-.+...|..||-.+ |-+-|..++|.- +-|-.|+..+.
T Consensus 71 a~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 71 AVIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred cchhccCcccCCchhhhhhhhcccccCCceEEEEcCccceeee
Confidence 34678999999764 788999999943 24999987654
No 48
>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=50.80 E-value=7.3 Score=21.08 Aligned_cols=30 Identities=27% Similarity=0.713 Sum_probs=18.4
Q ss_pred CcccccCccCCCC--cccCCCCCcccChhhhhh
Q 037152 8 RKCSHCETRHTPQ--WRVGPLGPKTLCNACGVR 38 (75)
Q Consensus 8 ~~C~~C~t~~Tp~--WR~gp~G~~~LCNaCGl~ 38 (75)
..|+-||.+.+.. .=.|++| ..+|+.|-..
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~-~~IC~~Cv~~ 33 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNG-AYICDECVEQ 33 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-S-EEEEHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCC-cEECHHHHHH
Confidence 5799999987643 3367767 6899999654
No 49
>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=48.71 E-value=9.6 Score=26.48 Aligned_cols=35 Identities=23% Similarity=0.501 Sum_probs=26.5
Q ss_pred CcccccCccCCCCc--ccCCCCC----cccChhhhhhhhhC
Q 037152 8 RKCSHCETRHTPQW--RVGPLGP----KTLCNACGVRYKSG 42 (75)
Q Consensus 8 ~~C~~C~t~~Tp~W--R~gp~G~----~~LCNaCGl~~~~~ 42 (75)
+.|..|+...|-.- |...+|. .--|.+||.+|--.
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTy 41 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTF 41 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcccee
Confidence 46999999998765 5566663 24799999998753
No 50
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=47.99 E-value=6.9 Score=28.57 Aligned_cols=31 Identities=29% Similarity=0.525 Sum_probs=21.8
Q ss_pred cCCcccccCccCCCCcccCCCCCcccChhhhhhhh
Q 037152 6 WQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYK 40 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~ 40 (75)
..+.|..||...... ..|....|.+||..+.
T Consensus 98 ~~~fC~~CG~~~~~~----~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 98 SHRFCGYCGHPMHPS----KTEWAMLCPHCRERYY 128 (256)
T ss_pred cCccccccCCCCeec----CCceeEECCCCCCEEC
Confidence 357899999975542 3454568999996554
No 51
>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=46.86 E-value=6.4 Score=21.25 Aligned_cols=28 Identities=18% Similarity=0.552 Sum_probs=16.4
Q ss_pred cccccCccCCCCcccCCCCCcccChhhhh
Q 037152 9 KCSHCETRHTPQWRVGPLGPKTLCNACGV 37 (75)
Q Consensus 9 ~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl 37 (75)
.|..||..-+-...-.. .....|-+||-
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 57778865544433333 33467888875
No 52
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=46.32 E-value=10 Score=26.56 Aligned_cols=28 Identities=21% Similarity=0.638 Sum_probs=23.0
Q ss_pred CcccccCccCCCCcccCCCCCcccChhhh
Q 037152 8 RKCSHCETRHTPQWRVGPLGPKTLCNACG 36 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~gp~G~~~LCNaCG 36 (75)
..|..||......+-.-.+| +.+|..|+
T Consensus 150 ~~C~~Cg~~~~~~~f~~~~g-g~~c~~c~ 177 (247)
T PRK00085 150 DHCAVCGAPGDHRYFSPKEG-GAVCSECG 177 (247)
T ss_pred hhHhcCCCCCCceEEecccC-Cccccccc
Confidence 47999998877677777777 78999997
No 53
>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=46.09 E-value=17 Score=22.72 Aligned_cols=34 Identities=29% Similarity=0.512 Sum_probs=24.3
Q ss_pred ccccCCcccccCccCCCCcccCCCCCcccChhhhhhhhh
Q 037152 3 EELWQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 3 ~~~~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~ 41 (75)
+......|.-|+...+-.+ -| ...|+||..+|+.
T Consensus 2 ~~~~~~~C~VCg~~a~g~h----yG-v~sC~aCk~FFRR 35 (90)
T cd07169 2 DRAEQRTCLICGDRATGLH----YG-IISCEGCKGFFKR 35 (90)
T ss_pred ccccCCCCeecCCcCcceE----EC-cceehhhHHHHHH
Confidence 4456778999987554433 23 4679999999986
No 54
>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=45.77 E-value=8.3 Score=21.02 Aligned_cols=27 Identities=26% Similarity=0.522 Sum_probs=17.1
Q ss_pred CcccccCccCCCCcccCCCCCcccChhhhh
Q 037152 8 RKCSHCETRHTPQWRVGPLGPKTLCNACGV 37 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl 37 (75)
-.|.+||.+ ..-+-++ .+ ..-|++|+.
T Consensus 19 ~~CP~Cg~~-~~~~~~~-~~-~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST-KHYRLKT-RG-RYRCKACRK 45 (46)
T ss_pred CCCCCCCCe-eeEEeCC-CC-eEECCCCCC
Confidence 458899887 4444333 33 567888863
No 55
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=45.57 E-value=8.5 Score=22.66 Aligned_cols=21 Identities=14% Similarity=0.097 Sum_probs=12.0
Q ss_pred CcccccCccCCCCcccCCCCCcccChhhhhh
Q 037152 8 RKCSHCETRHTPQWRVGPLGPKTLCNACGVR 38 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~ 38 (75)
-.|.+||...-| +.+|. ||.|
T Consensus 28 ~~c~~cg~~~~p---------H~vc~-cG~Y 48 (60)
T PRK01110 28 SVDKTTGEYHLP---------HHVSP-KGYY 48 (60)
T ss_pred eEcCCCCceecc---------ceecC-Cccc
Confidence 346666655443 45677 7744
No 56
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=45.56 E-value=9.7 Score=21.08 Aligned_cols=26 Identities=23% Similarity=0.621 Sum_probs=18.2
Q ss_pred cccccCccCCCCcccCCCCCcccChhhhhhh
Q 037152 9 KCSHCETRHTPQWRVGPLGPKTLCNACGVRY 39 (75)
Q Consensus 9 ~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~ 39 (75)
.|.+||...+.. +.+ ..-|..||-+.
T Consensus 4 ~C~~Cg~~~~~~----~~~-~irC~~CG~rI 29 (44)
T smart00659 4 ICGECGRENEIK----SKD-VVRCRECGYRI 29 (44)
T ss_pred ECCCCCCEeecC----CCC-ceECCCCCceE
Confidence 699999977654 122 46799999544
No 57
>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=45.55 E-value=6.2 Score=24.08 Aligned_cols=36 Identities=19% Similarity=0.353 Sum_probs=26.5
Q ss_pred ccCCcccccCccCCCCc-ccCCCCCcccChhhhhhhhh
Q 037152 5 LWQRKCSHCETRHTPQW-RVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 5 ~~~~~C~~C~t~~Tp~W-R~gp~G~~~LCNaCGl~~~~ 41 (75)
+..-.|-.|.+..|-+| +... ....-|-+||..-..
T Consensus 6 IAGa~CP~C~~~D~i~~~~e~~-ve~vECV~CGy~e~~ 42 (71)
T PF09526_consen 6 IAGAVCPKCQAMDTIMMWRENG-VEYVECVECGYTERQ 42 (71)
T ss_pred ecCccCCCCcCccEEEEEEeCC-ceEEEecCCCCeecc
Confidence 45678999999998664 5544 435569999987764
No 58
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=45.06 E-value=13 Score=30.60 Aligned_cols=30 Identities=27% Similarity=0.613 Sum_probs=20.9
Q ss_pred CcccccCccCCCCcccCCCCCcccChhhhhhhh
Q 037152 8 RKCSHCETRHTPQWRVGPLGPKTLCNACGVRYK 40 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~ 40 (75)
+.|.||+.+.-- ++.-.| ...|++||.-..
