Query psy7550
Match_columns 144
No_of_seqs 161 out of 1088
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 21:15:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7550.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7550hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0706|consensus 100.0 4.2E-46 9.2E-51 315.5 11.5 136 4-140 3-138 (454)
2 KOG0704|consensus 100.0 4.7E-42 1E-46 284.0 8.2 113 11-124 6-120 (386)
3 PLN03114 ADP-ribosylation fact 100.0 7.3E-40 1.6E-44 272.4 11.0 122 10-132 8-130 (395)
4 COG5347 GTPase-activating prot 100.0 1.1E-39 2.3E-44 270.7 8.7 119 8-127 4-124 (319)
5 KOG0703|consensus 100.0 6.7E-39 1.5E-43 261.1 7.3 114 7-122 8-121 (287)
6 PF01412 ArfGap: Putative GTPa 100.0 1.3E-38 2.8E-43 230.3 7.0 105 13-118 2-111 (116)
7 smart00105 ArfGap Putative GTP 100.0 1.1E-36 2.3E-41 219.2 9.1 97 22-119 1-103 (112)
8 PLN03119 putative ADP-ribosyla 100.0 1.5E-30 3.3E-35 226.5 9.7 119 1-124 1-121 (648)
9 PLN03131 hypothetical protein; 100.0 4.4E-30 9.5E-35 225.1 9.6 89 6-98 5-93 (705)
10 KOG0705|consensus 99.9 4.6E-25 1E-29 192.5 7.4 83 12-95 501-583 (749)
11 KOG0521|consensus 99.8 1.2E-21 2.5E-26 178.5 2.5 83 14-97 416-498 (785)
12 KOG0818|consensus 99.8 1.7E-20 3.6E-25 162.1 2.1 107 19-126 3-118 (669)
13 KOG1117|consensus 99.7 5E-18 1.1E-22 153.6 3.5 86 13-98 287-373 (1186)
14 KOG0702|consensus 99.3 1.3E-12 2.7E-17 113.2 5.4 93 1-95 1-95 (524)
15 KOG0521|consensus 94.6 0.0084 1.8E-07 55.9 -0.2 70 21-93 627-697 (785)
16 PRK00085 recO DNA repair prote 88.2 0.34 7.4E-06 38.3 2.1 32 20-51 145-177 (247)
17 TIGR00613 reco DNA repair prot 83.4 0.82 1.8E-05 36.0 2.1 36 18-53 141-177 (241)
18 PRK12495 hypothetical protein; 82.5 0.97 2.1E-05 36.4 2.1 28 22-53 40-67 (226)
19 PF00643 zf-B_box: B-box zinc 81.5 0.96 2.1E-05 26.1 1.4 34 23-56 2-36 (42)
20 PF00320 GATA: GATA zinc finge 80.2 0.99 2.1E-05 25.8 1.1 32 27-58 1-34 (36)
21 TIGR02419 C4_traR_proteo phage 79.4 1.1 2.4E-05 28.9 1.3 34 20-54 27-62 (63)
22 PF01286 XPA_N: XPA protein N- 78.2 0.7 1.5E-05 26.5 0.0 27 25-51 4-31 (34)
23 PRK11019 hypothetical protein; 78.2 1.4 2.9E-05 30.6 1.5 43 17-60 29-73 (88)
24 smart00401 ZnF_GATA zinc finge 77.8 2.1 4.5E-05 26.5 2.1 38 23-60 2-41 (52)
25 COG1381 RecO Recombinational D 75.0 1.8 3.9E-05 35.0 1.6 31 21-51 151-182 (251)
26 PF08271 TF_Zn_Ribbon: TFIIB z 74.9 0.93 2E-05 26.7 -0.0 27 26-53 2-28 (43)
27 PRK13715 conjugal transfer pro 72.8 1.8 3.9E-05 28.8 1.0 33 24-56 34-67 (73)
28 PF11781 RRN7: RNA polymerase 68.8 2.8 6.1E-05 24.1 1.1 27 22-51 6-32 (36)
29 PF01258 zf-dskA_traR: Prokary 68.7 0.83 1.8E-05 26.0 -1.2 29 26-54 5-34 (36)
30 cd07171 NR_DBD_ER DNA-binding 67.0 3.8 8.3E-05 27.7 1.6 31 23-56 2-32 (82)
31 cd07173 NR_DBD_AR DNA-binding 66.3 4.3 9.4E-05 27.4 1.8 32 22-56 1-32 (82)
32 PF10764 Gin: Inhibitor of sig 65.6 3.1 6.8E-05 25.3 0.9 27 26-53 1-27 (46)
33 PF12760 Zn_Tnp_IS1595: Transp 64.6 7.5 0.00016 23.1 2.4 43 7-51 2-44 (46)
34 cd06968 NR_DBD_ROR DNA-binding 63.2 4.7 0.0001 28.0 1.5 31 23-56 4-34 (95)
35 COG1734 DksA DnaK suppressor p 62.9 4.1 8.9E-05 29.7 1.2 30 25-54 81-111 (120)
36 TIGR02890 spore_yteA sporulati 62.1 5.5 0.00012 30.3 1.8 42 13-56 76-119 (159)
37 cd00202 ZnF_GATA Zinc finger D 61.2 8.1 0.00018 24.1 2.2 34 26-59 1-36 (54)
38 COG1997 RPL43A Ribosomal prote 60.8 7.1 0.00015 27.1 2.0 33 19-53 30-62 (89)
39 cd07170 NR_DBD_ERR DNA-binding 59.7 5.5 0.00012 27.9 1.3 30 24-56 4-33 (97)
40 PHA00080 DksA-like zinc finger 58.9 6.7 0.00014 26.0 1.6 33 22-55 29-63 (72)
41 cd07169 NR_DBD_GCNF_like DNA-b 57.2 7 0.00015 26.8 1.5 32 22-56 4-35 (90)
42 PF14803 Nudix_N_2: Nudix N-te 56.2 2.5 5.3E-05 24.1 -0.7 29 25-54 1-32 (34)
43 PRK10778 dksA RNA polymerase-b 56.1 8.7 0.00019 29.0 2.0 37 20-56 107-144 (151)
44 smart00782 PhnA_Zn_Ribbon PhnA 54.1 9.4 0.0002 23.3 1.5 30 23-52 6-44 (47)
45 PF07282 OrfB_Zn_ribbon: Putat 53.8 5.5 0.00012 25.4 0.5 27 23-51 27-53 (69)
46 PRK11788 tetratricopeptide rep 53.6 12 0.00025 30.6 2.6 38 11-55 341-379 (389)
47 cd07160 NR_DBD_LXR DNA-binding 53.3 8.5 0.00018 27.1 1.5 31 23-56 17-47 (101)
48 cd06966 NR_DBD_CAR DNA-binding 51.1 6 0.00013 27.4 0.4 29 25-56 1-29 (94)
49 COG2174 RPL34A Ribosomal prote 49.2 12 0.00026 26.2 1.6 34 19-52 29-79 (93)
50 cd07162 NR_DBD_PXR DNA-binding 49.2 12 0.00025 25.5 1.6 28 26-56 1-28 (87)
51 cd07158 NR_DBD_Ppar_like The D 48.5 11 0.00025 24.5 1.4 27 27-56 1-27 (73)
52 cd07165 NR_DBD_DmE78_like DNA- 48.5 12 0.00025 25.1 1.5 27 27-56 1-27 (81)
53 KOG3362|consensus 47.5 7 0.00015 29.6 0.3 35 21-56 115-150 (156)
54 cd03031 GRX_GRX_like Glutaredo 47.4 9.2 0.0002 28.6 0.9 40 9-57 84-123 (147)
55 cd07161 NR_DBD_EcR DNA-binding 46.4 13 0.00028 25.6 1.5 28 26-56 3-30 (91)
56 cd06956 NR_DBD_RXR DNA-binding 45.6 14 0.00031 24.4 1.5 28 26-56 2-29 (77)
57 cd07156 NR_DBD_VDR_like The DN 45.0 12 0.00027 24.3 1.2 27 27-56 1-27 (72)
58 cd07172 NR_DBD_GR_PR DNA-bindi 44.9 14 0.0003 24.6 1.4 29 25-56 3-31 (78)
59 cd07168 NR_DBD_DHR4_like DNA-b 44.6 16 0.00034 25.1 1.7 31 23-56 5-35 (90)
60 PF14471 DUF4428: Domain of un 44.5 12 0.00026 23.1 1.0 31 26-57 1-33 (51)
61 cd06965 NR_DBD_Ppar DNA-bindin 44.0 11 0.00025 25.4 0.9 27 27-56 2-28 (84)
62 TIGR02420 dksA RNA polymerase- 43.5 16 0.00034 25.8 1.6 30 22-51 78-108 (110)
63 PRK00423 tfb transcription ini 41.9 12 0.00026 31.1 0.9 32 22-54 9-40 (310)
64 smart00290 ZnF_UBP Ubiquitin C 41.7 15 0.00032 21.7 1.0 23 26-48 1-23 (50)
65 PF00105 zf-C4: Zinc finger, C 41.2 12 0.00027 23.9 0.7 26 25-53 1-26 (70)
66 cd07155 NR_DBD_ER_like DNA-bin 40.8 19 0.0004 23.7 1.5 27 27-56 1-27 (75)
67 cd06958 NR_DBD_COUP_TF DNA-bin 40.2 18 0.00039 23.7 1.3 27 27-56 1-27 (73)
68 cd07166 NR_DBD_REV_ERB DNA-bin 39.2 20 0.00043 24.5 1.5 30 24-56 3-32 (89)
69 cd07164 NR_DBD_PNR_like_1 DNA- 38.7 18 0.0004 23.9 1.3 27 27-56 1-27 (78)
70 cd07179 2DBD_NR_DBD2 The secon 38.0 21 0.00045 23.5 1.4 27 27-56 1-27 (74)
71 cd07163 NR_DBD_TLX DNA-binding 37.9 11 0.00023 26.0 -0.0 31 23-56 5-35 (92)
72 cd06955 NR_DBD_VDR DNA-binding 37.8 15 0.00032 26.1 0.7 30 24-56 6-35 (107)
73 cd06961 NR_DBD_TR DNA-binding 37.3 20 0.00043 24.2 1.3 27 27-56 2-28 (85)
74 smart00659 RPOLCX RNA polymera 36.9 11 0.00025 22.5 0.0 23 26-51 4-26 (44)
75 cd07157 2DBD_NR_DBD1 The first 36.6 12 0.00025 25.5 0.0 28 26-56 2-29 (86)
76 PF14376 Haem_bd: Haem-binding 36.6 18 0.0004 26.5 1.1 15 24-38 41-55 (137)
77 smart00399 ZnF_C4 c4 zinc fing 36.3 16 0.00035 23.5 0.7 27 27-56 2-28 (70)
78 TIGR00373 conserved hypothetic 34.9 17 0.00037 27.4 0.7 27 26-53 111-137 (158)
79 PF06689 zf-C4_ClpX: ClpX C4-t 34.2 23 0.00051 20.6 1.1 29 25-53 2-33 (41)
80 PF06827 zf-FPG_IleRS: Zinc fi 34.2 9.7 0.00021 20.5 -0.6 28 25-52 2-29 (30)
81 cd06963 NR_DBD_GR_like The DNA 34.1 24 0.00051 23.1 1.2 27 27-56 1-27 (73)
82 KOG3507|consensus 33.9 16 0.00036 23.5 0.4 25 24-51 20-44 (62)
83 cd06962 NR_DBD_FXR DNA-binding 33.3 15 0.00032 24.9 0.1 28 26-56 3-30 (84)
84 cd06960 NR_DBD_HNF4A DNA-bindi 33.2 17 0.00036 23.9 0.3 27 27-56 1-27 (76)
85 cd07167 NR_DBD_Lrh-1_like The 33.1 29 0.00062 24.0 1.5 27 27-56 1-27 (93)
86 cd06959 NR_DBD_EcR_like The DN 32.9 24 0.00052 23.0 1.1 27 27-56 2-28 (73)
87 COG2158 Uncharacterized protei 32.9 17 0.00038 26.1 0.4 24 36-59 52-77 (112)
88 PF13119 DUF3973: Domain of un 32.8 13 0.00028 22.1 -0.2 15 45-59 2-16 (41)
89 PTZ00255 60S ribosomal protein 32.7 37 0.0008 23.6 2.0 39 12-52 23-62 (90)
90 PF13462 Thioredoxin_4: Thiore 32.1 24 0.00052 25.1 1.1 28 31-58 8-35 (162)
91 cd06967 NR_DBD_TR2_like DNA-bi 32.0 15 0.00033 25.0 -0.0 29 25-56 4-32 (87)
92 TIGR01385 TFSII transcription 31.5 30 0.00065 28.9 1.7 30 22-51 256-293 (299)
93 cd06970 NR_DBD_PNR DNA-binding 31.3 18 0.00039 25.0 0.2 31 23-56 5-35 (92)
94 smart00834 CxxC_CXXC_SSSS Puta 31.0 14 0.0003 20.8 -0.3 27 26-52 7-34 (41)
95 PF03604 DNA_RNApol_7kD: DNA d 30.8 17 0.00038 20.3 0.1 23 26-51 2-24 (32)
96 PF00641 zf-RanBP: Zn-finger i 30.3 17 0.00037 19.5 -0.0 17 20-36 14-30 (30)
97 TIGR01384 TFS_arch transcripti 30.1 23 0.00049 24.4 0.6 28 24-51 62-97 (104)
98 PTZ00218 40S ribosomal protein 29.3 28 0.00061 22.0 0.9 30 21-52 13-42 (54)
99 PF04770 ZF-HD_dimer: ZF-HD pr 29.0 21 0.00046 23.0 0.3 30 27-57 21-52 (60)
100 PF08792 A2L_zn_ribbon: A2L zi 28.7 15 0.00032 20.7 -0.4 29 24-54 3-31 (33)
101 COG0675 Transposase and inacti 28.5 17 0.00038 28.9 -0.2 24 23-53 308-331 (364)
102 PRK00420 hypothetical protein; 28.5 49 0.0011 23.9 2.1 28 23-53 22-49 (112)
103 smart00661 RPOL9 RNA polymeras 28.2 20 0.00043 21.3 0.1 30 25-56 1-32 (52)
104 TIGR00100 hypA hydrogenase nic 28.0 18 0.0004 25.8 -0.2 30 21-54 67-96 (115)
105 PF06677 Auto_anti-p27: Sjogre 27.5 21 0.00046 21.1 0.1 25 23-50 16-40 (41)
106 PHA02942 putative transposase; 27.2 21 0.00046 30.7 0.1 26 24-52 325-350 (383)
107 PF12156 ATPase-cat_bd: Putati 27.1 52 0.0011 22.3 2.0 31 26-56 2-38 (88)
108 PRK06266 transcription initiat 27.1 27 0.00057 26.9 0.6 28 26-54 119-146 (178)
109 PRK03681 hypA hydrogenase nick 26.2 18 0.00039 25.8 -0.5 31 21-54 67-97 (114)
110 TIGR00598 rad14 DNA repair pro 25.5 18 0.00039 28.1 -0.6 28 27-54 1-29 (172)
111 PF11342 DUF3144: Protein of u 25.3 2.2E+02 0.0047 19.1 5.6 55 76-130 23-77 (78)
112 PF08274 PhnA_Zn_Ribbon: PhnA 25.0 24 0.00053 19.5 0.0 24 26-52 4-27 (30)
113 PF13746 Fer4_18: 4Fe-4S diclu 24.5 52 0.0011 21.2 1.5 22 11-32 36-57 (69)
114 PF10281 Ish1: Putative stress 24.2 1.4E+02 0.0031 16.7 3.6 21 70-102 2-22 (38)
115 PTZ00074 60S ribosomal protein 24.1 58 0.0013 24.3 1.9 32 21-52 38-86 (135)
116 PF01780 Ribosomal_L37ae: Ribo 23.9 31 0.00068 24.0 0.4 31 19-51 30-60 (90)
117 cd07154 NR_DBD_PNR_like The DN 23.8 24 0.00052 23.0 -0.2 27 27-56 1-27 (73)
118 cd06957 NR_DBD_PNR_like_2 DNA- 23.3 24 0.00052 23.7 -0.3 27 27-56 1-27 (82)
119 COG4012 Uncharacterized protei 23.2 90 0.0019 26.4 3.0 29 116-144 262-292 (342)
120 cd06964 NR_DBD_RAR DNA-binding 23.2 28 0.00061 23.5 0.1 29 25-56 5-33 (85)
121 TIGR00382 clpX endopeptidase C 22.8 46 0.00099 29.1 1.3 29 24-52 7-37 (413)
122 cd06916 NR_DBD_like DNA-bindin 22.7 26 0.00056 22.8 -0.2 27 27-56 1-27 (72)
123 PRK00432 30S ribosomal protein 22.5 41 0.00088 20.6 0.7 26 23-51 19-44 (50)
124 PRK00564 hypA hydrogenase nick 22.3 23 0.00051 25.3 -0.5 30 22-54 69-98 (117)
125 TIGR02605 CxxC_CxxC_SSSS putat 21.7 28 0.00061 20.8 -0.2 27 26-52 7-34 (52)
126 PF13248 zf-ribbon_3: zinc-rib 21.7 45 0.00098 17.4 0.7 12 22-33 14-25 (26)
127 KOG1416|consensus 21.4 1.2E+02 0.0025 27.2 3.4 45 73-118 115-166 (475)
128 KOG0457|consensus 20.8 1.5E+02 0.0032 26.3 4.0 62 21-82 10-85 (438)
129 PF13453 zf-TFIIB: Transcripti 20.8 33 0.00071 19.7 -0.0 28 26-53 1-28 (41)
130 PF11261 IRF-2BP1_2: Interfero 20.7 32 0.00069 21.6 -0.1 28 25-52 4-32 (54)
131 KOG0686|consensus 20.7 3.3E+02 0.0072 24.3 6.1 52 73-134 283-334 (466)
No 1
>KOG0706|consensus
Probab=100.00 E-value=4.2e-46 Score=315.54 Aligned_cols=136 Identities=66% Similarity=1.148 Sum_probs=132.0
Q ss_pred CCCChhHHHHHHHHHhcCCCCCCccCCCCCCCCceeeccchhcchhhhhhhhcCCCCCcceeeccCCCCCCHHHHHHHHh
Q psy7550 4 EGPNKNDIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQL 83 (144)
Q Consensus 4 ~~~~~~~~~~~~~~L~~~~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~lg~~iS~VkS~~ld~~w~~~~l~~m~~ 83 (144)
..+.+.+.+.+|+.|+..++||.|||||+++|+|+||+||||||++||++||.||+|||||||++||+ |+..||+.|+.
