Query psy521
Match_columns 173
No_of_seqs 127 out of 289
Neff 5.6
Searched_HMMs 46136
Date Fri Aug 16 20:11:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy521.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/521hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3233|consensus 100.0 1.1E-45 2.3E-50 314.3 11.4 144 27-173 130-274 (297)
2 PF05158 RNA_pol_Rpc34: RNA po 100.0 3.6E-47 7.9E-52 332.5 1.8 149 25-173 128-304 (327)
3 COG5111 RPC34 DNA-directed RNA 100.0 2.3E-40 5.1E-45 276.9 11.5 144 27-173 131-278 (301)
4 PF05158 RNA_pol_Rpc34: RNA po 99.2 2.5E-12 5.5E-17 113.1 1.4 34 2-35 135-168 (327)
5 KOG3233|consensus 99.2 9.7E-12 2.1E-16 106.9 2.4 75 2-82 135-217 (297)
6 COG5111 RPC34 DNA-directed RNA 99.1 1.7E-11 3.7E-16 103.6 2.3 34 2-35 136-169 (301)
7 PF09012 FeoC: FeoC like trans 95.2 0.032 7E-07 38.1 3.9 25 119-143 24-48 (69)
8 PF01475 FUR: Ferric uptake re 94.9 0.18 3.8E-06 37.5 7.5 68 69-155 7-74 (120)
9 cd07153 Fur_like Ferric uptake 94.2 0.38 8.2E-06 35.2 7.9 64 72-154 3-66 (116)
10 PF08672 APC2: Anaphase promot 93.7 0.054 1.2E-06 36.8 2.4 49 100-153 10-60 (60)
11 PRK09462 fur ferric uptake reg 92.2 0.96 2.1E-05 35.0 7.8 52 100-154 32-83 (148)
12 COG0735 Fur Fe2+/Zn2+ uptake r 89.8 2.2 4.9E-05 33.3 7.7 54 100-156 35-88 (145)
13 PF04703 FaeA: FaeA-like prote 89.4 0.62 1.3E-05 31.9 3.8 44 102-153 16-60 (62)
14 PF08784 RPA_C: Replication pr 82.8 2.2 4.8E-05 30.8 4.1 55 68-143 45-99 (102)
15 COG3682 Predicted transcriptio 81.1 4.3 9.3E-05 31.5 5.2 50 100-154 19-68 (123)
16 PF01978 TrmB: Sugar-specific 80.7 6.8 0.00015 26.1 5.6 46 100-155 21-66 (68)
17 PF06648 DUF1160: Protein of u 77.5 4 8.7E-05 31.6 4.1 67 56-143 24-90 (122)
18 smart00550 Zalpha Z-DNA-bindin 76.9 12 0.00026 25.4 5.9 43 102-154 23-65 (68)
19 PF08461 HTH_12: Ribonuclease 75.8 6.8 0.00015 26.7 4.5 39 101-142 13-51 (66)
20 smart00420 HTH_DEOR helix_turn 74.6 16 0.00035 22.0 6.0 35 101-143 14-48 (53)
21 PHA02943 hypothetical protein; 74.5 23 0.0005 28.7 7.8 36 100-143 23-58 (165)
22 PRK11639 zinc uptake transcrip 74.1 13 0.00027 29.7 6.3 42 100-144 40-81 (169)
23 PF01726 LexA_DNA_bind: LexA D 70.3 24 0.00051 24.0 6.1 36 101-143 25-60 (65)
24 PRK11367 hypothetical protein; 69.8 3 6.6E-05 38.9 2.0 27 53-79 18-47 (476)
25 PF09756 DDRGK: DDRGK domain; 69.2 6.9 0.00015 32.3 3.8 50 103-152 100-156 (188)
26 PF06224 HTH_42: Winged helix 69.2 23 0.0005 30.3 7.3 61 68-153 165-226 (327)
27 PF00538 Linker_histone: linke 68.8 12 0.00027 25.8 4.6 51 100-154 20-76 (77)
28 PRK14137 recX recombination re 68.2 21 0.00045 29.4 6.5 54 64-140 35-88 (195)
29 PF10007 DUF2250: Uncharacteri 67.9 10 0.00023 27.8 4.2 25 119-143 31-55 (92)
30 PRK09416 lstR lineage-specific 67.2 13 0.00028 29.3 4.8 55 102-156 56-110 (135)
31 PF04695 Pex14_N: Peroxisomal 66.3 21 0.00045 27.6 5.8 49 69-137 3-51 (136)
32 PRK15431 ferrous iron transpor 64.1 19 0.00041 25.8 4.8 41 103-143 3-50 (78)
33 PRK10857 DNA-binding transcrip 63.1 27 0.00058 27.8 6.1 47 101-157 25-71 (164)
34 PF03965 Penicillinase_R: Peni 61.7 35 0.00075 25.1 6.1 49 102-155 18-66 (115)
35 PF10557 Cullin_Nedd8: Cullin 59.4 45 0.00098 22.5 5.9 60 66-142 4-63 (68)
36 TIGR02702 SufR_cyano iron-sulf 57.6 62 0.0013 26.1 7.4 48 101-156 15-66 (203)
37 COG0826 Collagenase and relate 57.0 20 0.00042 32.2 4.7 78 91-171 113-196 (347)
38 PF13833 EF-hand_8: EF-hand do 56.9 20 0.00044 22.3 3.6 35 100-136 3-37 (54)
39 PF04539 Sigma70_r3: Sigma-70 56.5 47 0.001 22.3 5.6 25 101-133 20-44 (78)
40 smart00049 DEP Domain found in 55.8 45 0.00098 22.4 5.5 42 99-143 18-59 (77)
41 PF04157 EAP30: EAP30/Vps36 fa 55.5 15 0.00033 30.3 3.6 39 100-138 112-150 (223)
42 PF13034 DUF3895: Protein of u 54.9 69 0.0015 23.0 6.3 56 72-144 6-68 (78)
43 KOG2165|consensus 54.5 26 0.00056 34.6 5.3 51 99-154 712-764 (765)
44 PF07106 TBPIP: Tat binding pr 54.4 36 0.00077 26.8 5.4 61 72-156 3-64 (169)
45 PF03979 Sigma70_r1_1: Sigma-7 54.3 31 0.00068 24.1 4.5 34 99-137 19-52 (82)
46 PF02082 Rrf2: Transcriptional 53.0 23 0.00049 24.5 3.6 46 102-157 26-71 (83)
47 PRK11920 rirA iron-responsive 51.5 36 0.00078 26.6 4.9 47 101-157 24-70 (153)
48 PF13453 zf-TFIIB: Transcripti 51.4 3.5 7.7E-05 25.3 -0.7 13 53-65 25-37 (41)
49 PF05402 PqqD: Coenzyme PQQ sy 51.4 27 0.00059 22.9 3.7 54 67-140 14-68 (68)
50 PRK04280 arginine repressor; P 50.6 68 0.0015 25.3 6.4 46 100-153 17-63 (148)
51 PRK00117 recX recombination re 50.1 43 0.00094 25.8 5.2 54 65-141 7-60 (157)
52 TIGR00738 rrf2_super rrf2 fami 48.2 31 0.00067 25.5 3.9 45 101-155 25-69 (132)
53 PF03551 PadR: Transcriptional 48.2 68 0.0015 21.5 5.4 54 102-155 10-67 (75)
54 PF07574 SMC_Nse1: Nse1 non-SM 48.0 44 0.00096 27.2 5.1 103 36-147 73-188 (200)
55 COG3743 Uncharacterized conser 46.9 14 0.0003 29.1 1.9 34 108-141 80-117 (133)
56 PF09382 RQC: RQC domain; Int 46.8 74 0.0016 22.6 5.6 42 102-143 20-76 (106)
57 cd00052 EH Eps15 homology doma 46.4 61 0.0013 20.4 4.7 32 99-135 13-44 (67)
58 PF10941 DUF2620: Protein of u 46.0 43 0.00094 25.8 4.4 34 100-134 80-113 (117)
59 PRK11106 queuosine biosynthesi 45.9 17 0.00037 30.6 2.4 40 119-172 161-201 (231)
60 PF10264 Stork_head: Winged he 45.9 1.1E+02 0.0024 22.0 7.3 49 100-154 28-77 (80)
61 PRK14134 recX recombination re 44.5 75 0.0016 27.5 6.3 58 60-140 43-109 (283)
62 TIGR03433 padR_acidobact trans 43.8 1.2E+02 0.0026 21.7 7.0 55 102-156 18-76 (100)
63 PF13412 HTH_24: Winged helix- 43.4 76 0.0016 19.3 5.4 46 70-140 3-48 (48)
64 PF06897 DUF1269: Protein of u 43.3 27 0.00059 25.9 2.9 63 58-133 35-99 (102)
65 COG4189 Predicted transcriptio 43.2 1.3E+02 0.0029 26.3 7.4 33 101-141 37-69 (308)
66 PF03801 Ndc80_HEC: HEC/Ndc80p 42.9 1.3E+02 0.0028 23.8 6.9 72 64-140 34-112 (157)
67 TIGR02698 CopY_TcrY copper tra 41.3 1E+02 0.0023 23.4 6.0 48 101-154 18-66 (130)
68 PRK06266 transcription initiat 40.5 1.2E+02 0.0026 24.5 6.5 34 101-142 36-69 (178)
69 PF13099 DUF3944: Domain of un 40.0 24 0.00051 21.6 1.7 17 120-136 12-28 (35)
70 smart00418 HTH_ARSR helix_turn 40.0 86 0.0019 19.0 5.1 45 101-154 10-54 (66)
71 PF06479 Ribonuc_2-5A: Ribonuc 39.7 8.4 0.00018 29.8 -0.4 58 48-130 31-88 (129)
72 COG1959 Predicted transcriptio 39.6 31 0.00068 27.0 2.9 47 101-157 25-71 (150)
73 cd05029 S-100A6 S-100A6: S-100 39.2 1.4E+02 0.003 21.1 6.1 53 67-134 8-61 (88)
74 PRK06474 hypothetical protein; 38.7 1.9E+02 0.004 23.2 7.4 65 69-156 10-78 (178)
75 PF14418 OHA: OST-HTH Associat 38.4 51 0.0011 23.1 3.5 38 103-140 11-49 (75)
76 PF13592 HTH_33: Winged helix- 37.8 43 0.00092 22.0 2.9 31 101-133 4-34 (60)
77 smart00657 RPOL4c DNA-directed 37.7 1.1E+02 0.0023 22.9 5.5 29 102-133 83-111 (118)
78 cd07977 TFIIE_beta_winged_heli 37.4 1.4E+02 0.0031 20.8 5.7 28 71-113 10-37 (75)
79 PF14848 HU-DNA_bdg: DNA-bindi 37.3 58 0.0012 24.6 4.0 40 99-141 26-72 (124)
80 PF10357 Kin17_mid: Domain of 37.2 57 0.0012 25.4 4.0 55 61-124 19-84 (127)
81 TIGR01529 argR_whole arginine 36.8 1.9E+02 0.0041 22.6 6.9 47 100-153 15-61 (146)
82 smart00753 PAM PCI/PINT associ 36.8 1.4E+02 0.0029 20.3 6.7 37 100-144 23-59 (88)
83 smart00088 PINT motif in prote 36.8 1.4E+02 0.0029 20.3 6.7 37 100-144 23-59 (88)
84 smart00345 HTH_GNTR helix_turn 36.7 87 0.0019 19.1 4.2 35 101-143 20-54 (60)
85 cd08767 Cdt1_c The C-terminal 36.5 1.4E+02 0.003 22.8 6.0 34 99-134 59-92 (126)
86 PF01454 MAGE: MAGE family; I 36.5 1.1E+02 0.0023 24.4 5.6 90 36-143 72-166 (195)
87 PF15630 CENP-S: Kinetochore c 35.6 92 0.002 22.0 4.5 48 60-130 23-70 (76)
88 smart00346 HTH_ICLR helix_turn 35.3 1.4E+02 0.003 20.2 5.4 44 101-155 20-63 (91)
89 COG5126 FRQ1 Ca2+-binding prot 35.2 73 0.0016 25.7 4.4 39 98-139 105-145 (160)
90 PF08220 HTH_DeoR: DeoR-like h 34.5 1E+02 0.0023 19.9 4.4 36 100-143 13-48 (57)
91 PRK03341 arginine repressor; P 34.3 2.5E+02 0.0054 22.6 7.6 48 100-154 28-76 (168)
92 TIGR03791 TTQ_mauG tryptophan 33.7 73 0.0016 27.8 4.5 43 91-134 225-276 (291)
93 cd04755 Commd7 COMM_Domain con 33.1 1.2E+02 0.0026 24.8 5.4 21 61-81 5-25 (180)
94 PRK00441 argR arginine repress 32.7 2.4E+02 0.0053 22.1 7.6 47 100-153 17-63 (149)
95 PF00610 DEP: Domain found in 32.5 99 0.0021 20.5 4.2 45 99-144 15-59 (74)
96 TIGR00014 arsC arsenate reduct 32.3 63 0.0014 23.8 3.4 16 101-116 35-50 (114)
97 PF14394 DUF4423: Domain of un 32.3 2.6E+02 0.0057 22.3 7.4 47 102-158 40-86 (171)
98 PRK14136 recX recombination re 32.2 1.1E+02 0.0024 27.3 5.4 49 69-140 162-210 (309)
99 PF00536 SAM_1: SAM domain (St 32.2 41 0.00088 21.7 2.1 15 103-117 4-18 (64)
100 PF10931 DUF2735: Protein of u 31.9 11 0.00023 25.0 -0.8 16 48-63 31-46 (51)
101 PRK10906 DNA-binding transcrip 31.8 1.1E+02 0.0024 25.7 5.2 48 71-143 6-53 (252)
102 cd07979 TAF9 TATA Binding Prot 31.6 2.1E+02 0.0046 21.5 6.3 24 60-83 16-39 (117)
103 PF14178 YppF: YppF-like prote 31.5 1.5E+02 0.0033 20.2 4.8 35 102-137 19-53 (60)
104 cd07288 PX_SNX15 The phosphoin 31.4 78 0.0017 23.9 3.8 44 54-112 73-116 (118)
105 PF08671 SinI: Anti-repressor 31.3 1.1E+02 0.0025 17.9 3.9 14 100-113 15-28 (30)
106 smart00027 EH Eps15 homology d 31.3 1.8E+02 0.004 20.2 6.4 30 99-133 24-53 (96)
107 PRK05066 arginine repressor; P 31.1 2.7E+02 0.0058 22.1 8.2 49 100-154 22-70 (156)
108 PF01316 Arg_repressor: Argini 31.1 1.8E+02 0.0039 20.1 7.9 48 100-154 18-65 (70)
109 PF01885 PTS_2-RNA: RNA 2'-pho 31.0 55 0.0012 26.7 3.1 34 96-132 27-60 (186)
110 TIGR02944 suf_reg_Xantho FeS a 30.8 1E+02 0.0022 22.9 4.3 46 101-156 25-70 (130)
111 TIGR00373 conserved hypothetic 30.6 2.1E+02 0.0046 22.5 6.4 36 100-143 27-62 (158)
112 cd07284 PX_SNX7 The phosphoino 30.6 75 0.0016 23.9 3.6 22 61-82 76-97 (116)
113 TIGR02010 IscR iron-sulfur clu 30.0 83 0.0018 23.7 3.8 47 101-157 25-71 (135)
114 COG1695 Predicted transcriptio 29.9 2.3E+02 0.0051 21.0 6.4 55 102-156 23-81 (138)
115 cd01995 ExsB ExsB is a transcr 29.7 21 0.00046 27.5 0.5 7 166-172 152-158 (169)
116 KOG0833|consensus 29.7 17 0.00038 29.7 -0.0 8 164-171 101-108 (173)
117 PLN02701 alpha-mannosidase 29.3 2.5E+02 0.0054 29.1 8.0 106 13-143 8-121 (1050)
118 PF07524 Bromo_TP: Bromodomain 29.2 1.7E+02 0.0037 19.8 5.0 51 63-117 24-74 (77)
119 PRK14135 recX recombination re 29.1 1.7E+02 0.0037 24.4 5.9 59 60-141 39-106 (263)
120 PRK10411 DNA-binding transcrip 29.0 1.7E+02 0.0037 24.4 5.9 36 100-143 17-52 (240)
121 PF11303 DUF3105: Protein of u 29.0 1.1E+02 0.0025 23.6 4.4 62 53-114 49-117 (130)
122 PF13565 HTH_32: Homeodomain-l 28.6 1.7E+02 0.0036 19.3 4.8 29 102-130 49-77 (77)
123 cd07285 PX_SNX9 The phosphoino 28.5 88 0.0019 24.1 3.7 39 62-113 69-107 (126)
124 cd00090 HTH_ARSR Arsenical Res 28.4 1.5E+02 0.0033 18.3 6.7 44 102-154 21-64 (78)
125 cd04371 DEP DEP domain, named 28.1 1.5E+02 0.0033 19.7 4.5 41 100-143 27-67 (81)
126 PRK12411 cytidine deaminase; P 27.8 19 0.00041 27.8 -0.1 7 165-171 83-89 (132)
127 cd04448 DEP_PIKfyve DEP (Dishe 27.8 1.8E+02 0.0038 20.5 4.9 52 98-152 25-80 (81)
128 PF13811 DUF4186: Domain of un 27.7 2.8E+02 0.0061 21.2 6.6 64 68-134 32-106 (111)
129 TIGR01201 HU_rel DNA-binding p 27.3 1E+02 0.0022 24.0 3.9 40 99-142 28-74 (145)
130 cd03034 ArsC_ArsC Arsenate Red 27.3 85 0.0018 23.0 3.4 15 101-115 35-49 (112)
131 PF06569 DUF1128: Protein of u 27.3 1E+02 0.0022 21.7 3.5 30 100-133 37-66 (71)
132 PRK04338 N(2),N(2)-dimethylgua 27.2 4.2E+02 0.0091 23.9 8.4 80 52-133 272-380 (382)
133 cd03035 ArsC_Yffb Arsenate Red 27.1 90 0.0019 22.8 3.4 43 101-143 35-91 (105)
134 COG4840 Uncharacterized protei 27.0 77 0.0017 22.3 2.8 33 97-133 34-66 (71)
135 PRK14981 DNA-directed RNA poly 26.7 1E+02 0.0022 23.1 3.7 30 101-133 78-107 (112)
136 cd00166 SAM Sterile alpha moti 26.7 55 0.0012 20.4 2.0 13 103-115 3-15 (63)
137 PHA02046 hypothetical protein 26.6 1.7E+02 0.0037 21.9 4.7 32 102-133 38-69 (99)
138 PF08970 Sda: Sporulation inhi 26.5 67 0.0014 20.8 2.3 18 60-77 18-35 (46)
139 cd04450 DEP_RGS7-like DEP (Dis 26.4 2.3E+02 0.0051 19.9 5.5 52 100-154 27-83 (88)
140 PF11116 DUF2624: Protein of u 25.9 1.8E+02 0.0039 21.2 4.7 30 101-133 14-43 (85)
141 cd06872 PX_SNX19_like_plant Th 25.6 1.1E+02 0.0025 22.4 3.8 38 62-112 68-105 (107)
142 PF09279 EF-hand_like: Phospho 25.6 78 0.0017 21.5 2.7 34 100-134 14-47 (83)
143 PF03960 ArsC: ArsC family; I 25.4 75 0.0016 23.0 2.7 14 102-115 33-46 (110)
144 TIGR03830 CxxCG_CxxCG_HTH puta 25.4 1.1E+02 0.0024 22.2 3.7 41 61-117 40-80 (127)
145 PF15173 FAM180: FAM180 family 24.9 1.3E+02 0.0029 23.8 4.1 33 103-135 73-105 (137)
146 PF01466 Skp1: Skp1 family, di 24.9 1.4E+02 0.003 20.5 3.9 25 102-130 46-70 (78)
147 PF07647 SAM_2: SAM domain (St 24.9 78 0.0017 20.4 2.5 14 103-116 5-18 (66)
148 COG0220 Predicted S-adenosylme 24.7 94 0.002 26.1 3.5 43 101-143 82-124 (227)
149 smart00803 TAF TATA box bindin 24.4 2.3E+02 0.005 19.1 5.6 47 61-130 18-64 (65)
150 PF07079 DUF1347: Protein of u 24.4 97 0.0021 29.5 3.8 36 100-135 436-471 (549)
151 COG0295 Cdd Cytidine deaminase 24.1 21 0.00045 28.1 -0.5 8 164-171 84-91 (134)
152 PHA02605 54 baseplate subunit; 23.4 61 0.0013 28.7 2.2 74 42-135 24-106 (305)
153 PRK06848 hypothetical protein; 23.3 28 0.0006 27.2 0.1 8 164-171 93-100 (139)
154 cd06893 PX_SNX19 The phosphoin 23.2 90 0.002 24.0 2.9 22 61-82 92-113 (132)
155 COG2137 OraA Uncharacterized p 23.2 2.4E+02 0.0052 22.9 5.5 47 70-139 21-67 (174)
156 PF06207 DUF1002: Protein of u 23.1 3E+02 0.0064 23.3 6.2 33 102-134 172-205 (225)
157 cd08809 CARD_CARD9 Caspase act 23.1 62 0.0013 23.7 1.8 29 100-132 14-42 (86)
158 PRK11014 transcriptional repre 23.1 1.5E+02 0.0032 22.5 4.1 46 101-156 25-70 (141)
159 PF06508 QueC: Queuosine biosy 22.8 29 0.00063 28.6 0.1 38 120-172 160-197 (209)
160 PRK09834 DNA-binding transcrip 22.7 3.7E+02 0.0079 22.4 6.8 42 102-154 27-68 (263)
161 smart00526 H15 Domain in histo 22.6 1.9E+02 0.0041 19.0 4.1 43 100-142 22-64 (66)
162 PF02186 TFIIE_beta: TFIIE bet 22.6 2.6E+02 0.0056 19.0 5.6 53 73-153 8-61 (65)
163 PF03683 UPF0175: Uncharacteri 22.5 1.5E+02 0.0033 20.4 3.7 31 100-131 44-74 (76)
164 cd00092 HTH_CRP helix_turn_hel 22.5 1.9E+02 0.0042 18.2 4.0 36 100-143 24-59 (67)
165 smart00344 HTH_ASNC helix_turn 22.4 2.7E+02 0.0059 19.5 5.2 34 102-143 18-51 (108)
166 PRK08298 cytidine deaminase; V 22.4 29 0.00062 27.1 -0.0 8 165-172 86-93 (136)
167 PF04282 DUF438: Family of unk 22.3 2.5E+02 0.0054 19.6 4.7 39 101-141 28-68 (71)
168 cd04758 Commd10 COMM_Domain co 22.3 2.6E+02 0.0055 22.4 5.5 23 61-83 9-31 (186)
169 PF01136 Peptidase_U32: Peptid 22.3 2.9E+02 0.0064 22.2 6.0 52 91-143 36-91 (233)
170 PRK05578 cytidine deaminase; V 22.2 24 0.00053 27.2 -0.5 7 165-171 83-89 (131)
171 PRK06423 phosphoribosylformylg 22.2 2.6E+02 0.0057 19.0 4.9 22 121-142 47-68 (73)
172 PF09682 Holin_LLH: Phage holi 22.1 1.2E+02 0.0026 22.3 3.3 30 104-136 74-103 (108)
173 PF03962 Mnd1: Mnd1 family; I 22.0 96 0.0021 25.3 3.0 38 99-141 9-47 (188)
174 TIGR02147 Fsuc_second hypothet 22.0 5.2E+02 0.011 22.3 7.7 47 102-158 138-184 (271)
175 cd03033 ArsC_15kD Arsenate Red 22.0 1.3E+02 0.0027 22.4 3.4 43 101-143 36-91 (113)
176 cd06863 PX_Atg24p The phosphoi 21.7 86 0.0019 23.1 2.5 24 59-82 76-99 (118)
177 PF02005 TRM: N2,N2-dimethylgu 21.6 4.4E+02 0.0096 23.8 7.4 69 49-117 267-352 (377)
178 PF13463 HTH_27: Winged helix 21.6 2.3E+02 0.0049 18.0 4.3 47 101-155 18-66 (68)
179 PF11575 FhuF_C: FhuF 2Fe-2S C 21.4 45 0.00097 18.2 0.6 6 168-173 16-21 (22)
180 PF08385 DHC_N1: Dynein heavy 21.3 1.8E+02 0.0039 26.7 4.9 71 64-138 1-75 (579)
181 PF11829 DUF3349: Protein of u 21.2 1.5E+02 0.0033 21.9 3.6 33 102-136 56-88 (96)
182 TIGR00308 TRM1 tRNA(guanine-26 21.0 5.2E+02 0.011 23.3 7.8 78 52-132 263-370 (374)
183 PRK00285 ihfA integration host 20.9 1.5E+02 0.0033 21.1 3.6 28 102-133 3-30 (99)
184 KOG0121|consensus 20.9 34 0.00073 27.3 0.1 11 161-171 71-81 (153)
185 COG1799 Uncharacterized protei 20.9 1.3E+02 0.0027 24.6 3.4 53 99-155 82-142 (167)
186 PF09286 Pro-kuma_activ: Pro-k 20.8 65 0.0014 24.4 1.7 48 103-155 63-122 (143)
187 cd06870 PX_CISK The phosphoino 20.8 1.3E+02 0.0028 21.9 3.3 84 7-112 16-107 (109)
188 PRK05638 threonine synthase; V 20.6 3.5E+02 0.0076 24.6 6.6 64 68-156 369-433 (442)
189 TIGR00331 hrcA heat shock gene 20.5 1.3E+02 0.0029 26.6 3.8 62 69-153 6-71 (337)
190 smart00411 BHL bacterial (prok 20.3 1.7E+02 0.0037 20.1 3.6 27 103-133 2-28 (90)
191 PLN02182 cytidine deaminase 20.2 39 0.00083 30.5 0.3 7 165-171 129-135 (339)
192 smart00313 PXA Domain associat 20.2 88 0.0019 24.8 2.4 30 56-85 22-51 (176)
No 1
>KOG3233|consensus
Probab=100.00 E-value=1.1e-45 Score=314.29 Aligned_cols=144 Identities=49% Similarity=0.889 Sum_probs=133.6
Q ss_pred eeecccccccceeEEEeeccCCCcCcccccceecccccHHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHH
Q psy521 27 WYQDQDFEASKKKVYMLFDLEPDRSLTGGTWYQDQDFEVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKE 106 (173)
Q Consensus 27 ~~~d~sV~~~~rk~Yml~~l~Ps~eiTGG~WYtD~elD~eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~e 106 (173)
.++.++|++++||+||||+++||.++|||+|||||+||.|||+.|.++|++||+++++++.++..+|...++.+|+|++|
T Consensus 130 IKsVKsv~n~~~KvYmLy~leP~~elTGG~WytDqdlDvEfIe~L~~~c~~fl~~~~~~~~~~~~gp~~~~~~~~~t~~e 209 (297)
T KOG3233|consen 130 IKSVKSVKNSRKKVYMLYDLEPDSELTGGTWYTDQDLDVEFIEVLKQICVRFLESKRFPAEKNVEGPMFVRNESYPTVQE 209 (297)
T ss_pred HHHHHhhcCCCceEEEEecccccccccCCcccccccccHHHHHHHHHHHHHHHHhcccchhhccccchhhhhccCCCHHH
Confidence 34578889999999999999999999999999999999999999999999999999999887778998888889999999
Q ss_pred HHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeecCCcCCCCc-cccCccCCCC
Q psy521 107 VRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVSPYFAVTGL-STSPCGVCPD 173 (173)
Q Consensus 107 I~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~~~~~~~~~-~~~PCG~CP~ 173 (173)
|++||++.+|++|+|+.+|+++|+++|||||+||+.. ||. +||+++...++.++ +++|||.||+
T Consensus 210 i~~~i~~l~I~nV~Lsl~dleti~~vlvyDGkvE~r~--dG~-~yra~~~~~~~~~~~~~~Pcg~cPv 274 (297)
T KOG3233|consen 210 IKEFIRNLNILNVELSLEDLETILDVLVYDGKVEKRH--DGP-RYRAFGPNIPRAGLVAGIPCGICPV 274 (297)
T ss_pred HHHHHHHcCcccccccHHHHHHHhHHheecceeeeee--cCc-eeeecCCCCCCcCccCCCcccCCcc
Confidence 9999999999999999999999999999999999964 786 99999998877665 5599999996
No 2
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=100.00 E-value=3.6e-47 Score=332.51 Aligned_cols=149 Identities=45% Similarity=0.812 Sum_probs=14.8
Q ss_pred ceeeecccccccceeEEEeeccCCCcCcccccceecccccHHHHHHHHHHHHHHHhhhhhhccC------------CCCC
Q psy521 25 GTWYQDQDFEASKKKVYMLFDLEPDRSLTGGTWYQDQDFEVEFVDVLNQQCYRFLQLKREKTAN------------NTNG 92 (173)
Q Consensus 25 g~~~~d~sV~~~~rk~Yml~~l~Ps~eiTGG~WYtD~elD~eFI~~L~~~~~~~l~~k~~~~~~------------~~~~ 92 (173)
+..+..++|++++||+||||+|+||+|||||+||+|||||+|||+.|+++|++||++++.++.. ....
