Query psy13622
Match_columns 143
No_of_seqs 113 out of 1129
Neff 6.7
Searched_HMMs 46136
Date Fri Aug 16 15:54:50 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13622.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13622hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0703|consensus 100.0 1.8E-41 3.8E-46 273.7 6.8 99 1-105 29-127 (287)
2 smart00105 ArfGap Putative GTP 100.0 8.4E-41 1.8E-45 238.8 8.6 103 1-106 7-109 (112)
3 PF01412 ArfGap: Putative GTPa 100.0 2.8E-40 6.1E-45 237.3 4.6 100 1-104 17-116 (116)
4 KOG0705|consensus 100.0 6.6E-38 1.4E-42 269.9 7.5 134 1-138 517-650 (749)
5 KOG0818|consensus 100.0 4.4E-36 9.5E-41 255.5 9.6 141 2-142 13-163 (669)
6 COG5347 GTPase-activating prot 100.0 1.4E-35 3.1E-40 244.0 8.0 101 1-104 24-125 (319)
7 PLN03131 hypothetical protein; 100.0 1.1E-32 2.3E-37 239.3 7.8 102 1-108 27-128 (705)
8 PLN03119 putative ADP-ribosyla 100.0 1.7E-32 3.6E-37 236.5 8.5 99 1-105 27-125 (648)
9 KOG0704|consensus 100.0 4.2E-29 9.1E-34 205.2 5.2 104 1-104 23-127 (386)
10 PLN03114 ADP-ribosylation fact 99.9 4.5E-28 9.8E-33 200.2 6.9 102 1-103 26-127 (395)
11 KOG0706|consensus 99.9 4.5E-28 9.8E-33 204.1 4.7 70 1-70 27-96 (454)
12 KOG0521|consensus 99.9 1.3E-27 2.7E-32 215.6 5.3 104 1-106 430-533 (785)
13 KOG1117|consensus 99.9 5.2E-27 1.1E-31 209.2 5.1 138 1-142 302-443 (1186)
14 KOG0702|consensus 99.1 6.3E-11 1.4E-15 101.8 4.8 100 1-104 29-129 (524)
15 PF00023 Ank: Ankyrin repeat H 94.9 0.053 1.1E-06 29.6 3.6 28 115-142 5-32 (33)
16 KOG0521|consensus 94.3 0.0089 1.9E-07 55.3 -0.8 61 7-69 641-701 (785)
17 PF13606 Ank_3: Ankyrin repeat 94.2 0.075 1.6E-06 28.9 3.1 26 115-140 5-30 (30)
18 PF13637 Ank_4: Ankyrin repeat 90.9 0.29 6.3E-06 29.4 2.9 28 115-142 4-31 (54)
19 KOG0514|consensus 88.9 0.41 8.9E-06 41.1 3.1 31 113-143 341-371 (452)
20 PF13857 Ank_5: Ankyrin repeat 86.5 0.87 1.9E-05 27.7 2.8 29 114-142 18-46 (56)
21 KOG0511|consensus 86.1 1 2.2E-05 39.0 3.9 45 93-143 23-67 (516)
22 KOG0509|consensus 76.4 2.2 4.8E-05 38.6 2.7 29 114-142 114-142 (600)
23 PF12796 Ank_2: Ankyrin repeat 75.6 3.4 7.3E-05 26.6 2.8 28 115-142 62-89 (89)
24 PF12796 Ank_2: Ankyrin repeat 74.1 6.1 0.00013 25.4 3.8 28 115-142 29-56 (89)
25 PHA02791 ankyrin-like protein; 66.3 7.2 0.00016 31.8 3.4 27 116-142 198-224 (284)
26 smart00248 ANK ankyrin repeats 65.1 13 0.00028 17.0 3.3 25 115-139 5-29 (30)
27 KOG0512|consensus 61.1 6.7 0.00014 30.8 2.1 26 116-141 134-159 (228)
28 PHA02798 ankyrin-like protein; 59.0 10 0.00022 32.7 3.2 29 114-142 260-288 (489)
29 PHA02878 ankyrin repeat protei 58.7 11 0.00025 32.2 3.4 28 115-142 40-67 (477)
30 PHA03095 ankyrin-like protein; 57.8 12 0.00026 31.6 3.3 29 114-142 259-287 (471)
31 PHA02884 ankyrin repeat protei 57.1 14 0.0003 30.6 3.5 28 114-141 35-62 (300)
32 PRK00085 recO DNA repair prote 55.2 9.9 0.00022 29.7 2.3 23 2-24 154-177 (247)
33 KOG3676|consensus 53.3 14 0.00029 34.7 3.1 42 90-140 171-212 (782)
34 PHA02946 ankyin-like protein; 52.0 18 0.0004 31.1 3.6 29 114-142 74-102 (446)
35 PHA02884 ankyrin repeat protei 51.3 18 0.0004 29.8 3.4 28 114-141 72-99 (300)
36 PHA02875 ankyrin repeat protei 51.3 19 0.00042 29.9 3.6 29 114-142 170-198 (413)
37 PHA02874 ankyrin repeat protei 51.1 20 0.00042 30.3 3.6 29 114-142 37-65 (434)
38 PF00643 zf-B_box: B-box zinc 50.9 13 0.00028 21.0 1.8 27 3-29 9-36 (42)
39 PHA02989 ankyrin repeat protei 49.8 19 0.0004 31.1 3.3 29 114-142 258-286 (494)
40 PF13119 DUF3973: Domain of un 49.2 8.4 0.00018 22.6 0.7 14 18-31 2-15 (41)
41 TIGR00870 trp transient-recept 47.8 22 0.00047 32.4 3.6 30 113-142 18-49 (743)
42 PHA02791 ankyrin-like protein; 47.3 24 0.00051 28.8 3.4 30 113-142 161-190 (284)
43 PHA02795 ankyrin-like protein; 46.2 27 0.00058 30.6 3.7 29 114-142 223-251 (437)
44 PHA03100 ankyrin repeat protei 46.1 25 0.00055 29.7 3.5 29 114-142 252-280 (480)
45 KOG0502|consensus 45.9 18 0.00038 29.5 2.3 28 113-140 161-188 (296)
46 TIGR00613 reco DNA repair prot 45.0 35 0.00076 26.4 4.0 53 2-66 152-205 (241)
47 PTZ00322 6-phosphofructo-2-kin 43.6 33 0.00071 31.3 4.0 28 115-142 85-112 (664)
48 PLN03192 Voltage-dependent pot 40.9 32 0.0007 32.0 3.6 29 114-142 624-652 (823)
49 KOG4214|consensus 40.5 27 0.00059 24.8 2.3 78 48-138 16-93 (117)
50 PHA02874 ankyrin repeat protei 39.4 39 0.00084 28.5 3.6 29 114-142 126-154 (434)
51 PHA02736 Viral ankyrin protein 38.2 44 0.00095 23.7 3.3 29 114-142 94-123 (154)
52 PHA02875 ankyrin repeat protei 36.8 44 0.00096 27.7 3.5 28 115-142 138-165 (413)
53 PHA02730 ankyrin-like protein; 36.0 44 0.00095 30.9 3.6 29 114-142 43-74 (672)
54 PHA02878 ankyrin repeat protei 36.0 43 0.00094 28.6 3.4 29 114-142 170-198 (477)
55 PF01286 XPA_N: XPA protein N- 35.4 15 0.00033 20.7 0.4 24 1-24 7-31 (34)
56 PHA03100 ankyrin repeat protei 35.0 42 0.0009 28.4 3.1 29 114-142 37-65 (480)
57 PF10764 Gin: Inhibitor of sig 34.7 24 0.00052 21.1 1.2 22 3-25 5-26 (46)
58 PRK00523 hypothetical protein; 33.9 96 0.0021 20.5 4.0 35 90-124 23-57 (72)
59 PHA02859 ankyrin repeat protei 32.9 58 0.0013 24.8 3.4 28 115-142 54-83 (209)
60 KOG0515|consensus 31.7 46 0.00099 30.4 2.9 31 112-142 583-613 (752)
61 cd07170 NR_DBD_ERR DNA-binding 31.6 25 0.00054 24.3 1.0 18 12-29 16-33 (97)
62 cd07165 NR_DBD_DmE78_like DNA- 31.5 24 0.00052 23.3 0.9 24 3-29 4-27 (81)
63 KOG0502|consensus 31.2 49 0.0011 27.0 2.7 31 113-143 194-224 (296)
64 KOG0512|consensus 31.2 53 0.0012 25.9 2.8 29 114-142 99-127 (228)
65 cd07162 NR_DBD_PXR DNA-binding 31.2 31 0.00066 23.2 1.4 24 3-29 5-28 (87)
66 PF13462 Thioredoxin_4: Thiore 30.9 19 0.00041 25.5 0.3 28 4-31 8-35 (162)
67 PHA02876 ankyrin repeat protei 30.9 55 0.0012 29.4 3.4 29 114-142 180-208 (682)
68 cd07156 NR_DBD_VDR_like The DN 30.8 28 0.00062 22.4 1.1 24 3-29 4-27 (72)
69 PLN03192 Voltage-dependent pot 30.8 55 0.0012 30.5 3.4 31 112-142 525-555 (823)
70 cd07158 NR_DBD_Ppar_like The D 30.3 27 0.00059 22.5 1.0 24 3-29 4-27 (73)
71 PF08271 TF_Zn_Ribbon: TFIIB z 29.9 32 0.00069 19.8 1.1 24 2-26 5-28 (43)
72 cd06968 NR_DBD_ROR DNA-binding 29.4 29 0.00062 23.8 1.0 24 3-29 11-34 (95)
73 PHA02792 ankyrin-like protein; 29.3 51 0.0011 30.3 2.8 29 114-142 341-369 (631)
74 PF00320 GATA: GATA zinc finge 29.1 50 0.0011 18.4 1.9 30 2-31 3-34 (36)
75 PRK11032 hypothetical protein; 28.5 25 0.00053 26.7 0.6 13 13-25 120-132 (160)
76 PRK01844 hypothetical protein; 28.2 1.4E+02 0.003 19.8 4.0 33 90-122 22-54 (72)
77 PHA03095 ankyrin-like protein; 28.1 67 0.0014 27.0 3.2 28 115-142 50-80 (471)
78 PHA02741 hypothetical protein; 27.9 81 0.0018 22.9 3.3 29 114-142 100-129 (169)
79 PHA02795 ankyrin-like protein; 27.9 69 0.0015 28.1 3.3 30 112-141 116-147 (437)
80 PF09920 DUF2150: Uncharacteri 27.7 1.5E+02 0.0033 23.1 4.8 43 94-138 105-148 (190)
81 PHA02608 67 prohead core prote 27.6 70 0.0015 21.5 2.6 20 114-133 2-21 (80)
82 cd06966 NR_DBD_CAR DNA-binding 27.5 29 0.00063 23.7 0.8 18 12-29 12-29 (94)
83 PTZ00322 6-phosphofructo-2-kin 27.4 71 0.0015 29.1 3.4 30 113-142 116-145 (664)
84 KOG1710|consensus 27.2 65 0.0014 27.3 2.9 27 115-141 48-74 (396)
85 PF12417 DUF3669: Zinc finger 26.7 1.7E+02 0.0037 18.8 4.3 51 34-98 6-56 (72)
86 PF04170 NlpE: NlpE N-terminal 26.6 21 0.00046 23.8 -0.0 16 15-30 2-17 (87)
87 cd07157 2DBD_NR_DBD1 The first 26.3 26 0.00056 23.5 0.3 24 3-29 6-29 (86)
88 COG3763 Uncharacterized protei 26.3 1.7E+02 0.0036 19.3 4.1 23 90-112 22-44 (71)
89 cd07179 2DBD_NR_DBD2 The secon 25.9 43 0.00093 21.7 1.3 24 3-29 4-27 (74)
90 PF04770 ZF-HD_dimer: ZF-HD pr 25.7 31 0.00068 22.0 0.6 27 3-30 25-52 (60)
91 cd06956 NR_DBD_RXR DNA-binding 25.5 44 0.00096 21.8 1.4 18 12-29 12-29 (77)
92 PF03672 UPF0154: Uncharacteri 25.0 1.8E+02 0.0039 18.7 4.0 35 90-124 15-49 (64)
93 PF07295 DUF1451: Protein of u 24.1 33 0.00072 25.5 0.6 14 13-26 108-121 (146)
94 PHA02792 ankyrin-like protein; 24.0 89 0.0019 28.7 3.4 24 119-142 79-102 (631)
95 PF10609 ParA: ParA/MinD ATPas 23.9 35 0.00075 22.9 0.6 21 12-32 60-80 (81)
96 cd07164 NR_DBD_PNR_like_1 DNA- 23.7 41 0.00089 22.0 0.9 24 3-29 4-27 (78)
97 PHA02917 ankyrin-like protein; 23.6 91 0.002 28.6 3.4 29 114-142 105-133 (661)
98 TIGR02960 SigX5 RNA polymerase 23.5 1.3E+02 0.0028 24.2 4.1 30 108-137 205-234 (324)
99 PHA02730 ankyrin-like protein; 23.3 91 0.002 28.9 3.4 29 114-142 464-492 (672)
100 cd07169 NR_DBD_GCNF_like DNA-b 23.3 42 0.00092 22.7 1.0 19 11-29 17-35 (90)
101 PHA02876 ankyrin repeat protei 23.0 1.2E+02 0.0026 27.3 4.1 32 111-142 144-175 (682)
102 cd06960 NR_DBD_HNF4A DNA-bindi 22.9 40 0.00087 21.9 0.8 24 3-29 4-27 (76)
103 smart00399 ZnF_C4 c4 zinc fing 22.5 48 0.0011 21.0 1.1 18 12-29 11-28 (70)
104 PF00105 zf-C4: Zinc finger, C 22.3 45 0.00097 21.0 0.9 23 3-28 6-28 (70)
105 cd06963 NR_DBD_GR_like The DNA 21.6 42 0.00091 21.7 0.6 18 12-29 10-27 (73)
106 TIGR00870 trp transient-recept 21.4 92 0.002 28.4 3.0 28 114-141 130-157 (743)
107 PHA02716 CPXV016; CPX019; EVM0 21.3 92 0.002 29.3 3.0 29 114-142 214-244 (764)
108 PF06689 zf-C4_ClpX: ClpX C4-t 21.2 67 0.0015 18.5 1.4 17 10-26 17-33 (41)
109 COG4647 AcxC Acetone carboxyla 20.9 22 0.00048 26.4 -0.9 22 5-28 110-131 (165)
110 PRK09636 RNA polymerase sigma 20.9 1.3E+02 0.0029 24.0 3.6 30 107-136 171-200 (293)
111 PHA02743 Viral ankyrin protein 20.8 1.4E+02 0.003 21.7 3.4 29 114-142 130-158 (166)
112 cd06961 NR_DBD_TR DNA-binding 20.7 47 0.001 22.2 0.8 18 12-29 11-28 (85)
113 cd07161 NR_DBD_EcR DNA-binding 20.7 44 0.00096 22.7 0.6 18 12-29 13-30 (91)
114 cd07171 NR_DBD_ER DNA-binding 20.2 46 0.00099 22.1 0.6 18 12-29 15-32 (82)
115 KOG0510|consensus 20.2 99 0.0021 29.5 2.9 29 114-142 275-303 (929)
116 cd06962 NR_DBD_FXR DNA-binding 20.1 42 0.00092 22.4 0.4 18 12-29 13-30 (84)
No 1
>KOG0703|consensus
Probab=100.00 E-value=1.8e-41 Score=273.74 Aligned_cols=99 Identities=33% Similarity=0.643 Sum_probs=92.8
Q ss_pred CCCCCCCCCeeecccceeeccchhhhhhcCCCCcceeeeCCCCCCChHHHHHHHhhccCchhHHhccccccccCCCCCCC
Q psy13622 1 MSSRAADPKWGILNKGVLVCDACCSIHRSLGRHISQVKYLEPSTWPPSLLSMLMTLTNGGAPSLWEHSLCESKTKKKPVP 80 (143)
Q Consensus 1 ~DCga~~P~was~n~gvfiC~~CsgiHR~lg~~iskVks~~ld~w~~~~v~~~~~~GN~~~n~~~ea~~~~~~~~~kP~~ 80 (143)
.|||+++|+|||+|||||||++|+||||+||+||||||||+||.|++++|+.|+.+||.+||++||+.+|+ ...+|.+
T Consensus 29 ADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~~GN~~an~~~ea~~p~--~~~~p~~ 106 (287)
T KOG0703|consen 29 ADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMISMGNAKANSYYEAKLPD--PFRRPGP 106 (287)
T ss_pred cccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHHHcchhhhhhccccCCc--cccCCCh
Confidence 49999999999999999999999999999999999999999999999999999999999999999999975 4578776
Q ss_pred CCCChHHHHHHHHHHHhcCccccCC
Q psy13622 81 SDPLHPTKAEFIKAKYEQLSFMIRS 105 (143)
Q Consensus 81 ~~~~~~~r~~fI~~KY~~k~f~~~~ 105 (143)
+ ..++.|||+||+.|+|+.+.