T Consensus 3 ~~~~k~d~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDs-Ws~~qLR~M~~ 81 (454)
T KOG0706|consen 3 ATPNKQDIQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDS-WSWEQLRRMQV 81 (454)
T ss_pred CccchhhHHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeeccccc-CCHHHHhHhhh
Confidence 35689999999999999999999999999999999999999999999999999999999999999999 99999999999
Q ss_pred hChHHHHHHHhhcCCCCcchHHHhhHHHHHHHHHHHHHHHHHHHHHcCCeeeecCCC
Q psy7550 84 GGNANAVSFFNQHNCTSKDAQQKYNSRAAQLYREKLQHAAVQAMKIHGTKLFLDAMH 140 (144)
Q Consensus 84 gGN~~~~~~~e~~~~~~~~~~~ky~~~~~~~yr~kl~~~~~~~~~~~~~~~~~~~~~ 140 (144)
|||.+|+.||.+|+....+.+.||++++++.||++|+.++.++|+++++.+++|..+
T Consensus 82 GGN~nA~~FFkqhg~~t~d~~aKY~SraA~~Yr~kl~~lv~kam~~~~~~l~l~~~~ 138 (454)
T KOG0706|consen 82 GGNANARVFFKQHGCVTLDANAKYNSRAAKLYREKLKKLVQKAMAEHGTSLLLDSAV 138 (454)
T ss_pred cCchhHHHHHHHcCCcchhhhhhhccHHHHHHHHHHHHHHHHHHHhcCccccccCCC
Confidence 999999999999999999999999999999999999999999999999999998744
No 2
>KOG0704|consensus
Probab=100.00 E-value=4.7e-42 Score=284.02 Aligned_cols=113 Identities=45% Similarity=0.897 Sum_probs=105.6
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceeeccchhcchhhhhhhhcCCCCCcceeeccCCCCCCHHHHHHHHhhChHHHH
Q psy7550 11 IEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAV 90 (144)
Q Consensus 11 ~~~~~~~L~~~~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~lg~~iS~VkS~~ld~~w~~~~l~~m~~gGN~~~~ 90 (144)
..+.|+.|+...+|+.||||+++||+|||++||||||++|||+||+||+|||+||||+||+ |++.||+.|+.|||.+++
T Consensus 6 trr~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~-wkeiel~kMeaGGN~~~~ 84 (386)
T KOG0704|consen 6 TRRVLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDK-WKEIELKKMEAGGNERFR 84 (386)
T ss_pred HHHHHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeeccc-ccHHHHHHHHhccchhHH
Confidence 4566677766679999999999999999999999999999999999999999999999999 999999999999999999
Q ss_pred HHHhhcCCC--CcchHHHhhHHHHHHHHHHHHHHHH
Q psy7550 91 SFFNQHNCT--SKDAQQKYNSRAAQLYREKLQHAAV 124 (144)
Q Consensus 91 ~~~e~~~~~--~~~~~~ky~~~~~~~yr~kl~~~~~ 124 (144)
+||+.+++. .++|++||++++|..||+||..+|+
T Consensus 85 eFL~s~~~~~e~~~i~eKYns~aAa~yRdki~~lae 120 (386)
T KOG0704|consen 85 EFLSSQGIYKETWPIREKYNSRAAALYRDKIAALAE 120 (386)
T ss_pred HHHhhCccccccccHHHhhccHHHHHHHHHHHHHhc
Confidence 999999975 4589999999999999999999875
No 3
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=100.00 E-value=7.3e-40 Score=272.40 Aligned_cols=122 Identities=53% Similarity=0.915 Sum_probs=115.0
Q ss_pred HHHHHHHHHhcCCCCCCccCCCCCCCCceeeccchhcchhhhhhhhcCCCCCcceeeccCCCCCCHHHHHHHHhhChHHH
Q psy7550 10 DIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANA 89 (144)
Q Consensus 10 ~~~~~~~~L~~~~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~lg~~iS~VkS~~ld~~w~~~~l~~m~~gGN~~~ 89 (144)
+..++|+.|+..|+|+.|||||+++|+|+|++||||||+.|+|+||.||+|||+|||++||+ |++++|+.|+.|||.++
T Consensus 8 d~~~vfrkL~~kPgNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~-Ws~eqL~~Mk~GGN~rA 86 (395)
T PLN03114 8 DKISVFKKLKAKSDNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDS-WSSEQLKMMIYGGNNRA 86 (395)
T ss_pred cHHHHHHHHHhCcCCCcCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCC-CCHHHHHHHHHhcCHHH
Confidence 45678999999999999999999999999999999999999999999999999999999999 99999999999999999
Q ss_pred HHHHhhcCCCC-cchHHHhhHHHHHHHHHHHHHHHHHHHHHcCC
Q psy7550 90 VSFFNQHNCTS-KDAQQKYNSRAAQLYREKLQHAAVQAMKIHGT 132 (144)
Q Consensus 90 ~~~~e~~~~~~-~~~~~ky~~~~~~~yr~kl~~~~~~~~~~~~~ 132 (144)
+.||+.|+... .+++.||+++++++||++|.++|+++......
T Consensus 87 ~~fF~qhG~~~~~~~~~KY~S~aA~~Yre~L~keVa~~~a~~~~ 130 (395)
T PLN03114 87 QVFFKQYGWSDGGKTEAKYTSRAADLYKQILAKEVAKSKAEEEL 130 (395)
T ss_pred HHHHHHcCCCCCCCcccccCCHHHHHHHHHHHHHHHHhhhcccc
Confidence 99999999864 57899999999999999999999998875544
No 4
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=100.00 E-value=1.1e-39 Score=270.65 Aligned_cols=119 Identities=43% Similarity=0.740 Sum_probs=110.8
Q ss_pred hhHHHHHHHHHhcCCCCCCccCCCCCCCCceeeccchhcchhhhhhhhcCCCCCcceeeccCCCCCCHHHHHHHHhhChH
Q psy7550 8 KNDIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNA 87 (144)
Q Consensus 8 ~~~~~~~~~~L~~~~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~lg~~iS~VkS~~ld~~w~~~~l~~m~~gGN~ 87 (144)
+...++++..|++.++|+.|||||+++|+|+|+|||||||++||||||+||+|||+||||+||+ |+++||+.|..|||.
T Consensus 4 ~~~~~~~l~~l~~~~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~-wt~~~l~~m~~gGN~ 82 (319)
T COG5347 4 KSEDRKLLKLLKSDSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDN-WTEEELRRMEVGGNS 82 (319)
T ss_pred chHHHHHHHHHhhccccCccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeeccc-CCHHHHHHHHHhcch
Confidence 4456788999999999999999999999999999999999999999999999999999999999 999999999999999
Q ss_pred HHHHHHhhcCCCC--cchHHHhhHHHHHHHHHHHHHHHHHHH
Q psy7550 88 NAVSFFNQHNCTS--KDAQQKYNSRAAQLYREKLQHAAVQAM 127 (144)
Q Consensus 88 ~~~~~~e~~~~~~--~~~~~ky~~~~~~~yr~kl~~~~~~~~ 127 (144)
++|.||++++... .+++.+|.+..++.|++++..++.-.+
T Consensus 83 ~a~~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~ 124 (319)
T COG5347 83 NANRFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFID 124 (319)
T ss_pred hhhhHhccCCCcccccccccccCHHHHHHHHHHHHHhhhccc
Confidence 9999999999984 789999999999999988887765554
No 5
>KOG0703|consensus
Probab=100.00 E-value=6.7e-39 Score=261.06 Aligned_cols=114 Identities=36% Similarity=0.623 Sum_probs=99.4
Q ss_pred ChhHHHHHHHHHhcCCCCCCccCCCCCCCCceeeccchhcchhhhhhhhcCCCCCcceeeccCCCCCCHHHHHHHHhhCh
Q psy7550 7 NKNDIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGN 86 (144)
Q Consensus 7 ~~~~~~~~~~~L~~~~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~lg~~iS~VkS~~ld~~w~~~~l~~m~~gGN 86 (144)
..+..+++|+.|++.|+|+.|||||++.|+|||+|+|||||+.|+||||+||+|||+||||+||. |++|||+.|...||
T Consensus 8 ~~~~~~~~l~~Ll~~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~-W~~eqv~~m~~~GN 86 (287)
T KOG0703|consen 8 SNERNKRRLRELLREPDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDE-WTDEQVDFMISMGN 86 (287)
T ss_pred ccchHHHHHHHHHcCcccCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccc-cCHHHHHHHHHHcc
Confidence 45677899999999999999999999999999999999999999999999999999999999999 99999999999999
Q ss_pred HHHHHHHhhcCCCCcchHHHhhHHHHHHHHHHHHHH
Q psy7550 87 ANAVSFFNQHNCTSKDAQQKYNSRAAQLYREKLQHA 122 (144)
Q Consensus 87 ~~~~~~~e~~~~~~~~~~~ky~~~~~~~yr~kl~~~ 122 (144)
.++|+|||+. .|....+..-......|+|.||+..
T Consensus 87 ~~an~~~ea~-~p~~~~~p~~d~~~e~FIR~KYE~k 121 (287)
T KOG0703|consen 87 AKANSYYEAK-LPDPFRRPGPDDLVEQFIRDKYERK 121 (287)
T ss_pred hhhhhhcccc-CCccccCCChHHHHHHHHHHHHhhh
Confidence 9999999987 3322222222336677888888864
No 6
>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=100.00 E-value=1.3e-38 Score=230.32 Aligned_cols=105 Identities=39% Similarity=0.781 Sum_probs=82.1
Q ss_pred HHHHHHhcCCCCCCccCCCCCCCCceeeccchhcchhhhhhhhcCCCCCcceeeccCCCCCCHHHHHHHHhhChHHHHHH
Q psy7550 13 VIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAVSF 92 (144)
Q Consensus 13 ~~~~~L~~~~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~lg~~iS~VkS~~ld~~w~~~~l~~m~~gGN~~~~~~ 92 (144)
++|+.|++.|+|+.|||||+++|+|+|++||||||+.|+|+||.||+|+|+||||+||+ |++++|+.|+.+||..+|++
T Consensus 2 ~~l~~l~~~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~VkSi~~d~-w~~~ev~~~~~~GN~~~n~~ 80 (116)
T PF01412_consen 2 KILRELLKKPGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRVKSITMDN-WSPEEVQRMREGGNKRANSI 80 (116)
T ss_dssp HHHHHHHCSTTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--EEETTTS----HHHHHHHHHSHHHHHHHH
T ss_pred HHHHHHHcCcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhccccccCC-CCHHHHHHHHHHChHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999 99999999999999999999
Q ss_pred HhhcCCC-----CcchHHHhhHHHHHHHHHH
Q psy7550 93 FNQHNCT-----SKDAQQKYNSRAAQLYREK 118 (144)
Q Consensus 93 ~e~~~~~-----~~~~~~ky~~~~~~~yr~k 118 (144)
|+++..+ ......+|+...+..|+++
T Consensus 81 ~e~~~~~~~~~~~~~~~~~~~~fI~~KY~~k 111 (116)
T PF01412_consen 81 WEANSPPPKKPPPSSDQEKREQFIRAKYVEK 111 (116)
T ss_dssp HTTTSTTTTTHCTTSHHHHHHHHHHHHHTTH
T ss_pred HHcCCCCCCCCCCCCcHHHHHHHHHHHHHhh
Confidence 9998322 1234455666555555544
No 7
>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=100.00 E-value=1.1e-36 Score=219.20 Aligned_cols=97 Identities=58% Similarity=0.955 Sum_probs=86.8
Q ss_pred CCCCCccCCCCCCCCceeeccchhcchhhhhhhhcCCCCCcceeeccCCCCCCHHHHHHHHhhChHHHHHHHhhcCCCCc
Q psy7550 22 PTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAVSFFNQHNCTSK 101 (144)
Q Consensus 22 ~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~lg~~iS~VkS~~ld~~w~~~~l~~m~~gGN~~~~~~~e~~~~~~~ 101 (144)
|+|+.|||||+++|+|+|++||||||+.|+|+||.||+|||+||||+||+ |++++|+.|+.+||.++|+||+++..+..
T Consensus 1 ~~N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~VkSl~md~-w~~~~i~~~~~~GN~~~n~~~e~~~~~~~ 79 (112)
T smart00105 1 PGNKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLDT-WTEEELRLLQKGGNENANSIWESNLDDFS 79 (112)
T ss_pred CCCCcccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCeeeecccCC-CCHHHHHHHHHhhhHHHHHHHHhhCCccc
Confidence 68999999999999999999999999999999999999999999999998 99999999999999999999999876531
Q ss_pred ------chHHHhhHHHHHHHHHHH
Q psy7550 102 ------DAQQKYNSRAAQLYREKL 119 (144)
Q Consensus 102 ------~~~~ky~~~~~~~yr~kl 119 (144)
+...+|++.++.+|+++.
T Consensus 80 ~~~~~~~~~~~~~~fI~~KY~~k~ 103 (112)
T smart00105 80 LKPPDSDDQQKYESFIAAKYEEKL 103 (112)
T ss_pred cCCCCCchHHHHHHHHHHHHHhhh
Confidence 245677777777776653
No 8
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=99.97 E-value=1.5e-30 Score=226.46 Aligned_cols=119 Identities=22% Similarity=0.485 Sum_probs=95.7
Q ss_pred CCCCCCChhHHHHHHHHHhcCCCCCCccCCCCCCCCceeeccchhcchhhhhhhhcCCCCCcceeeccCCCCCCHHHHHH
Q psy7550 1 MSGEGPNKNDIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQ 80 (144)
Q Consensus 1 m~~~~~~~~~~~~~~~~L~~~~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~lg~~iS~VkS~~ld~~w~~~~l~~ 80 (144)
|++. +.+++.+++|++|++.|+|+.|+|||+.+|+|+|+|+|||||+.|+||||.|| ++||||+||+ |+.+||+.
