Query psy12696
Match_columns 267
No_of_seqs 225 out of 1340
Neff 7.2
Searched_HMMs 46136
Date Fri Aug 16 17:17:38 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12696.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12696hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5034 TNG2 Chromatin remodel 100.0 4.8E-39 1E-43 277.9 20.0 256 3-263 4-270 (271)
2 KOG1973|consensus 100.0 6.8E-36 1.5E-40 269.1 13.1 239 3-266 7-271 (274)
3 PF12998 ING: Inhibitor of gro 99.9 4.7E-27 1E-31 182.4 12.4 103 4-106 1-105 (105)
4 PF00628 PHD: PHD-finger; Int 98.8 7.8E-10 1.7E-14 74.6 0.1 44 216-262 1-50 (51)
5 smart00249 PHD PHD zinc finger 98.7 1.7E-08 3.7E-13 65.8 2.9 42 216-260 1-47 (47)
6 KOG1512|consensus 97.9 3.1E-06 6.7E-11 75.5 1.2 44 215-261 315-361 (381)
7 KOG4323|consensus 97.9 3.7E-06 8E-11 80.2 1.4 49 214-265 171-226 (464)
8 KOG0954|consensus 97.8 8.8E-06 1.9E-10 80.6 1.5 49 211-262 268-320 (893)
9 KOG0825|consensus 97.7 2E-05 4.3E-10 78.6 2.1 48 212-261 213-264 (1134)
10 KOG4299|consensus 97.7 1.4E-05 3E-10 78.2 1.0 46 214-262 253-304 (613)
11 KOG1244|consensus 97.6 2E-05 4.2E-10 70.0 0.4 52 212-266 279-334 (336)
12 PF13831 PHD_2: PHD-finger; PD 97.4 1.6E-05 3.5E-10 49.8 -1.2 34 225-261 2-36 (36)
13 KOG1245|consensus 97.0 0.00016 3.5E-09 77.9 -0.6 50 212-264 1106-1159(1404)
14 KOG0955|consensus 96.9 0.00061 1.3E-08 71.2 3.3 50 212-264 217-270 (1051)
15 KOG0383|consensus 96.7 0.00066 1.4E-08 68.3 1.8 46 213-263 46-94 (696)
16 KOG0956|consensus 96.6 0.00059 1.3E-08 67.5 0.4 39 225-264 20-58 (900)
17 COG5141 PHD zinc finger-contai 96.3 0.0011 2.3E-08 63.6 0.4 45 215-262 194-242 (669)
18 KOG1632|consensus 96.1 0.0023 5.1E-08 59.8 1.4 48 214-264 60-114 (345)
19 KOG0957|consensus 95.7 0.28 6.1E-06 47.6 13.1 44 215-261 545-596 (707)
20 KOG0957|consensus 94.4 0.038 8.2E-07 53.4 3.6 49 211-262 116-178 (707)
21 KOG1632|consensus 93.4 0.016 3.5E-07 54.3 -1.0 51 209-262 234-294 (345)
22 KOG2752|consensus 91.4 0.096 2.1E-06 47.9 1.5 31 213-246 127-165 (345)
23 KOG1844|consensus 91.2 0.2 4.3E-06 49.0 3.5 50 212-264 84-136 (508)
24 KOG4443|consensus 88.6 0.26 5.5E-06 49.2 1.9 46 214-262 68-117 (694)
25 COG1382 GimC Prefoldin, chaper 86.8 14 0.0003 29.3 13.2 102 13-114 1-111 (119)
26 PF07227 DUF1423: Protein of u 85.7 0.59 1.3E-05 44.9 2.6 43 218-263 133-192 (446)
27 PF10158 LOH1CR12: Tumour supp 82.1 25 0.00054 28.4 11.1 77 5-87 36-112 (131)
28 PF13341 RAG2_PHD: RAG2 PHD do 81.3 0.47 1E-05 33.9 0.0 32 226-259 29-67 (78)
29 PF13832 zf-HC5HC2H_2: PHD-zin 81.3 0.69 1.5E-05 35.6 0.9 31 214-246 55-86 (110)
30 PF10796 Anti-adapt_IraP: Sigm 81.1 14 0.00031 27.7 7.8 77 20-99 5-81 (87)
31 PF13771 zf-HC5HC2H: PHD-like 81.0 0.85 1.8E-05 33.7 1.3 31 214-246 36-67 (90)
32 KOG1493|consensus 80.9 0.74 1.6E-05 33.6 0.9 48 216-263 22-79 (84)
33 PF11932 DUF3450: Protein of u 80.9 23 0.00051 31.3 10.8 50 36-85 105-154 (251)
34 TIGR02338 gimC_beta prefoldin, 80.5 24 0.00053 27.2 11.9 46 67-112 61-106 (110)
35 PRK09343 prefoldin subunit bet 79.5 29 0.00062 27.4 12.2 100 14-113 3-111 (121)
36 PRK15365 type III secretion sy 79.4 26 0.00056 26.8 10.1 79 23-106 7-92 (107)
37 KOG1473|consensus 78.8 1.2 2.6E-05 47.3 1.9 42 215-261 345-389 (1414)
38 KOG0994|consensus 75.5 35 0.00076 37.0 11.3 45 67-111 1564-1608(1758)
39 KOG4443|consensus 75.4 0.85 1.8E-05 45.7 -0.2 46 214-262 18-70 (694)
40 PF05384 DegS: Sensor protein 74.7 49 0.0011 27.6 11.9 100 8-107 17-125 (159)
41 COG5034 TNG2 Chromatin remodel 72.6 23 0.0005 31.8 8.0 54 55-111 55-108 (271)
42 PF03194 LUC7: LUC7 N_terminus 71.9 31 0.00068 30.9 9.0 67 25-94 90-160 (254)
43 smart00744 RINGv The RING-vari 71.2 1 2.3E-05 29.9 -0.5 30 232-261 18-49 (49)
44 KOG4552|consensus 70.9 72 0.0016 27.9 11.1 87 22-112 12-99 (272)
45 PF10146 zf-C4H2: Zinc finger- 70.9 38 0.00083 29.9 9.1 41 10-50 10-50 (230)
46 KOG4360|consensus 70.4 71 0.0015 31.6 11.4 77 25-107 205-281 (596)
47 PF11690 DUF3287: Protein of u 70.3 17 0.00036 28.4 5.9 54 54-107 31-85 (109)
48 PF10497 zf-4CXXC_R1: Zinc-fin 69.8 3.6 7.8E-05 31.9 2.2 51 211-262 4-69 (105)
49 PF13901 DUF4206: Domain of un 69.1 3.3 7.2E-05 35.8 2.0 42 216-267 154-202 (202)
50 PF01627 Hpt: Hpt domain; Int 67.2 41 0.00089 23.7 8.1 86 5-100 2-88 (90)
51 PF07649 C1_3: C1-like domain; 66.4 1.5 3.3E-05 25.8 -0.4 27 216-245 2-30 (30)
52 COG5194 APC11 Component of SCF 66.3 1.7 3.6E-05 32.1 -0.3 43 216-262 22-78 (88)
53 PHA02562 46 endonuclease subun 65.9 84 0.0018 30.9 11.5 25 17-41 298-322 (562)
54 KOG3579|consensus 65.8 6.6 0.00014 35.8 3.3 52 206-259 260-316 (352)
55 PRK10244 anti-RssB factor; Pro 65.3 43 0.00093 25.1 7.0 77 20-99 5-81 (88)
56 COG5415 Predicted integral mem 64.0 4.2 9E-05 35.4 1.6 34 15-48 12-45 (251)
57 PF05781 MRVI1: MRVI1 protein; 63.5 1.3E+02 0.0027 30.1 11.8 28 85-112 290-317 (538)
58 KOG4460|consensus 63.2 82 0.0018 31.6 10.3 35 4-38 570-605 (741)
59 TIGR00634 recN DNA repair prot 60.5 69 0.0015 31.9 9.8 10 63-72 330-339 (563)
60 PRK10869 recombination and rep 60.4 69 0.0015 32.0 9.7 19 57-75 319-337 (553)
61 PF13639 zf-RING_2: Ring finge 59.9 2.5 5.4E-05 26.9 -0.3 36 218-261 5-44 (44)
62 PF07139 DUF1387: Protein of u 58.0 1.6E+02 0.0034 27.3 11.5 49 62-110 204-259 (302)
63 PF11793 FANCL_C: FANCL C-term 57.0 5.5 0.00012 28.4 1.0 47 216-263 4-64 (70)
64 KOG1937|consensus 55.8 1.8E+02 0.004 28.4 11.1 28 14-42 335-362 (521)
65 PF11781 RRN7: RNA polymerase 55.3 8.7 0.00019 23.8 1.6 25 227-261 8-32 (36)
66 PF05103 DivIVA: DivIVA protei 55.2 6.9 0.00015 30.8 1.4 34 6-42 23-56 (131)
67 KOG3047|consensus 55.1 1.1E+02 0.0024 24.7 10.5 45 67-111 99-143 (157)
68 COG4575 ElaB Uncharacterized c 54.6 99 0.0021 23.9 9.2 62 28-93 11-73 (104)
69 smart00502 BBC B-Box C-termina 54.0 93 0.002 23.4 12.2 23 79-101 71-93 (127)
70 PF05010 TACC: Transforming ac 53.9 1.5E+02 0.0032 25.8 13.8 33 62-94 125-157 (207)
71 PF01765 RRF: Ribosome recycli 53.0 72 0.0016 26.4 7.3 34 77-110 131-164 (165)
72 KOG1829|consensus 52.4 3.1 6.8E-05 41.5 -1.2 32 227-266 531-562 (580)
73 PF08702 Fib_alpha: Fibrinogen 52.4 1.3E+02 0.0028 24.6 13.6 37 71-107 95-131 (146)
74 KOG1512|consensus 52.0 3.9 8.4E-05 37.2 -0.6 45 214-261 261-315 (381)
75 KOG1853|consensus 51.5 1.9E+02 0.0041 26.2 12.0 10 213-222 284-293 (333)
76 KOG1244|consensus 51.3 4.1 9E-05 36.8 -0.5 45 214-261 224-282 (336)
77 TIGR00496 frr ribosome recycli 50.7 85 0.0019 26.5 7.4 33 79-111 142-174 (176)
78 PF04380 BMFP: Membrane fusoge 50.4 96 0.0021 22.5 8.4 43 65-107 35-77 (79)
79 PF04949 Transcrip_act: Transc 50.2 1.5E+02 0.0032 24.6 12.1 86 23-113 32-117 (159)
80 PF06008 Laminin_I: Laminin Do 49.9 1.9E+02 0.004 25.7 15.5 84 13-96 75-169 (264)
81 cd00632 Prefoldin_beta Prefold 49.8 1.1E+02 0.0024 23.1 11.9 96 9-112 4-102 (105)
82 PHA02825 LAP/PHD finger-like p 49.7 9.2 0.0002 31.9 1.3 47 213-262 7-56 (162)
83 PF13851 GAS: Growth-arrest sp 49.4 1.7E+02 0.0037 25.1 14.9 86 21-107 23-113 (201)
84 PF12252 SidE: Dot/Icm substra 48.9 2.7E+02 0.0058 30.4 11.8 52 3-54 1178-1229(1439)
85 KOG2932|consensus 48.4 8.2 0.00018 35.6 0.9 39 214-262 90-131 (389)
86 PF00130 C1_1: Phorbol esters/ 48.2 14 0.00031 24.1 1.9 33 213-248 10-46 (53)
87 PF12761 End3: Actin cytoskele 47.8 1.7E+02 0.0037 25.3 8.8 29 16-44 94-122 (195)
88 KOG4299|consensus 47.4 13 0.00029 37.2 2.3 45 214-263 47-95 (613)
89 PF08746 zf-RING-like: RING-li 47.4 5.3 0.00012 25.7 -0.3 32 228-260 12-43 (43)
90 PHA02862 5L protein; Provision 47.2 7.4 0.00016 32.0 0.4 25 238-262 26-50 (156)
91 PHA02562 46 endonuclease subun 47.1 2.9E+02 0.0062 27.1 12.6 26 66-91 221-246 (562)
92 PRK10780 periplasmic chaperone 46.9 1.6E+02 0.0035 24.2 11.3 43 28-70 53-95 (165)
93 KOG4515|consensus 46.8 1.9E+02 0.0041 24.9 10.4 39 6-44 101-139 (217)
94 PF07496 zf-CW: CW-type Zinc F 46.8 9.6 0.00021 25.2 0.8 28 227-259 3-34 (50)
95 KOG1937|consensus 46.6 2.9E+02 0.0064 27.0 13.7 59 53-111 441-512 (521)
96 PF06464 DMAP_binding: DMAP1-b 46.4 37 0.0008 26.4 4.2 21 13-36 2-22 (111)
97 PF04849 HAP1_N: HAP1 N-termin 46.4 2.4E+02 0.0053 26.1 11.4 47 61-108 237-283 (306)
98 COG0216 PrfA Protein chain rel 46.1 2.5E+02 0.0054 26.5 10.1 27 87-113 76-102 (363)
99 PF03938 OmpH: Outer membrane 46.1 1.6E+02 0.0034 23.7 10.5 53 29-81 47-99 (158)
100 KOG1671|consensus 45.9 10 0.00022 32.8 1.0 19 240-258 154-173 (210)
101 COG1645 Uncharacterized Zn-fin 45.3 14 0.0003 29.8 1.7 22 229-261 30-51 (131)
102 PRK14127 cell division protein 45.2 83 0.0018 24.6 6.0 37 6-45 28-64 (109)
103 PRK00083 frr ribosome recyclin 44.3 1.2E+02 0.0026 25.8 7.4 31 81-111 153-183 (185)
104 KOG2626|consensus 44.2 15 0.00033 36.2 2.1 47 214-263 20-76 (544)
105 PRK11637 AmiB activator; Provi 44.0 2.9E+02 0.0064 26.3 12.4 27 82-108 91-117 (428)
106 PF10046 BLOC1_2: Biogenesis o 43.6 63 0.0014 24.5 5.1 29 8-36 49-77 (99)
107 KOG0964|consensus 43.5 4.6E+02 0.01 28.4 13.0 26 87-112 748-773 (1200)
108 PF04012 PspA_IM30: PspA/IM30 43.4 2.1E+02 0.0046 24.5 12.1 104 5-112 27-130 (221)
109 COG3937 Uncharacterized conser 43.0 1.6E+02 0.0035 23.0 10.6 54 38-94 23-76 (108)
110 PF10168 Nup88: Nuclear pore c 42.8 3.1E+02 0.0067 28.5 11.3 19 7-25 550-568 (717)
111 KOG2846|consensus 42.6 17 0.00036 33.8 2.0 36 225-265 218-253 (328)
112 COG0233 Frr Ribosome recycling 41.5 1.4E+02 0.0031 25.6 7.3 34 78-111 152-185 (187)
113 cd07599 BAR_Rvs167p The Bin/Am 41.0 1.5E+02 0.0033 25.4 7.7 21 77-97 153-173 (216)
114 KOG1666|consensus 41.0 2.5E+02 0.0054 24.6 10.6 83 26-113 4-91 (220)
115 PHA03386 P10 fibrous body prot 40.6 1.6E+02 0.0035 22.3 7.2 31 17-47 4-34 (94)
116 KOG0412|consensus 40.4 4.4E+02 0.0096 27.4 11.8 38 18-55 24-64 (773)
117 PF15450 DUF4631: Domain of un 40.3 3.9E+02 0.0084 26.6 14.1 42 66-110 387-428 (531)
118 PF03148 Tektin: Tektin family 40.2 3.3E+02 0.0071 25.8 13.2 105 6-112 253-370 (384)
119 cd04476 RPA1_DBD_C RPA1_DBD_C: 40.0 19 0.00041 29.6 1.8 25 239-263 32-60 (166)
120 COG1579 Zn-ribbon protein, pos 40.0 2.7E+02 0.0059 24.8 11.0 76 16-111 1-76 (239)
121 KOG0996|consensus 40.0 4E+02 0.0087 29.3 11.6 46 65-110 885-930 (1293)
122 PF06008 Laminin_I: Laminin Do 39.6 2.7E+02 0.0059 24.7 11.6 43 65-107 188-233 (264)
123 PF10367 Vps39_2: Vacuolar sor 39.3 22 0.00048 26.5 2.0 28 214-246 78-108 (109)
124 PRK00808 hypothetical protein; 38.9 2.1E+02 0.0045 23.1 10.6 48 63-110 83-130 (150)
125 PF08946 Osmo_CC: Osmosensory 38.2 42 0.0009 22.0 2.7 27 83-109 8-34 (46)
126 KOG2856|consensus 38.1 3.7E+02 0.008 25.8 10.7 71 27-98 179-249 (472)
127 PF15290 Syntaphilin: Golgi-lo 37.9 3.2E+02 0.007 25.0 9.9 39 12-50 69-107 (305)
128 COG3404 Methenyl tetrahydrofol 37.2 2.8E+02 0.006 24.1 11.5 85 14-98 53-139 (208)
129 cd00890 Prefoldin Prefoldin is 36.8 1.7E+02 0.0037 22.5 6.8 46 67-112 81-126 (129)
130 KOG2041|consensus 36.7 34 0.00074 35.3 3.3 51 207-262 1109-1164(1189)
131 TIGR00595 priA primosomal prot 36.2 30 0.00065 34.1 2.8 35 228-263 223-262 (505)
132 PF12718 Tropomyosin_1: Tropom 35.8 2.4E+02 0.0052 22.9 12.6 32 76-107 97-128 (143)
133 PF07319 DnaI_N: Primosomal pr 35.4 1.4E+02 0.003 22.3 5.8 47 28-81 15-64 (94)
134 PF14446 Prok-RING_1: Prokaryo 35.3 23 0.0005 24.1 1.3 30 213-245 4-36 (54)
135 PF15079 DUF4546: Domain of un 34.9 2.8E+02 0.0061 23.5 8.1 54 19-84 51-104 (205)
136 PF02891 zf-MIZ: MIZ/SP-RING z 34.8 5.5 0.00012 26.5 -1.8 23 240-262 22-49 (50)
137 PF09726 Macoilin: Transmembra 34.7 5E+02 0.011 26.9 11.3 27 87-113 538-564 (697)
138 PF00038 Filament: Intermediat 34.6 2.3E+02 0.0051 25.5 8.3 31 10-40 208-238 (312)
139 PF07011 DUF1313: Protein of u 34.5 98 0.0021 23.1 4.6 34 16-49 40-73 (87)
140 smart00547 ZnF_RBZ Zinc finger 34.2 18 0.00039 20.1 0.5 11 253-263 1-11 (26)
141 KOG4628|consensus 34.1 33 0.0007 32.3 2.5 47 215-265 231-278 (348)
142 PF06160 EzrA: Septation ring 34.0 4.9E+02 0.011 26.0 13.1 45 61-105 167-212 (560)
143 PRK08032 fliD flagellar cappin 34.0 2.2E+02 0.0048 27.7 8.4 95 9-107 362-458 (462)
144 KOG3564|consensus 33.9 4.1E+02 0.0089 26.4 9.8 50 63-112 50-102 (604)
145 PF09755 DUF2046: Uncharacteri 33.9 3.9E+02 0.0085 24.8 13.7 39 71-109 155-193 (310)
146 TIGR02977 phageshock_pspA phag 33.9 3.1E+02 0.0068 23.7 13.6 105 4-112 13-131 (219)
147 PF00645 zf-PARP: Poly(ADP-rib 33.7 11 0.00024 27.3 -0.5 10 238-247 39-48 (82)
148 PF12861 zf-Apc11: Anaphase-pr 33.5 19 0.00041 26.9 0.7 24 239-263 55-80 (85)
149 PRK10807 paraquat-inducible pr 33.3 5.1E+02 0.011 25.9 14.1 20 4-25 420-439 (547)
150 KOG1246|consensus 33.3 36 0.00078 36.1 3.0 48 213-263 154-204 (904)
151 KOG4643|consensus 33.3 6.1E+02 0.013 27.6 11.5 8 93-100 529-536 (1195)
152 PF10498 IFT57: Intra-flagella 33.2 4.2E+02 0.0092 25.0 11.2 12 18-29 248-259 (359)
153 KOG4466|consensus 33.1 3.8E+02 0.0083 24.5 10.4 32 76-107 105-136 (291)
154 KOG1300|consensus 33.0 2.1E+02 0.0045 28.9 7.9 61 34-94 293-359 (593)
155 PRK04778 septation ring format 32.8 5.1E+02 0.011 25.9 13.5 20 88-107 304-323 (569)
156 PF03234 CDC37_N: Cdc37 N term 32.8 3.1E+02 0.0067 23.3 9.7 104 7-112 42-156 (177)
157 PRK14154 heat shock protein Gr 32.7 3.4E+02 0.0073 23.7 9.2 9 72-80 94-102 (208)
158 PF00641 zf-RanBP: Zn-finger i 32.6 23 0.0005 20.6 0.9 12 252-263 2-13 (30)
159 cd00520 RRF Ribosome recycling 32.5 1.9E+02 0.0042 24.3 6.8 32 79-110 147-178 (179)
160 PF08580 KAR9: Yeast cortical 32.1 5.9E+02 0.013 26.3 12.9 47 62-108 98-144 (683)
161 PF05064 Nsp1_C: Nsp1-like C-t 32.1 39 0.00084 26.5 2.3 28 28-55 18-45 (116)
162 PF10732 DUF2524: Protein of u 31.9 2.1E+02 0.0047 21.2 8.2 61 4-64 5-69 (84)
163 PF11221 Med21: Subunit 21 of 31.6 2.8E+02 0.006 22.4 10.3 56 43-98 83-140 (144)
164 PF04668 Tsg: Twisted gastrula 31.6 18 0.00039 29.3 0.3 27 235-261 100-131 (132)
165 PRK12495 hypothetical protein; 31.2 33 0.00073 30.1 1.9 11 252-262 56-66 (226)
166 PRK14011 prefoldin subunit alp 31.1 1.5E+02 0.0033 24.2 5.7 49 67-115 82-130 (144)
167 TIGR01149 mtrG N5-methyltetrah 30.9 1.4E+02 0.0031 21.4 4.7 31 17-47 11-41 (70)
168 PHA02414 hypothetical protein 30.6 2.5E+02 0.0054 21.5 8.6 70 30-108 2-78 (111)
169 PRK14873 primosome assembly pr 30.2 42 0.0009 34.4 2.8 43 214-263 383-431 (665)
170 PRK10132 hypothetical protein; 30.2 2.6E+02 0.0057 21.7 9.7 46 30-75 10-58 (108)
171 PF12906 RINGv: RING-variant d 30.0 6.3 0.00014 25.8 -2.1 23 238-260 25-47 (47)
172 PF08432 Vfa1: AAA-ATPase Vps4 29.9 30 0.00064 29.4 1.4 28 214-246 13-41 (182)
173 PRK05658 RNA polymerase sigma 29.3 4.4E+02 0.0095 26.7 9.9 27 14-40 214-240 (619)
174 PF12889 DUF3829: Protein of u 28.9 2.2E+02 0.0048 24.9 7.0 29 83-111 168-202 (276)
175 PF15272 BBP1_C: Spindle pole 28.8 3.8E+02 0.0083 23.1 12.1 28 5-36 3-30 (196)
176 PF04961 FTCD_C: Formiminotran 28.6 3.6E+02 0.0078 22.8 9.2 74 18-91 52-127 (184)
177 PF12095 DUF3571: Protein of u 28.0 1.4E+02 0.003 22.2 4.5 32 4-39 31-62 (83)
178 KOG0971|consensus 27.8 8E+02 0.017 26.5 11.6 94 20-113 260-358 (1243)
179 PRK05580 primosome assembly pr 27.8 44 0.00095 34.2 2.5 10 254-263 421-430 (679)
180 PF13865 FoP_duplication: C-te 27.7 1.1E+02 0.0024 21.9 3.9 23 29-51 44-70 (74)
181 KOG1318|consensus 27.7 4.7E+02 0.01 25.3 9.1 27 29-55 228-258 (411)
182 KOG2751|consensus 27.6 5.8E+02 0.013 24.8 10.5 17 25-41 143-159 (447)
183 PF12678 zf-rbx1: RING-H2 zinc 27.6 21 0.00045 25.5 0.1 20 238-261 52-73 (73)
184 PF10058 DUF2296: Predicted in 27.6 39 0.00085 22.9 1.4 30 228-262 23-52 (54)
185 PF09755 DUF2046: Uncharacteri 27.4 5.1E+02 0.011 24.1 13.5 23 68-90 109-131 (310)
186 PF10146 zf-C4H2: Zinc finger- 27.3 4.4E+02 0.0094 23.3 11.8 26 225-263 192-217 (230)
187 PF15619 Lebercilin: Ciliary p 27.3 4E+02 0.0086 22.8 14.1 37 6-42 49-85 (194)
188 PF13747 DUF4164: Domain of un 27.0 2.7E+02 0.0058 20.7 7.5 7 79-85 46-52 (89)
189 COG1773 Rubredoxin [Energy pro 26.8 56 0.0012 22.3 2.1 11 252-262 34-44 (55)
190 KOG1011|consensus 26.8 2.2E+02 0.0048 29.4 7.0 85 22-107 863-954 (1283)
191 PF15066 CAGE1: Cancer-associa 26.5 6.4E+02 0.014 24.9 12.0 86 16-111 416-502 (527)
192 PF12999 PRKCSH-like: Glucosid 26.4 4E+02 0.0087 22.6 7.8 25 83-107 149-173 (176)
193 TIGR01005 eps_transp_fam exopo 26.4 4.3E+02 0.0094 27.2 9.5 75 25-99 288-364 (754)
194 PF03107 C1_2: C1 domain; Int 26.2 55 0.0012 19.1 1.7 26 217-245 3-30 (30)
195 TIGR01562 FdhE formate dehydro 26.1 51 0.0011 30.5 2.3 8 255-262 253-260 (305)
196 PRK01026 tetrahydromethanopter 26.1 1.8E+02 0.004 21.2 4.7 31 17-47 14-44 (77)
197 smart00109 C1 Protein kinase C 26.0 38 0.00082 21.2 1.1 32 213-247 10-44 (49)
198 PF13949 ALIX_LYPXL_bnd: ALIX 25.9 4.7E+02 0.01 23.2 10.5 23 19-41 26-48 (296)
199 PF00301 Rubredoxin: Rubredoxi 25.9 36 0.00077 22.4 0.9 13 252-264 32-44 (47)
200 KOG1655|consensus 25.7 1.4E+02 0.0029 26.0 4.6 30 83-112 22-51 (218)
201 KOG4302|consensus 25.6 2.2E+02 0.0047 29.3 6.8 9 92-100 359-367 (660)
202 PF13922 PHD_3: PHD domain of 25.5 23 0.0005 25.1 -0.0 28 214-247 33-60 (69)
203 TIGR03545 conserved hypothetic 25.5 6.6E+02 0.014 25.3 10.2 39 69-107 219-257 (555)
204 PF08822 DUF1804: Protein of u 25.4 4.1E+02 0.0088 22.3 11.3 57 51-107 88-151 (165)
205 PF00412 LIM: LIM domain; Int 25.4 26 0.00055 23.1 0.2 24 238-261 20-54 (58)
206 COG0497 RecN ATPase involved i 25.4 7.1E+02 0.015 25.1 13.5 22 90-111 338-359 (557)
207 TIGR00606 rad50 rad50. This fa 25.4 9.7E+02 0.021 26.7 13.3 42 7-48 884-925 (1311)
208 PLN02678 seryl-tRNA synthetase 25.3 3.6E+02 0.0079 26.3 8.1 22 92-113 83-104 (448)
209 KOG2077|consensus 25.3 4.1E+02 0.0088 27.0 8.3 44 70-113 327-376 (832)
210 KOG2272|consensus 25.3 40 0.00087 30.3 1.4 47 216-264 139-193 (332)
211 PF15254 CCDC14: Coiled-coil d 25.0 8.3E+02 0.018 25.8 11.7 28 80-107 515-542 (861)
212 PF10737 GerPC: Spore germinat 25.0 3.7E+02 0.008 22.8 7.1 40 15-54 95-140 (176)
213 KOG1973|consensus 24.9 1E+02 0.0022 27.8 4.1 99 5-107 27-126 (274)
214 PF02996 Prefoldin: Prefoldin 24.9 3E+02 0.0065 20.9 6.3 43 69-111 73-115 (120)
215 KOG4451|consensus 24.8 4.3E+02 0.0092 23.6 7.6 39 5-43 51-89 (286)
216 PRK00409 recombination and DNA 24.6 8.3E+02 0.018 25.6 11.6 6 9-14 521-526 (782)
217 COG0266 Nei Formamidopyrimidin 24.6 39 0.00084 30.8 1.2 13 250-262 261-273 (273)
218 KOG2196|consensus 24.1 5.3E+02 0.011 23.1 12.8 37 76-112 167-203 (254)
219 COG0723 QcrA Rieske Fe-S prote 23.9 45 0.00098 27.8 1.5 18 241-258 110-129 (177)
220 PF14257 DUF4349: Domain of un 23.9 4.4E+02 0.0095 23.2 7.9 12 5-16 106-117 (262)
221 PF09789 DUF2353: Uncharacteri 23.9 6E+02 0.013 23.7 12.8 48 57-105 125-179 (319)
222 PF10267 Tmemb_cc2: Predicted 23.7 6.6E+02 0.014 24.1 12.3 35 15-49 209-243 (395)
223 KOG0250|consensus 23.4 1E+03 0.022 26.1 13.3 43 1-43 204-246 (1074)
224 PF02977 CarbpepA_inh: Carboxy 23.2 24 0.00052 23.1 -0.2 8 255-262 22-29 (46)
225 cd04772 HTH_TioE_rpt1 First He 23.2 1.1E+02 0.0023 23.0 3.3 23 87-109 76-98 (99)
226 PRK01103 formamidopyrimidine/5 23.2 46 0.00099 30.0 1.4 12 251-262 262-273 (274)
227 PF05478 Prominin: Prominin; 23.1 8.9E+02 0.019 25.4 12.5 35 9-43 185-220 (806)
228 KOG0976|consensus 23.0 9.5E+02 0.02 25.7 11.9 30 20-49 247-276 (1265)
229 PF05164 ZapA: Cell division p 23.0 2.9E+02 0.0062 19.7 10.2 25 33-57 22-46 (89)
230 PRK14127 cell division protein 23.0 1.9E+02 0.0041 22.6 4.7 39 4-42 30-68 (109)
231 KOG0612|consensus 22.9 1E+03 0.023 26.4 11.3 26 13-38 436-461 (1317)
232 PTZ00007 (NAP-L) nucleosome as 22.7 1.7E+02 0.0037 27.5 5.1 36 12-47 31-66 (337)
233 PF06717 DUF1202: Protein of u 22.7 3.7E+02 0.008 24.7 7.0 44 7-50 134-180 (308)
234 PF08535 KorB: KorB domain; I 22.7 3.1E+02 0.0068 20.0 7.0 22 3-25 17-38 (93)
235 KOG4057|consensus 22.7 4.5E+02 0.0097 21.8 7.8 35 74-113 32-66 (180)
236 CHL00154 rpl29 ribosomal prote 22.5 2.8E+02 0.006 19.6 5.1 22 60-81 42-63 (67)
237 PF12773 DZR: Double zinc ribb 22.5 76 0.0017 20.4 2.1 22 213-234 11-36 (50)
238 smart00787 Spc7 Spc7 kinetocho 22.4 6.2E+02 0.013 23.4 12.2 20 13-32 142-161 (312)
239 KOG4484|consensus 22.4 4.9E+02 0.011 22.1 9.7 29 6-41 36-64 (199)
240 PRK03564 formate dehydrogenase 22.3 76 0.0017 29.4 2.7 8 255-262 253-260 (309)
241 PF13758 Prefoldin_3: Prefoldi 22.3 3.7E+02 0.0079 20.7 6.3 84 23-112 3-93 (99)
242 PF10979 DUF2786: Protein of u 22.2 2.2E+02 0.0049 18.2 4.3 15 80-94 23-37 (43)
243 KOG4674|consensus 22.1 1.1E+03 0.024 27.5 11.7 108 6-113 574-687 (1822)
244 PF10046 BLOC1_2: Biogenesis o 22.0 3.5E+02 0.0076 20.3 12.9 27 79-105 72-98 (99)
245 TIGR03185 DNA_S_dndD DNA sulfu 22.0 8.4E+02 0.018 24.7 14.1 37 5-41 377-414 (650)
246 KOG3540|consensus 22.0 6.2E+02 0.013 25.2 8.7 98 5-107 331-436 (615)
247 cd02338 ZZ_PCMF_like Zinc fing 22.0 52 0.0011 21.6 1.2 31 228-262 1-32 (49)
248 KOG4721|consensus 22.0 9E+02 0.019 25.0 10.7 37 76-112 428-467 (904)
249 COG5293 Predicted ATPase [Gene 21.9 7.9E+02 0.017 24.4 12.6 51 62-112 403-453 (591)
250 PRK14811 formamidopyrimidine-D 21.7 56 0.0012 29.4 1.7 15 251-265 252-266 (269)
251 PF08400 phage_tail_N: Prophag 21.6 2.8E+02 0.0062 22.4 5.6 34 5-38 85-120 (134)
252 PF07195 FliD_C: Flagellar hoo 21.6 4.3E+02 0.0092 23.0 7.3 46 5-50 179-225 (239)
253 PRK05683 flgK flagellar hook-a 21.6 8.6E+02 0.019 25.1 10.3 34 64-97 165-201 (676)
254 cd07681 F-BAR_PACSIN3 The F-BA 21.5 6E+02 0.013 22.9 8.7 38 60-97 202-239 (258)
255 PF06827 zf-FPG_IleRS: Zinc fi 21.5 42 0.0009 19.4 0.6 13 250-262 17-29 (30)
256 PF13376 OmdA: Bacteriocin-pro 21.5 2.7E+02 0.0059 18.9 5.9 51 15-67 5-55 (63)
257 PF05769 DUF837: Protein of un 21.5 5E+02 0.011 21.9 11.1 95 12-110 4-104 (181)
258 PF11855 DUF3375: Protein of u 21.4 7.7E+02 0.017 24.1 13.8 33 6-38 180-212 (478)
259 PF11985 DUF3486: Protein of u 21.3 4.8E+02 0.01 21.7 7.7 29 12-40 6-35 (180)
260 COG5560 UBP12 Ubiquitin C-term 21.2 23 0.0005 36.0 -1.0 13 252-264 693-705 (823)
261 PF09730 BicD: Microtubule-ass 21.2 9.5E+02 0.021 25.1 10.9 73 10-82 365-439 (717)
262 COG3599 DivIVA Cell division i 21.1 5.6E+02 0.012 22.3 14.3 36 5-43 27-62 (212)
263 TIGR01069 mutS2 MutS2 family p 21.1 9.7E+02 0.021 25.1 13.0 14 29-42 508-521 (771)
264 TIGR02168 SMC_prok_B chromosom 21.1 1E+03 0.022 25.3 13.0 105 6-112 167-271 (1179)
265 COG4064 MtrG Tetrahydromethano 21.1 2.8E+02 0.006 19.9 4.7 31 17-47 14-44 (75)
266 TIGR00606 rad50 rad50. This fa 21.0 1.2E+03 0.025 26.0 13.2 23 88-110 1069-1091(1311)
267 PF14992 TMCO5: TMCO5 family 21.0 4.4E+02 0.0095 24.1 7.2 21 66-86 134-154 (280)
268 PRK06798 fliD flagellar cappin 20.9 2.1E+02 0.0046 27.7 5.6 72 5-81 366-437 (440)
269 PF04810 zf-Sec23_Sec24: Sec23 20.9 63 0.0014 20.2 1.4 12 252-263 22-33 (40)
270 PRK01917 cation-binding hemery 20.9 4.3E+02 0.0094 21.0 11.2 28 82-109 100-127 (139)
271 PF11101 DUF2884: Protein of u 20.8 5.7E+02 0.012 22.3 9.4 60 54-113 42-111 (229)
272 cd04777 HTH_MerR-like_sg1 Heli 20.8 2.7E+02 0.0058 21.0 5.1 24 87-110 81-104 (107)
273 KOG4796|consensus 20.7 8.7E+02 0.019 24.4 11.7 86 18-109 508-596 (604)
274 cd00162 RING RING-finger (Real 20.7 22 0.00048 21.4 -0.9 24 239-263 21-44 (45)
275 PF02403 Seryl_tRNA_N: Seryl-t 20.3 3.8E+02 0.0082 20.1 9.7 21 92-112 79-99 (108)
276 TIGR03185 DNA_S_dndD DNA sulfu 20.3 9.1E+02 0.02 24.5 11.1 24 79-102 479-502 (650)
277 PRK10626 hypothetical protein; 20.3 5.4E+02 0.012 23.0 7.5 40 54-93 64-106 (239)
278 PF07851 TMPIT: TMPIT-like pro 20.2 7.2E+02 0.016 23.3 10.4 44 63-110 47-91 (330)
279 KOG0995|consensus 20.1 9.1E+02 0.02 24.4 14.2 103 4-109 280-393 (581)
280 PRK09841 cryptic autophosphory 20.1 9.7E+02 0.021 24.7 15.0 51 5-57 249-302 (726)
281 TIGR01013 2a58 Phosphate:Na+ S 20.1 7.8E+02 0.017 23.7 10.4 20 81-100 413-432 (456)
282 PF05596 Taeniidae_ag: Taeniid 20.1 3E+02 0.0066 19.3 4.8 32 21-52 30-61 (64)
No 1
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=100.00 E-value=4.8e-39 Score=277.89 Aligned_cols=256 Identities=26% Similarity=0.436 Sum_probs=157.4
Q ss_pred hhHHHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHH--HHHHHHhcCCCChhHHH-HHHHHHHHHHHHHHHhHH
Q psy12696 3 TSYLEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRV--AEDYLDNMKHYSKDKKK-ETLAEIQKYFDKTKEYGD 79 (267)
Q Consensus 3 ~~yLedfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~--~~~~~k~~~~~~~~~~~-~~~~~I~~~~~~~~~lsd 79 (267)
...|+||+|.|+|+|.|+.+.|++|.++|.++.++++.+.+. +.+|+.+.++++++++. .+...|++.|-.+..+..