T Consensus 107 d----~~~e~FIR~KYE~kkf~~~~ 127 (287)
T KOG0703|consen 107 D----DLVEQFIRDKYERKKFLDPE 127 (287)
T ss_pred H----HHHHHHHHHHHhhhhhccch
Confidence 5 48999999999999999873
No 2
>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=8.4e-41 Score=238.76 Aligned_cols=103 Identities=38% Similarity=0.646 Sum_probs=92.6
Q ss_pred CCCCCCCCCeeecccceeeccchhhhhhcCCCCcceeeeCCCCCCChHHHHHHHhhccCchhHHhccccccccCCCCCCC
Q psy13622 1 MSSRAADPKWGILNKGVLVCDACCSIHRSLGRHISQVKYLEPSTWPPSLLSMLMTLTNGGAPSLWEHSLCESKTKKKPVP 80 (143)
Q Consensus 1 ~DCga~~P~was~n~gvfiC~~CsgiHR~lg~~iskVks~~ld~w~~~~v~~~~~~GN~~~n~~~ea~~~~~~~~~kP~~ 80 (143)
+|||+++|+|||+|+|||||+.|||+||+||+|||+||||+||+|++++|++|+.+||+++|++||++++++. .+| |
T Consensus 7 aDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~VkSl~md~w~~~~i~~~~~~GN~~~n~~~e~~~~~~~--~~~-~ 83 (112)
T smart00105 7 FDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLDTWTEEELRLLQKGGNENANSIWESNLDDFS--LKP-P 83 (112)
T ss_pred cCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCeeeecccCCCCHHHHHHHHHhhhHHHHHHHHhhCCccc--cCC-C
Confidence 6999999999999999999999999999999999999999999999999999999999999999999997432 233 3
Q ss_pred CCCChHHHHHHHHHHHhcCccccCCC
Q psy13622 81 SDPLHPTKAEFIKAKYEQLSFMIRSN 106 (143)
Q Consensus 81 ~~~~~~~r~~fI~~KY~~k~f~~~~~ 106 (143)
.++..+.|++||++||++++|+.+..
T Consensus 84 ~~~~~~~~~~fI~~KY~~k~f~~~~~ 109 (112)
T smart00105 84 DSDDQQKYESFIAAKYEEKLFVPPES 109 (112)
T ss_pred CCchHHHHHHHHHHHHHhhhcccccc
Confidence 33334899999999999999998854
No 3
>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=2.8e-40 Score=237.27 Aligned_cols=100 Identities=37% Similarity=0.693 Sum_probs=80.8
Q ss_pred CCCCCCCCCeeecccceeeccchhhhhhcCCCCcceeeeCCCCCCChHHHHHHHhhccCchhHHhccccccccCCCCCCC
Q psy13622 1 MSSRAADPKWGILNKGVLVCDACCSIHRSLGRHISQVKYLEPSTWPPSLLSMLMTLTNGGAPSLWEHSLCESKTKKKPVP 80 (143)
Q Consensus 1 ~DCga~~P~was~n~gvfiC~~CsgiHR~lg~~iskVks~~ld~w~~~~v~~~~~~GN~~~n~~~ea~~~~~~~~~kP~~ 80 (143)
+|||+++|+|||+|||||||+.|||+||+||+|+|+|||++||+|++++|+.|+.+||..+|++||++.+ ...+|.+
T Consensus 17 aDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~VkSi~~d~w~~~ev~~~~~~GN~~~n~~~e~~~~---~~~~~~~ 93 (116)
T PF01412_consen 17 ADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRVKSITMDNWSPEEVQRMREGGNKRANSIWEANSP---PPKKPPP 93 (116)
T ss_dssp TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--EEETTTS---HHHHHHHHHSHHHHHHHHHTTTST---TTTTHCT
T ss_pred CCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhccccccCCCCHHHHHHHHHHChHHHHHHHHcCCC---CCCCCCC
Confidence 6999999999999999999999999999999999999999999999999999999999999999999942 2244554
Q ss_pred CCCChHHHHHHHHHHHhcCccccC
Q psy13622 81 SDPLHPTKAEFIKAKYEQLSFMIR 104 (143)
Q Consensus 81 ~~~~~~~r~~fI~~KY~~k~f~~~ 104 (143)
+++ .+.+++||++||++++|+.+
T Consensus 94 ~~~-~~~~~~fI~~KY~~k~f~~~ 116 (116)
T PF01412_consen 94 SSD-QEKREQFIRAKYVEKAFISK 116 (116)
T ss_dssp TSH-HHHHHHHHHHHHTTHTTS-C
T ss_pred CCc-HHHHHHHHHHHHHhhhhccC
Confidence 444 48999999999999999863
No 4
>KOG0705|consensus
Probab=100.00 E-value=6.6e-38 Score=269.93 Aligned_cols=134 Identities=40% Similarity=0.682 Sum_probs=127.6
Q ss_pred CCCCCCCCCeeecccceeeccchhhhhhcCCCCcceeeeCCCCCCChHHHHHHHhhccCchhHHhccccccccCCCCCCC
Q psy13622 1 MSSRAADPKWGILNKGVLVCDACCSIHRSLGRHISQVKYLEPSTWPPSLLSMLMTLTNGGAPSLWEHSLCESKTKKKPVP 80 (143)
Q Consensus 1 ~DCga~~P~was~n~gvfiC~~CsgiHR~lg~~iskVks~~ld~w~~~~v~~~~~~GN~~~n~~~ea~~~~~~~~~kP~~ 80 (143)
.|||+++|.|||+|+|+.+|++|+||||.||+|+|||||+.||.|+.+.+.+|..+||+.||++||... .+..||.|
T Consensus 517 ~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~aiGN~~AN~vWE~~~---~G~~KPs~ 593 (749)
T KOG0705|consen 517 VDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSAIGNDLANSVWEGSS---QGQTKPSP 593 (749)
T ss_pred eecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHHhhhhHHHHHhhhhc---cCCcCCCc
Confidence 499999999999999999999999999999999999999999999999999999999999999999865 57789999
Q ss_pred CCCChHHHHHHHHHHHhcCccccCCCCCHHHHHHHHHHhhhcCCHHHHHHHHHcCCCC
Q psy13622 81 SDPLHPTKAEFIKAKYEQLSFMIRSNDTQEELNQQLHSSVRTSNLDTSLRLLSQGADP 138 (143)
Q Consensus 81 ~~~~~~~r~~fI~~KY~~k~f~~~~~~~~~~~~~~l~~av~~~~~~~~~~ll~~Ga~~ 138 (143)
+++. +++|+||++||++|.|..|.+.+...+.++|+.||...|+.+++.|||+|...
T Consensus 594 ~s~R-EEkErwIr~KYeqklFLaPl~~te~~lgqqLl~A~~~~Dl~t~~lLLAhg~~~ 650 (749)
T KOG0705|consen 594 DSSR-EEKERWIRAKYEQKLFLAPLPCTEEPLGQQLLRAVAAEDLQTAILLLAHGSRE 650 (749)
T ss_pred cccH-HHHHHHHHHHHHHHhhcCCCCCCCCchHHHHHHHHHHHHHHHHHHHHhccCch
Confidence 8765 99999999999999999999888999999999999999999999999999754
No 5
>KOG0818|consensus
Probab=100.00 E-value=4.4e-36 Score=255.46 Aligned_cols=141 Identities=55% Similarity=0.990 Sum_probs=133.3
Q ss_pred CCCCCCCCeeecccceeeccchhhhhhcCCCCcceeeeCCCCCCChHHHHHHHhhccCchhHHhcccccccc----CCCC
Q psy13622 2 SSRAADPKWGILNKGVLVCDACCSIHRSLGRHISQVKYLEPSTWPPSLLSMLMTLTNGGAPSLWEHSLCESK----TKKK 77 (143)
Q Consensus 2 DCga~~P~was~n~gvfiC~~CsgiHR~lg~~iskVks~~ld~w~~~~v~~~~~~GN~~~n~~~ea~~~~~~----~~~k 77 (143)
|||+++|.|||||-|+|+|.+|..+||+||.|||.||++....|.++.+++...+.|..+|.|||..+.+|. +.+|
T Consensus 13 DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~Lld~st~~sg~rk 92 (669)
T KOG0818|consen 13 DCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHSLLDPATIMSGRRK 92 (669)
T ss_pred ccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhhccCchhhhcccCC
Confidence 899999999999999999999999999999999999999999999999999999999999999999999884 4688
Q ss_pred CCCCCCChHHHHHHHHHHHhcCccccCC----C--CCHHHHHHHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 78 PVPSDPLHPTKAEFIKAKYEQLSFMIRS----N--DTQEELNQQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 78 P~~~~~~~~~r~~fI~~KY~~k~f~~~~----~--~~~~~~~~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
|.|.|..|..+++||++||+...|+.+. . -.+.++++||+.+|+++++++.++||++||++||++
T Consensus 93 ~~pqD~~Hp~K~eFIkaKy~~LtFv~~~~~rDdD~~~~~~LsrQLhasvRt~nlet~LRll~lGA~~N~~h 163 (669)
T KOG0818|consen 93 ANPQDKVHPNKAEFIRAKYQMLAFVHRLPCRDDDSVTAKDLSKQLHSSVRTGNLETCLRLLSLGAQANFFH 163 (669)
T ss_pred CCCcCCCCccHHHHHHHHHHheeeeccCCCCCcchhhHHHHHHHHHHHhhcccHHHHHHHHHcccccCCCC
Confidence 9999999999999999999999999852 2 257789999999999999999999999999999986
No 6
>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=1.4e-35 Score=244.02 Aligned_cols=101 Identities=31% Similarity=0.528 Sum_probs=89.9
Q ss_pred CCCCCCCCCeeecccceeeccchhhhhhcCCCCcceeeeCCCCCCChHHHHHHHhhccCchhHHhcccccccc-CCCCCC
Q psy13622 1 MSSRAADPKWGILNKGVLVCDACCSIHRSLGRHISQVKYLEPSTWPPSLLSMLMTLTNGGAPSLWEHSLCESK-TKKKPV 79 (143)
Q Consensus 1 ~DCga~~P~was~n~gvfiC~~CsgiHR~lg~~iskVks~~ld~w~~~~v~~~~~~GN~~~n~~~ea~~~~~~-~~~kP~ 79 (143)
||||+++|+|||+|||||||++||||||+||+|||+||||+||+|++++|++|..+||.+||.|||.++-++. ...+..
T Consensus 24 aDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~gGN~~a~~~~e~~~~~~~~~~~k~~ 103 (319)
T COG5347 24 ADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEVGGNSNANRFYEKNLLDQLLLPIKAK 103 (319)
T ss_pred ccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHHhcchhhhhHhccCCCcccccccccc
Confidence 7999999999999999999999999999999999999999999999999999999999999999999975421 112333
Q ss_pred CCCCChHHHHHHHHHHHhcCccccC
Q psy13622 80 PSDPLHPTKAEFIKAKYEQLSFMIR 104 (143)
Q Consensus 80 ~~~~~~~~r~~fI~~KY~~k~f~~~ 104 (143)
.+ ...+++||+.||++++|...
T Consensus 104 yd---~~v~~~y~~~ky~~~~~~~~ 125 (319)
T COG5347 104 YD---SSVAKKYIRKKYELKKFIDD 125 (319)
T ss_pred cC---HHHHHHHHHHHHHhhhcccc
Confidence 32 36899999999999999985
No 7
>PLN03131 hypothetical protein; Provisional
Probab=99.97 E-value=1.1e-32 Score=239.31 Aligned_cols=102 Identities=19% Similarity=0.293 Sum_probs=88.8
Q ss_pred CCCCCCCCCeeecccceeeccchhhhhhcCCCCcceeeeCCCCCCChHHHHHHHhhccCchhHHhccccccccCCCCCCC
Q psy13622 1 MSSRAADPKWGILNKGVLVCDACCSIHRSLGRHISQVKYLEPSTWPPSLLSMLMTLTNGGAPSLWEHSLCESKTKKKPVP 80 (143)
Q Consensus 1 ~DCga~~P~was~n~gvfiC~~CsgiHR~lg~~iskVks~~ld~w~~~~v~~~~~~GN~~~n~~~ea~~~~~~~~~kP~~ 80 (143)
+|||+++|+|||+|||||||+.|+||||.|| +|||||+||+|++++|+.|+.+||+++|++||++|+.. . ++.|
T Consensus 27 ADCga~~P~WASiNlGIFICi~CSGIHRsLg---hRVKSVTLD~WtdeEV~~Mk~gGN~~AN~iyeanwd~~-r--~~lP 100 (705)
T PLN03131 27 INCNSLGPQFVCTNFWTFICMTCSGIHREFT---HRVKSVSMSKFTSQDVEALQNGGNQRAREIYLKDWDQQ-R--QRLP 100 (705)
T ss_pred ccCCCCCCCeeEeccceEEchhchhhhcccC---cccccccCCCCCHHHHHHHHHhccHHHHHHHHhhcccc-c--CCCC
Confidence 6999999999999999999999999999997 49999999999999999999999999999999999632 2 2333
Q ss_pred CCCChHHHHHHHHHHHhcCccccCCCCC
Q psy13622 81 SDPLHPTKAEFIKAKYEQLSFMIRSNDT 108 (143)
Q Consensus 81 ~~~~~~~r~~fI~~KY~~k~f~~~~~~~ 108 (143)
.....+.+++|||.||++|+|+.+...+
T Consensus 101 ~~sd~ekrr~FIR~KYVeKRFa~~~s~d 128 (705)
T PLN03131 101 DNSKVDKIREFIKDIYVDKKYAGGKTHD 128 (705)
T ss_pred CCccHHHHHHHHHHHHhhhhhhcCCCCC
Confidence 3333367899999999999999985433
No 8
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=99.97 E-value=1.7e-32 Score=236.47 Aligned_cols=99 Identities=21% Similarity=0.317 Sum_probs=87.7
Q ss_pred CCCCCCCCCeeecccceeeccchhhhhhcCCCCcceeeeCCCCCCChHHHHHHHhhccCchhHHhccccccccCCCCCCC
Q psy13622 1 MSSRAADPKWGILNKGVLVCDACCSIHRSLGRHISQVKYLEPSTWPPSLLSMLMTLTNGGAPSLWEHSLCESKTKKKPVP 80 (143)
Q Consensus 1 ~DCga~~P~was~n~gvfiC~~CsgiHR~lg~~iskVks~~ld~w~~~~v~~~~~~GN~~~n~~~ea~~~~~~~~~kP~~ 80 (143)
+|||+++|+|||+|||||||++|+||||.|| +|||||+||+|++++|++|+.+||+++|++||++|++. . ++.|
T Consensus 27 ADCgs~~P~WASiNlGIFICi~CSGIHRsLG---hRVKSLSLDkWT~EEVe~Mk~gGN~~AN~iyeanw~~~-~--~~~P 100 (648)
T PLN03119 27 INCNSLGPQYVCTTFWTFVCMACSGIHREFT---HRVKSVSMSKFTSKEVEVLQNGGNQRAREIYLKNWDHQ-R--QRLP 100 (648)
T ss_pred ccCCCCCCCceeeccceEEeccchhhhccCC---ceeeccccCCCCHHHHHHHHHhchHHHHHHHHhhcccc-c--CCCC
Confidence 6999999999999999999999999999998 59999999999999999999999999999999999743 2 2333
Q ss_pred CCCChHHHHHHHHHHHhcCccccCC
Q psy13622 81 SDPLHPTKAEFIKAKYEQLSFMIRS 105 (143)
Q Consensus 81 ~~~~~~~r~~fI~~KY~~k~f~~~~ 105 (143)
.....+.+++|||.||++|+|+.+.