T Consensus 1 M~SK-R~qERnekILreLlklPgNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsLG---hRVKSLSLDk-WT~EEVe~ 75 (648)
T PLN03119 1 MGSK-REEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREFT---HRVKSVSMSK-FTSKEVEV 75 (648)
T ss_pred Ccch-HHHHHHHHHHHHHhhCcCCCccccCCCCCCCceeeccceEEeccchhhhccCC---ceeeccccCC-CCHHHHHH
Confidence 4443 35677789999999999999999999999999999999999999999999998 4899999999 99999999
Q ss_pred HHhhChHHHHHHHhhcCCCCcc--hHHHhhHHHHHHHHHHHHHHHH
Q psy7550 81 MQLGGNANAVSFFNQHNCTSKD--AQQKYNSRAAQLYREKLQHAAV 124 (144)
Q Consensus 81 m~~gGN~~~~~~~e~~~~~~~~--~~~ky~~~~~~~yr~kl~~~~~ 124 (144)
|+.+||.++|+||+++...... ....-..+.+.|+|.||..+-+
T Consensus 76 Mk~gGN~~AN~iyeanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF 121 (648)
T PLN03119 76 LQNGGNQRAREIYLKNWDHQRQRLPENSNAERVREFIKNVYVQKKY 121 (648)
T ss_pred HHHhchHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhc
Confidence 9999999999999987643210 0000122334566666665543
No 9
>PLN03131 hypothetical protein; Provisional
Probab=99.96 E-value=4.4e-30 Score=225.09 Aligned_cols=89 Identities=27% Similarity=0.577 Sum_probs=83.4
Q ss_pred CChhHHHHHHHHHhcCCCCCCccCCCCCCCCceeeccchhcchhhhhhhhcCCCCCcceeeccCCCCCCHHHHHHHHhhC
Q psy7550 6 PNKNDIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGG 85 (144)
Q Consensus 6 ~~~~~~~~~~~~L~~~~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~lg~~iS~VkS~~ld~~w~~~~l~~m~~gG 85 (144)
..+++.+++|++|++.|+|+.|+|||+++|+|+|++||||||+.|+||||.|| ++||||+||+ |+.+||+.|+.+|
T Consensus 5 kqqErnekiLreLlk~PgNk~CADCga~~P~WASiNlGIFICi~CSGIHRsLg---hRVKSVTLD~-WtdeEV~~Mk~gG 80 (705)
T PLN03131 5 KEEERNEKIIRGLMKLPPNRRCINCNSLGPQFVCTNFWTFICMTCSGIHREFT---HRVKSVSMSK-FTSQDVEALQNGG 80 (705)
T ss_pred HHHHHHHHHHHHHhhCcCCCccccCCCCCCCeeEeccceEEchhchhhhcccC---cccccccCCC-CCHHHHHHHHHhc
Confidence 35667789999999999999999999999999999999999999999999997 3899999999 9999999999999
Q ss_pred hHHHHHHHhhcCC
Q psy7550 86 NANAVSFFNQHNC 98 (144)
Q Consensus 86 N~~~~~~~e~~~~ 98 (144)
|.++|+||+++..
T Consensus 81 N~~AN~iyeanwd 93 (705)
T PLN03131 81 NQRAREIYLKDWD 93 (705)
T ss_pred cHHHHHHHHhhcc
Confidence 9999999997653
No 10
>KOG0705|consensus
Probab=99.91 E-value=4.6e-25 Score=192.52 Aligned_cols=83 Identities=42% Similarity=0.823 Sum_probs=79.7
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCCCceeeccchhcchhhhhhhhcCCCCCcceeeccCCCCCCHHHHHHHHhhChHHHHH
Q psy7550 12 EVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAVS 91 (144)
Q Consensus 12 ~~~~~~L~~~~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~lg~~iS~VkS~~ld~~w~~~~l~~m~~gGN~~~~~ 91 (144)
.-.++.++..+||..|+||+.++|.|||+|+|+.+|++|+||||.||+|+|+|+|+.||. |+.|-+..|..+||+.||+
T Consensus 501 a~a~qairn~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDd-WPvEl~~Vm~aiGN~~AN~ 579 (749)
T KOG0705|consen 501 AMALQAIRNMRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDD-WPVELLKVMSAIGNDLANS 579 (749)
T ss_pred HHHHHHHhcCcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhcccccc-CcHHHHHHHHHhhhhHHHH
Confidence 346788999999999999999999999999999999999999999999999999999999 9999999999999999999
Q ss_pred HHhh
Q psy7550 92 FFNQ 95 (144)
Q Consensus 92 ~~e~ 95 (144)
+||.
T Consensus 580 vWE~ 583 (749)
T KOG0705|consen 580 VWEG 583 (749)
T ss_pred Hhhh
Confidence 9984
No 11
>KOG0521|consensus
Probab=99.83 E-value=1.2e-21 Score=178.47 Aligned_cols=83 Identities=40% Similarity=0.794 Sum_probs=79.3
Q ss_pred HHHHHhcCCCCCCccCCCCCCCCceeeccchhcchhhhhhhhcCCCCCcceeeccCCCCCCHHHHHHHHhhChHHHHHHH
Q psy7550 14 IFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAVSFF 93 (144)
Q Consensus 14 ~~~~L~~~~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~lg~~iS~VkS~~ld~~w~~~~l~~m~~gGN~~~~~~~ 93 (144)
.+..+++.|+|..|+|||++.|+|+|+|+||.+|++|+|+||+||+|+|+|+|++||. |.++.+..|+..||...|.+|
T Consensus 416 ~~~~vq~~pgN~~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~-~~~~l~~l~~~lgn~~~N~i~ 494 (785)
T KOG0521|consen 416 VIEEVQSVPGNAQCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDV-WEPELLLLFKNLGNKYVNEIY 494 (785)
T ss_pred hhhhhhcCCchhhhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhc-cCcHHHHHHHHhCcchhhhhh
Confidence 4678899999999999999999999999999999999999999999999999999999 999999999999999999999
Q ss_pred hhcC
Q psy7550 94 NQHN 97 (144)
Q Consensus 94 e~~~ 97 (144)
++.-
T Consensus 495 e~~l 498 (785)
T KOG0521|consen 495 EALL 498 (785)
T ss_pred hccc
Confidence 8643
No 12
>KOG0818|consensus
Probab=99.79 E-value=1.7e-20 Score=162.11 Aligned_cols=107 Identities=30% Similarity=0.566 Sum_probs=94.0
Q ss_pred hcCCCCCCccCCCCCCCCceeeccchhcchhhhhhhhcCCCCCcceeeccCCCCCCHHHHHHHHhhChHHHHHHHhhcCC
Q psy7550 19 RNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAVSFFNQHNC 98 (144)
Q Consensus 19 ~~~~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~lg~~iS~VkS~~ld~~w~~~~l~~m~~gGN~~~~~~~e~~~~ 98 (144)
++.+..+.|+|||+++|.||||+-|+|||.+|..+||+||.|||.||++.-.. |.+.-|++.....|..+|.+||.+-.
T Consensus 3 k~~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~-W~pt~l~~V~tLn~~gaNsIWEh~Ll 81 (669)
T KOG0818|consen 3 KRLLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTP-WPPTLLQMVETLNNNGANSIWEHSLL 81 (669)
T ss_pred ccchhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCC-CCHHHHHHHHHHHhcCcchhhhhhcc
Confidence 34567789999999999999999999999999999999999999999999988 99999999999999999999997654
Q ss_pred CC---------cchHHHhhHHHHHHHHHHHHHHHHHH
Q psy7550 99 TS---------KDAQQKYNSRAAQLYREKLQHAAVQA 126 (144)
Q Consensus 99 ~~---------~~~~~ky~~~~~~~yr~kl~~~~~~~ 126 (144)
+. ..++.+..-..++|+|.||..+++.-
T Consensus 82 d~st~~sg~rk~~pqD~~Hp~K~eFIkaKy~~LtFv~ 118 (669)
T KOG0818|consen 82 DPATIMSGRRKANPQDKVHPNKAEFIRAKYQMLAFVH 118 (669)
T ss_pred CchhhhcccCCCCCcCCCCccHHHHHHHHHHheeeec
Confidence 42 23556666678899999999998765
No 13
>KOG1117|consensus
Probab=99.70 E-value=5e-18 Score=153.57 Aligned_cols=86 Identities=30% Similarity=0.552 Sum_probs=79.5
Q ss_pred HHHHHHhcCCCCCCccCCCCCCCCceeeccchhcchhhhhhhhcCCCCCcceeeccCCC-CCCHHHHHHHHhhChHHHHH
Q psy7550 13 VIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDT-NWTWVQLRQMQLGGNANAVS 91 (144)
Q Consensus 13 ~~~~~L~~~~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~lg~~iS~VkS~~ld~-~w~~~~l~~m~~gGN~~~~~ 91 (144)
....++....+|+.|+|||++.|.|||+|+++.||-.|+|-||+||..+|+|+|++||. .|+.+-++.+...||.++|.
T Consensus 287 evaeriW~ne~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~ 366 (1186)
T KOG1117|consen 287 EVAERIWLNEENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANR 366 (1186)
T ss_pred HHHHHHHhccccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCccccc
Confidence 44567788999999999999999999999999999999999999999999999999997 49999999999999999999
Q ss_pred HHhhcCC
Q psy7550 92 FFNQHNC 98 (144)
Q Consensus 92 ~~e~~~~ 98 (144)
||..+-.
T Consensus 367 Fwa~nl~ 373 (1186)
T KOG1117|consen 367 FWAGNLP 373 (1186)
T ss_pred ccccCCC
Confidence 9986543
No 14
>KOG0702|consensus
Probab=99.33 E-value=1.3e-12 Score=113.17 Aligned_cols=93 Identities=26% Similarity=0.437 Sum_probs=82.3
Q ss_pred CCCCCCChhHH-HHHHHHHhcCCCCCCccCCCCCCC-CceeeccchhcchhhhhhhhcCCCCCcceeeccCCCCCCHHHH
Q psy7550 1 MSGEGPNKNDI-EVIFKKLRNIPTNKECFDCNAKNP-TWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQL 78 (144)
Q Consensus 1 m~~~~~~~~~~-~~~~~~L~~~~~N~~C~DCg~~~p-~w~s~~~GiflC~~CsgiHR~lg~~iS~VkS~~ld~~w~~~~l 78 (144)
|++-..+.|+. +++++.|++.|+|++|++|....+ +|+.+.-|-|+|..|+|.-|.| ..-.+||||.|.+ ++..|+
T Consensus 1 ~a~~~ke~E~~~ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l-~~ahRvksiSmtt-ft~qev 78 (524)
T KOG0702|consen 1 YAGYKKEDEYDYEKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGL-NPAHRVKSISMTT-FTDQEV 78 (524)
T ss_pred CCcccccchhHHHHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccC-CCccccceeeeee-ccccch
Confidence 44444544444 899999999999999999999988 9999999999999999999998 4456899999998 999999
Q ss_pred HHHHhhChHHHHHHHhh
Q psy7550 79 RQMQLGGNANAVSFFNQ 95 (144)
Q Consensus 79 ~~m~~gGN~~~~~~~e~ 95 (144)
..++.+||+...++|-+
T Consensus 79 s~lQshgNq~~k~i~fk 95 (524)
T KOG0702|consen 79 SFLQSHGNQVCKEIWFK 95 (524)
T ss_pred HHHhhcchhhhhhhhhc
Confidence 99999999999999964
No 15
>KOG0521|consensus
Probab=94.64 E-value=0.0084 Score=55.87 Aligned_cols=70 Identities=19% Similarity=0.213 Sum_probs=54.9
Q ss_pred CCCCCCccCCCCC-CCCceeeccchhcchhhhhhhhcCCCCCcceeeccCCCCCCHHHHHHHHhhChHHHHHHH
Q psy7550 21 IPTNKECFDCNAK-NPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAVSFF 93 (144)
Q Consensus 21 ~~~N~~C~DCg~~-~p~w~s~~~GiflC~~CsgiHR~lg~~iS~VkS~~ld~~w~~~~l~~m~~gGN~~~~~~~ 93 (144)
...+..|++|++. ...|+++++.+-+|..|+++|+..+.+.+...++.+++ ..+ +.....-|+...+.-+
T Consensus 627 ~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~-ga~--vn~~d~~g~~plh~~~ 697 (785)
T KOG0521|consen 627 ASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQN-GAD--VNALDSKGRTPLHHAT 697 (785)
T ss_pred hccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhc-CCc--chhhhccCCCcchhhh
Confidence 3457889999984 68999999999999999999999999999999999987 655 4434434444444433
No 16
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=88.25 E-value=0.34 Score=38.31 Aligned_cols=32 Identities=22% Similarity=0.383 Sum_probs=27.5
Q ss_pred cCCCCCCccCCCCCCC-Cceeeccchhcchhhh
Q psy7550 20 NIPTNKECFDCNAKNP-TWSSVTYGVFICIDCS 51 (144)
Q Consensus 20 ~~~~N~~C~DCg~~~p-~w~s~~~GiflC~~Cs 51 (144)
-.|.-..|+-||.+.. .|.+...|.++|..|.
T Consensus 145 ~~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 145 YGLDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred CccchhhHhcCCCCCCceEEecccCCccccccc
Confidence 3567789999999755 7889999999999997
No 17
>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=83.36 E-value=0.82 Score=35.99 Aligned_cols=36 Identities=28% Similarity=0.544 Sum_probs=28.7
Q ss_pred HhcCCCCCCccCCCCCCC-Cceeeccchhcchhhhhh
Q psy7550 18 LRNIPTNKECFDCNAKNP-TWSSVTYGVFICIDCSAV 53 (144)
Q Consensus 18 L~~~~~N~~C~DCg~~~p-~w~s~~~GiflC~~Csgi 53 (144)
+--.|.-..|+.||..++ .+.|...|.++|..|+..
T Consensus 141 ~G~~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 141 LGYALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred cCCCcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 333577789999998544 678999999999999764
No 18
>PRK12495 hypothetical protein; Provisional
Probab=82.46 E-value=0.97 Score=36.36 Aligned_cols=28 Identities=25% Similarity=0.418 Sum_probs=23.9
Q ss_pred CCCCCccCCCCCCCCceeeccchhcchhhhhh
Q psy7550 22 PTNKECFDCNAKNPTWSSVTYGVFICIDCSAV 53 (144)
Q Consensus 22 ~~N~~C~DCg~~~p~w~s~~~GiflC~~Csgi 53 (144)
..+..|-+||.+-|.. -|+.+|..|..+
T Consensus 40 msa~hC~~CG~PIpa~----pG~~~Cp~CQ~~ 67 (226)
T PRK12495 40 MTNAHCDECGDPIFRH----DGQEFCPTCQQP 67 (226)
T ss_pred cchhhcccccCcccCC----CCeeECCCCCCc
Confidence 5799999999999932 699999999865
No 19
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=81.52 E-value=0.96 Score=26.10 Aligned_cols=34 Identities=15% Similarity=0.400 Sum_probs=28.6
Q ss_pred CCCCccCCCCCCCCceeeccchhcchhhhhh-hhc
Q psy7550 23 TNKECFDCNAKNPTWSSVTYGVFICIDCSAV-HRG 56 (144)
Q Consensus 23 ~N~~C~DCg~~~p~w~s~~~GiflC~~Csgi-HR~ 56 (144)
.+..|..|+.....+-..+-+++||..|... |+.
T Consensus 2 ~~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~ 36 (42)
T PF00643_consen 2 QEPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG 36 (42)
T ss_dssp SSSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT
T ss_pred cCccCccCCccceEEEecCCCCccCccCCCCCCCC
Confidence 3578999998878899999999999999987 876
No 20
>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=80.16 E-value=0.99 Score=25.82 Aligned_cols=32 Identities=25% Similarity=0.717 Sum_probs=23.1
Q ss_pred ccCCCCC-CCCceeeccchh-cchhhhhhhhcCC
Q psy7550 27 CFDCNAK-NPTWSSVTYGVF-ICIDCSAVHRGLG 58 (144)
Q Consensus 27 C~DCg~~-~p~w~s~~~Gif-lC~~CsgiHR~lg 58 (144)
|..|+.. .|.|-....|-. ||..|.-.+|..|
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~ 34 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYG 34 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhC
Confidence 7899996 699998888887 9999987776644
No 21
>TIGR02419 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA.
Probab=79.40 E-value=1.1 Score=28.90 Aligned_cols=34 Identities=29% Similarity=0.608 Sum_probs=24.0
Q ss_pred cCCCCCCccCCCCCCC--Cceeeccchhcchhhhhhh
Q psy7550 20 NIPTNKECFDCNAKNP--TWSSVTYGVFICIDCSAVH 54 (144)
Q Consensus 20 ~~~~N~~C~DCg~~~p--~w~s~~~GiflC~~CsgiH 54 (144)
..++...|.|||.+=| .+.- .-|+..|+.|...+
T Consensus 27 ~~~s~g~C~~Cg~~Ip~~Rl~a-~p~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 27 IGPSLRECEDCGEPIPEARREA-LPGVTRCVSCQEIL 62 (63)
T ss_pred cCCCCCeeccCCCcChHHHHhh-cCCcCCcHHHHhhc
Confidence 3466789999999754 3332 33788999997653
No 22
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=78.16 E-value=0.7 Score=26.53 Aligned_cols=27 Identities=15% Similarity=0.541 Sum_probs=16.5
Q ss_pred CCccCCCCC-CCCceeeccchhcchhhh
Q psy7550 25 KECFDCNAK-NPTWSSVTYGVFICIDCS 51 (144)
Q Consensus 25 ~~C~DCg~~-~p~w~s~~~GiflC~~Cs 51 (144)
..|.+||.+ .-+|..-+|+.-||..|.