T Consensus 4 ~~~Lnd~~d~l~n~P~et~~~~t~l~~iD~k~~d~~k~l~q~~si~k~~~~~~~~t~~e~ed~l~k~i~Ell~~a~~~~~ 83 (271)
T COG5034 4 FPGLNDITDHLANVPSETDIRFTELSEIDAKVCDIIKNLRQMISILKKIIDLDSQTYEEVEDGLLKEIRELLLKAIYIQK 83 (271)
T ss_pred hHHHHHHHHHHHhCChhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhhcccCccccchhHHHHHHHHHHHHHHHHHH
Confidence 457999999999999999999999999999999999998765 55777788888888877 455789999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHhhcCCC---CCCCCCCCCCCCCCCCCCCCC-cccccccccc--c
Q psy12696 80 DKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQE-KALKNTTG---GAGGGGSGTGSGSGSAGGAAS-KSKRGRKKAK--D 152 (267)
Q Consensus 80 EKv~LA~~a~dlVd~hirrLD~dl~~~e~el~~-~~~~~~~~---~~~~~~~~~~~~s~~~~~~~~-~~~~~r~~~~--~ 152 (267)
+|..|++.+.-+++||+++||..+.+...+... .+++.... ...++.+.. ...+++...+ .+.-|+++++ .
T Consensus 84 ~~~~l~d~~~~l~~Rh~~~~d~~~a~~~h~~~~~~ie~~~~~~s~~~~~~~ss~--a~~ss~~~~saassqgs~~t~~~~ 161 (271)
T COG5034 84 EKSDLADRAEKLLRRHRKLLDDRIAKRPHEKVAARIENCHDAVSRLERNSYSSA--ARRSSGEHRSAASSQGSRHTKLKK 161 (271)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhHHHhhhhhhhhhhhhhhhhhhhhhhccccchh--hhccccccccccccccccCchhHH
Confidence 999999999999999999999998776654433 22222100 000111100 0000000000 0000111111 0
Q ss_pred ccccccccCCCCCCCchhhhhccccCCCCCccccccccccCCC-CCCCCCCCCCCCCCCCCCCceeecCCCCCCCccccc
Q psy12696 153 KAESATDAAGDDKSSNSKKKVAKKITGVGGVVGVLNAIVAADP-DVAAPSHDVLDMPVDPNEPTYCVCQQVSYGEMIGCD 231 (267)
Q Consensus 153 ~~~~~~~~~~~~~~~~~kk~~~~~~~~~~~~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~C~C~~~~~~~mi~Cd 231 (267)
+.........++ ...+++.+.... .++..+.......... ....+.-.+......+++++||+|++++||+||+||
T Consensus 162 R~n~~~~k~~~p-~~~S~r~~~~t~--~sp~v~~t~t~v~e~~~~~s~~~~~vss~d~se~e~lYCfCqqvSyGqMVaCD 238 (271)
T COG5034 162 RKNIHNLKRRSP-ELSSKREVSFTL--ESPSVPDTATRVKEGNNGGSTKSRGVSSEDNSEGEELYCFCQQVSYGQMVACD 238 (271)
T ss_pred HHhhcccccCCc-chhhhccCCccC--CCCCcccchhhhhcccCCCCccccCcCccccccCceeEEEecccccccceecC
Confidence 110000000011 000111111100 0010000000000000 000011111112234678999999999999999999
Q ss_pred CCCCCCcceecccCccCCCCCCceeCcCCcCc
Q psy12696 232 NPDCPIEWFHFACVSLTTKPKGKWYCPKCTSD 263 (267)
Q Consensus 232 ~~~c~~~wfH~~Cv~l~~~p~~~w~C~~C~~~ 263 (267)
+.+|+++|||+.||||..+|+|+|||+.|...
T Consensus 239 n~nCkrEWFH~~CVGLk~pPKG~WYC~eCk~~ 270 (271)
T COG5034 239 NANCKREWFHLECVGLKEPPKGKWYCPECKKA 270 (271)
T ss_pred CCCCchhheeccccccCCCCCCcEeCHHhHhc
Confidence 99999999999999999999999999999753
No 2
>KOG1973|consensus
Probab=100.00 E-value=6.8e-36 Score=269.07 Aligned_cols=239 Identities=37% Similarity=0.680 Sum_probs=160.3
Q ss_pred hhHHHHHHHH----hhcchHHHHHhHHHHHHHHHH--HHHHHHHHH-HHHHHHHHhcCC-CChhHHHHHHHHHHHHHHHH
Q psy12696 3 TSYLEQYLDS----LDSLPIELQRNFTLMRELDSR--AQDVMKTID-RVAEDYLDNMKH-YSKDKKKETLAEIQKYFDKT 74 (267)
Q Consensus 3 ~~yLedfld~----ie~LP~El~r~l~~irelD~~--~~~~~~~i~-~~~~~~~k~~~~-~~~~~~~~~~~~I~~~~~~~ 74 (267)
+++++++++. +.+||..++++|..|.++|.. ......+++ ..+..|++...+ ++.......+..|+..+...
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~f~~l~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (274)
T KOG1973|consen 7 AILIEEVDDDIDMAVQNLPRNLQHNFDVIEDIDIFGRSENQKKELDLKVAVEYMSKGRSQLSKPQKDPLLEAIRSALRKC 86 (274)
T ss_pred hhhhhhcccccccccccCCccchhHHHHHhhhhccchhHHHHhhhhhhhhhccccccccccCccccchhHHHHHHHHhhh
Confidence 3577788888 999999999999999999995 466666666 667778876663 34445667888999999999
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCccccccc--cccc
Q psy12696 75 KEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQEKALKNTTGGAGGGGSGTGSGSGSAGGAASKSKRGRK--KAKD 152 (267)
Q Consensus 75 ~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~r~--~~~~ 152 (267)
.+++|||+++|.++++++.+||+++|..+..|+.++..... .+....+. + .+..+.+++ ....
T Consensus 87 ~~~~~ek~~~~~~~~e~~~~~~~~~~~~~~~~e~~~~~~~~----~~~~~~~~-------~----~~~~~~~~~~~~~~~ 151 (274)
T KOG1973|consen 87 KELSDEKVQIAMQTVELIPKHIGRLETALKSFEVELELAKA----ESSSKRSS-------S----LKSAKKKEREVFKEK 151 (274)
T ss_pred hhhhhHHHHHHHHHHHhhHhhhcchhHHHHhcccchhhhhh----hccccccc-------c----hhccCccccccccch
Confidence 99999999999999999999999999999988877765420 00110000 0 000110000 0000
Q ss_pred cccc-ccccCCCCCCCc-------------hhhhhccccCCCCCccccccccccCCCCCCC--CCCCCCCCCCCCCCCce
Q psy12696 153 KAES-ATDAAGDDKSSN-------------SKKKVAKKITGVGGVVGVLNAIVAADPDVAA--PSHDVLDMPVDPNEPTY 216 (267)
Q Consensus 153 ~~~~-~~~~~~~~~~~~-------------~kk~~~~~~~~~~~~~g~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~ 216 (267)
.... +.....+..+.. ++++.+... . ........... .+..+.+...|+++++|
T Consensus 152 ~~s~~~~~~~~s~~~~~~~~~~~~~~~~~~rekk~~v~~----~------~~~~t~~~~~s~~~~~~~~~~~~d~~e~~y 221 (274)
T KOG1973|consen 152 KESKQGSSEKPSSVDKAKKGSKVNRRPCGAREKKRKVVE----A------KKEKTPKNKSSRPAESMESEEAVDPDEPTY 221 (274)
T ss_pred hhcCCCCCCCcccccccccccccccccchhhhhhhhhcc----c------cccccccCCCCCcccccccccccCCCCCEE
Confidence 0000 000000000000 111111000 0 00000001111 44456677889999999
Q ss_pred eecCCCCCCCcccccCCCCCCcceecccCccCCCCCCceeCcCCcCcccC
Q psy12696 217 CVCQQVSYGEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPKCTSDRKK 266 (267)
Q Consensus 217 C~C~~~~~~~mi~Cd~~~c~~~wfH~~Cv~l~~~p~~~w~C~~C~~~~~~ 266 (267)
|+|++++||.||.|||.+||++||||.||||+..|.|+||||.|...+++
T Consensus 222 C~Cnqvsyg~Mi~CDn~~C~~eWFH~~CVGL~~~PkgkWyC~~C~~~~~~ 271 (274)
T KOG1973|consen 222 CICNQVSYGKMIGCDNPGCPIEWFHFTCVGLKTKPKGKWYCPRCKAENKK 271 (274)
T ss_pred EEecccccccccccCCCCCCcceEEEeccccccCCCCcccchhhhhhhhc
Confidence 99999999999999999999999999999999999999999999987764
No 3
>PF12998 ING: Inhibitor of growth proteins N-terminal histone-binding; InterPro: IPR024610 Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterised C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail. This entry represents the N-terminal histone binding domain found in inhibitor proteins.; PDB: 4AFL_A.
Probab=99.95 E-value=4.7e-27 Score=182.38 Aligned_cols=103 Identities=47% Similarity=0.834 Sum_probs=96.8
Q ss_pred hHHHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC--CChhHHHHHHHHHHHHHHHHHHhHHHH
Q psy12696 4 SYLEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKH--YSKDKKKETLAEIQKYFDKTKEYGDDK 81 (267)
Q Consensus 4 ~yLedfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~--~~~~~~~~~~~~I~~~~~~~~~lsdEK 81 (267)
+||++|+|+|++||.||+|+|++||+||.++++...++++.+.+|++..++ ++++.+...+.+|+..+.+++.+++||
T Consensus 1 ~~le~f~d~~~~LP~el~r~l~~irelD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~~l~deK 80 (105)
T PF12998_consen 1 TYLEDFLDSLENLPAELQRNLTLIRELDAKSQDLLEELDQQIQKFIKNHGSPSLSPEKRRELLKEIQEEYERALELSDEK 80 (105)
T ss_dssp HHHHHHHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTS--S-HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHChHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhcccccCChHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 699999999999999999999999999999999999999999999999988 888888899999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 82 VQLAIQTYEMVDKYIRKLDTDLARF 106 (267)
Q Consensus 82 v~LA~~a~dlVd~hirrLD~dl~~~ 106 (267)
|+||+++|++|++|++|||.++++|
T Consensus 81 v~lA~~~~d~v~~hi~rLD~dl~~f 105 (105)
T PF12998_consen 81 VALAQQAYDLVDRHIRRLDQDLKKF 105 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCT---
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 9999999999999999999999887
No 4
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=98.81 E-value=7.8e-10 Score=74.58 Aligned_cols=44 Identities=48% Similarity=1.254 Sum_probs=36.4
Q ss_pred ee-ecCCCC-CCCcccccCCCCCCcceecccCccCCCC----CCceeCcCCcC
Q psy12696 216 YC-VCQQVS-YGEMIGCDNPDCPIEWFHFACVSLTTKP----KGKWYCPKCTS 262 (267)
Q Consensus 216 ~C-~C~~~~-~~~mi~Cd~~~c~~~wfH~~Cv~l~~~p----~~~w~C~~C~~ 262 (267)
|| +|++.. .+.||.||.|. .|||..|+++...+ .+.|+|+.|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~---~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCN---RWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTS---CEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCC---hhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 68 998864 47899999987 89999999977652 56899999864
No 5
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG1512|consensus
Probab=97.93 E-value=3.1e-06 Score=75.51 Aligned_cols=44 Identities=34% Similarity=0.792 Sum_probs=38.1
Q ss_pred cee-ecCCCCC-CCcccccCCCCCCcceecccCccCCCCCCceeCc-CCc
Q psy12696 215 TYC-VCQQVSY-GEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCP-KCT 261 (267)
Q Consensus 215 ~~C-~C~~~~~-~~mi~Cd~~~c~~~wfH~~Cv~l~~~p~~~w~C~-~C~ 261 (267)
..| +|++|.- .+|++||-|+ ..||..||||...|.|.|.|. .|.
T Consensus 315 ~lC~IC~~P~~E~E~~FCD~CD---RG~HT~CVGL~~lP~G~WICD~~C~ 361 (381)
T KOG1512|consen 315 ELCRICLGPVIESEHLFCDVCD---RGPHTLCVGLQDLPRGEWICDMRCR 361 (381)
T ss_pred HhhhccCCcccchheecccccc---CCCCccccccccccCccchhhhHHH
Confidence 346 8999864 7899999988 789999999999999999998 464
No 7
>KOG4323|consensus
Probab=97.91 E-value=3.7e-06 Score=80.20 Aligned_cols=49 Identities=29% Similarity=0.739 Sum_probs=37.6
Q ss_pred CceeecCCCC-CCCcccccCCCCCCcceecccCccC------CCCCCceeCcCCcCccc
Q psy12696 214 PTYCVCQQVS-YGEMIGCDNPDCPIEWFHFACVSLT------TKPKGKWYCPKCTSDRK 265 (267)
Q Consensus 214 ~~~C~C~~~~-~~~mi~Cd~~~c~~~wfH~~Cv~l~------~~p~~~w~C~~C~~~~~ 265 (267)
..||+|+++. +..||+|+.|+ .|||-.|.--. ..|...|||..|....+
T Consensus 171 c~vC~~g~~~~~NrmlqC~~C~---~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~ 226 (464)
T KOG4323|consen 171 CSVCYCGGPGAGNRMLQCDKCR---QWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPK 226 (464)
T ss_pred eeeeecCCcCccceeeeecccc---cHHHHHhccCCCCHhhccCccceEeehhhccchh
Confidence 5677777774 34799999998 99999998722 23467899999987654
No 8
>KOG0954|consensus
Probab=97.77 E-value=8.8e-06 Score=80.59 Aligned_cols=49 Identities=33% Similarity=0.754 Sum_probs=43.0
Q ss_pred CCCCcee-ecCCCCC---CCcccccCCCCCCcceecccCccCCCCCCceeCcCCcC
Q psy12696 211 PNEPTYC-VCQQVSY---GEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPKCTS 262 (267)
Q Consensus 211 ~~~~~~C-~C~~~~~---~~mi~Cd~~~c~~~wfH~~Cv~l~~~p~~~w~C~~C~~ 262 (267)
.+|.+.| +|+.++. .+||+||.|+ .-.|..|.||...|.|.|+|.-|.-
T Consensus 268 ~dedviCDvCrspD~e~~neMVfCd~Cn---~cVHqaCyGIle~p~gpWlCr~Cal 320 (893)
T KOG0954|consen 268 YDEDVICDVCRSPDSEEANEMVFCDKCN---ICVHQACYGILEVPEGPWLCRTCAL 320 (893)
T ss_pred ccccceeceecCCCccccceeEEeccch---hHHHHhhhceeecCCCCeeehhccc
Confidence 3589999 9999854 5699999988 5699999999999999999999964
No 9
>KOG0825|consensus
Probab=97.66 E-value=2e-05 Score=78.61 Aligned_cols=48 Identities=25% Similarity=0.793 Sum_probs=38.9
Q ss_pred CCCcee-ecCCCCC-CCcccccCCCCCCcceecccCcc--CCCCCCceeCcCCc
Q psy12696 212 NEPTYC-VCQQVSY-GEMIGCDNPDCPIEWFHFACVSL--TTKPKGKWYCPKCT 261 (267)
Q Consensus 212 ~~~~~C-~C~~~~~-~~mi~Cd~~~c~~~wfH~~Cv~l--~~~p~~~w~C~~C~ 261 (267)
.|..-| +|..++- ..||.||.|+ ...||..|+.. ...|.+.|||+.|.
T Consensus 213 ~E~~~C~IC~~~DpEdVLLLCDsCN--~~~YH~YCLDPdl~eiP~~eWYC~NC~ 264 (1134)
T KOG0825|consen 213 QEEVKCDICTVHDPEDVLLLCDSCN--KVYYHVYCLDPDLSESPVNEWYCTNCS 264 (1134)
T ss_pred cccccceeeccCChHHhheeecccc--cceeeccccCcccccccccceecCcch
Confidence 455678 9988865 5599999977 45599999994 45899999999995
No 10
>KOG4299|consensus
Probab=97.66 E-value=1.4e-05 Score=78.18 Aligned_cols=46 Identities=35% Similarity=1.108 Sum_probs=36.1
Q ss_pred Ccee-ecCCCC-CCCcccccCCCCCCcceecccCc----cCCCCCCceeCcCCcC
Q psy12696 214 PTYC-VCQQVS-YGEMIGCDNPDCPIEWFHFACVS----LTTKPKGKWYCPKCTS 262 (267)
Q Consensus 214 ~~~C-~C~~~~-~~~mi~Cd~~~c~~~wfH~~Cv~----l~~~p~~~w~C~~C~~ 262 (267)
..|| .|++.. |...|+||. ||. -||+.|+. .+..|.|.|||+.|..
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD~--Cp~-sFH~~CLePPl~~eniP~g~W~C~ec~~ 304 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCDG--CPR-SFHQTCLEPPLEPENIPPGSWFCPECKI 304 (613)
T ss_pred HHHHHHhCCccccccceeecC--Cch-HHHHhhcCCCCCcccCCCCccccCCCee
Confidence 3499 998883 445699999 666 49999998 3346789999999964
No 11
>KOG1244|consensus
Probab=97.56 E-value=2e-05 Score=70.03 Aligned_cols=52 Identities=31% Similarity=0.811 Sum_probs=42.9
Q ss_pred CCCcee-ecCCCCC-CCcccccCCCCCCcceecccCc--cCCCCCCceeCcCCcCcccC
Q psy12696 212 NEPTYC-VCQQVSY-GEMIGCDNPDCPIEWFHFACVS--LTTKPKGKWYCPKCTSDRKK 266 (267)
Q Consensus 212 ~~~~~C-~C~~~~~-~~mi~Cd~~~c~~~wfH~~Cv~--l~~~p~~~w~C~~C~~~~~~ 266 (267)
-|-.|| +|+...+ .++++||.|+ ..||..|+. |..+|.|.|-|-.|...-++
T Consensus 279 ieck~csicgtsenddqllfcddcd---rgyhmyclsppm~eppegswsc~KOG~~~~e 334 (336)
T KOG1244|consen 279 IECKYCSICGTSENDDQLLFCDDCD---RGYHMYCLSPPMVEPPEGSWSCHLCLEELKE 334 (336)
T ss_pred eecceeccccCcCCCceeEeecccC---CceeeEecCCCcCCCCCCchhHHHHHHHHhh
Confidence 356788 8987765 6799999988 779999998 77788999999999766554
No 12
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=97.45 E-value=1.6e-05 Score=49.79 Aligned_cols=34 Identities=29% Similarity=0.834 Sum_probs=20.0
Q ss_pred CCcccccCCCCCCcceecccCccCCCCCC-ceeCcCCc
Q psy12696 225 GEMIGCDNPDCPIEWFHFACVSLTTKPKG-KWYCPKCT 261 (267)
Q Consensus 225 ~~mi~Cd~~~c~~~wfH~~Cv~l~~~p~~-~w~C~~C~ 261 (267)
..||.|++|. -.+|..|-|+...|.+ .|+|..|.
T Consensus 2 n~ll~C~~C~---v~VH~~CYGv~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCN---VAVHQSCYGVSEVPDGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS-----EEEHHHHT-SS--SS-----HHH-
T ss_pred CceEEeCCCC---CcCChhhCCcccCCCCCcEECCcCC
Confidence 4689999977 6899999999999865 89998874
No 13
>KOG1245|consensus
Probab=96.95 E-value=0.00016 Score=77.87 Aligned_cols=50 Identities=32% Similarity=0.840 Sum_probs=41.9
Q ss_pred CCCcee-ecCCCCC-CCcccccCCCCCCcceecccCc--cCCCCCCceeCcCCcCcc
Q psy12696 212 NEPTYC-VCQQVSY-GEMIGCDNPDCPIEWFHFACVS--LTTKPKGKWYCPKCTSDR 264 (267)
Q Consensus 212 ~~~~~C-~C~~~~~-~~mi~Cd~~~c~~~wfH~~Cv~--l~~~p~~~w~C~~C~~~~ 264 (267)
.....| +|+.-.. ..|+.|+.|+ .|||+.|+. +...|.+.|+||.|+.+.
T Consensus 1106 ~~~~~c~~cr~k~~~~~m~lc~~c~---~~~h~~C~rp~~~~~~~~dW~C~~c~~e~ 1159 (1404)
T KOG1245|consen 1106 AVNALCKVCRRKKQDEKMLLCDECL---SGFHLFCLRPALSSVPPGDWMCPSCRKEH 1159 (1404)
T ss_pred cchhhhhhhhhcccchhhhhhHhhh---hhHHHHhhhhhhccCCcCCccCCccchhh
Confidence 345678 8876644 4699999999 999999988 778899999999998876
No 14
>KOG0955|consensus
Probab=96.92 E-value=0.00061 Score=71.23 Aligned_cols=50 Identities=24% Similarity=0.671 Sum_probs=40.0
Q ss_pred CCCcee-ecCCCCC---CCcccccCCCCCCcceecccCccCCCCCCceeCcCCcCcc
Q psy12696 212 NEPTYC-VCQQVSY---GEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPKCTSDR 264 (267)
Q Consensus 212 ~~~~~C-~C~~~~~---~~mi~Cd~~~c~~~wfH~~Cv~l~~~p~~~w~C~~C~~~~ 264 (267)
+++..| +|....- ...|+||.|+ --+|..|.|+...|.|.|+|..|.-..
T Consensus 217 ~~D~~C~iC~~~~~~n~n~ivfCD~Cn---l~VHq~Cygi~~ipeg~WlCr~Cl~s~ 270 (1051)
T KOG0955|consen 217 EEDAVCCICLDGECQNSNVIVFCDGCN---LAVHQECYGIPFIPEGQWLCRRCLQSP 270 (1051)
T ss_pred CCCccceeecccccCCCceEEEcCCCc---chhhhhccCCCCCCCCcEeehhhccCc
Confidence 344455 9987742 5689999987 459999999999999999999997543
No 15
>KOG0383|consensus
Probab=96.74 E-value=0.00066 Score=68.34 Aligned_cols=46 Identities=41% Similarity=1.101 Sum_probs=36.5
Q ss_pred CCcee-ecCCCCCCCcccccCCCCCCcceecccCc--cCCCCCCceeCcCCcCc
Q psy12696 213 EPTYC-VCQQVSYGEMIGCDNPDCPIEWFHFACVS--LTTKPKGKWYCPKCTSD 263 (267)
Q Consensus 213 ~~~~C-~C~~~~~~~mi~Cd~~~c~~~wfH~~Cv~--l~~~p~~~w~C~~C~~~ 263 (267)
+..+| +|... |..|+||. || .|||..|++ +...|.+.|.|+.|...
T Consensus 46 ~~e~c~ic~~~--g~~l~c~t--C~-~s~h~~cl~~pl~~~p~~~~~c~Rc~~p 94 (696)
T KOG0383|consen 46 EQEACRICADG--GELLWCDT--CP-ASFHASCLGPPLTPQPNGEFICPRCFCP 94 (696)
T ss_pred hhhhhhhhcCC--CcEEEecc--cc-HHHHHHccCCCCCcCCccceeeeeeccC
Confidence 45566 99877 99999999 55 699999998 55666677999999543
No 16
>KOG0956|consensus
Probab=96.61 E-value=0.00059 Score=67.53 Aligned_cols=39 Identities=33% Similarity=0.974 Sum_probs=34.7
Q ss_pred CCcccccCCCCCCcceecccCccCCCCCCceeCcCCcCcc
Q psy12696 225 GEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPKCTSDR 264 (267)
Q Consensus 225 ~~mi~Cd~~~c~~~wfH~~Cv~l~~~p~~~w~C~~C~~~~ 264 (267)
..+|.||+-.|... .|-.|.||..+|.|.|||..|....
T Consensus 20 NPLVYCDG~nCsVA-VHQaCYGIvqVPtGpWfCrKCesqe 58 (900)
T KOG0956|consen 20 NPLVYCDGHNCSVA-VHQACYGIVQVPTGPWFCRKCESQE 58 (900)
T ss_pred CceeeecCCCceee-eehhcceeEecCCCchhhhhhhhhh
Confidence 55899999889886 9999999999999999999997543
No 17
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=96.34 E-value=0.0011 Score=63.56 Aligned_cols=45 Identities=27% Similarity=0.707 Sum_probs=37.5
Q ss_pred cee-ecCCCCC---CCcccccCCCCCCcceecccCccCCCCCCceeCcCCcC
Q psy12696 215 TYC-VCQQVSY---GEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPKCTS 262 (267)
Q Consensus 215 ~~C-~C~~~~~---~~mi~Cd~~~c~~~wfH~~Cv~l~~~p~~~w~C~~C~~ 262 (267)
..| +|..... ...|.||+|+ --.|-+|-|+...|.|.|+|..|.-
T Consensus 194 ~~C~~c~~t~~eN~naiVfCdgC~---i~VHq~CYGI~f~peG~WlCrkCi~ 242 (669)
T COG5141 194 DICTKCTSTHNENSNAIVFCDGCE---ICVHQSCYGIQFLPEGFWLCRKCIY 242 (669)
T ss_pred hhhHhccccccCCcceEEEecCcc---hhhhhhcccceecCcchhhhhhhcc
Confidence 457 8877754 4589999987 4599999999999999999999953
No 18
>KOG1632|consensus
Probab=96.11 E-value=0.0023 Score=59.79 Aligned_cols=48 Identities=25% Similarity=0.627 Sum_probs=39.2
Q ss_pred CceeecCCCCCC--CcccccCCCCCCcceeccc--CccCC---CCCCceeCcCCcCcc
Q psy12696 214 PTYCVCQQVSYG--EMIGCDNPDCPIEWFHFAC--VSLTT---KPKGKWYCPKCTSDR 264 (267)
Q Consensus 214 ~~~C~C~~~~~~--~mi~Cd~~~c~~~wfH~~C--v~l~~---~p~~~w~C~~C~~~~ 264 (267)
..||.|..+... .|+.|+.|. .|||..| ||+.. .+...|+|..|....
T Consensus 60 ~~~~~~~~~~~p~~~~~~cd~C~---~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~ 114 (345)
T KOG1632|consen 60 QRYCKCYKPCDPDDLMEQCDLCE---DWYHGECWEVGTAEKEAPKEDPKVCDECKEAQ 114 (345)
T ss_pred hchhhcccccCchhhhhcccccc---ccccccccccCchhhcCCccccccccccchhh
Confidence 348999888765 799999988 8999999 99665 336889999997654
No 19
>KOG0957|consensus
Probab=95.66 E-value=0.28 Score=47.60 Aligned_cols=44 Identities=32% Similarity=0.828 Sum_probs=34.1
Q ss_pred cee-ecCCCCC-CCcccccCCCCCCcceecccCc--cCCCCCC----ceeCcCCc
Q psy12696 215 TYC-VCQQVSY-GEMIGCDNPDCPIEWFHFACVS--LTTKPKG----KWYCPKCT 261 (267)
Q Consensus 215 ~~C-~C~~~~~-~~mi~Cd~~~c~~~wfH~~Cv~--l~~~p~~----~w~C~~C~ 261 (267)
.-| +|.+... -.+++||-|. --||+.|+. |+..|.. -|.|..|-
T Consensus 545 ysCgiCkks~dQHll~~CDtC~---lhYHlGCL~PPLTR~Pkk~kn~gWqCsECd 596 (707)
T KOG0957|consen 545 YSCGICKKSTDQHLLTQCDTCH---LHYHLGCLSPPLTRLPKKNKNFGWQCSECD 596 (707)
T ss_pred eeeeeeccchhhHHHhhcchhh---ceeeccccCCccccCcccccCcceeecccc
Confidence 348 8987754 3488999976 569999998 8888832 59999993
No 20
>KOG0957|consensus
Probab=94.42 E-value=0.038 Score=53.36 Aligned_cols=49 Identities=29% Similarity=0.731 Sum_probs=33.8
Q ss_pred CCCC-ceeecCC-C--CCCCcccccCCCCCCcceecccCccCC---CC-------CCceeCcCCcC
Q psy12696 211 PNEP-TYCVCQQ-V--SYGEMIGCDNPDCPIEWFHFACVSLTT---KP-------KGKWYCPKCTS 262 (267)
Q Consensus 211 ~~~~-~~C~C~~-~--~~~~mi~Cd~~~c~~~wfH~~Cv~l~~---~p-------~~~w~C~~C~~ 262 (267)
|-.. .+|+|-. . +-++.|+||+|. .-.|-.|.|+.. .| ...|||..|.-
T Consensus 116 pkk~~iCcVClg~rs~da~ei~qCd~CG---i~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~ 178 (707)
T KOG0957|consen 116 PKKAVICCVCLGQRSVDAGEILQCDKCG---INVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLY 178 (707)
T ss_pred cccceEEEEeecCccccccceeeccccC---ceecccccccccccccCCCCccCCCCchhhhhHhc
Confidence 3334 4569943 2 348899999976 459999999542 12 25799999864
No 21
>KOG1632|consensus
Probab=93.41 E-value=0.016 Score=54.26 Aligned_cols=51 Identities=27% Similarity=0.572 Sum_probs=39.0
Q ss_pred CCCCCCcee-ecCCCCC--CCcccccCCCCCCcceecccCccCCCC---CCc----eeCcCCcC
Q psy12696 209 VDPNEPTYC-VCQQVSY--GEMIGCDNPDCPIEWFHFACVSLTTKP---KGK----WYCPKCTS 262 (267)
Q Consensus 209 ~~~~~~~~C-~C~~~~~--~~mi~Cd~~~c~~~wfH~~Cv~l~~~p---~~~----w~C~~C~~ 262 (267)
.++.+..+| .|+.... ..||+|+.|. .|||..||.+...+ ... ++|+.|.-
T Consensus 234 ~~~~~~~~~~~cg~~~~~~~~~~~~~~~e---~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~ 294 (345)
T KOG1632|consen 234 APDYSKLICDPCGLSDANKKFEICCDLCE---SWFHGDCVQIFEARKRLNEIRNEVYKCPHCTV 294 (345)
T ss_pred ccccccccccccCcchHHHHHHHHHHHHH---HHhcccccccccchhhhhhhhccceecCceee
Confidence 455666788 5655432 4699999998 89999999998877 334 99999964
No 22
>KOG2752|consensus
Probab=91.41 E-value=0.096 Score=47.86 Aligned_cols=31 Identities=32% Similarity=0.868 Sum_probs=24.3
Q ss_pred CCceeecCCCCC-------CCcccccCCCCCCccee-cccCc
Q psy12696 213 EPTYCVCQQVSY-------GEMIGCDNPDCPIEWFH-FACVS 246 (267)
Q Consensus 213 ~~~~C~C~~~~~-------~~mi~Cd~~~c~~~wfH-~~Cv~ 246 (267)
.-.||.|..+.. |.|++|-.|. .||| -.|.-
T Consensus 127 qG~~C~Cd~~Ypdp~~~~e~~m~QC~iCE---DWFHce~c~~ 165 (345)
T KOG2752|consen 127 QGLFCKCDTPYPDPVRTEEGEMLQCVICE---DWFHCEGCMQ 165 (345)
T ss_pred cceeEEecCCCCCccccccceeeeEEecc---chhcccccCc
Confidence 467999988754 4699999988 9999 55543
No 23
>KOG1844|consensus
Probab=91.17 E-value=0.2 Score=49.01 Aligned_cols=50 Identities=30% Similarity=0.573 Sum_probs=39.8
Q ss_pred CCCceeecCCC-C-CCCcccccCCCCCCcceecccCccCCCC-CCceeCcCCcCcc
Q psy12696 212 NEPTYCVCQQV-S-YGEMIGCDNPDCPIEWFHFACVSLTTKP-KGKWYCPKCTSDR 264 (267)
Q Consensus 212 ~~~~~C~C~~~-~-~~~mi~Cd~~~c~~~wfH~~Cv~l~~~p-~~~w~C~~C~~~~ 264 (267)
.....|.|+.. . .|.||+|+.|. .|-|.-|+|....- +..|.|..|....