T Consensus 128 ~lIK~vksv~~~~rK~Yml~~l~Ps~eiTGG~wy~d~e~D~efi~~l~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~ 207 (327)
T PF05158_consen 128 KLIKSVKSVKNPNRKVYMLYDLEPSEEITGGPWYTDGEFDTEFIDVLREQCLRFIQQKSFPSSEQISQKTSSSSADPQAL 207 (327)
T ss_dssp TSEEEE--SS-SS--EEEESSS----------------------------------------------------------
T ss_pred CCEEEecCcCCCCeEEEEEccCCcCcccCCCCcccCCcccHHHHHHHHHHHHHHHHhCcCcccccccccccccccccccc
Confidence 4567789999999999999999999999999999999999999999999999999999886432 4578
Q ss_pred CcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeE----------------EeecC
Q psy521 93 PLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMY----------------RAVSP 156 (173)
Q Consensus 93 p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~Y----------------R~~~~ 156 (173)
|+++++++|||++||++||+++||++++|+++||++||++|||||+||++...+|...| |+...
T Consensus 208 ~~~~~~~~~~T~~eI~~fI~~sgIs~v~Ls~eDI~~LL~tLVyDgkIE~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 (327)
T PF05158_consen 208 PYPAGYASYPTLEEIAEFINKSGISNVELSEEDIESLLDTLVYDGKIEEVRSGDGYEYYRAPGQSVLYCSKRRYYRAVGP 287 (327)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ccccccCCCCCHHHHHHHHHHcCCCceecCHHHHHHHHHHHhhCceeEEEeccCCceeeeeecccceeeecccccccccc
Confidence 88899999999999999999999999999999999999999999999999865443333 33444
Q ss_pred CcCCCCccccCccCCCC
Q psy521 157 YFAVTGLSTSPCGVCPD 173 (173)
Q Consensus 157 ~~~~~~~~~~PCG~CP~ 173 (173)
....++++++|||+||+
T Consensus 288 ~~~~~~~~~~PCg~CPV 304 (327)
T PF05158_consen 288 EPSASGLTEVPCGVCPV 304 (327)
T ss_dssp -----------------
T ss_pred ccCCCCccCCCCCCCCc
Confidence 55678999999999996
No 3
>COG5111 RPC34 DNA-directed RNA polymerase III, subunit C34 [Transcription]
Probab=100.00 E-value=2.3e-40 Score=276.88 Aligned_cols=144 Identities=26% Similarity=0.510 Sum_probs=127.4
Q ss_pred eeecccccccceeEEEeeccCCCcCcccccceecccccHHHHHHHHHHHHHHHhhhhhhccCCCCCC---cccccCCCCC
Q psy521 27 WYQDQDFEASKKKVYMLFDLEPDRSLTGGTWYQDQDFEVEFVDVLNQQCYRFLQLKREKTANNTNGP---LVAQRLACAT 103 (173)
Q Consensus 27 ~~~d~sV~~~~rk~Yml~~l~Ps~eiTGG~WYtD~elD~eFI~~L~~~~~~~l~~k~~~~~~~~~~p---~~~~~~~~~T 103 (173)
.++.++|++|+||+||||+++||+||||||||||||+|.|||+.|.+++++||.++.++.++...+| +.+.+..|||
T Consensus 131 vKSvKsvKnptRKiYmLYdlvPS~eiTGGpWFtD~elDvEfi~~ll~ii~rf~~~n~fp~kn~~~gpnv~~~P~y~~ypT 210 (301)
T COG5111 131 VKSVKSVKNPTRKIYMLYDLVPSEEITGGPWFTDNELDVEFIARLLEIIERFLEKNLFPRKNFEEGPNVFYAPKYEDYPT 210 (301)
T ss_pred HHHhhhhcCCCceEEEEecccccccccCCCccccCcccHHHHHHHHHHHHHHHHhccCCccchhcCCccccCCccCCCcc
Confidence 4557889999999999999999999999999999999999999999999999999999987766666 3456778999
Q ss_pred HHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeecC-CcCCCCccccCccCCCC
Q psy521 104 PKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVSP-YFAVTGLSTSPCGVCPD 173 (173)
Q Consensus 104 ~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~~-~~~~~~~~~~PCG~CP~ 173 (173)
++||++||+..+|.+|+|+.+++++|.++||||||+|+++ +|. .||+... ....+.+++-|||.||.
T Consensus 211 ~~~I~n~vr~~ni~~v~L~l~n~~sL~dvLvyDgKvEK~~--~g~-~yR~~~~~~~~~nq~~~ep~gn~~l 278 (301)
T COG5111 211 LEDIMNYVRNVNILSVPLRLDNLESLADVLVYDGKVEKLH--SGP-IYRYRAFKPYAKNQGEGEPAGNKAL 278 (301)
T ss_pred HHHHHHHHHhceeeeccccHHHHHHHhHheeecCeeeeec--cCc-ceeeeecChhhhcccCCCCCCCCcc
Confidence 9999999999999999999999999999999999999986 463 5766432 23357899999999984
No 4
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=99.22 E-value=2.5e-12 Score=113.07 Aligned_cols=34 Identities=50% Similarity=1.057 Sum_probs=10.7
Q ss_pred CcccCcceEEEeeccccCCCCCCceeeecccccc
Q psy521 2 SEIASKKKVYMLFDLEPDRSLTGGTWYQDQDFEA 35 (173)
Q Consensus 2 ~~~~~~~k~y~~~~~~p~~~~tgg~~~~d~sV~~ 35 (173)
||++++|||||||+||||+|+|||+||+|+.||.
T Consensus 135 sv~~~~rK~Yml~~l~Ps~eiTGG~wy~d~e~D~ 168 (327)
T PF05158_consen 135 SVKNPNRKVYMLYDLEPSEEITGGPWYTDGEFDT 168 (327)
T ss_dssp -SS-SS--EEEESSS-------------------
T ss_pred CcCCCCeEEEEEccCCcCcccCCCCcccCCcccH
Confidence 7899999999999999999999999999999985
No 5
>KOG3233|consensus
Probab=99.17 E-value=9.7e-12 Score=106.86 Aligned_cols=75 Identities=37% Similarity=0.612 Sum_probs=50.5
Q ss_pred CcccCcceEEEeeccccCCCCCCceeeeccccccc-----ceeEEE--eeccCCCcCccccc-ceecccccHHHHHHHHH
Q psy521 2 SEIASKKKVYMLFDLEPDRSLTGGTWYQDQDFEAS-----KKKVYM--LFDLEPDRSLTGGT-WYQDQDFEVEFVDVLNQ 73 (173)
Q Consensus 2 ~~~~~~~k~y~~~~~~p~~~~tgg~~~~d~sV~~~-----~rk~Ym--l~~l~Ps~eiTGG~-WYtD~elD~eFI~~L~~ 73 (173)
||++++||+||||++|||.|+|||+||+|+.|+.. +.++++ -.+.+|.++--=|| ++-..++=+ .+
T Consensus 135 sv~n~~~KvYmLy~leP~~elTGG~WytDqdlDvEfIe~L~~~c~~fl~~~~~~~~~~~~gp~~~~~~~~~t------~~ 208 (297)
T KOG3233|consen 135 SVKNSRKKVYMLYDLEPDSELTGGTWYTDQDLDVEFIEVLKQICVRFLESKRFPAEKNVEGPMFVRNESYPT------VQ 208 (297)
T ss_pred hhcCCCceEEEEecccccccccCCcccccccccHHHHHHHHHHHHHHHHhcccchhhccccchhhhhccCCC------HH
Confidence 67899999999999999999999999999999842 333333 33344544333366 222222222 25
Q ss_pred HHHHHHhhh
Q psy521 74 QCYRFLQLK 82 (173)
Q Consensus 74 ~~~~~l~~k 82 (173)
.+++||.+.
T Consensus 209 ei~~~i~~l 217 (297)
T KOG3233|consen 209 EIKEFIRNL 217 (297)
T ss_pred HHHHHHHHc
Confidence 677788874
No 6
>COG5111 RPC34 DNA-directed RNA polymerase III, subunit C34 [Transcription]
Probab=99.14 E-value=1.7e-11 Score=103.59 Aligned_cols=34 Identities=38% Similarity=0.930 Sum_probs=32.3
Q ss_pred CcccCcceEEEeeccccCCCCCCceeeecccccc
Q psy521 2 SEIASKKKVYMLFDLEPDRSLTGGTWYQDQDFEA 35 (173)
Q Consensus 2 ~~~~~~~k~y~~~~~~p~~~~tgg~~~~d~sV~~ 35 (173)
||++++||+|||||++||.|||||+|++|+.+|.
T Consensus 136 svKnptRKiYmLYdlvPS~eiTGGpWFtD~elDv 169 (301)
T COG5111 136 SVKNPTRKIYMLYDLVPSEEITGGPWFTDNELDV 169 (301)
T ss_pred hhcCCCceEEEEecccccccccCCCccccCcccH
Confidence 6789999999999999999999999999999984
No 7
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=95.17 E-value=0.032 Score=38.12 Aligned_cols=25 Identities=28% Similarity=0.549 Sum_probs=21.0
Q ss_pred eecCHHHHHHHHHHHcccCeeEEEe
Q psy521 119 VELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 119 v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
..++.+.|+.+|+.|+--|+|+++.
T Consensus 24 ~~~s~~~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 24 FGISPEAVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp TT--HHHHHHHHHHHHCCTSCEEEE
T ss_pred HCcCHHHHHHHHHHHHHCCcEEEec
Confidence 3579999999999999999999985
No 8
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=94.85 E-value=0.18 Score=37.50 Aligned_cols=68 Identities=19% Similarity=0.190 Sum_probs=54.4
Q ss_pred HHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCC
Q psy521 69 DVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGT 148 (173)
Q Consensus 69 ~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~ 148 (173)
...|.+++++|.+.. ..+|++||.+.+++.+ ..++..=|-..|+.|+=.|.|.++...+|.
T Consensus 7 T~~R~~Il~~l~~~~----------------~~~ta~ei~~~l~~~~---~~is~~TVYR~L~~L~e~Gli~~~~~~~~~ 67 (120)
T PF01475_consen 7 TPQRLAILELLKESP----------------EHLTAEEIYDKLRKKG---PRISLATVYRTLDLLEEAGLIRKIEFGDGE 67 (120)
T ss_dssp HHHHHHHHHHHHHHS----------------SSEEHHHHHHHHHHTT---TT--HHHHHHHHHHHHHTTSEEEEEETTSE
T ss_pred CHHHHHHHHHHHcCC----------------CCCCHHHHHHHhhhcc---CCcCHHHHHHHHHHHHHCCeEEEEEcCCCc
Confidence 345788888998852 3589999999999766 345888999999999999999999876677
Q ss_pred eeEEeec
Q psy521 149 DMYRAVS 155 (173)
Q Consensus 149 ~~YR~~~ 155 (173)
..|....
T Consensus 68 ~~Y~~~~ 74 (120)
T PF01475_consen 68 SRYELST 74 (120)
T ss_dssp EEEEESS
T ss_pred ceEeecC
Confidence 7888765
No 9
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=94.23 E-value=0.38 Score=35.21 Aligned_cols=64 Identities=20% Similarity=0.168 Sum_probs=50.6
Q ss_pred HHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeE
Q psy521 72 NQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMY 151 (173)
Q Consensus 72 ~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~Y 151 (173)
|..++++|... ...+|++||++.+++.+ -.++..-|-..|+.|+=.|.|.++...+|...|
T Consensus 3 R~~Il~~l~~~----------------~~~~sa~ei~~~l~~~~---~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y 63 (116)
T cd07153 3 RLAILEVLLES----------------DGHLTAEEIYERLRKKG---PSISLATVYRTLELLEEAGLVREIELGDGKARY 63 (116)
T ss_pred HHHHHHHHHhC----------------CCCCCHHHHHHHHHhcC---CCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEE
Confidence 56677777753 13589999999999875 257889999999999999999999765665677
Q ss_pred Eee
Q psy521 152 RAV 154 (173)
Q Consensus 152 R~~ 154 (173)
...
T Consensus 64 ~~~ 66 (116)
T cd07153 64 ELN 66 (116)
T ss_pred EeC
Confidence 754
No 10
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=93.75 E-value=0.054 Score=36.81 Aligned_cols=49 Identities=18% Similarity=0.377 Sum_probs=35.6
Q ss_pred CCCCHHHHHHHHHHh--CCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEe
Q psy521 100 ACATPKEVRKFITDL--GISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRA 153 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~--~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~ 153 (173)
+..+++.||..++=. +-...+.|.+++++.|+.||-||+++.. +| .||.
T Consensus 10 gsl~l~RIh~mLkmf~~~~~~~~~s~~eL~~fL~~lv~e~~L~~~---~G--~YkL 60 (60)
T PF08672_consen 10 GSLPLDRIHSMLKMFPKDPGGYDISLEELQEFLDRLVEEGKLECS---GG--SYKL 60 (60)
T ss_dssp -SEEHHHHHHHHHHH-GGG--TT--HHHHHHHHHHHHHTTSEE-----TT--EEEE
T ss_pred CCCCHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHCCcEEec---CC--EEeC
Confidence 346799999999976 3334689999999999999999999985 45 4874
No 11
>PRK09462 fur ferric uptake regulator; Provisional
Probab=92.24 E-value=0.96 Score=35.03 Aligned_cols=52 Identities=15% Similarity=0.273 Sum_probs=43.6
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEee
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAV 154 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~ 154 (173)
..+|++||.+.+++.+ ..++..-|-..|+.|+=.|.|.++...+|...|...
T Consensus 32 ~h~sa~eI~~~l~~~~---~~i~~aTVYR~L~~L~e~Gli~~~~~~~~~~~y~~~ 83 (148)
T PRK09462 32 HHVSAEDLYKRLIDMG---EEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVFELT 83 (148)
T ss_pred CCCCHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHCCCEEEEEcCCCcEEEEeC
Confidence 3589999999999877 347889999999999999999999765676677653
No 12
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=89.77 E-value=2.2 Score=33.27 Aligned_cols=54 Identities=17% Similarity=0.193 Sum_probs=44.8
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeecC
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVSP 156 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~~ 156 (173)
..+|+++|++.+++.+ ..+|..-|-..|+.|+--|.|.++...+|...|.....
T Consensus 35 ~~~sAeei~~~l~~~~---p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y~~~~~ 88 (145)
T COG0735 35 GHLSAEELYEELREEG---PGISLATVYRTLKLLEEAGLVHRLEFEGGKTRYELNSE 88 (145)
T ss_pred CCCCHHHHHHHHHHhC---CCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEEecCCC
Confidence 3499999999999965 46789999999999999999999986666666765544
No 13
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=89.41 E-value=0.62 Score=31.87 Aligned_cols=44 Identities=27% Similarity=0.333 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCC-eeEEe
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGT-DMYRA 153 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~-~~YR~ 153 (173)
+|..||++-+ .+|.-.++.+|+.|+-+|+|++.+...|. ..+|.
T Consensus 16 ~~T~eiA~~~--------gls~~~aR~yL~~Le~eG~V~~~~~~rG~~~~W~l 60 (62)
T PF04703_consen 16 LKTREIADAL--------GLSIYQARYYLEKLEKEGKVERSPVRRGKSTYWRL 60 (62)
T ss_dssp EEHHHHHHHH--------TS-HHHHHHHHHHHHHCTSEEEES-SSSSS-EEEE
T ss_pred CCHHHHHHHh--------CCCHHHHHHHHHHHHHCCCEEEecCCCCcceeeee
Confidence 6677777653 57888999999999999999997644454 23443
No 14
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=82.84 E-value=2.2 Score=30.84 Aligned_cols=55 Identities=18% Similarity=0.312 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEe
Q psy521 68 VDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 68 I~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
...+++.|+.||++... . .-.+++++|++-+ .++.++|+..|+.|+-+|.|-...
T Consensus 45 ~~~~~~~Vl~~i~~~~~----~---------~~Gv~v~~I~~~l--------~~~~~~v~~al~~L~~eG~IYsTi 99 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPN----S---------EEGVHVDEIAQQL--------GMSENEVRKALDFLSNEGHIYSTI 99 (102)
T ss_dssp S-HHHHHHHHHHHC-----------------TTTEEHHHHHHHS--------TS-HHHHHHHHHHHHHTTSEEESS
T ss_pred CCHHHHHHHHHHHhcCC----C---------CCcccHHHHHHHh--------CcCHHHHHHHHHHHHhCCeEeccc
Confidence 56788999999998211 0 1347899998766 468999999999999999997654
No 15
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=81.06 E-value=4.3 Score=31.49 Aligned_cols=50 Identities=20% Similarity=0.239 Sum_probs=41.4
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEee
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAV 154 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~ 154 (173)
+..|++||+++|.+- -+++..-|..||+.|+--|.|-+.+. .+...||+.
T Consensus 19 ~~~t~~eI~~~l~~~----~ews~sTV~TLl~RL~KKg~l~~~kd-gr~~~y~pL 68 (123)
T COG3682 19 GPATVREIIEELPAD----REWSYSTVKTLLNRLVKKGLLTRKKD-GRAFRYSPL 68 (123)
T ss_pred CCccHHHHHHHHhhc----ccccHHHHHHHHHHHHhccchhhhhc-CCeeeeecc
Confidence 458999999999985 58999999999999999999988762 334667764
No 16
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=80.75 E-value=6.8 Score=26.05 Aligned_cols=46 Identities=26% Similarity=0.369 Sum_probs=35.8
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeec
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVS 155 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~ 155 (173)
+..|++||++.+ .++...|..+|+.|+-.|.|++... ....|+++.
T Consensus 21 ~~~t~~eIa~~l--------~i~~~~v~~~L~~L~~~GlV~~~~~--~~~~Y~a~~ 66 (68)
T PF01978_consen 21 GPATAEEIAEEL--------GISRSTVYRALKSLEEKGLVEREEG--RPKVYRAVP 66 (68)
T ss_dssp CHEEHHHHHHHH--------TSSHHHHHHHHHHHHHTTSEEEEEE--CCEEEEEE-
T ss_pred CCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEEcC--ceEEEEEeC
Confidence 347888888754 4688899999999999999999862 346788764
No 17
>PF06648 DUF1160: Protein of unknown function (DUF1160); InterPro: IPR010594 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf75; it is a family of uncharacterised viral proteins.
Probab=77.51 E-value=4 Score=31.61 Aligned_cols=67 Identities=13% Similarity=0.219 Sum_probs=56.7
Q ss_pred cceecccccHHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcc
Q psy521 56 TWYQDQDFEVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLF 135 (173)
Q Consensus 56 ~WYtD~elD~eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~ 135 (173)
-|..|.+=|.-|-+-|.+++..||+++ .+.+.+.+-+.... ...||..++.=+.+....
T Consensus 24 ~ylkel~~d~tf~~Kl~~Il~mFl~~e-------------------id~e~~y~l~~~~d--~~~LT~~Qi~Yl~~~~~~ 82 (122)
T PF06648_consen 24 KYLKELERDETFLDKLIKILKMFLNDE-------------------IDVEDMYNLFGAVD--GLKLTRSQIDYLYNRVYN 82 (122)
T ss_pred HHHHHhccCchHHHHHHHHHHHHHhCC-------------------CCHHHHHHHHhccc--HhhcCHHHHHHHHHHHHc
Confidence 377888899999999999999999987 78999999887642 238999999999999999
Q ss_pred cCeeEEEe
Q psy521 136 DGKIEQIN 143 (173)
Q Consensus 136 Dg~iE~~~ 143 (173)
|+.|..+.
T Consensus 83 n~~I~~Il 90 (122)
T PF06648_consen 83 NRYIINIL 90 (122)
T ss_pred cHHHHHHH
Confidence 98887653
No 18
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=76.89 E-value=12 Score=25.38 Aligned_cols=43 Identities=16% Similarity=0.326 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEee
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAV 154 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~ 154 (173)
.|+.||++-+ .++...|.++|..|.-+|.|++... . ...|+..
T Consensus 23 ~ta~eLa~~l--------gl~~~~v~r~L~~L~~~G~V~~~~~-~-~~~W~i~ 65 (68)
T smart00550 23 STALQLAKNL--------GLPKKEVNRVLYSLEKKGKVCKQGG-T-PPLWKLT 65 (68)
T ss_pred cCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEecCC-C-CCceEee
Confidence 5666666543 4677799999999999999998532 2 1346654
No 19
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=75.77 E-value=6.8 Score=26.68 Aligned_cols=39 Identities=28% Similarity=0.307 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEE
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQI 142 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~ 142 (173)
.++..+|.+.+...| .++|.+-|..-|+.|.-||.+++.
T Consensus 13 P~g~~~l~~~L~~~g---~~~se~avRrrLr~me~~Glt~~~ 51 (66)
T PF08461_consen 13 PLGRKQLAEELKLRG---EELSEEAVRRRLRAMERDGLTRKV 51 (66)
T ss_pred CCCHHHHHHHHHhcC---hhhhHHHHHHHHHHHHHCCCcccc
Confidence 488999999999876 789999999999999999977764
No 20
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=74.58 E-value=16 Score=22.00 Aligned_cols=35 Identities=23% Similarity=0.332 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEe
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
.+|..+|++.+ .++..-+...|+.|+-.|.|++..
T Consensus 14 ~~s~~~l~~~l--------~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 14 KVSVEELAELL--------GVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred CcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEEee
Confidence 47999999886 568889999999999999999864
No 21
>PHA02943 hypothetical protein; Provisional
Probab=74.50 E-value=23 Score=28.74 Aligned_cols=36 Identities=19% Similarity=0.338 Sum_probs=30.1
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEe
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
+..|..||++-+ .+|..+++-+|.+|.=+|+|+++.
T Consensus 23 G~~TtseIAkaL--------GlS~~qa~~~LyvLErEG~VkrV~ 58 (165)
T PHA02943 23 GCKTTSRIANKL--------GVSHSMARNALYQLAKEGMVLKVE 58 (165)
T ss_pred CCccHHHHHHHH--------CCCHHHHHHHHHHHHHcCceEEEe
Confidence 556777776643 478999999999999999999987
No 22
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=74.12 E-value=13 Score=29.68 Aligned_cols=42 Identities=10% Similarity=0.224 Sum_probs=36.3
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEec
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINN 144 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~ 144 (173)
..+|++||.+.+++.+. .++..-|-..|+.|+=.|.|.++..
T Consensus 40 ~hlSa~eI~~~L~~~~~---~is~aTVYRtL~~L~e~Glv~~~~~ 81 (169)
T PRK11639 40 GAISAYDLLDLLREAEP---QAKPPTVYRALDFLLEQGFVHKVES 81 (169)
T ss_pred CCCCHHHHHHHHHhhCC---CCCcchHHHHHHHHHHCCCEEEEec
Confidence 56899999999998872 3566889999999999999999864
No 23
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=70.32 E-value=24 Score=23.98 Aligned_cols=36 Identities=22% Similarity=0.302 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEe
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
.||+.||++.+ |++ |..-|+.-|+.|+-.|.|.+..
T Consensus 25 ~Pt~rEIa~~~---g~~----S~~tv~~~L~~Le~kG~I~r~~ 60 (65)
T PF01726_consen 25 PPTVREIAEAL---GLK----STSTVQRHLKALERKGYIRRDP 60 (65)
T ss_dssp ---HHHHHHHH---TSS----SHHHHHHHHHHHHHTTSEEEGC
T ss_pred CCCHHHHHHHh---CCC----ChHHHHHHHHHHHHCcCccCCC
Confidence 38999999886 332 5788999999999999999853
No 24
>PRK11367 hypothetical protein; Provisional
Probab=69.80 E-value=3 Score=38.91 Aligned_cols=27 Identities=26% Similarity=0.516 Sum_probs=20.4
Q ss_pred ccccceecccccHH---HHHHHHHHHHHHH
Q psy521 53 TGGTWYQDQDFEVE---FVDVLNQQCYRFL 79 (173)
Q Consensus 53 TGG~WYtD~elD~e---FI~~L~~~~~~~l 79 (173)
|||+|||......+ +|+.+++.+.+..
T Consensus 18 tGgsWYTGk~iE~~~~~~v~~~N~~l~~~~ 47 (476)
T PRK11367 18 GGGTWYTGTQIQPGVEKFIKDFNDAKKKGE 47 (476)
T ss_pred ccccceechHHHHHHHHHHHHHHHHHHhcC
Confidence 89999999988888 5666666554433
No 25
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=69.25 E-value=6.9 Score=32.32 Aligned_cols=50 Identities=16% Similarity=0.305 Sum_probs=32.0
Q ss_pred CHHHHHHHHHHhCCce-------eecCHHHHHHHHHHHcccCeeEEEecCCCCeeEE
Q psy521 103 TPKEVRKFITDLGISK-------VELSEEDIRTILETLLFDGKIEQINNIDGTDMYR 152 (173)
Q Consensus 103 T~~eI~~~I~~~~is~-------v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR 152 (173)
.+.+..+||+...|.. ..|+.+|+-.-|+.|.-+|.|--|.+..|..+|-
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyI 156 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYI 156 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE-
T ss_pred HHHHHHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEe
Confidence 4555566666555543 4689999999999999999999998767876664
No 26
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=69.23 E-value=23 Score=30.31 Aligned_cols=61 Identities=21% Similarity=0.382 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCC
Q psy521 68 VDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDG 147 (173)
Q Consensus 68 I~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g 147 (173)
=+.+.+.+.+|+.. ++.+|++++..|. | |+..+++..++.|+-.|.++++.-.+|
T Consensus 165 ~ea~~~Lv~Ryl~~-----------------~GPat~~d~a~w~---g-----l~~~~~r~~l~~l~~~~~L~~v~~~~G 219 (327)
T PF06224_consen 165 EEALAELVRRYLRA-----------------YGPATLADFAWWS---G-----LPKTQARRALAQLVEEGELVEVEVEGG 219 (327)
T ss_pred HHHHHHHHHHHHHH-----------------cCCccHHHHHHHh---c-----cCHHHHHHHHHhhccCCcEEEEEEcCc
Confidence 34466777889987 3669999999994 3 788899999999999888888864336
Q ss_pred Ce-eEEe
Q psy521 148 TD-MYRA 153 (173)
Q Consensus 148 ~~-~YR~ 153 (173)
.. .|-.
T Consensus 220 ~~~~~~~ 226 (327)
T PF06224_consen 220 KEPLYDL 226 (327)
T ss_pred ceeEEec
Confidence 54 4443
No 27
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=68.84 E-value=12 Score=25.76 Aligned_cols=51 Identities=20% Similarity=0.371 Sum_probs=38.7
Q ss_pred CCCCHHHHHHHHHHhCCceeecCH----HHHHHHHHHHcccCeeEEEec--CCCCeeEEee
Q psy521 100 ACATPKEVRKFITDLGISKVELSE----EDIRTILETLLFDGKIEQINN--IDGTDMYRAV 154 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~----~dI~~iL~~Lv~Dg~iE~~~~--~~g~~~YR~~ 154 (173)
..+|...|..||...- .+.+.. ..+..-|+.+|-.|.++++.. ..| .||+.