T Consensus 1 ~~C~~C~~s~fe--~d~a~g-~~~C~~CG~v~E 30 (521)
T KOG1598|consen 1 MVCKNCGGSNFE--RDEATG-NLYCTACGTVLE 30 (521)
T ss_pred CcCCCCCCCCcc--cccccC-Cceeccccceee
Confidence 479999986532 333456 578999997665
No 59
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=45.05 E-value=8.6 Score=21.82 Aligned_cols=29 Identities=17% Similarity=0.334 Sum_probs=19.6
Q ss_pred cCCcccccCccCCCCcccCCCCCcccChhhhhhh
Q 037152 6 WQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRY 39 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~ 39 (75)
....|..|+.. -+.... + ...|..||.-+
T Consensus 19 ~~~fCP~Cg~~--~m~~~~--~-r~~C~~Cgyt~ 47 (50)
T PRK00432 19 KNKFCPRCGSG--FMAEHL--D-RWHCGKCGYTE 47 (50)
T ss_pred ccCcCcCCCcc--hheccC--C-cEECCCcCCEE
Confidence 45689999974 333322 3 67899999754
No 60
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=44.71 E-value=14 Score=22.36 Aligned_cols=16 Identities=19% Similarity=0.596 Sum_probs=12.2
Q ss_pred CCcccccCccC-CCCcc
Q 037152 7 QRKCSHCETRH-TPQWR 22 (75)
Q Consensus 7 ~~~C~~C~t~~-Tp~WR 22 (75)
+..|.+||++. |+.|.
T Consensus 17 ~~~Cp~Cgs~~~S~~w~ 33 (64)
T PRK06393 17 EKTCPVHGDEKTTTEWF 33 (64)
T ss_pred CCcCCCCCCCcCCcCcc
Confidence 34799999887 67785
No 61
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=43.39 E-value=12 Score=28.81 Aligned_cols=32 Identities=22% Similarity=0.604 Sum_probs=23.5
Q ss_pred cccccCccCCCCcccCCCCCcccChhhhhhhhh
Q 037152 9 KCSHCETRHTPQWRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 9 ~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~ 41 (75)
.|..|......+--+--.| .++|-.|||-+..
T Consensus 2 ~c~~C~~~~~~~V~d~~~g-dtvC~~CGlVl~~ 33 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAG-DTVCSECGLVLED 33 (308)
T ss_pred CCCCCCCCCCCeeeeccCC-ceecccCCeeecc
Confidence 5888887665555555566 6899999987764
No 62
>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=42.81 E-value=8.3 Score=21.15 Aligned_cols=29 Identities=17% Similarity=0.449 Sum_probs=15.3
Q ss_pred CcccccCccCCCC-cccCCCCCcccChhhh
Q 037152 8 RKCSHCETRHTPQ-WRVGPLGPKTLCNACG 36 (75)
Q Consensus 8 ~~C~~C~t~~Tp~-WR~gp~G~~~LCNaCG 36 (75)
..|-.|+.+.-=. |.+....-..+|+.|+
T Consensus 4 ~pCP~CGG~DrFri~~d~~~~G~~~C~~C~ 33 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFDDKDGRGTWICRQCG 33 (40)
T ss_dssp E--TTTT-TTTEEEETT----S-EEETTTT
T ss_pred CCCCCCcCccccccCcCcccCCCEECCCCC
Confidence 3688898877655 7653332268999993
No 63
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=42.66 E-value=11 Score=28.36 Aligned_cols=31 Identities=19% Similarity=0.515 Sum_probs=20.7
Q ss_pred CcccccCccCCCCcccCCCCCcccChhhhhhhhh
Q 037152 8 RKCSHCETRHTPQWRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~ 41 (75)
..|.+|+++ -.=.+-..| ..+|..||+=...
T Consensus 2 ~~CpeCg~~--~~~~d~~~g-e~VC~~CG~Vi~~ 32 (285)
T COG1405 2 MSCPECGST--NIITDYERG-EIVCADCGLVLED 32 (285)
T ss_pred CCCCCCCCc--cceeeccCC-eEEeccCCEEecc
Confidence 469999988 111222356 6899999987654
No 64
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=42.58 E-value=14 Score=26.04 Aligned_cols=32 Identities=28% Similarity=0.759 Sum_probs=20.6
Q ss_pred CcccccCccCCCCccc-------CCCCCcccChhhhhhh
Q 037152 8 RKCSHCETRHTPQWRV-------GPLGPKTLCNACGVRY 39 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~-------gp~G~~~LCNaCGl~~ 39 (75)
..|.+|++..--.|-- ++.-....|+.||..|
T Consensus 40 ~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 40 TSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPY 78 (158)
T ss_pred HHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCC
Confidence 3578888776555533 2233345899999877
No 65
>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=42.39 E-value=10 Score=21.92 Aligned_cols=35 Identities=17% Similarity=0.256 Sum_probs=23.5
Q ss_pred cccCCcccccCccCCCCcccCCCCCcccChhhhhh
Q 037152 4 ELWQRKCSHCETRHTPQWRVGPLGPKTLCNACGVR 38 (75)
Q Consensus 4 ~~~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~ 38 (75)
+....+|.+|.....-.-+....--.+.|-.||.+
T Consensus 19 ~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 19 NRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred CceeEECcccchhhcccccccCCceEEEcCCCCCc
Confidence 45677899999876544344444446788888753
No 66
>COG3952 Predicted membrane protein [Function unknown]
Probab=41.84 E-value=5.2 Score=26.78 Aligned_cols=18 Identities=33% Similarity=0.462 Sum_probs=13.1
Q ss_pred cccCCCCCcccChhhhhhhh
Q 037152 21 WRVGPLGPKTLCNACGVRYK 40 (75)
Q Consensus 21 WR~gp~G~~~LCNaCGl~~~ 40 (75)
||.+|-+ .+|++||++..
T Consensus 77 ~~~DpV~--Vl~~~~glF~~ 94 (113)
T COG3952 77 RRQDPVF--VLGQACGLFIY 94 (113)
T ss_pred HhcchHH--HHHHhhhHHHH
Confidence 4555554 69999998765
No 67
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=41.14 E-value=14 Score=31.01 Aligned_cols=29 Identities=28% Similarity=0.655 Sum_probs=24.8
Q ss_pred cCCcccccCccCCCCcccCCCCCcccChhhh
Q 037152 6 WQRKCSHCETRHTPQWRVGPLGPKTLCNACG 36 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCG 36 (75)
..+.|.+|+... |.|-.-..| ..||-.|.
T Consensus 22 gNk~CADCgs~~-P~WASiNlG-IFICi~CS 50 (648)
T PLN03119 22 PNRRCINCNSLG-PQYVCTTFW-TFVCMACS 50 (648)
T ss_pred CCCccccCCCCC-CCceeeccc-eEEeccch
Confidence 457899999865 999998888 78999994
No 68
>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=39.92 E-value=16 Score=21.63 Aligned_cols=28 Identities=21% Similarity=0.755 Sum_probs=21.3
Q ss_pred CCcccccCccCCCCcccCCCCCcccC-hhhhhhhhhC
Q 037152 7 QRKCSHCETRHTPQWRVGPLGPKTLC-NACGVRYKSG 42 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~WR~gp~G~~~LC-NaCGl~~~~~ 42 (75)
-+.|.+||.+.-| + ...| ..|+..|.+.
T Consensus 3 HkHC~~CG~~Ip~-------~-~~fCS~~C~~~~~k~ 31 (59)
T PF09889_consen 3 HKHCPVCGKPIPP-------D-ESFCSPKCREEYRKR 31 (59)
T ss_pred CCcCCcCCCcCCc-------c-hhhhCHHHHHHHHHH
Confidence 3679999987765 2 5789 5999998764
No 69
>PF12553 DUF3742: Protein of unknown function (DUF3742); InterPro: IPR022213 This domain family is found in bacteria, and is approximately 50 amino acids in length. There is a single completely conserved residue Y that may be functionally important.