T Consensus 4 ~~C~eC~~~f~dSyL~~~F~~~VCD~CR 31 (34)
T PF01286_consen 4 PKCDECGKPFMDSYLLNNFDLPVCDKCR 31 (34)
T ss_dssp EE-TTT--EES-SSCCCCTS-S--TTT-
T ss_pred chHhHhCCHHHHHHHHHhCCcccccccc
Confidence 479999997 568999999999999994
No 23
>PRK11019 hypothetical protein; Provisional
Probab=78.16 E-value=1.4 Score=30.58 Aligned_cols=43 Identities=21% Similarity=0.442 Sum_probs=28.6
Q ss_pred HHhcCCCCCCccCCCCCCC--CceeeccchhcchhhhhhhhcCCCC
Q psy7550 17 KLRNIPTNKECFDCNAKNP--TWSSVTYGVFICIDCSAVHRGLGVH 60 (144)
Q Consensus 17 ~L~~~~~N~~C~DCg~~~p--~w~s~~~GiflC~~CsgiHR~lg~~ 60 (144)
.+...++-..|.|||.+=| .+.-++ ++-.|+.|...+-..+.+
T Consensus 29 r~~~g~syg~C~~CG~~Ip~~Rl~A~P-~a~~Cv~Cq~~~E~~~k~ 73 (88)
T PRK11019 29 ELPRGESLTECEECGEPIPEARRKAIP-GVRLCVACQQEKDLQQAA 73 (88)
T ss_pred hcccCCcCCeeCcCCCcCcHHHHhhcC-CccccHHHHHHHHHHHhH
Confidence 3333334679999999754 444444 788999999876544443
No 24
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=77.85 E-value=2.1 Score=26.49 Aligned_cols=38 Identities=21% Similarity=0.577 Sum_probs=30.7
Q ss_pred CCCCccCCCCC-CCCceeeccch-hcchhhhhhhhcCCCC
Q psy7550 23 TNKECFDCNAK-NPTWSSVTYGV-FICIDCSAVHRGLGVH 60 (144)
Q Consensus 23 ~N~~C~DCg~~-~p~w~s~~~Gi-flC~~CsgiHR~lg~~ 60 (144)
....|..|+.. .|.|=.-..|- +||..|.-..+..|..
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 46789999996 58898888886 9999998877776554
No 25
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=75.04 E-value=1.8 Score=34.98 Aligned_cols=31 Identities=29% Similarity=0.676 Sum_probs=27.2
Q ss_pred CCCCCCccCCCCCC-CCceeeccchhcchhhh
Q psy7550 21 IPTNKECFDCNAKN-PTWSSVTYGVFICIDCS 51 (144)
Q Consensus 21 ~~~N~~C~DCg~~~-p~w~s~~~GiflC~~Cs 51 (144)
.|.=..|+.||.+. |...|+-.|-++|.+|+
T Consensus 151 ~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 151 GPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred ccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 46677999999985 47999999999999998
No 26
>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=74.90 E-value=0.93 Score=26.73 Aligned_cols=27 Identities=26% Similarity=0.667 Sum_probs=20.0
Q ss_pred CccCCCCCCCCceeeccchhcchhhhhh
Q psy7550 26 ECFDCNAKNPTWSSVTYGVFICIDCSAV 53 (144)
Q Consensus 26 ~C~DCg~~~p~w~s~~~GiflC~~Csgi 53 (144)
+|..||+.. .-..-..|-++|..|..+
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-BB
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCCCE
Confidence 588999976 444556899999999543
No 27
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=72.80 E-value=1.8 Score=28.81 Aligned_cols=33 Identities=24% Similarity=0.541 Sum_probs=22.7
Q ss_pred CCCccCCCCCCCC-ceeeccchhcchhhhhhhhc
Q psy7550 24 NKECFDCNAKNPT-WSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 24 N~~C~DCg~~~p~-w~s~~~GiflC~~CsgiHR~ 56 (144)
...|.|||.+=|. =.-.--|+..|+.|...+-.
T Consensus 34 ~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~E~ 67 (73)
T PRK13715 34 VYLCEACGNPIPEARRKIFPGVTLCVECQAYQER 67 (73)
T ss_pred cccHhhcCCcCCHHHHhcCCCcCCCHHHHHHHHH
Confidence 4589999997542 22223488899999876543
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=68.81 E-value=2.8 Score=24.11 Aligned_cols=27 Identities=26% Similarity=0.736 Sum_probs=22.4
Q ss_pred CCCCCccCCCCCCCCceeeccchhcchhhh
Q psy7550 22 PTNKECFDCNAKNPTWSSVTYGVFICIDCS 51 (144)
Q Consensus 22 ~~N~~C~DCg~~~p~w~s~~~GiflC~~Cs 51 (144)
..|..|..|++. |....=|-+.|..|-
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCc
Confidence 456679999987 888888999999984
No 29
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=68.65 E-value=0.83 Score=25.98 Aligned_cols=29 Identities=24% Similarity=0.607 Sum_probs=17.1
Q ss_pred CccCCCCCCC-Cceeeccchhcchhhhhhh
Q psy7550 26 ECFDCNAKNP-TWSSVTYGVFICIDCSAVH 54 (144)
Q Consensus 26 ~C~DCg~~~p-~w~s~~~GiflC~~CsgiH 54 (144)
.|.+||.+=| .-.-+--+..+|..|+..|
T Consensus 5 ~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 5 ICEDCGEPIPEERLVAVPGATLCVECQERR 34 (36)
T ss_dssp B-TTTSSBEEHHHHHHCTTECS-HHHHHHH
T ss_pred CccccCChHHHHHHHhCCCcEECHHHhCcc
Confidence 4999998632 1222234778999998765
No 30
>cd07171 NR_DBD_ER DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well-conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserv
Probab=67.04 E-value=3.8 Score=27.67 Aligned_cols=31 Identities=29% Similarity=0.630 Sum_probs=25.2
Q ss_pred CCCCccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 23 TNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 23 ~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
.|..|.-||.+. ....||++.|..|.+..|-
T Consensus 2 ~~~~C~VCg~~~---~g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYA---SGYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcC---cceEECceeehhhHHhHHH
Confidence 467899999754 3578999999999998764
No 31
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=66.33 E-value=4.3 Score=27.44 Aligned_cols=32 Identities=25% Similarity=0.740 Sum_probs=25.5
Q ss_pred CCCCCccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 22 PTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 22 ~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
|..+.|.-||.+.. ...||+..|..|.+..|-
T Consensus 1 ~~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 32 (82)
T cd07173 1 PPQKTCLICGDEAS---GCHYGALTCGSCKVFFKR 32 (82)
T ss_pred CCCCCCeecCCcCc---ceEECcchhhhHHHHHHH
Confidence 34667999997553 568999999999998764
No 32
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=65.61 E-value=3.1 Score=25.28 Aligned_cols=27 Identities=33% Similarity=0.764 Sum_probs=20.2
Q ss_pred CccCCCCCCCCceeeccchhcchhhhhh
Q psy7550 26 ECFDCNAKNPTWSSVTYGVFICIDCSAV 53 (144)
Q Consensus 26 ~C~DCg~~~p~w~s~~~GiflC~~Csgi 53 (144)
.|+=|+.+.+.=. .=+|.|||.+|-.-
T Consensus 1 ~CiiC~~~~~~GI-~I~~~fIC~~CE~~ 27 (46)
T PF10764_consen 1 KCIICGKEKEEGI-HIYGKFICSDCEKE 27 (46)
T ss_pred CeEeCCCcCCCCE-EEECeEehHHHHHH
Confidence 4888999887733 34699999999543
No 33
>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=64.55 E-value=7.5 Score=23.12 Aligned_cols=43 Identities=16% Similarity=0.412 Sum_probs=29.0
Q ss_pred ChhHHHHHHHHHhcCCCCCCccCCCCCCCCceeeccchhcchhhh
Q psy7550 7 NKNDIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCS 51 (144)
Q Consensus 7 ~~~~~~~~~~~L~~~~~N~~C~DCg~~~p~w~s~~~GiflC~~Cs 51 (144)
++++-.+.|..+ ..|..-+|.-||...+.+.. +.+.+-|..|.
T Consensus 2 ~e~~c~~~l~~~-RW~~g~~CP~Cg~~~~~~~~-~~~~~~C~~C~ 44 (46)
T PF12760_consen 2 DEEACREYLEEI-RWPDGFVCPHCGSTKHYRLK-TRGRYRCKACR 44 (46)
T ss_pred CHHHHHHHHHHh-cCCCCCCCCCCCCeeeEEeC-CCCeEECCCCC
Confidence 455556666665 45556889999998554443 36888888884
No 34
>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=63.19 E-value=4.7 Score=28.04 Aligned_cols=31 Identities=32% Similarity=0.683 Sum_probs=25.4
Q ss_pred CCCCccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 23 TNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 23 ~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
++..|.-||.+. ....||++.|..|.+..|-
T Consensus 4 ~~~~C~VCg~~~---~g~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 4 EVIPCKICGDKS---SGIHYGVITCEGCKGFFRR 34 (95)
T ss_pred cccCCcccCCcC---cceEECceeehhhHHhhHH
Confidence 567899999865 3468999999999998864
No 35
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=62.94 E-value=4.1 Score=29.71 Aligned_cols=30 Identities=20% Similarity=0.470 Sum_probs=21.1
Q ss_pred CCccCCCCCCC-Cceeeccchhcchhhhhhh
Q psy7550 25 KECFDCNAKNP-TWSSVTYGVFICIDCSAVH 54 (144)
Q Consensus 25 ~~C~DCg~~~p-~w~s~~~GiflC~~CsgiH 54 (144)
.+|.+||.+=| .=.-.--+..+|+.|...|
T Consensus 81 G~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~ 111 (120)
T COG1734 81 GICEECGEPIPEARLEARPTARLCIECQERA 111 (120)
T ss_pred cchhccCCcCCHHHHhhCcchHHHHHHHHHH
Confidence 38999999743 2222334678999998876
No 36
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=62.12 E-value=5.5 Score=30.31 Aligned_cols=42 Identities=17% Similarity=0.359 Sum_probs=25.7
Q ss_pred HHHHHHhcCCCCCCccCCCCCCC--Cceeeccchhcchhhhhhhhc
Q psy7550 13 VIFKKLRNIPTNKECFDCNAKNP--TWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 13 ~~~~~L~~~~~N~~C~DCg~~~p--~w~s~~~GiflC~~CsgiHR~ 56 (144)
+.|.+| ..+.=..|.+||.+=| ..-.++ .+-.|+.|+..+-.
T Consensus 76 ~AL~Ri-~~G~YG~Ce~CGe~I~~~RL~a~P-~a~~Ci~Cq~~~E~ 119 (159)
T TIGR02890 76 HALQKI-ENGTYGICEVCGKPIPYERLEAIP-TATTCVECQNRKEV 119 (159)
T ss_pred HHHHHH-hCCCCCeecccCCcccHHHHhhCC-CcchhHHHHHHhhh
Confidence 334444 2345568999999732 222222 56789999987643
No 37
>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=61.23 E-value=8.1 Score=24.08 Aligned_cols=34 Identities=26% Similarity=0.687 Sum_probs=27.2
Q ss_pred CccCCCCC-CCCceeec-cchhcchhhhhhhhcCCC
Q psy7550 26 ECFDCNAK-NPTWSSVT-YGVFICIDCSAVHRGLGV 59 (144)
Q Consensus 26 ~C~DCg~~-~p~w~s~~-~GiflC~~CsgiHR~lg~ 59 (144)
.|..|+.. -|.|=.-. -+..||..|.-..+..|.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~ 36 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGV 36 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCC
Confidence 58999996 57888765 788999999877777663
No 38
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=60.77 E-value=7.1 Score=27.11 Aligned_cols=33 Identities=21% Similarity=0.476 Sum_probs=25.3
Q ss_pred hcCCCCCCccCCCCCCCCceeeccchhcchhhhhh
Q psy7550 19 RNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAV 53 (144)
Q Consensus 19 ~~~~~N~~C~DCg~~~p~w~s~~~GiflC~~Csgi 53 (144)
.....-..|..|+.+ .---+..||+.|..|...
T Consensus 30 ~~~~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~~ 62 (89)
T COG1997 30 AQQRAKHVCPFCGRT--TVKRIATGIWKCRKCGAK 62 (89)
T ss_pred HHHhcCCcCCCCCCc--ceeeeccCeEEcCCCCCe
Confidence 334567789999998 555678999999999543
No 39
>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription
Probab=59.69 E-value=5.5 Score=27.86 Aligned_cols=30 Identities=27% Similarity=0.642 Sum_probs=24.0
Q ss_pred CCCccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 24 NKECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 24 N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
+..|.-||.+.. ...||++.|..|.+..|-
T Consensus 4 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 33 (97)
T cd07170 4 KRLCLVCGDIAS---GYHYGVASCEACKAFFKR 33 (97)
T ss_pred CCCCeecCCcCc---ceEECceeehhhhHHHHH
Confidence 356999997653 468999999999998764
No 40
>PHA00080 DksA-like zinc finger domain containing protein
Probab=58.89 E-value=6.7 Score=25.97 Aligned_cols=33 Identities=24% Similarity=0.703 Sum_probs=23.4
Q ss_pred CCCCCccCCCCCCC--Cceeeccchhcchhhhhhhh
Q psy7550 22 PTNKECFDCNAKNP--TWSSVTYGVFICIDCSAVHR 55 (144)
Q Consensus 22 ~~N~~C~DCg~~~p--~w~s~~~GiflC~~CsgiHR 55 (144)
++...|.|||.+=| .+.-++ |+..|+.|...+-
T Consensus 29 ~~~~~C~~Cg~~Ip~~Rl~a~P-~~~~Cv~Cq~~~E 63 (72)
T PHA00080 29 PSATHCEECGDPIPEARREAVP-GCRTCVSCQEILE 63 (72)
T ss_pred CCCCEecCCCCcCcHHHHHhCC-CccCcHHHHHHHH
Confidence 45668999999744 444434 6777999988653
No 41
>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=57.22 E-value=7 Score=26.84 Aligned_cols=32 Identities=19% Similarity=0.729 Sum_probs=26.0
Q ss_pred CCCCCccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 22 PTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 22 ~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
.++..|.-||.+. ....||+..|..|.+..|-
T Consensus 4 ~~~~~C~VCg~~a---~g~hyGv~sC~aCk~FFRR 35 (90)
T cd07169 4 AEQRTCLICGDRA---TGLHYGIISCEGCKGFFKR 35 (90)
T ss_pred ccCCCCeecCCcC---cceEECcceehhhHHHHHH
Confidence 4677899999754 4468999999999998754
No 42
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=56.20 E-value=2.5 Score=24.14 Aligned_cols=29 Identities=21% Similarity=0.449 Sum_probs=14.2
Q ss_pred CCccCCCCCCCCceee---ccchhcchhhhhhh
Q psy7550 25 KECFDCNAKNPTWSSV---TYGVFICIDCSAVH 54 (144)
Q Consensus 25 ~~C~DCg~~~p~w~s~---~~GiflC~~CsgiH 54 (144)
|.|..||.+- ++... +.-=++|..|.-||
T Consensus 1 kfC~~CG~~l-~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 1 KFCPQCGGPL-ERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp -B-TTT--B--EEE--TT-SS-EEEETTTTEEE
T ss_pred CccccccChh-hhhcCCCCCccceECCCCCCEE
Confidence 5788898862 22211 34456888888887
No 43
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=56.10 E-value=8.7 Score=28.96 Aligned_cols=37 Identities=16% Similarity=0.239 Sum_probs=24.2
Q ss_pred cCCCCCCccCCCCCCC-Cceeeccchhcchhhhhhhhc
Q psy7550 20 NIPTNKECFDCNAKNP-TWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 20 ~~~~N~~C~DCg~~~p-~w~s~~~GiflC~~CsgiHR~ 56 (144)
..+.-..|-+||.+=| .=.-+--+...|+.|...+-.
T Consensus 107 ~~gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E~ 144 (151)
T PRK10778 107 EDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEI 144 (151)
T ss_pred hCCCCceeccCCCcccHHHHhcCCCccccHHHHHHHHH
Confidence 3467789999999732 112222355789999987643
No 44
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=54.06 E-value=9.4 Score=23.31 Aligned_cols=30 Identities=20% Similarity=0.655 Sum_probs=21.4
Q ss_pred CCCCccCCCCCCC--Cc-------eeeccchhcchhhhh
Q psy7550 23 TNKECFDCNAKNP--TW-------SSVTYGVFICIDCSA 52 (144)
Q Consensus 23 ~N~~C~DCg~~~p--~w-------~s~~~GiflC~~Csg 52 (144)
.+..|-=||+..+ .| .+....|+||..|..