T Consensus 20 ~GsS~~aI~kyI~~~y--~~~~~~~~~~~~l~~aLk~~v~~G~l~~~kg~G~sg--sfkl~ 76 (77)
T PF00538_consen 20 KGSSLQAIKKYIKAKY--KVDLNPANFKSRLKRALKRGVEKGKLVQVKGKGASG--SFKLS 76 (77)
T ss_dssp SSEEHHHHHHHHHHHS--SCCCCHTTHHHHHHHHHHHHHHCTSEEECSCSTTSS--EEEES
T ss_pred CCCCHHHHHHHHHHhc--CcCCChHHHHHHHHHHHHHHHHCCcEEeecccCCcc--ceecC
Confidence 4689999999999855 344454 568889999999999999862 234 37764
No 28
>PRK14137 recX recombination regulator RecX; Provisional
Probab=68.23 E-value=21 Score=29.44 Aligned_cols=54 Identities=20% Similarity=0.171 Sum_probs=46.3
Q ss_pred cHHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeE
Q psy521 64 EVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIE 140 (173)
Q Consensus 64 D~eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE 140 (173)
+.|+-+.+...+++||..+- =|..|+.++|.+.| ++.+.|+.+|+-|.=.|.|-
T Consensus 35 ~~e~~~~~~~~Al~~Ls~R~------------------rS~~ELr~KL~~kg-----~~~e~Ie~vI~rL~e~gyLD 88 (195)
T PRK14137 35 PDEAREALLAYAFRALAARA------------------MTAAELRAKLERRS-----EDEALVTEVLERVQELGYQD 88 (195)
T ss_pred HHHHHHHHHHHHHHHHhcch------------------hhHHHHHHHHHhcC-----CCHHHHHHHHHHHHHcCCCC
Confidence 45999999999999999863 37899999999876 57899999999998888773
No 29
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=67.88 E-value=10 Score=27.81 Aligned_cols=25 Identities=28% Similarity=0.468 Sum_probs=23.3
Q ss_pred eecCHHHHHHHHHHHcccCeeEEEe
Q psy521 119 VELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 119 v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
..+..++|+.+|+.|+--|.||++.
T Consensus 31 l~~~~~~v~~~l~~Le~~GLler~~ 55 (92)
T PF10007_consen 31 LKIPLEEVREALEKLEEMGLLERVE 55 (92)
T ss_pred HCCCHHHHHHHHHHHHHCCCeEEec
Confidence 4789999999999999999999985
No 30
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=67.17 E-value=13 Score=29.26 Aligned_cols=55 Identities=22% Similarity=0.270 Sum_probs=44.1
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeecC
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVSP 156 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~~ 156 (173)
..-=+|.+.|.+.+.....++...|-.+|+.|+-+|.|+......+...|+.+..
T Consensus 56 ~yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~ 110 (135)
T PRK09416 56 KTGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDK 110 (135)
T ss_pred CCHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCCeEEeecCCCceEEEECHH
Confidence 4666899999988766778899999999999999999997543234577888753
No 31
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=66.35 E-value=21 Score=27.59 Aligned_cols=49 Identities=24% Similarity=0.278 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccC
Q psy521 69 DVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDG 137 (173)
Q Consensus 69 ~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg 137 (173)
+.|.+...+||++-. -.-.+.++=.+||++.| ||.+||+++|+..--+.
T Consensus 3 e~li~~A~~FL~~p~---------------V~~sp~~~k~~FL~sKG-----Lt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 3 EDLIEQAVKFLQDPK---------------VRNSPLEKKIAFLESKG-----LTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHHHHHHHHHCTTT---------------CCCS-HHHHHHHHHHCT-------HHHHHHHHHHHT--S
T ss_pred HHHHHHHHHHhCCcc---------------cccCCHHHHHHHHHcCC-----CCHHHHHHHHHhcCCcc
Confidence 456777888999732 12356888899999987 89999999999876666
No 32
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=64.15 E-value=19 Score=25.85 Aligned_cols=41 Identities=22% Similarity=0.265 Sum_probs=30.6
Q ss_pred CHHHHHHHHHHhCCce-------eecCHHHHHHHHHHHcccCeeEEEe
Q psy521 103 TPKEVRKFITDLGISK-------VELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 103 T~~eI~~~I~~~~is~-------v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
++-+|.++|...|-.. ...+.+=|+..|+.|+-=||||++.
T Consensus 3 ~L~qlRd~l~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 3 SLIQVRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred cHHHHHHHHHHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence 4556666666555222 3568889999999999999999985
No 33
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=63.07 E-value=27 Score=27.84 Aligned_cols=47 Identities=11% Similarity=0.104 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeecCC
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVSPY 157 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~~~ 157 (173)
.+|.++|++.+ .++..-+++||+.|.-.|.|+.....+| .|+..+.+
T Consensus 25 ~vs~~eIA~~~--------~ip~~~l~kIl~~L~~aGLv~s~rG~~G--Gy~Lar~p 71 (164)
T PRK10857 25 PVPLADISERQ--------GISLSYLEQLFSRLRKNGLVSSVRGPGG--GYLLGKDA 71 (164)
T ss_pred cCcHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEeCCCCCC--CeeccCCH
Confidence 58999998764 5688999999999999999998765556 49987654
No 34
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=61.70 E-value=35 Score=25.06 Aligned_cols=49 Identities=16% Similarity=0.254 Sum_probs=38.6
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeec
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVS 155 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~ 155 (173)
+|+.||++.+.+. -.++..-|..+|+.|+=-|.|.+-.. .....|++.-
T Consensus 18 ~t~~eI~~~l~~~----~~~~~sTv~t~L~rL~~Kg~l~~~~~-gr~~~Y~p~i 66 (115)
T PF03965_consen 18 ATVREIHEALPEE----RSWAYSTVQTLLNRLVEKGFLTREKI-GRAYVYSPLI 66 (115)
T ss_dssp EEHHHHHHHHCTT----SS--HHHHHHHHHHHHHTTSEEEEEE-TTCEEEEESS
T ss_pred CCHHHHHHHHHhc----cccchhHHHHHHHHHHhCCceeEeec-CCceEEEeCC
Confidence 8999999999886 35788999999999999999998753 2346788653
No 35
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=59.42 E-value=45 Score=22.47 Aligned_cols=60 Identities=15% Similarity=0.137 Sum_probs=44.6
Q ss_pred HHHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEE
Q psy521 66 EFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQI 142 (173)
Q Consensus 66 eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~ 142 (173)
+-...|..+|.+.+.++. -.+.+++...+.+.=-.....+..+|++-|+.|+-.+.|++-
T Consensus 4 ~R~~~I~AaIVrimK~~k-----------------~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd 63 (68)
T PF10557_consen 4 DRKYQIDAAIVRIMKQEK-----------------KLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERD 63 (68)
T ss_dssp HHHHHHHHHHHHHHHHSS-----------------EEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEE
T ss_pred hhhhhhhhheehhhhhcC-----------------ceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcC
Confidence 344567788888888753 267888888888754346789999999999999999999985
No 36
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=57.58 E-value=62 Score=26.13 Aligned_cols=48 Identities=23% Similarity=0.212 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEec--CCCC--eeEEeecC
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINN--IDGT--DMYRAVSP 156 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~--~~g~--~~YR~~~~ 156 (173)
.+|..+|++.+ .++..-|...|+.|+-+|.|++... ..|. ..|+++..
T Consensus 15 ~~t~~eLA~~l--------gis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~ 66 (203)
T TIGR02702 15 QATAAALAEAL--------AISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQ 66 (203)
T ss_pred CCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcc
Confidence 37888888876 4677889999999999999998742 2343 55676644
No 37
>COG0826 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]
Probab=57.05 E-value=20 Score=32.18 Aligned_cols=78 Identities=28% Similarity=0.310 Sum_probs=49.6
Q ss_pred CCCcccccCCCCCHHHHHHHHHHhCCcee----ecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeecCCcCCC--Ccc
Q psy521 91 NGPLVAQRLACATPKEVRKFITDLGISKV----ELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVSPYFAVT--GLS 164 (173)
Q Consensus 91 ~~p~~~~~~~~~T~~eI~~~I~~~~is~v----~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~~~~~~~--~~~ 164 (173)
+.|+..+.+..+|-.+=.+|..+.|...+ +||.++|.+|.+.+. |=.||-.. .|..|+-....-...+ ...
T Consensus 113 ~l~ih~S~q~~v~N~~~~~f~~~~G~~rvVl~rEls~~ei~~i~~~~~-~veiEvfV--hGalcia~SgRC~ls~~~~~~ 189 (347)
T COG0826 113 DLPIHVSTQANVTNAETAKFWKELGAKRVVLPRELSLEEIKEIKEQTP-DVEIEVFV--HGALCIAYSGRCLLSNYFTGR 189 (347)
T ss_pred CCcEEEeeeEecCCHHHHHHHHHcCCEEEEeCccCCHHHHHHHHHhCC-CceEEEEE--ecchhhccCchhhhhhhccCC
Confidence 45665555555666666788899997764 799999999999997 55566654 4655543332221111 234
Q ss_pred ccCccCC
Q psy521 165 TSPCGVC 171 (173)
Q Consensus 165 ~~PCG~C 171 (173)
+..||.|
T Consensus 190 ~~n~g~c 196 (347)
T COG0826 190 SANRGGC 196 (347)
T ss_pred CCCCCCc
Confidence 5666655
No 38
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=56.90 E-value=20 Score=22.27 Aligned_cols=35 Identities=31% Similarity=0.504 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHccc
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFD 136 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~D 136 (173)
+..|.+++..+++..|+.. ++.++++.|++.+=-|
T Consensus 3 G~i~~~~~~~~l~~~g~~~--~s~~e~~~l~~~~D~~ 37 (54)
T PF13833_consen 3 GKITREEFRRALSKLGIKD--LSEEEVDRLFREFDTD 37 (54)
T ss_dssp SEEEHHHHHHHHHHTTSSS--SCHHHHHHHHHHHTTS
T ss_pred CEECHHHHHHHHHHhCCCC--CCHHHHHHHHHhcccC
Confidence 5688999999997777544 9999999999887544
No 39
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=56.47 E-value=47 Score=22.29 Aligned_cols=25 Identities=24% Similarity=0.399 Sum_probs=18.9
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHH
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETL 133 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~L 133 (173)
.||.+||++++ .++.++|+.++...
T Consensus 20 ~Pt~eEiA~~l--------gis~~~v~~~l~~~ 44 (78)
T PF04539_consen 20 EPTDEEIAEEL--------GISVEEVRELLQAS 44 (78)
T ss_dssp --BHHHHHHHH--------TS-HHHHHHHHHHH
T ss_pred CCCHHHHHHHH--------cccHHHHHHHHHhC
Confidence 49999999997 47899999988764
No 40
>smart00049 DEP Domain found in Dishevelled, Egl-10, and Pleckstrin. Domain of unknown function present in signalling proteins that contain PH, rasGEF, rhoGEF, rhoGAP, RGS, PDZ domains. DEP domain in Drosophila dishevelled is essential to rescue planar polarity defects and induce JNK signalling (Cell 94, 109-118).
Probab=55.83 E-value=45 Score=22.40 Aligned_cols=42 Identities=24% Similarity=0.304 Sum_probs=36.4
Q ss_pred CCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEe
Q psy521 99 LACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 99 ~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
...-|-.|+.+||.+.+. ..+.++...|.+.|+--|.|+.+.
T Consensus 18 ~~~F~G~e~v~wL~~~~~---~~~r~eA~~l~~~ll~~g~i~~v~ 59 (77)
T smart00049 18 PNCFTGSELVDWLMDNLE---IIDREEAVHLGQLLLDEGLIHHVN 59 (77)
T ss_pred cceeEcHHHHHHHHHcCC---cCCHHHHHHHHHHHHHCCCEEEeC
Confidence 345788999999999774 368899999999999999999986
No 41
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=55.54 E-value=15 Score=30.34 Aligned_cols=39 Identities=15% Similarity=-0.023 Sum_probs=30.6
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCe
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGK 138 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~ 138 (173)
+..++.|+...+++...-.-.+|.+||.+-++.|.--|.
T Consensus 112 Gii~L~dl~~~~nr~R~g~~lISp~Di~~A~~~l~~lg~ 150 (223)
T PF04157_consen 112 GIISLSDLYCRYNRARGGSELISPEDILRACKLLEVLGL 150 (223)
T ss_dssp SEEEHHHHHHHHHHCTTTSST--HHHHHHHHHHHCCCTS
T ss_pred CEEEHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHcCC
Confidence 579999999999997644447899999999999976664
No 42
>PF13034 DUF3895: Protein of unknown function (DUF3895)
Probab=54.89 E-value=69 Score=23.01 Aligned_cols=56 Identities=21% Similarity=0.283 Sum_probs=42.6
Q ss_pred HHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCc-eeecC------HHHHHHHHHHHcccCeeEEEec
Q psy521 72 NQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGIS-KVELS------EEDIRTILETLLFDGKIEQINN 144 (173)
Q Consensus 72 ~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is-~v~Ls------~~dI~~iL~~Lv~Dg~iE~~~~ 144 (173)
++.+..||++- .-.|+.|+.+|+-+.+-+ +-..+ =-+|-..|+-|+..|+|.-+.+
T Consensus 6 ~~~i~~yi~n~-----------------~~Isa~elcE~LI~~~~~~~~rysTgKpkiY~~Vc~yLe~L~~eg~l~~i~~ 68 (78)
T PF13034_consen 6 KEFINWYIQNE-----------------EEISARELCEYLIENGGSPNKRYSTGKPKIYPYVCNYLEYLVKEGKLSFIEN 68 (78)
T ss_pred HHHHHHHHhcc-----------------ccccHHHHHHHHHHcCCCccccccCCCceeHHHHHHHHHHHHHCCeEEEEec
Confidence 45566688873 348999999999877644 43333 3589999999999999998863
No 43
>KOG2165|consensus
Probab=54.47 E-value=26 Score=34.62 Aligned_cols=51 Identities=20% Similarity=0.371 Sum_probs=42.4
Q ss_pred CCCCCHHHHHHHHHHhCCc--eeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEee
Q psy521 99 LACATPKEVRKFITDLGIS--KVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAV 154 (173)
Q Consensus 99 ~~~~T~~eI~~~I~~~~is--~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~ 154 (173)
.+...++-||++++=-... ..+.|.++++.-|+.+|-+|+++-+ +| .||..
T Consensus 712 lgsm~leRIHnmLkmF~~~~~~~~~TlqeL~~fLq~kV~e~kL~f~---~G--~Y~l~ 764 (765)
T KOG2165|consen 712 LGSMKLERIHNMLKMFVPPDGSAEITLQELQGFLQRKVREGKLEFI---AG--SYRLK 764 (765)
T ss_pred cccchHHHHHHHHeeeecCCCCCcccHHHHHHHHHHHhhccceEEe---cc--eeeec
Confidence 4667899999999865544 4689999999999999999999987 46 59875
No 44
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=54.38 E-value=36 Score=26.80 Aligned_cols=61 Identities=15% Similarity=0.363 Sum_probs=45.8
Q ss_pred HHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCC-ee
Q psy521 72 NQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGT-DM 150 (173)
Q Consensus 72 ~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~-~~ 150 (173)
..+|+.|+.+.. +| -|+.+|.+-+.+ .++-..|+.+|+.|+-+|+|..-. -|. .+
T Consensus 3 e~~Il~y~~~qN--------RP--------ys~~di~~nL~~------~~~K~~v~k~Ld~L~~~g~i~~K~--~GKqki 58 (169)
T PF07106_consen 3 EDAILEYMKEQN--------RP--------YSAQDIFDNLHN------KVGKTAVQKALDSLVEEGKIVEKE--YGKQKI 58 (169)
T ss_pred HHHHHHHHHHcC--------CC--------CcHHHHHHHHHh------hccHHHHHHHHHHHHhCCCeeeee--ecceEE
Confidence 467888998753 33 579999998887 467788999999999999998754 354 55
Q ss_pred EEeecC
Q psy521 151 YRAVSP 156 (173)
Q Consensus 151 YR~~~~ 156 (173)
|-+...
T Consensus 59 Y~~~Q~ 64 (169)
T PF07106_consen 59 YFANQD 64 (169)
T ss_pred EeeCcc
Confidence 655543
No 45
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=54.30 E-value=31 Score=24.14 Aligned_cols=34 Identities=26% Similarity=0.340 Sum_probs=23.0
Q ss_pred CCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccC
Q psy521 99 LACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDG 137 (173)
Q Consensus 99 ~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg 137 (173)
.++.|.++|.++|.. ..++.++|..|+..|.=-|
T Consensus 19 ~G~lT~~eI~~~L~~-----~~~~~e~id~i~~~L~~~g 52 (82)
T PF03979_consen 19 KGYLTYDEINDALPE-----DDLDPEQIDEIYDTLEDEG 52 (82)
T ss_dssp HSS-BHHHHHHH-S------S---HHHHHHHHHHHHTT-
T ss_pred cCcCCHHHHHHHcCc-----cCCCHHHHHHHHHHHHHCC
Confidence 378999999999874 3489999999999986444
No 46
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=52.97 E-value=23 Score=24.55 Aligned_cols=46 Identities=30% Similarity=0.411 Sum_probs=36.2
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeecCC
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVSPY 157 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~~~ 157 (173)
.|.+||++.+ .++...+++|++.|+-.|.|+..+..+| .|++.+.+
T Consensus 26 ~s~~eiA~~~--------~i~~~~l~kil~~L~~~Gli~s~~G~~G--Gy~L~~~~ 71 (83)
T PF02082_consen 26 VSSKEIAERL--------GISPSYLRKILQKLKKAGLIESSRGRGG--GYRLARPP 71 (83)
T ss_dssp BEHHHHHHHH--------TS-HHHHHHHHHHHHHTTSEEEETSTTS--EEEESS-C
T ss_pred CCHHHHHHHH--------CcCHHHHHHHHHHHhhCCeeEecCCCCC--ceeecCCH
Confidence 7999999854 4688999999999999999998764445 59988764
No 47
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=51.47 E-value=36 Score=26.65 Aligned_cols=47 Identities=23% Similarity=0.265 Sum_probs=37.7
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeecCC
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVSPY 157 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~~~ 157 (173)
..|.++|++-+ .++..-+++|+..|+-.|.|+..+...|. |++.+++
T Consensus 24 ~~s~~eIA~~~--------~is~~~L~kIl~~L~~aGlv~S~rG~~GG--y~La~~p 70 (153)
T PRK11920 24 LSRIPEIARAY--------GVSELFLFKILQPLVEAGLVETVRGRNGG--VRLGRPA 70 (153)
T ss_pred cCcHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEeecCCCCC--eeecCCH
Confidence 46888887653 46888999999999999999998866664 8887654
No 48
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=51.42 E-value=3.5 Score=25.34 Aligned_cols=13 Identities=31% Similarity=0.964 Sum_probs=10.8
Q ss_pred ccccceecccccH
Q psy521 53 TGGTWYQDQDFEV 65 (173)
Q Consensus 53 TGG~WYtD~elD~ 65 (173)
-||.||..+||+.
T Consensus 25 C~G~W~d~~el~~ 37 (41)
T PF13453_consen 25 CGGIWFDAGELEK 37 (41)
T ss_pred CCeEEccHHHHHH
Confidence 4899999898874
No 49
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=51.40 E-value=27 Score=22.87 Aligned_cols=54 Identities=24% Similarity=0.289 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHH-hCCceeecCHHHHHHHHHHHcccCeeE
Q psy521 67 FVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITD-LGISKVELSEEDIRTILETLLFDGKIE 140 (173)
Q Consensus 67 FI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~-~~is~v~Ls~~dI~~iL~~Lv~Dg~iE 140 (173)
-++..-..+++.+.. -.|+++|.+.+.+ -++..-.+ .+||.+.|+.|.--|.||
T Consensus 14 ~Ln~~a~~Iw~~~~g-------------------~~t~~ei~~~l~~~y~~~~~~~-~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 14 TLNETAAFIWELLDG-------------------PRTVEEIVDALAEEYDVDPEEA-EEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp ---THHHHHHHH--S-------------------SS-HHHHHHHHHHHTT--HHHH-HHHHHHHHHHHHHTT---
T ss_pred cccHHHHHHHHHccC-------------------CCCHHHHHHHHHHHcCCCHHHH-HHHHHHHHHHHHHCcCcC
Confidence 455555666666643 2689999999985 44444445 899999999998887775
No 50
>PRK04280 arginine repressor; Provisional
Probab=50.57 E-value=68 Score=25.26 Aligned_cols=46 Identities=17% Similarity=0.286 Sum_probs=31.3
Q ss_pred CCCCHHHHHHHHHHhCCceeecCH-HHHHHHHHHHcccCeeEEEecCCCCeeEEe
Q psy521 100 ACATPKEVRKFITDLGISKVELSE-EDIRTILETLLFDGKIEQINNIDGTDMYRA 153 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~-~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~ 153 (173)
...|=+|+.+.|++.|+.-.+=|+ .||++| .+.++++.+|...|..
T Consensus 17 ~I~tQeeL~~~L~~~Gi~vTQATiSRDikeL--------~lvKv~~~~G~~~Y~l 63 (148)
T PRK04280 17 EIETQDELVDRLREEGFNVTQATVSRDIKEL--------HLVKVPLPDGRYKYSL 63 (148)
T ss_pred CCCCHHHHHHHHHHcCCCeehHHHHHHHHHc--------CCEEeecCCCcEEEee
Confidence 457899999999999977433332 344433 5677777778766665
No 51
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=50.14 E-value=43 Score=25.80 Aligned_cols=54 Identities=22% Similarity=0.378 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEE
Q psy521 65 VEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQ 141 (173)
Q Consensus 65 ~eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~ 141 (173)
.+-+......+++||..+. -|..+|.+.|.+.| ++.+.|+++|+-|.-.|.|.-
T Consensus 7 ~~~~~~a~~~al~~L~~r~------------------~s~~el~~kL~~kg-----~~~~~i~~vl~~l~~~~~ldD 60 (157)
T PRK00117 7 RRMYASARARALRLLARRE------------------HSRAELRRKLAAKG-----FSEEVIEAVLDRLKEEGLLDD 60 (157)
T ss_pred ccHHHHHHHHHHHHHccch------------------hHHHHHHHHHHhcC-----CCHHHHHHHHHHHHHcCCCCH
Confidence 3556777888888998763 48999999999987 567999999999988887753
No 52
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=48.19 E-value=31 Score=25.48 Aligned_cols=45 Identities=27% Similarity=0.324 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeec
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVS 155 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~ 155 (173)
.+|.++|++.+ .++..-++++|+.|+-.|.|+.....+| .|+..+
T Consensus 25 ~~s~~eia~~~--------~i~~~~v~~il~~L~~~gli~~~~g~~g--gy~l~~ 69 (132)
T TIGR00738 25 PVSVKEIAERQ--------GISRSYLEKILRTLRRAGLVESVRGPGG--GYRLAR 69 (132)
T ss_pred cCcHHHHHHHH--------CcCHHHHHHHHHHHHHCCcEEeccCCCC--CccCCC
Confidence 58999998765 3578899999999999999987643333 366654
No 53
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=48.16 E-value=68 Score=21.55 Aligned_cols=54 Identities=19% Similarity=0.190 Sum_probs=41.5
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecC--CC--CeeEEeec
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNI--DG--TDMYRAVS 155 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~--~g--~~~YR~~~ 155 (173)
.+.-+|.+.|.+.--.-..++...|-..|+.|+-+|.|+..... +| ...|+.+.
T Consensus 10 ~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~ 67 (75)
T PF03551_consen 10 MHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITE 67 (75)
T ss_dssp EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESH
T ss_pred CcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECH
Confidence 47889999999862123688999999999999999999987642 22 26677764
No 54
>PF07574 SMC_Nse1: Nse1 non-SMC component of SMC5-6 complex; InterPro: IPR011513 Saccharomyces cerevisiae Nse1 (Q07913 from SWISSPROT) forms part of a complex with SMC5-SMC6. This non-structural maintenance of chromosomes (SMC) complex plays an essential role in genomic stability, being involved in DNA repair and DNA metabolism [, ]. It is conserved in eukaryotes from yeast to human.; PDB: 3NW0_A.
Probab=47.97 E-value=44 Score=27.18 Aligned_cols=103 Identities=15% Similarity=0.238 Sum_probs=46.2
Q ss_pred cceeEEEeeccCCCcCcccccceecccccHHHHHHHHHHHHHHHhhhhhhccC--------CCCCCcccccCCCCCHHHH
Q psy521 36 SKKKVYMLFDLEPDRSLTGGTWYQDQDFEVEFVDVLNQQCYRFLQLKREKTAN--------NTNGPLVAQRLACATPKEV 107 (173)
Q Consensus 36 ~~rk~Yml~~l~Ps~eiTGG~WYtD~elD~eFI~~L~~~~~~~l~~k~~~~~~--------~~~~p~~~~~~~~~T~~eI 107 (173)
.++.+|.+.+..+++..--++=|+..|+ +|+. ..+...+......... .....+... ...+....
T Consensus 73 ~g~~~y~lVN~~~D~~sklaT~ys~~Ei--~ffK---~lle~I~~~~~~~~~~~~~~~~~~~~~~~i~~~--~~~~~~~~ 145 (200)
T PF07574_consen 73 DGERYYALVNTSSDEISKLATTYSPNEI--AFFK---KLLEEIVESENTSRSESASSIMALNEVQAIKLK--RPGDPSQW 145 (200)
T ss_dssp T--EEEEEEESSS-TTHHHHTTS-HHHH--HHHH---HHHHHHHHSSSS-EEH----HHHHGGGTT-SSS-----H----
T ss_pred CCCEEEEEEeCCCCHHHHhcCCCCHHHH--HHHH---HHHHHHHhCCCCceehhhHHHHHHHHHHHHHHh--ccCccccc
Confidence 6778999999999988877787777763 4444 4444444442211100 000000000 00000111
Q ss_pred HHHHH---HhC--CceeecCHHHHHHHHHHHcccCeeEEEecCCC
Q psy521 108 RKFIT---DLG--ISKVELSEEDIRTILETLLFDGKIEQINNIDG 147 (173)
Q Consensus 108 ~~~I~---~~~--is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g 147 (173)
.++.. .+. -+...|+..+++++|+.||=||=+++.. +|
T Consensus 146 ~~~~~~~~~~~~~~~~~~L~~~eae~lL~~lv~~gWl~~s~--~G 188 (200)
T PF07574_consen 146 TQGVSYAGGSTQLAQDKGLSKSEAESLLDRLVEDGWLYRSR--EG 188 (200)
T ss_dssp ---------------------HHHHHHHHHHHHTTSE-EEE--TT
T ss_pred ccccccccccccccccccchHHHHHHHHHHHHHCCCceeCC--CC
Confidence 11111 111 1124799999999999999999998864 46
No 55
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=46.92 E-value=14 Score=29.07 Aligned_cols=34 Identities=38% Similarity=0.583 Sum_probs=29.6
Q ss_pred HHHHHHhCCcee----ecCHHHHHHHHHHHcccCeeEE
Q psy521 108 RKFITDLGISKV----ELSEEDIRTILETLLFDGKIEQ 141 (173)
Q Consensus 108 ~~~I~~~~is~v----~Ls~~dI~~iL~~Lv~Dg~iE~ 141 (173)
.+-|+..||+.. .+|.+||..|=+.|-|+|+|++
T Consensus 80 e~~Ln~~GI~tfaQIAAwt~~di~~id~~l~f~GRi~R 117 (133)
T COG3743 80 EKVLNELGIFTFAQIAAWTRADIAWIDDYLNFDGRIER 117 (133)
T ss_pred HHHHHHcCCccHHHHHhcCHHHHHHHHhhcCCcchhHH
Confidence 456788898873 6999999999999999999987
No 56
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=46.85 E-value=74 Score=22.57 Aligned_cols=42 Identities=14% Similarity=0.307 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHhCCce---------------eecCHHHHHHHHHHHcccCeeEEEe
Q psy521 102 ATPKEVRKFITDLGISK---------------VELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~---------------v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
.|...|.+.++.+.-.+ ..++.+++++|++.|+.+|-|+...
T Consensus 20 ~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~~Li~~g~L~~~~ 76 (106)
T PF09382_consen 20 FGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIRQLILEGYLSEDN 76 (106)
T ss_dssp S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred ccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHHHHHHcCCceecC
Confidence 67888888887654322 2589999999999999999997654
No 57
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=46.44 E-value=61 Score=20.36 Aligned_cols=32 Identities=16% Similarity=0.174 Sum_probs=26.0
Q ss_pred CCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcc
Q psy521 99 LACATPKEVRKFITDLGISKVELSEEDIRTILETLLF 135 (173)
Q Consensus 99 ~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~ 135 (173)
.+..|.+|+.+++++.|+ +.++++++++.+-.