Probab=39.52 E-value=10 Score=22.06 Aligned_cols=10 Identities=60% Similarity=1.401 Sum_probs=8.8
Q ss_pred CCcccCCCCC
Q 037152 19 PQWRVGPLGP 28 (75)
Q Consensus 19 p~WR~gp~G~ 28 (75)
|+||.||.|-
T Consensus 34 ~E~R~G~~Gf 43 (54)
T PF12553_consen 34 PEWREGPAGF 43 (54)
T ss_pred HhheecCCCc
Confidence 8899999984
No 70
>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=39.47 E-value=13 Score=19.80 Aligned_cols=29 Identities=21% Similarity=0.598 Sum_probs=14.5
Q ss_pred CcccccCccCCCCcccCCCCCcccChhhhhh
Q 037152 8 RKCSHCETRHTPQWRVGPLGPKTLCNACGVR 38 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~ 38 (75)
+.|..||.+---....... ..+|..||-.
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~--~~~Cd~cg~~ 30 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKV--EGVCDNCGGE 30 (36)
T ss_dssp EEETTTTEEEETTTB--SS--TTBCTTTTEB
T ss_pred cCcCCCCCccccccCCCCC--CCccCCCCCe
Confidence 3567777654443333222 2467777643
No 71
>PLN03131 hypothetical protein; Provisional
Probab=39.37 E-value=16 Score=31.01 Aligned_cols=29 Identities=24% Similarity=0.632 Sum_probs=24.6
Q ss_pred cCCcccccCccCCCCcccCCCCCcccChhhh
Q 037152 6 WQRKCSHCETRHTPQWRVGPLGPKTLCNACG 36 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCG 36 (75)
..+.|.+|+.. .|.|-.-..| ..||-.|.
T Consensus 22 gNk~CADCga~-~P~WASiNlG-IFICi~CS 50 (705)
T PLN03131 22 PNRRCINCNSL-GPQFVCTNFW-TFICMTCS 50 (705)
T ss_pred CCCccccCCCC-CCCeeEeccc-eEEchhch
Confidence 46789999975 4999998888 78999995
No 72
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=38.63 E-value=18 Score=29.62 Aligned_cols=34 Identities=21% Similarity=0.509 Sum_probs=21.1
Q ss_pred CCcccccCccCCCCccc-CCCCCc----------ccChhhhhhhh
Q 037152 7 QRKCSHCETRHTPQWRV-GPLGPK----------TLCNACGVRYK 40 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~WR~-gp~G~~----------~LCNaCGl~~~ 40 (75)
...|.+||......-+. +|++.. +.||+||---+
T Consensus 161 ~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~R 205 (500)
T KOG0909|consen 161 NPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETR 205 (500)
T ss_pred CCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCccc
Confidence 35799999877444444 333211 57999996443
No 73
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=38.40 E-value=12 Score=30.23 Aligned_cols=33 Identities=24% Similarity=0.630 Sum_probs=27.3
Q ss_pred cccCCcccccCccCCCCcccCCCCCcccChhhhhh
Q 037152 4 ELWQRKCSHCETRHTPQWRVGPLGPKTLCNACGVR 38 (75)
Q Consensus 4 ~~~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~ 38 (75)
.-..+.|..|+.. .|.|-.-+.| -+||--|.--
T Consensus 20 ~~~NKvCFDCgAk-nPtWaSVTYG-IFLCiDCSAv 52 (454)
T KOG0706|consen 20 QSENKVCFDCGAK-NPTWASVTYG-IFLCIDCSAV 52 (454)
T ss_pred CCCCceecccCCC-CCCceeecce-EEEEEecchh
Confidence 3467899999975 5999999999 7999999533
No 74
>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=37.45 E-value=10 Score=23.58 Aligned_cols=36 Identities=19% Similarity=0.438 Sum_probs=25.0
Q ss_pred cCCcccccCccCCC----CcccCCCCCc--ccChhhhhhhhh
Q 037152 6 WQRKCSHCETRHTP----QWRVGPLGPK--TLCNACGVRYKS 41 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp----~WR~gp~G~~--~LCNaCGl~~~~ 41 (75)
....|..||-...- +=|.+.+|.. +.|-.||..|+.
T Consensus 61 ~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~ 102 (104)
T TIGR01384 61 TRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWRE 102 (104)
T ss_pred ccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEe
Confidence 46789999966532 3366666632 469999988874
No 75
>TIGR03573 WbuX N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an
Probab=37.01 E-value=25 Score=26.43 Aligned_cols=30 Identities=27% Similarity=0.545 Sum_probs=20.7
Q ss_pred CcccccCccCC-CCcccCCCCCcccChhhhhhhh
Q 037152 8 RKCSHCETRHT-PQWRVGPLGPKTLCNACGVRYK 40 (75)
Q Consensus 8 ~~C~~C~t~~T-p~WR~gp~G~~~LCNaCGl~~~ 40 (75)
+.|..|.-++| |.-.=..+| +||+|--+..
T Consensus 2 ~~C~~C~~~~t~p~i~fd~~G---vC~~C~~~~~ 32 (343)
T TIGR03573 2 KFCKRCVMPTTRPGITFDEDG---VCSACRNFEE 32 (343)
T ss_pred CcCCCCCCCCCCCCeeECCCC---CchhhhhHHh
Confidence 57999998775 432334445 9999987654
No 76
>PHA02998 RNA polymerase subunit; Provisional
Probab=36.97 E-value=13 Score=26.94 Aligned_cols=36 Identities=22% Similarity=0.651 Sum_probs=27.7
Q ss_pred cCCcccccCccCCCCc----ccCCCCCc--ccChhhhhhhhh
Q 037152 6 WQRKCSHCETRHTPQW----RVGPLGPK--TLCNACGVRYKS 41 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~W----R~gp~G~~--~LCNaCGl~~~~ 41 (75)
....|..|+-..+--| |.++++.- +.|..||-.|+.
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 4568999998876644 88888843 269999999983
No 77
>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=35.87 E-value=22 Score=18.49 Aligned_cols=26 Identities=27% Similarity=0.676 Sum_probs=15.3
Q ss_pred cccccCccCCCCcccCCCCCcccChhhhhhh
Q 037152 9 KCSHCETRHTPQWRVGPLGPKTLCNACGVRY 39 (75)
Q Consensus 9 ~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~ 39 (75)
.|..|++... .. .+...-|..||-+.
T Consensus 2 ~C~~Cg~~~~--~~---~~~~irC~~CG~RI 27 (32)
T PF03604_consen 2 ICGECGAEVE--LK---PGDPIRCPECGHRI 27 (32)
T ss_dssp BESSSSSSE---BS---TSSTSSBSSSS-SE
T ss_pred CCCcCCCeeE--cC---CCCcEECCcCCCeE
Confidence 5889998776 11 12235699998553
No 78
>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=35.38 E-value=13 Score=28.07 Aligned_cols=34 Identities=24% Similarity=0.604 Sum_probs=23.6
Q ss_pred CCcccccCccCCCCc----ccCCCCCc--ccChhhhhhhh
Q 037152 7 QRKCSHCETRHTPQW----RVGPLGPK--TLCNACGVRYK 40 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~W----R~gp~G~~--~LCNaCGl~~~ 40 (75)
...|..|+-....-| |.++++-. +.|..||.+|+
T Consensus 258 ~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 468999997665433 55555522 37999998875
No 79
>PF14122 YokU: YokU-like protein
Probab=35.19 E-value=12 Score=23.97 Aligned_cols=33 Identities=27% Similarity=0.750 Sum_probs=21.2
Q ss_pred cccccCccCC-----CCcccCCCCC---------cccChhhhhhhhh
Q 037152 9 KCSHCETRHT-----PQWRVGPLGP---------KTLCNACGVRYKS 41 (75)
Q Consensus 9 ~C~~C~t~~T-----p~WR~gp~G~---------~~LCNaCGl~~~~ 41 (75)
.|..|+..++ .....-|+|. ...|+.||+-|..
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~ 47 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQD 47 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEeh
Confidence 3888987543 2223345553 3579999998864
No 80
>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=34.87 E-value=12 Score=22.43 Aligned_cols=35 Identities=20% Similarity=0.566 Sum_probs=25.5
Q ss_pred ccCCcccccCccCCCC-cccCCCCCcccChhhhhhhh
Q 037152 5 LWQRKCSHCETRHTPQ-WRVGPLGPKTLCNACGVRYK 40 (75)
Q Consensus 5 ~~~~~C~~C~t~~Tp~-WR~gp~G~~~LCNaCGl~~~ 40 (75)
+..-.|-.|.+..|-+ |+.+..- ..-|-+||..-.