T Consensus 6 s~~kCELC~a~~~L~vy~Vpp~~~~~~d~~iliC~tC~~ 44 (47)
T smart00782 6 CESKCELCGSDSPLVVYAVPPSSDVTADNSVMLCDTCHS 44 (47)
T ss_pred cCCcccCcCCCCCceEEecCCCCCCCccceeeechHHHH
Confidence 4556999998653 11 355778999999975
No 45
>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=53.79 E-value=5.5 Score=25.37 Aligned_cols=27 Identities=30% Similarity=0.696 Sum_probs=22.7
Q ss_pred CCCCccCCCCCCCCceeeccchhcchhhh
Q psy7550 23 TNKECFDCNAKNPTWSSVTYGVFICIDCS 51 (144)
Q Consensus 23 ~N~~C~DCg~~~p~w~s~~~GiflC~~Cs 51 (144)
.-+.|..||..... ..+..+|.|..|.
T Consensus 27 TSq~C~~CG~~~~~--~~~~r~~~C~~Cg 53 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK--RRSGRVFTCPNCG 53 (69)
T ss_pred CccCccCccccccc--ccccceEEcCCCC
Confidence 46789999998887 7788899999984
No 46
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=53.62 E-value=12 Score=30.64 Aligned_cols=38 Identities=21% Similarity=0.511 Sum_probs=28.4
Q ss_pred HHHHHHH-HhcCCCCCCccCCCCCCCCceeeccchhcchhhhhhhh
Q psy7550 11 IEVIFKK-LRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHR 55 (144)
Q Consensus 11 ~~~~~~~-L~~~~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR 55 (144)
.+++++. +...|.|. |--||.....|. ++|..|.+.|-
T Consensus 341 ~~~~~~~~~~~~p~~~-c~~cg~~~~~~~------~~c~~c~~~~~ 379 (389)
T PRK11788 341 LRDLVGEQLKRKPRYR-CRNCGFTARTLY------WHCPSCKAWET 379 (389)
T ss_pred HHHHHHHHHhCCCCEE-CCCCCCCCccce------eECcCCCCccC
Confidence 3455553 45566655 999999999997 68999988873
No 47
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=53.33 E-value=8.5 Score=27.10 Aligned_cols=31 Identities=29% Similarity=0.639 Sum_probs=25.4
Q ss_pred CCCCccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 23 TNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 23 ~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
++..|.-||.+.. ...||+..|..|.+..|-
T Consensus 17 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 47 (101)
T cd07160 17 GNEVCSVCGDKAS---GFHYNVLSCEGCKGFFRR 47 (101)
T ss_pred CCCCCeecCCcCc---ceEECcceehhhhhhhhh
Confidence 5678999998543 468999999999998764
No 48
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian
Probab=51.15 E-value=6 Score=27.41 Aligned_cols=29 Identities=28% Similarity=0.563 Sum_probs=22.6
Q ss_pred CCccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 25 KECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 25 ~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
+.|.-||.+.. ...||+..|..|.+..|-
T Consensus 1 ~~C~VCg~~a~---g~hyGv~sC~aC~~FFRR 29 (94)
T cd06966 1 KICGVCGDKAL---GYNFNAITCESCKAFFRR 29 (94)
T ss_pred CCCeeCCCcCc---ceEECcceeeeehheehh
Confidence 45888887543 458999999999998765
No 49
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=49.25 E-value=12 Score=26.16 Aligned_cols=34 Identities=26% Similarity=0.725 Sum_probs=23.7
Q ss_pred hcCCCCCCccCCCCCC-------C-Cc---------eeeccchhcchhhhh
Q psy7550 19 RNIPTNKECFDCNAKN-------P-TW---------SSVTYGVFICIDCSA 52 (144)
Q Consensus 19 ~~~~~N~~C~DCg~~~-------p-~w---------~s~~~GiflC~~Csg 52 (144)
++.|+--.|++||.+- | .+ .+=.||-.+|.+|..
T Consensus 29 kK~~~~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~ 79 (93)
T COG2174 29 KKKPTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVR 79 (93)
T ss_pred eccCCCCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHH
Confidence 3456777999999962 1 11 233599999999965
No 50
>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers. DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding
Probab=49.21 E-value=12 Score=25.46 Aligned_cols=28 Identities=18% Similarity=0.543 Sum_probs=21.8
Q ss_pred CccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 26 ECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 26 ~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
.|.-||.+... ..||+..|..|++..|-
T Consensus 1 ~C~VCg~~~~g---~hygv~sC~aC~~FFRR 28 (87)
T cd07162 1 ICRVCGDRATG---YHFNAMTCEGCKGFFRR 28 (87)
T ss_pred CCcccCCcCcc---eEECcceehhhHHHHHh
Confidence 37778875443 58999999999998764
No 51
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=48.52 E-value=11 Score=24.53 Aligned_cols=27 Identities=33% Similarity=0.753 Sum_probs=20.5
Q ss_pred ccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 27 CFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 27 C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
|.-||.+.. ...||++.|..|.+..|-
T Consensus 1 C~VCg~~~~---g~hyGv~~C~aC~~FFRR 27 (73)
T cd07158 1 CKVCGDKAS---GFHYGVHSCEGCKGFFRR 27 (73)
T ss_pred CcccCccCc---ceEECcchhhHHHHHHhh
Confidence 455776444 368999999999998864
No 52
>cd07165 NR_DBD_DmE78_like DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers. DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. The SmE78 may be involved in transduction of an ecdysone signal in S. mansoni,
Probab=48.47 E-value=12 Score=25.10 Aligned_cols=27 Identities=33% Similarity=0.712 Sum_probs=20.8
Q ss_pred ccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 27 CFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 27 C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
|.-||.+.. ...||+..|..|.+..|-
T Consensus 1 C~VCg~~~~---g~hyG~~sC~aC~~FFRR 27 (81)
T cd07165 1 CKVCGDKAS---GYHYGVTSCEGCKGFFRR 27 (81)
T ss_pred CCccCccCc---ceEECchhhhhHHHHHHh
Confidence 556776543 458999999999998865
No 53
>KOG3362|consensus
Probab=47.53 E-value=7 Score=29.63 Aligned_cols=35 Identities=29% Similarity=0.561 Sum_probs=26.5
Q ss_pred CCCCCCccCCCCCCCCceeeccchhcch-hhhhhhhc
Q psy7550 21 IPTNKECFDCNAKNPTWSSVTYGVFICI-DCSAVHRG 56 (144)
Q Consensus 21 ~~~N~~C~DCg~~~p~w~s~~~GiflC~-~CsgiHR~ 56 (144)
+|--+.|+-|| -...+.+++-|.-.|. .|-++|..
T Consensus 115 KP~r~fCaVCG-~~S~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 115 KPLRKFCAVCG-YDSKYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred CCcchhhhhcC-CCchhHHHhcCCceeechhhhhccc
Confidence 35668999999 5666888888888774 67777754
No 54
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=47.36 E-value=9.2 Score=28.63 Aligned_cols=40 Identities=15% Similarity=0.433 Sum_probs=29.2
Q ss_pred hHHHHHHHHHhcCCCCCCccCCCCCCCCceeeccchhcchhhhhhhhcC
Q psy7550 9 NDIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGL 57 (144)
Q Consensus 9 ~~~~~~~~~L~~~~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~l 57 (144)
-+++++|+.+....+...|.-||. .+-..|..|.|-|+.+
T Consensus 84 G~L~~lL~~~~~~~~~~~C~~Cgg---------~rfv~C~~C~Gs~k~~ 123 (147)
T cd03031 84 GELRKLLKGIRARAGGGVCEGCGG---------ARFVPCSECNGSCKVF 123 (147)
T ss_pred CCHHHHHhhcccccCCCCCCCCCC---------cCeEECCCCCCcceEE
Confidence 345667776655566777999985 4556899999998875
No 55
>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers. DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs h
Probab=46.40 E-value=13 Score=25.57 Aligned_cols=28 Identities=21% Similarity=0.662 Sum_probs=22.5
Q ss_pred CccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 26 ECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 26 ~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
.|.-||.+.. ...||++.|..|.+..|-
T Consensus 3 ~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 30 (91)
T cd07161 3 LCLVCGDRAS---GYHYNALTCEGCKGFFRR 30 (91)
T ss_pred CCeeCCCcCc---ceEECceeehhhHHHHHH
Confidence 4888887544 468999999999998764
No 56
>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear rec
Probab=45.58 E-value=14 Score=24.42 Aligned_cols=28 Identities=25% Similarity=0.706 Sum_probs=22.3
Q ss_pred CccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 26 ECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 26 ~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
.|.-||.+.. ...||+..|..|.+..|-
T Consensus 2 ~C~VC~~~~~---g~hygv~sC~aC~~FFRR 29 (77)
T cd06956 2 ICAICGDRAS---GKHYGVYSCEGCKGFFKR 29 (77)
T ss_pred CCcccCCcCc---ceEECceeehhHHHHHHH
Confidence 5778887554 468999999999998754
No 57
>cd07156 NR_DBD_VDR_like The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemi
Probab=45.04 E-value=12 Score=24.35 Aligned_cols=27 Identities=19% Similarity=0.572 Sum_probs=20.3
Q ss_pred ccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 27 CFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 27 C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
|.-||.+... ..||+..|..|.+..|-
T Consensus 1 C~VC~~~~~g---~hygv~sC~aC~~FFRR 27 (72)
T cd07156 1 CGVCGDRATG---YHFNAMTCEGCKGFFRR 27 (72)
T ss_pred CCccCccCcc---cEECcceehhhhhhhch
Confidence 4557765443 48999999999998764
No 58
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p
Probab=44.92 E-value=14 Score=24.63 Aligned_cols=29 Identities=28% Similarity=0.744 Sum_probs=23.0
Q ss_pred CCccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 25 KECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 25 ~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
+.|.-||.+.. ...||+..|..|.+..|-
T Consensus 3 ~~C~VCg~~a~---g~hyGv~sC~aC~~FFRR 31 (78)
T cd07172 3 KICLVCSDEAS---GCHYGVLTCGSCKVFFKR 31 (78)
T ss_pred CCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 46888987543 468999999999998754
No 59
>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=44.59 E-value=16 Score=25.05 Aligned_cols=31 Identities=26% Similarity=0.683 Sum_probs=24.8
Q ss_pred CCCCccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 23 TNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 23 ~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
....|.-||.+.. ...||+..|..|.+..|-
T Consensus 5 ~~~~C~VCg~~~~---g~hyGv~sC~aCk~FFRR 35 (90)
T cd07168 5 SPKLCSICEDKAT---GLHYGIITCEGCKGFFKR 35 (90)
T ss_pred cCCCCcccCCcCc---ceEECceehhhhhHhhhh
Confidence 4567999997543 568999999999998754
No 60
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=44.55 E-value=12 Score=23.08 Aligned_cols=31 Identities=29% Similarity=0.651 Sum_probs=20.7
Q ss_pred CccCCCCCCCCc--eeeccchhcchhhhhhhhcC
Q psy7550 26 ECFDCNAKNPTW--SSVTYGVFICIDCSAVHRGL 57 (144)
Q Consensus 26 ~C~DCg~~~p~w--~s~~~GiflC~~CsgiHR~l 57 (144)
.|+=||..-.-. .-+.=| +||.+|..--..+
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl~~~ 33 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKLSGF 33 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHhcCc
Confidence 478888875433 345667 8999998654333
No 61
>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=43.99 E-value=11 Score=25.40 Aligned_cols=27 Identities=33% Similarity=0.767 Sum_probs=21.3
Q ss_pred ccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 27 CFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 27 C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
|.-||.+.. ...||++.|..|.+..|-
T Consensus 2 C~VCg~~~~---g~hyGv~sC~aCk~FFRR 28 (84)
T cd06965 2 CRVCGDKAS---GFHYGVHACEGCKGFFRR 28 (84)
T ss_pred CcccCccCc---ceEEChhhhhhhhhheee
Confidence 677886543 457999999999998865
No 62
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=43.51 E-value=16 Score=25.78 Aligned_cols=30 Identities=20% Similarity=0.408 Sum_probs=18.1
Q ss_pred CCCCCccCCCCCCC-Cceeeccchhcchhhh
Q psy7550 22 PTNKECFDCNAKNP-TWSSVTYGVFICIDCS 51 (144)
Q Consensus 22 ~~N~~C~DCg~~~p-~w~s~~~GiflC~~Cs 51 (144)
+.-..|-|||.+=| .=.-.--+...|+.|.
T Consensus 78 g~yG~C~~Cge~I~~~RL~a~P~a~~Cv~Cq 108 (110)
T TIGR02420 78 GEYGYCEECGEEIGLRRLEARPTATLCIDCK 108 (110)
T ss_pred CCCCchhccCCcccHHHHhhCCCccccHHhH
Confidence 45679999999733 1111122446788885
No 63
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=41.92 E-value=12 Score=31.09 Aligned_cols=32 Identities=22% Similarity=0.506 Sum_probs=22.4
Q ss_pred CCCCCccCCCCCCCCceeeccchhcchhhhhhh
Q psy7550 22 PTNKECFDCNAKNPTWSSVTYGVFICIDCSAVH 54 (144)
Q Consensus 22 ~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiH 54 (144)
.....|.+||..+. =..-.-|-.||.+|.-|-
T Consensus 9 ~~~~~Cp~Cg~~~i-v~d~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 9 EEKLVCPECGSDKL-IYDYERGEIVCADCGLVI 40 (310)
T ss_pred ccCCcCcCCCCCCe-eEECCCCeEeecccCCcc
Confidence 34568999997432 223467999999997653
No 64
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=41.74 E-value=15 Score=21.74 Aligned_cols=23 Identities=26% Similarity=0.566 Sum_probs=17.4
Q ss_pred CccCCCCCCCCceeeccchhcch
Q psy7550 26 ECFDCNAKNPTWSSVTYGVFICI 48 (144)
Q Consensus 26 ~C~DCg~~~p~w~s~~~GiflC~ 48 (144)
+|.+|+..+.-|+++.-|-..|.
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c~ 23 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGCG 23 (50)
T ss_pred CcccCCCcCCeEEecCCCCcccC
Confidence 58999998878877776666663
No 65
>PF00105 zf-C4: Zinc finger, C4 type (two domains); InterPro: IPR001628 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences, connected via a linker region to a C-terminal ligand-binding domain (IPR000536 from INTERPRO). In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The DNA-binding domain can elicit either an activating or repressing effect by binding to specific regions of the DNA known as hormone-response elements [, ]. These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. The DNA-binding domain is furthermore involved in several other functions including nuclear localisation, and interaction with transcription factors and co-activators []. Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the two C4-type zinc finger modules involved in DNA-binding. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1DSZ_A 1LO1_A 3M9E_F 2EBL_A 1GA5_B 1A6Y_B 1HLZ_B 1HRA_A 1KB6_B 1KB4_B ....
Probab=41.24 E-value=12 Score=23.90 Aligned_cols=26 Identities=35% Similarity=0.756 Sum_probs=20.0
Q ss_pred CCccCCCCCCCCceeeccchhcchhhhhh
Q psy7550 25 KECFDCNAKNPTWSSVTYGVFICIDCSAV 53 (144)
Q Consensus 25 ~~C~DCg~~~p~w~s~~~GiflC~~Csgi 53 (144)
+.|.-||.+. ...+||++.|..|...