T Consensus 13 ~G~i~~~el~~~l~~~g~-----~~~~~~~i~~~~d~ 44 (67)
T cd00052 13 DGLISGDEARPFLGKSGL-----PRSVLAQIWDLADT 44 (67)
T ss_pred CCcCcHHHHHHHHHHcCC-----CHHHHHHHHHHhcC
Confidence 467999999999998763 78889999886643
No 58
>PF10941 DUF2620: Protein of unknown function DUF2620; InterPro: IPR021238 This is a bacterial family of proteins with unknown function.
Probab=46.00 E-value=43 Score=25.80 Aligned_cols=34 Identities=18% Similarity=0.421 Sum_probs=29.3
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHc
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLL 134 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv 134 (173)
.-|+-+||.+++.+ |-...-+|.+|+++++-+|+
T Consensus 80 ~~~~eeeI~~~v~~-GK~AFGft~~hie~vvP~l~ 113 (117)
T PF10941_consen 80 KIPSEEEIRKEVAE-GKKAFGFTAQHIEQVVPVLI 113 (117)
T ss_pred CCCCHHHHHHHHHc-CCeeeeccHHHHHHHHHHHH
Confidence 46899999999987 54677899999999998875
No 59
>PRK11106 queuosine biosynthesis protein QueC; Provisional
Probab=45.94 E-value=17 Score=30.63 Aligned_cols=40 Identities=18% Similarity=0.360 Sum_probs=26.0
Q ss_pred eecCHHHHHHHHHHHc-ccCeeEEEecCCCCeeEEeecCCcCCCCccccCccCCC
Q psy521 119 VELSEEDIRTILETLL-FDGKIEQINNIDGTDMYRAVSPYFAVTGLSTSPCGVCP 172 (173)
Q Consensus 119 v~Ls~~dI~~iL~~Lv-~Dg~iE~~~~~~g~~~YR~~~~~~~~~~~~~~PCG~CP 172 (173)
+.|+..||.++-..|= .|=-++... .||+.. .+ + |||.||
T Consensus 161 ~~lsK~eI~~l~~~lg~v~~~~~~T~-----SCy~g~------~g--~-~CG~C~ 201 (231)
T PRK11106 161 MWLNKAETWALADYYGQLDLVRHETL-----TCYNGI------KG--D-GCGHCA 201 (231)
T ss_pred CCCCHHHHHHHHHHcCCcccccCcee-----eccCcC------CC--C-CCCCCH
Confidence 4699999999987765 322224432 488732 12 3 999998
No 60
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=45.93 E-value=1.1e+02 Score=21.98 Aligned_cols=49 Identities=24% Similarity=0.193 Sum_probs=38.0
Q ss_pred CCCCHHHHHHHHHHhCCcee-ecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEee
Q psy521 100 ACATPKEVRKFITDLGISKV-ELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAV 154 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v-~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~ 154 (173)
..+|.+.|.++|.+.= ..+ .=|.+-|..-|-+|+-++||-.. +. .|..+
T Consensus 28 ~~at~E~l~~~L~~~y-p~i~~Ps~e~l~~~L~~Li~erkIY~t--g~---GYfiv 77 (80)
T PF10264_consen 28 QPATQETLREHLRKHY-PGIAIPSQEVLYNTLGTLIKERKIYHT--GE---GYFIV 77 (80)
T ss_pred CcchHHHHHHHHHHhC-CCCCCCCHHHHHHHHHHHHHcCceeeC--CC---ceEee
Confidence 4589999999999852 222 45899999999999999999874 23 37654
No 61
>PRK14134 recX recombination regulator RecX; Provisional
Probab=44.53 E-value=75 Score=27.48 Aligned_cols=58 Identities=10% Similarity=0.186 Sum_probs=44.3
Q ss_pred cccccHHHHHHHHH---------HHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHH
Q psy521 60 DQDFEVEFVDVLNQ---------QCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTIL 130 (173)
Q Consensus 60 D~elD~eFI~~L~~---------~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL 130 (173)
+.++|.+.++.|.. ..++||..+ .-|-.||.++|.+.| ++.+.|+.+|
T Consensus 43 G~eld~e~~~ei~~~~~~~~a~~~AL~~Ls~r------------------~rSe~Elr~KL~~k~-----~~~~~Ie~vI 99 (283)
T PRK14134 43 GKVIDVNSLNDIIKEDNYIKCKGYALKYIEKS------------------YKTEKQIKEKLYLKE-----YDEDAVNRVI 99 (283)
T ss_pred CCCcCHHHHHHHHHHHHHHHHHHHHHHHhccC------------------cchHHHHHHHHHhCC-----CCHHHHHHHH
Confidence 67888888888763 344455543 358999999999877 5689999999
Q ss_pred HHHcccCeeE
Q psy521 131 ETLLFDGKIE 140 (173)
Q Consensus 131 ~~Lv~Dg~iE 140 (173)
+-|.-.|.|-
T Consensus 100 ~~L~e~~yld 109 (283)
T PRK14134 100 RFLKEYNFID 109 (283)
T ss_pred HHHHHCCCCC
Confidence 9998877763
No 62
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=43.83 E-value=1.2e+02 Score=21.75 Aligned_cols=55 Identities=15% Similarity=0.164 Sum_probs=41.5
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEe--cCCC--CeeEEeecC
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQIN--NIDG--TDMYRAVSP 156 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~--~~~g--~~~YR~~~~ 156 (173)
.+--||.+.|.+..-....++..-|-.+|+.|+-+|.|+... ..+| ...|+.+..
T Consensus 18 ~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~ 76 (100)
T TIGR03433 18 LHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAA 76 (100)
T ss_pred CCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHH
Confidence 467789999988654456889999999999999999999842 2222 266877643
No 63
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=43.38 E-value=76 Score=19.33 Aligned_cols=46 Identities=22% Similarity=0.285 Sum_probs=31.8
Q ss_pred HHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeE
Q psy521 70 VLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIE 140 (173)
Q Consensus 70 ~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE 140 (173)
.....++.+|.++ +..|..||++-+ .+|..-+.+.|+-|+=+|.|+
T Consensus 3 ~~~~~Il~~l~~~-----------------~~~t~~ela~~~--------~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 3 ETQRKILNYLREN-----------------PRITQKELAEKL--------GISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHHC-----------------TTS-HHHHHHHH--------TS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHc-----------------CCCCHHHHHHHh--------CCCHHHHHHHHHHHHHCcCcC
Confidence 4456677777764 347788877653 467788899999999888875
No 64
>PF06897 DUF1269: Protein of unknown function (DUF1269); InterPro: IPR009200 There are currently no experimental data for members of this group or their homologues. However, these proteins are predicted to contain two or more transmembrane segments.
Probab=43.30 E-value=27 Score=25.90 Aligned_cols=63 Identities=24% Similarity=0.318 Sum_probs=43.0
Q ss_pred eecccccHHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhC--CceeecCHHHHHHHHHHH
Q psy521 58 YQDQDFEVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLG--ISKVELSEEDIRTILETL 133 (173)
Q Consensus 58 YtD~elD~eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~--is~v~Ls~~dI~~iL~~L 133 (173)
++|-.+|.+|++.+.+.+. .-+ ..+... ....+.+.+.+.+++.+ +.+..||.+|-++|-++|
T Consensus 35 l~d~gI~d~~~~ev~~~L~----~Gs--------sAl~~l-v~~~~~d~v~~~l~~~gg~v~~t~ls~~~e~~L~~al 99 (102)
T PF06897_consen 35 LSDYGIDDEFIKEVGEALK----PGS--------SALFLL-VDEATEDKVDAALRKFGGKVLRTSLSEEDEDELQEAL 99 (102)
T ss_pred HhhCCCCHHHHHHHHhhcC----CCc--------eEEEEE-eccCCHHHHHHHHHhcCCEEEeccCCHHHHHHHHHHH
Confidence 5688899999887776432 110 000000 12368999999999987 446689999999988776
No 65
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=43.16 E-value=1.3e+02 Score=26.34 Aligned_cols=33 Identities=18% Similarity=0.269 Sum_probs=22.0
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEE
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQ 141 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~ 141 (173)
..++.||++.+ | |...-+-.=+++|+--|.|+.
T Consensus 37 plNvneiAe~l---g-----Lpqst~s~~ik~Le~aGlirT 69 (308)
T COG4189 37 PLNVNEIAEAL---G-----LPQSTMSANIKVLEKAGLIRT 69 (308)
T ss_pred CCCHHHHHHHh---C-----CchhhhhhhHHHHHhcCceee
Confidence 46788888764 3 444445555778888888864
No 66
>PF03801 Ndc80_HEC: HEC/Ndc80p family; InterPro: IPR005550 Members of this family are components of the mitotic spindle. It has been shown that Ndc80 from yeast is part of a complex called the Ndc80p complex []. This complex is thought to bind to the microtubules of the spindle.; PDB: 3IZ0_E 2VE7_B 2IGP_A.
Probab=42.86 E-value=1.3e+02 Score=23.81 Aligned_cols=72 Identities=18% Similarity=0.289 Sum_probs=41.8
Q ss_pred cHHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHH---HHHHHHHhCCceeecC---HHHHHHHHHHHcccC
Q psy521 64 EVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKE---VRKFITDLGISKVELS---EEDIRTILETLLFDG 137 (173)
Q Consensus 64 D~eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~e---I~~~I~~~~is~v~Ls---~~dI~~iL~~Lv~Dg 137 (173)
|.++.....+.+..||....+. ..++.......||..+ |.+||-+.=..+..+. +|||-.+|+.|=|=.
T Consensus 34 Dk~~q~~~~~~I~~fL~~~~~~-----~~~is~k~l~~Pt~kdf~~I~~fL~~~idp~~~~~~k~eeev~~~lK~L~YP~ 108 (157)
T PF03801_consen 34 DKSYQQECIRKIYEFLSEHGFE-----SHPISPKTLKSPTQKDFVEIFNFLFRQIDPNFKFGKKFEEEVPFLLKALGYPF 108 (157)
T ss_dssp -HHHHHHHHHHHHHHHHHTT-------SS---TTTTSS--HHHHHHHHHHHHHTTSTT---SSTHHHHHHHHHHHTT-SS
T ss_pred CHHHHHHHHHHHHHHHHHcCCC-----CccccccccCCCCHHHHHHHHHHHHHHhCCCCCcCcCHHHHHHHHHHHhCCCc
Confidence 9999999999999999987550 2233333334567655 5667776532234444 778999999998877
Q ss_pred -eeE
Q psy521 138 -KIE 140 (173)
Q Consensus 138 -~iE 140 (173)
.|-
T Consensus 109 ~~is 112 (157)
T PF03801_consen 109 ATIS 112 (157)
T ss_dssp ----
T ss_pred cccC
Confidence 443
No 67
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=41.30 E-value=1e+02 Score=23.36 Aligned_cols=48 Identities=21% Similarity=0.418 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCC-eeEEee
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGT-DMYRAV 154 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~-~~YR~~ 154 (173)
-+|+.||++.+.+. ..++..=|..+|+.|+--|.|++.. +|. ..|+++
T Consensus 18 ~~t~~eI~~~l~~~----~~~~~tTv~T~L~rL~~KG~v~~~k--~gr~~~Y~p~ 66 (130)
T TIGR02698 18 ETTSRDIIRILAEK----KDWSDSTIKTLLGRLVDKGCLTTEK--EGRKFIYTAL 66 (130)
T ss_pred CCCHHHHHHHHhhc----cCCcHHHHHHHHHHHHHCCceeeec--CCCcEEEEec
Confidence 37999999999764 2577889999999999999998764 343 567764
No 68
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=40.50 E-value=1.2e+02 Score=24.50 Aligned_cols=34 Identities=18% Similarity=0.119 Sum_probs=26.4
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEE
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQI 142 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~ 142 (173)
..|.+++++-+ .++..+|+++|..|.-||.|...
T Consensus 36 ~~tdeeLA~~L--------gi~~~~VRk~L~~L~e~gLv~~~ 69 (178)
T PRK06266 36 EVTDEEIAEQT--------GIKLNTVRKILYKLYDARLADYK 69 (178)
T ss_pred CcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCeEEe
Confidence 45555555543 57899999999999999999944
No 69
>PF13099 DUF3944: Domain of unknown function (DUF3944)
Probab=39.99 E-value=24 Score=21.65 Aligned_cols=17 Identities=35% Similarity=0.647 Sum_probs=15.6
Q ss_pred ecCHHHHHHHHHHHccc
Q psy521 120 ELSEEDIRTILETLLFD 136 (173)
Q Consensus 120 ~Ls~~dI~~iL~~Lv~D 136 (173)
.+|.+|++.|.+.|++|
T Consensus 12 ~cs~edL~~L~~~Lt~d 28 (35)
T PF13099_consen 12 ECSNEDLKDLVDILTHD 28 (35)
T ss_pred HCCHHHHHHHHHHHhcC
Confidence 37899999999999998
No 70
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=39.97 E-value=86 Score=18.99 Aligned_cols=45 Identities=18% Similarity=0.173 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEee
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAV 154 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~ 154 (173)
..|..+|.+.+. ++...+...|+.|+-+|.|+.... .+...|+..
T Consensus 10 ~~~~~~i~~~l~--------is~~~v~~~l~~L~~~g~i~~~~~-~~~~~~~~~ 54 (66)
T smart00418 10 ELCVCELAEILG--------LSQSTVSHHLKKLREAGLVESRRE-GKRVYYSLT 54 (66)
T ss_pred CccHHHHHHHHC--------CCHHHHHHHHHHHHHCCCeeeeec-CCEEEEEEc
Confidence 368889988873 577889999999999999997642 222345544
No 71
>PF06479 Ribonuc_2-5A: Ribonuclease 2-5A; InterPro: IPR010513 The proteins listed below share a common architecture with a protein kinase homology domain (see PDOC00100 from PROSITEDOC) followed by an ~135-residue globular kinase-extension nuclease (KEN) domain made of eight helices []: - Mammalian 2-5A-dependent RNase or RNase L (EC 3.1.26.-), an interferon- induced enzyme implicated in both the molecular mechanisms of interferon action and the fundamental control of RNA stability. 2-5A-dependent RNase is a unique enzyme in that it requires 2-5A, unusual oligoadenylates with 2',5'-phosphodiester linkages. RNase L is catalytically active only after binding to an unusual activator molecule containing a 5'-phosphorylated 2', 5'-linked oligoadenylate (2-5A), in the N-terminal half. RNase L consists of three domains, namely the N-terminal ankyrin repeat domain (see PDOC50088 from PROSITEDOC), the protein kinase homology domain, and the C-terminal KEN domain [, , ]. - Eukaryotic Ire1/Ern1, an ancient transmembrane sensor of endoplasmic reticulum (ER) stress with dual protein kinase and ribonuclease activities. In response to ER stress Ire1/Ern1 catalyzes the splicing of target mRNAs in a spliceosome-independent manner. Ire1/Ern1 is a type 1 transmembrane receptor consisting of an N-terminal ER luminal domain, a transmembrane segment and a cytoplasmic region. The cytoplasmic region encompasses a protein kinase domain followed by a C-terminal KEN domain [, ]. The dimerisation of the kinase domain activates the ribonuclease function of the KEN domain [].; GO: 0016891 endoribonuclease activity, producing 5'-phosphomonoesters, 0006397 mRNA processing; PDB: 3SDJ_D 3FBV_L 3LJ2_A 3SDM_A 3LJ0_A 2RIO_A 3LJ1_A 3P23_A.
Probab=39.71 E-value=8.4 Score=29.81 Aligned_cols=58 Identities=24% Similarity=0.488 Sum_probs=37.6
Q ss_pred CCcCcccccceecccccHHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHH
Q psy521 48 PDRSLTGGTWYQDQDFEVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIR 127 (173)
Q Consensus 48 Ps~eiTGG~WYtD~elD~eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~ 127 (173)
.+..+.||.| +..+|.+|++.|.. | ++ -.+-++.++..+|++..-=--+| .++++
T Consensus 31 ~~~~v~~~~W--~~~ld~~l~~~l~~----~--R~----------------Y~~~sv~DLLR~IRNk~~Hy~el-~~~~k 85 (129)
T PF06479_consen 31 NAEDVLGGDW--DKKLDPELLDDLGK----Y--RK----------------YDGDSVRDLLRAIRNKKHHYQEL-PEEVK 85 (129)
T ss_dssp CCCCCTTS-C--GGCSBHHHHHCCTT----T--SS------------------TT-HHHHHHHHHHHHHTCCCS--HHHH
T ss_pred cCCCCCCccH--hHHhCHHHHHHHHh----c--cC----------------CCccCHHHHHHHHHcchHhHHHC-CHHHH
Confidence 3667889999 46899999998764 2 11 13468999999999865333455 56677
Q ss_pred HHH
Q psy521 128 TIL 130 (173)
Q Consensus 128 ~iL 130 (173)
++|
T Consensus 86 ~~l 88 (129)
T PF06479_consen 86 EIL 88 (129)
T ss_dssp HHC
T ss_pred HHh
Confidence 665
No 72
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=39.61 E-value=31 Score=26.98 Aligned_cols=47 Identities=21% Similarity=0.313 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeecCC
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVSPY 157 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~~~ 157 (173)
.+|.++|++. ..++..-+++|+..|.-.|.|+.++...|. ||+.+++
T Consensus 25 ~~s~~~IA~~--------~~is~~~L~kil~~L~kaGlV~S~rG~~GG--y~Lar~~ 71 (150)
T COG1959 25 PVSSAEIAER--------QGISPSYLEKILSKLRKAGLVKSVRGKGGG--YRLARPP 71 (150)
T ss_pred cccHHHHHHH--------hCcCHHHHHHHHHHHHHcCCEEeecCCCCC--ccCCCCh
Confidence 4778888875 346788999999999999999999866664 8887654
No 73
>cd05029 S-100A6 S-100A6: S-100A6 domain found in proteins similar to S100A6. S100A6 is a member of the S100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A6 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100A6 is normally expressed in the G1 phase of the cell cycle in neuronal cells. The function of S100A6 remains unclear, but evidence suggests that it is involved in cell cycle regulation and exocytosis. S100A6 may also be involved in tumorigenesis; the protein is overexpressed in several tumors. Ca2+ binding to S100A6 leads to a conformational change in the protein, which exposes a hydrophobic surface for interact
Probab=39.15 E-value=1.4e+02 Score=21.11 Aligned_cols=53 Identities=17% Similarity=0.248 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHh-CCceeecCHHHHHHHHHHHc
Q psy521 67 FVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDL-GISKVELSEEDIRTILETLL 134 (173)
Q Consensus 67 FI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~-~is~v~Ls~~dI~~iL~~Lv 134 (173)
-|..|-....+|-.+.. ..++.+.+|+.+.+++. .. ...++.++|+++++.+=
T Consensus 8 ~~~~~i~~F~~y~~~~~--------------~~g~Is~~EL~~~l~~~~~l-g~k~t~~ev~~m~~~~D 61 (88)
T cd05029 8 AIGLLVAIFHKYSGREG--------------DKNTLSKKELKELIQKELTI-GSKLQDAEIAKLMEDLD 61 (88)
T ss_pred HHHHHHHHHHHHHccCC--------------CCCEECHHHHHHHHHHHHhc-CCCCCHHHHHHHHHHhc
Confidence 45566666666666321 13689999999999752 11 23479999999999874
No 74
>PRK06474 hypothetical protein; Provisional
Probab=38.74 E-value=1.9e+02 Score=23.19 Aligned_cols=65 Identities=14% Similarity=0.241 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecC---
Q psy521 69 DVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNI--- 145 (173)
Q Consensus 69 ~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~--- 145 (173)
+-.+..|+++|.... ...|+.+|++.+. .++..-|-.-|+.|+-.|.|+.+...
T Consensus 10 ~p~R~~Il~~L~~~~----------------~~~ta~el~~~l~-------~is~aTvYrhL~~L~e~GLI~~~~~~~~~ 66 (178)
T PRK06474 10 HPVRMKICQVLMRNK----------------EGLTPLELVKILK-------DVPQATLYRHLQTMVDSGILHVVKEKKVR 66 (178)
T ss_pred CHHHHHHHHHHHhCC----------------CCCCHHHHHHHhc-------CCCHHHHHHHHHHHHHCCCEEEeeccccc
Confidence 345677788887631 1279999998874 36777888899999999999998642
Q ss_pred CCC-eeEEeecC
Q psy521 146 DGT-DMYRAVSP 156 (173)
Q Consensus 146 ~g~-~~YR~~~~ 156 (173)
+|. ..|++...
T Consensus 67 ~~~ek~y~~~~~ 78 (178)
T PRK06474 67 SVSEKYYAINEE 78 (178)
T ss_pred CceeEEEEeccc
Confidence 232 56777654
No 75
>PF14418 OHA: OST-HTH Associated domain
Probab=38.37 E-value=51 Score=23.11 Aligned_cols=38 Identities=21% Similarity=0.225 Sum_probs=33.7
Q ss_pred CHHHHHHHHHHhCCcee-ecCHHHHHHHHHHHcccCeeE
Q psy521 103 TPKEVRKFITDLGISKV-ELSEEDIRTILETLLFDGKIE 140 (173)
Q Consensus 103 T~~eI~~~I~~~~is~v-~Ls~~dI~~iL~~Lv~Dg~iE 140 (173)
.--+.+++|++.|.... .|+..+|-.|++.++..+++.
T Consensus 11 gRY~~A~~Lk~~gp~~lr~l~Lg~i~~iVqlai~~k~l~ 49 (75)
T PF14418_consen 11 GRYGMAQFLKKRGPPFLRSLSLGDICHIVQLAISKKKLI 49 (75)
T ss_pred cHHHHHHHHHhcCchhhcCCcHHHHHHHHHHHHhCCeee
Confidence 35678999999998876 799999999999999988887
No 76
>PF13592 HTH_33: Winged helix-turn helix
Probab=37.78 E-value=43 Score=21.97 Aligned_cols=31 Identities=26% Similarity=0.301 Sum_probs=21.8
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHH
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETL 133 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~L 133 (173)
+-|+.+|.++|.+ -..|.+|..-|..+|.-|
T Consensus 4 ~wt~~~i~~~I~~--~fgv~ys~~~v~~lL~r~ 34 (60)
T PF13592_consen 4 RWTLKEIAAYIEE--EFGVKYSPSGVYRLLKRL 34 (60)
T ss_pred cccHHHHHHHHHH--HHCCEEcHHHHHHHHHHc
Confidence 4577788888875 234667888887777765
No 77
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=37.67 E-value=1.1e+02 Score=22.94 Aligned_cols=29 Identities=28% Similarity=0.520 Sum_probs=18.6
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHHHHH
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTILETL 133 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~L 133 (173)
.|+.++..-|-..+ -.++++++++||+.+
T Consensus 83 ~s~~E~~~lI~sl~---~r~~ee~l~~iL~~i 111 (118)
T smart00657 83 ETAEEAQLLIPSLE---ERIDEEELEELLDDL 111 (118)
T ss_pred CCHHHHHHHhhhhh---ccCCHHHHHHHHHHH
Confidence 45666666665543 126788888888765
No 78
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=37.42 E-value=1.4e+02 Score=20.80 Aligned_cols=28 Identities=7% Similarity=0.151 Sum_probs=20.2
Q ss_pred HHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHH
Q psy521 71 LNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITD 113 (173)
Q Consensus 71 L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~ 113 (173)
....+..|++++.. ...|++||.++++.
T Consensus 10 ~l~~aV~ymK~r~~---------------~Plt~~EIl~~ls~ 37 (75)
T cd07977 10 QLAKIVDYMKKRHQ---------------HPLTLDEILDYLSL 37 (75)
T ss_pred hHHHHHHHHHhcCC---------------CCccHHHHHHHHhc
Confidence 34556678888630 33899999999886
No 79
>PF14848 HU-DNA_bdg: DNA-binding domain
Probab=37.34 E-value=58 Score=24.61 Aligned_cols=40 Identities=25% Similarity=0.384 Sum_probs=30.5
Q ss_pred CCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHH-------cccCeeEE
Q psy521 99 LACATPKEVRKFITDLGISKVELSEEDIRTILETL-------LFDGKIEQ 141 (173)
Q Consensus 99 ~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~L-------v~Dg~iE~ 141 (173)
.+-.|.++|++-|.+.+ ..++.+||+.+|+.| +.+|....
T Consensus 26 ~~~~tl~~Ia~~i~~~~---s~~t~~di~~vl~~~~~~~~~~l~~G~sV~ 72 (124)
T PF14848_consen 26 SGTLTLEDIAEEIAKEG---STLTRADIEAVLNALKDEMIEALMNGYSVN 72 (124)
T ss_pred cCccCHHHHHHHHHHhC---CCCCHHHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 46789999999998754 457888888888765 56666655
No 80
>PF10357 Kin17_mid: Domain of Kin17 curved DNA-binding protein; InterPro: IPR019447 This entry represents the conserved central 169 residue region of the Kin17 DNA/RNA-binding proteins. The N-terminal region of Kin17 contains a zinc-finger domain, while in the human and mouse proteins there is a RecA-like domain found in the C-terminal region. In humans, Kin17 protein forms intra-nuclear foci during cell proliferation and is re-distributed in the nucleoplasm during the cell cycle []. ; PDB: 2V1N_A.
Probab=37.24 E-value=57 Score=25.39 Aligned_cols=55 Identities=22% Similarity=0.385 Sum_probs=36.2
Q ss_pred ccccHHHHHHHHHHH-----------HHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHH
Q psy521 61 QDFEVEFVDVLNQQC-----------YRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEE 124 (173)
Q Consensus 61 ~elD~eFI~~L~~~~-----------~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~ 124 (173)
.+|..+|++.|+..- ..||++|.- ..-..+...|+.+-.+||.+.|+.+|+-++.
T Consensus 19 ~eFe~~Fl~lLr~~hg~krV~AN~vYnEyI~Dk~H---------vHMNaT~W~sLT~FvkyLgr~G~~~Vdetek 84 (127)
T PF10357_consen 19 EEFEKDFLRLLRRRHGTKRVNANKVYNEYIQDKDH---------VHMNATRWTSLTEFVKYLGREGKCKVDETEK 84 (127)
T ss_dssp HHHHHHHHHHHHHHTSS-EEEHHHHHHHHTTSS-------------GGGSS-SSHHHHHHHHTTTTSEEEEEETT
T ss_pred HHHHHHHHHHHHHhcCCCeechhHHHHHHhcCccc---------eeecccccchHHHHHHHHhhCCeeEeecCCC
Confidence 689999999887532 235554310 0111246899999999999999999875443
No 81
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=36.81 E-value=1.9e+02 Score=22.56 Aligned_cols=47 Identities=21% Similarity=0.445 Sum_probs=31.9
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEe
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRA 153 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~ 153 (173)
...|.+|+.+.+++.|+. .|..=|-..|+-| |.+ ++...+|...|..
T Consensus 15 ~i~tqeeL~~~L~~~G~~---vsqaTIsRdL~el---glv-k~~~~~g~~~Y~~ 61 (146)
T TIGR01529 15 KISTQEELVALLKAEGIE---VTQATVSRDLREL---GAV-KVRDEDGSYVYSL 61 (146)
T ss_pred CCCCHHHHHHHHHHhCCC---cCHHHHHHHHHHc---CCE-EEECCCCcEEEee
Confidence 568999999999999865 5666665544443 444 4444677666765
No 82
>smart00753 PAM PCI/PINT associated module.
Probab=36.81 E-value=1.4e+02 Score=20.34 Aligned_cols=37 Identities=16% Similarity=0.335 Sum_probs=28.5
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEec
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINN 144 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~ 144 (173)
+..+.++|.+- ..++.+++|.+|-.|+.+|.|.-..+
T Consensus 23 ~~i~~~~i~~~--------~~l~~~~vE~~i~~~i~~~~l~~~ID 59 (88)
T smart00753 23 SSISLSDLAKL--------LGLSVPEVEKLVSKAIRDGEISAKID 59 (88)
T ss_pred ceeeHHHHHHH--------hCcCHHHHHHHHHHHHHCCCeEEEEc
Confidence 34678887744 35678899999999999999976553
No 83
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=36.81 E-value=1.4e+02 Score=20.34 Aligned_cols=37 Identities=16% Similarity=0.335 Sum_probs=28.5
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEec
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINN 144 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~ 144 (173)
+..+.++|.+- ..++.+++|.+|-.|+.+|.|.-..+
T Consensus 23 ~~i~~~~i~~~--------~~l~~~~vE~~i~~~i~~~~l~~~ID 59 (88)
T smart00088 23 SSISLSDLAKL--------LGLSVPEVEKLVSKAIRDGEISAKID 59 (88)
T ss_pred ceeeHHHHHHH--------hCcCHHHHHHHHHHHHHCCCeEEEEc
Confidence 34678887744 35678899999999999999976553
No 84
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=36.74 E-value=87 Score=19.12 Aligned_cols=35 Identities=17% Similarity=0.293 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEe
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
.||..++++.+ .+|..-|.+.|+.|+-+|.|+...