T Consensus 7 IAGA~CP~C~~~Dtl~~~~e~~~e-~vECv~Cg~~~~ 42 (59)
T TIGR02443 7 IAGAVCPACSAQDTLAMWKENNIE-LVECVECGYQEQ 42 (59)
T ss_pred eccccCCCCcCccEEEEEEeCCce-EEEeccCCCccc
Confidence 4567899999998865 5554443 457999997765
No 81
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=34.78 E-value=12 Score=19.66 Aligned_cols=31 Identities=26% Similarity=0.757 Sum_probs=21.2
Q ss_pred cccccCccC-CCCcccCCCCCcccChhhhhhh
Q 037152 9 KCSHCETRH-TPQWRVGPLGPKTLCNACGVRY 39 (75)
Q Consensus 9 ~C~~C~t~~-Tp~WR~gp~G~~~LCNaCGl~~ 39 (75)
.|.+|++.- -+...=.+.|...-|-.||-.|
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 588888864 4556556667556688888654
No 82
>PRK05978 hypothetical protein; Provisional
Probab=34.43 E-value=23 Score=24.44 Aligned_cols=35 Identities=29% Similarity=0.714 Sum_probs=22.9
Q ss_pred cCCcccccCccCCCCcccCCCCCcccChhhhhhhhhCC
Q 037152 6 WQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYKSGR 43 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~~~ 43 (75)
+...|-+||.- .+++ +-..-..-|.+||+.|..++
T Consensus 32 l~grCP~CG~G--~LF~-g~Lkv~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 32 FRGRCPACGEG--KLFR-AFLKPVDHCAACGEDFTHHR 66 (148)
T ss_pred HcCcCCCCCCC--cccc-cccccCCCccccCCccccCC
Confidence 55678888853 3444 33333457999999998643
No 83
>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=34.40 E-value=17 Score=19.80 Aligned_cols=29 Identities=24% Similarity=0.562 Sum_probs=18.5
Q ss_pred CcccccCccCCCCcccCCCCCcccChhhhh
Q 037152 8 RKCSHCETRHTPQWRVGPLGPKTLCNACGV 37 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl 37 (75)
-.|.+|+..-+ .|+.-.+.....|-.||-
T Consensus 6 y~C~~Cg~~fe-~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFE-VLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeE-EEEecCCCCCCCCCCCCC
Confidence 36888987544 455433333457999996
No 84
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=34.38 E-value=18 Score=25.33 Aligned_cols=28 Identities=21% Similarity=0.444 Sum_probs=20.3
Q ss_pred cccCCcccccCccCCCCcccCCCCCcccChhhhhhhh
Q 037152 4 ELWQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYK 40 (75)
Q Consensus 4 ~~~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~ 40 (75)
...-..|..||. ..+....|..||..+.
T Consensus 306 ~~tS~~C~~cg~---------~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 306 YYTSKTCPCCGH---------LSGRLFKCPRCGFVHD 333 (364)
T ss_pred CCCcccccccCC---------ccceeEECCCCCCeeh
Confidence 345578999999 3344578999997654
No 85
>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=33.65 E-value=7.6 Score=20.02 Aligned_cols=33 Identities=27% Similarity=0.642 Sum_probs=20.1
Q ss_pred CcccccCccCC-CCcccCCCCCcccChhhhhhhh
Q 037152 8 RKCSHCETRHT-PQWRVGPLGPKTLCNACGVRYK 40 (75)
Q Consensus 8 ~~C~~C~t~~T-p~WR~gp~G~~~LCNaCGl~~~ 40 (75)
..|.+|++.-. +...-+..|....|-.||..+.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 46888988532 3333344454567888886553
No 86
>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=33.53 E-value=8.7 Score=24.91 Aligned_cols=16 Identities=38% Similarity=0.980 Sum_probs=12.7
Q ss_pred CCCcccChhhhhhhhh
Q 037152 26 LGPKTLCNACGVRYKS 41 (75)
Q Consensus 26 ~G~~~LCNaCGl~~~~ 41 (75)
.|..++|++||.+|..
T Consensus 49 ~g~~lvC~~C~~~~~~ 64 (102)
T PF10080_consen 49 EGDQLVCKNCGVRFNL 64 (102)
T ss_pred ECCEEEEecCCCEEeh
Confidence 3446899999999874
No 87
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=33.41 E-value=17 Score=27.82 Aligned_cols=35 Identities=29% Similarity=0.630 Sum_probs=21.5
Q ss_pred CCcccccCccCCCC-cc-cCCC-C-CcccChhhhhhhhh
Q 037152 7 QRKCSHCETRHTPQ-WR-VGPL-G-PKTLCNACGVRYKS 41 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~-WR-~gp~-G-~~~LCNaCGl~~~~ 41 (75)
-..|.+|+.++.=. |- .+.. + .-..|..|+-|+|.
T Consensus 226 R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 226 RVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred CccCCCCCCCCceeeeeecCCCcceEeeeccccccccee
Confidence 34689999754322 42 2221 1 23589999999885
No 88
>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=33.12 E-value=18 Score=17.95 Aligned_cols=24 Identities=25% Similarity=0.858 Sum_probs=13.6
Q ss_pred cccccCccCCCCcccCCCCCcccChhhhhhhh
Q 037152 9 KCSHCETRHTPQWRVGPLGPKTLCNACGVRYK 40 (75)
Q Consensus 9 ~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~ 40 (75)
.|-+|+... +.. ...|..||..|.
T Consensus 2 ~CP~C~~~V-------~~~-~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEV-------PES-AKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCc-------hhh-cCcCCCCCCCCc
Confidence 466666554 222 456777776543
No 89
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=33.10 E-value=23 Score=24.90 Aligned_cols=34 Identities=29% Similarity=0.604 Sum_probs=26.7
Q ss_pred CcccccCccCCCCc--ccCCCCCc----ccChhhhhhhhh
Q 037152 8 RKCSHCETRHTPQW--RVGPLGPK----TLCNACGVRYKS 41 (75)
Q Consensus 8 ~~C~~C~t~~Tp~W--R~gp~G~~----~LCNaCGl~~~~ 41 (75)
+.|..|+...|..- |...+|.. --|..||-+|--
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTT 40 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTT 40 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhcccccccccch
Confidence 46999999999875 66777743 479999998864
No 90
>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=33.01 E-value=29 Score=18.76 Aligned_cols=29 Identities=21% Similarity=0.584 Sum_probs=18.6
Q ss_pred cccccCccCCCCcccCCCCCcccChhhhh
Q 037152 9 KCSHCETRHTPQWRVGPLGPKTLCNACGV 37 (75)
Q Consensus 9 ~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl 37 (75)
.|..|....++.|+=..-..-.||..|=.
T Consensus 2 ~C~~C~~~~~~r~~C~~C~dfDLC~~C~~ 30 (41)
T cd02337 2 TCNECKHHVETRWHCTVCEDYDLCITCYN 30 (41)
T ss_pred cCCCCCCcCCCceECCCCcchhhHHHHhC
Confidence 47778776667776655443457887743
No 91
>PRK12496 hypothetical protein; Provisional
Probab=31.75 E-value=27 Score=23.99 Aligned_cols=32 Identities=22% Similarity=0.649 Sum_probs=20.1
Q ss_pred cCCcccccCccCCCCcccCCCCCcccChhhhhhhhhCC
Q 037152 6 WQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYKSGR 43 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~~~ 43 (75)
+...|..|+..-. ..+. ...|.-||...+++.