T Consensus 1 ~~C~VCg~~~---~~~~ygv~sC~~C~~F 26 (70)
T PF00105_consen 1 KKCKVCGDPA---SGYHYGVLSCNACKMF 26 (70)
T ss_dssp -BSTTTSSBE---SEEETTEEEEHHHHHH
T ss_pred CCCeECCCcc---Ccccccccccccceee
Confidence 4688898643 3568999999999984
No 66
>cd07155 NR_DBD_ER_like DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. E
Probab=40.78 E-value=19 Score=23.69 Aligned_cols=27 Identities=30% Similarity=0.705 Sum_probs=20.4
Q ss_pred ccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 27 CFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 27 C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
|.-||.+.. ...||+..|..|.+..|-
T Consensus 1 C~VC~~~~~---g~hygv~sC~aCk~FFRR 27 (75)
T cd07155 1 CLVCGDIAS---GYHYGVASCEACKAFFKR 27 (75)
T ss_pred CcccCccCc---ceEEChhhhhhhHHHHHH
Confidence 556776533 468999999999998754
No 67
>cd06958 NR_DBD_COUP_TF DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. COUP-TFs homodimerize or heterodimerize with retinoid X receptor (RXR) and a few other nuclear receptors and bind to a variety of response elements that are composed of imperfect AGGTCA direct or inverted repeats with various spacings. COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone recept
Probab=40.18 E-value=18 Score=23.66 Aligned_cols=27 Identities=30% Similarity=0.812 Sum_probs=20.2
Q ss_pred ccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 27 CFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 27 C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
|.-||.+.. ...||+..|..|.+..|-
T Consensus 1 C~VCg~~~~---g~hygv~sC~aC~~FFRR 27 (73)
T cd06958 1 CVVCGDKSS---GKHYGQFTCEGCKSFFKR 27 (73)
T ss_pred CCccCccCc---ceEEChhhhhhhhhhhhh
Confidence 455666443 458999999999998754
No 68
>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=39.25 E-value=20 Score=24.49 Aligned_cols=30 Identities=30% Similarity=0.615 Sum_probs=23.7
Q ss_pred CCCccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 24 NKECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 24 N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
+..|.-||.+.. ...||++.|..|.+..|-
T Consensus 3 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 32 (89)
T cd07166 3 VVLCKVCGDKAS---GFHYGVHACEGCKGFFRR 32 (89)
T ss_pred CCCCcccCccCc---ceEEChhhhhhHhhEecc
Confidence 456999997554 457999999999997764
No 69
>cd07164 NR_DBD_PNR_like_1 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-t
Probab=38.71 E-value=18 Score=23.89 Aligned_cols=27 Identities=26% Similarity=0.639 Sum_probs=20.3
Q ss_pred ccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 27 CFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 27 C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
|.-||.+.. ...||+..|..|.+..|-
T Consensus 1 C~VCg~~~~---g~hyG~~~C~~C~~FFRR 27 (78)
T cd07164 1 CRVCGDRAS---GKHYGVPSCDGCRGFFKR 27 (78)
T ss_pred CcccCccCc---ceEECcchhhhhhhhhhh
Confidence 555776443 358999999999998754
No 70
>cd07179 2DBD_NR_DBD2 The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type zinc fingers. The second DNA-binding domain (DBD) of the 2DBD nuclear receptor (NR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. The proteins contain two DBDs in tandem, probably resulting from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=37.98 E-value=21 Score=23.45 Aligned_cols=27 Identities=26% Similarity=0.746 Sum_probs=20.3
Q ss_pred ccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 27 CFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 27 C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
|.-||.+.. ...||+..|..|.+..|-
T Consensus 1 C~VCg~~~~---g~hygv~sC~aC~~FFRR 27 (74)
T cd07179 1 CRVCGGKSS---GFHFGALTCEGCKGFFRR 27 (74)
T ss_pred CcccCccCc---ceEECceeehhHHHHHHH
Confidence 555776543 358999999999998764
No 71
>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=37.86 E-value=11 Score=26.02 Aligned_cols=31 Identities=23% Similarity=0.679 Sum_probs=24.7
Q ss_pred CCCCccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 23 TNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 23 ~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
-|..|.-||.+.. ...||+..|..|++..|-
T Consensus 5 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (92)
T cd07163 5 LDIPCKVCGDRSS---GKHYGIYACDGCSGFFKR 35 (92)
T ss_pred cCCCCcccCCcCc---ccEECceeeeeeeeEEee
Confidence 3778999997544 368999999999998754
No 72
>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=37.78 E-value=15 Score=26.15 Aligned_cols=30 Identities=17% Similarity=0.535 Sum_probs=24.1
Q ss_pred CCCccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 24 NKECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 24 N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
.+.|.-||.+.. ...||+..|..|.+..|-
T Consensus 6 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (107)
T cd06955 6 PRICGVCGDRAT---GFHFNAMTCEGCKGFFRR 35 (107)
T ss_pred CCCCeecCCcCc---ccEECcceeeeecceecc
Confidence 467999997544 458999999999998764
No 73
>cd06961 NR_DBD_TR DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the he
Probab=37.33 E-value=20 Score=24.24 Aligned_cols=27 Identities=26% Similarity=0.669 Sum_probs=20.9
Q ss_pred ccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 27 CFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 27 C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
|.-||.+.. ...||+..|..|.+..|-
T Consensus 2 C~VCg~~~~---g~hygv~sC~aC~~FFRR 28 (85)
T cd06961 2 CVVCGDKAT---GYHYRCITCEGCKGFFRR 28 (85)
T ss_pred CceeCCcCc---ceEEChhhhhhhhHhhHh
Confidence 667776543 358999999999998764
No 74
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=36.92 E-value=11 Score=22.49 Aligned_cols=23 Identities=26% Similarity=0.614 Sum_probs=16.6
Q ss_pred CccCCCCCCCCceeeccchhcchhhh
Q psy7550 26 ECFDCNAKNPTWSSVTYGVFICIDCS 51 (144)
Q Consensus 26 ~C~DCg~~~p~w~s~~~GiflC~~Cs 51 (144)
.|.+||....-. ..+..-|..|.
T Consensus 4 ~C~~Cg~~~~~~---~~~~irC~~CG 26 (44)
T smart00659 4 ICGECGRENEIK---SKDVVRCRECG 26 (44)
T ss_pred ECCCCCCEeecC---CCCceECCCCC
Confidence 599999964432 45778888884
No 75
>cd07157 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers. The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=36.60 E-value=12 Score=25.49 Aligned_cols=28 Identities=18% Similarity=0.571 Sum_probs=22.2
Q ss_pred CccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 26 ECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 26 ~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
.|.-||.+. ....||+..|..|.+..|-
T Consensus 2 ~C~VCg~~a---~g~hyGv~sC~aCk~FFRR 29 (86)
T cd07157 2 TCQVCGEPA---AGFHHGAYVCEACKKFFMR 29 (86)
T ss_pred CCcccCCcC---cccEECcceeeEeeeEEec
Confidence 488888754 3469999999999998754
No 76
>PF14376 Haem_bd: Haem-binding domain
Probab=36.59 E-value=18 Score=26.53 Aligned_cols=15 Identities=27% Similarity=1.019 Sum_probs=11.7
Q ss_pred CCCccCCCCCCCCce
Q psy7550 24 NKECFDCNAKNPTWS 38 (144)
Q Consensus 24 N~~C~DCg~~~p~w~ 38 (144)
.+-|.||++.++.|-
T Consensus 41 ~~~CydCHSn~T~~P 55 (137)
T PF14376_consen 41 KNSCYDCHSNNTRYP 55 (137)
T ss_pred HccccccCCCCCCCc
Confidence 357999999886654
No 77
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=36.28 E-value=16 Score=23.49 Aligned_cols=27 Identities=30% Similarity=0.732 Sum_probs=20.6
Q ss_pred ccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 27 CFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 27 C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
|.-||.+.. ...||+..|..|.+..|-
T Consensus 2 C~vC~~~~~---~~hygv~~C~aC~~FFRR 28 (70)
T smart00399 2 CCVCGDHAS---GFHFGVCSCRACKAFFRR 28 (70)
T ss_pred CeEeCCcCc---ccEeCCcEechhhhhhhh
Confidence 666776543 348999999999998764
No 78
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=34.86 E-value=17 Score=27.35 Aligned_cols=27 Identities=19% Similarity=0.372 Sum_probs=18.0
Q ss_pred CccCCCCCCCCceeeccchhcchhhhhh
Q psy7550 26 ECFDCNAKNPTWSSVTYGVFICIDCSAV 53 (144)
Q Consensus 26 ~C~DCg~~~p~w~s~~~GiflC~~Csgi 53 (144)
.|..|+..-+.=-.+++ -|.|..|.+.
T Consensus 111 ~Cp~c~~r~tf~eA~~~-~F~Cp~Cg~~ 137 (158)
T TIGR00373 111 ICPNMCVRFTFNEAMEL-NFTCPRCGAM 137 (158)
T ss_pred ECCCCCcEeeHHHHHHc-CCcCCCCCCE
Confidence 69888865332223344 4999999776
No 79
>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=34.17 E-value=23 Score=20.65 Aligned_cols=29 Identities=28% Similarity=0.574 Sum_probs=16.9
Q ss_pred CCccCCCCCCC---Cceeeccchhcchhhhhh
Q psy7550 25 KECFDCNAKNP---TWSSVTYGVFICIDCSAV 53 (144)
Q Consensus 25 ~~C~DCg~~~p---~w~s~~~GiflC~~Csgi 53 (144)
+.|.=||.+.. .-++-+-|++||..|...
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNGAYICDECVEQ 33 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-SEEEEHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCCcEECHHHHHH
Confidence 46888998764 334445589999999753
No 80
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=34.15 E-value=9.7 Score=20.47 Aligned_cols=28 Identities=14% Similarity=0.381 Sum_probs=15.8
Q ss_pred CCccCCCCCCCCceeeccchhcchhhhh
Q psy7550 25 KECFDCNAKNPTWSSVTYGVFICIDCSA 52 (144)
Q Consensus 25 ~~C~DCg~~~p~w~s~~~GiflC~~Csg 52 (144)
+.|.-|+..-+.-..-....++|..|..
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCcC
Confidence 3577777765554455677888888864
No 81
>cd06963 NR_DBD_GR_like The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family of NRs includes four types of nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). The receptors bind to common DNA elements containing a partial palindrome of the core sequence 5'-TGTTCT-3' with a 3bp spacer. These four receptors regulate some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family have high sequence homology and sha
Probab=34.12 E-value=24 Score=23.13 Aligned_cols=27 Identities=30% Similarity=0.797 Sum_probs=20.1
Q ss_pred ccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 27 CFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 27 C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
|.-||.+. ....||++.|..|.+..|-
T Consensus 1 C~VCg~~a---~~~hygv~sC~aCk~FFRR 27 (73)
T cd06963 1 CLICGDEA---SGCHYGVLTCGSCKVFFKR 27 (73)
T ss_pred CcccCccC---cceEECceeehhhhHhHHH
Confidence 45566543 3568999999999998754
No 82
>KOG3507|consensus
Probab=33.86 E-value=16 Score=23.52 Aligned_cols=25 Identities=28% Similarity=0.494 Sum_probs=16.6
Q ss_pred CCCccCCCCCCCCceeeccchhcchhhh
Q psy7550 24 NKECFDCNAKNPTWSSVTYGVFICIDCS 51 (144)
Q Consensus 24 N~~C~DCg~~~p~w~s~~~GiflC~~Cs 51 (144)
--.|+|||+.|.-= .--++-|.+|.
T Consensus 20 iYiCgdC~~en~lk---~~D~irCReCG 44 (62)
T KOG3507|consen 20 IYICGDCGQENTLK---RGDVIRCRECG 44 (62)
T ss_pred EEEecccccccccc---CCCcEehhhcc
Confidence 34899999987411 22467788884
No 83
>cd06962 NR_DBD_FXR DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. FXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. FXR is a member of the nuclear receptor family of ligand activated transcription factors. Bile acids are endogenous ligands for FXRs. Upon binding of a ligand, FXR binds to FXR response element (FXRE), which is an inverted repeat of TGACCT spaced by one nucleotide, either as a monomer or as a heterodimer with retinoid X receptor (RXR), to regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, FXR has a central well conserved
Probab=33.26 E-value=15 Score=24.88 Aligned_cols=28 Identities=25% Similarity=0.646 Sum_probs=22.1
Q ss_pred CccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 26 ECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 26 ~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
.|.-||.+.. ...||++.|..|.+..|-
T Consensus 3 ~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 30 (84)
T cd06962 3 LCVVCGDKAS---GYHYNALTCEGCKGFFRR 30 (84)
T ss_pred CCeecCCcCc---ceEECcceeecceeeeee
Confidence 4888887544 358999999999998754
No 84
>cd06960 NR_DBD_HNF4A DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is
Probab=33.19 E-value=17 Score=23.92 Aligned_cols=27 Identities=30% Similarity=0.758 Sum_probs=20.3
Q ss_pred ccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 27 CFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 27 C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
|.-||.+.. ...||++.|..|.+..|-
T Consensus 1 C~vCg~~~~---~~hygv~~C~aC~~FFrR 27 (76)
T cd06960 1 CAVCGDRAT---GKHYGVLSCNGCKGFFRR 27 (76)
T ss_pred CCccCccCc---ccEECcceeeeehheeCc
Confidence 556776543 458999999999998754
No 85
>cd07167 NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which is required at several stages of development. Particularly, FTZ-F1 regulated genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development; SF-1 is an essential regu
Probab=33.12 E-value=29 Score=24.00 Aligned_cols=27 Identities=26% Similarity=0.710 Sum_probs=20.3
Q ss_pred ccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 27 CFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 27 C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
|.-||.+.. ...||+..|..|.+..|-
T Consensus 1 C~VCg~~a~---g~hyGv~sC~aCk~FFRR 27 (93)
T cd07167 1 CPVCGDKVS---GYHYGLLTCESCKGFFKR 27 (93)
T ss_pred CcccCccCc---ceEECchhhhhHHHHHHH
Confidence 555776433 468999999999998754
No 86
>cd06959 NR_DBD_EcR_like The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: Ecdysone receptor (EcR), Liver X receptor (LXR) and Farnesoid X receptor (FXR). The DNA binding activity is regulated by their corresponding ligands. The ligands for EcR are ecdysteroids; LXR is regulated by oxidized cholesterol derivatives or oxysterols; and bile acids control FXR's activities. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcR-like receptors have a central well conserved DNA binding domai
Probab=32.90 E-value=24 Score=23.03 Aligned_cols=27 Identities=33% Similarity=0.821 Sum_probs=20.8
Q ss_pred ccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 27 CFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 27 C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
|.-||.+.. ...||+..|..|.+..|-
T Consensus 2 C~vCg~~~~---~~hygv~sC~aC~~FFRR 28 (73)
T cd06959 2 CVVCGDKAS---GFHYGVLSCEGCKGFFRR 28 (73)
T ss_pred CceeCCcCc---ceEECceeehhhHHHHHH
Confidence 666776443 468999999999998764
No 87
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=32.87 E-value=17 Score=26.09 Aligned_cols=24 Identities=42% Similarity=0.864 Sum_probs=20.8
Q ss_pred Cceeeccc--hhcchhhhhhhhcCCC
Q psy7550 36 TWSSVTYG--VFICIDCSAVHRGLGV 59 (144)
Q Consensus 36 ~w~s~~~G--iflC~~CsgiHR~lg~ 59 (144)
.|++-.-| |.-|.+|-=|||.-++
T Consensus 52 ewi~~~~G~~VwSC~dC~~iH~ke~~ 77 (112)
T COG2158 52 EWISDSNGRKVWSCSDCHWIHRKEGA 77 (112)
T ss_pred ceeEcCCCCEEeeccccceecccchH
Confidence 89998889 9999999999987544
No 88
>PF13119 DUF3973: Domain of unknown function (DUF3973)
Probab=32.76 E-value=13 Score=22.06 Aligned_cols=15 Identities=40% Similarity=1.161 Sum_probs=11.4
Q ss_pred hcchhhhhhhhcCCC
Q psy7550 45 FICIDCSAVHRGLGV 59 (144)
Q Consensus 45 flC~~CsgiHR~lg~ 59 (144)
|-|+.||.+|-.-+.
T Consensus 2 yYCi~Cs~~h~e~~~ 16 (41)
T PF13119_consen 2 YYCINCSEIHHEKGI 16 (41)
T ss_pred EEEEEhHHhHHhhcc
Confidence 569999999976433
No 89
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=32.66 E-value=37 Score=23.62 Aligned_cols=39 Identities=18% Similarity=0.355 Sum_probs=27.1
Q ss_pred HHHHHHH-hcCCCCCCccCCCCCCCCceeeccchhcchhhhh
Q psy7550 12 EVIFKKL-RNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSA 52 (144)
Q Consensus 12 ~~~~~~L-~~~~~N~~C~DCg~~~p~w~s~~~GiflC~~Csg 52 (144)
++.++++ .+...-..|.-||........ .||+-|..|.-
T Consensus 23 RK~v~kie~~q~a~y~CpfCgk~~vkR~a--~GIW~C~~C~~ 62 (90)
T PTZ00255 23 RKQIKKIEISQHAKYFCPFCGKHAVKRQA--VGIWRCKGCKK 62 (90)
T ss_pred HHHHHHHHHHHhCCccCCCCCCCceeeee--eEEEEcCCCCC
Confidence 3333433 445677899999987766554 49999999943
No 90
>PF13462 Thioredoxin_4: Thioredoxin; PDB: 3FEU_A 3HZ8_A 3DVW_A 3A3T_E 3GMF_A 1Z6M_A 3GYK_C 3BCK_A 3BD2_A 3BCI_A ....