T Consensus 84 ~~~~~c~c~~~~~~~g~~i~c~~c~---~Wqh~~C~g~~~~~~p~~y~c~~c~~~~ 136 (508)
T KOG1844|consen 84 REISRCDCGLEDDMEGLMIQCDWCG---RWQHKICCGSFKSTKPDKYVCEICTPRN 136 (508)
T ss_pred CcccccccccccCCCceeeCCcccC---cccCceeeeecCCCCchhceeeeecccc
Confidence 35677999866 3 58899999977 79999999955443 5899999997654
No 24
>KOG4443|consensus
Probab=88.57 E-value=0.26 Score=49.25 Aligned_cols=46 Identities=28% Similarity=0.675 Sum_probs=35.1
Q ss_pred Ccee-ecCCCC-CCCcccccCCCCCCcceecccCc--cCCCCCCceeCcCCcC
Q psy12696 214 PTYC-VCQQVS-YGEMIGCDNPDCPIEWFHFACVS--LTTKPKGKWYCPKCTS 262 (267)
Q Consensus 214 ~~~C-~C~~~~-~~~mi~Cd~~~c~~~wfH~~Cv~--l~~~p~~~w~C~~C~~ 262 (267)
-+.| .|+... ....+.|+.|+ .-||..|.- ++.+|.|.|+|+.|..
T Consensus 68 crvCe~c~~~gD~~kf~~Ck~cD---vsyh~yc~~P~~~~v~sg~~~ckk~~~ 117 (694)
T KOG4443|consen 68 CRVCEACGTTGDPKKFLLCKRCD---VSYHCYCQKPPNDKVPSGPWLCKKCTR 117 (694)
T ss_pred ceeeeeccccCCccccccccccc---ccccccccCCccccccCcccccHHHHh
Confidence 4566 676442 24578899988 679999987 7778899999998854
No 25
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=86.83 E-value=14 Score=29.34 Aligned_cols=102 Identities=16% Similarity=0.245 Sum_probs=69.9
Q ss_pred hhcchHHHHHhHHHHHHHHHHHHHHHHHH---HHHHHH---HHHhcCCCChhHHHHH---HHHHHHHHHHHHHhHHHHHH
Q psy12696 13 LDSLPIELQRNFTLMRELDSRAQDVMKTI---DRVAED---YLDNMKHYSKDKKKET---LAEIQKYFDKTKEYGDDKVQ 83 (267)
Q Consensus 13 ie~LP~El~r~l~~irelD~~~~~~~~~i---~~~~~~---~~k~~~~~~~~~~~~~---~~~I~~~~~~~~~lsdEKv~ 83 (267)
+.+||.+++..+.....|-.+.+.+..+. +..+.+ -+.....++.+..... -.-|.....++..=.++++.
T Consensus 1 ~~~lpp~~q~~l~q~QqLq~ql~~~~~qk~~le~qL~E~~~al~Ele~l~eD~~vYk~VG~llvk~~k~~~~~eL~er~E 80 (119)
T COG1382 1 MEQLPPEVQAQLAQLQQLQQQLQKVILQKQQLEAQLKEIEKALEELEKLDEDAPVYKKVGNLLVKVSKEEAVDELEERKE 80 (119)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccHHHHHhhhHHhhhhHHHHHHHHHHHHH
Confidence 36899999999999999988888776553 332222 2222233433322210 11245566777788888888
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 84 LAIQTYEMVDKYIRKLDTDLARFEQEIQEKA 114 (267)
Q Consensus 84 LA~~a~dlVd~hirrLD~dl~~~e~el~~~~ 114 (267)
.-.-=...+++..++|+..++.+...|...+
T Consensus 81 ~Le~ri~tLekQe~~l~e~l~eLq~~i~~~l 111 (119)
T COG1382 81 TLELRIKTLEKQEEKLQERLEELQSEIQKAL 111 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 8888888899999999999999988887753
No 26
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=85.74 E-value=0.59 Score=44.91 Aligned_cols=43 Identities=26% Similarity=0.690 Sum_probs=30.2
Q ss_pred ecCCCCC--C--CcccccCCCCCCcceecccCc---c-----CC-C----CCCceeCcCCcCc
Q psy12696 218 VCQQVSY--G--EMIGCDNPDCPIEWFHFACVS---L-----TT-K----PKGKWYCPKCTSD 263 (267)
Q Consensus 218 ~C~~~~~--~--~mi~Cd~~~c~~~wfH~~Cv~---l-----~~-~----p~~~w~C~~C~~~ 263 (267)
+|++.++ + .+|.||.|. .|-|..|.= + +. . ..+.|+|..|...
T Consensus 133 iC~kfD~~~n~~~Wi~Cd~Cg---H~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~ 192 (446)
T PF07227_consen 133 ICSKFDDNKNTCSWIGCDVCG---HWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKT 192 (446)
T ss_pred ccCCcccCCCCeeEEeccCCC---ceehhhhhcccccccCCccCCCCCccCceEEEccCCCCh
Confidence 8877654 2 399999988 899999942 1 11 1 1347999999653
No 27
>PF10158 LOH1CR12: Tumour suppressor protein; InterPro: IPR018780 This entry represents a region of 130 amino acids that is the most conserved part of some hypothetical proteins involved in loss of heterozygosity, and thus, tumour suppression []. The exact function of these proteins is not known.
Probab=82.10 E-value=25 Score=28.35 Aligned_cols=77 Identities=9% Similarity=0.194 Sum_probs=40.1
Q ss_pred HHHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHH
Q psy12696 5 YLEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQL 84 (267)
Q Consensus 5 yLedfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~L 84 (267)
|-+.|-.+.+.+=.|=...-..||+.|.....+...+.+..+.|-+... ....+.+|...+.++..+-++=+.+
T Consensus 36 ~Q~HL~~cA~~Va~~Q~~L~~riKevd~~~~~l~~~~~erqk~~~k~ae------~L~kv~els~~L~~~~~lL~~~v~~ 109 (131)
T PF10158_consen 36 YQEHLNQCAEAVAFDQNALAKRIKEVDQEIAKLLQQMVERQKRFAKFAE------QLEKVNELSQQLSRCQSLLNQTVPS 109 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444444555555566777777777777777666665544221 1223444555555555444443333
Q ss_pred HHH
Q psy12696 85 AIQ 87 (267)
Q Consensus 85 A~~ 87 (267)
..+
T Consensus 110 ie~ 112 (131)
T PF10158_consen 110 IET 112 (131)
T ss_pred HHH
Confidence 333
No 28
>PF13341 RAG2_PHD: RAG2 PHD domain; PDB: 2JWO_A 2V86_B 2V85_B 2V87_A 2V83_C 2V89_A 2V88_A.
Probab=81.34 E-value=0.47 Score=33.87 Aligned_cols=32 Identities=28% Similarity=0.703 Sum_probs=19.2
Q ss_pred CcccccCCCCCCcceecccCccCCCC-------CCceeCcC
Q psy12696 226 EMIGCDNPDCPIEWFHFACVSLTTKP-------KGKWYCPK 259 (267)
Q Consensus 226 ~mi~Cd~~~c~~~wfH~~Cv~l~~~p-------~~~w~C~~ 259 (267)
.||.|...+ ..|.|..|..|...- ..+|||.+
T Consensus 29 AMI~cs~~~--GHWvhaqCm~LsE~~L~~LSq~n~KYfC~d 67 (78)
T PF13341_consen 29 AMIFCSRGG--GHWVHAQCMDLSETMLIQLSQENTKYFCND 67 (78)
T ss_dssp -EEEE-STT---EEEETGGGT--HHHHHHHHHSSS-B--TT
T ss_pred eEEEEeCCC--ceEeEeecccchHHHHHHHccCCceEEEhh
Confidence 499999864 689999999987632 56899964
No 29
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=81.27 E-value=0.69 Score=35.64 Aligned_cols=31 Identities=32% Similarity=0.817 Sum_probs=24.4
Q ss_pred Ccee-ecCCCCCCCcccccCCCCCCcceecccCc
Q psy12696 214 PTYC-VCQQVSYGEMIGCDNPDCPIEWFHFACVS 246 (267)
Q Consensus 214 ~~~C-~C~~~~~~~mi~Cd~~~c~~~wfH~~Cv~ 246 (267)
...| +|+.. .|..|.|...+|.. +||..|.-
T Consensus 55 ~~~C~iC~~~-~G~~i~C~~~~C~~-~fH~~CA~ 86 (110)
T PF13832_consen 55 KLKCSICGKS-GGACIKCSHPGCST-AFHPTCAR 86 (110)
T ss_pred CCcCcCCCCC-CceeEEcCCCCCCc-CCCHHHHH
Confidence 4456 99876 68899999977755 79999964
No 30
>PF10796 Anti-adapt_IraP: Sigma-S stabilisation anti-adaptor protein ; InterPro: IPR019732 This entry is conserved in Enterobacteriaceae. It is one of a series of proteins, expressed by these bacteria in response to stress, that help to regulate Sigma-S, the stationary phase sigma factor of Escherichia coli and Salmonella. IraP is essential for Sigma-S stabilisation in some but not all starvation conditions []. ; GO: 0005737 cytoplasm
Probab=81.14 E-value=14 Score=27.69 Aligned_cols=77 Identities=12% Similarity=0.286 Sum_probs=53.5
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 20 LQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKL 99 (267)
Q Consensus 20 l~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrL 99 (267)
|...|-.|-++|+...++..+++.+---...-...+.+..+.+.+..|...+..+..-+++=.. .-.+++.+|+++|
T Consensus 5 i~~lL~KlA~~e~esKeL~AqVEAleivitALL~~l~~~~~~~~i~~I~~Ai~~a~~~~~~~~~---sd~eLL~~~~~~L 81 (87)
T PF10796_consen 5 IAELLAKLAEKEAESKELTAQVEALEIVITALLRTLDQGGRQEMIESIEKAIEDASPSSDVPLK---SDAELLLQYVKKL 81 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHhcccCCccch---HHHHHHHHHHHHH
Confidence 5566788999999999999998876333222333556677888999999999888876655322 1345666666555
No 31
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=81.02 E-value=0.85 Score=33.70 Aligned_cols=31 Identities=35% Similarity=0.941 Sum_probs=24.9
Q ss_pred Ccee-ecCCCCCCCcccccCCCCCCcceecccCc
Q psy12696 214 PTYC-VCQQVSYGEMIGCDNPDCPIEWFHFACVS 246 (267)
Q Consensus 214 ~~~C-~C~~~~~~~mi~Cd~~~c~~~wfH~~Cv~ 246 (267)
...| +|+++ .|-.|.|....|.. +||+.|.-
T Consensus 36 ~~~C~~C~~~-~Ga~i~C~~~~C~~-~fH~~CA~ 67 (90)
T PF13771_consen 36 KLKCSICKKK-GGACIGCSHPGCSR-SFHVPCAR 67 (90)
T ss_pred CCCCcCCCCC-CCeEEEEeCCCCCc-EEChHHHc
Confidence 4467 88766 68899999988876 69999965
No 32
>KOG1493|consensus
Probab=80.94 E-value=0.74 Score=33.57 Aligned_cols=48 Identities=31% Similarity=0.848 Sum_probs=32.9
Q ss_pred ee-ecCCCCCCCccccc--CCCCCCcc------eecccCc-cCCCCCCceeCcCCcCc
Q psy12696 216 YC-VCQQVSYGEMIGCD--NPDCPIEW------FHFACVS-LTTKPKGKWYCPKCTSD 263 (267)
Q Consensus 216 ~C-~C~~~~~~~mi~Cd--~~~c~~~w------fH~~Cv~-l~~~p~~~w~C~~C~~~ 263 (267)
.| +|+.+.+|-=-.|. +.+||..| ||..|+- --..|...-.||.|+.+
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~ 79 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQT 79 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchhe
Confidence 67 99988777433443 23388866 8999976 22455666899999864
No 33
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=80.93 E-value=23 Score=31.34 Aligned_cols=50 Identities=14% Similarity=0.234 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q psy12696 36 DVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLA 85 (267)
Q Consensus 36 ~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA 85 (267)
-++.+.-..++.|+...-.+..++|...+..+...+..+.--.-||+...
T Consensus 105 p~m~~m~~~L~~~v~~d~Pf~~~eR~~Rl~~L~~~l~~~dv~~~ek~r~v 154 (251)
T PF11932_consen 105 PLMEQMIDELEQFVELDLPFLLEERQERLARLRAMLDDADVSLAEKFRRV 154 (251)
T ss_pred HHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHhhhccCCCHHHHHHHH
Confidence 33333344445555544444555566666666666666655555554433
No 34
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=80.49 E-value=24 Score=27.19 Aligned_cols=46 Identities=13% Similarity=0.176 Sum_probs=35.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 67 IQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQE 112 (267)
Q Consensus 67 I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el~~ 112 (267)
|......+..--.+++.........+++.+..|...+..++..+..
T Consensus 61 v~~~~~e~~~~l~~r~e~ie~~i~~lek~~~~l~~~l~e~q~~l~~ 106 (110)
T TIGR02338 61 VKTDKEEAIQELKEKKETLELRVKTLQRQEERLREQLKELQEKIQE 106 (110)
T ss_pred heecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566677777777777777888888888888888888888777664
No 35
>PRK09343 prefoldin subunit beta; Provisional
Probab=79.54 E-value=29 Score=27.43 Aligned_cols=100 Identities=14% Similarity=0.268 Sum_probs=64.5
Q ss_pred hcchHHHHHhHHHHHHHHHHHHHHHHHHHHHH---HH---HHHhcCCCChhHHHHH-H--HHHHHHHHHHHHhHHHHHHH
Q psy12696 14 DSLPIELQRNFTLMRELDSRAQDVMKTIDRVA---ED---YLDNMKHYSKDKKKET-L--AEIQKYFDKTKEYGDDKVQL 84 (267)
Q Consensus 14 e~LP~El~r~l~~irelD~~~~~~~~~i~~~~---~~---~~k~~~~~~~~~~~~~-~--~~I~~~~~~~~~lsdEKv~L 84 (267)
.+||.+|+..+..+..+-.+++.+..+..... .+ -++....++++.+.-. + --|.....++..--.+++..
T Consensus 3 ~~~~~~~q~~~~~~q~lq~~l~~~~~q~~~le~q~~e~~~~~~EL~~L~~d~~VYk~VG~vlv~qd~~e~~~~l~~r~E~ 82 (121)
T PRK09343 3 ENIPPEVQAQLAQLQQLQQQLERLLQQKSQIDLELREINKALEELEKLPDDTPIYKIVGNLLVKVDKTKVEKELKERKEL 82 (121)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcchhHHHhhHHHhhccHHHHHHHHHHHHHH
Confidence 36888888888888888777776665543322 21 1122223443333311 1 12566777787777888888
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 85 AIQTYEMVDKYIRKLDTDLARFEQEIQEK 113 (267)
Q Consensus 85 A~~a~dlVd~hirrLD~dl~~~e~el~~~ 113 (267)
...-...+++....|...+..++..+..-
T Consensus 83 ie~~ik~lekq~~~l~~~l~e~q~~l~~l 111 (121)
T PRK09343 83 LELRSRTLEKQEKKLREKLKELQAKINEM 111 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 88777888888888888888888777664
No 36
>PRK15365 type III secretion system chaperone SseA; Provisional
Probab=79.45 E-value=26 Score=26.83 Aligned_cols=79 Identities=13% Similarity=0.214 Sum_probs=45.8
Q ss_pred hHHHHHHHHHHHHHHHHHH------HHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHH-HhHHHHHHHHHHHHHHHHHH
Q psy12696 23 NFTLMRELDSRAQDVMKTI------DRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTK-EYGDDKVQLAIQTYEMVDKY 95 (267)
Q Consensus 23 ~l~~irelD~~~~~~~~~i------~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~-~lsdEKv~LA~~a~dlVd~h 95 (267)
.|+++++|..++..+...+ .+.+..+++.-...++..| +.+..+..++-.-. .+..||..+... |...
T Consensus 7 ~~~~l~DL~~rYs~L~s~lkKfkq~q~~I~q~L~eRA~~d~kaR-E~l~rLd~aFP~G~~~~~qE~~k~m~~----i~~~ 81 (107)
T PRK15365 7 AFSEYRDLEQSYMQLNHCLKKFHQIRAKVSQQLAERAESPKKSR-ETESILHNLFPQGVAGVNQEAEKDLKK----IVSL 81 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHH-HHHHHHHHHCcchhhHHhHHHHHHHHH----HHHH
Confidence 4789999999988776554 3445455554444454433 44445666664433 556777554443 3355
Q ss_pred HHHHHHHHHHH
Q psy12696 96 IRKLDTDLARF 106 (267)
Q Consensus 96 irrLD~dl~~~ 106 (267)
-++|+..|+.+
T Consensus 82 FKQLEt~LKnl 92 (107)
T PRK15365 82 FKQLEVRLKQL 92 (107)
T ss_pred HHHHHHHHHhc
Confidence 55555555444
No 37
>KOG1473|consensus
Probab=78.80 E-value=1.2 Score=47.27 Aligned_cols=42 Identities=31% Similarity=0.948 Sum_probs=34.4
Q ss_pred cee-ecCCCCCCCcccccCCCCCCcceecccCc--cCCCCCCceeCcCCc
Q psy12696 215 TYC-VCQQVSYGEMIGCDNPDCPIEWFHFACVS--LTTKPKGKWYCPKCT 261 (267)
Q Consensus 215 ~~C-~C~~~~~~~mi~Cd~~~c~~~wfH~~Cv~--l~~~p~~~w~C~~C~ 261 (267)
..| +|+.. |..+||++ ||.. +|+.||- +...|...|-|.-|.
T Consensus 345 dhcrf~~d~--~~~lc~Et--~prv-vhlEcv~hP~~~~~s~~~e~evc~ 389 (1414)
T KOG1473|consen 345 DHCRFCHDL--GDLLCCET--CPRV-VHLECVFHPRFAVPSAFWECEVCN 389 (1414)
T ss_pred ccccccCcc--cceeeccc--CCce-EEeeecCCccccCCCccchhhhhh
Confidence 357 88887 89999999 6775 8999998 445678889998885
No 38
>KOG0994|consensus
Probab=75.50 E-value=35 Score=37.02 Aligned_cols=45 Identities=20% Similarity=0.096 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 67 IQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQ 111 (267)
Q Consensus 67 I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el~ 111 (267)
-.+...++++.+|+-...|+.+..-++.-|+...+.|.+.+++..
T Consensus 1564 ~ae~V~eaL~~Ad~Aq~~a~~ai~~a~~~~~~a~~~l~kv~~~t~ 1608 (1758)
T KOG0994|consen 1564 QAEDVVEALEEADVAQGEAQDAIQGADRDIRLAQQLLAKVQEETA 1608 (1758)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Confidence 344455566666666666666666666666666666666655443
No 39
>KOG4443|consensus
Probab=75.38 E-value=0.85 Score=45.66 Aligned_cols=46 Identities=26% Similarity=0.750 Sum_probs=31.9
Q ss_pred Ccee-ecCCCC---CCCcccccCCCCCCcceecccCccCCCC---CCceeCcCCcC
Q psy12696 214 PTYC-VCQQVS---YGEMIGCDNPDCPIEWFHFACVSLTTKP---KGKWYCPKCTS 262 (267)
Q Consensus 214 ~~~C-~C~~~~---~~~mi~Cd~~~c~~~wfH~~Cv~l~~~p---~~~w~C~~C~~ 262 (267)
...| +|.... .|.|+.|.+|. .-||..||.+...- .+-|-||.|+.
T Consensus 18 ~~mc~l~~s~G~~~ag~m~ac~~c~---~~yH~~cvt~~~~~~~l~~gWrC~~crv 70 (694)
T KOG4443|consen 18 CLMCPLCGSSGKGRAGRLLACSDCG---QKYHPYCVTSWAQHAVLSGGWRCPSCRV 70 (694)
T ss_pred hhhhhhhccccccccCcchhhhhhc---ccCCcchhhHHHhHHHhcCCcccCCcee
Confidence 3445 665432 26799999987 67999999954332 34599999963
No 40
>PF05384 DegS: Sensor protein DegS; InterPro: IPR008595 This is a group of Bacillus DegS proteins. The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterise the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon []. The entry also contains one sequence Q8R9D3 from SWISSPROT from Thermoanaerobacter tengcongensis which is described as a sensory transduction histidine kinase.; GO: 0016301 kinase activity, 0007165 signal transduction
Probab=74.67 E-value=49 Score=27.60 Aligned_cols=100 Identities=13% Similarity=0.265 Sum_probs=58.3
Q ss_pred HHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHH---HHHHHHHHHHHHHHHhHHHHHHH
Q psy12696 8 QYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKK---ETLAEIQKYFDKTKEYGDDKVQL 84 (267)
Q Consensus 8 dfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~---~~~~~I~~~~~~~~~lsdEKv~L 84 (267)
+.++..++-=.|+.+.-.+|.++-..+.....++|.+-..+...-..+..-.+. ..-..|...|.+|..++-+..-+
T Consensus 17 qIf~I~E~~R~E~~~l~~EL~evk~~v~~~I~evD~Le~~er~aR~rL~eVS~~f~~ysE~dik~AYe~A~~lQ~~L~~~ 96 (159)
T PF05384_consen 17 QIFEIAEQARQEYERLRKELEEVKEEVSEVIEEVDKLEKRERQARQRLAEVSRNFDRYSEEDIKEAYEEAHELQVRLAML 96 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHHHHHHHHHH
Confidence 445555666677777777888888888888888777665554322221111111 12346888888888777666555
Q ss_pred HHHHHHH------HHHHHHHHHHHHHHHH
Q psy12696 85 AIQTYEM------VDKYIRKLDTDLARFE 107 (267)
Q Consensus 85 A~~a~dl------Vd~hirrLD~dl~~~e 107 (267)
-++-..| +++.+++|..-+.+-+
T Consensus 97 re~E~qLr~rRD~LErrl~~l~~tierAE 125 (159)
T PF05384_consen 97 REREKQLRERRDELERRLRNLEETIERAE 125 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5554444 4455555554444433
No 41
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=72.59 E-value=23 Score=31.77 Aligned_cols=54 Identities=9% Similarity=0.019 Sum_probs=44.1
Q ss_pred CChhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 55 YSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQ 111 (267)
Q Consensus 55 ~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el~ 111 (267)
.+.....+....|.+.+.+++..++.|+.++.+|.+-+++-|+|++. .++..+.
T Consensus 55 ~~~~t~~e~ed~l~k~i~Ell~~a~~~~~~~~~l~d~~~~l~~Rh~~---~~d~~~a 108 (271)
T COG5034 55 LDSQTYEEVEDGLLKEIRELLLKAIYIQKEKSDLADRAEKLLRRHRK---LLDDRIA 108 (271)
T ss_pred cccCccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---hhhhHHH
Confidence 33444557788899999999999999999999999999999999987 3444443
No 42
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=71.93 E-value=31 Score=30.90 Aligned_cols=67 Identities=22% Similarity=0.362 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCh--hHHH-HHHHHHHHHHHHHHHhHHH-HHHHHHHHHHHHHH
Q psy12696 25 TLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSK--DKKK-ETLAEIQKYFDKTKEYGDD-KVQLAIQTYEMVDK 94 (267)
Q Consensus 25 ~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~--~~~~-~~~~~I~~~~~~~~~lsdE-Kv~LA~~a~dlVd~ 94 (267)
.+|+++|.++......+......-.. .... ..+. .+-.+|...+.++-.|+.+ +|.-|+.+...|+.
T Consensus 90 ~~i~d~drrI~~~k~RL~~~~~~~~~---~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~ 160 (254)
T PF03194_consen 90 RLIRDCDRRIERAKERLEQTQEEQAK---EADEEKAEKIDELDEKIGELLKEAEELGEEGDVDEAQKLMEEVEK 160 (254)
T ss_pred HHHHHHHHHHHHHHHHHHhCcccccc---chhhhHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45666666666555555433222111 1111 1222 3446799999999999998 99999988888776
No 43
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=71.19 E-value=1 Score=29.87 Aligned_cols=30 Identities=20% Similarity=0.457 Sum_probs=18.6
Q ss_pred CCCCCC--cceecccCccCCCCCCceeCcCCc
Q psy12696 232 NPDCPI--EWFHFACVSLTTKPKGKWYCPKCT 261 (267)
Q Consensus 232 ~~~c~~--~wfH~~Cv~l~~~p~~~w~C~~C~ 261 (267)
-|.|.. .|||.+|+.--..-.+.-.|+.|.
T Consensus 18 PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 18 PCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred ccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 344553 699999997333333345788873
No 44
>KOG4552|consensus
Probab=70.93 E-value=72 Score=27.91 Aligned_cols=87 Identities=13% Similarity=0.223 Sum_probs=48.7
Q ss_pred HhHHHHHHHHHHHHHHHHHH-HHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 22 RNFTLMRELDSRAQDVMKTI-DRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLD 100 (267)
Q Consensus 22 r~l~~irelD~~~~~~~~~i-~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD 100 (267)
|.|..+-+|+.-+.++.+.+ ....++.+++ +.. ..-.+++..=...|+++++++.|--. ..++.+.++.|+.+=|
T Consensus 12 rLL~~~dDlE~i~kelie~l~~~~~qk~l~~-gE~--v~il~Ll~~kd~ef~~llkla~eq~k-~e~~m~~Lea~VEkrD 87 (272)
T KOG4552|consen 12 RLLESADDLEHIVKELIETLINRDKQKMLKN-GET--VNILKLLDSKDDEFKTLLKLAPEQQK-REQLMRTLEAHVEKRD 87 (272)
T ss_pred HHHHHhhHHHHHHHHHHHHHHhhhHHHHHhc-chH--HHHHHHHHhccHHHHHHHHHhHhHHH-HHHHHHHHHHHHHHhH
Confidence 45666666666666666654 3333444432 221 12334554445566666666655332 3456667777777777
Q ss_pred HHHHHHHHHHHH
Q psy12696 101 TDLARFEQEIQE 112 (267)
Q Consensus 101 ~dl~~~e~el~~ 112 (267)
.++.+|+..+..
T Consensus 88 ~~IQqLqk~LK~ 99 (272)
T KOG4552|consen 88 EVIQQLQKNLKS 99 (272)
T ss_pred HHHHHHHHHHHH
Confidence 777777665544
No 45
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=70.86 E-value=38 Score=29.94 Aligned_cols=41 Identities=10% Similarity=0.198 Sum_probs=29.9
Q ss_pred HHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 10 LDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLD 50 (267)
Q Consensus 10 ld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k 50 (267)
+..++-|=.+|...+..+...+..+.++..+++.+..++..
T Consensus 10 ~~~lek~k~~i~~e~~~~e~ee~~L~e~~kE~~~L~~Er~~ 50 (230)
T PF10146_consen 10 TLELEKLKNEILQEVESLENEEKCLEEYRKEMEELLQERMA 50 (230)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455566777777788888888888888888877777654
No 46
>KOG4360|consensus
Probab=70.43 E-value=71 Score=31.62 Aligned_cols=77 Identities=16% Similarity=0.268 Sum_probs=53.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 25 TLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLA 104 (267)
Q Consensus 25 ~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~ 104 (267)
.++|++..++..+.++|..+..+.... .++.-.++.+|-+...+++.+.-||-.+-..+..++|.| +.|.+++.
T Consensus 205 KelrdtN~q~~s~~eel~~kt~el~~q-----~Ee~skLlsql~d~qkk~k~~~~Ekeel~~~Lq~~~da~-~ql~aE~~ 278 (596)
T KOG4360|consen 205 KELRDTNTQARSGQEELQSKTKELSRQ-----QEENSKLLSQLVDLQKKIKYLRHEKEELDEHLQAYKDAQ-RQLTAELE 278 (596)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhhH-HHHHHHHH
Confidence 455555666666666666555554431 123346788899999999999999999999999998885 55665554
Q ss_pred HHH
Q psy12696 105 RFE 107 (267)
Q Consensus 105 ~~e 107 (267)
.++
T Consensus 279 Ele 281 (596)
T KOG4360|consen 279 ELE 281 (596)
T ss_pred HHH
Confidence 443
No 47
>PF11690 DUF3287: Protein of unknown function (DUF3287); InterPro: IPR021704 This eukaryotic family of proteins has no known function.
Probab=70.29 E-value=17 Score=28.43 Aligned_cols=54 Identities=26% Similarity=0.461 Sum_probs=44.3
Q ss_pred CCChhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Q psy12696 54 HYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEM-VDKYIRKLDTDLARFE 107 (267)
Q Consensus 54 ~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dl-Vd~hirrLD~dl~~~e 107 (267)
.+++..+.+.+.-|+..-.+-+.+.+|+-.|...+.+| |++-++.|+++-..-+
T Consensus 31 ~~~~kd~~ea~~F~~kV~~qH~~~~~e~r~L~kKi~~l~veRkmr~Les~p~~W~ 85 (109)
T PF11690_consen 31 HLPSKDKKEAYDFIDKVVDQHQRYCDERRKLRKKIQDLRVERKMRALESHPFDWE 85 (109)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCChHHHH
Confidence 35566677777778888888899999999999999997 9999999998755443
No 48
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=69.81 E-value=3.6 Score=31.89 Aligned_cols=51 Identities=24% Similarity=0.535 Sum_probs=30.2
Q ss_pred CCCCcee-ecCCCCCCCcccc------cCCC-CCCcceecccCccC-------CCCCCceeCcCCcC
Q psy12696 211 PNEPTYC-VCQQVSYGEMIGC------DNPD-CPIEWFHFACVSLT-------TKPKGKWYCPKCTS 262 (267)
Q Consensus 211 ~~~~~~C-~C~~~~~~~mi~C------d~~~-c~~~wfH~~Cv~l~-------~~p~~~w~C~~C~~ 262 (267)
+..-..| .|++-..+..+.| ..|. |... |=..|+-.. ......|.||.|+.
T Consensus 4 ~~~g~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~~~-fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 4 SVNGKTCHQCRQKTLDFKTICTGHWKNSSCRGCRGK-FCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred CCCCCCchhhcCCCCCCceEcCCCCCCCCCccCcce-ehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 3445577 8888766665666 4431 1443 556775411 12367899999974
No 49
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=69.13 E-value=3.3 Score=35.78 Aligned_cols=42 Identities=29% Similarity=0.764 Sum_probs=30.1
Q ss_pred ee-ecCCCC--C----CCcccccCCCCCCcceecccCccCCCCCCceeCcCCcCcccCC
Q psy12696 216 YC-VCQQVS--Y----GEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPKCTSDRKKK 267 (267)
Q Consensus 216 ~C-~C~~~~--~----~~mi~Cd~~~c~~~wfH~~Cv~l~~~p~~~w~C~~C~~~~~~~ 267 (267)
.| +|+... | ...+.|..|. .-||-.|..- -.||.|.+-+++|
T Consensus 154 iCe~C~~~~~IfPF~~~~~~~C~~C~---~v~H~~C~~~-------~~CpkC~R~~~r~ 202 (202)
T PF13901_consen 154 ICEICNSDDIIFPFQIDTTVRCPKCK---SVFHKSCFRK-------KSCPKCARRQKRK 202 (202)
T ss_pred CCccCCCCCCCCCCCCCCeeeCCcCc---cccchhhcCC-------CCCCCcHhHhccC
Confidence 57 777542 2 2467899976 5699999962 2299998887765
No 50
>PF01627 Hpt: Hpt domain; InterPro: IPR008207 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents a domain present at the N terminus in proteins which undergo autophosphorylation. The group includes, the gliding motility regulatory protein from Myxococcus xanthus and a number of bacterial chemotaxis proteins.; GO: 0004871 signal transducer activity, 0000160 two-component signal transduction system (phosphorelay); PDB: 3KYJ_A 3KYI_A 3IQT_A 1Y6D_A 2LD6_A 1TQG_A 2R25_A 1OXB_A 1QSP_B 1C03_B ....
Probab=67.21 E-value=41 Score=23.66 Aligned_cols=86 Identities=16% Similarity=0.278 Sum_probs=37.2
Q ss_pred HHHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHH-H
Q psy12696 5 YLEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKV-Q 83 (267)
Q Consensus 5 yLedfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv-~ 83 (267)
+++.|++.+...-..|...+ ..++ ..-...+.+.++.+-...+.+.- ..+..+-..+.....-.+..- .
T Consensus 2 ll~~f~~~~~~~~~~l~~~~---~~~~---~~d~~~l~~~~H~lkG~a~~~g~----~~l~~~~~~lE~~~~~~~~~~~~ 71 (90)
T PF01627_consen 2 LLDIFLEEAPEDLEQLEQAL---QALE---QEDWEELRRLAHRLKGSAGNLGA----PRLAELAEQLEQALKSGDKPEAE 71 (90)
T ss_dssp HHHHHHHHHHHHHHHHHHHH---CSSH---HCHHHHHHHHHHHHHHHHHHTTC----HHHHHHHHHHHHHHHTTHHHHSH
T ss_pred HHHHHHHHHHHHHHHHHHHH---HHHh---HhhHHHHHHHHHHHhhhHHhcCH----HHHHHHHHHHHHHHHcCCccchh
Confidence 45666665554444444333 1111 23333344444444333333322 233344444444444433333 4
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy12696 84 LAIQTYEMVDKYIRKLD 100 (267)
Q Consensus 84 LA~~a~dlVd~hirrLD 100 (267)
+..++++.|...+.+|.
T Consensus 72 ~~~~~~~~l~~~l~~l~ 88 (90)
T PF01627_consen 72 ELEQLLDELEAMLEQLR 88 (90)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 55555555555555543
No 51
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=66.39 E-value=1.5 Score=25.78 Aligned_cols=27 Identities=26% Similarity=0.479 Sum_probs=10.6
Q ss_pred ee-ecCCCCCC-CcccccCCCCCCcceecccC
Q psy12696 216 YC-VCQQVSYG-EMIGCDNPDCPIEWFHFACV 245 (267)
Q Consensus 216 ~C-~C~~~~~~-~mi~Cd~~~c~~~wfH~~Cv 245 (267)
.| .|+.+.++ .+-.|..|+ -++|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cd---f~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECD---FDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-TTT--------HHHH
T ss_pred cCCcCCCcCCCCceEECccCC---CccChhcC
Confidence 35 78877766 566798877 57888874
No 52
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=66.26 E-value=1.7 Score=32.05 Aligned_cols=43 Identities=35% Similarity=0.852 Sum_probs=28.1
Q ss_pred ee-ecCCCCCCCcccccC-----CCCCCcc------eecccCc--cCCCCCCceeCcCCcC
Q psy12696 216 YC-VCQQVSYGEMIGCDN-----PDCPIEW------FHFACVS--LTTKPKGKWYCPKCTS 262 (267)
Q Consensus 216 ~C-~C~~~~~~~mi~Cd~-----~~c~~~w------fH~~Cv~--l~~~p~~~w~C~~C~~ 262 (267)
.| +|+-...|.-+.|-. .+||..| ||+.|+. |.. +=.||.|..