T Consensus 126 w~~~C~gC~~~~~----~~~~--~~~C~~CG~~~~r~~ 157 (164)
T PRK12496 126 WRKVCKGCKKKYP----EDYP--DDVCEICGSPVKRKM 157 (164)
T ss_pred eeEECCCCCcccc----CCCC--CCcCCCCCChhhhcc
Confidence 4567999984331 1222 258999998887543
No 92
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=31.68 E-value=13 Score=20.08 Aligned_cols=14 Identities=43% Similarity=1.056 Sum_probs=11.3
Q ss_pred cccChhhhhhhhhC
Q 037152 29 KTLCNACGVRYKSG 42 (75)
Q Consensus 29 ~~LCNaCGl~~~~~ 42 (75)
...|..|||.|..+
T Consensus 13 ~~~C~~CgM~Y~~~ 26 (41)
T PF13878_consen 13 ATTCPTCGMLYSPG 26 (41)
T ss_pred CcCCCCCCCEECCC
Confidence 46899999999753
No 93
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=31.59 E-value=27 Score=27.25 Aligned_cols=29 Identities=24% Similarity=0.607 Sum_probs=20.6
Q ss_pred CCcccccCccCCCCcccCCCCCcccChhhhhh
Q 037152 7 QRKCSHCETRHTPQWRVGPLGPKTLCNACGVR 38 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~ 38 (75)
...|.|||...|+..- +|..-+|-+||--
T Consensus 315 ~nfc~ncG~~~t~~~~---ng~a~fcp~cgq~ 343 (345)
T COG4260 315 LNFCLNCGCGTTADFD---NGKAKFCPECGQG 343 (345)
T ss_pred cccccccCcccccCCc---cchhhhChhhcCC
Confidence 3478999987777553 4545589999853
No 94
>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=31.51 E-value=17 Score=18.65 Aligned_cols=29 Identities=21% Similarity=0.507 Sum_probs=17.0
Q ss_pred cccccCccCCCCcccCCCCCcccChhhhhh
Q 037152 9 KCSHCETRHTPQWRVGPLGPKTLCNACGVR 38 (75)
Q Consensus 9 ~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~ 38 (75)
.|..||..-+. |....++....|-.||..
T Consensus 7 ~C~~Cg~~fe~-~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 7 RCEDCGHTFEV-LQKISDDPLATCPECGGD 35 (41)
T ss_pred EcCCCCCEEEE-EEecCCCCCCCCCCCCCc
Confidence 58888875432 232222435579999873
No 95
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=31.18 E-value=54 Score=19.18 Aligned_cols=23 Identities=35% Similarity=0.840 Sum_probs=13.9
Q ss_pred CCcccccCccCCCCcccCCCCCcccChhhhhhh
Q 037152 7 QRKCSHCETRHTPQWRVGPLGPKTLCNACGVRY 39 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~ 39 (75)
-+.|.+|++.+. ...|-.||...
T Consensus 5 mr~C~~CgvYTL----------k~~CP~CG~~t 27 (56)
T PRK13130 5 IRKCPKCGVYTL----------KEICPVCGGKT 27 (56)
T ss_pred ceECCCCCCEEc----------cccCcCCCCCC
Confidence 356777777655 23666676543
No 96
>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=30.78 E-value=54 Score=21.34 Aligned_cols=16 Identities=38% Similarity=1.009 Sum_probs=10.6
Q ss_pred CCCcccChhhhhhhhh
Q 037152 26 LGPKTLCNACGVRYKS 41 (75)
Q Consensus 26 ~G~~~LCNaCGl~~~~ 41 (75)
.|.+.+|..||.+|.-
T Consensus 6 lGtKR~Cp~CG~kFYD 21 (108)
T PF09538_consen 6 LGTKRTCPSCGAKFYD 21 (108)
T ss_pred cCCcccCCCCcchhcc
Confidence 4656677777776663
No 97
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=30.46 E-value=22 Score=20.97 Aligned_cols=8 Identities=38% Similarity=1.182 Sum_probs=4.5
Q ss_pred cccChhhh
Q 037152 29 KTLCNACG 36 (75)
Q Consensus 29 ~~LCNaCG 36 (75)
+.+|-.||
T Consensus 40 Hrvc~~cg 47 (57)
T COG0333 40 HRVCLKCG 47 (57)
T ss_pred ceEcCCCC
Confidence 34566665
No 98
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=30.14 E-value=17 Score=21.97 Aligned_cols=26 Identities=27% Similarity=0.640 Sum_probs=14.5
Q ss_pred CCcccccCccCCCCcccCCCCCcccChhhh
Q 037152 7 QRKCSHCETRHTPQWRVGPLGPKTLCNACG 36 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCG 36 (75)
...|+.||....|. ..+-...|-.||
T Consensus 9 ~~~CtSCg~~i~p~----e~~v~F~CPnCG 34 (61)
T COG2888 9 PPVCTSCGREIAPG----ETAVKFPCPNCG 34 (61)
T ss_pred CceeccCCCEeccC----CceeEeeCCCCC
Confidence 45777777665442 222234566666
No 99
>PHA02942 putative transposase; Provisional
Probab=30.10 E-value=30 Score=26.74 Aligned_cols=33 Identities=18% Similarity=0.382 Sum_probs=22.1
Q ss_pred cccccCCcccccCccCCCCcccCCCCCcccChhhhhhh
Q 037152 2 NEELWQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRY 39 (75)
Q Consensus 2 ~~~~~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~ 39 (75)
++..--..|+.||..... ..+....|..||...
T Consensus 320 ~p~yTSq~Cs~CG~~~~~-----l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 320 NPSYSSVSCPKCGHKMVE-----IAHRYFHCPSCGYEN 352 (383)
T ss_pred CCCCCCccCCCCCCccCc-----CCCCEEECCCCCCEe
Confidence 444556789999986532 233357899999754
No 100
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=29.30 E-value=16 Score=25.29 Aligned_cols=31 Identities=29% Similarity=0.477 Sum_probs=22.5
Q ss_pred CcccccCccCCCCcccCCCCCcccChhhhhhh
Q 037152 8 RKCSHCETRHTPQWRVGPLGPKTLCNACGVRY 39 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~ 39 (75)
..|.-|+...|+.-+.+-.= ...|.|||-..
T Consensus 106 v~C~~c~s~dt~l~~~~R~~-~l~c~acGa~~ 136 (151)
T COG1601 106 VKCKECGSPDTELIKEERLL-FLKCEACGAIR 136 (151)
T ss_pred eEeccCCCCchhhhhhhhhH-hhHHHHhCCcc
Confidence 47999999999988772221 24599999543
No 101
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=29.13 E-value=16 Score=20.57 Aligned_cols=31 Identities=32% Similarity=0.546 Sum_probs=22.2
Q ss_pred cCCcccccCccCCCCc----ccCCCCCcccChhhhhh
Q 037152 6 WQRKCSHCETRHTPQW----RVGPLGPKTLCNACGVR 38 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~W----R~gp~G~~~LCNaCGl~ 38 (75)
....|..|+..-+|+. +.+ +. -..|..||-.
T Consensus 21 ~~~~C~gC~~~l~~~~~~~i~~~-~~-i~~Cp~CgRi 55 (56)
T PF02591_consen 21 EGGTCSGCHMELPPQELNEIRKG-DE-IVFCPNCGRI 55 (56)
T ss_pred eCCccCCCCEEcCHHHHHHHHcC-CC-eEECcCCCcc
Confidence 4568999999988874 555 22 4679999853
No 102
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=28.80 E-value=47 Score=25.97 Aligned_cols=34 Identities=21% Similarity=0.334 Sum_probs=22.8
Q ss_pred cccCCcccccCccCCCC--cccCCCCCcccChhhhhhh
Q 037152 4 ELWQRKCSHCETRHTPQ--WRVGPLGPKTLCNACGVRY 39 (75)
Q Consensus 4 ~~~~~~C~~C~t~~Tp~--WR~gp~G~~~LCNaCGl~~ 39 (75)
+.....|+-||.+.... --.||. .++|+.|--..