T Consensus 20 l~s~~~la~~~--------~vs~~tv~~~l~~L~~~g~i~~~~ 54 (60)
T smart00345 20 LPSERELAAQL--------GVSRTTVREALSRLEAEGLVQRRP 54 (60)
T ss_pred CcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEEec
Confidence 45899988876 457889999999999999998764
No 85
>cd08767 Cdt1_c The C-terminal fold of replication licensing factor Cdt1 is essential for Cdt1 activity and directly interacts with MCM2-7 helicase. Cdt1 is a replication licensing factor in eukaryotes that recruits the Minichromosome Maintenance Complex (MCM2-7) to the Origin Recognition Complex (ORC). The Cdt1 protein is divided into three regions based on sequence comparison and biochemical analyses: the N-terminal region (Cdt1_n) binds DNA in a sequence-, strand-, and conformation-independent manner; the middle winged helix fold (Cdt1_m) binds geminin to inhibit both binding of the MCM complex to origins of replication and DNA; and the C-terminal region (Cdt1_c) is essential for Cdt1 activity and directly interacts with the MCM2-7 helicase. Precise duplication of chromosomal DNA is required for genomic stability during replication. Assembly of replication factors to start DNA replication in eukaryotes must occur only once per cell cycle. To form a pre-replicative complex on replicat
Probab=36.53 E-value=1.4e+02 Score=22.76 Aligned_cols=34 Identities=15% Similarity=0.022 Sum_probs=29.3
Q ss_pred CCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHc
Q psy521 99 LACATPKEVRKFITDLGISKVELSEEDIRTILETLL 134 (173)
Q Consensus 99 ~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv 134 (173)
.+..|.+++...|.+|. ...++.+|++..|+.|.
T Consensus 59 k~~l~~e~l~~kl~~S~--~~~~s~~E~E~~l~LL~ 92 (126)
T cd08767 59 KTVLPLEELVYKLQASY--PSILSRGEVEEHLRLLA 92 (126)
T ss_pred cccccHHHHHHHHHHhC--CCCCCHHHHHHHHHHHH
Confidence 35689999999999976 45679999999999997
No 86
>PF01454 MAGE: MAGE family; InterPro: IPR002190 The first mammalian members of the MAGE (melanoma-associated antigen) gene family were originally described as completely silent in normal adult tissues, with the exception of male germ cells and, for some of them, placenta. By contrast, these genes were expressed in various kinds of tumors. However, other members of the family were recently found to be expressed in normal cells, indicating that the family is larger and more disparate than initially expected. MAGE-like genes have also been identified in non-mammalian species, including Drosophila melanogaster (Fruit fly) and Danio rerio (Zebrafish). Although no MAGE homologous sequences have been identified in Caenorhabditis elegans, Saccharomyces cerevisiae (Baker's yeast) or Schizosaccharomyces pombe (Fission yeast), MAGE sequences have been found in several vegetal species, including Arabidopsis thaliana (Mouse-ear cress) []. The only region of homology shared by all of the members of the family is a stretch of about 200 amino acids which has been named the MAGE conserved domain. The MAGE conserved domain is usually located close to the C-terminal, although it can also be found in a more central position in some proteins. The MAGE conserved domain is generally present as a single copy but it is duplicated in some proteins. It has been proposed that the MAGE conserved domain of MAGE-D proteins might interact with p75 neurotrophin or related receptors [].; PDB: 3NW0_B 2WA0_A 1I4F_C.
Probab=36.46 E-value=1.1e+02 Score=24.43 Aligned_cols=90 Identities=18% Similarity=0.247 Sum_probs=47.6
Q ss_pred cceeEEEeeccCCCcCcccccceecccccH-HHHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHh
Q psy521 36 SKKKVYMLFDLEPDRSLTGGTWYQDQDFEV-EFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDL 114 (173)
Q Consensus 36 ~~rk~Yml~~l~Ps~eiTGG~WYtD~elD~-eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~ 114 (173)
...+.|+|.+.-|...... +=.+.+... ---..|...++.+|.-+ .+.++-++++++|++.
T Consensus 72 ~~~~~yiL~n~L~~~~~~~--~~~~~~~~~~~~~~Gll~~IL~lI~~~----------------g~~i~E~~L~~~L~~l 133 (195)
T PF01454_consen 72 SSSKSYILVNTLPPEYRNE--LSDDSETPSNLAKTGLLMLILSLIFMS----------------GNSISEDDLWKFLRRL 133 (195)
T ss_dssp ---SEEEEEEGCG-S-----------SSH----HHHHHHHHHHHHHHC----------------TT-EEHHHHHHHHHHT
T ss_pred ccCCEEEEEecCCCcccee--ecCCCCCchhHhHhhHHHHHHHHHHhc----------------CCccCHHHHHHHHHhc
Confidence 3466899998887776422 112222221 11233445555555543 1347899999999999
Q ss_pred CCc---eeecCHHHHHHHH-HHHcccCeeEEEe
Q psy521 115 GIS---KVELSEEDIRTIL-ETLLFDGKIEQIN 143 (173)
Q Consensus 115 ~is---~v~Ls~~dI~~iL-~~Lv~Dg~iE~~~ 143 (173)
||. +...---|+..+| +.||=.+-|++..
T Consensus 134 gi~~~~~~~~~g~~~~~~i~~~~vkq~YL~~~k 166 (195)
T PF01454_consen 134 GIDEDEKHPILGMDIKKLILKEFVKQGYLVRYK 166 (195)
T ss_dssp T--TTS-BTTTB--HHHHHHCHHHHCTSE-EEE
T ss_pred CCCccccCccCCCCHHHHHHHHHHHhcCHHhee
Confidence 987 3333333788888 9999999996654
No 87
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=35.58 E-value=92 Score=21.95 Aligned_cols=48 Identities=17% Similarity=0.433 Sum_probs=33.9
Q ss_pred cccccHHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHH
Q psy521 60 DQDFEVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTIL 130 (173)
Q Consensus 60 D~elD~eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL 130 (173)
+-++..+||..|.+.+++++.. -..|+..|=+-.| +...+.+||.-+.
T Consensus 23 ~~~~s~~~i~al~ELv~~q~~~---------------------~a~DLe~FAkHA~--R~tI~~dDV~Ll~ 70 (76)
T PF15630_consen 23 GVEVSPQFIAALTELVYKQLEN---------------------LAKDLEAFAKHAG--RSTINMDDVKLLA 70 (76)
T ss_dssp TSEE-HHHHHHHHHHHHHHHHH---------------------HHHHHHHHHHHTT---SEE-HHHHHHHT
T ss_pred CCccCHHHHHHHHHHHHHHHHH---------------------HHHHHHHHHHhcC--CCeecHHHHHHHh
Confidence 3468889999999999999996 2677777777665 4446777876543
No 88
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=35.30 E-value=1.4e+02 Score=20.23 Aligned_cols=44 Identities=30% Similarity=0.285 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeec
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVS 155 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~ 155 (173)
..|+.||++.+ .++..-|..+|+.|+-.|.|++.. .+| .|+...
T Consensus 20 ~~t~~~ia~~l--------~i~~~tv~r~l~~L~~~g~l~~~~-~~~--~y~l~~ 63 (91)
T smart00346 20 GLTLAELAERL--------GLSKSTAHRLLNTLQELGYVEQDG-QNG--RYRLGP 63 (91)
T ss_pred CcCHHHHHHHh--------CCCHHHHHHHHHHHHHCCCeeecC-CCC--ceeecH
Confidence 47889998877 468889999999999999999853 233 477643
No 89
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=35.19 E-value=73 Score=25.66 Aligned_cols=39 Identities=28% Similarity=0.465 Sum_probs=32.7
Q ss_pred cCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcc--cCee
Q psy521 98 RLACATPKEVRKFITDLGISKVELSEEDIRTILETLLF--DGKI 139 (173)
Q Consensus 98 ~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~--Dg~i 139 (173)
+.++++..++...++..| -.+++++|+.+|+...- ||+|
T Consensus 105 ~dG~Is~~eL~~vl~~lg---e~~~deev~~ll~~~d~d~dG~i 145 (160)
T COG5126 105 HDGYISIGELRRVLKSLG---ERLSDEEVEKLLKEYDEDGDGEI 145 (160)
T ss_pred CCceecHHHHHHHHHhhc---ccCCHHHHHHHHHhcCCCCCceE
Confidence 468999999999999877 47999999999999885 4444
No 90
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=34.46 E-value=1e+02 Score=19.88 Aligned_cols=36 Identities=31% Similarity=0.338 Sum_probs=28.6
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEe
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
+.+|++|+++.+ | .|..-|+.=|+.|+-.|+|.++.
T Consensus 13 ~~~s~~ela~~~---~-----VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 13 GKVSVKELAEEF---G-----VSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred CCEEHHHHHHHH---C-----cCHHHHHHHHHHHHHCCCEEEEc
Confidence 457788877764 2 47778888899999999999985
No 91
>PRK03341 arginine repressor; Provisional
Probab=34.27 E-value=2.5e+02 Score=22.64 Aligned_cols=48 Identities=19% Similarity=0.329 Sum_probs=36.2
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCe-eEEee
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTD-MYRAV 154 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~-~YR~~ 154 (173)
...|-+|+.+.|++.||. .|..-|..-|+-|- +.++++.+|.. .|...
T Consensus 28 ~i~tQ~eL~~~L~~~Gi~---vTQaTiSRDl~eL~----~~Kv~~~~G~~~~Y~lp 76 (168)
T PRK03341 28 SVRSQAELAALLADEGIE---VTQATLSRDLDELG----AVKLRGADGGLGVYVVP 76 (168)
T ss_pred CCccHHHHHHHHHHcCCc---ccHHHHHHHHHHhc----CEeeecCCCCEEEEEec
Confidence 568999999999999975 57777777777774 45666677875 67653
No 92
>TIGR03791 TTQ_mauG tryptophan tryptophylquinone biosynthesis enzyme MauG. Members of this protein family are the tryptophan tryptophylquinone biosynthesis (TTQ) enzyme MauG, as found in Methylobacterium extorquens and related species. This protein is required to complete the maturation of the TTQ cofactor in the methylamine dehydrogenase light (beta) chain.
Probab=33.73 E-value=73 Score=27.82 Aligned_cols=43 Identities=19% Similarity=0.242 Sum_probs=31.8
Q ss_pred CCCcccccCCCCCHHHHHHHHHHhCCc---------eeecCHHHHHHHHHHHc
Q psy521 91 NGPLVAQRLACATPKEVRKFITDLGIS---------KVELSEEDIRTILETLL 134 (173)
Q Consensus 91 ~~p~~~~~~~~~T~~eI~~~I~~~~is---------~v~Ls~~dI~~iL~~Lv 134 (173)
..|+.+. -++.|++|+.+|-++-|.. ...||.+|++.|+.=|-
T Consensus 225 taPY~Hd-G~~~tL~evv~~y~~~g~~~~~~~~~~~~~~Lt~~E~~dLvaFL~ 276 (291)
T TIGR03791 225 EGPFMHD-GQLGSLDAVIDHYEKGGEKRPSISAEMKPFELSEREREDLIAFIE 276 (291)
T ss_pred CCCCCCC-CCcCCHHHHHHHHHccCccccccccccccCCCCHHHHHHHHHHHH
Confidence 4555542 4689999999998875532 24799999999987664
No 93
>cd04755 Commd7 COMM_Domain containing protein 7. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=33.06 E-value=1.2e+02 Score=24.83 Aligned_cols=21 Identities=14% Similarity=0.232 Sum_probs=18.4
Q ss_pred ccccHHHHHHHHHHHHHHHhh
Q psy521 61 QDFEVEFVDVLNQQCYRFLQL 81 (173)
Q Consensus 61 ~elD~eFI~~L~~~~~~~l~~ 81 (173)
+.||.+-...|.+.++.||..
T Consensus 5 n~l~~~~f~~l~~~i~~~L~~ 25 (180)
T cd04755 5 NQLSEQQFSRLTEILFEFLLE 25 (180)
T ss_pred ccCCHHHHHHHHHHHHHHHhc
Confidence 568889999999999999993
No 94
>PRK00441 argR arginine repressor; Provisional
Probab=32.74 E-value=2.4e+02 Score=22.09 Aligned_cols=47 Identities=17% Similarity=0.346 Sum_probs=34.6
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEe
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRA 153 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~ 153 (173)
+..|.+|+.+.+++.|+. .|..=|.+-|+.| .+.++++.+|...|..
T Consensus 17 ~~~~q~eL~~~L~~~G~~---vSqaTisRDl~~L----~lvKv~~~~G~~~Y~l 63 (149)
T PRK00441 17 EIETQEELAEELKKMGFD---VTQATVSRDIKEL----KLIKVLSNDGKYKYAT 63 (149)
T ss_pred CCCcHHHHHHHHHhcCCC---cCHHHHHHHHHHc----CcEEeECCCCCEEEEe
Confidence 567999999999998854 5777777777766 3566666678755654
No 95
>PF00610 DEP: Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP); InterPro: IPR000591 This entry represents the DEP (Dishevelled, Egl-10 and Pleckstrin) domain, a globular domain of about 80 residues that is found in over 50 proteins involved in G-protein signalling pathways. It was named after the three proteins it was initially found in: Dishevelled (Dsh and Dvl), which play a key role in the transduction of the Wg/Wnt signal from the cell surface to the nucleus; it is a segment polarity protein required to establish coherent arrays of polarized cells and segments in embryos, and plays a role in wingless signalling. Egl-10, which regulates G-protein signalling in the central nervous system. Pleckstrin, the major substrate of protein kinase C in platelets; Pleckstrin contains two PH domains flanking the DEP domain. Mammalian regulators of G-protein signalling also contain these domains, and regulate signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving them into their inactive GDP-bound form. It has been proposed that the DEP domain could play a selective role in targeting DEP domain-containing proteins to specific subcellular membranous sites, perhaps even to specific G protein-coupled signaling pathways [, ]. Nuclear magnetic resonance spectroscopy has revealed that the DEP domain comprises a three-helix bundle, a beta-hairpin 'arm' composed of two beta-strands and two short beta-strands in the C-terminal region [].; GO: 0035556 intracellular signal transduction; PDB: 1UHW_A 1V3F_A 2YSR_A 2CSO_A 1W4M_A 2PBI_C 1O7F_A 2BYV_E 1FSH_A 3ML6_D ....
Probab=32.50 E-value=99 Score=20.51 Aligned_cols=45 Identities=22% Similarity=0.323 Sum_probs=36.7
Q ss_pred CCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEec
Q psy521 99 LACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINN 144 (173)
Q Consensus 99 ~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~ 144 (173)
...-|-.|+.+||.+ .......+.++..+|.+.|+-.|.|+.+..
T Consensus 15 ~~~F~G~e~v~WL~~-~~~~~~~~r~eA~~l~q~Ll~~g~i~~v~~ 59 (74)
T PF00610_consen 15 PNCFTGSEAVDWLMD-NFEGFVRDREEAVQLGQELLDHGFIEHVSD 59 (74)
T ss_dssp CCEEEHHHHHHHHHH-TSCTSTSSHHHHHHHHHHHHHCTSEEESSS
T ss_pred CCEeEhHHHHHHHHH-hccccccCHHHHHHHHHHHHHCCCEEECCC
Confidence 455789999999996 223346789999999999999999999863
No 96
>TIGR00014 arsC arsenate reductase (glutaredoxin). composed of two polypeptides, the products of the arsA and arsB genes. The pump alone produces resistance to arsenite and antimonite. This protein, ArsC, catalyzes the reduction of arsenate to arsenite, and thus extends resistance to include arsenate.
Probab=32.34 E-value=63 Score=23.83 Aligned_cols=16 Identities=25% Similarity=0.441 Sum_probs=9.8
Q ss_pred CCCHHHHHHHHHHhCC
Q psy521 101 CATPKEVRKFITDLGI 116 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~i 116 (173)
.+|.+|+.+++...|+
T Consensus 35 p~t~~el~~~l~~~g~ 50 (114)
T TIGR00014 35 PPTKSELEAIFAKLGL 50 (114)
T ss_pred CcCHHHHHHHHHHcCC
Confidence 3666666666666554
No 97
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=32.25 E-value=2.6e+02 Score=22.29 Aligned_cols=47 Identities=28% Similarity=0.358 Sum_probs=37.6
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeecCCc
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVSPYF 158 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~~~~ 158 (173)
+++++|.+-++. .+|.++++..|+.|+==|.|++-. +| .|+.+...+
T Consensus 40 ~d~~~iak~l~p------~is~~ev~~sL~~L~~~gli~k~~--~g--~y~~t~~~l 86 (171)
T PF14394_consen 40 PDPEWIAKRLRP------KISAEEVRDSLEFLEKLGLIKKDG--DG--KYVQTDKSL 86 (171)
T ss_pred CCHHHHHHHhcC------CCCHHHHHHHHHHHHHCCCeEECC--CC--cEEEeccee
Confidence 488888887654 689999999999999999999853 45 488776543
No 98
>PRK14136 recX recombination regulator RecX; Provisional
Probab=32.20 E-value=1.1e+02 Score=27.27 Aligned_cols=49 Identities=12% Similarity=0.268 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeE
Q psy521 69 DVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIE 140 (173)
Q Consensus 69 ~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE 140 (173)
..|....++||..+. =|..||.+.|.+.| +..+.|+++|+-|.-.|.|-
T Consensus 162 ~~lk~kAL~lLSrRe------------------RSe~ELr~KL~kkG-----~~ee~IE~VIerLke~gYLD 210 (309)
T PRK14136 162 RSLKGRALGYLSRRE------------------YSRAELARKLAPYA-----DESDSVEPLLDALEREGWLS 210 (309)
T ss_pred HHHHHHHHHHhhccc------------------ccHHHHHHHHHHcC-----CCHHHHHHHHHHHHHcCCcC
Confidence 467777888888753 37999999999876 57799999999999888774
No 99
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=32.16 E-value=41 Score=21.73 Aligned_cols=15 Identities=20% Similarity=0.636 Sum_probs=10.3
Q ss_pred CHHHHHHHHHHhCCc
Q psy521 103 TPKEVRKFITDLGIS 117 (173)
Q Consensus 103 T~~eI~~~I~~~~is 117 (173)
|+++|.+|++..|..
T Consensus 4 ~~~~V~~WL~~~~l~ 18 (64)
T PF00536_consen 4 SVEDVSEWLKSLGLE 18 (64)
T ss_dssp SHHHHHHHHHHTTGG
T ss_pred CHHHHHHHHHHCCCH
Confidence 567777777776654
No 100
>PF10931 DUF2735: Protein of unknown function (DUF2735); InterPro: IPR021232 Some members in this family of proteins are annotated as glutamine synthetase translation inhibitor however this function can not be confirmed.
Probab=31.93 E-value=11 Score=24.97 Aligned_cols=16 Identities=19% Similarity=0.642 Sum_probs=11.4
Q ss_pred CCcCcccccceecccc
Q psy521 48 PDRSLTGGTWYQDQDF 63 (173)
Q Consensus 48 Ps~eiTGG~WYtD~el 63 (173)
.-..+++|.||+|.-.
T Consensus 31 ~~~~~~~~sWYHeeAI 46 (51)
T PF10931_consen 31 VCPAADSGSWYHEEAI 46 (51)
T ss_pred cCceecCccchHHHHH
Confidence 3456789999987543
No 101
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=31.82 E-value=1.1e+02 Score=25.75 Aligned_cols=48 Identities=17% Similarity=0.224 Sum_probs=38.7
Q ss_pred HHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEe
Q psy521 71 LNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 71 L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
=++.|..+|.++ +.+|+.|+.+.+ ..|.+-|++=|+.|.=.|+|.++.
T Consensus 6 R~~~Il~~l~~~-----------------~~~~~~ela~~l--------~vS~~TiRRdL~~Le~~g~l~r~~ 53 (252)
T PRK10906 6 RHDAIIELVKQQ-----------------GYVSTEELVEHF--------SVSPQTIRRDLNDLAEQNKILRHH 53 (252)
T ss_pred HHHHHHHHHHHc-----------------CCEeHHHHHHHh--------CCCHHHHHHHHHHHHHCCCEEEec
Confidence 356677777663 458899998865 578899999999999999999976
No 102
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=31.59 E-value=2.1e+02 Score=21.50 Aligned_cols=24 Identities=17% Similarity=0.267 Sum_probs=21.0
Q ss_pred cccccHHHHHHHHHHHHHHHhhhh
Q psy521 60 DQDFEVEFVDVLNQQCYRFLQLKR 83 (173)
Q Consensus 60 D~elD~eFI~~L~~~~~~~l~~k~ 83 (173)
..+++..++..|.+..++|..+-.
T Consensus 16 v~~~~~~v~~~Lle~~~ry~~~il 39 (117)
T cd07979 16 ITEYEPRVINQLLEFAYRYTTDVL 39 (117)
T ss_pred CCccCHHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999999754
No 103
>PF14178 YppF: YppF-like protein
Probab=31.54 E-value=1.5e+02 Score=20.23 Aligned_cols=35 Identities=23% Similarity=0.302 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccC
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTILETLLFDG 137 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg 137 (173)
.++.|+++|.+++= ..-+|+..+-+.+++.|.--|
T Consensus 19 ~~~NeLLDFar~~Y-i~gei~i~eYR~lvreLE~~G 53 (60)
T PF14178_consen 19 EDMNELLDFARKLY-IQGEISINEYRNLVRELEANG 53 (60)
T ss_pred ccHHHHHHHHHHHH-HhCcccHHHHHHHHHHHHHhC
Confidence 68999999999864 345899999999999987554
No 104
>cd07288 PX_SNX15 The phosphoinositide binding Phox Homology domain of Sorting Nexin 15. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX15 contains an N-terminal PX domain and a C-terminal Microtubule Interacting and Trafficking (MIT) domain. It plays a role in protein trafficking processes in the endocytic pathway and the trans-Golgi network. The PX domain of SNX15 interacts with the PDGF receptor and is responsible for the membrane association of t
Probab=31.36 E-value=78 Score=23.86 Aligned_cols=44 Identities=14% Similarity=0.255 Sum_probs=31.9
Q ss_pred cccceecccccHHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHH
Q psy521 54 GGTWYQDQDFEVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFIT 112 (173)
Q Consensus 54 GG~WYtD~elD~eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~ 112 (173)
+..|+. .||.+||+.=++...+||+.-.. .| ......++.+|+.
T Consensus 73 ~K~~~g--~f~~~fIeeRR~~Le~fL~~i~~-------~p------~l~~s~~~~~FL~ 116 (118)
T cd07288 73 RAQVFG--RFEAAVIEERRNAAEAMLLFTVN-------IP------ALYNSPQLKEFFR 116 (118)
T ss_pred Cceeec--cCCHHHHHHHHHHHHHHHHHHhC-------Ch------hhcCChHHHHHHh
Confidence 677775 69999999999999999997532 12 2234566777765
No 105
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=31.31 E-value=1.1e+02 Score=17.88 Aligned_cols=14 Identities=21% Similarity=0.425 Sum_probs=9.1
Q ss_pred CCCCHHHHHHHHHH
Q psy521 100 ACATPKEVRKFITD 113 (173)
Q Consensus 100 ~~~T~~eI~~~I~~ 113 (173)
...|.+||.+|+..
T Consensus 15 ~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 15 SGLSKEEIREFLEF 28 (30)
T ss_dssp TT--HHHHHHHHHH
T ss_pred cCCCHHHHHHHHHh
Confidence 35788888888864
No 106
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=31.30 E-value=1.8e+02 Score=20.25 Aligned_cols=30 Identities=13% Similarity=0.158 Sum_probs=24.8
Q ss_pred CCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHH
Q psy521 99 LACATPKEVRKFITDLGISKVELSEEDIRTILETL 133 (173)
Q Consensus 99 ~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~L 133 (173)
.+..+.+++.+.++..| ++.++++.++...
T Consensus 24 ~G~Is~~el~~~l~~~~-----~~~~ev~~i~~~~ 53 (96)
T smart00027 24 DGTVTGAQAKPILLKSG-----LPQTLLAKIWNLA 53 (96)
T ss_pred CCeEeHHHHHHHHHHcC-----CCHHHHHHHHHHh
Confidence 36799999999999865 5788999998864
No 107
>PRK05066 arginine repressor; Provisional
Probab=31.14 E-value=2.7e+02 Score=22.10 Aligned_cols=49 Identities=10% Similarity=0.212 Sum_probs=30.8
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEee
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAV 154 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~ 154 (173)
..-|=+|+.+.+++.|+..| |..=|-+-|+-| .+.++++.+|...|...
T Consensus 22 ~I~tQeeL~~~L~~~Gi~~v--TQATiSRDikeL----~lvKv~~~~G~~~Y~l~ 70 (156)
T PRK05066 22 KFGSQGEIVTALQEQGFDNI--NQSKVSRMLTKF----GAVRTRNAKMEMVYCLP 70 (156)
T ss_pred CCCCHHHHHHHHHHCCCCee--cHHHHHHHHHHc----CCEEeeCCCCCEEEEeC
Confidence 45789999999999997732 333332323322 56667666787667653
No 108
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=31.11 E-value=1.8e+02 Score=20.09 Aligned_cols=48 Identities=17% Similarity=0.288 Sum_probs=31.2
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEee
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAV 154 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~ 154 (173)
...|=+|+.+.|.+.||. .|..-|-.-|+-| .+.++++.+|...|.+.
T Consensus 18 ~i~sQ~eL~~~L~~~Gi~---vTQaTiSRDLkeL----~~vKv~~~~g~~~Y~l~ 65 (70)
T PF01316_consen 18 EISSQEELVELLEEEGIE---VTQATISRDLKEL----GAVKVPDGNGKYRYVLP 65 (70)
T ss_dssp ---SHHHHHHHHHHTT-T-----HHHHHHHHHHH----T-EEEECTTSSEEEE-T
T ss_pred CcCCHHHHHHHHHHcCCC---cchhHHHHHHHHc----CcEEeeCCCCCEEEEec
Confidence 457999999999999965 5666666667766 56777777787677654
No 109
>PF01885 PTS_2-RNA: RNA 2'-phosphotransferase, Tpt1 / KptA family; InterPro: IPR002745 The final step of tRNA splicing in Saccharomyces cerevisiae (Baker's yeast) requires 2'-phosphotransferase (Tpt1) to transfer the 2'-phosphate from ligated tRNA to NAD, producing mature tRNA and ADP ribose-1' '-2' '-cyclic phosphate. Yeast and Mus musculus (Mouse) Tpt1 protein and bacterial KptA protein can catalyze the conversion of the generated intermediate to both product and the original substrate, these enzymes likely use the same reaction mechanism. Step 1 of this reaction is strikingly similar to the ADP-ribosylation of proteins catalyzed by a number of bacterial toxins. KptA, a functional Tpt1 protein homologue from Escherichia coli is strikingly similar to yeast Tpt1 in its kinetic parameters, although E. coli is not known to have a 2'-phosphorylated RNA substrate [,].; GO: 0016772 transferase activity, transferring phosphorus-containing groups, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation; PDB: 1WFX_A.
Probab=30.97 E-value=55 Score=26.67 Aligned_cols=34 Identities=24% Similarity=0.332 Sum_probs=23.5
Q ss_pred cccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHH
Q psy521 96 AQRLACATPKEVRKFITDLGISKVELSEEDIRTILET 132 (173)
Q Consensus 96 ~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~ 132 (173)
.+..+|+.+++++++++..+. .+|.+||++++++
T Consensus 27 ~d~~G~v~v~dLL~~~~~~~~---~~t~~~i~~vV~~ 60 (186)
T PF01885_consen 27 MDPDGWVSVDDLLRALRFKGL---WVTEEDIREVVET 60 (186)
T ss_dssp --TT--EEHHHHHHHHHHT-T---T--HHHHHHHHHH
T ss_pred cCCCCCEeHHHHHHHHHHcCC---CCCHHHHHHHHhh
Confidence 345689999999999998643 3799999999988
No 110
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=30.85 E-value=1e+02 Score=22.89 Aligned_cols=46 Identities=17% Similarity=0.301 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeecC
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVSP 156 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~~ 156 (173)
..|..||++.+ .++..-+.++|+.|+=.|.|+.....+| .|+..+.