T Consensus 22 ~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T----k~~CPld~q 78 (88)
T COG5194 22 VCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT----KGVCPLDRQ 78 (88)
T ss_pred hhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh----CCCCCCCCc
Confidence 46 887776666666654 3477777 9999987 433 345666643
No 53
>PHA02562 46 endonuclease subunit; Provisional
Probab=65.94 E-value=84 Score=30.85 Aligned_cols=25 Identities=16% Similarity=0.263 Sum_probs=11.8
Q ss_pred hHHHHHhHHHHHHHHHHHHHHHHHH
Q psy12696 17 PIELQRNFTLMRELDSRAQDVMKTI 41 (267)
Q Consensus 17 P~El~r~l~~irelD~~~~~~~~~i 41 (267)
|..+...-..|.+|..++..+...+
T Consensus 298 ~~~~~~l~d~i~~l~~~l~~l~~~i 322 (562)
T PHA02562 298 PDRITKIKDKLKELQHSLEKLDTAI 322 (562)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444445555555444444443
No 54
>KOG3579|consensus
Probab=65.84 E-value=6.6 Score=35.78 Aligned_cols=52 Identities=27% Similarity=0.721 Sum_probs=36.3
Q ss_pred CCCCCCCCCcee-ecCCCC-CCCcccccCCCCCCcceecccCc--cCCCC-CCceeCcC
Q psy12696 206 DMPVDPNEPTYC-VCQQVS-YGEMIGCDNPDCPIEWFHFACVS--LTTKP-KGKWYCPK 259 (267)
Q Consensus 206 ~~~~~~~~~~~C-~C~~~~-~~~mi~Cd~~~c~~~wfH~~Cv~--l~~~p-~~~w~C~~ 259 (267)
+...-+..++.| +|+..- +-.+|+|-. -|..=|-|.|-. |...- .|+.|||-
T Consensus 260 ~s~~A~~apLcCTLC~ERLEDTHFVQCPS--Vp~HKFCFPCSResIK~Qg~sgevYCPS 316 (352)
T KOG3579|consen 260 DSGAAPSAPLCCTLCHERLEDTHFVQCPS--VPSHKFCFPCSRESIKQQGASGEVYCPS 316 (352)
T ss_pred ccccCCCCceeehhhhhhhccCceeecCC--CcccceecccCHHHHHhhcCCCceeCCC
Confidence 445667888899 998763 566899887 445556677765 54443 78999984
No 55
>PRK10244 anti-RssB factor; Provisional
Probab=65.28 E-value=43 Score=25.12 Aligned_cols=77 Identities=9% Similarity=0.234 Sum_probs=50.1
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 20 LQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKL 99 (267)
Q Consensus 20 l~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrL 99 (267)
|-..|-.|-+.|+...++..+++.+---.......+.++....+...|+..+..+.+-+++ +-..-.+++-.|++||
T Consensus 5 I~elL~KlA~ke~esKeL~AQVEAlellitAlL~~~~~~~~~~li~~Ie~Ai~~a~~~~~~---~~~~D~eLL~~~v~~L 81 (88)
T PRK10244 5 IAELLAKLAQKEEESKELTAQVEALELLVTAMLRTMGKNGQQELIEQVEGAINAVSKPDDS---VPDSDTELLLTYVNKL 81 (88)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhChhhHHHHHHHHHHHHHHhcccccc---ccchHHHHHHHHHHHH
Confidence 4456778889999999999998876332222223455555667778888887777544443 3344556777777665
No 56
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=64.03 E-value=4.2 Score=35.42 Aligned_cols=34 Identities=12% Similarity=0.160 Sum_probs=26.1
Q ss_pred cchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 15 SLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDY 48 (267)
Q Consensus 15 ~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~ 48 (267)
-+-.||.|.=..|-++|..+..++..+++..-.+
T Consensus 12 ~~~~~L~rle~qi~q~~~~~~~~qs~l~~~~~r~ 45 (251)
T COG5415 12 KYTADLSRLESQIHQLDVALKKSQSILSQWQSRL 45 (251)
T ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456888888999999999888887777655443
No 57
>PF05781 MRVI1: MRVI1 protein; InterPro: IPR008677 This family consists of mammalian MRVI1 proteins which are related to the lymphoid-restricted membrane protein (JAW1) and the IP3 receptor associated cGMP kinase substrates A and B (IRAGA and IRAGB). The function of MRVI1 is unknown although mutations in the Mrvi1 gene induces myeloid leukaemia by altering the expression of a gene important for myeloid cell growth and/or differentiation so it has been speculated that Mrvi1 is a tumour suppressor gene []. IRAG is very similar in sequence to MRVI1 and is an essential NO/cGKI-dependent regulator of IP3-induced calcium release. Activation of cGKI decreases IP3-stimulated elevations in intracellular calcium, induces smooth muscle relaxation and contributes to the antiproliferative and pro-apoptotic effects of NO/cGMP []. Jaw1 is a member of a class of proteins with COOH-terminal hydrophobic membrane anchors and is structurally similar to proteins involved in vesicle targeting and fusion. This suggests that the function and/or the structure of the ER in lymphocytes may be modified by lymphoid-restricted resident ER proteins [].
Probab=63.50 E-value=1.3e+02 Score=30.09 Aligned_cols=28 Identities=14% Similarity=0.215 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 85 AIQTYEMVDKYIRKLDTDLARFEQEIQE 112 (267)
Q Consensus 85 A~~a~dlVd~hirrLD~dl~~~e~el~~ 112 (267)
.+.|.+.+..|+..|..-+.+.-+++.+
T Consensus 290 ~SkAvevM~qhvenLkr~~~kehaeL~E 317 (538)
T PF05781_consen 290 VSKAVEVMIQHVENLKRMYEKEHAELEE 317 (538)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4578888888888888877777777665
No 58
>KOG4460|consensus
Probab=63.16 E-value=82 Score=31.57 Aligned_cols=35 Identities=29% Similarity=0.420 Sum_probs=26.4
Q ss_pred hHHHHHHHHhhcchHHHHHhHHHHHHH-HHHHHHHH
Q psy12696 4 SYLEQYLDSLDSLPIELQRNFTLMREL-DSRAQDVM 38 (267)
Q Consensus 4 ~yLedfld~ie~LP~El~r~l~~irel-D~~~~~~~ 38 (267)
.|-|+|+..-+-+-.||+|+..+|... |.+.|++.
T Consensus 570 vfrEqYi~~~dlV~~e~qrH~~~l~~~k~~QlQ~l~ 605 (741)
T KOG4460|consen 570 VFREQYILKQDLVKEEIQRHVKLLCDQKKKQLQDLS 605 (741)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466889998888999999999888654 55555543
No 59
>TIGR00634 recN DNA repair protein RecN. All proteins in this family for which functions are known are ATP binding proteins involved in the initiation of recombination and recombinational repair.
Probab=60.51 E-value=69 Score=31.93 Aligned_cols=10 Identities=20% Similarity=0.295 Sum_probs=3.8
Q ss_pred HHHHHHHHHH
Q psy12696 63 TLAEIQKYFD 72 (267)
Q Consensus 63 ~~~~I~~~~~ 72 (267)
.+.+++..+.
T Consensus 330 ~~~~l~~eL~ 339 (563)
T TIGR00634 330 YAEKIKEELD 339 (563)
T ss_pred HHHHHHHHHH
Confidence 3333333333
No 60
>PRK10869 recombination and repair protein; Provisional
Probab=60.41 E-value=69 Score=32.01 Aligned_cols=19 Identities=0% Similarity=0.008 Sum_probs=7.5
Q ss_pred hhHHHHHHHHHHHHHHHHH
Q psy12696 57 KDKKKETLAEIQKYFDKTK 75 (267)
Q Consensus 57 ~~~~~~~~~~I~~~~~~~~ 75 (267)
.++-.....+++..+..+.
T Consensus 319 ~~~~~~~~~~l~~eL~~L~ 337 (553)
T PRK10869 319 PEELPQHHQQLLEEQQQLD 337 (553)
T ss_pred HHHHHHHHHHHHHHHHHhh
Confidence 3333333444444444333
No 61
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=59.91 E-value=2.5 Score=26.87 Aligned_cols=36 Identities=28% Similarity=0.622 Sum_probs=20.5
Q ss_pred ecCCCC-CCC-cccccCCCCCCcceecccCc--cCCCCCCceeCcCCc
Q psy12696 218 VCQQVS-YGE-MIGCDNPDCPIEWFHFACVS--LTTKPKGKWYCPKCT 261 (267)
Q Consensus 218 ~C~~~~-~~~-mi~Cd~~~c~~~wfH~~Cv~--l~~~p~~~w~C~~C~ 261 (267)
+|.... .++ ++... |. ..||..|+. +... ..||.|+
T Consensus 5 IC~~~~~~~~~~~~l~-C~---H~fh~~Ci~~~~~~~----~~CP~CR 44 (44)
T PF13639_consen 5 ICLEEFEDGEKVVKLP-CG---HVFHRSCIKEWLKRN----NSCPVCR 44 (44)
T ss_dssp TTTCBHHTTSCEEEET-TS---EEEEHHHHHHHHHHS----SB-TTTH
T ss_pred CCChhhcCCCeEEEcc-CC---CeeCHHHHHHHHHhC----CcCCccC
Confidence 665553 233 33333 55 689999987 3222 3888884
No 62
>PF07139 DUF1387: Protein of unknown function (DUF1387); InterPro: IPR009816 This family represents a conserved region approximately 300 residues long within a number of hypothetical proteins of unknown function that seem to be restricted to mammals.
Probab=57.99 E-value=1.6e+02 Score=27.25 Aligned_cols=49 Identities=24% Similarity=0.296 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHH
Q psy12696 62 ETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDK-------YIRKLDTDLARFEQEI 110 (267)
Q Consensus 62 ~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~-------hirrLD~dl~~~e~el 110 (267)
.++.+|.+-..+++++.+.--.=|..+..+.|+ ++..|-+||+.|-.+.
T Consensus 204 aLl~EmdkVK~EAmeiL~aRqkkAeeLkrltd~A~~MsE~Ql~ELRadIK~fvs~r 259 (302)
T PF07139_consen 204 ALLAEMDKVKAEAMEILDARQKKAEELKRLTDRASQMSEEQLAELRADIKHFVSER 259 (302)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhhhh
Confidence 677788887788877777666656555555554 4555555555554443
No 63
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=57.03 E-value=5.5 Score=28.38 Aligned_cols=47 Identities=32% Similarity=0.696 Sum_probs=18.8
Q ss_pred ee-ecCCCC--CC--CcccccCCCCCCcceecccCc--cC---CCC----CCceeCcCCcCc
Q psy12696 216 YC-VCQQVS--YG--EMIGCDNPDCPIEWFHFACVS--LT---TKP----KGKWYCPKCTSD 263 (267)
Q Consensus 216 ~C-~C~~~~--~~--~mi~Cd~~~c~~~wfH~~Cv~--l~---~~p----~~~w~C~~C~~~ 263 (267)
.| +|-..- .+ .-+.|++..|... ||..|+- +. ... .-.+-||.|...
T Consensus 4 ~C~IC~~~~~~~~~~p~~~C~n~~C~~~-fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~ 64 (70)
T PF11793_consen 4 ECGICYSYRLDDGEIPDVVCPNPSCGKK-FHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSP 64 (70)
T ss_dssp S-SSS--SS-TT-----B--S-TT-----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SE
T ss_pred CCCcCCcEecCCCCcCceEcCCcccCCH-HHHHHHHHHHHHcccCCeeecccccCCcCCCCe
Confidence 45 665542 23 3588998888776 9999997 21 211 224679999764
No 64
>KOG1937|consensus
Probab=55.77 E-value=1.8e+02 Score=28.39 Aligned_cols=28 Identities=21% Similarity=0.325 Sum_probs=13.6
Q ss_pred hcchHHHHHhHHHHHHHHHHHHHHHHHHH
Q psy12696 14 DSLPIELQRNFTLMRELDSRAQDVMKTID 42 (267)
Q Consensus 14 e~LP~El~r~l~~irelD~~~~~~~~~i~ 42 (267)
.++-.|=.+ |..|+++.+.+...-.+++
T Consensus 335 ~~~e~e~~e-~~~IqeleqdL~a~~eei~ 362 (521)
T KOG1937|consen 335 KNLETEDEE-IRRIQELEQDLEAVDEEIE 362 (521)
T ss_pred hcccchHHH-HHHHHHHHHHHHHHHHHHH
Confidence 333334444 5555555555555555444
No 65
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=55.27 E-value=8.7 Score=23.82 Aligned_cols=25 Identities=32% Similarity=0.914 Sum_probs=17.2
Q ss_pred cccccCCCCCCcceecccCccCCCCCCceeCcCCc
Q psy12696 227 MIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPKCT 261 (267)
Q Consensus 227 mi~Cd~~~c~~~wfH~~Cv~l~~~p~~~w~C~~C~ 261 (267)
-+.|.. |...||. ...|.|||..|-
T Consensus 8 ~~~C~~--C~~~~~~--------~~dG~~yC~~cG 32 (36)
T PF11781_consen 8 NEPCPV--CGSRWFY--------SDDGFYYCDRCG 32 (36)
T ss_pred CCcCCC--CCCeEeE--------ccCCEEEhhhCc
Confidence 345777 5556763 457889999884
No 66
>PF05103 DivIVA: DivIVA protein; InterPro: IPR007793 The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate minicells []. Inactivation of divIVA produces a minicell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype []. These proteins appear to contain coiled-coils.; PDB: 2WUK_C 2WUJ_A.
Probab=55.24 E-value=6.9 Score=30.76 Aligned_cols=34 Identities=24% Similarity=0.405 Sum_probs=19.7
Q ss_pred HHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHH
Q psy12696 6 LEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTID 42 (267)
Q Consensus 6 Ledfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~ 42 (267)
+++||+.|. .++.....++.+|..++..+..++.
T Consensus 23 VD~fl~~l~---~~~~~l~~e~~~L~~~~~~l~~~l~ 56 (131)
T PF05103_consen 23 VDDFLDELA---EELERLQRENAELKEEIEELQAQLE 56 (131)
T ss_dssp HHHHHHHHH---HHHHHHHHHHHHHHHHHHCCCCT--
T ss_pred HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 567777666 5666666666666666555544443
No 67
>KOG3047|consensus
Probab=55.12 E-value=1.1e+02 Score=24.69 Aligned_cols=45 Identities=16% Similarity=0.240 Sum_probs=36.8
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 67 IQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQ 111 (267)
Q Consensus 67 I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el~ 111 (267)
+.-.++.++...|.|+.+-..+.+.+.+-..+|-++|-.+-+.+.
T Consensus 99 lElkLadAiKf~DRK~dlLkel~ekLqKdsmkiKa~ihMLLagl~ 143 (157)
T KOG3047|consen 99 LELKLADAIKFCDRKMDLLKELMEKLQKDSMKIKADIHMLLAGLD 143 (157)
T ss_pred eeehHHHHHHHHHHhHHHHHHHHHHHHHhHHHHHHHHHHHHHhhh
Confidence 345678899999999999999999999988888888877765444
No 68
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=54.63 E-value=99 Score=23.94 Aligned_cols=62 Identities=15% Similarity=0.281 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHH-HhHHHHHHHHHHHHHHHH
Q psy12696 28 RELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTK-EYGDDKVQLAIQTYEMVD 93 (267)
Q Consensus 28 relD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~-~lsdEKv~LA~~a~dlVd 93 (267)
-+|...++++...++ +.|+..++...++-.++-.+|+..+.++. .+++-+=.+++++.+.++
T Consensus 11 ~~l~~el~~L~d~lE----evL~ssg~~a~~e~~~lR~r~~~~Lk~~r~rl~~~~d~v~~~sk~a~~ 73 (104)
T COG4575 11 DQLLAELQELLDTLE----EVLKSSGSLAGDEAEELRSKAESALKEARDRLGDTGDAVVQRSKAAAD 73 (104)
T ss_pred HHHHHHHHHHHHHHH----HHHHhcccchhhHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence 344444444444444 55666666666666666667777776665 344444445555554444
No 69
>smart00502 BBC B-Box C-terminal domain. Coiled coil region C-terminal to (some) B-Box domains
Probab=53.98 E-value=93 Score=23.44 Aligned_cols=23 Identities=22% Similarity=0.310 Sum_probs=9.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 79 DDKVQLAIQTYEMVDKYIRKLDT 101 (267)
Q Consensus 79 dEKv~LA~~a~dlVd~hirrLD~ 101 (267)
.+|..-...-.+-+..++.+|..
T Consensus 71 ~~~~~~l~~q~~~l~~~l~~l~~ 93 (127)
T smart00502 71 ENKLKVLEQQLESLTQKQEKLSH 93 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333333333344444444433
No 70
>PF05010 TACC: Transforming acidic coiled-coil-containing protein (TACC); InterPro: IPR007707 This family contains the proteins TACC 1, 2 and 3, found concentrated in the centrosomes of eukaryotes which may play a conserved role in organising centrosomal microtubules. The human TACC proteins have been linked to cancer and TACC2 has been identified as a possible tumour suppressor (AZU-1) [].
Probab=53.94 E-value=1.5e+02 Score=25.81 Aligned_cols=33 Identities=18% Similarity=0.258 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q psy12696 62 ETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDK 94 (267)
Q Consensus 62 ~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~ 94 (267)
..+....+.|..++.-+.+|+.+|+.-++-|-+
T Consensus 125 ~~l~~~eqry~aLK~hAeekL~~ANeei~~v~~ 157 (207)
T PF05010_consen 125 ERLKKEEQRYQALKAHAEEKLEKANEEIAQVRS 157 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345566778888889999999999887776554
No 71
>PF01765 RRF: Ribosome recycling factor; InterPro: IPR023584 The ribosome recycling factor or ribosome release factor (RRF) dissociates ribosomes from mRNA after termination of translation, and is essential for bacterial growth []. Thus ribosomes are 'recycled' and ready for another round of protein synthesis. This entry represents a domain found in ribosome recycling factors.; PDB: 3R8N_Y 1Y69_8 1ISE_A 1EK8_A 1DD5_A 1WIH_A 2Z4L_6 2QBE_6 2V46_Y 1EH1_A ....
Probab=53.02 E-value=72 Score=26.42 Aligned_cols=34 Identities=35% Similarity=0.522 Sum_probs=25.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 77 YGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEI 110 (267)
Q Consensus 77 lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el 110 (267)
..|+.-.+-.++-.+.++++..+|.-++.-+.+|
T Consensus 131 s~D~~~~~~~~iq~l~~~~~~~id~~~~~kekel 164 (165)
T PF01765_consen 131 SEDDIKKLEKEIQKLTDKYIKKIDELLKKKEKEL 164 (165)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3455666777888888899999998887776654
No 72
>KOG1829|consensus
Probab=52.45 E-value=3.1 Score=41.53 Aligned_cols=32 Identities=25% Similarity=0.594 Sum_probs=23.9
Q ss_pred cccccCCCCCCcceecccCccCCCCCCceeCcCCcCcccC
Q psy12696 227 MIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPKCTSDRKK 266 (267)
Q Consensus 227 mi~Cd~~~c~~~wfH~~Cv~l~~~p~~~w~C~~C~~~~~~ 266 (267)
-.-|+.|. .|||-.|......- ||.|.+-+++
T Consensus 531 ~~rC~~C~---avfH~~C~~r~s~~-----CPrC~R~q~r 562 (580)
T KOG1829|consen 531 TRRCSTCL---AVFHKKCLRRKSPC-----CPRCERRQKR 562 (580)
T ss_pred ceeHHHHH---HHHHHHHHhccCCC-----CCchHHHHHH
Confidence 57799988 89999998754433 9999765443
No 73
>PF08702 Fib_alpha: Fibrinogen alpha/beta chain family; InterPro: IPR012290 Fibrinogen plays key roles in both blood clotting and platelet aggregation. During blood clot formation, the conversion of soluble fibrinogen to insoluble fibrin is triggered by thrombin, resulting in the polymerisation of fibrin, which forms a soft clot; this is then converted to a hard clot by factor XIIIA, which cross-links fibrin molecules. Platelet aggregation involves the binding of the platelet protein receptor integrin alpha(IIb)-beta(3) to the C-terminal D domain of fibrinogen []. In addition to platelet aggregation, platelet-fibrinogen interaction mediates both adhesion and fibrin clot retraction. Fibrinogen occurs as a dimer, where each monomer is composed of three non-identical chains, alpha, beta and gamma, linked together by several disulphide bonds []. The N-terminals of all six chains come together to form the centre of the molecule (E domain), from which the monomers extend in opposite directions as coiled coils, followed by C-terminal globular domains (D domains). Therefore, the domain composition is: D-coil-E-coil-D. At each end, the C-terminal of the alpha chain extends beyond the D domain as a protuberance that is important for cross-linking the molecule. During clot formation, the N-terminal fragments of the alpha and beta chains (within the E domain) in fibrinogen are cleaved by thrombin, releasing fibrinopeptides A and B, respectively, and producing fibrin. This cleavage results in the exposure of four binding sites on the E domain, each of which can bind to a D domain from different fibrin molecules. The binding of fibrin molecules produces a polymer consisting of a lattice network of fibrins that form a long, branching, flexible fibre [, ]. Fibrin fibres interact with platelets to increase the size of the clot, as well as with several different proteins and cells, thereby promoting the inflammatory response and concentrating the cells required for wound repair at the site of damage. This entry represents the coiled-coil domain and part of the N-terminal E domain found in all three fibrinogen polypeptides, namely the alpha, beta and gamma chains. More information about these proteins can be found at Protein of the Month: Fibrinogen [].; GO: 0005102 receptor binding, 0030674 protein binding, bridging, 0007165 signal transduction, 0030168 platelet activation, 0051258 protein polymerization, 0005577 fibrinogen complex; PDB: 1LWU_D 1N73_D 1M1J_B 1JY2_R 1JY3_R 1RF0_A 2H43_D 1RE4_D 2XNY_D 2HPC_D ....
Probab=52.38 E-value=1.3e+02 Score=24.61 Aligned_cols=37 Identities=11% Similarity=0.202 Sum_probs=21.4
Q ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 71 FDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFE 107 (267)
Q Consensus 71 ~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e 107 (267)
++...--...-+.+-+.+++.....|.+|+.++..++
T Consensus 95 ~e~~i~~~~~~I~~Lq~~~~~~~~ki~~Le~~i~~~~ 131 (146)
T PF08702_consen 95 LETKIINQPSNIRVLQNILRSNRQKIQRLEQDIDQQE 131 (146)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHhhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444455556666666666666666666665544
No 74
>KOG1512|consensus
Probab=52.04 E-value=3.9 Score=37.25 Aligned_cols=45 Identities=20% Similarity=0.290 Sum_probs=29.5
Q ss_pred CceeecCCCCC-----CCcccccCCCCCCcceecccCccCCCC-----CCceeCcCCc
Q psy12696 214 PTYCVCQQVSY-----GEMIGCDNPDCPIEWFHFACVSLTTKP-----KGKWYCPKCT 261 (267)
Q Consensus 214 ~~~C~C~~~~~-----~~mi~Cd~~~c~~~wfH~~Cv~l~~~p-----~~~w~C~~C~ 261 (267)
-..|+=.+.+. ..||+|..|. + -+|..||.++..- .=.|.|..|.
T Consensus 261 ~~~~~~~~~~~~~~r~~S~I~C~~C~--~-~~HP~Ci~M~~elv~~~KTY~W~C~~C~ 315 (381)
T KOG1512|consen 261 RKHFWDIQTNIIQSRRNSWIVCKPCA--T-RPHPYCVAMIPELVGQYKTYFWKCSSCE 315 (381)
T ss_pred hhhhhcchhhhhhhhhccceeecccc--c-CCCCcchhcCHHHHhHHhhcchhhcccH
Confidence 33454444443 3499999955 4 4999999976543 2358887774
No 75
>KOG1853|consensus
Probab=51.46 E-value=1.9e+02 Score=26.20 Aligned_cols=10 Identities=20% Similarity=0.401 Sum_probs=5.4
Q ss_pred CCceeecCCC
Q psy12696 213 EPTYCVCQQV 222 (267)
Q Consensus 213 ~~~~C~C~~~ 222 (267)
.+.-|+|+.+
T Consensus 284 g~g~~~~~i~ 293 (333)
T KOG1853|consen 284 GAGACINRIV 293 (333)
T ss_pred ccchhhhhhh
Confidence 3445666554
No 76
>KOG1244|consensus
Probab=51.29 E-value=4.1 Score=36.82 Aligned_cols=45 Identities=27% Similarity=0.670 Sum_probs=31.6
Q ss_pred Ccee-ecCCCCC--------CCcccccCCCCCCcceecccCccCCCC-----CCceeCcCCc
Q psy12696 214 PTYC-VCQQVSY--------GEMIGCDNPDCPIEWFHFACVSLTTKP-----KGKWYCPKCT 261 (267)
Q Consensus 214 ~~~C-~C~~~~~--------~~mi~Cd~~~c~~~wfH~~Cv~l~~~p-----~~~w~C~~C~ 261 (267)
.-|| +|-..+. .++|.|..|. .-=|.+|+-.+..- .=.|.|..|.
T Consensus 224 n~YCDFclgdsr~nkkt~~peelvscsdcg---rsghpsclqft~nm~~avk~yrwqcieck 282 (336)
T KOG1244|consen 224 NPYCDFCLGDSRENKKTGMPEELVSCSDCG---RSGHPSCLQFTANMIAAVKTYRWQCIECK 282 (336)
T ss_pred CcccceeccccccccccCCchhhcchhhcC---CCCCcchhhhhHHHHHHHHhheeeeeecc
Confidence 4589 9955431 3589999976 45799999866533 3468888774
No 77
>TIGR00496 frr ribosome recycling factor. This model finds only eubacterial proteins. Mitochondrial and/or chloroplast forms might be expected but are not currently known. This protein was previously called ribosome releasing factor. By releasing ribosomes from mRNA at the end of protein biosynthesis, it prevents inappropriate translation from 3-prime regions of the mRNA and frees the ribosome for new rounds of translation. EGAD|53116|YHR038W is part of the frr superfamily.
Probab=50.72 E-value=85 Score=26.50 Aligned_cols=33 Identities=30% Similarity=0.509 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 79 DDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQ 111 (267)
Q Consensus 79 dEKv~LA~~a~dlVd~hirrLD~dl~~~e~el~ 111 (267)
|+--.+-.++..+.|.++.++|.-++.-+.|+.
T Consensus 142 D~~k~~~~~iQkltd~~i~~id~~~~~Kekeim 174 (176)
T TIGR00496 142 DEERRLQEEIQKLTDEYIKKIDEILKDKEKELM 174 (176)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 555556678888899999999999888887764
No 78
>PF04380 BMFP: Membrane fusogenic activity; InterPro: IPR007475 BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro.
Probab=50.36 E-value=96 Score=22.53 Aligned_cols=43 Identities=16% Similarity=0.198 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 65 AEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFE 107 (267)
Q Consensus 65 ~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e 107 (267)
..++..+.+.--.+.|=..+-..++.-.-..|..|++.+..||
T Consensus 35 ~~l~~~l~kldlVtREEFd~q~~~L~~~r~kl~~LEarl~~LE 77 (79)
T PF04380_consen 35 ARLQSALSKLDLVTREEFDAQKAVLARTREKLEALEARLAALE 77 (79)
T ss_pred HHHHHHHHHCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3455555555555666666666666666666777777766665
No 79
>PF04949 Transcrip_act: Transcriptional activator; InterPro: IPR007033 Golgins are a family of coiled-coil proteins associated with the Golgi apparatus necessary for tethering events in membrane fusion and as structural supports for Golgi cisternae []. This entry represents proteins annotated as RAB6-interacting golgins.
Probab=50.18 E-value=1.5e+02 Score=24.58 Aligned_cols=86 Identities=14% Similarity=0.241 Sum_probs=57.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 23 NFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTD 102 (267)
Q Consensus 23 ~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~d 102 (267)
.++.++..|..+.....++.+.++..+.. .++....+..|...+.-.-.=-..=|...-.-.|.|++.++.|-..
T Consensus 32 als~f~AkEeeIErkKmeVrekVq~~Lgr-----veEetkrLa~ireeLE~l~dP~RkEv~~vRkkID~vNreLkpl~~~ 106 (159)
T PF04949_consen 32 ALSAFRAKEEEIERKKMEVREKVQAQLGR-----VEEETKRLAEIREELEVLADPMRKEVEMVRKKIDSVNRELKPLGQS 106 (159)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHhH-----HHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHhhHHHHH
Confidence 46777888888887777777777665531 2344466777777776555555556777777777888888877777
Q ss_pred HHHHHHHHHHH
Q psy12696 103 LARFEQEIQEK 113 (267)
Q Consensus 103 l~~~e~el~~~ 113 (267)
..+-+.+....
T Consensus 107 cqKKEkEykea 117 (159)
T PF04949_consen 107 CQKKEKEYKEA 117 (159)
T ss_pred HHHHHHHHHHH
Confidence 66666665543
No 80
>PF06008 Laminin_I: Laminin Domain I; InterPro: IPR009254 Laminins are glycoproteins that are major constituents of the basement membrane of cells. Laminins are trimeric molecules; laminin-1 is an alpha1 beta1 gamma1 trimer. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure []. Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organisation of cells into tissues during embryonic development by interacting with other extracellular matrix components.; GO: 0005102 receptor binding, 0030155 regulation of cell adhesion, 0030334 regulation of cell migration, 0045995 regulation of embryonic development, 0005606 laminin-1 complex
Probab=49.90 E-value=1.9e+02 Score=25.72 Aligned_cols=84 Identities=17% Similarity=0.283 Sum_probs=45.5
Q ss_pred hhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC---CCChhHHHHHHHHHHHHHHHH--------HHhHHHH
Q psy12696 13 LDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMK---HYSKDKKKETLAEIQKYFDKT--------KEYGDDK 81 (267)
Q Consensus 13 ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~---~~~~~~~~~~~~~I~~~~~~~--------~~lsdEK 81 (267)
...|-.+..+.+....+|+..+..+...|...+.+...-.. .++...-...+.+++..+.++ ...+++=
T Consensus 75 ~~~l~~~t~~t~~~a~~L~~~i~~l~~~i~~l~~~~~~l~~~~~~~~~~~l~~~l~ea~~mL~emr~r~f~~~~~~Ae~E 154 (264)
T PF06008_consen 75 AQQLNNNTERTLQRAQDLEQFIQNLQDNIQELIEQVESLNENGDQLPSEDLQRALAEAQRMLEEMRKRDFTPQRQNAEDE 154 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHHHHHHHHHHhccchhHHHHHHHH
Confidence 33444555556666666666666666666666555433222 333333334455555444444 4555555
Q ss_pred HHHHHHHHHHHHHHH
Q psy12696 82 VQLAIQTYEMVDKYI 96 (267)
Q Consensus 82 v~LA~~a~dlVd~hi 96 (267)
..-|..+++-|.+.+
T Consensus 155 l~~A~~LL~~v~~~~ 169 (264)
T PF06008_consen 155 LKEAEDLLSRVQKWF 169 (264)
T ss_pred HHHHHHHHHHHHHHH
Confidence 666666666666554
No 81
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=49.75 E-value=1.1e+02 Score=23.14 Aligned_cols=96 Identities=11% Similarity=0.241 Sum_probs=57.2
Q ss_pred HHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHH-HHH--HHHHHHHHHHHHhHHHHHHHH
Q psy12696 9 YLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKK-ETL--AEIQKYFDKTKEYGDDKVQLA 85 (267)
Q Consensus 9 fld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~-~~~--~~I~~~~~~~~~lsdEKv~LA 85 (267)
.+..+..|-.+++.....++.|+....+...-++. + . .++++.+. ..+ .-|.....++...-++++...
T Consensus 4 ~~~~~q~l~~~~~~l~~~~~~l~~~~~E~~~v~~E----L-~---~l~~d~~vy~~VG~vfv~~~~~ea~~~Le~~~e~l 75 (105)
T cd00632 4 QLAQLQQLQQQLQAYIVQRQKVEAQLNENKKALEE----L-E---KLADDAEVYKLVGNVLVKQEKEEARTELKERLETI 75 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----H-H---cCCCcchHHHHhhhHHhhccHHHHHHHHHHHHHHH
Confidence 34444444455555555555555555554333321 1 1 12222111 110 125666777888888888888
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 86 IQTYEMVDKYIRKLDTDLARFEQEIQE 112 (267)
Q Consensus 86 ~~a~dlVd~hirrLD~dl~~~e~el~~ 112 (267)
....+-++..+..|...+..++..+..
T Consensus 76 e~~i~~l~~~~~~l~~~~~elk~~l~~ 102 (105)
T cd00632 76 ELRIKRLERQEEDLQEKLKELQEKIQQ 102 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 888888888888888888888877754
No 82
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=49.71 E-value=9.2 Score=31.87 Aligned_cols=47 Identities=15% Similarity=0.364 Sum_probs=28.9
Q ss_pred CCcee-ecCCCCCCCcccccCCCCC--CcceecccCccCCCCCCceeCcCCcC
Q psy12696 213 EPTYC-VCQQVSYGEMIGCDNPDCP--IEWFHFACVSLTTKPKGKWYCPKCTS 262 (267)
Q Consensus 213 ~~~~C-~C~~~~~~~mi~Cd~~~c~--~~wfH~~Cv~l~~~p~~~w~C~~C~~ 262 (267)
....| +|..... ..+ .-|.|. ..|.|-+|+..-....+...|+.|..
T Consensus 7 ~~~~CRIC~~~~~-~~~--~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~ 56 (162)
T PHA02825 7 MDKCCWICKDEYD-VVT--NYCNCKNENKIVHKECLEEWINTSKNKSCKICNG 56 (162)
T ss_pred CCCeeEecCCCCC-Ccc--CCcccCCCchHHHHHHHHHHHhcCCCCcccccCC
Confidence 34567 8876643 222 233333 37999999985444556778888854
No 83
>PF13851 GAS: Growth-arrest specific micro-tubule binding
Probab=49.45 E-value=1.7e+02 Score=25.15 Aligned_cols=86 Identities=20% Similarity=0.293 Sum_probs=43.1
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHH---HHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHHH--HHHHHHHHH
Q psy12696 21 QRNFTLMRELDSRAQDVMKTIDRV---AEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAI--QTYEMVDKY 95 (267)
Q Consensus 21 ~r~l~~irelD~~~~~~~~~i~~~---~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~--~a~dlVd~h 95 (267)
.-+|.+|+.|-.++.++....... +......+..+. +|-.....++...-.....+..+|..|++ .-+..+++.
T Consensus 23 ~~NL~lIksLKeei~emkk~e~~~~k~m~ei~~eN~~L~-epL~~a~~e~~eL~k~L~~y~kdK~~L~~~k~rl~~~ek~ 101 (201)
T PF13851_consen 23 LNNLELIKSLKEEIAEMKKKEERNEKLMAEISQENKRLS-EPLKKAEEEVEELRKQLKNYEKDKQSLQNLKARLKELEKE 101 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345666666666666555543222 222222222222 22334445556666666677777777655 333445666
Q ss_pred HHHHHHHHHHHH
Q psy12696 96 IRKLDTDLARFE 107 (267)
Q Consensus 96 irrLD~dl~~~e 107 (267)
++.|..+..-++
T Consensus 102 l~~Lk~e~evL~ 113 (201)
T PF13851_consen 102 LKDLKWEHEVLE 113 (201)
T ss_pred HHHHHHHHHHHH
Confidence 666655544333
No 84
>PF12252 SidE: Dot/Icm substrate protein; InterPro: IPR021014 This entry represents bacterial proteins that are typically between 397 and 1543 amino acids in length including SidE protein in the Dot/Icm pathway of Legionella pneumophila bacteria. There is little literature describing the family.
Probab=48.87 E-value=2.7e+02 Score=30.41 Aligned_cols=52 Identities=17% Similarity=0.270 Sum_probs=47.0
Q ss_pred hhHHHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q psy12696 3 TSYLEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKH 54 (267)
Q Consensus 3 ~~yLedfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~ 54 (267)
-.||.+...-|+.|-.|+=++++.|+..-....+...+++...++-+|.++.