T Consensus 6 ~~~~~~CSFCGr~~~ev~~li~g~~--~~IC~~Ci~~~ 41 (412)
T PRK05342 6 SKKLLYCSFCGKSQHEVRKLIAGPG--VYICDECIELC 41 (412)
T ss_pred CCCccccCCCCCChhhccccccCCC--CcccchHHHHH
Confidence 34456899999976543 445653 47999995333
No 103
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=28.30 E-value=32 Score=23.89 Aligned_cols=29 Identities=28% Similarity=0.678 Sum_probs=18.9
Q ss_pred CcccccCccCCCCcccCCCCCcccChhhhh
Q 037152 8 RKCSHCETRHTPQWRVGPLGPKTLCNACGV 37 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl 37 (75)
..|..||......+=.-..| ..+|..|+-
T Consensus 148 ~~C~~cg~~~~~~~fs~~~g-g~~C~~c~~ 176 (241)
T TIGR00613 148 DKCAVCGSKEDLIYFSMTYG-GALCRQCGE 176 (241)
T ss_pred CccCCCCCcCCCceEchhcC-eEEChhhCc
Confidence 47999998433333333445 689999964
No 104
>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=28.22 E-value=20 Score=19.35 Aligned_cols=31 Identities=23% Similarity=0.544 Sum_probs=19.9
Q ss_pred cCCcccccCccCCCCcccCCCCCcccChhhhhhhhh
Q 037152 6 WQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~ 41 (75)
....|..|+..- |-.+.. .+.|..|++.+.+
T Consensus 10 ~~~~C~~C~~~i---~g~~~~--g~~C~~C~~~~H~ 40 (53)
T PF00130_consen 10 KPTYCDVCGKFI---WGLGKQ--GYRCSWCGLVCHK 40 (53)
T ss_dssp STEB-TTSSSBE---CSSSSC--EEEETTTT-EEET
T ss_pred CCCCCcccCccc---CCCCCC--eEEECCCCChHhh
Confidence 456788887765 553333 4789999998875
No 105
>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=27.90 E-value=35 Score=16.87 Aligned_cols=23 Identities=26% Similarity=0.712 Sum_probs=12.8
Q ss_pred ccccCccCCCCcccCCCCCcccChhhh
Q 037152 10 CSHCETRHTPQWRVGPLGPKTLCNACG 36 (75)
Q Consensus 10 C~~C~t~~Tp~WR~gp~G~~~LCNaCG 36 (75)
|..|+..-.|.=+ +..+.|-.||
T Consensus 1 C~sC~~~i~~r~~----~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQ----AVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCccc----CceEeCCCCC
Confidence 5566655554321 3356787777
No 106
>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=27.35 E-value=19 Score=18.63 Aligned_cols=26 Identities=31% Similarity=0.695 Sum_probs=12.6
Q ss_pred cccccCccCCCCcccCCCCCcccChhhhhhh
Q 037152 9 KCSHCETRHTPQWRVGPLGPKTLCNACGVRY 39 (75)
Q Consensus 9 ~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~ 39 (75)
.|-.|++..|= .+|..++|..||-.|
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 57778877664 556567899888543
No 107
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=27.23 E-value=26 Score=26.66 Aligned_cols=37 Identities=24% Similarity=0.560 Sum_probs=26.4
Q ss_pred CCcccccCccCCC-CcccC--CCCCccc-ChhhhhhhhhCC
Q 037152 7 QRKCSHCETRHTP-QWRVG--PLGPKTL-CNACGVRYKSGR 43 (75)
Q Consensus 7 ~~~C~~C~t~~Tp-~WR~g--p~G~~~L-CNaCGl~~~~~~ 43 (75)
...|--||+.-.- +-+.+ .+|.++| |+-|+..|.-.+
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R 224 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVR 224 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccC
Confidence 3489999997654 44554 4676665 999999998543
No 108
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=27.15 E-value=20 Score=22.43 Aligned_cols=14 Identities=36% Similarity=0.956 Sum_probs=11.1
Q ss_pred ccChhhhhhhhhCC
Q 037152 30 TLCNACGVRYKSGR 43 (75)
Q Consensus 30 ~LCNaCGl~~~~~~ 43 (75)
.-|.+||+.|...+
T Consensus 9 ~~C~~CG~d~~~~~ 22 (86)
T PF06170_consen 9 PRCPHCGLDYSHAR 22 (86)
T ss_pred CcccccCCccccCC
Confidence 46999999998644
No 109
>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=27.06 E-value=29 Score=28.05 Aligned_cols=36 Identities=25% Similarity=0.777 Sum_probs=27.0
Q ss_pred cCCcccccCccCCCCccc-----C--CCCCcccChhhhhhhhh
Q 037152 6 WQRKCSHCETRHTPQWRV-----G--PLGPKTLCNACGVRYKS 41 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~-----g--p~G~~~LCNaCGl~~~~ 41 (75)
.-..|-+||.-....|.. + +....+.|-.||-.+..
T Consensus 199 ~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 199 YYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred EEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCH
Confidence 456899999999988753 2 34446789999988763
No 110
>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=26.32 E-value=52 Score=20.73 Aligned_cols=32 Identities=16% Similarity=0.430 Sum_probs=22.3
Q ss_pred ccCCcccccCccCCCCcccCCCCCcccChhhhhhhhh
Q 037152 5 LWQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 5 ~~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~ 41 (75)
+....|.-|+...+-.+ -| ...|+||..+|+.
T Consensus 3 ~~~~~C~VCg~~~~g~h----yG-v~sC~aC~~FFRR 34 (95)
T cd06968 3 IEVIPCKICGDKSSGIH----YG-VITCEGCKGFFRR 34 (95)
T ss_pred ccccCCcccCCcCcceE----EC-ceeehhhHHhhHH
Confidence 34567999987554432 23 4579999999986
No 111
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=26.25 E-value=26 Score=30.70 Aligned_cols=25 Identities=28% Similarity=0.670 Sum_probs=18.0
Q ss_pred CCcccccCccCCCCcccCCCCCcccChhhhh
Q 037152 7 QRKCSHCETRHTPQWRVGPLGPKTLCNACGV 37 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl 37 (75)
...|.+||+. + -++|..++|..||.
T Consensus 924 ~~~c~~c~~~---~---~~~g~c~~c~~cg~ 948 (953)
T PRK06556 924 APLCPTCGTK---M---VRNGSCYVCEGCGS 948 (953)
T ss_pred CCcCCCccCe---e---eECCceEeccCCCC
Confidence 4569999752 2 24577899999984
No 112
>PF09698 GSu_C4xC__C2xCH: Geobacter CxxxxCH...CXXCH motif (GSu_C4xC__C2xCH); InterPro: IPR010176 This motif occurs from three to eight times in eight different proteins of Geobacter sulfurreducens. The final CXXCH motif matches the cytochrome c family haem-binding site signature, suggesting that the sequence may be involved in haem-binding.
Probab=26.08 E-value=41 Score=17.61 Aligned_cols=17 Identities=35% Similarity=0.970 Sum_probs=12.3
Q ss_pred cCCCCcccCCCCCcccChhh
Q 037152 16 RHTPQWRVGPLGPKTLCNAC 35 (75)
Q Consensus 16 ~~Tp~WR~gp~G~~~LCNaC 35 (75)
..+|.|-.+..+. |++|
T Consensus 19 ~~~p~W~~~~~~~---C~~C 35 (36)
T PF09698_consen 19 YTTPTWGSGATTA---CGSC 35 (36)
T ss_pred ccCceeCCCCCCc---cccc
Confidence 3567898877763 8887
No 113
>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=25.71 E-value=9.3 Score=28.01 Aligned_cols=36 Identities=22% Similarity=0.492 Sum_probs=17.0
Q ss_pred CCcccccCccCCCCcccCCC--CCccc-ChhhhhhhhhC
Q 037152 7 QRKCSHCETRHTPQWRVGPL--GPKTL-CNACGVRYKSG 42 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~WR~gp~--G~~~L-CNaCGl~~~~~ 42 (75)
...|--||+.-.--+-++.. |.++| |.-||..|.-.
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~ 210 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFV 210 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--EEE--
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeec
Confidence 46899999876655544444 76654 99999998743
No 114
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=25.59 E-value=34 Score=23.61 Aligned_cols=34 Identities=26% Similarity=0.572 Sum_probs=21.7
Q ss_pred CcccccCccCCCCcccC--CCCC----cccChhhhhhhhh
Q 037152 8 RKCSHCETRHTPQWRVG--PLGP----KTLCNACGVRYKS 41 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~g--p~G~----~~LCNaCGl~~~~ 41 (75)
+.|.+||...|-.--.- +.|. ..-|.+||..+..