T Consensus 25 ~~s~~eia~~l--------~is~~~v~~~l~~L~~~Gli~~~~g~~g--gy~l~~~ 70 (130)
T TIGR02944 25 PYSAAEIAEQT--------GLNAPTVSKILKQLSLAGIVTSKRGVEG--GYTLARA 70 (130)
T ss_pred CccHHHHHHHH--------CcCHHHHHHHHHHHHHCCcEEecCCCCC--ChhhcCC
Confidence 47888887754 4688899999999999999987653344 3666543
No 111
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=30.61 E-value=2.1e+02 Score=22.50 Aligned_cols=36 Identities=17% Similarity=0.146 Sum_probs=30.1
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEe
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
+..|-+||++-+ .++..+|+.+|..|.-+|.|...+
T Consensus 27 ~~~tdEeLa~~L--------gi~~~~VRk~L~~L~e~~Lv~~~r 62 (158)
T TIGR00373 27 GEFTDEEISLEL--------GIKLNEVRKALYALYDAGLADYKR 62 (158)
T ss_pred CCCCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCceeee
Confidence 457888888765 468999999999999999997554
No 112
>cd07284 PX_SNX7 The phosphoinositide binding Phox Homology domain of Sorting Nexin 7. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX7 harbors a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain, similar to the sorting nexins SNX1-2, SNX4-6, SNX8, SNX30,
Probab=30.59 E-value=75 Score=23.88 Aligned_cols=22 Identities=18% Similarity=0.436 Sum_probs=19.8
Q ss_pred ccccHHHHHHHHHHHHHHHhhh
Q psy521 61 QDFEVEFVDVLNQQCYRFLQLK 82 (173)
Q Consensus 61 ~elD~eFI~~L~~~~~~~l~~k 82 (173)
+.||.+||+.=++...+||++-
T Consensus 76 ~~~~~~fie~Rr~~Le~FL~ri 97 (116)
T cd07284 76 ERFNEDFIETRRKALHKFLNRI 97 (116)
T ss_pred ccCCHHHHHHHHHHHHHHHHHH
Confidence 6699999999999999999985
No 113
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=30.01 E-value=83 Score=23.73 Aligned_cols=47 Identities=15% Similarity=0.193 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeecCC
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVSPY 157 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~~~ 157 (173)
.+|.++|.+-+ .++..-+++||+.|.--|.|+..+...| .|+..+.+
T Consensus 25 ~~s~~~ia~~~--------~ip~~~l~kil~~L~~~glv~s~~G~~G--gy~l~~~~ 71 (135)
T TIGR02010 25 PVTLADISERQ--------GISLSYLEQLFAKLRKAGLVKSVRGPGG--GYQLGRPA 71 (135)
T ss_pred cCcHHHHHHHH--------CcCHHHHHHHHHHHHHCCceEEEeCCCC--CEeccCCH
Confidence 47899987643 5788999999999999999998765455 48887644
No 114
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=29.93 E-value=2.3e+02 Score=21.02 Aligned_cols=55 Identities=25% Similarity=0.230 Sum_probs=42.9
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEec-CCC---CeeEEeecC
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINN-IDG---TDMYRAVSP 156 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~-~~g---~~~YR~~~~ 156 (173)
.+--+|.+.|.....---..+..-|-.+|+.|+-+|.|+.... .++ ...|+.+..
T Consensus 23 ~~Gyei~k~~~~~~~~~~~~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~ 81 (138)
T COG1695 23 SHGYEIIKELEELSGGLWEPSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEK 81 (138)
T ss_pred chHHHHHHHHHHHcCCCCcCCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHH
Confidence 5677899999987655457899999999999999999998743 233 467887743
No 115
>cd01995 ExsB ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large ( 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown
Probab=29.74 E-value=21 Score=27.52 Aligned_cols=7 Identities=43% Similarity=1.236 Sum_probs=6.5
Q ss_pred cCccCCC
Q psy521 166 SPCGVCP 172 (173)
Q Consensus 166 ~PCG~CP 172 (173)
.|||.||
T Consensus 152 ~~CG~C~ 158 (169)
T cd01995 152 KHCGECD 158 (169)
T ss_pred CCCCCCH
Confidence 7999998
No 116
>KOG0833|consensus
Probab=29.70 E-value=17 Score=29.74 Aligned_cols=8 Identities=75% Similarity=1.738 Sum_probs=7.3
Q ss_pred cccCccCC
Q psy521 164 STSPCGVC 171 (173)
Q Consensus 164 ~~~PCG~C 171 (173)
-..|||+|
T Consensus 101 f~tPCG~C 108 (173)
T KOG0833|consen 101 FTTPCGVC 108 (173)
T ss_pred cCCCcHHH
Confidence 68999999
No 117
>PLN02701 alpha-mannosidase
Probab=29.27 E-value=2.5e+02 Score=29.09 Aligned_cols=106 Identities=17% Similarity=0.264 Sum_probs=60.0
Q ss_pred eeccccCCCCCCceeeeccccc-------ccceeEEEeeccCCCcCcccccce-ecccccHHHHHHHHHHHHHHHhhhhh
Q psy521 13 LFDLEPDRSLTGGTWYQDQDFE-------ASKKKVYMLFDLEPDRSLTGGTWY-QDQDFEVEFVDVLNQQCYRFLQLKRE 84 (173)
Q Consensus 13 ~~~~~p~~~~tgg~~~~d~sV~-------~~~rk~Yml~~l~Ps~eiTGG~WY-tD~elD~eFI~~L~~~~~~~l~~k~~ 84 (173)
+|+.-|=.+..||.|++-=.+. ....++ ++.|....==| || |=+|+=..-+..+...+...|.+...
T Consensus 8 ~y~~~~f~~~~gg~w~qg~~~~y~~~~~~~~~l~V----hlVpHSH~D~g-Wl~T~~eyy~~~~~~ild~vv~~L~~dp~ 82 (1050)
T PLN02701 8 LYDRIEFLDKDGGAWKQGWRVKYRGDEWDREKLKV----FVVPHSHNDPG-WILTVEEYYQEQSRHILDTIVESLSKDPR 82 (1050)
T ss_pred hhhcCcccCCCCCeeccccceeecccccCCcceEE----EEeCCCCCCHH-HcCcHHHHHHHHHHHHHHHHHHHHHhCcC
Confidence 5777777899999999944333 233444 45555555333 88 43443222333444444444544211
Q ss_pred hccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEe
Q psy521 85 KTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 85 ~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
+..-++-..=+..|+++.. .+.++.++.||-+|++|-+.
T Consensus 83 ------------rkFi~~E~~fl~~Ww~~~~--------pe~~~~vk~LV~~GrLE~vg 121 (1050)
T PLN02701 83 ------------RKFIWEEMSYLERWWRDAS--------PSKKEAFTKLVKNGQLEIVG 121 (1050)
T ss_pred ------------cceeeccHHHHHHHHHhcC--------HHHHHHHHHHHHcCCEEEEC
Confidence 1112232222556775522 37788899999999999874
No 118
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=29.22 E-value=1.7e+02 Score=19.85 Aligned_cols=51 Identities=18% Similarity=0.215 Sum_probs=34.1
Q ss_pred ccHHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCc
Q psy521 63 FEVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGIS 117 (173)
Q Consensus 63 lD~eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is 117 (173)
.....+|.|.+...+||++-...+..... .....-|++.+|...+.+.||.
T Consensus 24 ~~~~al~~Ltdi~~~yl~~l~~~~~~~ae----~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 24 ASPSALDTLTDILQRYLQELGRTAKRYAE----HAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHH----HcCCCCCCHHHHHHHHHHhCCC
Confidence 45678999999999999874432211100 0112457899999999998873
No 119
>PRK14135 recX recombination regulator RecX; Provisional
Probab=29.12 E-value=1.7e+02 Score=24.42 Aligned_cols=59 Identities=22% Similarity=0.383 Sum_probs=44.0
Q ss_pred cccccHHHHHHHHHH---------HHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHH
Q psy521 60 DQDFEVEFVDVLNQQ---------CYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTIL 130 (173)
Q Consensus 60 D~elD~eFI~~L~~~---------~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL 130 (173)
+.++|.+.++.|... +++||..+ .-|..||.+.|.+.| ++.+.|+.+|
T Consensus 39 g~~l~~~~~~~i~~~~~~~~a~~~Al~~L~~r------------------~~s~~el~~kL~~kg-----~~~~~Ie~vl 95 (263)
T PRK14135 39 GKELDEEDLEEIQYADQVSKGKNLALYYLSYQ------------------MRTEKEVRDYLKKHE-----ISEEIISEVI 95 (263)
T ss_pred CCcCCHHHHHHHHHHHHHHHHHHHHHHHhhhc------------------cccHHHHHHHHHHCC-----CCHHHHHHHH
Confidence 678888888877643 34444443 246799999999877 4679999999
Q ss_pred HHHcccCeeEE
Q psy521 131 ETLLFDGKIEQ 141 (173)
Q Consensus 131 ~~Lv~Dg~iE~ 141 (173)
+-|.-.|.|.-
T Consensus 96 ~~l~~~~~ldD 106 (263)
T PRK14135 96 DKLKEEKYIDD 106 (263)
T ss_pred HHHHHcCCCCH
Confidence 99988887753
No 120
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=29.05 E-value=1.7e+02 Score=24.40 Aligned_cols=36 Identities=28% Similarity=0.345 Sum_probs=30.7
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEe
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
+.++.+|+++.+ .+|..-|+.-|+.|.-.|+|.+..
T Consensus 17 ~~~~~~eLa~~l--------~VS~~TiRRdL~~L~~~~~l~r~~ 52 (240)
T PRK10411 17 TSLTTEALAEQL--------NVSKETIRRDLNELQTQGKILRNH 52 (240)
T ss_pred CCCcHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEec
Confidence 468999999988 378888999999999999998853
No 121
>PF11303 DUF3105: Protein of unknown function (DUF3105); InterPro: IPR021454 Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known.
Probab=29.04 E-value=1.1e+02 Score=23.59 Aligned_cols=62 Identities=18% Similarity=0.291 Sum_probs=37.9
Q ss_pred cccccee-cccccHHHHHHHHHHHHHHHhhhhhhccCCCCCCcccc------cCCCCCHHHHHHHHHHh
Q psy521 53 TGGTWYQ-DQDFEVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQ------RLACATPKEVRKFITDL 114 (173)
Q Consensus 53 TGG~WYt-D~elD~eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~------~~~~~T~~eI~~~I~~~ 114 (173)
=|+.|++ +-.++.+-|+.|+...-.+...---........|+... ....++...|.+||++-
T Consensus 49 HGaV~i~Y~p~~~~~~v~~L~~l~~~~~~~~visP~~~~~~pialtaWg~~l~~~~~d~~~i~~Fi~~~ 117 (130)
T PF11303_consen 49 HGAVWITYDPCLPPDQVAKLKALAKSCLPYVVISPYPGLDRPIALTAWGRQLKLDSADDPRIKQFIRKY 117 (130)
T ss_pred cCcEEEEECCCCCHHHHHHHHHHHhccCCcEEEecCCCCCCCEEEeecCCEeecCcCCHHHHHHHHHHH
Confidence 5887774 44499999999999777654421111111223444321 23567888999999864
No 122
>PF13565 HTH_32: Homeodomain-like domain
Probab=28.56 E-value=1.7e+02 Score=19.33 Aligned_cols=29 Identities=24% Similarity=0.350 Sum_probs=16.1
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHH
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTIL 130 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL 130 (173)
-|+.+|+++|.+..-.++.+|..-|..+|
T Consensus 49 wt~~~i~~~L~~~~g~~~~~S~~tv~R~L 77 (77)
T PF13565_consen 49 WTPREIAEYLEEEFGISVRVSRSTVYRIL 77 (77)
T ss_pred CCHHHHHHHHHHHhCCCCCccHhHHHHhC
Confidence 56777777777642222244655555543
No 123
>cd07285 PX_SNX9 The phosphoinositide binding Phox Homology domain of Sorting Nexin 9. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX9, also known as SH3PX1, is a cytosolic protein that interacts with proteins associated with clathrin-coated pits such as Cdc-42-associated tyrosine kinase 2 (ACK2). It contains an N-terminal Src Homology 3 (SH3) domain, a PX domain, and a C-terminal Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature. T
Probab=28.51 E-value=88 Score=24.12 Aligned_cols=39 Identities=15% Similarity=0.301 Sum_probs=28.1
Q ss_pred cccHHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHH
Q psy521 62 DFEVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITD 113 (173)
Q Consensus 62 elD~eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~ 113 (173)
.||.+||+.=++...+||++-.. .| -.....++..||.-
T Consensus 69 ~f~~~FIe~Rr~~Le~FL~ri~~-------hP------~L~~~~~l~~FL~~ 107 (126)
T cd07285 69 RFEEEFIKMRMERLQAWMTRMCR-------HP------VISESEVFQQFLNF 107 (126)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHc-------Cc------CcCCCcHHHHHhCC
Confidence 59999999999999999998532 22 22344667777764
No 124
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=28.41 E-value=1.5e+02 Score=18.32 Aligned_cols=44 Identities=20% Similarity=0.177 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEee
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAV 154 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~ 154 (173)
.+..||++.+ .++...|...|+.|+=.|.|...... ....|+..
T Consensus 21 ~~~~ei~~~~--------~i~~~~i~~~l~~L~~~g~i~~~~~~-~~~~~~~~ 64 (78)
T cd00090 21 LTVSELAERL--------GLSQSTVSRHLKKLEEAGLVESRREG-RRVYYSLT 64 (78)
T ss_pred cCHHHHHHHH--------CcCHhHHHHHHHHHHHCCCeEEEEec-cEEEEEeC
Confidence 6777877754 35778899999999999999987532 23456665
No 125
>cd04371 DEP DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction.
Probab=28.14 E-value=1.5e+02 Score=19.74 Aligned_cols=41 Identities=22% Similarity=0.348 Sum_probs=35.5
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEe
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
..-|-.|+.+||.+..-. .+.++..++.+.|+--|.|+.+.
T Consensus 27 ~~F~G~e~v~WL~~~~~~---~~r~ea~~~~~~ll~~g~i~~v~ 67 (81)
T cd04371 27 NCFTGSELVDWLLDNLEA---ITREEAVELGQALLKHGLIHHVS 67 (81)
T ss_pred ceeEcHHHHHHHHHhCCC---CCHHHHHHHHHHHHHCCCEEEeC
Confidence 445789999999987633 89999999999999999999985
No 126
>PRK12411 cytidine deaminase; Provisional
Probab=27.82 E-value=19 Score=27.82 Aligned_cols=7 Identities=57% Similarity=1.792 Sum_probs=6.0
Q ss_pred ccCccCC
Q psy521 165 TSPCGVC 171 (173)
Q Consensus 165 ~~PCG~C 171 (173)
-.|||.|
T Consensus 83 ~sPCG~C 89 (132)
T PRK12411 83 VPPCGAC 89 (132)
T ss_pred cCCchhH
Confidence 3799999
No 127
>cd04448 DEP_PIKfyve DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) PIKfyve-like proteins. PIKfyve contains N-terminal Fyve finger and DEP domains, a central chaperonin-like domain and a C-terminal PIPK (phosphatidylinositol phosphate kinase) domain. PIKfyve-like proteins are important phosphatidylinositol (3)-monophosphate (PtdIns(3)P)-5-kinases, producing PtdIns(3,5)P2, which plays a major role in multivesicular body (MVB) sorting and control of retrograde traffic from the vacuole back to the endosome and/or Golgi. PIKfyve itself has been shown to be play a role in regulating early-endosome-to-trans-Golgi network (TGN) retrograde trafficking.
Probab=27.79 E-value=1.8e+02 Score=20.47 Aligned_cols=52 Identities=23% Similarity=0.319 Sum_probs=40.1
Q ss_pred cCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEec----CCCCeeEE
Q psy521 98 RLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINN----IDGTDMYR 152 (173)
Q Consensus 98 ~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~----~~g~~~YR 152 (173)
+.+.-+-.|+.+||-+.+. ..+-++...+.+.|.-.|.|+-+.+ .|+...||
T Consensus 25 y~~cF~GselVdWL~~~~~---~~~R~eAv~~gq~Ll~~g~i~hV~~~~~F~D~~~~Yr 80 (81)
T cd04448 25 YTNCILGKELVNWLIRQGK---AATRVQAIAIGQALLDAGWIECVSDDDLFRDEYALYK 80 (81)
T ss_pred cCcccChHHHHHHHHHcCC---CCCHHHHHHHHHHHHHCCCEEecCCCCccccCccccC
Confidence 3455678999999998763 2788999999999999999999864 23444455
No 128
>PF13811 DUF4186: Domain of unknown function (DUF4186)
Probab=27.67 E-value=2.8e+02 Score=21.20 Aligned_cols=64 Identities=23% Similarity=0.408 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHhhhhhhccCCC--------CCCcccccCCCCC-HHH-HHHHHHHhCCce-eecCHHHHHHHHHHHc
Q psy521 68 VDVLNQQCYRFLQLKREKTANNT--------NGPLVAQRLACAT-PKE-VRKFITDLGISK-VELSEEDIRTILETLL 134 (173)
Q Consensus 68 I~~L~~~~~~~l~~k~~~~~~~~--------~~p~~~~~~~~~T-~~e-I~~~I~~~~is~-v~Ls~~dI~~iL~~Lv 134 (173)
.+.+++...+||.++-.+|.... ..|....++.-+| +.. +.+| -+|.+ .+||+++++-|++++.
T Consensus 32 ~~~I~~Ha~dfi~~RLapA~p~nDGkQTPmrGHPVFiAQHATatCCRgCL~KW---H~Ip~gr~Lt~~eq~yiv~vi~ 106 (111)
T PF13811_consen 32 LDTIREHARDFIAKRLAPAQPPNDGKQTPMRGHPVFIAQHATATCCRGCLEKW---HGIPKGRELTEEEQAYIVDVIM 106 (111)
T ss_pred HHHHHHHHHHHHHHHhCccCCCCCCCCCCCCCCCeeeecCCCccchHHHHHHH---hCCCCCCCCCHHHHHHHHHHHH
Confidence 46788889999999887654422 3344444554444 333 3333 35664 6899999999999874
No 129
>TIGR01201 HU_rel DNA-binding protein, histone-like, putative. This model describes a set of proteins related to but longer than DNA-binding protein HU. Its distinctive domain architecture compared to HU and related histone-like DNA-binding proteins justifies the designation as superfamily. Members include, so far, one from Bacteroides fragilis, a gut bacterium, and ten from Porphyromonas gingivalis, an oral anaerobe.
Probab=27.34 E-value=1e+02 Score=24.01 Aligned_cols=40 Identities=25% Similarity=0.439 Sum_probs=28.4
Q ss_pred CCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHH-------cccCeeEEE
Q psy521 99 LACATPKEVRKFITDLGISKVELSEEDIRTILETL-------LFDGKIEQI 142 (173)
Q Consensus 99 ~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~L-------v~Dg~iE~~ 142 (173)
.+-.|.+++.+.|.+.. .+|..||+.+|+.| +-+|...++
T Consensus 28 ~~~mt~~el~~~Ia~~s----~~s~~dv~~vl~~l~~~i~~~L~~G~~V~L 74 (145)
T TIGR01201 28 SGVIDFEEIAELIAEES----SLSPGDVKGIIDRLAYVLRRELANGKTVRL 74 (145)
T ss_pred CCCcCHHHHHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHHhCCCeEEe
Confidence 34689999999998742 57888888777765 345555555
No 130
>cd03034 ArsC_ArsC Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the detoxification of arsenic, using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX). ArsC contains a single catalytic cysteine, within a thioredoxin fold, that forms a covalent thiolate-As(V) intermediate, which is reduced by GRX through a mixed GSH-arsenate intermediate. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases.
Probab=27.33 E-value=85 Score=23.02 Aligned_cols=15 Identities=33% Similarity=0.609 Sum_probs=10.1
Q ss_pred CCCHHHHHHHHHHhC
Q psy521 101 CATPKEVRKFITDLG 115 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~ 115 (173)
.+|.+|+.+|+...|
T Consensus 35 ~~t~~el~~~l~~~~ 49 (112)
T cd03034 35 PPTAAELRELLAKLG 49 (112)
T ss_pred CcCHHHHHHHHHHcC
Confidence 367777777777666
No 131
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=27.32 E-value=1e+02 Score=21.70 Aligned_cols=30 Identities=17% Similarity=0.329 Sum_probs=24.9
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHH
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETL 133 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~L 133 (173)
.|=.+.+|++++.+.+ .+|..+++.|.+-|
T Consensus 37 ~yedl~diy~~V~~K~----~fS~sEm~aI~~EL 66 (71)
T PF06569_consen 37 KYEDLKDIYEMVMSKD----SFSPSEMQAIAEEL 66 (71)
T ss_pred hHHHHHHHHHHHHhcc----CCCHHHHHHHHHHH
Confidence 4567889999998755 89999999998876
No 132
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=27.19 E-value=4.2e+02 Score=23.89 Aligned_cols=80 Identities=16% Similarity=0.327 Sum_probs=48.0
Q ss_pred cccccceecccccHHHHHHHHHHHH----------HHHhhhhhhccCCCCCCccc--------ccCCCCCHHHHHHHHHH
Q psy521 52 LTGGTWYQDQDFEVEFVDVLNQQCY----------RFLQLKREKTANNTNGPLVA--------QRLACATPKEVRKFITD 113 (173)
Q Consensus 52 iTGG~WYtD~elD~eFI~~L~~~~~----------~~l~~k~~~~~~~~~~p~~~--------~~~~~~T~~eI~~~I~~ 113 (173)
..+||.|...=.|.||++.+.+.+. +.|..-.. ......|++- ...+.|..+.|.+.|++
T Consensus 272 ~~~GPlW~G~l~d~~fl~~~~~~~~~~~~~~~~~~~ll~~~~~--E~~~~~p~~y~~~~i~~~~k~~~p~~~~~~~~L~~ 349 (382)
T PRK04338 272 GTAGPLWLGPLHDKEFVEEMLEEAAKELGTSKKALKLLKTIEE--ESKLDTPTFYDLHELAKKLKVSAPPMDEILEALRE 349 (382)
T ss_pred eeccccccCccCCHHHHHHHHHHhhhhccchHHHHHHHHHHHh--ccCCCCCcEEcHHHHHhhcCCCCCCHHHHHHHHHH
Confidence 4688999999999999999987652 11111100 0011233211 12357888888888888
Q ss_pred hCCc-----------eeecCHHHHHHHHHHH
Q psy521 114 LGIS-----------KVELSEEDIRTILETL 133 (173)
Q Consensus 114 ~~is-----------~v~Ls~~dI~~iL~~L 133 (173)
.|.. +++-..++|..+++.+
T Consensus 350 ~Gy~as~tH~~p~~iKTdAp~~~i~~i~~~~ 380 (382)
T PRK04338 350 AGFEASRTHFSPTGFKTDAPYDEIKEAIKSL 380 (382)
T ss_pred CCCeEEeeEECCCcEecCCCHHHHHHHHHHh
Confidence 7632 2445566666666543
No 133
>cd03035 ArsC_Yffb Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine suggest that it is likely to function as a glutathione (GSH)-dependent thiol reductase. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from GSH via glutaredoxin, through a single catalytic cysteine.
Probab=27.15 E-value=90 Score=22.79 Aligned_cols=43 Identities=7% Similarity=0.178 Sum_probs=26.2
Q ss_pred CCCHHHHHHHHHHhCCce---------eecCHHH-----HHHHHHHHcccCeeEEEe
Q psy521 101 CATPKEVRKFITDLGISK---------VELSEED-----IRTILETLLFDGKIEQIN 143 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~---------v~Ls~~d-----I~~iL~~Lv~Dg~iE~~~ 143 (173)
.+|.+|+.+++.+.|+.. -+|..++ -+++++.|+-+..+.+++
T Consensus 35 p~s~~eL~~~l~~~g~~~li~~~~~~yk~l~l~~~~~~s~~e~~~~l~~~p~LikRP 91 (105)
T cd03035 35 GLDAATLERWLAKVGWETLLNKRGTTWRKLDDAQKAALDAAKAIALMLEHPSLIKRP 91 (105)
T ss_pred CCCHHHHHHHHHHhChHHHHccCchHHHhCChhhhccCCHHHHHHHHHhCcCeeecc
Confidence 478888888887776321 1233322 255677777777777653
No 134
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.99 E-value=77 Score=22.26 Aligned_cols=33 Identities=9% Similarity=0.258 Sum_probs=26.1
Q ss_pred ccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHH
Q psy521 97 QRLACATPKEVRKFITDLGISKVELSEEDIRTILETL 133 (173)
Q Consensus 97 ~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~L 133 (173)
....|-.+.+|+++|++.. .+|..+++.|-+.|
T Consensus 34 d~~~~edLtdiy~mvkkke----nfSpsEmqaiA~eL 66 (71)
T COG4840 34 DNANYEDLTDIYDMVKKKE----NFSPSEMQAIADEL 66 (71)
T ss_pred ccccHHHHHHHHHHHHHhc----cCCHHHHHHHHHHH
Confidence 3445667889999999866 78899999888776
No 135
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=26.75 E-value=1e+02 Score=23.11 Aligned_cols=30 Identities=27% Similarity=0.410 Sum_probs=24.3
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHH
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETL 133 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~L 133 (173)
.-|.+|+...|-+. +..++.+++++||+.|
T Consensus 78 P~~~dElrai~~~~---~~~~~~e~l~~ILd~l 107 (112)
T PRK14981 78 PETRDELRAIFAKE---RYTLSPEELDEILDIV 107 (112)
T ss_pred CCCHHHHHHHHHHh---ccCCCHHHHHHHHHHH
Confidence 36788888888775 4579999999999976
No 136
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=26.72 E-value=55 Score=20.45 Aligned_cols=13 Identities=31% Similarity=0.882 Sum_probs=6.9
Q ss_pred CHHHHHHHHHHhC
Q psy521 103 TPKEVRKFITDLG 115 (173)
Q Consensus 103 T~~eI~~~I~~~~ 115 (173)
|+++|.+|++..|
T Consensus 3 ~~~~V~~wL~~~~ 15 (63)
T cd00166 3 SPEDVAEWLESLG 15 (63)
T ss_pred CHHHHHHHHHHcC
Confidence 4555555555544
No 137
>PHA02046 hypothetical protein
Probab=26.58 E-value=1.7e+02 Score=21.87 Aligned_cols=32 Identities=22% Similarity=0.267 Sum_probs=25.7
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHHHHH
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTILETL 133 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~L 133 (173)
+...-|.+|+++.+|+.-.-+.++++.|=+.|
T Consensus 38 ad~aa~~KFLKDNnItcdpaD~~~m~~Lr~e~ 69 (99)
T PHA02046 38 ADKAAIAKFLKDNEITCDPADTINIDRLREEF 69 (99)
T ss_pred HHHHHHHHHhhcCCcccCcccHHHHHHHHHHH
Confidence 45778999999999998777888888776654
No 138
>PF08970 Sda: Sporulation inhibitor A; InterPro: IPR015064 Members of this protein group contain two antiparallel alpha helices that are linked by a highly structured inter-helix loop to form a helical hairpin; the structure is stabilised by numerous hydrophobic and electrostatic interactions. These sporulation inhibitors are antikinases that bind to the histidine kinase KinA phosphotransfer domain and act as a molecular barricade that inhibit productive interaction between the ATP binding site and the phosphorylatable KinA His residue. This results in the inhibition of sporulation (by preventing phosphorylation of spo0A) []. ; PDB: 3FYR_B 1PV0_A.