T Consensus 1178 dAyl~eitKqIsaLe~e~PKnltdvK~missf~d~laeiE~LrnErIKkHGa 1229 (1439)
T PF12252_consen 1178 DAYLVEITKQISALEKEKPKNLTDVKSMISSFNDRLAEIEFLRNERIKKHGA 1229 (1439)
T ss_pred HHHHHHHHHHHHHHHhhCCCchhhHHHHHHHHHhhhhHHHHHHHHHhhccCC
Confidence 3588888999999999999999999999999999999999998888988874
No 85
>KOG2932|consensus
Probab=48.45 E-value=8.2 Score=35.62 Aligned_cols=39 Identities=31% Similarity=0.815 Sum_probs=26.7
Q ss_pred Ccee-ecCCC--CCCCcccccCCCCCCcceecccCccCCCCCCceeCcCCcC
Q psy12696 214 PTYC-VCQQV--SYGEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPKCTS 262 (267)
Q Consensus 214 ~~~C-~C~~~--~~~~mi~Cd~~~c~~~wfH~~Cv~l~~~p~~~w~C~~C~~ 262 (267)
.-+| -|..+ -||.||-|+.- |-+.|..+.. +-.|+.|..
T Consensus 90 VHfCd~Cd~PI~IYGRmIPCkHv------FCl~CAr~~~----dK~Cp~C~d 131 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIYGRMIPCKHV------FCLECARSDS----DKICPLCDD 131 (389)
T ss_pred eEeecccCCcceeeecccccchh------hhhhhhhcCc----cccCcCccc
Confidence 4467 88887 37999999862 6677776544 346777743
No 86
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=48.17 E-value=14 Score=24.15 Aligned_cols=33 Identities=30% Similarity=0.512 Sum_probs=23.9
Q ss_pred CCcee-ecCCCC---CCCcccccCCCCCCcceecccCccC
Q psy12696 213 EPTYC-VCQQVS---YGEMIGCDNPDCPIEWFHFACVSLT 248 (267)
Q Consensus 213 ~~~~C-~C~~~~---~~~mi~Cd~~~c~~~wfH~~Cv~l~ 248 (267)
.+.+| +|++.- ....+.|..|. .-+|-.|+...
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~---~~~H~~C~~~~ 46 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCG---LVCHKKCLSKV 46 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT----EEETTGGCTS
T ss_pred CCCCCcccCcccCCCCCCeEEECCCC---ChHhhhhhhhc
Confidence 47789 998876 35578899966 46999998743
No 87
>PF12761 End3: Actin cytoskeleton-regulatory complex protein END3
Probab=47.84 E-value=1.7e+02 Score=25.25 Aligned_cols=29 Identities=17% Similarity=0.106 Sum_probs=24.2
Q ss_pred chHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q psy12696 16 LPIELQRNFTLMRELDSRAQDVMKTIDRV 44 (267)
Q Consensus 16 LP~El~r~l~~irelD~~~~~~~~~i~~~ 44 (267)
=+.|..|.=.++.+||.++..+.......
T Consensus 94 ~dwEevrLkrELa~Le~~l~~~~~~~~~~ 122 (195)
T PF12761_consen 94 TDWEEVRLKRELAELEEKLSKVEQAAESR 122 (195)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35699999999999999999988777654
No 88
>KOG4299|consensus
Probab=47.42 E-value=13 Score=37.20 Aligned_cols=45 Identities=27% Similarity=0.723 Sum_probs=32.7
Q ss_pred Ccee-ecCCCCCCCcccccCCCCCCcceecccCccCCCC---CCceeCcCCcCc
Q psy12696 214 PTYC-VCQQVSYGEMIGCDNPDCPIEWFHFACVSLTTKP---KGKWYCPKCTSD 263 (267)
Q Consensus 214 ~~~C-~C~~~~~~~mi~Cd~~~c~~~wfH~~Cv~l~~~p---~~~w~C~~C~~~ 263 (267)
...| +|.+. |...+|+.|. . -||+.|.+....| .+.|.|..|...
T Consensus 47 ~ts~~~~~~~--gn~~~~~~~~--~-s~h~~~~~~~~sp~~~~~~~~~~~~~~~ 95 (613)
T KOG4299|consen 47 ATSCGICKSG--GNLLCCDHCP--A-SFHLECDKPPLSPDLKGSEINCSRCPKG 95 (613)
T ss_pred hhhcchhhhc--CCccccccCc--c-ccchhccCcccCcccccccccccCCCcc
Confidence 4456 77666 8889999954 4 5999999966666 356777777653
No 89
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=47.36 E-value=5.3 Score=25.70 Aligned_cols=32 Identities=28% Similarity=0.722 Sum_probs=14.9
Q ss_pred ccccCCCCCCcceecccCccCCCCCCceeCcCC
Q psy12696 228 IGCDNPDCPIEWFHFACVSLTTKPKGKWYCPKC 260 (267)
Q Consensus 228 i~Cd~~~c~~~wfH~~Cv~l~~~p~~~w~C~~C 260 (267)
+.|.+.+|... +|..|+.--......-.||.|
T Consensus 12 ~~C~~~~C~~r-~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 12 QRCSNRDCNVR-LHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp EE-SS--S--E-E-HHHHHHHTTT-SS-B-TTT
T ss_pred ccCCCCccCch-HHHHHHHHHHhcCCCCCCcCC
Confidence 56888778887 699999832222211278887
No 90
>PHA02862 5L protein; Provisional
Probab=47.19 E-value=7.4 Score=31.98 Aligned_cols=25 Identities=24% Similarity=0.452 Sum_probs=20.0
Q ss_pred cceecccCccCCCCCCceeCcCCcC
Q psy12696 238 EWFHFACVSLTTKPKGKWYCPKCTS 262 (267)
Q Consensus 238 ~wfH~~Cv~l~~~p~~~w~C~~C~~ 262 (267)
.|.|-+|+..--.+.++-+|+.|.-
T Consensus 26 K~VHq~CL~~WIn~S~k~~CeLCkt 50 (156)
T PHA02862 26 KVVHIKCMQLWINYSKKKECNLCKT 50 (156)
T ss_pred hhHHHHHHHHHHhcCCCcCccCCCC
Confidence 8999999985556677789999964
No 91
>PHA02562 46 endonuclease subunit; Provisional
Probab=47.06 E-value=2.9e+02 Score=27.07 Aligned_cols=26 Identities=8% Similarity=0.175 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHH
Q psy12696 66 EIQKYFDKTKEYGDDKVQLAIQTYEM 91 (267)
Q Consensus 66 ~I~~~~~~~~~lsdEKv~LA~~a~dl 91 (267)
++.....++..+..+.-.|-..+.++
T Consensus 221 e~~~l~~~~~~l~~~l~~l~~~i~~l 246 (562)
T PHA02562 221 KYDELVEEAKTIKAEIEELTDELLNL 246 (562)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444545544454555544
No 92
>PRK10780 periplasmic chaperone; Provisional
Probab=46.87 E-value=1.6e+02 Score=24.18 Aligned_cols=43 Identities=5% Similarity=0.037 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHH
Q psy12696 28 RELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKY 70 (267)
Q Consensus 28 relD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~ 70 (267)
.....++.....+++.....|-+....+++..+.....+|...
T Consensus 53 ~~~q~el~~~~~elq~~~~~~q~~~~~ms~~~~~~~~~el~~~ 95 (165)
T PRK10780 53 KGRASELQRMETDLQAKMQKLQRDGSTMKGSDRTKLEKDVMAQ 95 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcccccCHHHHHHHHHHHHHH
Confidence 3344455555566677777887777888888777666666443
No 93
>KOG4515|consensus
Probab=46.76 E-value=1.9e+02 Score=24.88 Aligned_cols=39 Identities=3% Similarity=0.060 Sum_probs=19.5
Q ss_pred HHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q psy12696 6 LEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRV 44 (267)
Q Consensus 6 Ledfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~ 44 (267)
-+.|--+.+.+-.|=.+....+++.|..+..+.......
T Consensus 101 Q~Hl~~cA~aVA~dQn~lv~r~K~v~~s~~tLf~~~~~~ 139 (217)
T KOG4515|consen 101 QEHLAVCAKAVAADQNKLVARCKSVEASMITLFEETRAH 139 (217)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444555555555555555555554444333
No 94
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=46.75 E-value=9.6 Score=25.25 Aligned_cols=28 Identities=25% Similarity=0.765 Sum_probs=14.6
Q ss_pred cccccCCCCCCcceecccCccCC----CCCCceeCcC
Q psy12696 227 MIGCDNPDCPIEWFHFACVSLTT----KPKGKWYCPK 259 (267)
Q Consensus 227 mi~Cd~~~c~~~wfH~~Cv~l~~----~p~~~w~C~~ 259 (267)
.|+||.|. .|=.+. .++.. .|. .|||..
T Consensus 3 WVQCd~C~---KWR~lp-~~~~~~~~~~~d-~W~C~~ 34 (50)
T PF07496_consen 3 WVQCDSCL---KWRRLP-EEVDPIREELPD-PWYCSM 34 (50)
T ss_dssp EEE-TTT-----EEEE--CCHHCTSCCSST-T--GGG
T ss_pred EEECCCCC---ceeeCC-hhhCcccccCCC-eEEcCC
Confidence 68999987 798776 44332 233 899976
No 95
>KOG1937|consensus
Probab=46.60 E-value=2.9e+02 Score=27.05 Aligned_cols=59 Identities=20% Similarity=0.157 Sum_probs=27.1
Q ss_pred CCCChhHHH--HHHHHHHHHHHHHHHh-------HHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHH
Q psy12696 53 KHYSKDKKK--ETLAEIQKYFDKTKEY-------GDDKVQLAIQTYE----MVDKYIRKLDTDLARFEQEIQ 111 (267)
Q Consensus 53 ~~~~~~~~~--~~~~~I~~~~~~~~~l-------sdEKv~LA~~a~d----lVd~hirrLD~dl~~~e~el~ 111 (267)
...+.+.|. +.+..|.....++.+. -.|=..|-.+++- .+...+.+|-+|+..|..++.
T Consensus 441 akhddhvR~aykllt~iH~nc~ei~E~i~~tg~~~revrdlE~qI~~E~~k~~l~slEkl~~Dyqairqen~ 512 (521)
T KOG1937|consen 441 AKHDDHVRLAYKLLTRIHLNCMEILEMIRETGALKREVRDLESQIYVEEQKQYLKSLEKLHQDYQAIRQEND 512 (521)
T ss_pred hccCHHHHHHHHHHHHHHHHHHHHHHHHHHcchHHHHHHHHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 344555554 4455555544444422 2223333333332 233445555566666655443
No 96
>PF06464 DMAP_binding: DMAP1-binding Domain; InterPro: IPR010506 This domain binds DMAP1, a transcriptional co-repressor.; GO: 0008134 transcription factor binding, 0005634 nucleus
Probab=46.45 E-value=37 Score=26.44 Aligned_cols=21 Identities=38% Similarity=0.539 Sum_probs=16.2
Q ss_pred hhcchHHHHHhHHHHHHHHHHHHH
Q psy12696 13 LDSLPIELQRNFTLMRELDSRAQD 36 (267)
Q Consensus 13 ie~LP~El~r~l~~irelD~~~~~ 36 (267)
+..||.||+ ..+++||.++.+
T Consensus 2 ~s~LP~evq---~~L~~L~~el~~ 22 (111)
T PF06464_consen 2 PSSLPPEVQ---NRLQELDLELEE 22 (111)
T ss_pred cccCCHHHH---HHHHHHHHhhhc
Confidence 568999999 677778777654
No 97
>PF04849 HAP1_N: HAP1 N-terminal conserved region; InterPro: IPR006933 This family is defined by an N-terminal conserved region found in several huntingtin-associated protein 1 (HAP1) homologues. HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner. However, its possible role in the pathogenesis of Huntingtons disease is unclear. This family also includes a similar N-terminal conserved region from hypothetical protein products of ALS2CR3 genes found in the human juvenile amyotrophic lateral sclerosis critical region 2q33-2q34 [].
Probab=46.44 E-value=2.4e+02 Score=26.07 Aligned_cols=47 Identities=13% Similarity=0.228 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 61 KETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQ 108 (267)
Q Consensus 61 ~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~ 108 (267)
..++.+|.+...+++.++-|+-.|.+++...-+.|- +|-+++..|..
T Consensus 237 t~LlsqivdlQ~r~k~~~~EnEeL~q~L~~ske~Q~-~L~aEL~elqd 283 (306)
T PF04849_consen 237 TSLLSQIVDLQQRCKQLAAENEELQQHLQASKESQR-QLQAELQELQD 283 (306)
T ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHH-HHHHHHHHHHH
Confidence 367788888889999999999999999988888865 47777766654
No 98
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis]
Probab=46.12 E-value=2.5e+02 Score=26.47 Aligned_cols=27 Identities=22% Similarity=0.468 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 87 QTYEMVDKYIRKLDTDLARFEQEIQEK 113 (267)
Q Consensus 87 ~a~dlVd~hirrLD~dl~~~e~el~~~ 113 (267)
.|.++...-|..|+..+..++.+|..-
T Consensus 76 em~ema~~Ei~~~~~~~~~le~~L~~l 102 (363)
T COG0216 76 EMREMAEEEIKELEAKIEELEEELKIL 102 (363)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 677888888888888888888887654
No 99
>PF03938 OmpH: Outer membrane protein (OmpH-like); InterPro: IPR005632 This entry includes outer membrane proteins such as OmpH (Skp) among others. OmpH (outer membrane protein H) is a major structural protein of the outer membrane. In Pasteurella multocida it acts as a channel-forming transmembrane porin []. Porins act as molecular sieves to allow the diffusion of small hydrophilic solutes through the outer membrane and also acts as a receptor for bacteriophages and bacteriocins. Porins are highly immunogenic and are conserved in bacterial families, making them attractive vaccine candidates []. The 17kDa protein (Skp, OmpH) of Escherichia coli is a homotrimeric periplasmic chaperone for newly synthesised outer-membrane proteins, the X-ray structure of which has been reported at resolutions of 2.35 A and 2.30 A [, ]. Three hairpin-shaped alpha-helical extensions reach out by approximately 60 A from a trimerisation domain, which is composed of three intersubunit beta-sheets that wind around a central axis. The alpha-helical extensions approach each other at their distal turns, resulting in a fold that resembles a 'three-pronged grasping forcep'. The overall shape of Skp is reminiscent of the cytosolic chaperone prefoldin (IPR009053 from INTERPRO), although it is based on a radically different topology. The peculiar architecture, with apparent plasticity of the prongs and distinct electrostatic and hydrophobic surface properties, supports the recently proposed biochemical mechanism of this chaperone: formation of a Skp(3)-Omp complex protects the outer membrane protein from aggregation during passage through the bacterial periplasm. The ability of Skp to prevent the aggregation of model substrates in vitro is independent of ATP. Skp can interact directly with membrane lipids and lipopolysaccharide. These interactions are needed for efficient Skp-assisted folding of membrane proteins [].; GO: 0051082 unfolded protein binding; PDB: 1SG2_C 1U2M_C.
Probab=46.09 E-value=1.6e+02 Score=23.70 Aligned_cols=53 Identities=11% Similarity=0.250 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHH
Q psy12696 29 ELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDK 81 (267)
Q Consensus 29 elD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEK 81 (267)
.+..+.+....+++.....|-.....++.+.+...-.+|+........+....
T Consensus 47 ~~~~~l~~~~~el~~~~~~l~~~~~~ls~~~~~~~~~~l~~~~~~l~~~~~~~ 99 (158)
T PF03938_consen 47 ALQKELQAKQKELQKLQQKLQSQKATLSEEERQKRQQELQQKEQELQQFQQQA 99 (158)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTTS----SSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44445555555666666666665557777777666666665555555444433
No 100
>KOG1671|consensus
Probab=45.89 E-value=10 Score=32.77 Aligned_cols=19 Identities=37% Similarity=1.015 Sum_probs=15.5
Q ss_pred eecccCccCCCC-CCceeCc
Q psy12696 240 FHFACVSLTTKP-KGKWYCP 258 (267)
Q Consensus 240 fH~~Cv~l~~~p-~~~w~C~ 258 (267)
-|+.||-+..+- .|.||||
T Consensus 154 ThLGCVp~~~AGd~gg~~CP 173 (210)
T KOG1671|consen 154 THLGCVPIANAGDYGGYYCP 173 (210)
T ss_pred ccccccccccccccCceecc
Confidence 489999886666 5799999
No 101
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=45.28 E-value=14 Score=29.82 Aligned_cols=22 Identities=32% Similarity=0.981 Sum_probs=16.3
Q ss_pred cccCCCCCCcceecccCccCCCCCCceeCcCCc
Q psy12696 229 GCDNPDCPIEWFHFACVSLTTKPKGKWYCPKCT 261 (267)
Q Consensus 229 ~Cd~~~c~~~wfH~~Cv~l~~~p~~~w~C~~C~ 261 (267)
-|..|.+|. | ...|..|||.|.
T Consensus 30 hCp~Cg~PL--F---------~KdG~v~CPvC~ 51 (131)
T COG1645 30 HCPKCGTPL--F---------RKDGEVFCPVCG 51 (131)
T ss_pred hCcccCCcc--e---------eeCCeEECCCCC
Confidence 377777665 4 257889999996
No 102
>PRK14127 cell division protein GpsB; Provisional
Probab=45.25 E-value=83 Score=24.57 Aligned_cols=37 Identities=14% Similarity=0.302 Sum_probs=21.3
Q ss_pred HHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 6 LEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVA 45 (267)
Q Consensus 6 Ledfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~ 45 (267)
+++|||.|. .++.....++.+|-.+...+..++.+..
T Consensus 28 VD~FLd~V~---~dye~l~~e~~~Lk~e~~~l~~~l~e~~ 64 (109)
T PRK14127 28 VDKFLDDVI---KDYEAFQKEIEELQQENARLKAQVDELT 64 (109)
T ss_pred HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556666555 4556556666666666665555554433
No 103
>PRK00083 frr ribosome recycling factor; Reviewed
Probab=44.26 E-value=1.2e+02 Score=25.81 Aligned_cols=31 Identities=35% Similarity=0.424 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 81 KVQLAIQTYEMVDKYIRKLDTDLARFEQEIQ 111 (267)
Q Consensus 81 Kv~LA~~a~dlVd~hirrLD~dl~~~e~el~ 111 (267)
--.+-..+..+.|+++.++|.-++.-|.||.
T Consensus 153 ~k~~e~eiQkltd~~i~~id~~~~~Kekeim 183 (185)
T PRK00083 153 LKRAEDEIQKLTDKYIKKIDELLAAKEKEIM 183 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445567778888999999988888887764
No 104
>KOG2626|consensus
Probab=44.19 E-value=15 Score=36.18 Aligned_cols=47 Identities=23% Similarity=0.600 Sum_probs=33.8
Q ss_pred CceeecCCCCC--CCcccccCCCCCCcceecccCcc----C-CCC---CCceeCcCCcCc
Q psy12696 214 PTYCVCQQVSY--GEMIGCDNPDCPIEWFHFACVSL----T-TKP---KGKWYCPKCTSD 263 (267)
Q Consensus 214 ~~~C~C~~~~~--~~mi~Cd~~~c~~~wfH~~Cv~l----~-~~p---~~~w~C~~C~~~ 263 (267)
.++|+|+.... ..-++|..|. .|||..|+-. + ..| .-.+.|..|...
T Consensus 20 ~~~~y~e~~r~l~~~elqcs~cl---k~~~~~~~~~~~~~~s~~pf~t~y~fvc~~c~~~ 76 (544)
T KOG2626|consen 20 ATVCYCEGERNLGIVELQCSTCL---KWFHLPTLEAFHLIKSSLPFMTSYEFVCKECTPS 76 (544)
T ss_pred ccccccccccccCceeeEeeecc---cccccccccccccccccCCcccceeEEeccccCc
Confidence 67899987654 4589999988 9999866542 1 223 346899999876
No 105
>PRK11637 AmiB activator; Provisional
Probab=44.04 E-value=2.9e+02 Score=26.34 Aligned_cols=27 Identities=26% Similarity=0.448 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 82 VQLAIQTYEMVDKYIRKLDTDLARFEQ 108 (267)
Q Consensus 82 v~LA~~a~dlVd~hirrLD~dl~~~e~ 108 (267)
+.-.+.-...++..|..|+.++..++.
T Consensus 91 i~~~~~~i~~~~~ei~~l~~eI~~~q~ 117 (428)
T PRK11637 91 LRETQNTLNQLNKQIDELNASIAKLEQ 117 (428)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333333333344444444444333333
No 106
>PF10046 BLOC1_2: Biogenesis of lysosome-related organelles complex-1 subunit 2 ; InterPro: IPR019269 This entry represents a family of proteins that play a role in cellular proliferation, as well as in the biogenesis of specialised organelles of the endosomal-lysosomal system [].
Probab=43.56 E-value=63 Score=24.47 Aligned_cols=29 Identities=17% Similarity=0.324 Sum_probs=12.2
Q ss_pred HHHHHhhcchHHHHHhHHHHHHHHHHHHH
Q psy12696 8 QYLDSLDSLPIELQRNFTLMRELDSRAQD 36 (267)
Q Consensus 8 dfld~ie~LP~El~r~l~~irelD~~~~~ 36 (267)
.+++.+...=.+|+.+|..|-++|.++..
T Consensus 49 ~~~~~l~~k~~~l~~~l~~Id~Ie~~V~~ 77 (99)
T PF10046_consen 49 KNLEDLNQKYEELQPYLQQIDQIEEQVTE 77 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444444444444444444443
No 107
>KOG0964|consensus
Probab=43.55 E-value=4.6e+02 Score=28.42 Aligned_cols=26 Identities=23% Similarity=0.420 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 87 QTYEMVDKYIRKLDTDLARFEQEIQE 112 (267)
Q Consensus 87 ~a~dlVd~hirrLD~dl~~~e~el~~ 112 (267)
..++.|..|+..+.+....|++++..
T Consensus 748 ~~Le~i~~~l~~~~~~~~~~e~el~s 773 (1200)
T KOG0964|consen 748 KELEEIKTSLHKLESQSNYFESELGS 773 (1200)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHhH
Confidence 34455566666666666666666544
No 108
>PF04012 PspA_IM30: PspA/IM30 family; InterPro: IPR007157 This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma54-containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator [].
Probab=43.37 E-value=2.1e+02 Score=24.48 Aligned_cols=104 Identities=13% Similarity=0.190 Sum_probs=0.0
Q ss_pred HHHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHH
Q psy12696 5 YLEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQL 84 (267)
Q Consensus 5 yLedfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~L 84 (267)
.|++||..++.-=.+++..+..+.-.-.++..-..++...+.+|-.....--..-+.. +......-+.-..+.+.-
T Consensus 27 ~l~q~ird~e~~l~~a~~~~a~~~a~~~~le~~~~~~~~~~~~~~~~A~~Al~~g~ed----LAr~al~~k~~~e~~~~~ 102 (221)
T PF04012_consen 27 MLEQAIRDMEEQLRKARQALARVMANQKRLERKLDEAEEEAEKWEKQAELALAAGRED----LAREALQRKADLEEQAER 102 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHH----HHHHHHHHHHHHHHHHHH
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 85 AIQTYEMVDKYIRKLDTDLARFEQEIQE 112 (267)
Q Consensus 85 A~~a~dlVd~hirrLD~dl~~~e~el~~ 112 (267)
....++.+..++.+|...|..++..+..
T Consensus 103 l~~~~~~~~~~~~~l~~~l~~l~~kl~e 130 (221)
T PF04012_consen 103 LEQQLDQAEAQVEKLKEQLEELEAKLEE 130 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 109
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=42.99 E-value=1.6e+02 Score=22.95 Aligned_cols=54 Identities=7% Similarity=0.239 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q psy12696 38 MKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDK 94 (267)
Q Consensus 38 ~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~ 94 (267)
..++...+..+.+ -|.+++++-++...+|.+..+......++| +-.+|-++++.
T Consensus 23 ~ek~~klvDelVk-kGeln~eEak~~vddl~~q~k~~~~e~e~K--~~r~i~~ml~~ 76 (108)
T COG3937 23 AEKVQKLVDELVK-KGELNAEEAKRFVDDLLRQAKEAQGELEEK--IPRKIEEMLSD 76 (108)
T ss_pred HHHHHHHHHHHHH-cCCCCHHHHHHHHHHHHHHHHHHhhhHHHh--hhHHHHHHHhh
Confidence 3344555555554 367888887777777777777888888888 55666666554
No 110
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=42.81 E-value=3.1e+02 Score=28.50 Aligned_cols=19 Identities=32% Similarity=0.513 Sum_probs=7.5
Q ss_pred HHHHHHhhcchHHHHHhHH
Q psy12696 7 EQYLDSLDSLPIELQRNFT 25 (267)
Q Consensus 7 edfld~ie~LP~El~r~l~ 25 (267)
|+|++..+..=.+|++++.
T Consensus 550 eeYi~~~~~ar~ei~~rv~ 568 (717)
T PF10168_consen 550 EEYIEKQDLAREEIQRRVK 568 (717)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3344433333334444333
No 111
>KOG2846|consensus
Probab=42.64 E-value=17 Score=33.78 Aligned_cols=36 Identities=14% Similarity=0.229 Sum_probs=27.0
Q ss_pred CCcccccCCCCCCcceecccCccCCCCCCceeCcCCcCccc
Q psy12696 225 GEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPKCTSDRK 265 (267)
Q Consensus 225 ~~mi~Cd~~~c~~~wfH~~Cv~l~~~p~~~w~C~~C~~~~~ 265 (267)
..-+-|.+|. .|-.|+.....+.-.|+|+.|..-++
T Consensus 218 ryALIC~~C~-----~HNGla~~ee~~yi~F~C~~Cn~LN~ 253 (328)
T KOG2846|consen 218 RYALICSQCH-----HHNGLARKEEYEYITFRCPHCNALNP 253 (328)
T ss_pred hhhhcchhhc-----cccCcCChhhcCceEEECccccccCC
Confidence 3446688875 58888887677777899999976543
No 112
>COG0233 Frr Ribosome recycling factor [Translation, ribosomal structure and biogenesis]
Probab=41.53 E-value=1.4e+02 Score=25.56 Aligned_cols=34 Identities=29% Similarity=0.422 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 78 GDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQ 111 (267)
Q Consensus 78 sdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el~ 111 (267)
.||--..-..+.-+-|.+|.+||.-++.-|.++.
T Consensus 152 EDe~k~~e~~iQKlTd~yi~~iD~~~~~KEkEim 185 (187)
T COG0233 152 EDEVKKAEEEIQKLTDEYIKKIDELLKDKEKEIM 185 (187)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4555555566777778888888888888877764
No 113
>cd07599 BAR_Rvs167p The Bin/Amphiphysin/Rvs (BAR) domain of Saccharomyces cerevisiae Reduced viability upon starvation protein 167 and similar proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of fungal proteins with similarity to Saccharomyces cerevisiae Reduced viability upon starvation protein 167 (Rvs167p) and Schizosaccharomyces pombe Hob1 (homolog of Bin1). S. cerevisiae Rvs167p plays a role in regulation of the actin cytoskeleton, endocytosis, and sporulation. It forms a heterodimer with another BAR domain protein Rvs161p. Rvs161p and Rvs167p share common functions but are not interchangeable. Their BAR domains cannot be replaced with each other and the overexpression of one cannot suppress the mutant phenotypes of the other. Rvs167p also interacts with the GTPase activating protein (GAP) Gyp5p, which is involved in ER to Golgi vesicle trafficking. BAR domains fo
Probab=41.02 E-value=1.5e+02 Score=25.40 Aligned_cols=21 Identities=19% Similarity=0.368 Sum_probs=17.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHH
Q psy12696 77 YGDDKVQLAIQTYEMVDKYIR 97 (267)
Q Consensus 77 lsdEKv~LA~~a~dlVd~hir 97 (267)
-+++++..|...|+.++.+++
T Consensus 153 kae~~l~~a~~~y~~lN~~Lk 173 (216)
T cd07599 153 KLERKLEEAKEEYEALNELLK 173 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 347899999999999998875
No 114
>KOG1666|consensus
Probab=41.01 E-value=2.5e+02 Score=24.65 Aligned_cols=83 Identities=18% Similarity=0.330 Sum_probs=60.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHHH-----HHHHHHHHHHHHHH
Q psy12696 26 LMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAI-----QTYEMVDKYIRKLD 100 (267)
Q Consensus 26 ~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~-----~a~dlVd~hirrLD 100 (267)
.+-..+..+..+..+|...+...+. ++..+|...+.+|...+.++.++-+ ++.+.. .....+...+|---
T Consensus 4 ~fe~yEqqy~~l~a~it~k~~~~~~----~~~~ekk~~l~~i~~~leEa~ell~-qMdlEvr~lp~~~Rs~~~~KlR~yk 78 (220)
T KOG1666|consen 4 LFEGYEQQYRELSAEITKKIGRALS----LPGSEKKQLLSEIDSKLEEANELLD-QMDLEVRELPPNFRSSYLSKLREYK 78 (220)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHhc----CCchHHHHHHHHHHHhHHHHHHHHH-HHHHHHHhCCchhhhHHHHHHHHHH
Confidence 4456677788888888777776653 5567888899999999999888765 344443 23455667788888
Q ss_pred HHHHHHHHHHHHH
Q psy12696 101 TDLARFEQEIQEK 113 (267)
Q Consensus 101 ~dl~~~e~el~~~ 113 (267)
.+|++|..++...
T Consensus 79 sdl~~l~~e~k~~ 91 (220)
T KOG1666|consen 79 SDLKKLKRELKRT 91 (220)
T ss_pred HHHHHHHHHHHHh
Confidence 8899998888764
No 115
>PHA03386 P10 fibrous body protein; Provisional
Probab=40.60 E-value=1.6e+02 Score=22.31 Aligned_cols=31 Identities=19% Similarity=0.437 Sum_probs=25.7
Q ss_pred hHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 17 PIELQRNFTLMRELDSRAQDVMKTIDRVAED 47 (267)
Q Consensus 17 P~El~r~l~~irelD~~~~~~~~~i~~~~~~ 47 (267)
|+-|.-++.-|+++|.++..++.+++....+
T Consensus 4 pnILl~Ir~dIkavd~KVdaLQ~qV~dv~~n 34 (94)
T PHA03386 4 PSVLTQILDAVQEVDTKVDALQTQLNGLEED 34 (94)
T ss_pred chHHHHHHHHHHHHhhHHHHHHHHHHHHHhc
Confidence 7778889999999999999988888765543
No 116
>KOG0412|consensus
Probab=40.42 E-value=4.4e+02 Score=27.36 Aligned_cols=38 Identities=21% Similarity=0.312 Sum_probs=29.2
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHH---HHHHHHHHHHhcCCC
Q psy12696 18 IELQRNFTLMRELDSRAQDVMKT---IDRVAEDYLDNMKHY 55 (267)
Q Consensus 18 ~El~r~l~~irelD~~~~~~~~~---i~~~~~~~~k~~~~~ 55 (267)
.++.+.++.|+++|..++.+..+ +++.+..++.+...+
T Consensus 24 ~eli~d~t~i~qi~~~le~~~~ee~~~~~~L~~lL~q~~~i 64 (773)
T KOG0412|consen 24 GELIRDLTDISQIDLLLERIAREEARVDKDLEALLSQQQTI 64 (773)
T ss_pred HHHHhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcch
Confidence 46788888999999999888766 677777888765443
No 117
>PF15450 DUF4631: Domain of unknown function (DUF4631)
Probab=40.26 E-value=3.9e+02 Score=26.64 Aligned_cols=42 Identities=14% Similarity=0.250 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 66 EIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEI 110 (267)
Q Consensus 66 ~I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el 110 (267)
.+.........-+.+|+ .+..+.++.|++.|..-+..|-.+|
T Consensus 387 e~~~e~~~~~r~~lekl---~~~q~e~~~~l~~v~eKVd~LpqqI 428 (531)
T PF15450_consen 387 EAKNEWESDERKSLEKL---DQWQNEMEKHLKEVQEKVDSLPQQI 428 (531)
T ss_pred HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHhhhHHH
Confidence 34444444444444443 2344455555555555555444433
No 118
>PF03148 Tektin: Tektin family; InterPro: IPR000435 Tektin heteropolymers form unique protofilaments of flagellar microtubules []. The proteins are predicted to form extended rods composed of 2 alpha- helical segments (~180 residues long) capable of forming coiled coils, interrupted by non-helical linkers []. The 2 segments are similar in sequence, indicating a gene duplication event. Along each tektin rod, cysteine residues occur with a periodicity of ~8nm, coincident with the axial repeat of tubulin dimers in microtubules []. It is proposed that the assembly of tektin heteropolymers produces filaments with repeats of 8, 16, 24, 32, 40, 48 and 96nm, generating the basis for the complex spatial arrangements of axonemal components [].; GO: 0000226 microtubule cytoskeleton organization, 0005874 microtubule
Probab=40.25 E-value=3.3e+02 Score=25.81 Aligned_cols=105 Identities=14% Similarity=0.211 Sum_probs=68.3
Q ss_pred HHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc------C--CCCh-----hHHHHHHHHHHHHHH
Q psy12696 6 LEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNM------K--HYSK-----DKKKETLAEIQKYFD 72 (267)
Q Consensus 6 Ledfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~------~--~~~~-----~~~~~~~~~I~~~~~ 72 (267)
+.+..+....|-..+...+.+|.++...+..+...|.....- ++-+ + .... .+-..+..++ ..+.
T Consensus 253 i~et~~ak~~Le~ql~~~~~ei~~~e~~i~~L~~ai~~k~~~-lkvaqTRL~~R~~RP~vElcrD~~q~~L~~Ev-~~l~ 330 (384)
T PF03148_consen 253 IHETQEAKNELEWQLKKTLQEIAEMEKNIEDLEKAIRDKEGP-LKVAQTRLENRTQRPNVELCRDPPQYGLIEEV-KELR 330 (384)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhh-HHHHHHHHhhHhcCCchHHHHhhHHHHHHHHH-HHHH
Confidence 344555556677777777788888877777777666544322 2211 0 1110 0112334454 4556
Q ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 73 KTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQE 112 (267)
Q Consensus 73 ~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el~~ 112 (267)
....-..+|+.-|...+..|.++..+|+.||..-...+..
T Consensus 331 ~~i~~L~~~L~~a~~~l~~L~~~~~~Le~di~~K~~sL~i 370 (384)
T PF03148_consen 331 ESIEALQEKLDEAEASLQKLERTRLRLEEDIAVKNNSLFI 370 (384)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 6677778999999999999999999999999877766643
No 119
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=40.04 E-value=19 Score=29.63 Aligned_cols=25 Identities=28% Similarity=0.829 Sum_probs=16.6
Q ss_pred ceecccCc----cCCCCCCceeCcCCcCc
Q psy12696 239 WFHFACVS----LTTKPKGKWYCPKCTSD 263 (267)
Q Consensus 239 wfH~~Cv~----l~~~p~~~w~C~~C~~~ 263 (267)
||..+|-. +...+.+.|+|+.|...
T Consensus 32 ~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~ 60 (166)
T cd04476 32 WWYPACPGCNKKVVEEGNGTYRCEKCNKS 60 (166)
T ss_pred eEEccccccCcccEeCCCCcEECCCCCCc
Confidence 66666654 33333478999999764
No 120
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=40.03 E-value=2.7e+02 Score=24.80 Aligned_cols=76 Identities=8% Similarity=0.170 Sum_probs=0.0
Q ss_pred chHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q psy12696 16 LPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKY 95 (267)
Q Consensus 16 LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~h 95 (267)
++......|-.|..||.....+...+......+-+ ++..+..+..--.++ +..++-|++.