T Consensus 101 ~~sD~e~lr~FIR~KYVeKRF~~~~ 125 (648)
T PLN03119 101 ENSNAERVREFIKNVYVQKKYAGAN 125 (648)
T ss_pred CCccHHHHHHHHHHHHhhhhccCcC
Confidence 3333467889999999999999874
No 9
>KOG0704|consensus
Probab=99.95 E-value=4.2e-29 Score=205.19 Aligned_cols=104 Identities=19% Similarity=0.240 Sum_probs=83.2
Q ss_pred CCCCCCCCCeeecccceeeccchhhhhhcCCCCcceeeeCCCCCCChHHHHHHHhhccCchhHHhcccccc-ccCCCCCC
Q psy13622 1 MSSRAADPKWGILNKGVLVCDACCSIHRSLGRHISQVKYLEPSTWPPSLLSMLMTLTNGGAPSLWEHSLCE-SKTKKKPV 79 (143)
Q Consensus 1 ~DCga~~P~was~n~gvfiC~~CsgiHR~lg~~iskVks~~ld~w~~~~v~~~~~~GN~~~n~~~ea~~~~-~~~~~kP~ 79 (143)
|||++++|+|||++||||||.+|||+||.||+|||+|||||||+|.+.+|+.|+++||++++.|++..-.- +....+-.
T Consensus 23 feC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~~~eFL~s~~~~~e~~~i~eK 102 (386)
T KOG0704|consen 23 FECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNERFREFLSSQGIYKETWPIREK 102 (386)
T ss_pred eecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchhHHHHHhhCccccccccHHHh
Confidence 79999999999999999999999999999999999999999999999999999999999999999866310 00011112
Q ss_pred CCCCChHHHHHHHHHHHhcCccccC
Q psy13622 80 PSDPLHPTKAEFIKAKYEQLSFMIR 104 (143)
Q Consensus 80 ~~~~~~~~r~~fI~~KY~~k~f~~~ 104 (143)
.++......++-|.+--+.+.|-++
T Consensus 103 Yns~aAa~yRdki~~laegr~w~d~ 127 (386)
T KOG0704|consen 103 YNSRAAALYRDKIAALAEGREWNDP 127 (386)
T ss_pred hccHHHHHHHHHHHHHhcCCccccc
Confidence 2222234566777777777888443
No 10
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.95 E-value=4.5e-28 Score=200.20 Aligned_cols=102 Identities=25% Similarity=0.370 Sum_probs=83.3
Q ss_pred CCCCCCCCCeeecccceeeccchhhhhhcCCCCcceeeeCCCCCCChHHHHHHHhhccCchhHHhccccccccCCCCCCC
Q psy13622 1 MSSRAADPKWGILNKGVLVCDACCSIHRSLGRHISQVKYLEPSTWPPSLLSMLMTLTNGGAPSLWEHSLCESKTKKKPVP 80 (143)
Q Consensus 1 ~DCga~~P~was~n~gvfiC~~CsgiHR~lg~~iskVks~~ld~w~~~~v~~~~~~GN~~~n~~~ea~~~~~~~~~kP~~ 80 (143)
+|||+++|+|||+|+|||||+.|+|+||.||+|||+|||++||.|++++|++|+.+||.++|.||+.+.-......+-..
T Consensus 26 aDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~Ws~eqL~~Mk~GGN~rA~~fF~qhG~~~~~~~~~KY 105 (395)
T PLN03114 26 FDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSSEQLKMMIYGGNNRAQVFFKQYGWSDGGKTEAKY 105 (395)
T ss_pred ccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCCCCHHHHHHHHHhcCHHHHHHHHHcCCCCCCCccccc
Confidence 69999999999999999999999999999999999999999999999999999999999999999987542211112222
Q ss_pred CCCChHHHHHHHHHHHhcCcccc
Q psy13622 81 SDPLHPTKAEFIKAKYEQLSFMI 103 (143)
Q Consensus 81 ~~~~~~~r~~fI~~KY~~k~f~~ 103 (143)
++.. ..+=+-+.+|++.+.+..
T Consensus 106 ~S~a-A~~Yre~L~keVa~~~a~ 127 (395)
T PLN03114 106 TSRA-ADLYKQILAKEVAKSKAE 127 (395)
T ss_pred CCHH-HHHHHHHHHHHHHHhhhc
Confidence 2222 334444788888888874
No 11
>KOG0706|consensus
Probab=99.94 E-value=4.5e-28 Score=204.09 Aligned_cols=70 Identities=27% Similarity=0.586 Sum_probs=68.3
Q ss_pred CCCCCCCCCeeecccceeeccchhhhhhcCCCCcceeeeCCCCCCChHHHHHHHhhccCchhHHhccccc
Q psy13622 1 MSSRAADPKWGILNKGVLVCDACCSIHRSLGRHISQVKYLEPSTWPPSLLSMLMTLTNGGAPSLWEHSLC 70 (143)
Q Consensus 1 ~DCga~~P~was~n~gvfiC~~CsgiHR~lg~~iskVks~~ld~w~~~~v~~~~~~GN~~~n~~~ea~~~ 70 (143)
|||||++|+|+||+||||||++||++||.||+|||+|||+.||+|+..+|+.|+.+||.+|+.|+..+.-
T Consensus 27 FDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~~FFkqhg~ 96 (454)
T KOG0706|consen 27 FDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANARVFFKQHGC 96 (454)
T ss_pred cccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHHHHHHHcCC
Confidence 7999999999999999999999999999999999999999999999999999999999999999998863
No 12
>KOG0521|consensus
Probab=99.94 E-value=1.3e-27 Score=215.58 Aligned_cols=104 Identities=35% Similarity=0.629 Sum_probs=96.7
Q ss_pred CCCCCCCCCeeecccceeeccchhhhhhcCCCCcceeeeCCCCCCChHHHHHHHhhccCchhHHhccccccccCCCCCCC
Q psy13622 1 MSSRAADPKWGILNKGVLVCDACCSIHRSLGRHISQVKYLEPSTWPPSLLSMLMTLTNGGAPSLWEHSLCESKTKKKPVP 80 (143)
Q Consensus 1 ~DCga~~P~was~n~gvfiC~~CsgiHR~lg~~iskVks~~ld~w~~~~v~~~~~~GN~~~n~~~ea~~~~~~~~~kP~~ 80 (143)
.|||++.|+|+|+|+||.+|++|+|+||+||+|+|||+|++||.|.++.+.+|+.+||..+|.+||+++++. ...+|.+
T Consensus 430 ~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~lgn~~~N~i~e~~l~~~-~~~~~~~ 508 (785)
T KOG0521|consen 430 CDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKNLGNKYVNEIYEALLPSY-DSSKPTA 508 (785)
T ss_pred hhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHHhCcchhhhhhhcccccc-cccCCCC
Confidence 389999999999999999999999999999999999999999999999999999999999999999999854 3678888
Q ss_pred CCCChHHHHHHHHHHHhcCccccCCC
Q psy13622 81 SDPLHPTKAEFIKAKYEQLSFMIRSN 106 (143)
Q Consensus 81 ~~~~~~~r~~fI~~KY~~k~f~~~~~ 106 (143)
..+. ..|+.||++||++++|.....
T Consensus 509 ~~~~-~~r~~~i~~kyve~~F~~k~~ 533 (785)
T KOG0521|consen 509 SSSR-QAREAWIKAKYVERRFSVKEP 533 (785)
T ss_pred ccch-hhhhHhhhcccceeeEeeccc
Confidence 7764 899999999999999998743
No 13
>KOG1117|consensus
Probab=99.93 E-value=5.2e-27 Score=209.19 Aligned_cols=138 Identities=29% Similarity=0.512 Sum_probs=124.5
Q ss_pred CCCCCCCCCeeecccceeeccchhhhhhcCCCCcceeeeCCCC--CCChHHHHHHHhhccCchhHHhccccccccCCCCC
Q psy13622 1 MSSRAADPKWGILNKGVLVCDACCSIHRSLGRHISQVKYLEPS--TWPPSLLSMLMTLTNGGAPSLWEHSLCESKTKKKP 78 (143)
Q Consensus 1 ~DCga~~P~was~n~gvfiC~~CsgiHR~lg~~iskVks~~ld--~w~~~~v~~~~~~GN~~~n~~~ea~~~~~~~~~kP 78 (143)
.|||++.|.|||+||+|.||..|+|-||+||.-+|||+|++|| .|+.+.++++..+||.++|.||.+++++. ...
T Consensus 302 adC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~Fwa~nl~~~-e~l-- 378 (1186)
T KOG1117|consen 302 ADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANRFWAGNLPPN-EHL-- 378 (1186)
T ss_pred cccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCcccccccccCCCCc-ccc--
Confidence 3899999999999999999999999999999999999999997 69999999999999999999999999843 323
Q ss_pred CCCCCChHHHHHHHHHHHhcCccccCC--CCCHHHHHHHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 79 VPSDPLHPTKAEFIKAKYEQLSFMIRS--NDTQEELNQQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 79 ~~~~~~~~~r~~fI~~KY~~k~f~~~~--~~~~~~~~~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
.|+++. ..|++||++||.+..|.... ....+++.++|+.||...|+..++.+|.+|++++++.
T Consensus 379 h~dssp-~~r~~fi~~Kykeg~fRk~~~~~~~~sel~kalcaaV~~pdl~etma~l~sga~v~~f~ 443 (1186)
T KOG1117|consen 379 HPDSSP-STRRQFIKEKYKEGKFRKEHPVEICSSELPKALCAAVNVPDLLETMALLFSGADVMCFT 443 (1186)
T ss_pred CCCCCc-chhhhHHHHHhhccccccccccccccccCChhheeeeeCCchhhHHHHhhccccceeec
Confidence 344555 78999999999999998763 5567889999999999999999999999999999864
No 14
>KOG0702|consensus
Probab=99.11 E-value=6.3e-11 Score=101.80 Aligned_cols=100 Identities=18% Similarity=0.372 Sum_probs=86.2
Q ss_pred CCCCCCCC-CeeecccceeeccchhhhhhcCCCCcceeeeCCCCCCChHHHHHHHhhccCchhHHhccccccccCCCCCC
Q psy13622 1 MSSRAADP-KWGILNKGVLVCDACCSIHRSLGRHISQVKYLEPSTWPPSLLSMLMTLTNGGAPSLWEHSLCESKTKKKPV 79 (143)
Q Consensus 1 ~DCga~~P-~was~n~gvfiC~~CsgiHR~lg~~iskVks~~ld~w~~~~v~~~~~~GN~~~n~~~ea~~~~~~~~~kP~ 79 (143)
|+|....+ +|+...-|-|+|..|+|.-|.|. .-+||||++|.+++..++..++..||..+.++|..-. |.....-|.
T Consensus 29 ~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~-~ahRvksiSmttft~qevs~lQshgNq~~k~i~fkl~-D~q~S~vPD 106 (524)
T KOG0702|consen 29 INCNSLVAATYVVYTVGSFVCTMCSGLLSGLN-PAHRVKSISMTTFTDQEVSFLQSHGNQVCKEIWFKLF-DFQRSNVPD 106 (524)
T ss_pred eeccccccceEEEeeccceeeeccchhhccCC-CccccceeeeeeccccchHHHhhcchhhhhhhhhcch-hhhhccCCC
Confidence 68999988 99999999999999999999984 5689999999999999999999999999999998664 333334444
Q ss_pred CCCCChHHHHHHHHHHHhcCccccC
Q psy13622 80 PSDPLHPTKAEFIKAKYEQLSFMIR 104 (143)
Q Consensus 80 ~~~~~~~~r~~fI~~KY~~k~f~~~ 104 (143)
..+. ...++||+.||+.|+|+.+
T Consensus 107 ~rn~--~~~kef~q~~y~~kr~~v~ 129 (524)
T KOG0702|consen 107 SRNP--QKVKEFQQEKYVKKRYYVP 129 (524)
T ss_pred cccc--hhhHHHHhhhhccceeecC
Confidence 4433 5789999999999999987
No 15
>PF00023 Ank: Ankyrin repeat Hereditary spherocytosis; InterPro: IPR002110 The ankyrin repeat is one of the most common protein-protein interaction motifs in nature. Ankyrin repeats are tandemly repeated modules of about 33 amino acids. They occur in a large number of functionally diverse proteins mainly from eukaryotes. The few known examples from prokaryotes and viruses may be the result of horizontal gene transfers []. The repeat has been found in proteins of diverse function such as transcriptional initiators, cell-cycle regulators, cytoskeletal, ion transporters and signal transducers. The ankyrin fold appears to be defined by its structure rather than its function since there is no specific sequence or structure which is universally recognised by it. The conserved fold of the ankyrin repeat unit is known from several crystal and solution structures [, , , ]. Each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90o angle. The repeats stack together to form an L-shaped structure [, ].; GO: 0005515 protein binding; PDB: 1D9S_A 1NFI_F 1IKN_D 1WDY_A 1OT8_C 1QYM_A 1TR4_A 1UOH_A 1N11_A 1K1A_A ....
Probab=94.89 E-value=0.053 Score=29.62 Aligned_cols=28 Identities=32% Similarity=0.293 Sum_probs=26.1
Q ss_pred HHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 115 QLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 115 ~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
.|+.|+..++...+..||.+|+|+|..|
T Consensus 5 pLh~A~~~~~~~~v~~Ll~~ga~~~~~d 32 (33)
T PF00023_consen 5 PLHYAAQRGHPDIVKLLLKHGADINARD 32 (33)
T ss_dssp HHHHHHHTTCHHHHHHHHHTTSCTTCBC
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCCCCC
Confidence 5889999999999999999999999876
No 16
>KOG0521|consensus
Probab=94.33 E-value=0.0089 Score=55.29 Aligned_cols=61 Identities=15% Similarity=0.021 Sum_probs=51.6
Q ss_pred CCCeeecccceeeccchhhhhhcCCCCcceeeeCCCCCCChHHHHHHHhhccCchhHHhcccc
Q psy13622 7 DPKWGILNKGVLVCDACCSIHRSLGRHISQVKYLEPSTWPPSLLSMLMTLTNGGAPSLWEHSL 69 (143)
Q Consensus 7 ~P~was~n~gvfiC~~CsgiHR~lg~~iskVks~~ld~w~~~~v~~~~~~GN~~~n~~~ea~~ 69 (143)
.-.|+++|+.+.+|+.|+++|+..+.+++..+++.+++-.+ +.....-|+..++..+....