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~ 40 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTT 40 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceE
Confidence 46999998776543111 1231 2569999988863
No 115
>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=25.54 E-value=24 Score=22.67 Aligned_cols=33 Identities=24% Similarity=0.608 Sum_probs=18.0
Q ss_pred cCCcccccCccCCCCcccCCC---CCcccChhhhhh
Q 037152 6 WQRKCSHCETRHTPQWRVGPL---GPKTLCNACGVR 38 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~---G~~~LCNaCGl~ 38 (75)
....|..|+.+-+-.+..|-. =...+|..||.+
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 456788888776555544321 113567777766
No 116
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=25.39 E-value=56 Score=20.55 Aligned_cols=23 Identities=26% Similarity=0.700 Sum_probs=16.9
Q ss_pred cCCcccccCccCCCCcccCCCCCcccChhhhhh
Q 037152 6 WQRKCSHCETRHTPQWRVGPLGPKTLCNACGVR 38 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~ 38 (75)
....|..||..++ ..+|.+|-++
T Consensus 79 ~~~~C~~CG~pss----------~~iC~~C~l~ 101 (104)
T TIGR00269 79 DLRRCERCGEPTS----------GRICKACKFL 101 (104)
T ss_pred cCCcCCcCcCcCC----------ccccHhhhhh
Confidence 4567999997665 3589999764
No 117
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=24.60 E-value=39 Score=21.78 Aligned_cols=38 Identities=21% Similarity=0.509 Sum_probs=27.9
Q ss_pred ccCCcccccCccCCCCcccCCCCCcccChhhhhhhhhCCCCC
Q 037152 5 LWQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYKSGRLLP 46 (75)
Q Consensus 5 ~~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~~~~~p 46 (75)
...-.|..|+.+ .-++.-.| -..|..||--|..+.-.|
T Consensus 33 ~~~~~Cp~C~~~---~VkR~a~G-IW~C~kCg~~fAGgay~P 70 (89)
T COG1997 33 RAKHVCPFCGRT---TVKRIATG-IWKCRKCGAKFAGGAYTP 70 (89)
T ss_pred hcCCcCCCCCCc---ceeeeccC-eEEcCCCCCeeccccccc
Confidence 356679999987 55666677 578999999888654333
No 118
>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=24.55 E-value=34 Score=22.10 Aligned_cols=27 Identities=19% Similarity=0.461 Sum_probs=16.9
Q ss_pred cCCcccccCccCCCCcccCCCCCcccChhhhhh
Q 037152 6 WQRKCSHCETRHTPQWRVGPLGPKTLCNACGVR 38 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~ 38 (75)
....|.+|+...++... ...|-.||-+
T Consensus 69 ~~~~C~~Cg~~~~~~~~------~~~CP~Cgs~ 95 (115)
T TIGR00100 69 VECECEDCSEEVSPEID------LYRCPKCHGI 95 (115)
T ss_pred cEEEcccCCCEEecCCc------CccCcCCcCC
Confidence 34578888865555432 3568888854
No 119
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=23.93 E-value=25 Score=21.32 Aligned_cols=31 Identities=19% Similarity=0.488 Sum_probs=20.1
Q ss_pred CCcccccCccCCCCcccCCCCCcccChhhhhh
Q 037152 7 QRKCSHCETRHTPQWRVGPLGPKTLCNACGVR 38 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~ 38 (75)
.+.|-.||...--.=..+... ...|..||..
T Consensus 6 lKPCPFCG~~~~~v~~~~g~~-~v~C~~CgA~ 36 (64)
T PRK09710 6 VKPCPFCGCPSVTVKAISGYY-RAKCNGCESR 36 (64)
T ss_pred ccCCCCCCCceeEEEecCceE-EEEcCCCCcC
Confidence 578999998654333333333 3579999874
No 120
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=23.74 E-value=39 Score=18.79 Aligned_cols=31 Identities=29% Similarity=0.653 Sum_probs=18.0
Q ss_pred CcccccCccCCCCcccC--CC-CCcc-cChhhhhhh
Q 037152 8 RKCSHCETRHTPQWRVG--PL-GPKT-LCNACGVRY 39 (75)
Q Consensus 8 ~~C~~C~t~~Tp~WR~g--p~-G~~~-LCNaCGl~~ 39 (75)
+.|-.||...- .+|++ +. +..+ .|..||...
T Consensus 2 kPCPfCGg~~~-~~~~~~~~~~~~~~~~C~~Cga~~ 36 (53)
T TIGR03655 2 KPCPFCGGADV-YLRRGFDPLDLSHYFECSTCGASG 36 (53)
T ss_pred CCCCCCCCcce-eeEeccCCCCCEEEEECCCCCCCc
Confidence 67999998443 24422 22 2123 599998653
No 121
>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=22.96 E-value=41 Score=20.90 Aligned_cols=30 Identities=17% Similarity=0.455 Sum_probs=21.1
Q ss_pred CCcccccCccCCCCcccCCCCCcccChhhhhhhhh
Q 037152 7 QRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~ 41 (75)
...|.-|+...+-.+ -| ...|+||..+|+.
T Consensus 3 ~~~C~VCg~~a~g~h----yG-v~sC~aCk~FFRR 32 (89)
T cd07166 3 VVLCKVCGDKASGFH----YG-VHACEGCKGFFRR 32 (89)
T ss_pred CCCCcccCccCcceE----EC-hhhhhhHhhEecc
Confidence 346888987555332 23 4579999999986
No 122
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=22.48 E-value=18 Score=26.45 Aligned_cols=36 Identities=19% Similarity=0.446 Sum_probs=22.7
Q ss_pred ccCCcccccCccCCC--Cccc-CCCCCcccChhhhhhhhh
Q 037152 5 LWQRKCSHCETRHTP--QWRV-GPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 5 ~~~~~C~~C~t~~Tp--~WR~-gp~G~~~LCNaCGl~~~~ 41 (75)
.+-..|-+|+.-+++ .-+. |.+ .-.-|++||.-+..
T Consensus 4 ~iy~~Cp~Cg~eev~hEVik~~g~~-~lvrC~eCG~V~~~ 42 (201)
T COG1326 4 EIYIECPSCGSEEVSHEVIKERGRE-PLVRCEECGTVHPA 42 (201)
T ss_pred eEEEECCCCCcchhhHHHHHhcCCc-eEEEccCCCcEeec
Confidence 345689999955552 2344 333 23349999998854
No 123
>PLN00162 transport protein sec23; Provisional
Probab=22.30 E-value=33 Score=28.88 Aligned_cols=35 Identities=23% Similarity=0.354 Sum_probs=27.8
Q ss_pred cCCcccccCccCCCCcccCCCCCcccChhhhhhhh
Q 037152 6 WQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYK 40 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~ 40 (75)
..-+|..|++--.|--+-...|+...||-|+....
T Consensus 52 ~pvRC~~CraylNPf~~~d~~~~~W~C~~C~~~N~ 86 (761)
T PLN00162 52 DPLRCRTCRAVLNPYCRVDFQAKIWICPFCFQRNH 86 (761)
T ss_pred CCCccCCCcCEECCceEEecCCCEEEccCCCCCCC
Confidence 35789999999988766666777789999986653
No 124
>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=21.94 E-value=56 Score=17.34 Aligned_cols=29 Identities=21% Similarity=0.610 Sum_probs=17.4
Q ss_pred cCCcccccCccCCCCccc--CCCCC-cccChhh
Q 037152 6 WQRKCSHCETRHTPQWRV--GPLGP-KTLCNAC 35 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~--gp~G~-~~LCNaC 35 (75)
++..|..|+.++. .-|. ++.|. .++|-.|
T Consensus 4 i~v~CP~C~s~~~-v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 4 IDVHCPRCQSTEG-VKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred EeeeCCCCCCCCc-ceeCCCCCCCCEeEecCcC
Confidence 4567888887652 3344 34553 3678776
No 125
>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=21.84 E-value=41 Score=20.61 Aligned_cols=27 Identities=19% Similarity=0.571 Sum_probs=17.8
Q ss_pred ccccCccCCCCcccCCCCCcccChhhhhhhhh
Q 037152 10 CSHCETRHTPQWRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 10 C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~ 41 (75)
|.-|+...+-.+ -| ...|+||..+|+.