T Consensus 1 ~m~~~~~~L~~iq~lD~e~~rl~~~~~~~~~~l~k----------------~~~e~e~~~~~~~~~----~~e~e~le~q 60 (239)
T COG1579 1 MMNNNLKSLLAIQKLDLEKDRLEPRIKEIRKALKK----------------AKAELEALNKALEAL----EIELEDLENQ 60 (239)
T ss_pred CcchHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHH----------------HHHHHHHHHHHHHHH----HHHHHHHHHH
Q ss_pred HHHHHHHHHHHHHHHH
Q psy12696 96 IRKLDTDLARFEQEIQ 111 (267)
Q Consensus 96 irrLD~dl~~~e~el~ 111 (267)
+.+++.++..+..-+.
T Consensus 61 v~~~e~ei~~~r~r~~ 76 (239)
T COG1579 61 VSQLESEIQEIRERIK 76 (239)
T ss_pred HHHHHHHHHHHHHHHH
No 121
>KOG0996|consensus
Probab=40.00 E-value=4e+02 Score=29.33 Aligned_cols=46 Identities=30% Similarity=0.488 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 65 AEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEI 110 (267)
Q Consensus 65 ~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el 110 (267)
.+|.....++..+..+|++.-..=.+-|...|..|.+++.++..-+
T Consensus 885 ~~i~~lq~~i~~i~~e~~q~qk~kv~~~~~~~~~l~~~i~k~~~~i 930 (1293)
T KOG0996|consen 885 ARIKELQNKIDEIGGEKVQAQKDKVEKINEQLDKLEADIAKLTVAI 930 (1293)
T ss_pred HHHHHHHHHHHHhhchhhHHhHHHHHHHHHHHHHHHHHHHHhHHHH
Confidence 3455555566666666666666666666666666666666555444
No 122
>PF06008 Laminin_I: Laminin Domain I; InterPro: IPR009254 Laminins are glycoproteins that are major constituents of the basement membrane of cells. Laminins are trimeric molecules; laminin-1 is an alpha1 beta1 gamma1 trimer. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure []. Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organisation of cells into tissues during embryonic development by interacting with other extracellular matrix components.; GO: 0005102 receptor binding, 0030155 regulation of cell adhesion, 0030334 regulation of cell migration, 0045995 regulation of embryonic development, 0005606 laminin-1 complex
Probab=39.65 E-value=2.7e+02 Score=24.66 Aligned_cols=43 Identities=9% Similarity=0.137 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHhH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 65 AEIQKYFDKTKEYG---DDKVQLAIQTYEMVDKYIRKLDTDLARFE 107 (267)
Q Consensus 65 ~~I~~~~~~~~~ls---dEKv~LA~~a~dlVd~hirrLD~dl~~~e 107 (267)
.+....+..+..+. .+++.-|..+.......+..+......+.
T Consensus 188 ~~~~~kL~Dl~~~l~eA~~~~~ea~~ln~~n~~~l~~~~~k~~~l~ 233 (264)
T PF06008_consen 188 NDYNAKLQDLRDLLNEAQNKTREAEDLNRANQKNLEDLEKKKQELS 233 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333443344333 44777777777776666665555444444
No 123
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=39.28 E-value=22 Score=26.53 Aligned_cols=28 Identities=21% Similarity=0.438 Sum_probs=16.8
Q ss_pred Ccee-ecCCCCC-CCc-ccccCCCCCCcceecccCc
Q psy12696 214 PTYC-VCQQVSY-GEM-IGCDNPDCPIEWFHFACVS 246 (267)
Q Consensus 214 ~~~C-~C~~~~~-~~m-i~Cd~~~c~~~wfH~~Cv~ 246 (267)
...| +|+++-. +.. +..++ .-||+.|..
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~-----~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCG-----HVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCC-----eEEeccccc
Confidence 3458 9998854 332 33322 349999973
No 124
>PRK00808 hypothetical protein; Provisional
Probab=38.89 E-value=2.1e+02 Score=23.11 Aligned_cols=48 Identities=13% Similarity=0.043 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 63 TLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEI 110 (267)
Q Consensus 63 ~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el 110 (267)
.+.+|.....+...-.+--..+..-+.+.+-.||...|..+..|-...
T Consensus 83 fl~~l~~l~~~~~~g~~~~~~l~~~L~~WL~~HI~~~D~~~~~~l~~~ 130 (150)
T PRK00808 83 FIKRVEEYRERFQAGEDVADELHGMLSRWLFNHIRNDDAAYVDAVKAN 130 (150)
T ss_pred HHHHHHHHHHHHHccchHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHh
Confidence 344555544444332223345677788889999999999998885543
No 125
>PF08946 Osmo_CC: Osmosensory transporter coiled coil; InterPro: IPR015041 The osmosensory transporter coiled coil is a C-terminal domain found in various bacterial osmoprotective transporters, such as ProP, Proline/betaine transporter, Proline permease 2 and the citrate proton symporters. It adopts an antiparallel coiled-coil structure, and is essential for osmosensory and osmoprotectant transporter function []. ; PDB: 1R48_B.
Probab=38.23 E-value=42 Score=21.99 Aligned_cols=27 Identities=22% Similarity=0.530 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 83 QLAIQTYEMVDKYIRKLDTDLARFEQE 109 (267)
Q Consensus 83 ~LA~~a~dlVd~hirrLD~dl~~~e~e 109 (267)
.|-+..||.|+..|..||..++.|+.-
T Consensus 8 elLqe~~d~IEqkiedid~qIaeLe~K 34 (46)
T PF08946_consen 8 ELLQEHYDNIEQKIEDIDEQIAELEAK 34 (46)
T ss_dssp -------THHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhHHHhHHHHHHHHHHHHHH
Confidence 455778899999999999888877753
No 126
>KOG2856|consensus
Probab=38.07 E-value=3.7e+02 Score=25.75 Aligned_cols=71 Identities=11% Similarity=0.347 Sum_probs=43.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q psy12696 27 MRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRK 98 (267)
Q Consensus 27 irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirr 98 (267)
++.|-.+++.+.+++.+...+|-+....+... ....+..+..-|+.++..-...++.-..|+--|.+|+.-
T Consensus 179 ~kKlqdrveK~k~evqktkekYektl~el~~y-t~~YmE~MeqvFe~CQ~fE~~Rl~Ffkeil~~v~~hldl 249 (472)
T KOG2856|consen 179 LKKLQDRVEKCKQEVQKTKEKYEKTLAELNKY-TPVYMEDMEQVFEQCQQFEEKRLQFFKEILLKVQRHLDL 249 (472)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 33444455555555554444443332222211 113566788888888888888888888888888888543
No 127
>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp
Probab=37.91 E-value=3.2e+02 Score=25.03 Aligned_cols=39 Identities=13% Similarity=0.388 Sum_probs=29.3
Q ss_pred HhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 12 SLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLD 50 (267)
Q Consensus 12 ~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k 50 (267)
+|-+|-.-|+.....+.+-|.++.++..+|-+-...||.
T Consensus 69 ~iRHLkakLkes~~~l~dRetEI~eLksQL~RMrEDWIE 107 (305)
T PF15290_consen 69 CIRHLKAKLKESENRLHDRETEIDELKSQLARMREDWIE 107 (305)
T ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Confidence 466777777777777777788888887777777777775
No 128
>COG3404 Methenyl tetrahydrofolate cyclohydrolase [Amino acid transport and metabolism]
Probab=37.19 E-value=2.8e+02 Score=24.09 Aligned_cols=85 Identities=9% Similarity=0.188 Sum_probs=55.6
Q ss_pred hcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc--CCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q psy12696 14 DSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNM--KHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEM 91 (267)
Q Consensus 14 e~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~--~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dl 91 (267)
++.-.|+..+|.++.++-.....+.++=.+-...++... ...+.+++...-..|+..+..+.+.=-+=+.++-++.++
T Consensus 53 ~~~d~e~k~i~~~~~~ik~~l~~lidkD~eAf~~im~AyKlPK~teEEK~~R~~~lQ~Alk~Aa~vP~~ia~~~~~~l~l 132 (208)
T COG3404 53 EDYDDEMKEILEELQKIKAELLALIDKDEEAFNLIMAAYKLPKSTEEEKAARRKALQNALKEAAKVPLDIATLMVDLLEL 132 (208)
T ss_pred hhhhhhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHHhChHHHHHHHHHHHHH
Confidence 445567777888888888887777666554444444433 233556666677789999888887766666666666666
Q ss_pred HHHHHHH
Q psy12696 92 VDKYIRK 98 (267)
Q Consensus 92 Vd~hirr 98 (267)
+..-+..
T Consensus 133 ~e~l~~~ 139 (208)
T COG3404 133 LEKLVEK 139 (208)
T ss_pred HHHHHHh
Confidence 6554443
No 129
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=36.79 E-value=1.7e+02 Score=22.47 Aligned_cols=46 Identities=17% Similarity=0.421 Sum_probs=38.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 67 IQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQE 112 (267)
Q Consensus 67 I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el~~ 112 (267)
+...+.++.++-++|+.......+-+++.+.++...+..+...+..
T Consensus 81 ve~~~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~~l~~ 126 (129)
T cd00890 81 VEKSLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQEELQQ 126 (129)
T ss_pred EEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566777889999999999999999999999999999888877654
No 130
>KOG2041|consensus
Probab=36.74 E-value=34 Score=35.33 Aligned_cols=51 Identities=29% Similarity=0.671 Sum_probs=32.6
Q ss_pred CCCCCCCCc-ee-ecCCCCCCCcccccCCCCCCcceecccCccCCCC---CCceeCcCCcC
Q psy12696 207 MPVDPNEPT-YC-VCQQVSYGEMIGCDNPDCPIEWFHFACVSLTTKP---KGKWYCPKCTS 262 (267)
Q Consensus 207 ~~~~~~~~~-~C-~C~~~~~~~mi~Cd~~~c~~~wfH~~Cv~l~~~p---~~~w~C~~C~~ 262 (267)
.|+|++.+. -| +|+.+-..--++|..|. . =...|+.- ..| .--|.||.|..
T Consensus 1109 ~p~d~~~~~vdc~~cg~~i~~~~~~c~ec~---~-kfP~Cias-G~pIt~~~fWlC~~CkH 1164 (1189)
T KOG2041|consen 1109 PPVDPNSAKVDCSVCGAKIDPYDLQCSECQ---T-KFPVCIAS-GRPITDNIFWLCPRCKH 1164 (1189)
T ss_pred CCCCCCccceeeeecCCcCCccCCCChhhc---C-cCceeecc-CCccccceEEEcccccc
Confidence 356666654 48 88876555567898865 2 23678752 222 33699999964
No 131
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=36.17 E-value=30 Score=34.11 Aligned_cols=35 Identities=26% Similarity=0.536 Sum_probs=18.3
Q ss_pred ccccCCCCCCcceec-----ccCccCCCCCCceeCcCCcCc
Q psy12696 228 IGCDNPDCPIEWFHF-----ACVSLTTKPKGKWYCPKCTSD 263 (267)
Q Consensus 228 i~Cd~~~c~~~wfH~-----~Cv~l~~~p~~~w~C~~C~~~ 263 (267)
+.|.+|+-+.. ||. .|----....-.|.||.|...
T Consensus 223 ~~C~~C~~~l~-~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSLT-YHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCceE-EecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 56777664444 442 342211122234899999653
No 132
>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells. In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].
Probab=35.78 E-value=2.4e+02 Score=22.88 Aligned_cols=32 Identities=16% Similarity=0.267 Sum_probs=15.0
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 76 EYGDDKVQLAIQTYEMVDKYIRKLDTDLARFE 107 (267)
Q Consensus 76 ~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e 107 (267)
.-..+|+.-|....+-++|.+..|+.....++
T Consensus 97 ~e~~ekl~e~d~~ae~~eRkv~~le~~~~~~E 128 (143)
T PF12718_consen 97 KETTEKLREADVKAEHFERKVKALEQERDQWE 128 (143)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHhhHHHHH
Confidence 33344444444444444555555544444443
No 133
>PF07319 DnaI_N: Primosomal protein DnaI N-terminus; InterPro: IPR009928 This entry represents the N terminus (approximately 120 residues) of bacterial primosomal DnaI proteins, although one family member appears to be of viral origin. DnaI is one of the components of the Bacillus subtilis replication restart primosome, and is required for the DnaB75-dependent loading of the DnaC helicase [].; PDB: 2K7R_A.
Probab=35.43 E-value=1.4e+02 Score=22.33 Aligned_cols=47 Identities=17% Similarity=0.425 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHH--HHHHHHHHHhc-CCCChhHHHHHHHHHHHHHHHHHHhHHHH
Q psy12696 28 RELDSRAQDVMKTI--DRVAEDYLDNM-KHYSKDKKKETLAEIQKYFDKTKEYGDDK 81 (267)
Q Consensus 28 relD~~~~~~~~~i--~~~~~~~~k~~-~~~~~~~~~~~~~~I~~~~~~~~~lsdEK 81 (267)
+.+..+++++++++ +..++.||+.+ ..++.+ .|+..+.++-++..|+
T Consensus 15 ~~~~~~~~~l~~~vl~dp~V~~Fl~~h~~eLt~~-------~i~rsl~kLyEy~~e~ 64 (94)
T PF07319_consen 15 RNFEERYEQLKQEVLSDPEVQAFLQEHQPELTQE-------MIERSLSKLYEYVSER 64 (94)
T ss_dssp -HHHHHHHHHHHHHTT-HHHHHHHHHSTTT--HH-------HHHHTHHHHHHHHHS-
T ss_pred ccHHHHHHHHHHHHHcCHHHHHHHHHhHHhcCHH-------HHHHHHHHHHHHHHHH
Confidence 56677888888887 78899999988 556543 2444444444444443
No 134
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=35.32 E-value=23 Score=24.11 Aligned_cols=30 Identities=23% Similarity=0.480 Sum_probs=23.0
Q ss_pred CCcee-ecCCCC--CCCcccccCCCCCCcceecccC
Q psy12696 213 EPTYC-VCQQVS--YGEMIGCDNPDCPIEWFHFACV 245 (267)
Q Consensus 213 ~~~~C-~C~~~~--~~~mi~Cd~~~c~~~wfH~~Cv 245 (267)
+...| +|+++- .++.|.|..|. .=||..|.
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~Cg---apyHR~C~ 36 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECG---APYHRDCW 36 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCC---CcccHHHH
Confidence 34568 888886 57789999977 55899886
No 135
>PF15079 DUF4546: Domain of unknown function (DUF4546)
Probab=34.91 E-value=2.8e+02 Score=23.46 Aligned_cols=54 Identities=19% Similarity=0.319 Sum_probs=0.0
Q ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHH
Q psy12696 19 ELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQL 84 (267)
Q Consensus 19 El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~L 84 (267)
||+ .++||.-+++.+-+++|.+...-.-+ -...+.+.-+.+.+.+.--|||+.+
T Consensus 51 eLk---NeLREVREELkEKmeEIKQIKdiMDK---------DFDKL~EFVEIMKeMQkDMDEKMDv 104 (205)
T PF15079_consen 51 ELK---NELREVREELKEKMEEIKQIKDIMDK---------DFDKLHEFVEIMKEMQKDMDEKMDV 104 (205)
T ss_pred HHH---HHHHHHHHHHHHHHHHHHHHHHHHhh---------hHHHHHHHHHHHHHHHHhHHHhhhH
No 136
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=34.75 E-value=5.5 Score=26.50 Aligned_cols=23 Identities=35% Similarity=0.938 Sum_probs=8.9
Q ss_pred eecccCccCC----C-CCCceeCcCCcC
Q psy12696 240 FHFACVSLTT----K-PKGKWYCPKCTS 262 (267)
Q Consensus 240 fH~~Cv~l~~----~-p~~~w~C~~C~~ 262 (267)
-|+.|..+.. . ..+.|.||.|..
T Consensus 22 ~H~~CFDl~~fl~~~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 22 KHLQCFDLESFLESNQRTPKWKCPICNK 49 (50)
T ss_dssp -SS--EEHHHHHHHHHHS---B-TTT--
T ss_pred cccceECHHHHHHHhhccCCeECcCCcC
Confidence 5778877432 1 245699999975
No 137
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=34.75 E-value=5e+02 Score=26.94 Aligned_cols=27 Identities=22% Similarity=0.474 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 87 QTYEMVDKYIRKLDTDLARFEQEIQEK 113 (267)
Q Consensus 87 ~a~dlVd~hirrLD~dl~~~e~el~~~ 113 (267)
..-+..-.+.+.||.++.++..|+...
T Consensus 538 e~~e~~r~r~~~lE~E~~~lr~elk~k 564 (697)
T PF09726_consen 538 ECAESCRQRRRQLESELKKLRRELKQK 564 (697)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345566777888998888888887664
No 138
>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope. They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....
Probab=34.56 E-value=2.3e+02 Score=25.48 Aligned_cols=31 Identities=16% Similarity=0.197 Sum_probs=15.4
Q ss_pred HHHhhcchHHHHHhHHHHHHHHHHHHHHHHH
Q psy12696 10 LDSLDSLPIELQRNFTLMRELDSRAQDVMKT 40 (267)
Q Consensus 10 ld~ie~LP~El~r~l~~irelD~~~~~~~~~ 40 (267)
...+..+..|+.+.-..|..|..++..+...
T Consensus 208 ~~~~~~~~~E~~~~r~~~~~l~~el~~l~~~ 238 (312)
T PF00038_consen 208 SEELESAKEELKELRRQIQSLQAELESLRAK 238 (312)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccchhHhHHHHHHhhhhHhhhhhhccccc
Confidence 3344445555555555555555555544433
No 139
>PF07011 DUF1313: Protein of unknown function (DUF1313); InterPro: IPR009741 This family consists of several hypothetical plant proteins of around 100 residues in length. The function of this family is unknown.
Probab=34.48 E-value=98 Score=23.13 Aligned_cols=34 Identities=26% Similarity=0.494 Sum_probs=20.3
Q ss_pred chHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 16 LPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYL 49 (267)
Q Consensus 16 LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~ 49 (267)
.|.-|.|+..+||||..-+...+.-...+-..|.
T Consensus 40 ~PdnL~RNV~LIrELN~NI~rVv~lY~dLs~sFs 73 (87)
T PF07011_consen 40 IPDNLSRNVGLIRELNGNISRVVDLYSDLSSSFS 73 (87)
T ss_pred CCchhhHhHHHHHHHHhhHHHHHHHHHHHhHHHH
Confidence 5677777777777776665555554444444443
No 140
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=34.17 E-value=18 Score=20.11 Aligned_cols=11 Identities=55% Similarity=1.346 Sum_probs=8.5
Q ss_pred CceeCcCCcCc
Q psy12696 253 GKWYCPKCTSD 263 (267)
Q Consensus 253 ~~w~C~~C~~~ 263 (267)
|.|.|+.|.-.
T Consensus 1 g~W~C~~C~~~ 11 (26)
T smart00547 1 GDWECPACTFL 11 (26)
T ss_pred CcccCCCCCCc
Confidence 57999999543
No 141
>KOG4628|consensus
Probab=34.13 E-value=33 Score=32.31 Aligned_cols=47 Identities=23% Similarity=0.595 Sum_probs=26.6
Q ss_pred ceeecCCCC-CCCcccccCCCCCCcceecccCccCCCCCCceeCcCCcCccc
Q psy12696 215 TYCVCQQVS-YGEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPKCTSDRK 265 (267)
Q Consensus 215 ~~C~C~~~~-~~~mi~Cd~~~c~~~wfH~~Cv~l~~~p~~~w~C~~C~~~~~ 265 (267)
.+|+|-... .|+-+.==. |... ||..||.-.-... .-+||-|+.+-+
T Consensus 231 ~CaIClEdY~~GdklRiLP--C~H~-FH~~CIDpWL~~~-r~~CPvCK~di~ 278 (348)
T KOG4628|consen 231 TCAICLEDYEKGDKLRILP--CSHK-FHVNCIDPWLTQT-RTFCPVCKRDIR 278 (348)
T ss_pred eEEEeecccccCCeeeEec--CCCc-hhhccchhhHhhc-CccCCCCCCcCC
Confidence 344997653 366433333 2235 9999996211111 247999987543
No 142
>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane
Probab=34.03 E-value=4.9e+02 Score=26.00 Aligned_cols=45 Identities=16% Similarity=0.234 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHHhHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 61 KETLAEIQKYFDKTKEYGDD-KVQLAIQTYEMVDKYIRKLDTDLAR 105 (267)
Q Consensus 61 ~~~~~~I~~~~~~~~~lsdE-Kv~LA~~a~dlVd~hirrLD~dl~~ 105 (267)
...+..|...|.+...+... =..=|..++..+..++..|...+..
T Consensus 167 e~~L~~ie~~F~~f~~lt~~GD~~~A~eil~~l~~~~~~l~~~~e~ 212 (560)
T PF06160_consen 167 EKQLENIEEEFSEFEELTENGDYLEAREILEKLKEETDELEEIMED 212 (560)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35666677766666665554 4444566666666666666655433
No 143
>PRK08032 fliD flagellar capping protein; Reviewed
Probab=34.03 E-value=2.2e+02 Score=27.68 Aligned_cols=95 Identities=13% Similarity=0.201 Sum_probs=42.2
Q ss_pred HHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhH--HHHHHHHHHHHHHHHHHhHHHHHHHHH
Q psy12696 9 YLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDK--KKETLAEIQKYFDKTKEYGDDKVQLAI 86 (267)
Q Consensus 9 fld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~--~~~~~~~I~~~~~~~~~lsdEKv~LA~ 86 (267)
|-+.|++=|..|...|.-- ....-+...+...+..|+...+-+.... -...+.+|.+.++.....-+.+-+-=.
T Consensus 362 l~~al~~np~~V~~lF~~~----~~~~G~~~~l~~~l~~~~~~~G~l~~~~~~l~~~i~~l~~~i~~~~~rl~~~e~rl~ 437 (462)
T PRK08032 362 LTKALKEDPAGVKALFVGD----GKKTGITTQIATNLKSWLSTTGIIKTATDGVNKTLKKLTKQYNAVSDSIDATIARYK 437 (462)
T ss_pred HHHHHHHCHHHHHHHhCCC----CCCCcHHHHHHHHHHHHHcCCccchhHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5555666677777666421 0112344444444555554433332111 112333444444444433333333333
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q psy12696 87 QTYEMVDKYIRKLDTDLARFE 107 (267)
Q Consensus 87 ~a~dlVd~hirrLD~dl~~~e 107 (267)
.=|-.++.-|.+|......|.
T Consensus 438 ~qF~ame~~~s~mns~~s~L~ 458 (462)
T PRK08032 438 AQFTQLDKLMTSLNSTSSYLT 458 (462)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 344555555555555544443
No 144
>KOG3564|consensus
Probab=33.94 E-value=4.1e+02 Score=26.37 Aligned_cols=50 Identities=22% Similarity=0.236 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHH---HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 63 TLAEIQKYFDKTK---EYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQE 112 (267)
Q Consensus 63 ~~~~I~~~~~~~~---~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el~~ 112 (267)
-+.++++++.++. ..-|-|+.=|....++.-+.-++++.|.+++|..+.+
T Consensus 50 e~~~~~~~L~Ka~tk~~~ldvklkha~~~vda~ik~rr~ae~d~~~~E~~i~~ 102 (604)
T KOG3564|consen 50 ELGKYKDLLAKAETKRSALDVKLKHARNQVDAEIKRRRRAEADCEKLETQIQL 102 (604)
T ss_pred HHHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence 3455666666654 3457788889999999888899999999999987765
No 145
>PF09755 DUF2046: Uncharacterized conserved protein H4 (DUF2046); InterPro: IPR019152 This is the conserved N-terminal 350 residues of a family of proteins of unknown function possibly containing a coiled-coil domain.
Probab=33.90 E-value=3.9e+02 Score=24.80 Aligned_cols=39 Identities=15% Similarity=0.244 Sum_probs=24.8
Q ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 71 FDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQE 109 (267)
Q Consensus 71 ~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~e 109 (267)
......|..|||.|=+++-.-=+--+.+|...+.+++.+
T Consensus 155 q~~le~Lr~EKVdlEn~LE~EQE~lvN~L~Kqm~~l~~e 193 (310)
T PF09755_consen 155 QEELERLRREKVDLENTLEQEQEALVNRLWKQMDKLEAE 193 (310)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344558899999998876554444455555555555544
No 146
>TIGR02977 phageshock_pspA phage shock protein A. Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by PFAM model pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects.
Probab=33.86 E-value=3.1e+02 Score=23.66 Aligned_cols=105 Identities=18% Similarity=0.256 Sum_probs=0.0
Q ss_pred hHHHHHHHHhhcchH-HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHH--HHHHHHHHHH-----HHHH
Q psy12696 4 SYLEQYLDSLDSLPI-ELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKK--ETLAEIQKYF-----DKTK 75 (267)
Q Consensus 4 ~yLedfld~ie~LP~-El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~--~~~~~I~~~~-----~~~~ 75 (267)
..+++.+|.+++ |. -|. ..|+++...+......+-..+.........+...... .+..+....+ ..+.
T Consensus 13 a~~n~~~dk~ED-P~~~l~---q~irem~~~l~~ar~~lA~~~a~~k~~e~~~~~~~~~~~~~~~~A~~Al~~G~EdLAr 88 (219)
T TIGR02977 13 SNLNALLDKAED-PEKMIR---LIIQEMEDTLVEVRTTSARTIADKKELERRVSRLEAQVADWQEKAELALSKGREDLAR 88 (219)
T ss_pred HHHHHHHHhccC-HHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH
Q ss_pred HhHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 76 EYGDDKVQLAIQT------YEMVDKYIRKLDTDLARFEQEIQE 112 (267)
Q Consensus 76 ~lsdEKv~LA~~a------~dlVd~hirrLD~dl~~~e~el~~ 112 (267)
....+|.....++ ++-+...+.+|...+..|+..+..
T Consensus 89 ~Al~~k~~~~~~~~~l~~~~~~~~~~v~~l~~~l~~L~~ki~~ 131 (219)
T TIGR02977 89 AALIEKQKAQELAEALERELAAVEETLAKLQEDIAKLQAKLAE 131 (219)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 147
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=33.74 E-value=11 Score=27.30 Aligned_cols=10 Identities=30% Similarity=1.215 Sum_probs=8.6
Q ss_pred cceecccCcc
Q psy12696 238 EWFHFACVSL 247 (267)
Q Consensus 238 ~wfH~~Cv~l 247 (267)
.|||+.|+..
T Consensus 39 ~W~H~~C~~~ 48 (82)
T PF00645_consen 39 KWYHWDCFFK 48 (82)
T ss_dssp EEEEHHHHHH
T ss_pred ceECcccccc
Confidence 7999999873
No 148
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=33.55 E-value=19 Score=26.86 Aligned_cols=24 Identities=38% Similarity=0.815 Sum_probs=17.1
Q ss_pred ceecccCc--cCCCCCCceeCcCCcCc
Q psy12696 239 WFHFACVS--LTTKPKGKWYCPKCTSD 263 (267)
Q Consensus 239 wfH~~Cv~--l~~~p~~~w~C~~C~~~ 263 (267)
=||..|+- |... ..+=.||.|+..
T Consensus 55 ~FH~hCI~kWl~~~-~~~~~CPmCR~~ 80 (85)
T PF12861_consen 55 NFHMHCILKWLSTQ-SSKGQCPMCRQP 80 (85)
T ss_pred HHHHHHHHHHHccc-cCCCCCCCcCCe
Confidence 39999987 4443 334599999865
No 149
>PRK10807 paraquat-inducible protein B; Provisional
Probab=33.34 E-value=5.1e+02 Score=25.94 Aligned_cols=20 Identities=30% Similarity=0.474 Sum_probs=13.9
Q ss_pred hHHHHHHHHhhcchHHHHHhHH
Q psy12696 4 SYLEQYLDSLDSLPIELQRNFT 25 (267)
Q Consensus 4 ~yLedfld~ie~LP~El~r~l~ 25 (267)
.-+.++++.++.|| |-..+.
T Consensus 420 ~~~~~il~kin~lp--le~i~~ 439 (547)
T PRK10807 420 QKLMEALDKINNLP--LNPMIE 439 (547)
T ss_pred HHHHHHHHHHhcCC--HHHHHH
Confidence 35778888999999 444444
No 150
>KOG1246|consensus
Probab=33.32 E-value=36 Score=36.06 Aligned_cols=48 Identities=33% Similarity=0.847 Sum_probs=34.7
Q ss_pred CCcee-ecCCCCCCCcccccCCCCCCcceecccCc--cCCCCCCceeCcCCcCc
Q psy12696 213 EPTYC-VCQQVSYGEMIGCDNPDCPIEWFHFACVS--LTTKPKGKWYCPKCTSD 263 (267)
Q Consensus 213 ~~~~C-~C~~~~~~~mi~Cd~~~c~~~wfH~~Cv~--l~~~p~~~w~C~~C~~~ 263 (267)
....| .|.+.....++.|+.|. .=+|..|.. ++..+.+.|.|+.|...
T Consensus 154 ~~~~~~~~~k~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 204 (904)
T KOG1246|consen 154 DYPQCNTCSKGKEEKLLLCDSCD---DSYHTYCLRPPLTRVPDGDWRCPKCIPT 204 (904)
T ss_pred cchhhhccccCCCccceeccccc---CcccccccCCCCCcCCcCcccCCccccc
Confidence 33446 77666433445899976 569999987 55667899999999765
No 151
>KOG4643|consensus
Probab=33.26 E-value=6.1e+02 Score=27.62 Aligned_cols=8 Identities=13% Similarity=0.430 Sum_probs=2.8
Q ss_pred HHHHHHHH
Q psy12696 93 DKYIRKLD 100 (267)
Q Consensus 93 d~hirrLD 100 (267)
++|+..|.
T Consensus 529 ~~k~eeLe 536 (1195)
T KOG4643|consen 529 SNKLEELE 536 (1195)
T ss_pred HHHHHHHH
Confidence 33333333
No 152
>PF10498 IFT57: Intra-flagellar transport protein 57 ; InterPro: IPR019530 Eukaryotic cilia and flagella are specialised organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bi-directional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated []. This protein is known as Huntington-interacting protein-1 in humans.
Probab=33.16 E-value=4.2e+02 Score=25.00 Aligned_cols=12 Identities=0% Similarity=0.277 Sum_probs=5.0
Q ss_pred HHHHHhHHHHHH
Q psy12696 18 IELQRNFTLMRE 29 (267)
Q Consensus 18 ~El~r~l~~ire 29 (267)
.+|.+.|..|.-
T Consensus 248 ~~i~~~lekI~s 259 (359)
T PF10498_consen 248 QDISKTLEKIES 259 (359)
T ss_pred HHHHHHHHHHHH
Confidence 444444444433
No 153
>KOG4466|consensus
Probab=33.12 E-value=3.8e+02 Score=24.48 Aligned_cols=32 Identities=19% Similarity=0.288 Sum_probs=20.4
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 76 EYGDDKVQLAIQTYEMVDKYIRKLDTDLARFE 107 (267)
Q Consensus 76 ~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e 107 (267)
++-.+|+.|=..++.-|+..+++|+.+-..|+
T Consensus 105 e~E~~~~lLke~l~seleeKkrkieeeR~smD 136 (291)
T KOG4466|consen 105 EYESKKKLLKENLISELEEKKRKIEEERLSMD 136 (291)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 45566666666777777777777766544443
No 154
>KOG1300|consensus
Probab=33.05 E-value=2.1e+02 Score=28.91 Aligned_cols=61 Identities=15% Similarity=0.274 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHH------HHHHHHHHHHHH
Q psy12696 34 AQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKV------QLAIQTYEMVDK 94 (267)
Q Consensus 34 ~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv------~LA~~a~dlVd~ 94 (267)
..+..+.|.+.+++|...++.+....+..-.+.+++.+..+-+++.++- .||+..+.....
T Consensus 293 Iadvse~l~~~~k~f~~~nk~~~~~~k~~S~kDL~~mv~~lpqy~k~~~Kls~Hl~LA~eC~~~~~~ 359 (593)
T KOG1300|consen 293 IADVSERLTKKMKNFSSKNKRLQTKSKETSTKDLSKMVKKLPQYQKELDKLSLHLELAEECMKKFQE 359 (593)
T ss_pred HHHHHHHHHHHHHHHHhhhhhhhccccccchHHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455566777777887766544433443445666777777777777764 444444444443
No 155
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=32.85 E-value=5.1e+02 Score=25.86 Aligned_cols=20 Identities=20% Similarity=0.135 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q psy12696 88 TYEMVDKYIRKLDTDLARFE 107 (267)
Q Consensus 88 a~dlVd~hirrLD~dl~~~e 107 (267)
|...|++++.+|...+....
T Consensus 304 A~~~vek~~~~l~~~l~~~~ 323 (569)
T PRK04778 304 ARKYVEKNSDTLPDFLEHAK 323 (569)
T ss_pred HHHHHHHhhHHHHHHHHHHH
Confidence 33334444444444443333
No 156
>PF03234 CDC37_N: Cdc37 N terminal kinase binding; InterPro: IPR013855 In Saccharomyces cerevisiae (Baker's yeast), cell division control protein Cdc37 is required for the productive formation of Cdc28-cyclin complexes. Cdc37 may be a kinase targeting subunit of Hsp90 [].
Probab=32.81 E-value=3.1e+02 Score=23.27 Aligned_cols=104 Identities=17% Similarity=0.224 Sum_probs=61.3
Q ss_pred HHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHH---HHHHHHHHHhcCC-------CChhHHH-HHHHHHHHHHHHHH
Q psy12696 7 EQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTI---DRVAEDYLDNMKH-------YSKDKKK-ETLAEIQKYFDKTK 75 (267)
Q Consensus 7 edfld~ie~LP~El~r~l~~irelD~~~~~~~~~i---~~~~~~~~k~~~~-------~~~~~~~-~~~~~I~~~~~~~~ 75 (267)
+++-..++.|-.+..-+-.++.+++..+..+...- .+.+..++..... ..+.+.. ..-.-|...+.++.
T Consensus 42 ~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~~~~~~~~~~e~~~~~~~~~~~p~y~~Mi~~L~~qvk 121 (177)
T PF03234_consen 42 EERKQEIEELKYERKINEKLLKRIQKLLSALDKEEEADKQEVMESLNEPFDKKEKPGVENKDPEQPTYDEMIEDLLDQVK 121 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccchHHHHHHHHhcccccccccccccCCCCCCCHHHHHHHHHHHHh
Confidence 45556667777777777777777777776665441 1223333332211 1111111 22234566666666
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 76 EYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQE 112 (267)
Q Consensus 76 ~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el~~ 112 (267)
...|++- ...+...|..|..+|+.....+...+..