T Consensus 641 ~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~~~~~g~ 701 (785)
T KOG0521|consen 641 LAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHHATASGH 701 (785)
T ss_pred hcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchhhhhhcc
Confidence 56899999999999999999999999999999999988877 77777777777776655443
No 17
>PF13606 Ank_3: Ankyrin repeat
Probab=94.23 E-value=0.075 Score=28.85 Aligned_cols=26 Identities=35% Similarity=0.466 Sum_probs=23.9
Q ss_pred HHHHhhhcCCHHHHHHHHHcCCCCCC
Q psy13622 115 QLHSSVRTSNLDTSLRLLSQGADPNY 140 (143)
Q Consensus 115 ~l~~av~~~~~~~~~~ll~~Ga~~n~ 140 (143)
.|+.|++.++++.+-.||..|+|+|.
T Consensus 5 ~Lh~A~~~g~~e~v~~Ll~~gadvn~ 30 (30)
T PF13606_consen 5 PLHLAASNGNIEIVKYLLEHGADVNA 30 (30)
T ss_pred HHHHHHHhCCHHHHHHHHHcCCCCCC
Confidence 58899999999999999999999983
No 18
>PF13637 Ank_4: Ankyrin repeats (many copies); PDB: 3B95_A 3B7B_A 3F6Q_A 2KBX_A 3IXE_A 2DWZ_C 2DVW_A 3AJI_A 1S70_B 2HE0_A ....
Probab=90.88 E-value=0.29 Score=29.35 Aligned_cols=28 Identities=39% Similarity=0.425 Sum_probs=23.2
Q ss_pred HHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 115 QLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 115 ~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
.|+.|++.|+++.+..|+..|+|+|..|
T Consensus 4 ~lh~A~~~g~~~~~~~Ll~~~~din~~d 31 (54)
T PF13637_consen 4 PLHWAARSGNLEIVKLLLEHGADINAQD 31 (54)
T ss_dssp HHHHHHHTT-HHHHHHHHHTTSGTT-B-
T ss_pred HHHHHHHhCCHHHHHHHHHCCCCCCCCC
Confidence 5789999999999999999999999875
No 19
>KOG0514|consensus
Probab=88.87 E-value=0.41 Score=41.07 Aligned_cols=31 Identities=29% Similarity=0.273 Sum_probs=28.5
Q ss_pred HHHHHHhhhcCCHHHHHHHHHcCCCCCCcCC
Q psy13622 113 NQQLHSSVRTSNLDTSLRLLSQGADPNYFYQ 143 (143)
Q Consensus 113 ~~~l~~av~~~~~~~~~~ll~~Ga~~n~~~~ 143 (143)
+.+|..||.+|.+..+--||+.|||+|.-|+
T Consensus 341 QTALMLAVSHGr~d~vk~LLacgAdVNiQDd 371 (452)
T KOG0514|consen 341 QTALMLAVSHGRVDMVKALLACGADVNIQDD 371 (452)
T ss_pred chhhhhhhhcCcHHHHHHHHHccCCCccccC
Confidence 4689999999999999999999999999875
No 20
>PF13857 Ank_5: Ankyrin repeats (many copies); PDB: 1SW6_A 3EHR_B 3EHQ_A.
Probab=86.51 E-value=0.87 Score=27.72 Aligned_cols=29 Identities=34% Similarity=0.380 Sum_probs=21.1
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..|+.|+..++.+.+..||..|+|+|..|
T Consensus 18 T~LH~A~~~g~~~~v~~Ll~~g~d~~~~d 46 (56)
T PF13857_consen 18 TPLHWAARYGHSEVVRLLLQNGADPNAKD 46 (56)
T ss_dssp -HHHHHHHHT-HHHHHHHHHCT--TT---
T ss_pred cHHHHHHHcCcHHHHHHHHHCcCCCCCCc
Confidence 58999999999999999999999999876
No 21
>KOG0511|consensus
Probab=86.09 E-value=1 Score=38.98 Aligned_cols=45 Identities=16% Similarity=0.194 Sum_probs=36.1
Q ss_pred HHHHhcCccccCCCCCHHHHHHHHHHhhhcCCHHHHHHHHHcCCCCCCcCC
Q psy13622 93 KAKYEQLSFMIRSNDTQEELNQQLHSSVRTSNLDTSLRLLSQGADPNYFYQ 143 (143)
Q Consensus 93 ~~KY~~k~f~~~~~~~~~~~~~~l~~av~~~~~~~~~~ll~~Ga~~n~~~~ 143 (143)
..||.--.|..+.+ ...|++|.++||+..+-.|+.-|+++|.+||
T Consensus 23 ~~~~~~s~~~~~~~------f~elceacR~GD~d~v~~LVetgvnVN~vD~ 67 (516)
T KOG0511|consen 23 LQDYKPSVPLKKVP------FGELCEACRAGDVDRVRYLVETGVNVNAVDR 67 (516)
T ss_pred hhhcCcccccccCc------hHHHHHHhhcccHHHHHHHHHhCCCcchhhc
Confidence 34555555555532 5689999999999999999999999999986
No 22
>KOG0509|consensus
Probab=76.40 E-value=2.2 Score=38.57 Aligned_cols=29 Identities=31% Similarity=0.411 Sum_probs=27.3
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
.-|+.|.+.|.+..+..|+.+|||++.+|
T Consensus 114 tPLHWAar~G~~~vv~lLlqhGAdpt~~D 142 (600)
T KOG0509|consen 114 TPLHWAARNGHISVVDLLLQHGADPTLKD 142 (600)
T ss_pred CcchHHHHcCcHHHHHHHHHcCCCCceec
Confidence 57999999999999999999999999987
No 23
>PF12796 Ank_2: Ankyrin repeats (3 copies); InterPro: IPR020683 This entry represents the ankyrin repeat-containing domain. These domains contain multiple repeats of a beta(2)-alpha(2) motif. The ankyrin repeat is one of the most common protein-protein interaction motifs in nature. Ankyrin repeats are tandemly repeated modules of about 33 amino acids. They occur in a large number of functionally diverse proteins mainly from eukaryotes. The few known examples from prokaryotes and viruses may be the result of horizontal gene transfers []. The repeat has been found in proteins of diverse function such as transcriptional initiators, cell-cycle regulators, cytoskeletal, ion transporters and signal transducers. The ankyrin fold appears to be defined by its structure rather than its function since there is no specific sequence or structure which is universally recognised by it. The conserved fold of the ankyrin repeat unit is known from several crystal and solution structures [, , , ]. Each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90o angle. The repeats stack together to form an L-shaped structure [, ].; PDB: 3AAA_C 3F6Q_A 2KBX_A 3IXE_A 3TWR_D 3TWV_A 3TWT_B 3TWQ_A 3TWS_A 3TWX_B ....
Probab=75.61 E-value=3.4 Score=26.62 Aligned_cols=28 Identities=36% Similarity=0.415 Sum_probs=22.7
Q ss_pred HHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 115 QLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 115 ~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
.|+.|+..++...+-.|+..|+++|..|
T Consensus 62 ~L~~A~~~~~~~~~~~Ll~~g~~~~~~n 89 (89)
T PF12796_consen 62 ALHYAAENGNLEIVKLLLEHGADVNIRN 89 (89)
T ss_dssp HHHHHHHTTHHHHHHHHHHTTT-TTSS-
T ss_pred HHHHHHHcCCHHHHHHHHHcCCCCCCcC
Confidence 6888999999998888999999998764
No 24
>PF12796 Ank_2: Ankyrin repeats (3 copies); InterPro: IPR020683 This entry represents the ankyrin repeat-containing domain. These domains contain multiple repeats of a beta(2)-alpha(2) motif. The ankyrin repeat is one of the most common protein-protein interaction motifs in nature. Ankyrin repeats are tandemly repeated modules of about 33 amino acids. They occur in a large number of functionally diverse proteins mainly from eukaryotes. The few known examples from prokaryotes and viruses may be the result of horizontal gene transfers []. The repeat has been found in proteins of diverse function such as transcriptional initiators, cell-cycle regulators, cytoskeletal, ion transporters and signal transducers. The ankyrin fold appears to be defined by its structure rather than its function since there is no specific sequence or structure which is universally recognised by it. The conserved fold of the ankyrin repeat unit is known from several crystal and solution structures [, , , ]. Each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90o angle. The repeats stack together to form an L-shaped structure [, ].; PDB: 3AAA_C 3F6Q_A 2KBX_A 3IXE_A 3TWR_D 3TWV_A 3TWT_B 3TWQ_A 3TWS_A 3TWX_B ....
Probab=74.12 E-value=6.1 Score=25.36 Aligned_cols=28 Identities=36% Similarity=0.376 Sum_probs=25.1
Q ss_pred HHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 115 QLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 115 ~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
.|+.|+..+++..+..|+..|+|+|..|
T Consensus 29 ~l~~A~~~~~~~~~~~Ll~~g~~~~~~~ 56 (89)
T PF12796_consen 29 ALHYAAENGNLEIVKLLLENGADINSQD 56 (89)
T ss_dssp HHHHHHHTTTHHHHHHHHHTTTCTT-BS
T ss_pred HHHHHHHcCCHHHHHHHHHhcccccccC
Confidence 8999999999999999999999999865
No 25
>PHA02791 ankyrin-like protein; Provisional
Probab=66.31 E-value=7.2 Score=31.80 Aligned_cols=27 Identities=7% Similarity=0.107 Sum_probs=19.1
Q ss_pred HHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 116 LHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 116 l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
|+.|+..++++.+-.||..|||+|..|
T Consensus 198 L~~Aa~~~~~e~v~lLl~~Ga~in~~~ 224 (284)
T PHA02791 198 IKLAIDNKDLEMLQALFKYDINIYSVN 224 (284)
T ss_pred HHHHHHcCCHHHHHHHHHCCCCCccCc
Confidence 666777777777777777777777654
No 26
>smart00248 ANK ankyrin repeats. Ankyrin repeats are about 33 amino acids long and occur in at least four consecutive copies. They are involved in protein-protein interactions. The core of the repeat seems to be an helix-loop-helix structure.
Probab=65.15 E-value=13 Score=17.04 Aligned_cols=25 Identities=40% Similarity=0.538 Sum_probs=20.3
Q ss_pred HHHHhhhcCCHHHHHHHHHcCCCCC
Q psy13622 115 QLHSSVRTSNLDTSLRLLSQGADPN 139 (143)
Q Consensus 115 ~l~~av~~~~~~~~~~ll~~Ga~~n 139 (143)
.++.++..++...+-.++..|.++|
T Consensus 5 ~l~~~~~~~~~~~~~~ll~~~~~~~ 29 (30)
T smart00248 5 PLHLAAENGNLEVVKLLLDKGADIN 29 (30)
T ss_pred HHHHHHHcCCHHHHHHHHHcCCCCC
Confidence 4667888889888888888898876
No 27
>KOG0512|consensus
Probab=61.14 E-value=6.7 Score=30.79 Aligned_cols=26 Identities=42% Similarity=0.560 Sum_probs=15.0
Q ss_pred HHHhhhcCCHHHHHHHHHcCCCCCCc
Q psy13622 116 LHSSVRTSNLDTSLRLLSQGADPNYF 141 (143)
Q Consensus 116 l~~av~~~~~~~~~~ll~~Ga~~n~~ 141 (143)
|++|++=.+.+.+-+||.+|||+|..
T Consensus 134 LhSAckWnN~~va~~LLqhgaDVnA~ 159 (228)
T KOG0512|consen 134 LHSACKWNNFEVAGRLLQHGADVNAQ 159 (228)
T ss_pred hhhhhcccchhHHHHHHhccCccccc
Confidence 34555555555555666666666654
No 28
>PHA02798 ankyrin-like protein; Provisional
Probab=58.98 E-value=10 Score=32.67 Aligned_cols=29 Identities=31% Similarity=0.214 Sum_probs=26.1
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
.-|+.|+..++...+..||..|||+|..|
T Consensus 260 TPL~~A~~~~~~~~v~~LL~~GAdin~~d 288 (489)
T PHA02798 260 NPLYYSVSHNNRKIFEYLLQLGGDINIIT 288 (489)
T ss_pred cHHHHHHHcCcHHHHHHHHHcCCcccccC
Confidence 47888999999999999999999999876
No 29
>PHA02878 ankyrin repeat protein; Provisional
Probab=58.72 E-value=11 Score=32.17 Aligned_cols=28 Identities=36% Similarity=0.444 Sum_probs=25.8
Q ss_pred HHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 115 QLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 115 ~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
-|+.|+..|++..+-.|+..|+|+|..|
T Consensus 40 PLh~A~~~g~~e~vk~Ll~~gadvn~~d 67 (477)
T PHA02878 40 PLHQAVEARNLDVVKSLLTRGHNVNQPD 67 (477)
T ss_pred hHHHHHHcCCHHHHHHHHHCCCCCCCCC
Confidence 4899999999999999999999999875
No 30
>PHA03095 ankyrin-like protein; Provisional
Probab=57.83 E-value=12 Score=31.58 Aligned_cols=29 Identities=31% Similarity=0.316 Sum_probs=26.2
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..|+.|+..++...+..||..|||+|..|
T Consensus 259 TpLh~A~~~~~~~~v~~LL~~gad~n~~~ 287 (471)
T PHA03095 259 TPLHYAAVFNNPRACRRLIALGADINAVS 287 (471)
T ss_pred CHHHHHHHcCCHHHHHHHHHcCCCCcccC
Confidence 47899999999999999999999999876
No 31
>PHA02884 ankyrin repeat protein; Provisional
Probab=57.13 E-value=14 Score=30.56 Aligned_cols=28 Identities=32% Similarity=0.298 Sum_probs=21.1
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCc
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYF 141 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~ 141 (143)
..|+.|+..+++..+-.||.+|||+|..
T Consensus 35 ~lL~~A~~~~~~eivk~LL~~GAdiN~~ 62 (300)
T PHA02884 35 NILYSSIKFHYTDIIDAILKLGADPEAP 62 (300)
T ss_pred HHHHHHHHcCCHHHHHHHHHCCCCcccc
Confidence 4677777777777777777888887764
No 32
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=55.22 E-value=9.9 Score=29.70 Aligned_cols=23 Identities=22% Similarity=0.388 Sum_probs=19.6
Q ss_pred CCCCCCC-Ceeecccceeeccchh
Q psy13622 2 SSRAADP-KWGILNKGVLVCDACC 24 (143)
Q Consensus 2 DCga~~P-~was~n~gvfiC~~Cs 24 (143)
-||.+.. .|.+..-|-++|..|.
T Consensus 154 ~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 154 VCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred cCCCCCCceEEecccCCccccccc
Confidence 4887754 7899999999999997
No 33
>KOG3676|consensus
Probab=53.26 E-value=14 Score=34.65 Aligned_cols=42 Identities=21% Similarity=0.321 Sum_probs=32.7
Q ss_pred HHHHHHHhcCccccCCCCCHHHHHHHHHHhhhcCCHHHHHHHHHcCCCCCC
Q psy13622 90 EFIKAKYEQLSFMIRSNDTQEELNQQLHSSVRTSNLDTSLRLLSQGADPNY 140 (143)
Q Consensus 90 ~fI~~KY~~k~f~~~~~~~~~~~~~~l~~av~~~~~~~~~~ll~~Ga~~n~ 140 (143)
++|-+-|..-.|+.. .+|+-||...|...+..|++.|||+|.