Probab=26.52 E-value=67 Score=20.81 Aligned_cols=18 Identities=17% Similarity=0.569 Sum_probs=12.5
Q ss_pred cccccHHHHHHHHHHHHH
Q psy521 60 DQDFEVEFVDVLNQQCYR 77 (173)
Q Consensus 60 D~elD~eFI~~L~~~~~~ 77 (173)
+-.+|.+||..|.+-+.+
T Consensus 18 el~L~~dFI~Ll~~Ei~r 35 (46)
T PF08970_consen 18 ELNLDPDFIRLLEEEIQR 35 (46)
T ss_dssp HTT--HHHHHHHHHHHHH
T ss_pred HhCCCHHHHHHHHHHHHH
Confidence 467899999999887653
No 139
>cd04450 DEP_RGS7-like DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in RGS (regulator of G-protein signaling) proteins of the subfamily R7. This subgroup contains RGS7, RGS6, RGS9 and RGS11. They share a common domain architecture, containing, beside the RGS domain, a DEP domain and a GGL (G-protein gamma subunit-like ) domain. RGS proteins are GTPase-activating (GAP) proteins of heterotrimeric G proteins by increasing the rate of GTP hydrolysis of the alpha subunit. The fungal homologs, like yeast Sst2, share a related common domain architecture, containing RGS and DEP domains. Sst2 has been identified as the principal regulator of mating pheromone signaling and recently the DEP domain of Sst2 has been shown to be necessary and sufficient to mediate receptor interaction.
Probab=26.45 E-value=2.3e+02 Score=19.89 Aligned_cols=52 Identities=15% Similarity=0.213 Sum_probs=42.1
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecC-----CCCeeEEee
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNI-----DGTDMYRAV 154 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~-----~g~~~YR~~ 154 (173)
..-|-.++.+||-+.. . ..+.++...|-+.|+--|.|+.+... ++...||..
T Consensus 27 ~~F~G~~~v~WL~~~~--~-~~~~~EA~~~~~~ll~~gli~~V~~~~~~~~~~~~~yr~~ 83 (88)
T cd04450 27 YAFTGKAIVQWLMDCT--D-VVDPSEALEIAALFVKYGLITPVSDHRSLLKPDETLYRFQ 83 (88)
T ss_pred ceeEhHHHHHHHHHCC--C-CCCHHHHHHHHHHHHHCCCEEEecCCcccccCCCceEecc
Confidence 4567899999999854 3 38999999999999999999999742 344678865
No 140
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=25.93 E-value=1.8e+02 Score=21.15 Aligned_cols=30 Identities=20% Similarity=0.358 Sum_probs=25.5
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHH
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETL 133 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~L 133 (173)
..|++|..+|=++-| +.+|.++.+.|++.|
T Consensus 14 ~iT~~eLlkyskqy~---i~it~~QA~~I~~~l 43 (85)
T PF11116_consen 14 NITAKELLKYSKQYN---ISITKKQAEQIANIL 43 (85)
T ss_pred cCCHHHHHHHHHHhC---CCCCHHHHHHHHHHH
Confidence 489999999988877 568999999998876
No 141
>cd06872 PX_SNX19_like_plant The phosphoinositide binding Phox Homology domain of uncharacterized SNX19-like plant proteins. The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to PI-enriched membranes. Members in this subfamily are uncharacterized plant proteins containing an N-terminal PXA domain, a central PX domain, and a C-terminal domain that is conserved in some sorting nexins (SNXs). This is the same domain architecture found in SNX19. SNX13 and SNX14 also contain these three domains but also contain a regulator of G protein signaling (RGS) domain in between the PXA and PX domains. SNXs make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction dom
Probab=25.60 E-value=1.1e+02 Score=22.42 Aligned_cols=38 Identities=16% Similarity=0.197 Sum_probs=27.2
Q ss_pred cccHHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHH
Q psy521 62 DFEVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFIT 112 (173)
Q Consensus 62 elD~eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~ 112 (173)
.+|.+||+.=+.....||+.-... .......++.+|+.
T Consensus 68 ~~~~~fie~Rr~~Le~yL~~l~~~-------------p~i~~s~~~~~FL~ 105 (107)
T cd06872 68 SLDGAFIEERCKLLDKYLKDLLVI-------------EKVAESHEVWSFLS 105 (107)
T ss_pred CCCHHHHHHHHHHHHHHHHHHhcC-------------hhhhcCHHHHHHhc
Confidence 379999999999999999974211 12345666777764
No 142
>PF09279 EF-hand_like: Phosphoinositide-specific phospholipase C, efhand-like; InterPro: IPR015359 This domain is predominantly found in the enzyme phosphoinositol-specific phospholipase C. It adopts a structure consisting of a core of four alpha helices, in an EF like fold, and is required for functioning of the enzyme []. ; PDB: 3OHM_B 3QR0_A 2ZKM_X 2FJU_B 3QR1_D 1DJW_B 1DJI_B 1DJG_B 1QAS_B 2ISD_B ....
Probab=25.59 E-value=78 Score=21.54 Aligned_cols=34 Identities=21% Similarity=0.448 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHc
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLL 134 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv 134 (173)
.+.|+++..+|+++.. -...++.+++++|++.-.
T Consensus 14 ~~mt~~~f~~FL~~eQ-~~~~~~~~~~~~li~~~~ 47 (83)
T PF09279_consen 14 EYMTAEEFRRFLREEQ-GEPRLTDEQAKELIEKFE 47 (83)
T ss_dssp SSEEHHHHHHHHHHTS-S-TTSSHHHHHHHHHHHH
T ss_pred CcCCHHHHHHHHHHHh-ccccCcHHHHHHHHHHHc
Confidence 5789999999998644 122359999999998743
No 143
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=25.39 E-value=75 Score=22.99 Aligned_cols=14 Identities=29% Similarity=0.698 Sum_probs=6.4
Q ss_pred CCHHHHHHHHHHhC
Q psy521 102 ATPKEVRKFITDLG 115 (173)
Q Consensus 102 ~T~~eI~~~I~~~~ 115 (173)
+|.+++.+++...|
T Consensus 33 ~s~~el~~~l~~~~ 46 (110)
T PF03960_consen 33 LSREELRELLSKLG 46 (110)
T ss_dssp --HHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHhc
Confidence 45555555555554
No 144
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=25.35 E-value=1.1e+02 Score=22.23 Aligned_cols=41 Identities=22% Similarity=0.261 Sum_probs=25.8
Q ss_pred ccccHHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCc
Q psy521 61 QDFEVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGIS 117 (173)
Q Consensus 61 ~elD~eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is 117 (173)
..||.+-.+.+.+.+..+..++. +..+..+|.....+.|++
T Consensus 40 ~~~~~e~~~~~~~~i~~~~~~~~----------------~~~~~~~i~~~r~~~glt 80 (127)
T TIGR03830 40 ELLDPEESKRNSAALADFYRKVD----------------GLLTPPEIRRIRKKLGLS 80 (127)
T ss_pred EEEcHHHHHHHHHHHHHHHHHcc----------------CCcCHHHHHHHHHHcCCC
Confidence 45667777888888888777652 335555665555555543
No 145
>PF15173 FAM180: FAM180 family
Probab=24.93 E-value=1.3e+02 Score=23.77 Aligned_cols=33 Identities=27% Similarity=0.444 Sum_probs=26.4
Q ss_pred CHHHHHHHHHHhCCceeecCHHHHHHHHHHHcc
Q psy521 103 TPKEVRKFITDLGISKVELSEEDIRTILETLLF 135 (173)
Q Consensus 103 T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~ 135 (173)
++.+|.+.+.+.---...|+.+|.|+.+=||+|
T Consensus 73 ~l~di~rl~~~ls~~~g~L~~~DFErtlLTlvy 105 (137)
T PF15173_consen 73 SLPDIRRLSAQLSQHRGPLSPEDFERTLLTLVY 105 (137)
T ss_pred cHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Confidence 577887777765434458999999999999998
No 146
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=24.89 E-value=1.4e+02 Score=20.52 Aligned_cols=25 Identities=36% Similarity=0.741 Sum_probs=15.3
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHH
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTIL 130 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL 130 (173)
-|+++|.+++ ||.+ +++.++-++|-
T Consensus 46 ks~eeir~~f---gi~~-d~t~eee~~i~ 70 (78)
T PF01466_consen 46 KSPEEIRKYF---GIEN-DLTPEEEEEIR 70 (78)
T ss_dssp S-HHHHHHHH---T----TSSHHHHHHHH
T ss_pred CCHHHHHHHc---CCCC-CCCHHHHHHHH
Confidence 5888888887 4443 57877776653
No 147
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=24.88 E-value=78 Score=20.42 Aligned_cols=14 Identities=29% Similarity=0.890 Sum_probs=8.7
Q ss_pred CHHHHHHHHHHhCC
Q psy521 103 TPKEVRKFITDLGI 116 (173)
Q Consensus 103 T~~eI~~~I~~~~i 116 (173)
|+++|.+|+...|.
T Consensus 5 ~~~~v~~WL~~~gl 18 (66)
T PF07647_consen 5 SPEDVAEWLKSLGL 18 (66)
T ss_dssp CHHHHHHHHHHTTC
T ss_pred CHHHHHHHHHHCCc
Confidence 56666666666554
No 148
>COG0220 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]
Probab=24.73 E-value=94 Score=26.13 Aligned_cols=43 Identities=26% Similarity=0.397 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEe
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
.+.+..+++.+.+.++.++.+...|..++|+.|.=||-|+++.
T Consensus 82 ~~~v~~~l~k~~~~~l~Nlri~~~DA~~~l~~~~~~~sl~~I~ 124 (227)
T COG0220 82 VPGVAKALKKIKELGLKNLRLLCGDAVEVLDYLIPDGSLDKIY 124 (227)
T ss_pred hHHHHHHHHHHHHcCCCcEEEEcCCHHHHHHhcCCCCCeeEEE
Confidence 4678999999999999999999999999999999999999985
No 149
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=24.45 E-value=2.3e+02 Score=19.11 Aligned_cols=47 Identities=19% Similarity=0.246 Sum_probs=35.1
Q ss_pred ccccHHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHH
Q psy521 61 QDFEVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTIL 130 (173)
Q Consensus 61 ~elD~eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL 130 (173)
..+..+....|.+.+..++.+- .++-.+|.+.++ +..|+.+||..-|
T Consensus 18 ~ris~~a~~~l~~~~e~rl~~i---------------------~~~A~k~~~hak--Rktlt~~DI~~Al 64 (65)
T smart00803 18 GNLSDEAAKLLAEDVEYRIKEI---------------------VQEALKFMRHSK--RTTLTTSDIDSAL 64 (65)
T ss_pred ccccHHHHHHHHHHHHHHHHHH---------------------HHHHHHHHHHhC--CCeecHHHHHHHh
Confidence 4567777888888888888763 677778888776 5668899987654
No 150
>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length. Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.
Probab=24.37 E-value=97 Score=29.54 Aligned_cols=36 Identities=28% Similarity=0.529 Sum_probs=30.8
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcc
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLF 135 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~ 135 (173)
..|-+=.+.+||.+.||+++..++++|...|.--.|
T Consensus 436 ~~~rLlkLe~fi~e~gl~~i~i~e~eian~LaDAEy 471 (549)
T PF07079_consen 436 AIPRLLKLEDFITEVGLTPITISEEEIANFLADAEY 471 (549)
T ss_pred hHHHHHHHHHHHHhcCCCcccccHHHHHHHHHHHHH
Confidence 567788999999999999999999999888765443
No 151
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=24.10 E-value=21 Score=28.06 Aligned_cols=8 Identities=63% Similarity=1.659 Sum_probs=6.6
Q ss_pred cccCccCC
Q psy521 164 STSPCGVC 171 (173)
Q Consensus 164 ~~~PCG~C 171 (173)
.-.|||.|
T Consensus 84 ~~sPCG~C 91 (134)
T COG0295 84 PVSPCGAC 91 (134)
T ss_pred CcCCcHHH
Confidence 46799999
No 152
>PHA02605 54 baseplate subunit; Provisional
Probab=23.41 E-value=61 Score=28.73 Aligned_cols=74 Identities=18% Similarity=0.311 Sum_probs=53.4
Q ss_pred EeeccCCCcC------cccccceecccccHHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhC
Q psy521 42 MLFDLEPDRS------LTGGTWYQDQDFEVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLG 115 (173)
Q Consensus 42 ml~~l~Ps~e------iTGG~WYtD~elD~eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~ 115 (173)
..+.-.||.. -.||.-|.+--|+.+|....+.-+-+-+.. .-.+.+..-|+++|
T Consensus 24 vvfat~pssk~~~l~~~~~~~~~~n~p~~~d~~~~~~g~~~~~~~~--------------------~~~~~~~~~~~ksg 83 (305)
T PHA02605 24 VVFATTPSSKSQALIDGFGGFLYNNLPLNNDFFGLTQGDISQGLTT--------------------LVTAGTQSLIRKSG 83 (305)
T ss_pred EEEecCCCcchHHHHHHhhHHHhhcCCcchhhhhhhcccHHHHHHH--------------------HHHHHHHHHHHhcc
Confidence 3455566654 368888999999999988777655544443 23567888899999
Q ss_pred Cce---eecCHHHHHHHHHHHcc
Q psy521 116 ISK---VELSEEDIRTILETLLF 135 (173)
Q Consensus 116 is~---v~Ls~~dI~~iL~~Lv~ 135 (173)
+++ ..+|..-|++||-..++
T Consensus 84 ~sk~ligams~r~v~sl~g~~~~ 106 (305)
T PHA02605 84 VSKYLIGAMSSRTVQSLLGQFEV 106 (305)
T ss_pred chhHhhhccCHHHHHHhcCchhH
Confidence 998 46888888888865433
No 153
>PRK06848 hypothetical protein; Validated
Probab=23.28 E-value=28 Score=27.18 Aligned_cols=8 Identities=63% Similarity=1.601 Sum_probs=6.6
Q ss_pred cccCccCC
Q psy521 164 STSPCGVC 171 (173)
Q Consensus 164 ~~~PCG~C 171 (173)
.-.|||.|
T Consensus 93 ~~~PCG~C 100 (139)
T PRK06848 93 VVSPCGAC 100 (139)
T ss_pred ccCCChhh
Confidence 45799999
No 154
>cd06893 PX_SNX19 The phosphoinositide binding Phox Homology domain of Sorting Nexin 19. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX19 contains an N-terminal PXA domain, a central PX domain, and a C-terminal domain that is conserved in some SNXs. These domains are also found in SNX13 and SNX14, which also contain a regulator of G protein signaling (RGS) domain in between the PXA and PX domains. SNX19 interacts with IA-2, a major autoantigen found
Probab=23.18 E-value=90 Score=24.01 Aligned_cols=22 Identities=9% Similarity=0.138 Sum_probs=19.9
Q ss_pred ccccHHHHHHHHHHHHHHHhhh
Q psy521 61 QDFEVEFVDVLNQQCYRFLQLK 82 (173)
Q Consensus 61 ~elD~eFI~~L~~~~~~~l~~k 82 (173)
+.+|.+||+.=+....+||++-
T Consensus 92 g~~d~~fie~Rr~~Le~fL~~l 113 (132)
T cd06893 92 GNMDKDKIEARRGLLETFLRQL 113 (132)
T ss_pred CCCCHHHHHHHHHHHHHHHHHH
Confidence 5699999999999999999984
No 155
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=23.16 E-value=2.4e+02 Score=22.88 Aligned_cols=47 Identities=23% Similarity=0.335 Sum_probs=33.0
Q ss_pred HHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCee
Q psy521 70 VLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKI 139 (173)
Q Consensus 70 ~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~i 139 (173)
..+..++.||..+. -|..|+..+|.+.++ +.+.|+.+|+.|-=-|.+
T Consensus 21 ~~~~~Al~~Ls~R~------------------rse~ELr~kL~k~~~-----~~~~Ie~Vi~~l~~~~~l 67 (174)
T COG2137 21 KGLNRALRLLSRRD------------------RSEKELRRKLAKKEF-----SEEIIEEVIDRLAEEGYL 67 (174)
T ss_pred HHHHHHHHHHHHHH------------------HHHHHHHHHHHhccC-----CHHHHHHHHHHHHHcCcc
Confidence 34456788888764 378888888888764 455588888877655554
No 156
>PF06207 DUF1002: Protein of unknown function (DUF1002); InterPro: IPR009343 This protein family has no known function. Its members are about 300 amino acids in length. It has so far been detected in Firmicute bacteria and some archaebacteria.
Probab=23.11 E-value=3e+02 Score=23.32 Aligned_cols=33 Identities=24% Similarity=0.495 Sum_probs=24.1
Q ss_pred CCHHHHHHHHHHh-CCceeecCHHHHHHHHHHHc
Q psy521 102 ATPKEVRKFITDL-GISKVELSEEDIRTILETLL 134 (173)
Q Consensus 102 ~T~~eI~~~I~~~-~is~v~Ls~~dI~~iL~~Lv 134 (173)
-|.+||.+-|++. +--.+.||.+|+++|.+.|.
T Consensus 172 ~t~~eI~~IV~~~~~~~~i~ls~~q~~~i~~l~~ 205 (225)
T PF06207_consen 172 KTDEEIRNIVNNVLNNYNINLSDEQIQQIVNLMK 205 (225)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 3888888888752 11234599999999998874
No 157
>cd08809 CARD_CARD9 Caspase activation and recruitment domain of CARD9-like proteins. Caspase activation and recruitment domain (CARD) similar to that found in CARD9. CARD9 is a central regulator of innate immunity and is highly expressed in dendritic cells and macrophages. Together with BCL10 (B-cell lymphoma 10) and Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1), it forms the M-CBM signalosome (the CBM complex in myeloid immune cells), which mediates activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. CARD9 associates with BCL10 via a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating wi
Probab=23.09 E-value=62 Score=23.68 Aligned_cols=29 Identities=14% Similarity=0.438 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHH
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILET 132 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~ 132 (173)
...+++.|+.|+++.+| |+.+|.|+|++.
T Consensus 14 ~~i~p~rl~pyLrQ~~V----l~~~deEeI~~~ 42 (86)
T cd08809 14 SVIDPSRITPYLRQCKV----LNSDDEEQVLND 42 (86)
T ss_pred eeeCHhhcChHHHHhCC----CChhhHHHHHcC
Confidence 35789999999999984 667777777665
No 158
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=23.06 E-value=1.5e+02 Score=22.47 Aligned_cols=46 Identities=20% Similarity=0.286 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeecC
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVSP 156 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~~ 156 (173)
.++.++|++-+ .++..-|+++|..|.-.|.|+..+...| .|+..+.
T Consensus 25 ~~s~~~ia~~~--------~is~~~vrk~l~~L~~~Glv~s~~G~~G--G~~l~~~ 70 (141)
T PRK11014 25 MTSISEVTEVY--------GVSRNHMVKIINQLSRAGYVTAVRGKNG--GIRLGKP 70 (141)
T ss_pred ccCHHHHHHHH--------CcCHHHHHHHHHHHHhCCEEEEecCCCC--CeeecCC
Confidence 46788887643 4577789999999999999999875444 3776543
No 159
>PF06508 QueC: Queuosine biosynthesis protein QueC; InterPro: IPR018317 This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In Rhizobium meliloti (Sinorhizobium meliloti), a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA [, ]. In Arthrobacter viscosus, the homologous gene is designated alu1 and is associated with an aluminum tolerance phenotype. When expressed in Escherichia coli, it conferred aliminium tolerance []. The entry also contains the gene queC, which is responsible for the conversion of GTP to 7-cyano-7-deazaguanine (preQ0). The biosynthesis of hypermodified tRNA nucleoside queuosine only occurs in eubacteria. It occupies the wobble position for all known tRNAs that are specific for Asp, Asn, His or Tyr [].; PDB: 3BL5_B 2PG3_A.
Probab=22.80 E-value=29 Score=28.58 Aligned_cols=38 Identities=29% Similarity=0.483 Sum_probs=18.1
Q ss_pred ecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeecCCcCCCCccccCccCCC
Q psy521 120 ELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVSPYFAVTGLSTSPCGVCP 172 (173)
Q Consensus 120 ~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~~~~~~~~~~~~PCG~CP 172 (173)
.++..||-++...|- --++.. -.||+ ++-...|||.||
T Consensus 160 ~~tK~eiv~~~~~lg--~~~~~T-----~SCy~--------~~~~~~~CG~C~ 197 (209)
T PF06508_consen 160 DLTKAEIVKLGVELG--VPLELT-----WSCYR--------GGEKGKHCGRCP 197 (209)
T ss_dssp T--HHHHHHHHHHTT--HHHHH------B-STT--------S--BTTTTSSSH
T ss_pred CCCHHHHHHHHHHcC--CCHHHc-----cCCCC--------CCCCCCCCCCCH
Confidence 467777766665543 111111 13554 223358999997
No 160
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=22.70 E-value=3.7e+02 Score=22.42 Aligned_cols=42 Identities=26% Similarity=0.385 Sum_probs=33.7
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEee
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAV 154 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~ 154 (173)
.|+.||.+-+ .++..-+..+|++|+-.|.|++... ++ .|++.
T Consensus 27 ls~~eia~~l--------gl~kstv~RlL~tL~~~g~v~~~~~-~~--~Y~Lg 68 (263)
T PRK09834 27 ATVGLLAELT--------GLHRTTVRRLLETLQEEGYVRRSAS-DD--SFRLT 68 (263)
T ss_pred CCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEecC-CC--cEEEc
Confidence 7888988876 5777889999999999999998642 23 48775
No 161
>smart00526 H15 Domain in histone families 1 and 5.
Probab=22.63 E-value=1.9e+02 Score=19.00 Aligned_cols=43 Identities=16% Similarity=0.188 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEE
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQI 142 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~ 142 (173)
+.+|...|.+||...--....=-...+..-|+.+|-.|+++++
T Consensus 22 ~GsS~~aI~kyi~~~~~~~~~~~~~~l~~~Lk~~v~~G~l~q~ 64 (66)
T smart00526 22 KGSSLQAIKKYIEANYKVLPNNFRSLLKLALKKLVASGKLVQV 64 (66)
T ss_pred CCCCHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcCceeec
Confidence 4589999999999852110011123466668999999999886
No 162
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=22.58 E-value=2.6e+02 Score=19.00 Aligned_cols=53 Identities=21% Similarity=0.369 Sum_probs=28.7
Q ss_pred HHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCC-CeeE
Q psy521 73 QQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDG-TDMY 151 (173)
Q Consensus 73 ~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g-~~~Y 151 (173)
..+..|++++. ...|++||.++++ ..+. ..+.++|+ -..||+--. +| +..|
T Consensus 8 ~~~VeymK~r~----------------~Plt~~eI~d~l~-~d~~------~~~~~~Lk---~npKI~~d~--~~~~f~f 59 (65)
T PF02186_consen 8 AKAVEYMKKRD----------------HPLTLEEILDYLS-LDIG------KKLKQWLK---NNPKIEYDP--DGNTFSF 59 (65)
T ss_dssp HHHHHHHHHH-----------------S-B-HHHHHHHHT-SSS-------HHHHHHHH---H-TTEEEE---TT-CEEE
T ss_pred HHHHHHHHhcC----------------CCcCHHHHHHHHc-CCCC------HHHHHHHH---cCCCEEEec--CCCEEEe
Confidence 34566888863 2389999999988 4442 23444444 566666532 44 6666
Q ss_pred Ee
Q psy521 152 RA 153 (173)
Q Consensus 152 R~ 153 (173)
|.
T Consensus 60 kp 61 (65)
T PF02186_consen 60 KP 61 (65)
T ss_dssp --
T ss_pred cc
Confidence 63
No 163
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=22.48 E-value=1.5e+02 Score=20.42 Aligned_cols=31 Identities=26% Similarity=0.401 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHH
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILE 131 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~ 131 (173)
...|..+.++++++.||+ ..++.+|+++=++
T Consensus 44 ag~s~~eF~~~L~~~gI~-~~~~~eel~~dle 74 (76)
T PF03683_consen 44 AGMSRWEFLELLKERGIP-INYDEEELEEDLE 74 (76)
T ss_pred hCCCHHHHHHHHHHCCCC-CCCCHHHHHHHHH
Confidence 346899999999999999 9999999987554
No 164
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=22.47 E-value=1.9e+02 Score=18.16 Aligned_cols=36 Identities=22% Similarity=0.334 Sum_probs=29.7
Q ss_pred CCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEe
Q psy521 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 100 ~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
...|..+|++.+. ++..-+.++|+.|+-+|.|+...
T Consensus 24 ~~~s~~ela~~~g--------~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 24 LPLTRQEIADYLG--------LTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred CCcCHHHHHHHHC--------CCHHHHHHHHHHHHHCCCEEecC
Confidence 3478888888754 57889999999999999999853
No 165
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=22.44 E-value=2.7e+02 Score=19.53 Aligned_cols=34 Identities=21% Similarity=0.241 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEe
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
.|..+|++.+ .++..-+...++.|.-+|.|.+..
T Consensus 18 ~~~~~la~~l--------~~s~~tv~~~l~~L~~~g~i~~~~ 51 (108)
T smart00344 18 ISLAELAKKV--------GLSPSTVHNRVKRLEEEGVIKGYT 51 (108)
T ss_pred CCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeeceE
Confidence 6788888765 578899999999999999998554
No 166
>PRK08298 cytidine deaminase; Validated
Probab=22.43 E-value=29 Score=27.10 Aligned_cols=8 Identities=75% Similarity=1.717 Sum_probs=6.4
Q ss_pred ccCccCCC
Q psy521 165 TSPCGVCP 172 (173)
Q Consensus 165 ~~PCG~CP 172 (173)
-.|||.|-
T Consensus 86 ~sPCG~CR 93 (136)
T PRK08298 86 LSPCGVCQ 93 (136)
T ss_pred cCCChhHH
Confidence 46999993
No 167
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=22.33 E-value=2.5e+02 Score=19.65 Aligned_cols=39 Identities=21% Similarity=0.394 Sum_probs=24.5
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHH--HcccCeeEE
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILET--LLFDGKIEQ 141 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~--Lv~Dg~iE~ 141 (173)
-+++.||+.-=.+ +.+-.++.++|+.++++ -+|.|.|+.
T Consensus 28 ~Vs~~EI~~~Eq~--Li~eG~~~eeiq~LCdvH~~lf~~~i~~ 68 (71)
T PF04282_consen 28 DVSASEISAAEQE--LIQEGMPVEEIQKLCDVHAALFKGSIEE 68 (71)
T ss_pred CCCHHHHHHHHHH--HHHcCCCHHHHHHHhHHHHHHHHHHHHh
Confidence 3788888754332 22224889999999885 455555543
No 168
>cd04758 Commd10 COMM_Domain containing protein 10. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=22.31 E-value=2.6e+02 Score=22.45 Aligned_cols=23 Identities=22% Similarity=0.275 Sum_probs=17.5
Q ss_pred ccccHHHHHHHHHHHHHHHhhhh
Q psy521 61 QDFEVEFVDVLNQQCYRFLQLKR 83 (173)
Q Consensus 61 ~elD~eFI~~L~~~~~~~l~~k~ 83 (173)
+.+|.+--..|.+.+..++..+.
T Consensus 9 n~l~~~~f~~ll~~i~~~l~~~~ 31 (186)
T cd04758 9 NSIDTEKFPRLLSRLFQKLHLKA 31 (186)
T ss_pred hcCCHHHHHHHHHHHHHHhcccc
Confidence 45777777888888888888654
No 169
>PF01136 Peptidase_U32: Peptidase family U32 This is family U32 in the peptidase classification. ; InterPro: IPR001539 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This is a group of peptidases belonging to MEROPS peptidase family U32 (clan U-). The type example is collagenase (gene prtC) from Porphyromonas gingivalis (Bacteroides gingivalis) [], which is an enzyme that degrades type I collagen and that seems to require a metal cofactor. The product of PrtC is evolutionary related to a number of uncharacterised proteins with a well conserved region containing two cysteines.; GO: 0008233 peptidase activity, 0006508 proteolysis
Probab=22.25 E-value=2.9e+02 Score=22.22 Aligned_cols=52 Identities=29% Similarity=0.367 Sum_probs=36.9
Q ss_pred CCCcccccCCCCCHHHHHHHHHHhCCcee----ecCHHHHHHHHHHHcccCeeEEEe
Q psy521 91 NGPLVAQRLACATPKEVRKFITDLGISKV----ELSEEDIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 91 ~~p~~~~~~~~~T~~eI~~~I~~~~is~v----~Ls~~dI~~iL~~Lv~Dg~iE~~~ 143 (173)
..++..+..-.++=.+=++|+.+.|+..+ +|+.++|++|.+..= +-.+|-+.