T Consensus 122 ~~~de~~--~~~~~~~l~~H~~kl~~~~ke~~~kLee 156 (177)
T PF03234_consen 122 KEPDEKS--GKAELEELQEHRAKLEKEQKELKKKLEE 156 (177)
T ss_pred cccCccc--HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6666655 7888889999999988877666655543
No 157
>PRK14154 heat shock protein GrpE; Provisional
Probab=32.69 E-value=3.4e+02 Score=23.68 Aligned_cols=9 Identities=11% Similarity=0.423 Sum_probs=3.4
Q ss_pred HHHHHhHHH
Q psy12696 72 DKTKEYGDD 80 (267)
Q Consensus 72 ~~~~~lsdE 80 (267)
..+..++-+
T Consensus 94 e~~~~~a~e 102 (208)
T PRK14154 94 ADIIKFGSK 102 (208)
T ss_pred HHHHHHHHH
Confidence 333333333
No 158
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=32.64 E-value=23 Score=20.55 Aligned_cols=12 Identities=50% Similarity=1.326 Sum_probs=9.5
Q ss_pred CCceeCcCCcCc
Q psy12696 252 KGKWYCPKCTSD 263 (267)
Q Consensus 252 ~~~w~C~~C~~~ 263 (267)
.|.|.|+.|...
T Consensus 2 ~g~W~C~~C~~~ 13 (30)
T PF00641_consen 2 EGDWKCPSCTFM 13 (30)
T ss_dssp SSSEEETTTTEE
T ss_pred CcCccCCCCcCC
Confidence 478999999654
No 159
>cd00520 RRF Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another round of protein synthesis. RRF is believed to bind the ribosome at the A-site in a manner that mimics tRNA, but the specific mechanisms remain unclear. RRF is essential for bacterial growth. It is not necessary for cell growth in archaea or eukaryotes, but is found in mitochondria or chloroplasts of some eukaryotic species.
Probab=32.47 E-value=1.9e+02 Score=24.35 Aligned_cols=32 Identities=28% Similarity=0.440 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 79 DDKVQLAIQTYEMVDKYIRKLDTDLARFEQEI 110 (267)
Q Consensus 79 dEKv~LA~~a~dlVd~hirrLD~dl~~~e~el 110 (267)
|+--.+-..+..+.|+++.++|.-++.-+.|+
T Consensus 147 D~~k~~~~~iqkltd~~i~~id~~~~~Kekei 178 (179)
T cd00520 147 DEVKKAEEDLQKLTDEYIKKIDELLKSKEKEL 178 (179)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34444456677778888888888777766654
No 160
>PF08580 KAR9: Yeast cortical protein KAR9; InterPro: IPR013889 The KAR9 protein in Saccharomyces cerevisiae (Baker's yeast) is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules []. KAR9 localises at the shmoo tip in mating cells and at the tip of the growing bud in anaphase [].
Probab=32.11 E-value=5.9e+02 Score=26.33 Aligned_cols=47 Identities=17% Similarity=0.252 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 62 ETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQ 108 (267)
Q Consensus 62 ~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~ 108 (267)
+...++...+++.+..-.+.|+||-.=.||.+.||.-|+.+++.+-.
T Consensus 98 e~vsqm~~~vK~~L~~vK~qveiAmE~~EL~~~vlg~l~~EIe~~~~ 144 (683)
T PF08580_consen 98 EEVSQMELDVKKTLISVKKQVEIAMEWEELWNDVLGDLDNEIEECIR 144 (683)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence 44455666777778888899999999999999999999998876643
No 161
>PF05064 Nsp1_C: Nsp1-like C-terminal region; InterPro: IPR007758 The NSP1-like protein appears to be an essential component of the nuclear pore complex, for example preribosome nuclear export requires the Nup82p-Nup159p-Nsp1p complex. The C-terminal of Nsp1 is involved in binding Nup82 [], probably via coiled-coil formation [, ]. The family is related to the rotavirus nonstructural protein NSP1 which is the least conserved protein in the rotavirus genome. Its function in the replication process is not fully understood.; GO: 0017056 structural constituent of nuclear pore, 0005643 nuclear pore; PDB: 3T97_C.
Probab=32.08 E-value=39 Score=26.47 Aligned_cols=28 Identities=7% Similarity=0.229 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q psy12696 28 RELDSRAQDVMKTIDRVAEDYLDNMKHY 55 (267)
Q Consensus 28 relD~~~~~~~~~i~~~~~~~~k~~~~~ 55 (267)
+.||.-+..-..+|+.....|...+..+
T Consensus 18 k~Leeiin~W~~eLe~q~k~F~~qA~~V 45 (116)
T PF05064_consen 18 KTLEEIINKWNKELEEQEKEFNEQATQV 45 (116)
T ss_dssp ----------------------------
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455555555666677777776655443
No 162
>PF10732 DUF2524: Protein of unknown function (DUF2524); InterPro: IPR019668 This entry represents proteins with unknown function, and appear to be restricted to the Bacillaceae.
Probab=31.87 E-value=2.1e+02 Score=21.19 Aligned_cols=61 Identities=7% Similarity=0.102 Sum_probs=43.3
Q ss_pred hHHHHHHHHhhcchHHHHHhHHHHHHH----HHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHH
Q psy12696 4 SYLEQYLDSLDSLPIELQRNFTLMREL----DSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETL 64 (267)
Q Consensus 4 ~yLedfld~ie~LP~El~r~l~~irel----D~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~ 64 (267)
-++++|++..+..=...+..|.+=... |..+.+.+..|+..+.++-+-..+.++.+|+.+.
T Consensus 5 qs~~~~lq~~e~~i~~a~eQ~~~~~rqehynd~eYt~Aq~~LE~a~neL~~l~~sAN~qQREqL~ 69 (84)
T PF10732_consen 5 QSVDEFLQQCEQAIRFAQEQFEEGSRQEHYNDEEYTEAQQMLEEAYNELEKLAHSANPQQREQLH 69 (84)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHH
Confidence 378888888776655555555544433 7778888888888888887777777877777543
No 163
>PF11221 Med21: Subunit 21 of Mediator complex; InterPro: IPR021384 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator []. ; PDB: 1YKE_B 1YKH_B.
Probab=31.63 E-value=2.8e+02 Score=22.39 Aligned_cols=56 Identities=18% Similarity=0.278 Sum_probs=35.7
Q ss_pred HHHHHHHHhcCCC--ChhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q psy12696 43 RVAEDYLDNMKHY--SKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRK 98 (267)
Q Consensus 43 ~~~~~~~k~~~~~--~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirr 98 (267)
+.+..+|.....+ +++...+.+.++...+..+-.--.++|.-+...+..|+.-|+.
T Consensus 83 kqIe~LIdsLPg~~~see~Q~~~i~~L~~E~~~~~~el~~~v~e~e~ll~~v~~~i~~ 140 (144)
T PF11221_consen 83 KQIEYLIDSLPGIEVSEEEQLKRIKELEEENEEAEEELQEAVKEAEELLKQVQELIRE 140 (144)
T ss_dssp HHHHHHHHHSTTSSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455667666553 3444556667777777777777777777777777666665543
No 164
>PF04668 Tsg: Twisted gastrulation (Tsg) protein conserved region; InterPro: IPR006761 Tsg was identified in Drosophila melanogaster as being required to specify the dorsal-most structures in the embryo, for example the amnioserosa. Biochemical experiments have revealed three key properties of Tsg: it can synergistically inhibit Dpp/BMP action in both D. melanogaster and vertebrates by forming a tripartite complete between itself, SOG/chordin and a BMP ligand; Tsg seems to enhance the Tld/BMP-1-mediated cleavage rate of SOG/chordin and may change the preference of site utilisation; Tsg can promote the dissociation of chordin cysteine-rich-containing fragments from the ligand to inhibit BMP signalling [, ].
Probab=31.55 E-value=18 Score=29.26 Aligned_cols=27 Identities=30% Similarity=0.668 Sum_probs=15.2
Q ss_pred CCCcceeccc---CccCCCC--CCceeCcCCc
Q psy12696 235 CPIEWFHFAC---VSLTTKP--KGKWYCPKCT 261 (267)
Q Consensus 235 c~~~wfH~~C---v~l~~~p--~~~w~C~~C~ 261 (267)
-.|.|||-.| ||-+=.. ...-.|..|.
T Consensus 100 ssYRWFHdgCCECVG~~CinYGinesrC~~Cp 131 (132)
T PF04668_consen 100 SSYRWFHDGCCECVGPTCINYGINESRCSNCP 131 (132)
T ss_pred ccceeeccchhhccCchhhhccCCcHhHhcCC
Confidence 3579999965 6632222 3345566663
No 165
>PRK12495 hypothetical protein; Provisional
Probab=31.18 E-value=33 Score=30.11 Aligned_cols=11 Identities=36% Similarity=1.220 Sum_probs=6.4
Q ss_pred CCceeCcCCcC
Q psy12696 252 KGKWYCPKCTS 262 (267)
Q Consensus 252 ~~~w~C~~C~~ 262 (267)
.|.-||+.|..
T Consensus 56 pG~~~Cp~CQ~ 66 (226)
T PRK12495 56 DGQEFCPTCQQ 66 (226)
T ss_pred CCeeECCCCCC
Confidence 44566777653
No 166
>PRK14011 prefoldin subunit alpha; Provisional
Probab=31.08 E-value=1.5e+02 Score=24.22 Aligned_cols=49 Identities=18% Similarity=0.254 Sum_probs=40.7
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy12696 67 IQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQEKAL 115 (267)
Q Consensus 67 I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el~~~~~ 115 (267)
+.....+|.++-+.|+.......+.|...|.++...+..+..++...+.
T Consensus 82 VEk~~~eA~~~~~~ri~~l~~~~~~l~~~i~~~~~~~~~l~~~L~~k~~ 130 (144)
T PRK14011 82 LEKDVSEVIEDFKKSVEELDKTKKEGNKKIEELNKEITKLRKELEKRAQ 130 (144)
T ss_pred EEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5667788888889999999999999999999999998888877776533
No 167
>TIGR01149 mtrG N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit G. coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranfersae is membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.
Probab=30.95 E-value=1.4e+02 Score=21.37 Aligned_cols=31 Identities=13% Similarity=0.226 Sum_probs=24.7
Q ss_pred hHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 17 PIELQRNFTLMRELDSRAQDVMKTIDRVAED 47 (267)
Q Consensus 17 P~El~r~l~~irelD~~~~~~~~~i~~~~~~ 47 (267)
|.|+...+..+-++|.++.-...++.++.-+
T Consensus 11 ~~d~~~i~~rLd~iEeKVEf~~~E~~Qr~Gk 41 (70)
T TIGR01149 11 PDEFNEVMKRLDEIEEKVEFVNGEVAQRIGK 41 (70)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 6888888888888888888888777766554
No 168
>PHA02414 hypothetical protein
Probab=30.61 E-value=2.5e+02 Score=21.54 Aligned_cols=70 Identities=11% Similarity=0.265 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCC----hhHH---HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 30 LDSRAQDVMKTIDRVAEDYLDNMKHYS----KDKK---KETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTD 102 (267)
Q Consensus 30 lD~~~~~~~~~i~~~~~~~~k~~~~~~----~~~~---~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~d 102 (267)
.|..++++..+++..-.+. +.+.++ ..+- ..-++.|--.+++-..+..|| +.-|--+|.|||..
T Consensus 2 ~D~~in~Lv~~v~~ledKi--Q~Gelt~kgdn~eL~~av~ELRdivvslDKd~Av~sEK-------qshi~yQi~~Lee~ 72 (111)
T PHA02414 2 MDKEINNLVSQVETLEDKI--QEGELTDKGDNKELEVAVAELRDIVVSLDKDVAVNSEK-------QSHIYYQIERLEEK 72 (111)
T ss_pred cchHHHHHHHHHHHHHHHH--hcCccccCCchHHHHHHHHHHHHHHHHhhhHhhhhHHH-------hhHHHHHHHHHHHH
Confidence 4566666666665544443 222222 1111 123344444444444555555 44455567777777
Q ss_pred HHHHHH
Q psy12696 103 LARFEQ 108 (267)
Q Consensus 103 l~~~e~ 108 (267)
+..++.
T Consensus 73 i~aL~~ 78 (111)
T PHA02414 73 ISALAE 78 (111)
T ss_pred HHHHHh
Confidence 766653
No 169
>PRK14873 primosome assembly protein PriA; Provisional
Probab=30.24 E-value=42 Score=34.41 Aligned_cols=43 Identities=26% Similarity=0.651 Sum_probs=25.2
Q ss_pred Ccee-ecCCCCCCCcccccCCCCCCcceec-----ccCccCCCCCCceeCcCCcCc
Q psy12696 214 PTYC-VCQQVSYGEMIGCDNPDCPIEWFHF-----ACVSLTTKPKGKWYCPKCTSD 263 (267)
Q Consensus 214 ~~~C-~C~~~~~~~mi~Cd~~~c~~~wfH~-----~Cv~l~~~p~~~w~C~~C~~~ 263 (267)
.++| -|+.+ +.|.+|+-+.. ||. .|----... ..|.||.|...
T Consensus 383 ~l~C~~Cg~~-----~~C~~C~~~L~-~h~~~~~l~Ch~CG~~~-~p~~Cp~Cgs~ 431 (665)
T PRK14873 383 SLACARCRTP-----ARCRHCTGPLG-LPSAGGTPRCRWCGRAA-PDWRCPRCGSD 431 (665)
T ss_pred eeEhhhCcCe-----eECCCCCCcee-EecCCCeeECCCCcCCC-cCccCCCCcCC
Confidence 3467 67554 77888775555 563 353211111 26999999654
No 170
>PRK10132 hypothetical protein; Provisional
Probab=30.17 E-value=2.6e+02 Score=21.66 Aligned_cols=46 Identities=20% Similarity=0.338 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHHH---HHHHHhcCCCChhHHHHHHHHHHHHHHHHH
Q psy12696 30 LDSRAQDVMKTIDRVA---EDYLDNMKHYSKDKKKETLAEIQKYFDKTK 75 (267)
Q Consensus 30 lD~~~~~~~~~i~~~~---~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~ 75 (267)
||.+...+..+|...+ ++.++.......++-..+-.++...+..+.
T Consensus 10 ~~~q~e~L~~Dl~~L~~~le~ll~~~~~~~~~~~~~lR~r~~~~L~~ar 58 (108)
T PRK10132 10 VDDGVQDIQNDVNQLADSLESVLKSWGSDAKGEAEAARRKAQALLKETR 58 (108)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 4444444444443332 233443333332222233344444444443
No 171
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=30.03 E-value=6.3 Score=25.80 Aligned_cols=23 Identities=22% Similarity=0.622 Sum_probs=12.7
Q ss_pred cceecccCccCCCCCCceeCcCC
Q psy12696 238 EWFHFACVSLTTKPKGKWYCPKC 260 (267)
Q Consensus 238 ~wfH~~Cv~l~~~p~~~w~C~~C 260 (267)
.|.|..|+---..-.+...|+.|
T Consensus 25 ~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 25 KYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp GSEECCHHHHHHHHHT-SB-TTT
T ss_pred chhHHHHHHHHHHhcCCCcCCCC
Confidence 78999998722222344556655
No 172
>PF08432 Vfa1: AAA-ATPase Vps4-associated protein 1; InterPro: IPR013640 This is a family of fungal proteins of unknown function.
Probab=29.93 E-value=30 Score=29.35 Aligned_cols=28 Identities=32% Similarity=0.634 Sum_probs=21.4
Q ss_pred Ccee-ecCCCCCCCcccccCCCCCCcceecccCc
Q psy12696 214 PTYC-VCQQVSYGEMIGCDNPDCPIEWFHFACVS 246 (267)
Q Consensus 214 ~~~C-~C~~~~~~~mi~Cd~~~c~~~wfH~~Cv~ 246 (267)
..-| +|..|+...||.=++. .||| .|-.
T Consensus 13 ~k~C~IC~KpsttVL~t~~~~----DfFY-~C~~ 41 (182)
T PF08432_consen 13 AKACFICYKPSTTVLITPDNK----DFFY-VCPS 41 (182)
T ss_pred CCceeEecCCCceEEecCCCC----CeEE-eCcc
Confidence 4468 9999988888876665 4887 8866
No 173
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=29.27 E-value=4.4e+02 Score=26.68 Aligned_cols=27 Identities=11% Similarity=0.262 Sum_probs=16.8
Q ss_pred hcchHHHHHhHHHHHHHHHHHHHHHHH
Q psy12696 14 DSLPIELQRNFTLMRELDSRAQDVMKT 40 (267)
Q Consensus 14 e~LP~El~r~l~~irelD~~~~~~~~~ 40 (267)
..+|..+...|..|+++-.++..+...
T Consensus 214 ~~~~~~v~~~~~~i~~~~~~~~~~~~k 240 (619)
T PRK05658 214 SELPEKVLEKFKALAKQYKKLRKAQEK 240 (619)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345666777777777666555554443
No 174
>PF12889 DUF3829: Protein of unknown function (DUF3829); InterPro: IPR024291 This is a small family of proteins from several bacterial species, whose function is not known. It may, however, be related to the GvpL_GvpF family of proteins (PF06386 from PFAM).; PDB: 3RH3_B 3IEE_A.
Probab=28.86 E-value=2.2e+02 Score=24.93 Aligned_cols=29 Identities=28% Similarity=0.257 Sum_probs=13.0
Q ss_pred HHHHHHHHHH---H---HHHHHHHHHHHHHHHHHH
Q psy12696 83 QLAIQTYEMV---D---KYIRKLDTDLARFEQEIQ 111 (267)
Q Consensus 83 ~LA~~a~dlV---d---~hirrLD~dl~~~e~el~ 111 (267)
..|.++.++| + -.+..+++.+..|+..+.
T Consensus 168 ~~a~~i~~~l~~~~~~~~d~~~~~~~l~~~~~~~~ 202 (276)
T PF12889_consen 168 IDAEQIIDELQSDDNQKFDMAALDAALAELEKLLK 202 (276)
T ss_dssp HHHHHHHHHHT-TTS--HHHHHHH--HHHHHHHHH
T ss_pred HHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHHHH
Confidence 4455555555 1 334444444555554444
No 175
>PF15272 BBP1_C: Spindle pole body component BBP1, C-terminal
Probab=28.84 E-value=3.8e+02 Score=23.14 Aligned_cols=28 Identities=29% Similarity=0.611 Sum_probs=17.7
Q ss_pred HHHHHHHHhhcchHHHHHhHHHHHHHHHHHHH
Q psy12696 5 YLEQYLDSLDSLPIELQRNFTLMRELDSRAQD 36 (267)
Q Consensus 5 yLedfld~ie~LP~El~r~l~~irelD~~~~~ 36 (267)
|..+|++.++ +|.++=..|..|+..+..
T Consensus 3 ~t~eY~~lld----~l~~Nnr~L~~L~~dl~~ 30 (196)
T PF15272_consen 3 YTSEYLELLD----QLDQNNRALSDLNQDLRE 30 (196)
T ss_pred chHHHHHHHH----HHHHhHHHHHHHHHHHHH
Confidence 7788888876 445555555555555544
No 176
>PF04961 FTCD_C: Formiminotransferase-cyclodeaminase; InterPro: IPR007044 Enzymes containing the cyclodeaminase domain function in channeling one-carbon units to the folate pool. In most cases, this domain catalyses the cyclisation of formimidoyltetrahydrofolate to methenyltetrahydrofolate as shown in reaction (1). In the methylotrophic bacterium Methylobacterium extorquens, however, it catalyses the interconversion of formyltetrahydrofolate and methylenetetrahydrofolate [],as shown in reaction (2) (1) 5-formimidoyltetrahydrofolate = 5,10-methenyltetrahydrofolate + NH(3) (2) 10- formyltetrahydrofolate = 5,10-methenyltetrahydrofolate + H(2)O In prokaryotes, this domain mostly occurs on its own, while in eukaryotes it is fused to a glutamate formiminotransferase domain (which catalyses the previous step in the pathway) to form the bifunctional enzyme formiminotransferase-cyclodeaminase []. The eukaryotic enzyme is a circular tetramer of homodimers [], while the prokaryotic enzyme is a dimer [, ]. The crystal structure of the cyclodeaminase enzyme (Q9X1P6 from SWISSPROT) from Thermaotogoa maritima has been studied []. It is a homodimer, where each monomer is composed of six alpha helices arranged in an up and down helical bundle, forming a novel fold. The location of the active site is not known, but sequence alignments revealed two clusters of conserved residues located in a deep pocket within the dimmer interface. This pocket was large enough to accommodate the reaction product and it was postulated that this is the active site.; GO: 0003824 catalytic activity, 0044237 cellular metabolic process; PDB: 2PFD_C 1O5H_B.
Probab=28.62 E-value=3.6e+02 Score=22.76 Aligned_cols=74 Identities=16% Similarity=0.197 Sum_probs=38.3
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--CCChhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q psy12696 18 IELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMK--HYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEM 91 (267)
Q Consensus 18 ~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~--~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dl 91 (267)
.+++..+..+.++-.+...+.++=.+-...|++..+ .-+++++...-..|++.+..+...-=+=+.++..++++
T Consensus 52 ~~~~~~~~~~~~~~~~ll~l~d~D~~af~~~~~a~klPk~T~eek~~R~~~i~~al~~A~~vPl~~a~~~~~~l~~ 127 (184)
T PF04961_consen 52 EELKEIIEKLEELREELLDLADEDAEAFNAVMAAYKLPKETDEEKAARSEAIQEALKEAAEVPLEIARLCLELLEL 127 (184)
T ss_dssp HHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHCCCTS---SGGGTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555555555554444444443444445554332 23456666666778888888775554433333333333
No 177
>PF12095 DUF3571: Protein of unknown function (DUF3571); InterPro: IPR021954 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 85 to 97 amino acids in length. ; PDB: 2KRX_A.
Probab=27.98 E-value=1.4e+02 Score=22.17 Aligned_cols=32 Identities=25% Similarity=0.466 Sum_probs=21.0
Q ss_pred hHHHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHH
Q psy12696 4 SYLEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMK 39 (267)
Q Consensus 4 ~yLedfld~ie~LP~El~r~l~~irelD~~~~~~~~ 39 (267)
..|.+++...++||.+|++.- -+|.+++.+++
T Consensus 31 ~~Lk~~L~~~~~LP~dL~~~~----s~~~qa~~Lld 62 (83)
T PF12095_consen 31 EKLKEWLQNQDDLPPDLAKFS----SVEEQAQYLLD 62 (83)
T ss_dssp HHHHHHHHHTTTS-HHHHH-------HHHHHHHHHH
T ss_pred HHHHHHHHcCCCCCHHHHhCC----CHHHHHHHHHH
Confidence 478899999999999998543 34555555544
No 178
>KOG0971|consensus
Probab=27.84 E-value=8e+02 Score=26.53 Aligned_cols=94 Identities=19% Similarity=0.339 Sum_probs=0.0
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHH--HHHHHHHHHHHHH---HHhHHHHHHHHHHHHHHHHH
Q psy12696 20 LQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKK--ETLAEIQKYFDKT---KEYGDDKVQLAIQTYEMVDK 94 (267)
Q Consensus 20 l~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~--~~~~~I~~~~~~~---~~lsdEKv~LA~~a~dlVd~ 94 (267)
++-.|..+.|.-.++..-...+++.+..--+..+....-..+ ..+.++.+.+.-+ +++++|+..--+.=.+.+.-
T Consensus 260 mkiqleqlqEfkSkim~qqa~Lqrel~raR~e~keaqe~ke~~k~emad~ad~iEmaTldKEmAEERaesLQ~eve~lkE 339 (1243)
T KOG0971|consen 260 MKIQLEQLQEFKSKIMEQQADLQRELKRARKEAKEAQEAKERYKEEMADTADAIEMATLDKEMAEERAESLQQEVEALKE 339 (1243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy12696 95 YIRKLDTDLARFEQEIQEK 113 (267)
Q Consensus 95 hirrLD~dl~~~e~el~~~ 113 (267)
.+..|+.||+-|.+|++.+
T Consensus 340 r~deletdlEILKaEmeek 358 (1243)
T KOG0971|consen 340 RVDELETDLEILKAEMEEK 358 (1243)
T ss_pred HHHHHHHHHHHHHHHHHhc
No 179
>PRK05580 primosome assembly protein PriA; Validated
Probab=27.78 E-value=44 Score=34.23 Aligned_cols=10 Identities=40% Similarity=0.886 Sum_probs=7.4
Q ss_pred ceeCcCCcCc
Q psy12696 254 KWYCPKCTSD 263 (267)
Q Consensus 254 ~w~C~~C~~~ 263 (267)
.|.||.|...
T Consensus 421 ~~~Cp~Cg~~ 430 (679)
T PRK05580 421 PKACPECGST 430 (679)
T ss_pred CCCCCCCcCC
Confidence 4899999543
No 180
>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1
Probab=27.67 E-value=1.1e+02 Score=21.93 Aligned_cols=23 Identities=26% Similarity=0.515 Sum_probs=14.2
Q ss_pred HHHHHHHHHH----HHHHHHHHHHHHh
Q psy12696 29 ELDSRAQDVM----KTIDRVAEDYLDN 51 (267)
Q Consensus 29 elD~~~~~~~----~~i~~~~~~~~k~ 51 (267)
|||+++.++| ..||..+..|+..
T Consensus 44 eLDaELD~Ym~~~~~~LD~~Ld~Y~~~ 70 (74)
T PF13865_consen 44 ELDAELDAYMSKTKSKLDAELDSYMSK 70 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 4555555554 4467777788764
No 181
>KOG1318|consensus
Probab=27.66 E-value=4.7e+02 Score=25.32 Aligned_cols=27 Identities=22% Similarity=0.396 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHH----HHHHHHHhcCCC
Q psy12696 29 ELDSRAQDVMKTIDR----VAEDYLDNMKHY 55 (267)
Q Consensus 29 elD~~~~~~~~~i~~----~~~~~~k~~~~~ 55 (267)
+.|.+-.+..++|++ .|+.+|+..+.+
T Consensus 228 ~rdr~Krd~HNeVERRRR~nIN~~IkeLg~l 258 (411)
T KOG1318|consen 228 ERDRRKRDNHNEVERRRRENINDRIKELGQL 258 (411)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHh
Confidence 344555555555543 467777766543
No 182
>KOG2751|consensus
Probab=27.65 E-value=5.8e+02 Score=24.84 Aligned_cols=17 Identities=24% Similarity=0.503 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy12696 25 TLMRELDSRAQDVMKTI 41 (267)
Q Consensus 25 ~~irelD~~~~~~~~~i 41 (267)
.++-.+|..+..+.+++
T Consensus 143 ~l~~~ld~e~~~~~~e~ 159 (447)
T KOG2751|consen 143 VLLNKLDKEVEDAEDEV 159 (447)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34445555555444443
No 183
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=27.61 E-value=21 Score=25.50 Aligned_cols=20 Identities=45% Similarity=1.037 Sum_probs=13.5
Q ss_pred cceecccCc--cCCCCCCceeCcCCc
Q psy12696 238 EWFHFACVS--LTTKPKGKWYCPKCT 261 (267)
Q Consensus 238 ~wfH~~Cv~--l~~~p~~~w~C~~C~ 261 (267)
--||+.|+. |... ..||.|+
T Consensus 52 H~FH~~Ci~~Wl~~~----~~CP~CR 73 (73)
T PF12678_consen 52 HIFHFHCISQWLKQN----NTCPLCR 73 (73)
T ss_dssp EEEEHHHHHHHHTTS----SB-TTSS
T ss_pred CCEEHHHHHHHHhcC----CcCCCCC
Confidence 359999997 4333 2899885
No 184
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=27.60 E-value=39 Score=22.87 Aligned_cols=30 Identities=17% Similarity=0.290 Sum_probs=18.2
Q ss_pred ccccCCCCCCcceecccCccCCCCCCceeCcCCcC
Q psy12696 228 IGCDNPDCPIEWFHFACVSLTTKPKGKWYCPKCTS 262 (267)
Q Consensus 228 i~Cd~~~c~~~wfH~~Cv~l~~~p~~~w~C~~C~~ 262 (267)
+-|.+|. .|-.++--.....-.|.|+.|..
T Consensus 23 LIC~~C~-----~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 23 LICSKCF-----SHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred EECcccc-----hhhcccccccCCceEEEcCCCCC
Confidence 4477764 56666642222234899999964
No 185
>PF09755 DUF2046: Uncharacterized conserved protein H4 (DUF2046); InterPro: IPR019152 This is the conserved N-terminal 350 residues of a family of proteins of unknown function possibly containing a coiled-coil domain.
Probab=27.36 E-value=5.1e+02 Score=24.07 Aligned_cols=23 Identities=22% Similarity=0.219 Sum_probs=18.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHH
Q psy12696 68 QKYFDKTKEYGDDKVQLAIQTYE 90 (267)
Q Consensus 68 ~~~~~~~~~lsdEKv~LA~~a~d 90 (267)
.....++.++.+||++|.+++-.
T Consensus 109 n~L~rkl~qLr~EK~~lE~~Le~ 131 (310)
T PF09755_consen 109 NDLSRKLNQLRQEKVELENQLEQ 131 (310)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 44567888999999999998864
No 186
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=27.35 E-value=4.4e+02 Score=23.29 Aligned_cols=26 Identities=27% Similarity=0.636 Sum_probs=17.5
Q ss_pred CCcccccCCCCCCcceecccCccCCCCCCceeCcCCcCc
Q psy12696 225 GEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCPKCTSD 263 (267)
Q Consensus 225 ~~mi~Cd~~~c~~~wfH~~Cv~l~~~p~~~w~C~~C~~~ 263 (267)
..|=.|..|. .-.|- .+| .||.|..+
T Consensus 192 PPMK~C~sC~---qqIHR------NAP----iCPlCK~K 217 (230)
T PF10146_consen 192 PPMKTCQSCH---QQIHR------NAP----ICPLCKAK 217 (230)
T ss_pred CCcchhHhHH---HHHhc------CCC----CCcccccc
Confidence 3488899987 66662 333 59999643
No 187
>PF15619 Lebercilin: Ciliary protein causing Leber congenital amaurosis disease
Probab=27.25 E-value=4e+02 Score=22.82 Aligned_cols=37 Identities=30% Similarity=0.353 Sum_probs=30.0
Q ss_pred HHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHH
Q psy12696 6 LEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTID 42 (267)
Q Consensus 6 Ledfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~ 42 (267)
|..|-++=..||.-|+++-.+||-|-.++........
T Consensus 49 L~k~e~~e~~Lpqll~~h~eEvr~Lr~~LR~~q~~~r 85 (194)
T PF15619_consen 49 LQKYEDTEAELPQLLQRHNEEVRVLRERLRKSQEQER 85 (194)
T ss_pred HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6778888889999999999999998888777666543
No 188
>PF13747 DUF4164: Domain of unknown function (DUF4164)
Probab=26.98 E-value=2.7e+02 Score=20.73 Aligned_cols=7 Identities=43% Similarity=0.667 Sum_probs=2.6
Q ss_pred HHHHHHH
Q psy12696 79 DDKVQLA 85 (267)
Q Consensus 79 dEKv~LA 85 (267)
.++-.||
T Consensus 46 ~dr~rLa 52 (89)
T PF13747_consen 46 ADRSRLA 52 (89)
T ss_pred hhHHHHH
Confidence 3333333
No 189
>COG1773 Rubredoxin [Energy production and conversion]
Probab=26.83 E-value=56 Score=22.33 Aligned_cols=11 Identities=36% Similarity=1.295 Sum_probs=9.2
Q ss_pred CCceeCcCCcC
Q psy12696 252 KGKWYCPKCTS 262 (267)
Q Consensus 252 ~~~w~C~~C~~ 262 (267)
...|+||.|..
T Consensus 34 Pd~w~CP~Cg~ 44 (55)
T COG1773 34 PDDWVCPECGV 44 (55)
T ss_pred CCccCCCCCCC
Confidence 56899999975
No 190
>KOG1011|consensus
Probab=26.81 E-value=2.2e+02 Score=29.35 Aligned_cols=85 Identities=24% Similarity=0.379 Sum_probs=50.2
Q ss_pred HhHHHH--HHHHHHHHHHHHHHHHHHHHHHHhc-----CCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q psy12696 22 RNFTLM--RELDSRAQDVMKTIDRVAEDYLDNM-----KHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDK 94 (267)
Q Consensus 22 r~l~~i--relD~~~~~~~~~i~~~~~~~~k~~-----~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~ 94 (267)
..|.-| +|||+.+.+.+.+++-.++..+... -++.++ ..+...++-..+.++..-+..|-.+|+.+-..+.-
T Consensus 863 kmfeamggkeld~ea~d~lk~lqvkln~vldels~~f~tsfqph-i~e~v~qmg~il~qvkgt~~a~~sva~dad~vl~p 941 (1283)
T KOG1011|consen 863 KMFEAMGGKELDEEAGDVLKELQVKLNSVLDELSAVFVTSFQPH-IHECVIQMGDILVQVKGTGLAKTSVAQDADAVLEP 941 (1283)
T ss_pred HHHHHhcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCcc-HHHHHHHHHHHHhhhcccccchhhcccchHHHHHH
Confidence 334444 4788888888887765555444322 123332 12344556666777777777777777776666665
Q ss_pred HHHHHHHHHHHHH
Q psy12696 95 YIRKLDTDLARFE 107 (267)
Q Consensus 95 hirrLD~dl~~~e 107 (267)
-+.-||..|..|.
T Consensus 942 lmdlldgnlt~fa 954 (1283)
T KOG1011|consen 942 LMDLLDGNLTLFA 954 (1283)
T ss_pred HHHHHhchHHHHH
Confidence 5566665555553
No 191
>PF15066 CAGE1: Cancer-associated gene protein 1 family
Probab=26.48 E-value=6.4e+02 Score=24.91 Aligned_cols=86 Identities=16% Similarity=0.280 Sum_probs=38.5
Q ss_pred chHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChh-HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q psy12696 16 LPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKD-KKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDK 94 (267)
Q Consensus 16 LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~-~~~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~ 94 (267)
|-.+|.+.=.....|-.++..-+.+-+..+..|+...+.++.- +-...+.++...+.++ +..|++++.+
T Consensus 416 LqlelkK~k~nyv~LQEry~~eiQqKnksvsqclEmdk~LskKeeeverLQ~lkgelEka----------t~SALdlLkr 485 (527)
T PF15066_consen 416 LQLELKKIKANYVHLQERYMTEIQQKNKSVSQCLEMDKTLSKKEEEVERLQQLKGELEKA----------TTSALDLLKR 485 (527)
T ss_pred HHHHHHHHhhhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH----------HHHHHHHHHH
Confidence 3334444444444444444444444455555565555554422 1123333333333322 2345555555
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy12696 95 YIRKLDTDLARFEQEIQ 111 (267)
Q Consensus 95 hirrLD~dl~~~e~el~ 111 (267)
--.-.++++-.|..++.
T Consensus 486 EKe~~EqefLslqeEfQ 502 (527)
T PF15066_consen 486 EKETREQEFLSLQEEFQ 502 (527)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 55555555555544443
No 192
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=26.41 E-value=4e+02 Score=22.59 Aligned_cols=25 Identities=16% Similarity=0.282 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 83 QLAIQTYEMVDKYIRKLDTDLARFE 107 (267)
Q Consensus 83 ~LA~~a~dlVd~hirrLD~dl~~~e 107 (267)
.-|....+-+.+.+..|+.+|...+
T Consensus 149 ~~a~~~~~e~~~~l~~l~~ei~~~~ 173 (176)
T PF12999_consen 149 EEAKKKREELEKKLEELEKEIQAAK 173 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3344444444555555555554443
No 193
>TIGR01005 eps_transp_fam exopolysaccharide transport protein family. The model describes the exopolysaccharide transport protein family in bacteria. The transport protein is part of a large genetic locus which is associated with exopolysaccharide (EPS) biosynthesis. Detailed molecular characterization and gene fusion analysis revealed atleast seven gene products are involved in the overall regulation, which among other things, include exopolysaccharide biosynthesis, property of conferring virulence and exopolysaccharide export.