T Consensus 171 ~lind~~~~eeY~Gq---------SaLHiAIv~~~~~~V~lLl~~gADV~a 212 (782)
T KOG3676|consen 171 KLINDIYTSEEYYGQ---------SALHIAIVNRDAELVRLLLAAGADVHA 212 (782)
T ss_pred HHhhhhhhhHhhcCc---------chHHHHHHhccHHHHHHHHHcCCchhh
Confidence 445555555555543 489999999999999999999999984
No 34
>PHA02946 ankyin-like protein; Provisional
Probab=51.97 E-value=18 Score=31.13 Aligned_cols=29 Identities=34% Similarity=0.408 Sum_probs=25.8
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..|+.|+..++.+.+-.||.+|||+|..|
T Consensus 74 TpLh~Aa~~g~~eiv~lLL~~GAdin~~d 102 (446)
T PHA02946 74 YPLHIASKINNNRIVAMLLTHGADPNACD 102 (446)
T ss_pred CHHHHHHHcCCHHHHHHHHHCcCCCCCCC
Confidence 47899999999999999999999999765
No 35
>PHA02884 ankyrin repeat protein; Provisional
Probab=51.35 E-value=18 Score=29.84 Aligned_cols=28 Identities=29% Similarity=0.360 Sum_probs=23.6
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCc
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYF 141 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~ 141 (143)
..|+.|++.+++..+..|+.+|||+|..
T Consensus 72 TpLh~Aa~~~~~eivklLL~~GADVN~~ 99 (300)
T PHA02884 72 NPLIYAIDCDNDDAAKLLIRYGADVNRY 99 (300)
T ss_pred CHHHHHHHcCCHHHHHHHHHcCCCcCcc
Confidence 3678888999998888888999999864
No 36
>PHA02875 ankyrin repeat protein; Provisional
Probab=51.29 E-value=19 Score=29.90 Aligned_cols=29 Identities=24% Similarity=0.382 Sum_probs=20.3
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..|+.|+..+++..+..|+..|+|+|..+
T Consensus 170 TpL~~A~~~g~~eiv~~Ll~~ga~~n~~~ 198 (413)
T PHA02875 170 TPLIIAMAKGDIAICKMLLDSGANIDYFG 198 (413)
T ss_pred CHHHHHHHcCCHHHHHHHHhCCCCCCcCC
Confidence 35667777777777777777777777654
No 37
>PHA02874 ankyrin repeat protein; Provisional
Probab=51.12 E-value=20 Score=30.30 Aligned_cols=29 Identities=21% Similarity=0.303 Sum_probs=25.7
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..|+.|++.|++..+-.|+..|+++|..+
T Consensus 37 tpL~~A~~~g~~~iv~~Ll~~Ga~~n~~~ 65 (434)
T PHA02874 37 TPLIDAIRSGDAKIVELFIKHGADINHIN 65 (434)
T ss_pred CHHHHHHHcCCHHHHHHHHHCCCCCCCCC
Confidence 47889999999999999999999998764
No 38
>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=50.86 E-value=13 Score=20.96 Aligned_cols=27 Identities=11% Similarity=0.161 Sum_probs=20.9
Q ss_pred CCCCCCCeeecccceeeccchhhh-hhc
Q psy13622 3 SRAADPKWGILNKGVLVCDACCSI-HRS 29 (143)
Q Consensus 3 Cga~~P~was~n~gvfiC~~Csgi-HR~ 29 (143)
|+.....+...+=++++|..|... |+.
T Consensus 9 H~~~~~~~~C~~C~~~~C~~C~~~~H~~ 36 (42)
T PF00643_consen 9 HPEEPLSLFCEDCNEPLCSECTVSGHKG 36 (42)
T ss_dssp TTTSBEEEEETTTTEEEEHHHHHTSTTT
T ss_pred CCccceEEEecCCCCccCccCCCCCCCC
Confidence 334445677888899999999998 876
No 39
>PHA02989 ankyrin repeat protein; Provisional
Probab=49.80 E-value=19 Score=31.13 Aligned_cols=29 Identities=24% Similarity=0.187 Sum_probs=25.7
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..|+.|+..++...+-.||..|||+|..|
T Consensus 258 TpL~~Aa~~~~~~~v~~LL~~Gadin~~d 286 (494)
T PHA02989 258 NPLLISAKVDNYEAFNYLLKLGDDIYNVS 286 (494)
T ss_pred CHHHHHHHhcCHHHHHHHHHcCCCccccC
Confidence 46888999999999999999999999876
No 40
>PF13119 DUF3973: Domain of unknown function (DUF3973)
Probab=49.16 E-value=8.4 Score=22.58 Aligned_cols=14 Identities=36% Similarity=0.795 Sum_probs=11.3
Q ss_pred eeccchhhhhhcCC
Q psy13622 18 LVCDACCSIHRSLG 31 (143)
Q Consensus 18 fiC~~CsgiHR~lg 31 (143)
+-|+.||.+|-.-+
T Consensus 2 yYCi~Cs~~h~e~~ 15 (41)
T PF13119_consen 2 YYCINCSEIHHEKG 15 (41)
T ss_pred EEEEEhHHhHHhhc
Confidence 56999999997643
No 41
>TIGR00870 trp transient-receptor-potential calcium channel protein. after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
Probab=47.81 E-value=22 Score=32.43 Aligned_cols=30 Identities=13% Similarity=0.130 Sum_probs=18.1
Q ss_pred HHHHHHhhhcCCHHHHHHHHHc--CCCCCCcC
Q psy13622 113 NQQLHSSVRTSNLDTSLRLLSQ--GADPNYFY 142 (143)
Q Consensus 113 ~~~l~~av~~~~~~~~~~ll~~--Ga~~n~~~ 142 (143)
.++++.|++.||+..+.+++.. |+++|+.|
T Consensus 18 ~~~~l~A~~~g~~~~v~~lL~~~~~~~in~~d 49 (743)
T TIGR00870 18 EKAFLPAAERGDLASVYRDLEEPKKLNINCPD 49 (743)
T ss_pred HHHHHHHHHcCCHHHHHHHhccccccCCCCcC
Confidence 3566666666666666666665 66666543
No 42
>PHA02791 ankyrin-like protein; Provisional
Probab=47.34 E-value=24 Score=28.77 Aligned_cols=30 Identities=17% Similarity=0.204 Sum_probs=26.5
Q ss_pred HHHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 113 NQQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 113 ~~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
...|+.|+..|++..+-.||..|||+|..|
T Consensus 161 ~TpLh~Aa~~g~~eiv~lLL~~gAd~n~~d 190 (284)
T PHA02791 161 LSCIHITIKNGHVDMMILLLDYMTSTNTNN 190 (284)
T ss_pred ccHHHHHHHcCCHHHHHHHHHCCCCCCccc
Confidence 458999999999999999999999998754
No 43
>PHA02795 ankyrin-like protein; Provisional
Probab=46.25 E-value=27 Score=30.60 Aligned_cols=29 Identities=24% Similarity=0.269 Sum_probs=26.0
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..|+.|+..++...+-.|+..|||+|..|
T Consensus 223 TpLh~Aa~~g~~eiVelLL~~GAdIN~~d 251 (437)
T PHA02795 223 TLLYRAIYAGYIDLVSWLLENGANVNAVM 251 (437)
T ss_pred CHHHHHHHcCCHHHHHHHHHCCCCCCCcC
Confidence 47899999999999999999999999876
No 44
>PHA03100 ankyrin repeat protein; Provisional
Probab=46.12 E-value=25 Score=29.70 Aligned_cols=29 Identities=34% Similarity=0.430 Sum_probs=21.1
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..|+.|+..++...+-.|+..|+|+|..|
T Consensus 252 TpL~~A~~~~~~~iv~~Ll~~gad~n~~d 280 (480)
T PHA03100 252 TPLHYAVYNNNPEFVKYLLDLGANPNLVN 280 (480)
T ss_pred CHHHHHHHcCCHHHHHHHHHcCCCCCccC
Confidence 35677777777777777777788777655
No 45
>KOG0502|consensus
Probab=45.88 E-value=18 Score=29.49 Aligned_cols=28 Identities=25% Similarity=0.290 Sum_probs=24.1
Q ss_pred HHHHHHhhhcCCHHHHHHHHHcCCCCCC
Q psy13622 113 NQQLHSSVRTSNLDTSLRLLSQGADPNY 140 (143)
Q Consensus 113 ~~~l~~av~~~~~~~~~~ll~~Ga~~n~ 140 (143)
...|++|.++|.+..+..||..|||+..
T Consensus 161 fTpLiWAaa~G~i~vV~fLL~~GAdp~~ 188 (296)
T KOG0502|consen 161 FTPLIWAAAKGHIPVVQFLLNSGADPDA 188 (296)
T ss_pred chHhHHHHhcCchHHHHHHHHcCCChhh
Confidence 3578999999999999999999999864
No 46
>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=45.01 E-value=35 Score=26.44 Aligned_cols=53 Identities=19% Similarity=0.252 Sum_probs=34.0
Q ss_pred CCCCCCC-CeeecccceeeccchhhhhhcCCCCcceeeeCCCCCCChHHHHHHHhhccCchhHHhc
Q psy13622 2 SSRAADP-KWGILNKGVLVCDACCSIHRSLGRHISQVKYLEPSTWPPSLLSMLMTLTNGGAPSLWE 66 (143)
Q Consensus 2 DCga~~P-~was~n~gvfiC~~CsgiHR~lg~~iskVks~~ld~w~~~~v~~~~~~GN~~~n~~~e 66 (143)
.||..++ .+.|..-|-++|..|..... +. ..++++.+..+..+=+.....+.+
T Consensus 152 ~cg~~~~~~~fs~~~gg~~C~~c~~~~~----~~--------~~~~~~~l~~~~~l~~~~~~~~~~ 205 (241)
T TIGR00613 152 VCGSKEDLIYFSMTYGGALCRQCGEKDP----HA--------IPIDPKLLRLLRYLLKLDLEKLLS 205 (241)
T ss_pred CCCCcCCCceEchhcCeEEChhhCccCC----Cc--------eecCHHHHHHHHHHHcCCHHHhce
Confidence 4777544 68899999999999976421 10 134566777776665554444444
No 47
>PTZ00322 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional
Probab=43.60 E-value=33 Score=31.26 Aligned_cols=28 Identities=29% Similarity=0.293 Sum_probs=15.7
Q ss_pred HHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 115 QLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 115 ~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
.|+.++..|++..+-.|+..|+|+|..|
T Consensus 85 ~L~~aa~~G~~~~vk~LL~~Gadin~~d 112 (664)
T PTZ00322 85 ELCQLAASGDAVGARILLTGGADPNCRD 112 (664)
T ss_pred HHHHHHHcCCHHHHHHHHHCCCCCCCcC
Confidence 4555555566555555555566555443
No 48
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=40.95 E-value=32 Score=31.98 Aligned_cols=29 Identities=21% Similarity=0.255 Sum_probs=25.8
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..|+.|+..+++..+-.|+.+|+|+|..|
T Consensus 624 ~~L~~Aa~~g~~~~v~~Ll~~Gadin~~d 652 (823)
T PLN03192 624 DLLCTAAKRNDLTAMKELLKQGLNVDSED 652 (823)
T ss_pred hHHHHHHHhCCHHHHHHHHHCCCCCCCCC
Confidence 46889999999999999999999999876
No 49
>KOG4214|consensus
Probab=40.48 E-value=27 Score=24.75 Aligned_cols=78 Identities=14% Similarity=0.013 Sum_probs=43.2
Q ss_pred HHHHHHHhhccCchhHHhccccccccCCCCCCCCCCChHHHHHHHHHHHhcCccccCCCCCHHHHHHHHHHhhhcCCHHH
Q psy13622 48 SLLSMLMTLTNGGAPSLWEHSLCESKTKKKPVPSDPLHPTKAEFIKAKYEQLSFMIRSNDTQEELNQQLHSSVRTSNLDT 127 (143)
Q Consensus 48 ~~v~~~~~~GN~~~n~~~ea~~~~~~~~~kP~~~~~~~~~r~~fI~~KY~~k~f~~~~~~~~~~~~~~l~~av~~~~~~~ 127 (143)
++|+....-| ..+|.++..+-| - .-..+-.. -...+|+-.+=-+- -.++- ---.-|++||..|....
T Consensus 16 DeVk~~v~~g-~nVn~~~ggR~p--l---hyAAD~GQ-l~ilefli~iGA~i--~~kDK----ygITPLLsAvwEGH~~c 82 (117)
T KOG4214|consen 16 DEVKQSVNEG-LNVNEIYGGRTP--L---HYAADYGQ-LSILEFLISIGANI--QDKDK----YGITPLLSAVWEGHRDC 82 (117)
T ss_pred HHHHHHHHcc-ccHHHHhCCccc--c---hHhhhcch-HHHHHHHHHhcccc--CCccc----cCCcHHHHHHHHhhHHH
Confidence 5566555556 668888865542 1 11111122 33444544332111 11110 01125889999999999
Q ss_pred HHHHHHcCCCC
Q psy13622 128 SLRLLSQGADP 138 (143)
Q Consensus 128 ~~~ll~~Ga~~ 138 (143)
+-.||..|||-
T Consensus 83 VklLL~~GAdr 93 (117)
T KOG4214|consen 83 VKLLLQNGADR 93 (117)
T ss_pred HHHHHHcCccc
Confidence 99999999984
No 50
>PHA02874 ankyrin repeat protein; Provisional
Probab=39.39 E-value=39 Score=28.49 Aligned_cols=29 Identities=28% Similarity=0.352 Sum_probs=25.6
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..|+.|+..+++..+-.|+..|+++|..|
T Consensus 126 T~Lh~A~~~~~~~~v~~Ll~~gad~n~~d 154 (434)
T PHA02874 126 TFLHYAIKKGDLESIKMLFEYGADVNIED 154 (434)
T ss_pred cHHHHHHHCCCHHHHHHHHhCCCCCCCcC
Confidence 47889999999999999999999998765
No 51
>PHA02736 Viral ankyrin protein; Provisional
Probab=38.18 E-value=44 Score=23.75 Aligned_cols=29 Identities=28% Similarity=0.348 Sum_probs=23.7
Q ss_pred HHHHHhhhcCCHHHHHHHHHc-CCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQ-GADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~-Ga~~n~~~ 142 (143)
..|+.|+..++...+..|+.+ |+|+|..|
T Consensus 94 T~Lh~A~~~~~~~i~~~Ll~~~g~d~n~~~ 123 (154)
T PHA02736 94 TPLHIAVYTQNYELATWLCNQPGVNMEILN 123 (154)
T ss_pred cHHHHHHHhCCHHHHHHHHhCCCCCCcccc
Confidence 478889999999888888874 99998654
No 52
>PHA02875 ankyrin repeat protein; Provisional
Probab=36.81 E-value=44 Score=27.73 Aligned_cols=28 Identities=18% Similarity=0.086 Sum_probs=18.5
Q ss_pred HHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 115 QLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 115 ~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
.|+.|+..++...+-.|+..|+++|..|
T Consensus 138 pLh~A~~~~~~~~v~~Ll~~g~~~~~~d 165 (413)
T PHA02875 138 PLHLAVMMGDIKGIELLIDHKACLDIED 165 (413)
T ss_pred HHHHHHHcCCHHHHHHHHhcCCCCCCCC
Confidence 5666667777766666666677666544
No 53
>PHA02730 ankyrin-like protein; Provisional
Probab=36.04 E-value=44 Score=30.91 Aligned_cols=29 Identities=24% Similarity=0.279 Sum_probs=23.7
Q ss_pred HHHHHhhhcC---CHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTS---NLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~---~~~~~~~ll~~Ga~~n~~~ 142 (143)
-.|+.|+..+ +.+.+-.||.+|||+|..|
T Consensus 43 TaLh~A~~~~~~~~~eivklLLs~GAdin~kD 74 (672)
T PHA02730 43 NALHCYVSNKCDTDIKIVRLLLSRGVERLCRN 74 (672)
T ss_pred cHHHHHHHcCCcCcHHHHHHHHhCCCCCcccC
Confidence 4788888886 4777778888999999876
No 54
>PHA02878 ankyrin repeat protein; Provisional
Probab=35.99 E-value=43 Score=28.64 Aligned_cols=29 Identities=28% Similarity=0.230 Sum_probs=25.4
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..|+.|+..+++..+-.|+..|+|+|..|
T Consensus 170 tpLh~A~~~~~~~iv~~Ll~~gad~n~~d 198 (477)
T PHA02878 170 TALHYATENKDQRLTELLLSYGANVNIPD 198 (477)
T ss_pred CHHHHHHhCCCHHHHHHHHHCCCCCCCcC
Confidence 46889999999999999999999998765
No 55
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=35.40 E-value=15 Score=20.71 Aligned_cols=24 Identities=21% Similarity=0.289 Sum_probs=13.4
Q ss_pred CCCCCC-CCCeeecccceeeccchh
Q psy13622 1 MSSRAA-DPKWGILNKGVLVCDACC 24 (143)
Q Consensus 1 ~DCga~-~P~was~n~gvfiC~~Cs 24 (143)
++||.+ .-+|..-+|+.-||.+|.