Probab=32.09 E-value=24 Score=25.11 Aligned_cols=28 Identities=18% Similarity=0.396 Sum_probs=22.4
Q ss_pred CCCCCCceeeccchhcchhhhhhhhcCC
Q psy7550 31 NAKNPTWSSVTYGVFICIDCSAVHRGLG 58 (144)
Q Consensus 31 g~~~p~w~s~~~GiflC~~CsgiHR~lg 58 (144)
|.++.....+-|.-|.|..|+..|..++
T Consensus 8 G~~~a~~~v~~f~d~~Cp~C~~~~~~~~ 35 (162)
T PF13462_consen 8 GNPDAPITVTEFFDFQCPHCAKFHEELE 35 (162)
T ss_dssp S-TTTSEEEEEEE-TTSHHHHHHHHHHH
T ss_pred cCCCCCeEEEEEECCCCHhHHHHHHHHh
Confidence 5677778888999999999999998764
No 91
>cd06967 NR_DBD_TR2_like DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. It has been shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or
Probab=32.00 E-value=15 Score=24.97 Aligned_cols=29 Identities=24% Similarity=0.622 Sum_probs=22.8
Q ss_pred CCccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 25 KECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 25 ~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
..|.-||.+... ..||+..|..|.+..|-
T Consensus 4 ~~C~VCg~~~~g---~hyGv~sC~aC~~FFRR 32 (87)
T cd06967 4 ELCVVCGDKASG---RHYGAVSCEGCKGFFKR 32 (87)
T ss_pred CCCeecCCcCCc---CEeCcceEeeeeeEeee
Confidence 458889975543 58999999999997754
No 92
>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=31.48 E-value=30 Score=28.95 Aligned_cols=30 Identities=20% Similarity=0.448 Sum_probs=21.5
Q ss_pred CCCCCccCCCCCCCCceeec--------cchhcchhhh
Q psy7550 22 PTNKECFDCNAKNPTWSSVT--------YGVFICIDCS 51 (144)
Q Consensus 22 ~~N~~C~DCg~~~p~w~s~~--------~GiflC~~Cs 51 (144)
.+...|..||..+..|.-+- .-.|+|..|.
T Consensus 256 t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg 293 (299)
T TIGR01385 256 TDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECG 293 (299)
T ss_pred cccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCC
Confidence 34679999999988876431 3355888885
No 93
>cd06970 NR_DBD_PNR DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of the nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hing
Probab=31.31 E-value=18 Score=24.97 Aligned_cols=31 Identities=23% Similarity=0.634 Sum_probs=24.2
Q ss_pred CCCCccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 23 TNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 23 ~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
-...|.-||.+.. ...||+..|..|.+..|-
T Consensus 5 p~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (92)
T cd06970 5 PGLLCRVCGDTSS---GKHYGIYACNGCSGFFKR 35 (92)
T ss_pred CCCCCeecCCcCc---ccEECccEEeeeeeEeee
Confidence 3456999997654 358999999999998754
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=31.04 E-value=14 Score=20.79 Aligned_cols=27 Identities=19% Similarity=0.532 Sum_probs=18.4
Q ss_pred CccCCCCCCCCceeec-cchhcchhhhh
Q psy7550 26 ECFDCNAKNPTWSSVT-YGVFICIDCSA 52 (144)
Q Consensus 26 ~C~DCg~~~p~w~s~~-~GiflC~~Csg 52 (144)
.|.+||..-..|.++. -....|..|.+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 5788888665566554 45667888866
No 95
>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=30.82 E-value=17 Score=20.33 Aligned_cols=23 Identities=22% Similarity=0.488 Sum_probs=13.6
Q ss_pred CccCCCCCCCCceeeccchhcchhhh
Q psy7550 26 ECFDCNAKNPTWSSVTYGVFICIDCS 51 (144)
Q Consensus 26 ~C~DCg~~~p~w~s~~~GiflC~~Cs 51 (144)
.|.+||+... .. .....-|..|.
T Consensus 2 ~C~~Cg~~~~--~~-~~~~irC~~CG 24 (32)
T PF03604_consen 2 ICGECGAEVE--LK-PGDPIRCPECG 24 (32)
T ss_dssp BESSSSSSE---BS-TSSTSSBSSSS
T ss_pred CCCcCCCeeE--cC-CCCcEECCcCC
Confidence 5889998755 11 22345777774
No 96
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=30.26 E-value=17 Score=19.47 Aligned_cols=17 Identities=29% Similarity=0.714 Sum_probs=9.6
Q ss_pred cCCCCCCccCCCCCCCC
Q psy7550 20 NIPTNKECFDCNAKNPT 36 (144)
Q Consensus 20 ~~~~N~~C~DCg~~~p~ 36 (144)
..+.+..|.-|+++.|.
T Consensus 14 N~~~~~~C~~C~~~rp~ 30 (30)
T PF00641_consen 14 NPASRSKCVACGAPRPG 30 (30)
T ss_dssp EESSSSB-TTT--BTTB
T ss_pred chHHhhhhhCcCCCCcC
Confidence 34667788888887763
No 97
>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=30.08 E-value=23 Score=24.35 Aligned_cols=28 Identities=21% Similarity=0.572 Sum_probs=21.9
Q ss_pred CCCccCCCCCCCCceeec--------cchhcchhhh
Q psy7550 24 NKECFDCNAKNPTWSSVT--------YGVFICIDCS 51 (144)
Q Consensus 24 N~~C~DCg~~~p~w~s~~--------~GiflC~~Cs 51 (144)
+..|..||.....|..+. .-.|+|.+|.
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~ 97 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCG 97 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCC
Confidence 789999999988887553 3478888885
No 98
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=29.26 E-value=28 Score=21.98 Aligned_cols=30 Identities=20% Similarity=0.501 Sum_probs=22.2
Q ss_pred CCCCCCccCCCCCCCCceeeccchhcchhhhh
Q psy7550 21 IPTNKECFDCNAKNPTWSSVTYGVFICIDCSA 52 (144)
Q Consensus 21 ~~~N~~C~DCg~~~p~w~s~~~GiflC~~Csg 52 (144)
-++-+.|.-||.+. =.--.||..+|..|-.
T Consensus 13 GkGsr~C~vCg~~~--gliRkygL~~CRqCFR 42 (54)
T PTZ00218 13 GKGSRQCRVCSNRH--GLIRKYGLNVCRQCFR 42 (54)
T ss_pred CCCCCeeecCCCcc--hhhhhcCcchhhHHHH
Confidence 35778999999853 2333799999999854
No 99
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
Probab=29.05 E-value=21 Score=23.00 Aligned_cols=30 Identities=27% Similarity=0.534 Sum_probs=23.1
Q ss_pred ccC-CCCCCCC-ceeeccchhcchhhhhhhhcC
Q psy7550 27 CFD-CNAKNPT-WSSVTYGVFICIDCSAVHRGL 57 (144)
Q Consensus 27 C~D-Cg~~~p~-w~s~~~GiflC~~CsgiHR~l 57 (144)
..| ||.-.|. +..-+...+.|..| |-||+|
T Consensus 21 a~DGCgEFm~~~g~eg~~~al~CaAC-gCHRnF 52 (60)
T PF04770_consen 21 AVDGCGEFMPSPGEEGTPEALKCAAC-GCHRNF 52 (60)
T ss_pred ccccccccccCCCCCCCcccceeccc-Ccchhc
Confidence 455 8887777 66667788999988 789886
No 100
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=28.73 E-value=15 Score=20.69 Aligned_cols=29 Identities=21% Similarity=0.398 Sum_probs=20.4
Q ss_pred CCCccCCCCCCCCceeeccchhcchhhhhhh
Q psy7550 24 NKECFDCNAKNPTWSSVTYGVFICIDCSAVH 54 (144)
Q Consensus 24 N~~C~DCg~~~p~w~s~~~GiflC~~CsgiH 54 (144)
.+.|-.|+...--| -+-+..+|..|..++
T Consensus 3 ~~~C~~C~~~~i~~--~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVN--KEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEE--ecCCeEEcccCCcEe
Confidence 45788888876443 467888888886543
No 101
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=28.55 E-value=17 Score=28.92 Aligned_cols=24 Identities=33% Similarity=0.676 Sum_probs=19.6
Q ss_pred CCCCccCCCCCCCCceeeccchhcchhhhhh
Q psy7550 23 TNKECFDCNAKNPTWSSVTYGVFICIDCSAV 53 (144)
Q Consensus 23 ~N~~C~DCg~~~p~w~s~~~GiflC~~Csgi 53 (144)
.-+.|.-||. +.-+.|.|..|...
T Consensus 308 tS~~C~~cg~-------~~~r~~~C~~cg~~ 331 (364)
T COG0675 308 TSKTCPCCGH-------LSGRLFKCPRCGFV 331 (364)
T ss_pred CcccccccCC-------ccceeEECCCCCCe
Confidence 3479999999 66789999999753
No 102
>PRK00420 hypothetical protein; Validated
Probab=28.50 E-value=49 Score=23.86 Aligned_cols=28 Identities=21% Similarity=0.315 Sum_probs=21.3
Q ss_pred CCCCccCCCCCCCCceeeccchhcchhhhhh
Q psy7550 23 TNKECFDCNAKNPTWSSVTYGVFICIDCSAV 53 (144)
Q Consensus 23 ~N~~C~DCg~~~p~w~s~~~GiflC~~Csgi 53 (144)
-+..|..||.+-.. +.-|-.+|..|...
T Consensus 22 l~~~CP~Cg~pLf~---lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 22 LSKHCPVCGLPLFE---LKDGEVVCPVHGKV 49 (112)
T ss_pred ccCCCCCCCCccee---cCCCceECCCCCCe
Confidence 46899999976543 26789999999653
No 103
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=28.24 E-value=20 Score=21.26 Aligned_cols=30 Identities=20% Similarity=0.309 Sum_probs=18.8
Q ss_pred CCccCCCCCC--CCceeeccchhcchhhhhhhhc
Q psy7550 25 KECFDCNAKN--PTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 25 ~~C~DCg~~~--p~w~s~~~GiflC~~CsgiHR~ 56 (144)
+.|.+||..- +.+.. --.++|..|.-.++.
T Consensus 1 ~FCp~Cg~~l~~~~~~~--~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 1 KFCPKCGNMLIPKEGKE--KRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCCCccccccCCC--CCEEECCcCCCeEEC
Confidence 4799999843 22221 127889999766554
No 104
>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=27.98 E-value=18 Score=25.77 Aligned_cols=30 Identities=27% Similarity=0.652 Sum_probs=20.2
Q ss_pred CCCCCCccCCCCCCCCceeeccchhcchhhhhhh
Q psy7550 21 IPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVH 54 (144)
Q Consensus 21 ~~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiH 54 (144)
.|.--.|.+||.. ..+..-.+.|..|.+..
T Consensus 67 ~p~~~~C~~Cg~~----~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 67 EPVECECEDCSEE----VSPEIDLYRCPKCHGIM 96 (115)
T ss_pred eCcEEEcccCCCE----EecCCcCccCcCCcCCC
Confidence 5677799999953 22222257899998754
No 105
>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=27.46 E-value=21 Score=21.10 Aligned_cols=25 Identities=24% Similarity=0.632 Sum_probs=16.8
Q ss_pred CCCCccCCCCCCCCceeeccchhcchhh
Q psy7550 23 TNKECFDCNAKNPTWSSVTYGVFICIDC 50 (144)
Q Consensus 23 ~N~~C~DCg~~~p~w~s~~~GiflC~~C 50 (144)
-+..|.+||.+--+ ..-|..+|..|
T Consensus 16 L~~~Cp~C~~PL~~---~k~g~~~Cv~C 40 (41)
T PF06677_consen 16 LDEHCPDCGTPLMR---DKDGKIYCVSC 40 (41)
T ss_pred hcCccCCCCCeeEE---ecCCCEECCCC
Confidence 37889999876433 24566777776
No 106
>PHA02942 putative transposase; Provisional
Probab=27.19 E-value=21 Score=30.65 Aligned_cols=26 Identities=23% Similarity=0.531 Sum_probs=19.8
Q ss_pred CCCccCCCCCCCCceeeccchhcchhhhh
Q psy7550 24 NKECFDCNAKNPTWSSVTYGVFICIDCSA 52 (144)
Q Consensus 24 N~~C~DCg~~~p~w~s~~~GiflC~~Csg 52 (144)
-+.|..||...+ .++-.+|.|..|.-
T Consensus 325 Sq~Cs~CG~~~~---~l~~r~f~C~~CG~ 350 (383)
T PHA02942 325 SVSCPKCGHKMV---EIAHRYFHCPSCGY 350 (383)
T ss_pred CccCCCCCCccC---cCCCCEEECCCCCC
Confidence 468999998765 34567899999954
No 107
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=27.12 E-value=52 Score=22.32 Aligned_cols=31 Identities=29% Similarity=0.636 Sum_probs=22.9
Q ss_pred CccCCCCCCCC---ceeeccc---hhcchhhhhhhhc
Q psy7550 26 ECFDCNAKNPT---WSSVTYG---VFICIDCSAVHRG 56 (144)
Q Consensus 26 ~C~DCg~~~p~---w~s~~~G---iflC~~CsgiHR~ 56 (144)
.|+-||.+-|. +...--| .|-|..|.+|...
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~~~ 38 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVYQL 38 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHHHH
Confidence 69999998763 3333334 8999999998765
No 108
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=27.06 E-value=27 Score=26.92 Aligned_cols=28 Identities=21% Similarity=0.519 Sum_probs=18.2
Q ss_pred CccCCCCCCCCceeeccchhcchhhhhhh
Q psy7550 26 ECFDCNAKNPTWSSVTYGVFICIDCSAVH 54 (144)
Q Consensus 26 ~C~DCg~~~p~w~s~~~GiflC~~CsgiH 54 (144)
.|..|+..-+.=--+++ -|.|..|.+.-
T Consensus 119 ~Cp~C~~rytf~eA~~~-~F~Cp~Cg~~L 146 (178)
T PRK06266 119 FCPNCHIRFTFDEAMEY-GFRCPQCGEML 146 (178)
T ss_pred ECCCCCcEEeHHHHhhc-CCcCCCCCCCC
Confidence 68888865332223444 59999997753
No 109
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=26.16 E-value=18 Score=25.82 Aligned_cols=31 Identities=19% Similarity=0.250 Sum_probs=21.5
Q ss_pred CCCCCCccCCCCCCCCceeeccchhcchhhhhhh
Q psy7550 21 IPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVH 54 (144)
Q Consensus 21 ~~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiH 54 (144)
.|..-.|.+||.. +....+..+.|..|.+..
T Consensus 67 ~p~~~~C~~Cg~~---~~~~~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 67 QEAECWCETCQQY---VTLLTQRVRRCPQCHGDM 97 (114)
T ss_pred eCcEEEcccCCCe---eecCCccCCcCcCcCCCC
Confidence 4677789999963 333344557899998654
No 110
>TIGR00598 rad14 DNA repair protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.52 E-value=18 Score=28.05 Aligned_cols=28 Identities=14% Similarity=0.427 Sum_probs=20.6
Q ss_pred ccCCCCCCCC-ceeeccchhcchhhhhhh
Q psy7550 27 CFDCNAKNPT-WSSVTYGVFICIDCSAVH 54 (144)
Q Consensus 27 C~DCg~~~p~-w~s~~~GiflC~~CsgiH 54 (144)
|.+||...-. |.--+|++-||..|..-+
T Consensus 1 C~eCg~~~~D~~l~~~F~~~vC~~C~~~~ 29 (172)
T TIGR00598 1 CEECGKIFMDSYLFDHFDCAVCDNCRDKD 29 (172)
T ss_pred CccccchhhhHHHHHHCCChhhhhhhccc
Confidence 8899985332 334489999999998754
No 111
>PF11342 DUF3144: Protein of unknown function (DUF3144); InterPro: IPR021490 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=25.28 E-value=2.2e+02 Score=19.14 Aligned_cols=55 Identities=15% Similarity=0.098 Sum_probs=36.8
Q ss_pred HHHHHHHhhChHHHHHHHhhcCCCCcchHHHhhHHHHHHHHHHHHHHHHHHHHHc
Q psy7550 76 VQLRQMQLGGNANAVSFFNQHNCTSKDAQQKYNSRAAQLYREKLQHAAVQAMKIH 130 (144)
Q Consensus 76 ~~l~~m~~gGN~~~~~~~e~~~~~~~~~~~ky~~~~~~~yr~kl~~~~~~~~~~~ 130 (144)
.+|..--.-+..++|.|.-+....+...-..-+..+-.+|.+.++.+....+..|
T Consensus 23 g~VsaallyAaARfnAf~~a~~~~~~~~~~~~ke~~i~~f~~qy~~mL~~nlddy 77 (78)
T PF11342_consen 23 GQVSAALLYAAARFNAFVAASSFESKADMAAEKEEAIDYFTEQYRKMLEENLDDY 77 (78)
T ss_pred chHHHHHHHHHHHHHHHHHHHccCcHHHHHHhHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4444433457889999998877776544344456666778888888777666544
No 112
>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=24.98 E-value=24 Score=19.49 Aligned_cols=24 Identities=17% Similarity=0.623 Sum_probs=11.9
Q ss_pred CccCCCCCCCCceeeccchhcchhhhh
Q psy7550 26 ECFDCNAKNPTWSSVTYGVFICIDCSA 52 (144)
Q Consensus 26 ~C~DCg~~~p~w~s~~~GiflC~~Csg 52 (144)
.|--|++... | ..-.+|||..|..