T Consensus 36 ~~~i~~~~~~nv~N~~s~~~~~~~G~~~i~ls~EL~~~ei~~i~~~~~-~~~~Ev~v 91 (233)
T PF01136_consen 36 DLKIIADYSLNVFNSESARFLKELGASRITLSPELSLEEIKEIAENSP-GVPLEVIV 91 (233)
T ss_pred CCcEEEecCccCCCHHHHHHHHHcCCCEEEECccCCHHHHHHHHHhCC-CCeEEEEE
Confidence 34555555555666677788888898875 688899999988774 55666654
No 170
>PRK05578 cytidine deaminase; Validated
Probab=22.25 E-value=24 Score=27.20 Aligned_cols=7 Identities=71% Similarity=1.716 Sum_probs=6.0
Q ss_pred ccCccCC
Q psy521 165 TSPCGVC 171 (173)
Q Consensus 165 ~~PCG~C 171 (173)
-.|||.|
T Consensus 83 ~sPCG~C 89 (131)
T PRK05578 83 LSPCGRC 89 (131)
T ss_pred cCccHHH
Confidence 4799999
No 171
>PRK06423 phosphoribosylformylglycinamidine synthase; Provisional
Probab=22.19 E-value=2.6e+02 Score=18.97 Aligned_cols=22 Identities=18% Similarity=0.173 Sum_probs=20.1
Q ss_pred cCHHHHHHHHHHHcccCeeEEE
Q psy521 121 LSEEDIRTILETLLFDGKIEQI 142 (173)
Q Consensus 121 Ls~~dI~~iL~~Lv~Dg~iE~~ 142 (173)
++.++++.+.+.|..|-.||..
T Consensus 47 ~~~~~~~~i~~~lL~Npvie~~ 68 (73)
T PRK06423 47 DSYNEVDEIAGKILTNPVIHSY 68 (73)
T ss_pred CCHHHHHHHHHHhcCCceeeEE
Confidence 7899999999999999999875
No 172
>PF09682 Holin_LLH: Phage holin protein (Holin_LLH); InterPro: IPR010026 This entry represents the Bacteriophage LL-H, Orf107, holin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. It is thought that the temporal precision of holin-mediated lysis may occur through the build-up of a holin oligomer which causes the lysis [].
Probab=22.08 E-value=1.2e+02 Score=22.32 Aligned_cols=30 Identities=20% Similarity=0.381 Sum_probs=24.4
Q ss_pred HHHHHHHHHHhCCceeecCHHHHHHHHHHHccc
Q psy521 104 PKEVRKFITDLGISKVELSEEDIRTILETLLFD 136 (173)
Q Consensus 104 ~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~D 136 (173)
.+-+.+++++.|| .+|+++|+..++.-|.+
T Consensus 74 ~~~v~~~L~~~gi---~~t~~~i~~~IEaAV~~ 103 (108)
T PF09682_consen 74 VQYVKERLKKKGI---KVTDEQIEGAIEAAVKE 103 (108)
T ss_pred HHHHHHHHHHcCC---CCCHHHHHHHHHHHHHH
Confidence 4567788888887 78999999999987754
No 173
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=22.02 E-value=96 Score=25.29 Aligned_cols=38 Identities=26% Similarity=0.384 Sum_probs=29.6
Q ss_pred CCCCCHHHHHHHHHH-hCCceeecCHHHHHHHHHHHcccCeeEE
Q psy521 99 LACATPKEVRKFITD-LGISKVELSEEDIRTILETLLFDGKIEQ 141 (173)
Q Consensus 99 ~~~~T~~eI~~~I~~-~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~ 141 (173)
..+=|+.|+-+.+-+ .||+ ...|+.+|+.||-||+|..
T Consensus 9 ~~~y~lKELEK~~pK~~gI~-----~~~VKdvlq~LvDDglV~~ 47 (188)
T PF03962_consen 9 KDFYTLKELEKLAPKEKGIV-----SMSVKDVLQSLVDDGLVHV 47 (188)
T ss_pred CCcccHHHHHHHcccccCCc-----hhhHHHHHHHHhccccchh
Confidence 356789999888877 6654 4567777999999999965
No 174
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=22.00 E-value=5.2e+02 Score=22.32 Aligned_cols=47 Identities=26% Similarity=0.356 Sum_probs=35.9
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCCeeEEeecCCc
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAVSPYF 158 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~~~YR~~~~~~ 158 (173)
.++++|++-+.- .+|.++|+..|+.|+==|.|++. .+| .|+.+.+.+
T Consensus 138 ~~~~~ia~~l~p------~is~~ev~~sL~~L~~~glikk~--~~g--~y~~t~~~l 184 (271)
T TIGR02147 138 DDPEELAKRCFP------KISAEQVKESLDLLERLGLIKKN--EDG--FYKQTDKAV 184 (271)
T ss_pred CCHHHHHHHhCC------CCCHHHHHHHHHHHHHCCCeeEC--CCC--cEEeeccee
Confidence 467777766543 57999999999999999999974 356 488776543
No 175
>cd03033 ArsC_15kD Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also encodes dinitrogenase reductase ADP-ribosyltransferase (DRAT) and dinitrogenase reductase activating glycohydrolase (DRAG). ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via glutaredoxin, through a single catalytic cysteine.
Probab=21.99 E-value=1.3e+02 Score=22.42 Aligned_cols=43 Identities=23% Similarity=0.261 Sum_probs=24.0
Q ss_pred CCCHHHHHHHHHHhCCce-----------eecCHH--HHHHHHHHHcccCeeEEEe
Q psy521 101 CATPKEVRKFITDLGISK-----------VELSEE--DIRTILETLLFDGKIEQIN 143 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~-----------v~Ls~~--dI~~iL~~Lv~Dg~iE~~~ 143 (173)
.+|.+|+.+|+.+.|+.. ..+..+ ..+++++.|+-+..+.+++
T Consensus 36 p~s~~eL~~~l~~~g~~~l~n~~~~~~r~~~~~~~~ls~~e~~~ll~~~P~LikRP 91 (113)
T cd03033 36 PWTAETLRPFFGDLPVAEWFNPAAPRVKSGEVVPEALDEEEALALMIADPLLIRRP 91 (113)
T ss_pred CCCHHHHHHHHHHcCHHHHHhcccHHHHhcCCCccCCCHHHHHHHHHhCcceeeCC
Confidence 467777777777666332 111111 1244577777777776653
No 176
>cd06863 PX_Atg24p The phosphoinositide binding Phox Homology domain of yeast Atg24p, an autophagic degradation protein. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. The yeast Atg24p is a sorting nexin (SNX) which is involved in membrane fusion events at the vacuolar surface during pexophagy. This is facilitated via binding of Atg24p to phosphatidylinositol 3-phosphate (PI3P) through its PX domain. SNXs make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway.
Probab=21.73 E-value=86 Score=23.13 Aligned_cols=24 Identities=29% Similarity=0.389 Sum_probs=20.5
Q ss_pred ecccccHHHHHHHHHHHHHHHhhh
Q psy521 59 QDQDFEVEFVDVLNQQCYRFLQLK 82 (173)
Q Consensus 59 tD~elD~eFI~~L~~~~~~~l~~k 82 (173)
..+.||.+||+.=++....||+.-
T Consensus 76 ~~~~~~~~~ie~Rr~~Le~fL~~i 99 (118)
T cd06863 76 TGDRFSPEFITRRAQSLQRFLRRI 99 (118)
T ss_pred cccCCCHHHHHHHHHHHHHHHHHH
Confidence 345689999999999999999985
No 177
>PF02005 TRM: N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA: S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs []. The enzyme is found in both eukaryotes and archaea [].; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing; PDB: 2YTZ_B 2DUL_A 2EJU_A 2EJT_A 3AXT_A 3AXS_A.
Probab=21.57 E-value=4.4e+02 Score=23.77 Aligned_cols=69 Identities=10% Similarity=0.181 Sum_probs=36.7
Q ss_pred CcCcccccceecccccHHHHHHHHHHHHHHH----hhhhhh----ccCC-CCCCcccc--------cCCCCCHHHHHHHH
Q psy521 49 DRSLTGGTWYQDQDFEVEFVDVLNQQCYRFL----QLKREK----TANN-TNGPLVAQ--------RLACATPKEVRKFI 111 (173)
Q Consensus 49 s~eiTGG~WYtD~elD~eFI~~L~~~~~~~l----~~k~~~----~~~~-~~~p~~~~--------~~~~~T~~eI~~~I 111 (173)
+.-..+||.+...=.|.+||+.+.+...+.- ..+... .... ...|++-. ..+.|..++|.+.|
T Consensus 267 ~~~~~~GPlWlGpL~d~~fl~~ml~~~~~~~~~~~~~ri~~lL~~i~eE~~~~P~yY~l~~ias~lk~~~P~~~~ii~aL 346 (377)
T PF02005_consen 267 SKLHISGPLWLGPLHDKEFLEKMLEEAEEMPELNTSKRIEKLLETIKEELIDPPFYYDLHEIASRLKCNPPPLDKIISAL 346 (377)
T ss_dssp SCCCEEEEEE-S-SB-HHHHHHHHHHHCT-S-TTTHHHHHHHHHHHHHCHS-SSS-EEHHHHHHHHT-SC--HHHHHHHH
T ss_pred CccceecCccccccCCHHHHHHHHhhhhccchhhhHHHHhhhcchhhhhcccceeEEeHHHHHHhcCCCCCCHHHHHHHH
Confidence 3445789999999999999999887665421 111100 0001 23444221 23568889999999
Q ss_pred HHhCCc
Q psy521 112 TDLGIS 117 (173)
Q Consensus 112 ~~~~is 117 (173)
++.|..
T Consensus 347 ~~~Gy~ 352 (377)
T PF02005_consen 347 RNAGYR 352 (377)
T ss_dssp HHTTTT
T ss_pred hhcceE
Confidence 888743
No 178
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=21.55 E-value=2.3e+02 Score=17.98 Aligned_cols=47 Identities=19% Similarity=0.297 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEec-CCCC-eeEEeec
Q psy521 101 CATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINN-IDGT-DMYRAVS 155 (173)
Q Consensus 101 ~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~-~~g~-~~YR~~~ 155 (173)
.+|..+|.+.+ .++...+-.+|+.|+=.|.|++..+ .|+. ..|+++.
T Consensus 18 ~~t~~~l~~~~--------~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~ 66 (68)
T PF13463_consen 18 PMTQSDLAERL--------GISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTP 66 (68)
T ss_dssp -BEHHHHHHHT--------T--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-H
T ss_pred CcCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCC
Confidence 46788887764 3466788899999999999999875 3554 5677653
No 179
>PF11575 FhuF_C: FhuF 2Fe-2S C-terminal domain; InterPro: IPR024726 Ferric iron reductase (FhuF) is involved in the reduction of ferric iron in cytoplasmic ferrioxamine B []. This entry represents the C-terminal domain that contains 4 conserved cysteine residues found to be part of a 2Fe-2S cluster [].; GO: 0051537 2 iron, 2 sulfur cluster binding
Probab=21.41 E-value=45 Score=18.19 Aligned_cols=6 Identities=67% Similarity=1.841 Sum_probs=5.1
Q ss_pred ccCCCC
Q psy521 168 CGVCPD 173 (173)
Q Consensus 168 CG~CP~ 173 (173)
|+.||+
T Consensus 16 C~~CP~ 21 (22)
T PF11575_consen 16 CGTCPL 21 (22)
T ss_pred cCCCCC
Confidence 999985
No 180
>PF08385 DHC_N1: Dynein heavy chain, N-terminal region 1; InterPro: IPR013594 Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit []. The region featured in this family includes the sequences implicated in mediating these interactions []. It is thought to be flexible and not to adopt a rigid conformation [].
Probab=21.30 E-value=1.8e+02 Score=26.68 Aligned_cols=71 Identities=15% Similarity=0.206 Sum_probs=42.3
Q ss_pred cHHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhC--Cc--eeecCHHHHHHHHHHHcccCe
Q psy521 64 EVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLG--IS--KVELSEEDIRTILETLLFDGK 138 (173)
Q Consensus 64 D~eFI~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~--is--~v~Ls~~dI~~iL~~Lv~Dg~ 138 (173)
|.+||+.|...+.+|+.+-..--....... . ...+++.+=.+|-+... +. .-+|...+|+.++++|..-+.
T Consensus 1 D~~~~~~le~~v~~W~~qI~~vl~~~~~~~-~---~~~~~p~~Ei~fW~~r~~~L~~i~~QL~s~~v~~~~~iL~~~~s 75 (579)
T PF08385_consen 1 DPEFLNSLESIVIQWIKQIQKVLSLSSDPR-S---GDNPGPLDEIEFWRSREENLSSIYEQLKSPEVQKILEILEKAKS 75 (579)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhcCcccc-c---CCCCChHHHHHHHHHHHHHHHHHHHHHcchHHHHHHHHHHHhcc
Confidence 789999999999999997443211111000 0 12345444444444322 22 246888999999998875543
No 181
>PF11829 DUF3349: Protein of unknown function (DUF3349); InterPro: IPR021784 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. ; PDB: 2KVC_A 3OL3_B 3OL4_A 2LKY_A.
Probab=21.19 E-value=1.5e+02 Score=21.94 Aligned_cols=33 Identities=18% Similarity=0.170 Sum_probs=23.2
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHHHHHccc
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTILETLLFD 136 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~D 136 (173)
+|..+|..+|.+ ++.-.=+.+||+++...|.--
T Consensus 56 ~~~~dI~~~I~~--vt~~~P~~~di~RV~~~Laa~ 88 (96)
T PF11829_consen 56 VDRIDIGVAITR--VTDELPTPEDIERVRARLAAA 88 (96)
T ss_dssp BSCCHHHHHHHH--HCSS-S-HHHHHHHHHHHHTT
T ss_pred CCHHHHHHHHHH--HHcCCcCHHHHHHHHHHHHhC
Confidence 367777777776 666777889999988887543
No 182
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=21.04 E-value=5.2e+02 Score=23.29 Aligned_cols=78 Identities=19% Similarity=0.282 Sum_probs=46.0
Q ss_pred cccccceecccccHHHHHHHHHHHHH-----------HHhhhhhhccCCCCCCccc--------ccCCCCCHHHHHHHHH
Q psy521 52 LTGGTWYQDQDFEVEFVDVLNQQCYR-----------FLQLKREKTANNTNGPLVA--------QRLACATPKEVRKFIT 112 (173)
Q Consensus 52 iTGG~WYtD~elD~eFI~~L~~~~~~-----------~l~~k~~~~~~~~~~p~~~--------~~~~~~T~~eI~~~I~ 112 (173)
..+||.|...=.|.||++.+.+.... .|..-.. .....|++- ...+.|..+.+.+.|+
T Consensus 263 ~~~GPlW~G~l~d~~fl~~m~~~~~~~~~~~~~~~~~lL~~~~~---E~~~~p~~y~~~~i~~~~k~~~p~~~~~~~~L~ 339 (374)
T TIGR00308 263 HLAGPLYAGPLHDKEFIEEVLRIAEEKEYGTRKRVLKMLSLIKN---ELSDPPGYYSPHHIASVLKLSVPPLKDVVAGLK 339 (374)
T ss_pred eeecCcccCccCCHHHHHHHHHhhhhccccchHHHHHHHHHHHh---ccCCCCeEEeHHHHHHhcCCCCCCHHHHHHHHH
Confidence 35889999999999999998765422 2211100 011223211 1235788888888888
Q ss_pred HhCCc-----------eeecCHHHHHHHHHH
Q psy521 113 DLGIS-----------KVELSEEDIRTILET 132 (173)
Q Consensus 113 ~~~is-----------~v~Ls~~dI~~iL~~ 132 (173)
+.|.. +++-+.++|..|++.
T Consensus 340 ~~Gy~as~tH~~p~~iKTdAp~~~i~~i~~~ 370 (374)
T TIGR00308 340 SLGFEASRTHYQPSGIKTDAPWDAIWEVLQK 370 (374)
T ss_pred HCCCeEEeeeeCCCcEecCCCHHHHHHHHHh
Confidence 87632 244556666666653
No 183
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=20.93 E-value=1.5e+02 Score=21.12 Aligned_cols=28 Identities=18% Similarity=0.336 Sum_probs=19.5
Q ss_pred CCHHHHHHHHHHhCCceeecCHHHHHHHHHHH
Q psy521 102 ATPKEVRKFITDLGISKVELSEEDIRTILETL 133 (173)
Q Consensus 102 ~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~L 133 (173)
.|-+|+.+.|.+. ..++..|++.+++.+
T Consensus 3 mtk~el~~~ia~~----~~~s~~~v~~vl~~~ 30 (99)
T PRK00285 3 LTKADLAEALFEK----VGLSKREAKELVELF 30 (99)
T ss_pred cCHHHHHHHHHHH----hCcCHHHHHHHHHHH
Confidence 5778888888753 346777777766653
No 184
>KOG0121|consensus
Probab=20.89 E-value=34 Score=27.28 Aligned_cols=11 Identities=36% Similarity=1.210 Sum_probs=8.7
Q ss_pred CCccccCccCC
Q psy521 161 TGLSTSPCGVC 171 (173)
Q Consensus 161 ~~~~~~PCG~C 171 (173)
.-++..|||.|
T Consensus 71 dr~kktpCGFC 81 (153)
T KOG0121|consen 71 DRFKKTPCGFC 81 (153)
T ss_pred ccCCcCccceE
Confidence 34678999998
No 185
>COG1799 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.85 E-value=1.3e+02 Score=24.62 Aligned_cols=53 Identities=13% Similarity=0.382 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHhCCcee---ecCHHHHHHHHHHH-----cccCeeEEEecCCCCeeEEeec
Q psy521 99 LACATPKEVRKFITDLGISKV---ELSEEDIRTILETL-----LFDGKIEQINNIDGTDMYRAVS 155 (173)
Q Consensus 99 ~~~~T~~eI~~~I~~~~is~v---~Ls~~dI~~iL~~L-----v~Dg~iE~~~~~~g~~~YR~~~ 155 (173)
+.|..+.+|.++|++....-+ .++.++-++|||=| +++|.+.+| |..+|=++.
T Consensus 82 r~yeda~~ia~~lk~~k~Vvinl~~m~~~qArRivDFlaG~~~al~G~~qkV----g~~ifL~tP 142 (167)
T COG1799 82 RKYEDAQEIADYLKNRKAVVINLQRMDPAQARRIVDFLAGAVFALRGSIQKV----GSKIFLLTP 142 (167)
T ss_pred ccHHHHHHHHHHHhcCceEEEEeeeCCHHHHHHHHHHhcchhhhhcccHHhh----cceeEEecc
Confidence 468899999999999876654 58899999999965 789999887 334665544
No 186
>PF09286 Pro-kuma_activ: Pro-kumamolisin, activation domain ; InterPro: IPR015366 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found at the N terminus of peptidases belonging to MEROPS peptidase family S53 (sedolisin, clan SB). The domain adopts a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase []. ; GO: 0008236 serine-type peptidase activity; PDB: 1T1E_A 3EDY_A 3EE6_A.
Probab=20.81 E-value=65 Score=24.40 Aligned_cols=48 Identities=13% Similarity=0.140 Sum_probs=29.7
Q ss_pred CHHHHHHHHHHhCCce-----------eecCHHHHHHHHHHHcccCeeEEEec-CCCCeeEEeec
Q psy521 103 TPKEVRKFITDLGISK-----------VELSEEDIRTILETLLFDGKIEQINN-IDGTDMYRAVS 155 (173)
Q Consensus 103 T~~eI~~~I~~~~is~-----------v~Ls~~dI~~iL~~Lv~Dg~iE~~~~-~~g~~~YR~~~ 155 (173)
+++.|.+|+++.|++. +..++.++++++++= +..... .+|...+|...
T Consensus 63 ~v~~V~~wL~~~G~~~~~~~~~~~~i~~~~tv~~~e~~f~t~-----~~~y~~~~~~~~~~~~~~ 122 (143)
T PF09286_consen 63 DVAAVKSWLKSHGLTVVEVSANGDWITVSGTVAQAERAFGTK-----FHVYQHKDGGQFYARTSE 122 (143)
T ss_dssp HHHHHHHHHHHCT-EEEEEETTTTEEEEEEEHHHHHHHCT--------EEEEETTTTEEEEESCS
T ss_pred HHHHHHHHHHHcCCceeEEeCCCCEEEEEEeHHHHHHHhCcc-----eEEEEecCCCeEEEeCCC
Confidence 4677888999988764 468999999998873 333332 34444455544
No 187
>cd06870 PX_CISK The phosphoinositide binding Phox Homology Domain of Cytokine-Independent Survival Kinase. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Cytokine-independent survival kinase (CISK), also called Serum- and Glucocorticoid-induced Kinase 3 (SGK3), plays a role in cell growth and survival. It is expressed in most tissues and is most abundant in the embryo and adult heart and spleen. It was originally discovered in a screen for antiapoptotic genes. It phosphorylates and inhibits the proapoptotic proteins, Bad and FKHRL1. CISK/SGK3 also regulates many transporters, ion channels, and receptors. It plays a critical role in hair follicle morphogenesis and hair cycling. N-terminal to a catalytic kinase domain, CISK contains a PX domain which binds highly phosphorylated PIs, directs membrane localization, and regulates the enzyme's activity.
Probab=20.80 E-value=1.3e+02 Score=21.89 Aligned_cols=84 Identities=18% Similarity=0.378 Sum_probs=47.0
Q ss_pred cceEEEeeccccCCCCCCceeeeccccc---ccce---eEEE--eeccCCCcCcccccceecccccHHHHHHHHHHHHHH
Q psy521 7 KKKVYMLFDLEPDRSLTGGTWYQDQDFE---ASKK---KVYM--LFDLEPDRSLTGGTWYQDQDFEVEFVDVLNQQCYRF 78 (173)
Q Consensus 7 ~~k~y~~~~~~p~~~~tgg~~~~d~sV~---~~~r---k~Ym--l~~l~Ps~eiTGG~WYtD~elD~eFI~~L~~~~~~~ 78 (173)
++|-|+.|.++-.. .|+.|..-.... .-.+ +.|= ...+ |++.+.| . .+|.+||+.=+.....|
T Consensus 16 ~~~~~~~Y~I~v~~--~~~~~~v~RRYseF~~L~~~L~~~~~~~~~~l-P~K~~~~-----~-~~~~~~ie~Rr~~Le~f 86 (109)
T cd06870 16 KKKRFTVYKVVVSV--GRSSWFVFRRYAEFDKLYESLKKQFPASNLKI-PGKRLFG-----N-NFDPDFIKQRRAGLDEF 86 (109)
T ss_pred CCCCeEEEEEEEEE--CCeEEEEEeehHHHHHHHHHHHHHCcccCcCC-CCCcccc-----c-CCCHHHHHHHHHHHHHH
Confidence 56788888886532 356665422211 1000 0010 0012 4444443 2 68999999999999999
Q ss_pred HhhhhhhccCCCCCCcccccCCCCCHHHHHHHHH
Q psy521 79 LQLKREKTANNTNGPLVAQRLACATPKEVRKFIT 112 (173)
Q Consensus 79 l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~ 112 (173)
|++-... ....+.+++.+|+.
T Consensus 87 L~~ll~~-------------p~l~~s~~~~~FL~ 107 (109)
T cd06870 87 IQRLVSD-------------PKLLNHPDVRAFLQ 107 (109)
T ss_pred HHHHhCC-------------HhhhcChHHHHHhC
Confidence 9974321 12345666777764
No 188
>PRK05638 threonine synthase; Validated
Probab=20.61 E-value=3.5e+02 Score=24.59 Aligned_cols=64 Identities=16% Similarity=0.149 Sum_probs=47.0
Q ss_pred HHHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCC
Q psy521 68 VDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDG 147 (173)
Q Consensus 68 I~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g 147 (173)
.+..+..|+.+|.++ -.+..||.+.|.. .+|..-|.+.|+.|.=+|.|+.... .|
T Consensus 369 ~~~~r~~IL~~L~~~------------------~~~~~el~~~l~~------~~s~~~v~~hL~~Le~~GLV~~~~~-~g 423 (442)
T PRK05638 369 IGGTKLEILKILSER------------------EMYGYEIWKALGK------PLKYQAVYQHIKELEELGLIEEAYR-KG 423 (442)
T ss_pred ccchHHHHHHHHhhC------------------CccHHHHHHHHcc------cCCcchHHHHHHHHHHCCCEEEeec-CC
Confidence 345678888888763 2578899988874 3688889999999999999987422 34
Q ss_pred C-eeEEeecC
Q psy521 148 T-DMYRAVSP 156 (173)
Q Consensus 148 ~-~~YR~~~~ 156 (173)
. ..|+++..
T Consensus 424 ~~~~Y~Lt~~ 433 (442)
T PRK05638 424 RRVYYKLTEK 433 (442)
T ss_pred CcEEEEECcH
Confidence 4 45777654
No 189
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=20.53 E-value=1.3e+02 Score=26.58 Aligned_cols=62 Identities=21% Similarity=0.210 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHhhhhhhccCCCCCCcccccCCCCCHHHHHHHHHHhCCceeecCHHHHHHHHHHHcccCeeEEEecCCCC
Q psy521 69 DVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGT 148 (173)
Q Consensus 69 ~~L~~~~~~~l~~k~~~~~~~~~~p~~~~~~~~~T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~Lv~Dg~iE~~~~~~g~ 148 (173)
..|..++..|+.+. ..++.+++++- ....+|.+=|+.-+..|.-.|.|++.+++.|.
T Consensus 6 ~il~aIV~~~l~~~-----------------~pv~s~~l~~~------~~~~vS~aTiR~d~~~Le~~G~l~~~h~sagr 62 (337)
T TIGR00331 6 KILKAIVEEYIKTG-----------------QPVGSKTLLEK------YNLGLSSATIRNDMADLEDLGFIEKPHTSSGR 62 (337)
T ss_pred HHHHHHHHHHHhcC-----------------CCcCHHHHHhh------cCCCCChHHHHHHHHHHHHCCCccCCCCCCCc
Confidence 45677777888874 34788887764 22356788899999999999999998876663
Q ss_pred ----eeEEe
Q psy521 149 ----DMYRA 153 (173)
Q Consensus 149 ----~~YR~ 153 (173)
..||.
T Consensus 63 ipt~kGYR~ 71 (337)
T TIGR00331 63 IPTDKGYRY 71 (337)
T ss_pred CcChhHHHH
Confidence 44664
No 190
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=20.26 E-value=1.7e+02 Score=20.07 Aligned_cols=27 Identities=22% Similarity=0.369 Sum_probs=16.0
Q ss_pred CHHHHHHHHHHhCCceeecCHHHHHHHHHHH
Q psy521 103 TPKEVRKFITDLGISKVELSEEDIRTILETL 133 (173)
Q Consensus 103 T~~eI~~~I~~~~is~v~Ls~~dI~~iL~~L 133 (173)
|-+|+.+.|.+. ..++..|++.+|+.|
T Consensus 2 tk~eli~~ia~~----~~~~~~~v~~vl~~l 28 (90)
T smart00411 2 TKSELIDAIAEK----AGLSKKDAKAAVDAF 28 (90)
T ss_pred CHHHHHHHHHHH----hCCCHHHHHHHHHHH
Confidence 456777777652 235667766666543
No 191
>PLN02182 cytidine deaminase
Probab=20.21 E-value=39 Score=30.52 Aligned_cols=7 Identities=57% Similarity=1.692 Sum_probs=6.1
Q ss_pred ccCccCC
Q psy521 165 TSPCGVC 171 (173)
Q Consensus 165 ~~PCG~C 171 (173)
-.|||+|
T Consensus 129 ~sPCG~C 135 (339)
T PLN02182 129 GTPCGHC 135 (339)
T ss_pred cCCCchh
Confidence 4699999
No 192
>smart00313 PXA Domain associated with PX domains. unpubl. observations
Probab=20.18 E-value=88 Score=24.80 Aligned_cols=30 Identities=17% Similarity=0.332 Sum_probs=25.0
Q ss_pred cceecccccHHHHHHHHHHHHHHHhhhhhh
Q psy521 56 TWYQDQDFEVEFVDVLNQQCYRFLQLKREK 85 (173)
Q Consensus 56 ~WYtD~elD~eFI~~L~~~~~~~l~~k~~~ 85 (173)
+||..=--|.+|++.+++.+..++.+-...
T Consensus 22 sWY~~is~d~~F~~~i~~~l~~~~~~l~~R 51 (176)
T smart00313 22 GWYKGVSEDPSFLREIEQTLEYILRQLYRR 51 (176)
T ss_pred HHhccCCCChhHHHHHHHHHHHHHHHHHHH
Confidence 699887788899999999999988875543
Done!