T Consensus 7 ~eC~~~f~dSyL~~~F~~~VCD~CR 31 (34)
T PF01286_consen 7 DECGKPFMDSYLLNNFDLPVCDKCR 31 (34)
T ss_dssp TTT--EES-SSCCCCTS-S--TTT-
T ss_pred hHhCCHHHHHHHHHhCCcccccccc
Confidence 357765 347888999999999984
No 56
>PHA03100 ankyrin repeat protein; Provisional
Probab=35.02 E-value=42 Score=28.37 Aligned_cols=29 Identities=31% Similarity=0.248 Sum_probs=24.4
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..|+.|++.++...+-.|+..|+++|..+
T Consensus 37 t~L~~A~~~~~~~ivk~Ll~~g~~~~~~~ 65 (480)
T PHA03100 37 LPLYLAKEARNIDVVKILLDNGADINSST 65 (480)
T ss_pred hhhhhhhccCCHHHHHHHHHcCCCCCCcc
Confidence 57888999999988888898999988654
No 57
>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=34.66 E-value=24 Score=21.12 Aligned_cols=22 Identities=23% Similarity=0.516 Sum_probs=14.4
Q ss_pred CCCCCCCeeecccceeeccchhh
Q psy13622 3 SRAADPKWGILNKGVLVCDACCS 25 (143)
Q Consensus 3 Cga~~P~was~n~gvfiC~~Csg 25 (143)
|+.+.+. --.=+|.|||.+|-.
T Consensus 5 C~~~~~~-GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 5 CGKEKEE-GIHIYGKFICSDCEK 26 (46)
T ss_pred CCCcCCC-CEEEECeEehHHHHH
Confidence 5555554 334478899999954
No 58
>PRK00523 hypothetical protein; Provisional
Probab=33.94 E-value=96 Score=20.47 Aligned_cols=35 Identities=11% Similarity=0.038 Sum_probs=19.4
Q ss_pred HHHHHHHhcCccccCCCCCHHHHHHHHHHhhhcCC
Q psy13622 90 EFIKAKYEQLSFMIRSNDTQEELNQQLHSSVRTSN 124 (143)
Q Consensus 90 ~fI~~KY~~k~f~~~~~~~~~~~~~~l~~av~~~~ 124 (143)
=||..||.+|.+.+.++-+++.+..-...--+..+
T Consensus 23 ffiark~~~k~l~~NPpine~mir~M~~QMGqKPS 57 (72)
T PRK00523 23 YFVSKKMFKKQIRENPPITENMIRAMYMQMGRKPS 57 (72)
T ss_pred HHHHHHHHHHHHHHCcCCCHHHHHHHHHHhCCCcc
Confidence 47777787777776554454444443333333333
No 59
>PHA02859 ankyrin repeat protein; Provisional
Probab=32.92 E-value=58 Score=24.81 Aligned_cols=28 Identities=25% Similarity=0.373 Sum_probs=17.9
Q ss_pred HHHHhhhcC--CHHHHHHHHHcCCCCCCcC
Q psy13622 115 QLHSSVRTS--NLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 115 ~l~~av~~~--~~~~~~~ll~~Ga~~n~~~ 142 (143)
.|+.|+..+ ++..+-.||..|+|+|..+
T Consensus 54 pLh~a~~~~~~~~eiv~~Ll~~gadvn~~~ 83 (209)
T PHA02859 54 PIFSCLEKDKVNVEILKFLIENGADVNFKT 83 (209)
T ss_pred HHHHHHHcCCCCHHHHHHHHHCCCCCCccC
Confidence 455566543 6666666777788877653
No 60
>KOG0515|consensus
Probab=31.66 E-value=46 Score=30.36 Aligned_cols=31 Identities=19% Similarity=0.150 Sum_probs=27.6
Q ss_pred HHHHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 112 LNQQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 112 ~~~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
.-.+|+.||=.|..+-+-.||-.||++|..|
T Consensus 583 GITaLHNAiCaghyeIVkFLi~~ganVNa~D 613 (752)
T KOG0515|consen 583 GITALHNAICAGHYEIVKFLIEFGANVNAAD 613 (752)
T ss_pred chhHHhhhhhcchhHHHHHHHhcCCcccCcc
Confidence 4568899999999999999999999999887
No 61
>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=31.61 E-value=25 Score=24.27 Aligned_cols=18 Identities=28% Similarity=0.597 Sum_probs=15.8
Q ss_pred ecccceeeccchhhhhhc
Q psy13622 12 ILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 12 s~n~gvfiC~~CsgiHR~ 29 (143)
...||+..|..|.++.|-
T Consensus 16 g~hyGv~sC~aCk~FFRR 33 (97)
T cd07170 16 GYHYGVASCEACKAFFKR 33 (97)
T ss_pred ceEECceeehhhhHHHHH
Confidence 468999999999998874
No 62
>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=31.54 E-value=24 Score=23.34 Aligned_cols=24 Identities=21% Similarity=0.418 Sum_probs=18.9
Q ss_pred CCCCCCCeeecccceeeccchhhhhhc
Q psy13622 3 SRAADPKWGILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 3 Cga~~P~was~n~gvfiC~~CsgiHR~ 29 (143)
||.+.- ...||+..|..|.++.|-
T Consensus 4 Cg~~~~---g~hyG~~sC~aC~~FFRR 27 (81)
T cd07165 4 CGDKAS---GYHYGVTSCEGCKGFFRR 27 (81)
T ss_pred cCccCc---ceEECchhhhhHHHHHHh
Confidence 565443 469999999999998884
No 63
>KOG0502|consensus
Probab=31.24 E-value=49 Score=26.99 Aligned_cols=31 Identities=23% Similarity=0.202 Sum_probs=24.3
Q ss_pred HHHHHHhhhcCCHHHHHHHHHcCCCCCCcCC
Q psy13622 113 NQQLHSSVRTSNLDTSLRLLSQGADPNYFYQ 143 (143)
Q Consensus 113 ~~~l~~av~~~~~~~~~~ll~~Ga~~n~~~~ 143 (143)
..+|..|.+.|-+.-+-.||-.++|+|.||+
T Consensus 194 esALsLAt~ggytdiV~lLL~r~vdVNvyDw 224 (296)
T KOG0502|consen 194 ESALSLATRGGYTDIVELLLTREVDVNVYDW 224 (296)
T ss_pred hhhHhHHhcCChHHHHHHHHhcCCCcceecc
Confidence 3577888888877777778888999998885
No 64
>KOG0512|consensus
Probab=31.24 E-value=53 Score=25.85 Aligned_cols=29 Identities=28% Similarity=0.311 Sum_probs=25.4
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..|+.|+-.+.+.-+-.||+.||+++..+
T Consensus 99 TpLHRAaYn~h~div~~ll~~gAn~~a~T 127 (228)
T KOG0512|consen 99 TPLHRAAYNGHLDIVHELLLSGANKEAKT 127 (228)
T ss_pred cHHHHHHhcCchHHHHHHHHccCCccccc
Confidence 47889999999999999999999998764
No 65
>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=31.15 E-value=31 Score=23.17 Aligned_cols=24 Identities=13% Similarity=0.333 Sum_probs=18.5
Q ss_pred CCCCCCCeeecccceeeccchhhhhhc
Q psy13622 3 SRAADPKWGILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 3 Cga~~P~was~n~gvfiC~~CsgiHR~ 29 (143)
||.+.- ...||+..|..|+++.|-
T Consensus 5 Cg~~~~---g~hygv~sC~aC~~FFRR 28 (87)
T cd07162 5 CGDRAT---GYHFNAMTCEGCKGFFRR 28 (87)
T ss_pred cCCcCc---ceEECcceehhhHHHHHh
Confidence 565443 458999999999998874
No 66
>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=30.94 E-value=19 Score=25.53 Aligned_cols=28 Identities=18% Similarity=0.302 Sum_probs=22.8
Q ss_pred CCCCCCeeecccceeeccchhhhhhcCC
Q psy13622 4 RAADPKWGILNKGVLVCDACCSIHRSLG 31 (143)
Q Consensus 4 ga~~P~was~n~gvfiC~~CsgiHR~lg 31 (143)
|.++.....+-|+-+.|..|+..|..++
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 6777888889999999999999998774
No 67
>PHA02876 ankyrin repeat protein; Provisional
Probab=30.92 E-value=55 Score=29.43 Aligned_cols=29 Identities=31% Similarity=0.313 Sum_probs=21.4
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..|+.|+..|++..+-.|+..|||+|..+
T Consensus 180 TpLh~Aa~~G~~~iv~~LL~~Gad~n~~~ 208 (682)
T PHA02876 180 TPIHYAAERGNAKMVNLLLSYGADVNIIA 208 (682)
T ss_pred CHHHHHHHCCCHHHHHHHHHCCCCcCccC
Confidence 36777788888877777777788877543
No 68
>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=30.83 E-value=28 Score=22.41 Aligned_cols=24 Identities=13% Similarity=0.333 Sum_probs=18.3
Q ss_pred CCCCCCCeeecccceeeccchhhhhhc
Q psy13622 3 SRAADPKWGILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 3 Cga~~P~was~n~gvfiC~~CsgiHR~ 29 (143)
||.+.- ..+||+..|..|.++.|-
T Consensus 4 C~~~~~---g~hygv~sC~aC~~FFRR 27 (72)
T cd07156 4 CGDRAT---GYHFNAMTCEGCKGFFRR 27 (72)
T ss_pred cCccCc---ccEECcceehhhhhhhch
Confidence 554433 358999999999998874
No 69
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=30.83 E-value=55 Score=30.46 Aligned_cols=31 Identities=23% Similarity=0.182 Sum_probs=24.2
Q ss_pred HHHHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 112 LNQQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 112 ~~~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
....|+.|+..|+...+-.|+..|+|+|..|
T Consensus 525 ~~~~L~~Aa~~g~~~~l~~Ll~~G~d~n~~d 555 (823)
T PLN03192 525 MASNLLTVASTGNAALLEELLKAKLDPDIGD 555 (823)
T ss_pred chhHHHHHHHcCCHHHHHHHHHCCCCCCCCC
Confidence 3466888888888888888888888888765
No 70
>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=30.34 E-value=27 Score=22.49 Aligned_cols=24 Identities=21% Similarity=0.437 Sum_probs=18.5
Q ss_pred CCCCCCCeeecccceeeccchhhhhhc
Q psy13622 3 SRAADPKWGILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 3 Cga~~P~was~n~gvfiC~~CsgiHR~ 29 (143)
||.+.- ...+|++.|..|.++.|-
T Consensus 4 Cg~~~~---g~hyGv~~C~aC~~FFRR 27 (73)
T cd07158 4 CGDKAS---GFHYGVHSCEGCKGFFRR 27 (73)
T ss_pred cCccCc---ceEECcchhhHHHHHHhh
Confidence 554433 468999999999999874
No 71
>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=29.90 E-value=32 Score=19.79 Aligned_cols=24 Identities=21% Similarity=0.336 Sum_probs=15.1
Q ss_pred CCCCCCCCeeecccceeeccchhhh
Q psy13622 2 SSRAADPKWGILNKGVLVCDACCSI 26 (143)
Q Consensus 2 DCga~~P~was~n~gvfiC~~Csgi 26 (143)
.||+.. .-.--.-|-++|..|--|
T Consensus 5 ~Cg~~~-~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 5 NCGSKE-IVFDPERGELVCPNCGLV 28 (43)
T ss_dssp TTSSSE-EEEETTTTEEEETTT-BB
T ss_pred CCcCCc-eEEcCCCCeEECCCCCCE
Confidence 366654 233456899999999433
No 72
>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=29.38 E-value=29 Score=23.82 Aligned_cols=24 Identities=21% Similarity=0.538 Sum_probs=18.7
Q ss_pred CCCCCCCeeecccceeeccchhhhhhc
Q psy13622 3 SRAADPKWGILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 3 Cga~~P~was~n~gvfiC~~CsgiHR~ 29 (143)
||.+. ....+|+..|..|.++.|-
T Consensus 11 Cg~~~---~g~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 11 CGDKS---SGIHYGVITCEGCKGFFRR 34 (95)
T ss_pred cCCcC---cceEECceeehhhHHhhHH
Confidence 55443 3568999999999998874
No 73
>PHA02792 ankyrin-like protein; Provisional
Probab=29.35 E-value=51 Score=30.30 Aligned_cols=29 Identities=7% Similarity=-0.063 Sum_probs=23.3
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..++.|+..++++.+-.|+.+|||+|..|
T Consensus 341 n~~~~Aa~~gn~eIVelLIs~GADIN~kD 369 (631)
T PHA02792 341 NKYFQKFDNRDPKVVEYILKNGNVVVEDD 369 (631)
T ss_pred hHHHHHHHcCCHHHHHHHHHcCCchhhhc
Confidence 34677788888888888889999998755
No 74
>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=29.10 E-value=50 Score=18.37 Aligned_cols=30 Identities=23% Similarity=0.563 Sum_probs=21.8
Q ss_pred CCCCC-CCCeeeccccee-eccchhhhhhcCC
Q psy13622 2 SSRAA-DPKWGILNKGVL-VCDACCSIHRSLG 31 (143)
Q Consensus 2 DCga~-~P~was~n~gvf-iC~~CsgiHR~lg 31 (143)
.|++. .|.|=....|-. ||..|--.+|..|
T Consensus 3 ~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~ 34 (36)
T PF00320_consen 3 NCGTTETPQWRRGPNGNRTLCNACGLYYKKYG 34 (36)
T ss_dssp TT--ST-SSEEEETTSEE-EEHHHHHHHHHHS
T ss_pred CCcCCCCchhhcCCCCCCHHHHHHHHHHHHhC
Confidence 57766 689998888888 9999988777544
No 75
>PRK11032 hypothetical protein; Provisional
Probab=28.46 E-value=25 Score=26.69 Aligned_cols=13 Identities=38% Similarity=0.915 Sum_probs=11.0
Q ss_pred cccceeeccchhh
Q psy13622 13 LNKGVLVCDACCS 25 (143)
Q Consensus 13 ~n~gvfiC~~Csg 25 (143)
+.+|+++|.+|--
T Consensus 120 vg~G~LvC~~Cg~ 132 (160)
T PRK11032 120 VGLGNLVCEKCHH 132 (160)
T ss_pred eecceEEecCCCC
Confidence 5799999999943
No 76
>PRK01844 hypothetical protein; Provisional
Probab=28.18 E-value=1.4e+02 Score=19.76 Aligned_cols=33 Identities=15% Similarity=0.077 Sum_probs=18.0
Q ss_pred HHHHHHHhcCccccCCCCCHHHHHHHHHHhhhc
Q psy13622 90 EFIKAKYEQLSFMIRSNDTQEELNQQLHSSVRT 122 (143)
Q Consensus 90 ~fI~~KY~~k~f~~~~~~~~~~~~~~l~~av~~ 122 (143)
=||..||.++.+.+.++-+++.+..-...--+.