T Consensus 4 ~Cp~C~se~~-y--~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYT-Y--EDGELLVCPECGH 27 (30)
T ss_dssp --TTT------E--E-SSSEEETTTTE
T ss_pred CCCCCCCcce-e--ccCCEEeCCcccc
Confidence 4666666433 2 6778899999863
No 113
>PF13746 Fer4_18: 4Fe-4S dicluster domain
Probab=24.50 E-value=52 Score=21.15 Aligned_cols=22 Identities=23% Similarity=0.442 Sum_probs=18.2
Q ss_pred HHHHHHHHhcCCCCCCccCCCC
Q psy7550 11 IEVIFKKLRNIPTNKECFDCNA 32 (144)
Q Consensus 11 ~~~~~~~L~~~~~N~~C~DCg~ 32 (144)
..+.+.++....+...|.+||.
T Consensus 36 r~r~~~k~~~~~~~~~CVgCgr 57 (69)
T PF13746_consen 36 RYRFMHKLRDRYGEGDCVGCGR 57 (69)
T ss_pred chhhhhhhhhhcCCccCCCcCh
Confidence 4567788888889999999998
No 114
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=24.15 E-value=1.4e+02 Score=16.68 Aligned_cols=21 Identities=29% Similarity=0.594 Sum_probs=14.1
Q ss_pred CCCCCHHHHHHHHhhChHHHHHHHhhcCCCCcc
Q psy7550 70 DTNWTWVQLRQMQLGGNANAVSFFNQHNCTSKD 102 (144)
Q Consensus 70 d~~w~~~~l~~m~~gGN~~~~~~~e~~~~~~~~ 102 (144)
|+ |+.++|+ .+++.||++...
T Consensus 2 dt-Ws~~~L~-----------~wL~~~gi~~~~ 22 (38)
T PF10281_consen 2 DT-WSDSDLK-----------SWLKSHGIPVPK 22 (38)
T ss_pred CC-CCHHHHH-----------HHHHHcCCCCCC
Confidence 55 8876654 577788887543
No 115
>PTZ00074 60S ribosomal protein L34; Provisional
Probab=24.10 E-value=58 Score=24.30 Aligned_cols=32 Identities=28% Similarity=0.584 Sum_probs=21.2
Q ss_pred CCCCCCccCCCCCC-------C----------Cceeeccchhcchhhhh
Q psy7550 21 IPTNKECFDCNAKN-------P----------TWSSVTYGVFICIDCSA 52 (144)
Q Consensus 21 ~~~N~~C~DCg~~~-------p----------~w~s~~~GiflC~~Csg 52 (144)
.+.--.|.|||.+- | .-++=.||-.+|..|-.
T Consensus 38 ~~~~pkC~~cg~~L~GI~~~Rp~e~~rlsK~~KtvsRaYGG~lC~~CVr 86 (135)
T PTZ00074 38 KSSGPKCGDCGKVLAGIKALRPTEYKQLSRRERTVSRAYGGVLCHKCVR 86 (135)
T ss_pred CCCCCCCCCCCCccCCccCCchHHHHHccccCCCccCCCccchhHHHHH
Confidence 34445799999962 1 22344589999998853
No 116
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=23.92 E-value=31 Score=23.96 Aligned_cols=31 Identities=19% Similarity=0.470 Sum_probs=23.5
Q ss_pred hcCCCCCCccCCCCCCCCceeeccchhcchhhh
Q psy7550 19 RNIPTNKECFDCNAKNPTWSSVTYGVFICIDCS 51 (144)
Q Consensus 19 ~~~~~N~~C~DCg~~~p~w~s~~~GiflC~~Cs 51 (144)
.+....-.|.-||..... -+..||+-|..|.
T Consensus 30 ~~q~~ky~Cp~Cgk~~vk--R~a~GIW~C~~C~ 60 (90)
T PF01780_consen 30 ISQHAKYTCPFCGKTSVK--RVATGIWKCKKCG 60 (90)
T ss_dssp HHHHS-BEESSSSSSEEE--EEETTEEEETTTT
T ss_pred HHHhCCCcCCCCCCceeE--EeeeEEeecCCCC
Confidence 445578899999998744 4578999999995
No 117
>cd07154 NR_DBD_PNR_like The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family. The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear
Probab=23.79 E-value=24 Score=22.97 Aligned_cols=27 Identities=30% Similarity=0.803 Sum_probs=20.0
Q ss_pred ccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 27 CFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 27 C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
|.-||.+.. ...||+..|..|.+..|-
T Consensus 1 C~vCg~~~~---~~hyGv~sC~aC~~FFRR 27 (73)
T cd07154 1 CKVCGDRSS---GKHYGVYACDGCSGFFKR 27 (73)
T ss_pred CcccCccCc---ceEECcceeeeeeeEeee
Confidence 455776443 458999999999998754
No 118
>cd06957 NR_DBD_PNR_like_2 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like is composed of two C4-type zinc fingers. The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members
Probab=23.31 E-value=24 Score=23.65 Aligned_cols=27 Identities=33% Similarity=0.763 Sum_probs=19.7
Q ss_pred ccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 27 CFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 27 C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
|.-||.+.. ...||+..|..|.+..|-
T Consensus 1 C~VCg~~~~---g~hyGv~sC~aCk~FFRR 27 (82)
T cd06957 1 CKVCGDKSY---GKHYGVYCCDGCSCFFKR 27 (82)
T ss_pred CCccCccCc---ceEECcceEeeeeeEEEE
Confidence 455665433 468999999999998653
No 119
>COG4012 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.24 E-value=90 Score=26.35 Aligned_cols=29 Identities=24% Similarity=0.487 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHH--cCCeeeecCCCcccC
Q psy7550 116 REKLQHAAVQAMKI--HGTKLFLDAMHGCYT 144 (144)
Q Consensus 116 r~kl~~~~~~~~~~--~~~~~~~~~~~~~~~ 144 (144)
++||+....+.... ..++|+.||++|||.
T Consensus 262 pekled~I~rf~~GeL~neeV~~DgGHGch~ 292 (342)
T COG4012 262 PEKLEDQIIRFVEGELENEEVYRDGGHGCHN 292 (342)
T ss_pred HHHHHHHHHHHHhcccccceeecCCCCceee
Confidence 34444444433333 378999999999983
No 120
>cd06964 NR_DBD_RAR DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RARs mediate the biological effect of retinoids, including both natural dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RAR function as a heterodimer with retinoic X receptor by binding to specific RAR response elements (RAREs), which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair and found in the promoter reg
Probab=23.18 E-value=28 Score=23.51 Aligned_cols=29 Identities=38% Similarity=0.834 Sum_probs=23.2
Q ss_pred CCccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 25 KECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 25 ~~C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
..|.-||.+.. ...||+..|..|.+..|-
T Consensus 5 ~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 33 (85)
T cd06964 5 KPCFVCQDKSS---GYHYGVSACEGCKGFFRR 33 (85)
T ss_pred CCCcccCCcCc---ccEECcceeeeeeeEEee
Confidence 46888997543 468999999999998764
No 121
>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=22.82 E-value=46 Score=29.08 Aligned_cols=29 Identities=24% Similarity=0.529 Sum_probs=20.7
Q ss_pred CCCccCCCCCCCCceeec--cchhcchhhhh
Q psy7550 24 NKECFDCNAKNPTWSSVT--YGVFICIDCSA 52 (144)
Q Consensus 24 N~~C~DCg~~~p~w~s~~--~GiflC~~Csg 52 (144)
+..|.-||.+..+--.+- -|++||.+|..
T Consensus 7 ~~~c~fc~~~~~~~~~~~~~~~~~ic~~c~~ 37 (413)
T TIGR00382 7 TLYCSFCGKSQDEVRKLIAGPGVYICDECIE 37 (413)
T ss_pred CeecCCCCCChhhcccccCCCCCcCCCchHH
Confidence 448999999765543333 35899999975
No 122
>cd06916 NR_DBD_like DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Most nuclear receptors bind as homodimers or hetero
Probab=22.69 E-value=26 Score=22.79 Aligned_cols=27 Identities=33% Similarity=0.791 Sum_probs=19.9
Q ss_pred ccCCCCCCCCceeeccchhcchhhhhhhhc
Q psy7550 27 CFDCNAKNPTWSSVTYGVFICIDCSAVHRG 56 (144)
Q Consensus 27 C~DCg~~~p~w~s~~~GiflC~~CsgiHR~ 56 (144)
|.-||.+.. ...||+..|..|.+..|-
T Consensus 1 C~vC~~~~~---~~hygv~sC~aC~~FFRR 27 (72)
T cd06916 1 CAVCGDKAS---GYHYGVLTCEGCKGFFRR 27 (72)
T ss_pred CCccCccCc---ccEECcceeeeeeeeEeE
Confidence 455666443 468999999999997754
No 123
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=22.52 E-value=41 Score=20.60 Aligned_cols=26 Identities=23% Similarity=0.546 Sum_probs=17.8
Q ss_pred CCCCccCCCCCCCCceeeccchhcchhhh
Q psy7550 23 TNKECFDCNAKNPTWSSVTYGVFICIDCS 51 (144)
Q Consensus 23 ~N~~C~DCg~~~p~w~s~~~GiflC~~Cs 51 (144)
-++.|..||+. ......+.+.|..|.
T Consensus 19 ~~~fCP~Cg~~---~m~~~~~r~~C~~Cg 44 (50)
T PRK00432 19 KNKFCPRCGSG---FMAEHLDRWHCGKCG 44 (50)
T ss_pred ccCcCcCCCcc---hheccCCcEECCCcC
Confidence 46689999973 333345788888883
No 124
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.26 E-value=23 Score=25.32 Aligned_cols=30 Identities=20% Similarity=0.503 Sum_probs=18.7
Q ss_pred CCCCCccCCCCCCCCceeeccchhcchhhhhhh
Q psy7550 22 PTNKECFDCNAKNPTWSSVTYGVFICIDCSAVH 54 (144)
Q Consensus 22 ~~N~~C~DCg~~~p~w~s~~~GiflC~~CsgiH 54 (144)
|.--.|.+||.. |....+..+.|..|.+..
T Consensus 69 p~~~~C~~Cg~~---~~~~~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 69 KVELECKDCSHV---FKPNALDYGVCEKCHSKN 98 (117)
T ss_pred CCEEEhhhCCCc---cccCCccCCcCcCCCCCc
Confidence 344579999943 222234455699998753
No 125
>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=21.70 E-value=28 Score=20.76 Aligned_cols=27 Identities=15% Similarity=0.505 Sum_probs=18.8
Q ss_pred CccCCCCCCCCceeecc-chhcchhhhh
Q psy7550 26 ECFDCNAKNPTWSSVTY-GVFICIDCSA 52 (144)
Q Consensus 26 ~C~DCg~~~p~w~s~~~-GiflC~~Csg 52 (144)
.|-+||..--.|.++.- ....|..|.+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 58888886666766543 4556888876
No 126
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=21.65 E-value=45 Score=17.35 Aligned_cols=12 Identities=50% Similarity=0.944 Sum_probs=6.8
Q ss_pred CCCCCccCCCCC
Q psy7550 22 PTNKECFDCNAK 33 (144)
Q Consensus 22 ~~N~~C~DCg~~ 33 (144)
++.+.|..||++
T Consensus 14 ~~~~fC~~CG~~ 25 (26)
T PF13248_consen 14 PDAKFCPNCGAK 25 (26)
T ss_pred cccccChhhCCC
Confidence 445666666653
No 127
>KOG1416|consensus
Probab=21.39 E-value=1.2e+02 Score=27.23 Aligned_cols=45 Identities=20% Similarity=0.291 Sum_probs=30.5
Q ss_pred CCHHHHHHHHhhChHHHHHHHhhc--CC-----CCcchHHHhhHHHHHHHHHH
Q psy7550 73 WTWVQLRQMQLGGNANAVSFFNQH--NC-----TSKDAQQKYNSRAAQLYREK 118 (144)
Q Consensus 73 w~~~~l~~m~~gGN~~~~~~~e~~--~~-----~~~~~~~ky~~~~~~~yr~k 118 (144)
-+.++|..|+..|+. +.++.++- +. .....++||-.+..++|-++
T Consensus 115 Lt~EeI~~mr~eg~~-g~EiI~kLienSkTF~~KT~fSQeKYv~rK~kKy~~~ 166 (475)
T KOG1416|consen 115 LTQEEIEEMRQEGLS-GEEIIEKLIENSKTFHNKTVFSQEKYVLRKKKKYAKR 166 (475)
T ss_pred CCHHHHHHHHHhccC-HHHHHHHHHhcCcccccchhhhHHHHHHHHhhhhhhh
Confidence 678999999998774 44444321 11 12357899999998888665
No 128
>KOG0457|consensus
Probab=20.82 E-value=1.5e+02 Score=26.31 Aligned_cols=62 Identities=21% Similarity=0.397 Sum_probs=28.9
Q ss_pred CCCCCC-ccCCCCC--CCCceeeccc--hhcchhhhhhhhcCCCC-----Ccceeecc---CCCCCCH-HHHHHHH
Q psy7550 21 IPTNKE-CFDCNAK--NPTWSSVTYG--VFICIDCSAVHRGLGVH-----LSFVRSTQ---LDTNWTW-VQLRQMQ 82 (144)
Q Consensus 21 ~~~N~~-C~DCg~~--~p~w~s~~~G--iflC~~CsgiHR~lg~~-----iS~VkS~~---ld~~w~~-~~l~~m~ 82 (144)
.++++. |.-|..- ++..+...-. ..||+.|-..=-.+|+| .-.|...+ ++..|+. +|+..++
T Consensus 10 ~~g~ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLe 85 (438)
T KOG0457|consen 10 DPGGKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSVGAETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLE 85 (438)
T ss_pred cCCCCCCCccHhHHhccceEEEeecCCCcchhHHHHhcccccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHH
Confidence 455554 3336552 3333322221 47899997543334433 11222211 1224985 6776654
No 129
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=20.77 E-value=33 Score=19.74 Aligned_cols=28 Identities=14% Similarity=0.422 Sum_probs=16.2
Q ss_pred CccCCCCCCCCceeeccchhcchhhhhh
Q psy7550 26 ECFDCNAKNPTWSSVTYGVFICIDCSAV 53 (144)
Q Consensus 26 ~C~DCg~~~p~w~s~~~GiflC~~Csgi 53 (144)
.|..|+..-..-..-.+-|..|..|.|+
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCGGI 28 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCCeE
Confidence 3666776433222244566778888665
No 130
>PF11261 IRF-2BP1_2: Interferon regulatory factor 2-binding protein zinc finger; InterPro: IPR022750 IRF-2BP1 and IRF-2BP2 are nuclear transcriptional repressor proteins and can inhibit both enhancer-activated and basal transcription. They both contain N-terminal zinc finger and C-terminal RING finger domains []. This entry represents the N-terminal zinc finger domain of IRF-2BP1 and IRF-2BP2.
Probab=20.74 E-value=32 Score=21.59 Aligned_cols=28 Identities=18% Similarity=0.774 Sum_probs=23.5
Q ss_pred CCccCCCCCCCCceee-ccchhcchhhhh
Q psy7550 25 KECFDCNAKNPTWSSV-TYGVFICIDCSA 52 (144)
Q Consensus 25 ~~C~DCg~~~p~w~s~-~~GiflC~~Csg 52 (144)
..|+-|--+.+.|+-+ .|+-.||..|..
T Consensus 4 q~CyLCdlPr~PWami~df~EpVCRgCvN 32 (54)
T PF11261_consen 4 QQCYLCDLPRMPWAMIWDFSEPVCRGCVN 32 (54)
T ss_pred eeEEeccCCCCchHHHhhccchhhhhhcC
Confidence 4699999999999965 789999999853
No 131
>KOG0686|consensus
Probab=20.66 E-value=3.3e+02 Score=24.29 Aligned_cols=52 Identities=12% Similarity=0.229 Sum_probs=32.6
Q ss_pred CCHHHHHHHHhhChHHHHHHHhhcCCCCcchHHHhhHHHHHHHHHHHHHHHHHHHHHcCCee
Q psy7550 73 WTWVQLRQMQLGGNANAVSFFNQHNCTSKDAQQKYNSRAAQLYREKLQHAAVQAMKIHGTKL 134 (144)
Q Consensus 73 w~~~~l~~m~~gGN~~~~~~~e~~~~~~~~~~~ky~~~~~~~yr~kl~~~~~~~~~~~~~~~ 134 (144)
|+..++. +...+|..++.|++- ..+.+....+||..+|.+- ..-+++-...|
T Consensus 283 fdr~~Lk-~~vi~n~~Fk~flel--------~Pqlr~il~~fy~sky~~c-l~~L~~~k~~l 334 (466)
T KOG0686|consen 283 FDRQDLK-LNVIKNESFKLFLEL--------EPQLREILFKFYSSKYASC-LELLREIKPRL 334 (466)
T ss_pred CCHHHHH-HHHHcchhhhhHHhc--------ChHHHHHHHHHhhhhHHHH-HHHHHHhccce
Confidence 8888886 567799999999973 2334555566666666543 33344443333
Done!