T Consensus 2 C~VCg~~~~g~h----yG-v~sC~aCk~FFRR 28 (84)
T cd06965 2 CRVCGDKASGFH----YG-VHACEGCKGFFRR 28 (84)
T ss_pred CcccCccCcceE----EC-hhhhhhhhhheee
Confidence 667775444322 23 4579999999986
No 126
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.52 E-value=48 Score=21.50 Aligned_cols=28 Identities=18% Similarity=0.530 Sum_probs=15.0
Q ss_pred cCCcccccCccCCCCcccCCCCCcccChhhhhh
Q 037152 6 WQRKCSHCETRHTPQWRVGPLGPKTLCNACGVR 38 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~ 38 (75)
....|.+|+...+.... . ...|-.||-+
T Consensus 70 ~~~~C~~Cg~~~~~~~~----~-~~~CP~Cgs~ 97 (117)
T PRK00564 70 VELECKDCSHVFKPNAL----D-YGVCEKCHSK 97 (117)
T ss_pred CEEEhhhCCCccccCCc----c-CCcCcCCCCC
Confidence 34568888855444321 1 1238888754
No 127
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=21.41 E-value=41 Score=21.69 Aligned_cols=27 Identities=19% Similarity=0.300 Sum_probs=15.9
Q ss_pred cCCcccccCccCCCCcccCCCCCcccChhhhhh
Q 037152 6 WQRKCSHCETRHTPQWRVGPLGPKTLCNACGVR 38 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~ 38 (75)
....|.+|+........ ...|-.||-+
T Consensus 69 ~~~~C~~Cg~~~~~~~~------~~~CP~Cgs~ 95 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQH------DAQCPHCHGE 95 (113)
T ss_pred cEEEcccCCCEEecCCc------CccCcCCCCC
Confidence 34578888855444321 3458888743
No 128
>PF06869 DUF1258: Protein of unknown function (DUF1258); InterPro: IPR009667 This family represents a conserved region approximately 260 residues long within a number of hypothetical proteins of unknown function that seem to be specific to Caenorhabditis elegans. Note that this family contains a number of conserved cysteine and histidine residues.
Probab=21.33 E-value=32 Score=25.97 Aligned_cols=19 Identities=21% Similarity=0.616 Sum_probs=12.6
Q ss_pred ccCCCCCcccChhhhhhhh
Q 037152 22 RVGPLGPKTLCNACGVRYK 40 (75)
Q Consensus 22 R~gp~G~~~LCNaCGl~~~ 40 (75)
+++.-..+++||.||....
T Consensus 11 ~~~~~S~h~~CN~CG~~~~ 29 (258)
T PF06869_consen 11 KKNNFSTHFICNSCGKVVE 29 (258)
T ss_pred ccCcceeehhhhhhhhhhc
Confidence 3344444689999998444
No 129
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=21.21 E-value=59 Score=23.31 Aligned_cols=24 Identities=17% Similarity=0.482 Sum_probs=13.3
Q ss_pred CCcccccCccCCCCcccCCCCCcccChhhhhh
Q 037152 7 QRKCSHCETRHTPQWRVGPLGPKTLCNACGVR 38 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~ 38 (75)
+..|.+||.+.+ .| ..+|..||-+
T Consensus 354 ~~~c~~cg~~~~-~~-------~~~c~~c~~~ 377 (389)
T PRK11788 354 RYRCRNCGFTAR-TL-------YWHCPSCKAW 377 (389)
T ss_pred CEECCCCCCCCc-cc-------eeECcCCCCc
Confidence 456777776543 34 3466666543
No 130
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=21.18 E-value=34 Score=18.20 Aligned_cols=25 Identities=24% Similarity=0.654 Sum_probs=15.8
Q ss_pred ccccCccCCCCcccCCCCCcccChhhhhhhhh
Q 037152 10 CSHCETRHTPQWRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 10 C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~ 41 (75)
|.-|+. .++.+.-..|..|+..|..
T Consensus 2 C~vC~~-------~~~~~~~i~C~~C~~~~H~ 26 (51)
T PF00628_consen 2 CPVCGQ-------SDDDGDMIQCDSCNRWYHQ 26 (51)
T ss_dssp BTTTTS-------SCTTSSEEEBSTTSCEEET
T ss_pred CcCCCC-------cCCCCCeEEcCCCChhhCc
Confidence 556665 3344434569999987764
No 131
>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=21.07 E-value=44 Score=21.66 Aligned_cols=32 Identities=22% Similarity=0.452 Sum_probs=22.4
Q ss_pred ccCCcccccCccCCCCcccCCCCCcccChhhhhhhhh
Q 037152 5 LWQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 5 ~~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~ 41 (75)
.....|.-|+...+-.+ -| ...|+||..+|+.
T Consensus 4 ~~~~~C~VCg~~a~g~h----yG-v~sC~aCk~FFRR 35 (107)
T cd06955 4 NVPRICGVCGDRATGFH----FN-AMTCEGCKGFFRR 35 (107)
T ss_pred CCCCCCeecCCcCcccE----EC-cceeeeecceecc
Confidence 35677999987554332 13 4579999999986
No 132
>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=21.01 E-value=80 Score=24.89 Aligned_cols=31 Identities=23% Similarity=0.444 Sum_probs=20.1
Q ss_pred CCcccccCccCCCC--cccCCCCCcccChhhhhhh
Q 037152 7 QRKCSHCETRHTPQ--WRVGPLGPKTLCNACGVRY 39 (75)
Q Consensus 7 ~~~C~~C~t~~Tp~--WR~gp~G~~~LCNaCGl~~ 39 (75)
...|+-||-..... .=.|+. .++|+.|-...
T Consensus 7 ~~~c~fc~~~~~~~~~~~~~~~--~~ic~~c~~~~ 39 (413)
T TIGR00382 7 TLYCSFCGKSQDEVRKLIAGPG--VYICDECIELC 39 (413)
T ss_pred CeecCCCCCChhhcccccCCCC--CcCCCchHHHH
Confidence 34799999876542 233433 37999995443
No 133
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=20.73 E-value=27 Score=26.99 Aligned_cols=31 Identities=19% Similarity=0.487 Sum_probs=20.5
Q ss_pred cCCcccccCccCCCCcccCCCCCcccChhhhhhhhh
Q 037152 6 WQRKCSHCETRHTPQWRVGPLGPKTLCNACGVRYKS 41 (75)
Q Consensus 6 ~~~~C~~C~t~~Tp~WR~gp~G~~~LCNaCGl~~~~ 41 (75)
....|.+|+...+..| + . ...|.-||-.+..
T Consensus 243 ~~~~C~~c~~~~~~~~---~-~-~~~C~~c~~~~~~ 273 (382)
T PRK04338 243 YVYYCPKCLYREEVEG---L-P-PEECPVCGGKFGT 273 (382)
T ss_pred eEEECCCCCcEEEecC---C-C-CCCCCCCCCccee
Confidence 4567888988777666 1 1 2468888766554
No 134
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=20.20 E-value=29 Score=22.61 Aligned_cols=32 Identities=28% Similarity=0.777 Sum_probs=23.6
Q ss_pred cccccCccCCCCc----ccCCCCCc--ccChhhhhhhh
Q 037152 9 KCSHCETRHTPQW----RVGPLGPK--TLCNACGVRYK 40 (75)
Q Consensus 9 ~C~~C~t~~Tp~W----R~gp~G~~--~LCNaCGl~~~ 40 (75)
.|..||-.+---| |.++++.. +.|-.||-.|+
T Consensus 74 ~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 74 KCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred cCCCCCCceeEEEeeehhccCCCceEEEEecccCCEee
Confidence 5888887765444 88888743 35999998886
Done!