T Consensus 22 ff~ark~~~k~lk~NPpine~mir~Mm~QMGqk 54 (72)
T PRK01844 22 FFIARKYMMNYLQKNPPINEQMLKMMMMQMGQK 54 (72)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCC
Confidence 467777777777766544444444333333333
No 77
>PHA03095 ankyrin-like protein; Provisional
Probab=28.05 E-value=67 Score=26.99 Aligned_cols=28 Identities=36% Similarity=0.215 Sum_probs=17.3
Q ss_pred HHHHhhhcC---CHHHHHHHHHcCCCCCCcC
Q psy13622 115 QLHSSVRTS---NLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 115 ~l~~av~~~---~~~~~~~ll~~Ga~~n~~~ 142 (143)
.|+.|++.+ +.+.+..|+..|+|+|..|
T Consensus 50 ~Lh~a~~~~~~~~~~iv~~Ll~~Gadin~~~ 80 (471)
T PHA03095 50 PLHLYLHYSSEKVKDIVRLLLEAGADVNAPE 80 (471)
T ss_pred HHHHHHHhcCCChHHHHHHHHHCCCCCCCCC
Confidence 455566655 5666666666677777654
No 78
>PHA02741 hypothetical protein; Provisional
Probab=27.95 E-value=81 Score=22.93 Aligned_cols=29 Identities=21% Similarity=0.280 Sum_probs=24.1
Q ss_pred HHHHHhhhcCCHHHHHHHHH-cCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLS-QGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~-~Ga~~n~~~ 142 (143)
..|+.|+..++...+-.|+. .|+++|..|
T Consensus 100 TpLh~A~~~~~~~iv~~Ll~~~g~~~~~~n 129 (169)
T PHA02741 100 TALHLAAHRRDHDLAEWLCCQPGIDLHFCN 129 (169)
T ss_pred CHHHHHHHcCCHHHHHHHHhCCCCCCCcCC
Confidence 46899999999998888887 499998754
No 79
>PHA02795 ankyrin-like protein; Provisional
Probab=27.93 E-value=69 Score=28.07 Aligned_cols=30 Identities=13% Similarity=0.066 Sum_probs=24.9
Q ss_pred HHHHHHHhhh--cCCHHHHHHHHHcCCCCCCc
Q psy13622 112 LNQQLHSSVR--TSNLDTSLRLLSQGADPNYF 141 (143)
Q Consensus 112 ~~~~l~~av~--~~~~~~~~~ll~~Ga~~n~~ 141 (143)
....|+.++. .++++.+-.||.+|||+|..
T Consensus 116 ~~~~L~~~~~n~~n~~eiV~~LI~~GADIn~~ 147 (437)
T PHA02795 116 VQDLLLYYLSNAYVEIDIVDFMVDHGAVIYKI 147 (437)
T ss_pred ccHHHHHHHHhcCCCHHHHHHHHHCCCCCCCC
Confidence 4567888888 78899999999999999864
No 80
>PF09920 DUF2150: Uncharacterized protein conserved in archaea (DUF2150); InterPro: IPR014518 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=27.65 E-value=1.5e+02 Score=23.15 Aligned_cols=43 Identities=21% Similarity=0.225 Sum_probs=34.2
Q ss_pred HHHhcCccccCCCCCHHHHHHHHHHhhhcCCHHHHHHHHHc-CCCC
Q psy13622 94 AKYEQLSFMIRSNDTQEELNQQLHSSVRTSNLDTSLRLLSQ-GADP 138 (143)
Q Consensus 94 ~KY~~k~f~~~~~~~~~~~~~~l~~av~~~~~~~~~~ll~~-Ga~~ 138 (143)
.+|+...|... .+.+++-+.-..+-+.+|+..++.+.++ ||.+
T Consensus 105 e~yi~g~~~~~--~~i~~lvk~A~~aE~~edle~Al~~~a~~GA~V 148 (190)
T PF09920_consen 105 EEYIAGGYDEE--ADIEELVKAAVEAEAEEDLEAALGYAAQIGARV 148 (190)
T ss_pred HHHHcCCCCCc--CCHHHHHHHHHHHhhccCHHHHHHHHHHhCcee
Confidence 46777777543 5788888888888899999999999988 6653
No 81
>PHA02608 67 prohead core protein; Provisional
Probab=27.57 E-value=70 Score=21.48 Aligned_cols=20 Identities=10% Similarity=0.312 Sum_probs=15.7
Q ss_pred HHHHHhhhcCCHHHHHHHHH
Q psy13622 114 QQLHSSVRTSNLDTSLRLLS 133 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~ 133 (143)
..|++||++|||..+-.+++
T Consensus 2 e~lIeAIKS~DLV~akK~F~ 21 (80)
T PHA02608 2 EDLIEAIKSGDLVEAKKEFA 21 (80)
T ss_pred hHHHHHHhcCcHHHHHHHHH
Confidence 47899999999987766544
No 82
>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=27.55 E-value=29 Score=23.72 Aligned_cols=18 Identities=22% Similarity=0.552 Sum_probs=15.8
Q ss_pred ecccceeeccchhhhhhc
Q psy13622 12 ILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 12 s~n~gvfiC~~CsgiHR~ 29 (143)
...||+..|..|+++.|-
T Consensus 12 g~hyGv~sC~aC~~FFRR 29 (94)
T cd06966 12 GYNFNAITCESCKAFFRR 29 (94)
T ss_pred ceEECcceeeeehheehh
Confidence 468999999999998874
No 83
>PTZ00322 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional
Probab=27.43 E-value=71 Score=29.14 Aligned_cols=30 Identities=27% Similarity=0.390 Sum_probs=27.0
Q ss_pred HHHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 113 NQQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 113 ~~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
...|+.|+..+++..+..|+..|+|+|..|
T Consensus 116 ~TpLh~Aa~~g~~eiv~~LL~~Gadvn~~d 145 (664)
T PTZ00322 116 RTPLHIACANGHVQVVRVLLEFGADPTLLD 145 (664)
T ss_pred CcHHHHHHHCCCHHHHHHHHHCCCCCCCCC
Confidence 457999999999999999999999999765
No 84
>KOG1710|consensus
Probab=27.24 E-value=65 Score=27.29 Aligned_cols=27 Identities=33% Similarity=0.225 Sum_probs=23.3
Q ss_pred HHHHhhhcCCHHHHHHHHHcCCCCCCc
Q psy13622 115 QLHSSVRTSNLDTSLRLLSQGADPNYF 141 (143)
Q Consensus 115 ~l~~av~~~~~~~~~~ll~~Ga~~n~~ 141 (143)
-|..|.-.|++..+..||-.|+|+|.-
T Consensus 48 ~LahAaykGnl~~v~lll~~gaDvN~~ 74 (396)
T KOG1710|consen 48 VLAHAAYKGNLTLVELLLELGADVNDK 74 (396)
T ss_pred HHHHHHhcCcHHHHHHHHHhCCCcCcc
Confidence 566778899999999999999999963
No 85
>PF12417 DUF3669: Zinc finger protein ; InterPro: IPR022137 This domain family is found in eukaryotes, and is typically between 64 and 80 amino acids in length.
Probab=26.73 E-value=1.7e+02 Score=18.79 Aligned_cols=51 Identities=10% Similarity=0.255 Sum_probs=24.2
Q ss_pred cceeeeCCCCCCChHHHHHHHhhccCchhHHhccccccccCCCCCCCCCCChHHHHHHHHHHHhc
Q psy13622 34 ISQVKYLEPSTWPPSLLSMLMTLTNGGAPSLWEHSLCESKTKKKPVPSDPLHPTKAEFIKAKYEQ 98 (143)
Q Consensus 34 iskVks~~ld~w~~~~v~~~~~~GN~~~n~~~ea~~~~~~~~~kP~~~~~~~~~r~~fI~~KY~~ 98 (143)
++.++.++++ ++.+..+ ++.+|..- | .++||...+....+--.-.+.+|..
T Consensus 6 F~~~~~i~~~---e~gv~~a-------v~af~~Nd---p-y~PRp~~~~~~~~~lW~~F~~~Yl~ 56 (72)
T PF12417_consen 6 FDQCRPIEMD---EAGVAQA-------VEAFWRND---P-YYPRPLDCEKTDKELWNQFRSRYLE 56 (72)
T ss_pred hhhhcccccc---hhHHHHH-------HHHhccCC---C-CCCCCCccchHHHHHHHHHHHHHHH
Confidence 4555666665 4444443 55566522 2 4466664433322222334555543
No 86
>PF04170 NlpE: NlpE N-terminal domain; InterPro: IPR007298 This family represents a bacterial outer membrane lipoprotein that is necessary for signalling by the Cpx pathway []. This pathway responds to cell envelope disturbances and increases the expression of periplasmic protein folding and degradation factors. While the molecular function of the NlpE protein is unknown, it may be involved in detecting bacterial adhesion to abiotic surfaces. NlpE from Escherichia coli and Salmonella typhi is also known to confer copper tolerance in copper-sensitive strains of E. coli, and may be involved in copper efflux and delivery of copper to copper-dependent enzymes [].; PDB: 3LHN_A 2Z4I_B 2Z4H_A.
Probab=26.60 E-value=21 Score=23.82 Aligned_cols=16 Identities=38% Similarity=0.825 Sum_probs=13.3
Q ss_pred cceeeccchhhhhhcC
Q psy13622 15 KGVLVCDACCSIHRSL 30 (143)
Q Consensus 15 ~gvfiC~~CsgiHR~l 30 (143)
-|++-|-.|.||.-.|
T Consensus 2 ~G~LPCADC~GI~t~L 17 (87)
T PF04170_consen 2 EGTLPCADCPGIKTTL 17 (87)
T ss_dssp EEEEEETTSSEEEEEE
T ss_pred ccEeECCCCCCeEEEE
Confidence 3899999999987654
No 87
>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=26.31 E-value=26 Score=23.55 Aligned_cols=24 Identities=21% Similarity=0.465 Sum_probs=18.6
Q ss_pred CCCCCCCeeecccceeeccchhhhhhc
Q psy13622 3 SRAADPKWGILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 3 Cga~~P~was~n~gvfiC~~CsgiHR~ 29 (143)
||.+. ...+||+..|..|+++.|-
T Consensus 6 Cg~~a---~g~hyGv~sC~aCk~FFRR 29 (86)
T cd07157 6 CGEPA---AGFHHGAYVCEACKKFFMR 29 (86)
T ss_pred cCCcC---cccEECcceeeEeeeEEec
Confidence 55433 3569999999999998874
No 88
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.29 E-value=1.7e+02 Score=19.31 Aligned_cols=23 Identities=17% Similarity=0.069 Sum_probs=14.8
Q ss_pred HHHHHHHhcCccccCCCCCHHHH
Q psy13622 90 EFIKAKYEQLSFMIRSNDTQEEL 112 (143)
Q Consensus 90 ~fI~~KY~~k~f~~~~~~~~~~~ 112 (143)
-||..||.++.+.+.++=+++.+
T Consensus 22 ~fiark~~~k~lk~NPpine~~i 44 (71)
T COG3763 22 FFIARKQMKKQLKDNPPINEEMI 44 (71)
T ss_pred HHHHHHHHHHHHhhCCCCCHHHH
Confidence 47788888887776654444433
No 89
>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=25.88 E-value=43 Score=21.71 Aligned_cols=24 Identities=21% Similarity=0.492 Sum_probs=18.4
Q ss_pred CCCCCCCeeecccceeeccchhhhhhc
Q psy13622 3 SRAADPKWGILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 3 Cga~~P~was~n~gvfiC~~CsgiHR~ 29 (143)
||.+.- ...||+..|..|+++.|-
T Consensus 4 Cg~~~~---g~hygv~sC~aC~~FFRR 27 (74)
T cd07179 4 CGGKSS---GFHFGALTCEGCKGFFRR 27 (74)
T ss_pred cCccCc---ceEECceeehhHHHHHHH
Confidence 554432 468999999999998874
No 90
>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=25.74 E-value=31 Score=21.97 Aligned_cols=27 Identities=26% Similarity=0.360 Sum_probs=19.6
Q ss_pred CCCCCCC-eeecccceeeccchhhhhhcC
Q psy13622 3 SRAADPK-WGILNKGVLVCDACCSIHRSL 30 (143)
Q Consensus 3 Cga~~P~-was~n~gvfiC~~CsgiHR~l 30 (143)
||.-.|. +..-+...+.|..| |-||.|
T Consensus 25 CgEFm~~~g~eg~~~al~CaAC-gCHRnF 52 (60)
T PF04770_consen 25 CGEFMPSPGEEGTPEALKCAAC-GCHRNF 52 (60)
T ss_pred ccccccCCCCCCCcccceeccc-Ccchhc
Confidence 6666666 55566778899888 678876
No 91
>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=25.52 E-value=44 Score=21.81 Aligned_cols=18 Identities=22% Similarity=0.532 Sum_probs=15.8
Q ss_pred ecccceeeccchhhhhhc
Q psy13622 12 ILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 12 s~n~gvfiC~~CsgiHR~ 29 (143)
...||+..|..|+++.|-
T Consensus 12 g~hygv~sC~aC~~FFRR 29 (77)
T cd06956 12 GKHYGVYSCEGCKGFFKR 29 (77)
T ss_pred ceEECceeehhHHHHHHH
Confidence 468999999999998874
No 92
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=24.97 E-value=1.8e+02 Score=18.73 Aligned_cols=35 Identities=14% Similarity=0.147 Sum_probs=19.2
Q ss_pred HHHHHHHhcCccccCCCCCHHHHHHHHHHhhhcCC
Q psy13622 90 EFIKAKYEQLSFMIRSNDTQEELNQQLHSSVRTSN 124 (143)
Q Consensus 90 ~fI~~KY~~k~f~~~~~~~~~~~~~~l~~av~~~~ 124 (143)
-||..||-+|.+.+.++-+++.+..-...--++.+
T Consensus 15 ff~ar~~~~k~l~~NPpine~mir~M~~QMG~kpS 49 (64)
T PF03672_consen 15 FFIARKYMEKQLKENPPINEKMIRAMMMQMGRKPS 49 (64)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCcc
Confidence 46777777777766554444544444444334433
No 93
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=24.14 E-value=33 Score=25.51 Aligned_cols=14 Identities=36% Similarity=0.859 Sum_probs=11.4
Q ss_pred cccceeeccchhhh
Q psy13622 13 LNKGVLVCDACCSI 26 (143)
Q Consensus 13 ~n~gvfiC~~Csgi 26 (143)
+..|+++|.+|-..
T Consensus 108 ~g~G~l~C~~Cg~~ 121 (146)
T PF07295_consen 108 VGPGTLVCENCGHE 121 (146)
T ss_pred ecCceEecccCCCE
Confidence 57899999999543
No 94
>PHA02792 ankyrin-like protein; Provisional
Probab=24.05 E-value=89 Score=28.74 Aligned_cols=24 Identities=17% Similarity=0.200 Sum_probs=18.0
Q ss_pred hhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 119 SVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 119 av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
+...++++.+-.|+.+|||+|..+
T Consensus 79 ~s~n~~lElvk~LI~~GAdvN~~~ 102 (631)
T PHA02792 79 CSDNIDIELLKLLISKGLEINSIK 102 (631)
T ss_pred HHhcccHHHHHHHHHcCCCccccc
Confidence 446678888888888888888654
No 95
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=23.88 E-value=35 Score=22.94 Aligned_cols=21 Identities=24% Similarity=0.480 Sum_probs=13.9
Q ss_pred ecccceeeccchhhhhhcCCC
Q psy13622 12 ILNKGVLVCDACCSIHRSLGR 32 (143)
Q Consensus 12 s~n~gvfiC~~CsgiHR~lg~ 32 (143)
.-|.+-|.|..|...+.-||.
T Consensus 60 VENMs~~~Cp~Cg~~~~iFg~ 80 (81)
T PF10609_consen 60 VENMSYFVCPHCGERIYIFGK 80 (81)
T ss_dssp EECT-EEE-TTT--EEETTTT
T ss_pred EECCCccCCCCCCCeecCCCC
Confidence 458889999999999988873
No 96
>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=23.73 E-value=41 Score=21.99 Aligned_cols=24 Identities=21% Similarity=0.380 Sum_probs=18.3
Q ss_pred CCCCCCCeeecccceeeccchhhhhhc
Q psy13622 3 SRAADPKWGILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 3 Cga~~P~was~n~gvfiC~~CsgiHR~ 29 (143)
||.+. ....+|+..|..|.++.|-
T Consensus 4 Cg~~~---~g~hyG~~~C~~C~~FFRR 27 (78)
T cd07164 4 CGDRA---SGKHYGVPSCDGCRGFFKR 27 (78)
T ss_pred cCccC---cceEECcchhhhhhhhhhh
Confidence 55443 2458999999999998864
No 97
>PHA02917 ankyrin-like protein; Provisional
Probab=23.65 E-value=91 Score=28.57 Aligned_cols=29 Identities=14% Similarity=0.031 Sum_probs=22.5
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..++.|+..++++.+-.||..|||+|..|
T Consensus 105 ~~~~~a~~~~~~e~vk~Ll~~Gadin~~d 133 (661)
T PHA02917 105 IFSYMKSKNVDVDLIKVLVEHGFDLSVKC 133 (661)
T ss_pred hHHHHHhhcCCHHHHHHHHHcCCCCCccC
Confidence 34567778888888888888899988765
No 98
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=23.52 E-value=1.3e+02 Score=24.17 Aligned_cols=30 Identities=20% Similarity=0.291 Sum_probs=25.6
Q ss_pred CHHHHHHHHHHhhhcCCHHHHHHHHHcCCC
Q psy13622 108 TQEELNQQLHSSVRTSNLDTSLRLLSQGAD 137 (143)
Q Consensus 108 ~~~~~~~~l~~av~~~~~~~~~~ll~~Ga~ 137 (143)
...++.++.+.|+.+||+..+..||+.++-
T Consensus 205 ~~~~~v~~~~~a~~~gD~~~l~~Lla~Dv~ 234 (324)
T TIGR02960 205 EEQDLLERYIAAFESYDLDALTALLHEDAI 234 (324)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHhcCCeE
Confidence 455678999999999999999999988753
No 99
>PHA02730 ankyrin-like protein; Provisional
Probab=23.34 E-value=91 Score=28.89 Aligned_cols=29 Identities=31% Similarity=0.281 Sum_probs=25.7
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..|+-|+..++...+-.|+.+|||+|..|
T Consensus 464 TPLh~Aa~~~~~eive~LI~~GAdIN~~d 492 (672)
T PHA02730 464 TLLYYAVDVNNIQFARRLLEYGASVNTTS 492 (672)
T ss_pred CHHHHHHHhCCHHHHHHHHHCCCCCCCCC
Confidence 47888999999998989999999999876
No 100
>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=23.28 E-value=42 Score=22.71 Aligned_cols=19 Identities=21% Similarity=0.635 Sum_probs=16.2
Q ss_pred eecccceeeccchhhhhhc
Q psy13622 11 GILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 11 as~n~gvfiC~~CsgiHR~ 29 (143)
....||+..|..|.++.|-
T Consensus 17 ~g~hyGv~sC~aCk~FFRR 35 (90)
T cd07169 17 TGLHYGIISCEGCKGFFKR 35 (90)
T ss_pred cceEECcceehhhHHHHHH
Confidence 3578999999999998874
No 101
>PHA02876 ankyrin repeat protein; Provisional
Probab=23.01 E-value=1.2e+02 Score=27.25 Aligned_cols=32 Identities=25% Similarity=0.224 Sum_probs=27.7
Q ss_pred HHHHHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 111 ELNQQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 111 ~~~~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
+....+..+++.+++.-+-.|+..|+|+|..|
T Consensus 144 ~~~~~l~~~i~~~~~~i~k~Ll~~Gadvn~~d 175 (682)
T PHA02876 144 EYMKLIKERIQQDELLIAEMLLEGGADVNAKD 175 (682)
T ss_pred hhhHHHHHHHHCCcHHHHHHHHhCCCCCCCCC
Confidence 44567889999999999999999999999865
No 102
>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=22.94 E-value=40 Score=21.87 Aligned_cols=24 Identities=25% Similarity=0.432 Sum_probs=18.5
Q ss_pred CCCCCCCeeecccceeeccchhhhhhc
Q psy13622 3 SRAADPKWGILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 3 Cga~~P~was~n~gvfiC~~CsgiHR~ 29 (143)
||.+. ....+|+..|..|.++.|-
T Consensus 4 Cg~~~---~~~hygv~~C~aC~~FFrR 27 (76)
T cd06960 4 CGDRA---TGKHYGVLSCNGCKGFFRR 27 (76)
T ss_pred cCccC---cccEECcceeeeehheeCc
Confidence 55543 2568999999999998874
No 103
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=22.54 E-value=48 Score=21.03 Aligned_cols=18 Identities=33% Similarity=0.587 Sum_probs=15.5
Q ss_pred ecccceeeccchhhhhhc
Q psy13622 12 ILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 12 s~n~gvfiC~~CsgiHR~ 29 (143)
...+|+..|..|.++.|-
T Consensus 11 ~~hygv~~C~aC~~FFRR 28 (70)
T smart00399 11 GFHFGVCSCRACKAFFRR 28 (70)
T ss_pred ccEeCCcEechhhhhhhh
Confidence 458999999999998874
No 104
>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=22.28 E-value=45 Score=21.04 Aligned_cols=23 Identities=30% Similarity=0.520 Sum_probs=16.8
Q ss_pred CCCCCCCeeecccceeeccchhhhhh
Q psy13622 3 SRAADPKWGILNKGVLVCDACCSIHR 28 (143)
Q Consensus 3 Cga~~P~was~n~gvfiC~~CsgiHR 28 (143)
||.+. ...++|+..|..|..+=|
T Consensus 6 Cg~~~---~~~~ygv~sC~~C~~FFr 28 (70)
T PF00105_consen 6 CGDPA---SGYHYGVLSCNACKMFFR 28 (70)
T ss_dssp TSSBE---SEEETTEEEEHHHHHHHH
T ss_pred CCCcc---Ccccccccccccceeeee
Confidence 55433 357999999999999433
No 105
>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=21.56 E-value=42 Score=21.72 Aligned_cols=18 Identities=28% Similarity=0.573 Sum_probs=15.9
Q ss_pred ecccceeeccchhhhhhc
Q psy13622 12 ILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 12 s~n~gvfiC~~CsgiHR~ 29 (143)
..++|++.|..|.++.|-
T Consensus 10 ~~hygv~sC~aCk~FFRR 27 (73)
T cd06963 10 GCHYGVLTCGSCKVFFKR 27 (73)
T ss_pred ceEECceeehhhhHhHHH
Confidence 569999999999998874
No 106
>TIGR00870 trp transient-receptor-potential calcium channel protein. after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
Probab=21.35 E-value=92 Score=28.42 Aligned_cols=28 Identities=25% Similarity=0.254 Sum_probs=25.1
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCc
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYF 141 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~ 141 (143)
..|+.|+..++.+.+-.|+..|||+|..
T Consensus 130 TpLhlAa~~~~~eiVklLL~~GAdv~~~ 157 (743)
T TIGR00870 130 TALHLAAHRQNYEIVKLLLERGASVPAR 157 (743)
T ss_pred cHHHHHHHhCCHHHHHHHHhCCCCCCcC
Confidence 4689999999999999999999999853
No 107
>PHA02716 CPXV016; CPX019; EVM010; Provisional
Probab=21.29 E-value=92 Score=29.27 Aligned_cols=29 Identities=21% Similarity=0.328 Sum_probs=21.2
Q ss_pred HHHHHhhhcCCH--HHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNL--DTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~--~~~~~ll~~Ga~~n~~~ 142 (143)
-.|+.|++.++. +.+-.||..|||+|..|
T Consensus 214 TPLH~Aa~~g~~~~eIVklLLe~GADVN~kD 244 (764)
T PHA02716 214 TPLHTYLITGNVCASVIKKIIELGGDMDMKC 244 (764)
T ss_pred CHHHHHHHcCCCCHHHHHHHHHcCCCCCCCC
Confidence 467788888853 55666778899988765
No 108
>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=21.19 E-value=67 Score=18.45 Aligned_cols=17 Identities=24% Similarity=0.477 Sum_probs=11.4
Q ss_pred eeecccceeeccchhhh
Q psy13622 10 WGILNKGVLVCDACCSI 26 (143)
Q Consensus 10 was~n~gvfiC~~Csgi 26 (143)
-++-+-+++||..|...
T Consensus 17 li~g~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 17 LISGPNGAYICDECVEQ 33 (41)
T ss_dssp EEEES-SEEEEHHHHHH
T ss_pred eecCCCCcEECHHHHHH
Confidence 34445579999999753
No 109
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=20.92 E-value=22 Score=26.38 Aligned_cols=22 Identities=27% Similarity=0.798 Sum_probs=17.9
Q ss_pred CCCCCeeecccceeeccchhhhhh
Q psy13622 5 AADPKWGILNKGVLVCDACCSIHR 28 (143)
Q Consensus 5 a~~P~was~n~gvfiC~~CsgiHR 28 (143)
.++|+|- -+--|+|.+|.-+|-
T Consensus 110 ipdp~wm--e~reficpecg~l~e 131 (165)
T COG4647 110 IPDPQWM--EIREFICPECGILHE 131 (165)
T ss_pred CCCchHH--HHHHhhCccccceee
Confidence 5789997 456799999998885
No 110
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=20.90 E-value=1.3e+02 Score=24.04 Aligned_cols=30 Identities=20% Similarity=0.395 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHHhhhcCCHHHHHHHHHcCC
Q psy13622 107 DTQEELNQQLHSSVRTSNLDTSLRLLSQGA 136 (143)
Q Consensus 107 ~~~~~~~~~l~~av~~~~~~~~~~ll~~Ga 136 (143)
....++.++++.|+..||+..+..||+..+
T Consensus 171 ~~~~~~v~~f~~A~~~gD~~~l~~Lla~Dv 200 (293)
T PRK09636 171 EEGAELVEAFFAALASGDLDALVALLAPDV 200 (293)
T ss_pred hHHHHHHHHHHHHHHhCCHHHHHHHHhhCe
Confidence 346678899999999999999999998865
No 111
>PHA02743 Viral ankyrin protein; Provisional
Probab=20.84 E-value=1.4e+02 Score=21.73 Aligned_cols=29 Identities=14% Similarity=0.009 Sum_probs=22.5
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..|+.|+..++...+-.|+..|+++|-.+
T Consensus 130 tpL~~A~~~~~~~iv~~Ll~~ga~~~~~~ 158 (166)
T PHA02743 130 TAYHIAYKMRDRRMMEILRANGAVCDDPL 158 (166)
T ss_pred CHHHHHHHcCCHHHHHHHHHcCCCCCCcc
Confidence 46788888888887777888888887543
No 112
>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=20.71 E-value=47 Score=22.16 Aligned_cols=18 Identities=17% Similarity=0.475 Sum_probs=15.6
Q ss_pred ecccceeeccchhhhhhc
Q psy13622 12 ILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 12 s~n~gvfiC~~CsgiHR~ 29 (143)
...||+..|..|+++.|-
T Consensus 11 g~hygv~sC~aC~~FFRR 28 (85)
T cd06961 11 GYHYRCITCEGCKGFFRR 28 (85)
T ss_pred ceEEChhhhhhhhHhhHh
Confidence 468999999999998874
No 113
>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=20.71 E-value=44 Score=22.70 Aligned_cols=18 Identities=22% Similarity=0.525 Sum_probs=15.8
Q ss_pred ecccceeeccchhhhhhc
Q psy13622 12 ILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 12 s~n~gvfiC~~CsgiHR~ 29 (143)
...||++.|..|+++.|-
T Consensus 13 g~hyGv~sC~aCk~FFRR 30 (91)
T cd07161 13 GYHYNALTCEGCKGFFRR 30 (91)
T ss_pred ceEECceeehhhHHHHHH
Confidence 468999999999998874
No 114
>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=20.20 E-value=46 Score=22.14 Aligned_cols=18 Identities=22% Similarity=0.571 Sum_probs=16.0
Q ss_pred ecccceeeccchhhhhhc
Q psy13622 12 ILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 12 s~n~gvfiC~~CsgiHR~ 29 (143)
...||+..|..|+++.|-
T Consensus 15 g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 15 GYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred ceEECceeehhhHHhHHH
Confidence 579999999999998874
No 115
>KOG0510|consensus
Probab=20.19 E-value=99 Score=29.53 Aligned_cols=29 Identities=28% Similarity=0.251 Sum_probs=26.1
Q ss_pred HHHHHhhhcCCHHHHHHHHHcCCCCCCcC
Q psy13622 114 QQLHSSVRTSNLDTSLRLLSQGADPNYFY 142 (143)
Q Consensus 114 ~~l~~av~~~~~~~~~~ll~~Ga~~n~~~ 142 (143)
..|+.|++.|.++.+-.|+..||++|..+
T Consensus 275 tpLH~a~r~G~~~svd~Ll~~Ga~I~~kn 303 (929)
T KOG0510|consen 275 TPLHYAARQGGPESVDNLLGFGASINSKN 303 (929)
T ss_pred chHHHHHHcCChhHHHHHHHcCCcccccC
Confidence 36889999999999999999999999764
No 116
>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=20.14 E-value=42 Score=22.42 Aligned_cols=18 Identities=22% Similarity=0.525 Sum_probs=15.6
Q ss_pred ecccceeeccchhhhhhc
Q psy13622 12 ILNKGVLVCDACCSIHRS 29 (143)
Q Consensus 12 s~n~gvfiC~~CsgiHR~ 29 (143)
...||+..|..|+++.|-
T Consensus 13 g~hyGv~sC~aCk~FFRR 30 (84)
T cd06962 13 GYHYNALTCEGCKGFFRR 30 (84)
T ss_pred ceEECcceeecceeeeee
Confidence 468999999999998874
Done!