Probab=26.37 E-value=4.3e+02 Score=27.18 Aligned_cols=75 Identities=16% Similarity=0.136 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCh--hHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 25 TLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSK--DKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKL 99 (267)
Q Consensus 25 ~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~--~~~~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrL 99 (267)
..|.+|-.+..++..++.+....|..++..+-. .+...+-.+|.+.+.++....+.-++.+.+-...+...+..+
T Consensus 288 ~~i~~L~~~l~~l~~~~~~l~~~y~~~hP~v~~l~~qi~~l~~~i~~e~~~~~~~~~~~~~~a~~~~~~L~~~l~~~ 364 (754)
T TIGR01005 288 DLIQRLRERQAELRATIADLSTTMLANHPRVVAAKSSLADLDAQIRSELQKITKSLLMQADAAQARESQLVSDVNQL 364 (754)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555555555555554444444332221110 011122233444444444433444444444444555544444
No 194
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=26.21 E-value=55 Score=19.05 Aligned_cols=26 Identities=27% Similarity=0.665 Sum_probs=17.9
Q ss_pred e-ecCCCCCCC-cccccCCCCCCcceecccC
Q psy12696 217 C-VCQQVSYGE-MIGCDNPDCPIEWFHFACV 245 (267)
Q Consensus 217 C-~C~~~~~~~-mi~Cd~~~c~~~wfH~~Cv 245 (267)
| +|++...+. +-.|+.|. +. +|..|+
T Consensus 3 C~~C~~~~~~~~~Y~C~~c~--f~-lh~~Ca 30 (30)
T PF03107_consen 3 CDVCRRKIDGFYFYHCSECC--FT-LHVRCA 30 (30)
T ss_pred CCCCCCCcCCCEeEEeCCCC--Ce-EcCccC
Confidence 5 777777777 77787753 43 787774
No 195
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=26.14 E-value=51 Score=30.48 Aligned_cols=8 Identities=25% Similarity=0.692 Sum_probs=5.2
Q ss_pred eeCcCCcC
Q psy12696 255 WYCPKCTS 262 (267)
Q Consensus 255 w~C~~C~~ 262 (267)
-.|..|..
T Consensus 253 e~C~~C~~ 260 (305)
T TIGR01562 253 ETCDSCQG 260 (305)
T ss_pred eecccccc
Confidence 46777753
No 196
>PRK01026 tetrahydromethanopterin S-methyltransferase subunit G; Provisional
Probab=26.12 E-value=1.8e+02 Score=21.24 Aligned_cols=31 Identities=10% Similarity=0.127 Sum_probs=24.4
Q ss_pred hHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 17 PIELQRNFTLMRELDSRAQDVMKTIDRVAED 47 (267)
Q Consensus 17 P~El~r~l~~irelD~~~~~~~~~i~~~~~~ 47 (267)
|.|+...+..+-++|+++.-...++.+++-+
T Consensus 14 ~~d~~~i~~rLD~iEeKVEftn~Ei~Qr~Gk 44 (77)
T PRK01026 14 PKDFKEIQKRLDEIEEKVEFTNAEIFQRIGK 44 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 6678888888888888888888877766554
No 197
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=25.95 E-value=38 Score=21.20 Aligned_cols=32 Identities=28% Similarity=0.706 Sum_probs=22.2
Q ss_pred CCcee-ecCCCCCC--CcccccCCCCCCcceecccCcc
Q psy12696 213 EPTYC-VCQQVSYG--EMIGCDNPDCPIEWFHFACVSL 247 (267)
Q Consensus 213 ~~~~C-~C~~~~~~--~mi~Cd~~~c~~~wfH~~Cv~l 247 (267)
.+.+| +|++.-.+ ..+.|..|. +. .|..|+..
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~--~~-~H~~C~~~ 44 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCK--VK-CHKKCAEK 44 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCC--ch-HHHHHHhh
Confidence 35688 88877544 367788854 44 89888763
No 198
>PF13949 ALIX_LYPXL_bnd: ALIX V-shaped domain binding to HIV ; PDB: 2XS1_A 2XS8_A 2R03_A 2R02_A 2OEX_B 2OEV_A 2OJQ_A 2R05_A.
Probab=25.88 E-value=4.7e+02 Score=23.18 Aligned_cols=23 Identities=17% Similarity=0.442 Sum_probs=9.9
Q ss_pred HHHHhHHHHHHHHHHHHHHHHHH
Q psy12696 19 ELQRNFTLMRELDSRAQDVMKTI 41 (267)
Q Consensus 19 El~r~l~~irelD~~~~~~~~~i 41 (267)
.|...|..|.++-.++.+...++
T Consensus 26 ~l~~~l~~l~~~~~~~~~~L~e~ 48 (296)
T PF13949_consen 26 KLEESLQELPELSQEVRSILDEI 48 (296)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444444443
No 199
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=25.87 E-value=36 Score=22.42 Aligned_cols=13 Identities=31% Similarity=1.127 Sum_probs=8.0
Q ss_pred CCceeCcCCcCcc
Q psy12696 252 KGKWYCPKCTSDR 264 (267)
Q Consensus 252 ~~~w~C~~C~~~~ 264 (267)
.+.|.||.|...+
T Consensus 32 p~~w~CP~C~a~K 44 (47)
T PF00301_consen 32 PDDWVCPVCGAPK 44 (47)
T ss_dssp -TT-B-TTTSSBG
T ss_pred CCCCcCcCCCCcc
Confidence 4679999998764
No 200
>KOG1655|consensus
Probab=25.68 E-value=1.4e+02 Score=25.97 Aligned_cols=30 Identities=27% Similarity=0.510 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 83 QLAIQTYEMVDKYIRKLDTDLARFEQEIQE 112 (267)
Q Consensus 83 ~LA~~a~dlVd~hirrLD~dl~~~e~el~~ 112 (267)
.-.+..-+.|+..|.+||++|.+|...+..
T Consensus 22 ~~v~~r~dSve~KIskLDaeL~k~~~Qi~k 51 (218)
T KOG1655|consen 22 DSVNKRSDSVEKKISKLDAELCKYKDQIKK 51 (218)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHHHHHHHHh
Confidence 334566788999999999999999877654
No 201
>KOG4302|consensus
Probab=25.57 E-value=2.2e+02 Score=29.31 Aligned_cols=9 Identities=33% Similarity=0.704 Sum_probs=3.5
Q ss_pred HHHHHHHHH
Q psy12696 92 VDKYIRKLD 100 (267)
Q Consensus 92 Vd~hirrLD 100 (267)
+|.+|+++.
T Consensus 359 ~d~~i~k~k 367 (660)
T KOG4302|consen 359 IDNLIKKYK 367 (660)
T ss_pred HHHHHHHHH
Confidence 333444333
No 202
>PF13922 PHD_3: PHD domain of transcriptional enhancer, Asx
Probab=25.54 E-value=23 Score=25.09 Aligned_cols=28 Identities=25% Similarity=0.597 Sum_probs=22.7
Q ss_pred CceeecCCCCCCCcccccCCCCCCcceecccCcc
Q psy12696 214 PTYCVCQQVSYGEMIGCDNPDCPIEWFHFACVSL 247 (267)
Q Consensus 214 ~~~C~C~~~~~~~mi~Cd~~~c~~~wfH~~Cv~l 247 (267)
..-|.|.-. -||-|-.|. ..-|-.|+|-
T Consensus 33 ~~~C~C~Lk---AMi~Cq~CG---AFCHDDCIgp 60 (69)
T PF13922_consen 33 SNKCACSLK---AMIMCQGCG---AFCHDDCIGP 60 (69)
T ss_pred ccccccchH---HHHHHhhcc---chhccccccH
Confidence 456888654 799999988 8899999984
No 203
>TIGR03545 conserved hypothetical protein TIGR03545. This model represents a relatively rare but broadly distributed uncharacterized protein family, distributed in 1-2 percent of bacterial genomes, all of which have outer membranes. In many of these genomes, it is part of a two-gene pair.
Probab=25.48 E-value=6.6e+02 Score=25.26 Aligned_cols=39 Identities=26% Similarity=0.312 Sum_probs=17.7
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 69 KYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFE 107 (267)
Q Consensus 69 ~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e 107 (267)
+.+++++.-.....+.+..+..-|..-..+|.+++..++
T Consensus 219 ~e~d~lk~e~~~~~~~i~~~~~~l~~~~~~~~~~~~~lk 257 (555)
T TIGR03545 219 EEFDKLKKEGKADKQKIKSAKNDLQNDKKQLKADLAELK 257 (555)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence 333333333344444444444444444555555554444
No 204
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=25.44 E-value=4.1e+02 Score=22.33 Aligned_cols=57 Identities=19% Similarity=0.330 Sum_probs=43.3
Q ss_pred hcCCCChhHHHHHHHHHHHHHHHHHHhHH------HHHHHHHHHHHHHHHHHHHHH-HHHHHHH
Q psy12696 51 NMKHYSKDKKKETLAEIQKYFDKTKEYGD------DKVQLAIQTYEMVDKYIRKLD-TDLARFE 107 (267)
Q Consensus 51 ~~~~~~~~~~~~~~~~I~~~~~~~~~lsd------EKv~LA~~a~dlVd~hirrLD-~dl~~~e 107 (267)
....+++.+|.++|..+.+.|.++...+. .++.+|....+++-.+++.-- +.+..|-
T Consensus 88 ~~~~~~~~~k~~~LasLaDsf~K~vaaskr~lPets~LavA~~vl~~l~~fv~e~~P~h~~af~ 151 (165)
T PF08822_consen 88 ENEDMPPQEKVELLASLADSFSKMVAASKRVLPETSELAVAMEVLELLAAFVQERYPQHLAAFL 151 (165)
T ss_pred cccCCCHHHHHHHHHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHHHhcCHHHHHHHH
Confidence 45678899999999999999988886664 578888888888887777554 3444443
No 205
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=25.43 E-value=26 Score=23.09 Aligned_cols=24 Identities=33% Similarity=0.821 Sum_probs=13.9
Q ss_pred cceecccCc-------cCCCC----CCceeCcCCc
Q psy12696 238 EWFHFACVS-------LTTKP----KGKWYCPKCT 261 (267)
Q Consensus 238 ~wfH~~Cv~-------l~~~p----~~~w~C~~C~ 261 (267)
..||..|.. |.... .+..||..|-
T Consensus 20 ~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~ 54 (58)
T PF00412_consen 20 KFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCY 54 (58)
T ss_dssp EEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHH
T ss_pred cEEEccccccCCCCCccCCCeeEeECCEEECHHHH
Confidence 347887765 22222 5677777663
No 206
>COG0497 RecN ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=25.42 E-value=7.1e+02 Score=25.11 Aligned_cols=22 Identities=9% Similarity=0.391 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q psy12696 90 EMVDKYIRKLDTDLARFEQEIQ 111 (267)
Q Consensus 90 dlVd~hirrLD~dl~~~e~el~ 111 (267)
+-.+.|+..|+.++..+..++.
T Consensus 338 ~~~~~~~~~Le~~~~~l~~~~~ 359 (557)
T COG0497 338 DNSEESLEALEKEVKKLKAELL 359 (557)
T ss_pred hhhhhHHHHHHHHHHHHHHHHH
Confidence 3344556666666555555443
No 207
>TIGR00606 rad50 rad50. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.42 E-value=9.7e+02 Score=26.67 Aligned_cols=42 Identities=12% Similarity=0.246 Sum_probs=25.2
Q ss_pred HHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 7 EQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDY 48 (267)
Q Consensus 7 edfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~ 48 (267)
.++-..++.|=.++...-..|.+++.....+..+++.....+
T Consensus 884 ~~le~~L~el~~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 925 (1311)
T TIGR00606 884 QQFEEQLVELSTEVQSLIREIKDAKEQDSPLETFLEKDQQEK 925 (1311)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHH
Confidence 344555555556666666666666666666666665554444
No 208
>PLN02678 seryl-tRNA synthetase
Probab=25.34 E-value=3.6e+02 Score=26.28 Aligned_cols=22 Identities=14% Similarity=0.294 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q psy12696 92 VDKYIRKLDTDLARFEQEIQEK 113 (267)
Q Consensus 92 Vd~hirrLD~dl~~~e~el~~~ 113 (267)
|...|..|+.++..++.++...
T Consensus 83 Lk~ei~~le~~~~~~~~~l~~~ 104 (448)
T PLN02678 83 LKKEITEKEAEVQEAKAALDAK 104 (448)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4455777888887777777654
No 209
>KOG2077|consensus
Probab=25.34 E-value=4.1e+02 Score=27.05 Aligned_cols=44 Identities=20% Similarity=0.256 Sum_probs=31.9
Q ss_pred HHHHHHHhHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 70 YFDKTKEYGDDKVQ------LAIQTYEMVDKYIRKLDTDLARFEQEIQEK 113 (267)
Q Consensus 70 ~~~~~~~lsdEKv~------LA~~a~dlVd~hirrLD~dl~~~e~el~~~ 113 (267)
++.++.+|.-||.. -++++...++..|+.|+.+|+++..+....
T Consensus 327 LIakVDeL~~E~~vLrgElea~kqak~Klee~i~elEEElk~~k~ea~~a 376 (832)
T KOG2077|consen 327 LIAKVDELTCEKDVLRGELEAVKQAKLKLEEKIRELEEELKKAKAEAEDA 376 (832)
T ss_pred HHHHHHhhccHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555543 367888889999999999999998877654
No 210
>KOG2272|consensus
Probab=25.27 E-value=40 Score=30.32 Aligned_cols=47 Identities=28% Similarity=0.661 Sum_probs=27.9
Q ss_pred ee-ecCCCCCCCcccccCCCCCCcceecccCc----cCCCC---CCceeCcCCcCcc
Q psy12696 216 YC-VCQQVSYGEMIGCDNPDCPIEWFHFACVS----LTTKP---KGKWYCPKCTSDR 264 (267)
Q Consensus 216 ~C-~C~~~~~~~mi~Cd~~~c~~~wfH~~Cv~----l~~~p---~~~w~C~~C~~~~ 264 (267)
.| -|..--+.+.+---+ =|+.-|||.|.. |+... .|..||+.|...+
T Consensus 139 vC~KCh~~iD~~~l~fr~--d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~m 193 (332)
T KOG2272|consen 139 VCQKCHAHIDEQPLTFRG--DPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKM 193 (332)
T ss_pred ehhhhhhhcccccccccC--CCCCccceecccccccccchhhhhccceecccccccc
Confidence 35 555443334333333 245668999977 44433 6889999997644
No 211
>PF15254 CCDC14: Coiled-coil domain-containing protein 14
Probab=25.01 E-value=8.3e+02 Score=25.76 Aligned_cols=28 Identities=14% Similarity=0.313 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 80 DKVQLAIQTYEMVDKYIRKLDTDLARFE 107 (267)
Q Consensus 80 EKv~LA~~a~dlVd~hirrLD~dl~~~e 107 (267)
-|++-|..=...+.--+|+=|+++.+|.
T Consensus 515 ~kLe~sekEN~iL~itlrQrDaEi~RL~ 542 (861)
T PF15254_consen 515 FKLEASEKENQILGITLRQRDAEIERLR 542 (861)
T ss_pred hhHHHHHhhhhHhhhHHHHHHHHHHHHH
Confidence 4555555555555555666666665554
No 212
>PF10737 GerPC: Spore germination protein GerPC; InterPro: IPR019673 GerPC is required for the formation of functionally normal spores. The gerP locus encodes a number of proteins which are thought to be involved in the establishment of normal spore coat structure and/or permeability, which allows the access of germinants to their receptor [].
Probab=24.98 E-value=3.7e+02 Score=22.82 Aligned_cols=40 Identities=20% Similarity=0.288 Sum_probs=23.8
Q ss_pred cchHHHHHhHHHHH-HHHHHHH-----HHHHHHHHHHHHHHHhcCC
Q psy12696 15 SLPIELQRNFTLMR-ELDSRAQ-----DVMKTIDRVAEDYLDNMKH 54 (267)
Q Consensus 15 ~LP~El~r~l~~ir-elD~~~~-----~~~~~i~~~~~~~~k~~~~ 54 (267)
.+|..|.+.-.... .||..+. ++++++.+++.-|+++...
T Consensus 95 e~p~~l~~~e~~~~~~ld~~y~~~IieDIrKQl~~RI~~YlqQ~~~ 140 (176)
T PF10737_consen 95 EAPQRLEQLEQQYNVPLDDSYRSFIIEDIRKQLPQRIQFYLQQVQP 140 (176)
T ss_pred HHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHhHHHHHHHHhcCCC
Confidence 45555554444332 3444444 5667788888888887654
No 213
>KOG1973|consensus
Probab=24.95 E-value=1e+02 Score=27.85 Aligned_cols=99 Identities=15% Similarity=0.178 Sum_probs=65.2
Q ss_pred HHHHHHHHhhcchHHHHHhHHHHHHHH-HHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHHH
Q psy12696 5 YLEQYLDSLDSLPIELQRNFTLMRELD-SRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQ 83 (267)
Q Consensus 5 yLedfld~ie~LP~El~r~l~~irelD-~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~ 83 (267)
++...++.|..+.... +......++| ..+...+..... .|...............+..+.....+-.+++...+.
T Consensus 27 ~~~~~f~~l~~~~~~~-~~~~~~~e~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~ek~~~~~~~~e 102 (274)
T KOG1973|consen 27 NLQHNFDVIEDIDIFG-RSENQKKELDLKVAVEYMSKGRS---QLSKPQKDPLLEAIRSALRKCKELSDEKVQIAMQTVE 102 (274)
T ss_pred cchhHHHHHhhhhccc-hhHHHHhhhhhhhhhcccccccc---ccCccccchhHHHHHHHHhhhhhhhhHHHHHHHHHHH
Confidence 3444555555555544 6777778888 555555554443 1111111111222335666788888889999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 84 LAIQTYEMVDKYIRKLDTDLARFE 107 (267)
Q Consensus 84 LA~~a~dlVd~hirrLD~dl~~~e 107 (267)
+....+..++.|+.+++.++....
T Consensus 103 ~~~~~~~~~~~~~~~~e~~~~~~~ 126 (274)
T KOG1973|consen 103 LIPKHIGRLETALKSFEVELELAK 126 (274)
T ss_pred hhHhhhcchhHHHHhcccchhhhh
Confidence 999999999999999998888774
No 214
>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits. Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal alpha subunit, eukaryotic prefoldin subunits 3 and 5 and the UXT (ubiquitously expressed transcript) family. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 1FXK_C 2ZDI_C.
Probab=24.94 E-value=3e+02 Score=20.86 Aligned_cols=43 Identities=16% Similarity=0.340 Sum_probs=28.0
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 69 KYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQ 111 (267)
Q Consensus 69 ~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el~ 111 (267)
..+.+|.++.+.++...+...+.+...+..+...+..++..+.
T Consensus 73 ~s~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~~~~~l~ 115 (120)
T PF02996_consen 73 MSLEEAIEFLKKRIKELEEQLEKLEKELAELQAQIEQLEQTLQ 115 (120)
T ss_dssp EEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHH
T ss_pred ecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566666777777677777777777777766666665554
No 215
>KOG4451|consensus
Probab=24.77 E-value=4.3e+02 Score=23.58 Aligned_cols=39 Identities=21% Similarity=0.322 Sum_probs=32.0
Q ss_pred HHHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHH
Q psy12696 5 YLEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDR 43 (267)
Q Consensus 5 yLedfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~ 43 (267)
-||+|-..++.|=.|=.-++++||++-+.+.++.+.|++
T Consensus 51 ~leey~~em~~lL~ekm~Hveelr~iHadiN~men~ikq 89 (286)
T KOG4451|consen 51 NLEEYELEMGVLLLEKMGHVEELREIHADINEMENDIKQ 89 (286)
T ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Confidence 478888888888888888899999998888887776643
No 216
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=24.57 E-value=8.3e+02 Score=25.61 Aligned_cols=6 Identities=33% Similarity=0.634 Sum_probs=2.2
Q ss_pred HHHHhh
Q psy12696 9 YLDSLD 14 (267)
Q Consensus 9 fld~ie 14 (267)
.++.++
T Consensus 521 li~~l~ 526 (782)
T PRK00409 521 LIASLE 526 (782)
T ss_pred HHHHHH
Confidence 333333
No 217
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=24.55 E-value=39 Score=30.75 Aligned_cols=13 Identities=31% Similarity=1.048 Sum_probs=10.2
Q ss_pred CCCCceeCcCCcC
Q psy12696 250 KPKGKWYCPKCTS 262 (267)
Q Consensus 250 ~p~~~w~C~~C~~ 262 (267)
...+.||||.|..
T Consensus 261 ~gR~t~~CP~CQ~ 273 (273)
T COG0266 261 GGRSTFYCPVCQK 273 (273)
T ss_pred cCCcCEeCCCCCC
Confidence 3467899999974
No 218
>KOG2196|consensus
Probab=24.08 E-value=5.3e+02 Score=23.14 Aligned_cols=37 Identities=16% Similarity=0.290 Sum_probs=28.0
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 76 EYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQE 112 (267)
Q Consensus 76 ~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el~~ 112 (267)
.-.|++-.=+-++.+-||.++++|+.||..+-..+-.
T Consensus 167 ~~~D~eR~qty~~a~nidsqLk~l~~dL~~ii~~lN~ 203 (254)
T KOG2196|consen 167 SRADVEREQTYKMAENIDSQLKRLSEDLKQIIKSLNT 203 (254)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHh
Confidence 3455666666777888999999999999888766643
No 219
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=23.92 E-value=45 Score=27.82 Aligned_cols=18 Identities=28% Similarity=0.877 Sum_probs=12.7
Q ss_pred ecccCccCC--CCCCceeCc
Q psy12696 241 HFACVSLTT--KPKGKWYCP 258 (267)
Q Consensus 241 H~~Cv~l~~--~p~~~w~C~ 258 (267)
|+.|..... ...+.|+||
T Consensus 110 HlGC~~~~~~~~~~~~~~CP 129 (177)
T COG0723 110 HLGCTVPWNNAGAEGGFFCP 129 (177)
T ss_pred CCCCccCcccCCCCCeEEcc
Confidence 777766543 456889998
No 220
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=23.86 E-value=4.4e+02 Score=23.22 Aligned_cols=12 Identities=33% Similarity=0.708 Sum_probs=6.6
Q ss_pred HHHHHHHHhhcc
Q psy12696 5 YLEQYLDSLDSL 16 (267)
Q Consensus 5 yLedfld~ie~L 16 (267)
-+++|++.|..+
T Consensus 106 ~~~~~l~~l~~~ 117 (262)
T PF14257_consen 106 KFDSFLDELSEL 117 (262)
T ss_pred HHHHHHHHHhcc
Confidence 455666655544
No 221
>PF09789 DUF2353: Uncharacterized coiled-coil protein (DUF2353); InterPro: IPR019179 Members of this family have been annotated as being coiled-coil domain-containing protein 149, however they currently have no known function.
Probab=23.86 E-value=6e+02 Score=23.69 Aligned_cols=48 Identities=10% Similarity=0.231 Sum_probs=24.9
Q ss_pred hhHHHHHHHHH-------HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 57 KDKKKETLAEI-------QKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLAR 105 (267)
Q Consensus 57 ~~~~~~~~~~I-------~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~ 105 (267)
++++..++.++ .......+.+.|||-.+...- |..-..+.||+.+|..
T Consensus 125 ~~ere~lV~qLEk~~~q~~qLe~d~qs~lDEkeEl~~ER-D~yk~K~~RLN~ELn~ 179 (319)
T PF09789_consen 125 PHEREDLVEQLEKLREQIEQLERDLQSLLDEKEELVTER-DAYKCKAHRLNHELNY 179 (319)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Confidence 35666554443 334444556667776665542 3333345566655543
No 222
>PF10267 Tmemb_cc2: Predicted transmembrane and coiled-coil 2 protein; InterPro: IPR019394 This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.
Probab=23.66 E-value=6.6e+02 Score=24.13 Aligned_cols=35 Identities=20% Similarity=0.415 Sum_probs=19.9
Q ss_pred cchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 15 SLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYL 49 (267)
Q Consensus 15 ~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~ 49 (267)
..+..+...+.+++|+-.....+...++.+...|.
T Consensus 209 ~~~~~l~~~~~el~eik~~~~~L~~~~e~Lk~~~~ 243 (395)
T PF10267_consen 209 QQNLGLQKILEELREIKESQSRLEESIEKLKEQYQ 243 (395)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455666666666666666665555555544433
No 223
>KOG0250|consensus
Probab=23.36 E-value=1e+03 Score=26.10 Aligned_cols=43 Identities=21% Similarity=0.269 Sum_probs=22.3
Q ss_pred ChhhHHHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHH
Q psy12696 1 MSTSYLEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDR 43 (267)
Q Consensus 1 m~~~yLedfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~ 43 (267)
|-++-|++.-+++...=.-+.+...+|..+...+..+.+++..
T Consensus 204 mkaT~L~qi~~~~~~~~~~~~~~~~~i~~~~e~i~~l~k~i~e 246 (1074)
T KOG0250|consen 204 MKATQLEQITESYSEIMESLDHAKELIDLKEEEIKNLKKKIKE 246 (1074)
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence 3455566555555555555555555555555555555444433
No 224
>PF02977 CarbpepA_inh: Carboxypeptidase A inhibitor; InterPro: IPR004231 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. This family is represented by the well-characterised metallocarboxypeptidase A inhibitor (MCPI) from potatoes, which belongs to the MEROPS inhibitor family I37, clan IE. It inhibits metallopeptidases belonging to MEROPS peptidase family M14, carboxypeptidase A. In Russet Burbank potatoes, it is a mixture of approximately equal amounts of two polypeptide chains containing 38 or 39 amino acid residues. The chains differ in their amino terminal sequence only [] and are resistant to fragmentation by proteases []. The structure of the complex between bovine carboxypeptidase A and the 39-amino-acid carboxypeptidase A inhibitor from potatoes has been determined at 2.5-A resolution []. The potato inhibitor is synthesised as a precursor, having a 29 residue N-terminal signal peptide, a 27 residue pro-peptide, the 39 residue mature inhibitor region and a 7 residue C-terminal extension. The 7 residue C-terminal extension is involved in inhibitor inactivation and may be required for targeting to the vacuole where the mature active inhibitor accumulates []. The N-terminal region and the mature inhibitor are weakly related to other solananaceous proteins found in this entry, from potato, tomato and henbane, which have been incorrectly described as metallocarboxipeptidase inhibitors [].; GO: 0008191 metalloendopeptidase inhibitor activity; PDB: 4CPA_I 1H20_A 2HLG_A.
Probab=23.25 E-value=24 Score=23.13 Aligned_cols=8 Identities=25% Similarity=0.518 Sum_probs=4.3
Q ss_pred eeCcCCcC
Q psy12696 255 WYCPKCTS 262 (267)
Q Consensus 255 w~C~~C~~ 262 (267)
|||+.|.+
T Consensus 22 tlC~~C~k 29 (46)
T PF02977_consen 22 TLCQWCWK 29 (46)
T ss_dssp SSS-EE-C
T ss_pred eehHHHHh
Confidence 77777743
No 225
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=23.16 E-value=1.1e+02 Score=23.03 Aligned_cols=23 Identities=22% Similarity=0.237 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 87 QTYEMVDKYIRKLDTDLARFEQE 109 (267)
Q Consensus 87 ~a~dlVd~hirrLD~dl~~~e~e 109 (267)
.+.++++.|+..|+..++.++.+
T Consensus 76 ~~~~ll~~~~~~l~~~i~~L~~~ 98 (99)
T cd04772 76 SALALVDAAHALLQRYRQQLDQE 98 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 67899999999999999888765
No 226
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=23.16 E-value=46 Score=29.99 Aligned_cols=12 Identities=25% Similarity=1.212 Sum_probs=10.0
Q ss_pred CCCceeCcCCcC
Q psy12696 251 PKGKWYCPKCTS 262 (267)
Q Consensus 251 p~~~w~C~~C~~ 262 (267)
..+.||||.|..
T Consensus 262 gR~t~~CP~CQ~ 273 (274)
T PRK01103 262 GRSTFFCPRCQK 273 (274)
T ss_pred CCCcEECcCCCC
Confidence 367899999975
No 227
>PF05478 Prominin: Prominin; InterPro: IPR008795 The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and Homo sapiens prominin and (Mus musculus) prominin-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain []. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration [].; GO: 0016021 integral to membrane
Probab=23.07 E-value=8.9e+02 Score=25.40 Aligned_cols=35 Identities=14% Similarity=0.229 Sum_probs=15.9
Q ss_pred HHHHhhcchHHHHHhHHH-HHHHHHHHHHHHHHHHH
Q psy12696 9 YLDSLDSLPIELQRNFTL-MRELDSRAQDVMKTIDR 43 (267)
Q Consensus 9 fld~ie~LP~El~r~l~~-irelD~~~~~~~~~i~~ 43 (267)
.-..+.+.|.+|++.+.. ..++..++.+.++.+..
T Consensus 185 l~~~l~~~~~qi~~l~~~ny~~~~~~v~~~L~~~~~ 220 (806)
T PF05478_consen 185 LRTFLNDTPQQIDHLLVQNYSELKDHVSSDLDNIGS 220 (806)
T ss_pred HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 333344445555555444 44444444444444433
No 228
>KOG0976|consensus
Probab=23.01 E-value=9.5e+02 Score=25.70 Aligned_cols=30 Identities=20% Similarity=0.297 Sum_probs=23.5
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 20 LQRNFTLMRELDSRAQDVMKTIDRVAEDYL 49 (267)
Q Consensus 20 l~r~l~~irelD~~~~~~~~~i~~~~~~~~ 49 (267)
++..-+.|+|.|.-.+...++|.+...+|-
T Consensus 247 ~rk~~s~i~E~d~~lq~sak~ieE~m~qlk 276 (1265)
T KOG0976|consen 247 LRKTCSMIEEQDMDLQASAKEIEEKMRQLK 276 (1265)
T ss_pred HhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456678889999999888888887776664
No 229
>PF05164 ZapA: Cell division protein ZapA; InterPro: IPR007838 This entry a structural domain found in the cell division protein ZapA, as well as in related proteins. This domain has a core structure consisting of two layers alpha/beta, and has a long C-terminal helix that forms dimeric parallel and tetrameric antiparallel coiled coils []. ZapA interacts with FtsZ, where FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle. ZapA drives the polymerisation and filament bundling of FtsZ, thereby contributing to the spatio-temporal tuning of the Z-ring.; PDB: 1T3U_B 1W2E_B 3HNW_A.
Probab=23.01 E-value=2.9e+02 Score=19.68 Aligned_cols=25 Identities=8% Similarity=0.081 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCh
Q psy12696 33 RAQDVMKTIDRVAEDYLDNMKHYSK 57 (267)
Q Consensus 33 ~~~~~~~~i~~~~~~~~k~~~~~~~ 57 (267)
.+..+.+.|++.+..+-...+.++.
T Consensus 22 ~l~~~a~~i~~~i~~~~~~~~~~~~ 46 (89)
T PF05164_consen 22 YLRKAAELINEKINEIKKKYPKLSP 46 (89)
T ss_dssp HHHHHHHHHHHHHHHHCTTCCTSSH
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCH
Confidence 3455666677777777666555554
No 230
>PRK14127 cell division protein GpsB; Provisional
Probab=22.99 E-value=1.9e+02 Score=22.55 Aligned_cols=39 Identities=10% Similarity=0.305 Sum_probs=25.3
Q ss_pred hHHHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHH
Q psy12696 4 SYLEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTID 42 (267)
Q Consensus 4 ~yLedfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~ 42 (267)
.||++-++.++.|=.|+.+.-.++..|..++.++..++.
T Consensus 30 ~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~~ 68 (109)
T PRK14127 30 KFLDDVIKDYEAFQKEIEELQQENARLKAQVDELTKQVS 68 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 366666666666666666666666666666666665554
No 231
>KOG0612|consensus
Probab=22.86 E-value=1e+03 Score=26.43 Aligned_cols=26 Identities=27% Similarity=0.319 Sum_probs=19.1
Q ss_pred hhcchHHHHHhHHHHHHHHHHHHHHH
Q psy12696 13 LDSLPIELQRNFTLMRELDSRAQDVM 38 (267)
Q Consensus 13 ie~LP~El~r~l~~irelD~~~~~~~ 38 (267)
+.-|+..+...+..++.+|.+++.+.
T Consensus 436 ~~~le~~l~~~~~~~~~~~~~~~~~~ 461 (1317)
T KOG0612|consen 436 LQILEQSLVNEMQEKEKLDEKCQAVA 461 (1317)
T ss_pred hhhcccchhhHHHHhhhHHHHHHHHh
Confidence 34466667777888888888888765
No 232
>PTZ00007 (NAP-L) nucleosome assembly protein -L; Provisional
Probab=22.74 E-value=1.7e+02 Score=27.47 Aligned_cols=36 Identities=14% Similarity=0.150 Sum_probs=28.6
Q ss_pred HhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 12 SLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAED 47 (267)
Q Consensus 12 ~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~ 47 (267)
.|..||..+++.+..|+.|..++..+..+..+.+..
T Consensus 31 ~i~~Lp~~~~~rv~aL~~lQ~e~~~le~ef~~ev~~ 66 (337)
T PTZ00007 31 KLSHLTDEQRETLKKLQLLQKEFDDLEVEYNAELRK 66 (337)
T ss_pred hhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 366899999999999999999988887775544433
No 233
>PF06717 DUF1202: Protein of unknown function (DUF1202); InterPro: IPR009592 This family consists of several hypothetical bacterial proteins of around 335 residues in length. Members of this family are found exclusively in Escherichia coli and Salmonella species and are often referred to as YggM proteins. The function of this family is unknown.
Probab=22.71 E-value=3.7e+02 Score=24.70 Aligned_cols=44 Identities=14% Similarity=0.268 Sum_probs=35.6
Q ss_pred HHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHH---HHHHHHHHH
Q psy12696 7 EQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTI---DRVAEDYLD 50 (267)
Q Consensus 7 edfld~ie~LP~El~r~l~~irelD~~~~~~~~~i---~~~~~~~~k 50 (267)
++|.+.|..|-.++.+.=..|-.|..+..++..++ .+.+..|..
T Consensus 134 ~~F~~rf~~Ied~~~~kK~~I~~L~~qisaLdkqi~ai~Kkid~yWg 180 (308)
T PF06717_consen 134 QDFNYRFNQIEDEYNRKKNKIPGLNKQISALDKQIVAINKKIDRYWG 180 (308)
T ss_pred hhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 57888999999999999999999988888887774 455666664
No 234
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=22.70 E-value=3.1e+02 Score=20.04 Aligned_cols=22 Identities=27% Similarity=0.378 Sum_probs=16.3
Q ss_pred hhHHHHHHHHhhcchHHHHHhHH
Q psy12696 3 TSYLEQYLDSLDSLPIELQRNFT 25 (267)
Q Consensus 3 ~~yLedfld~ie~LP~El~r~l~ 25 (267)
-.|+..|+- +-+||.+|+..+.
T Consensus 17 ~s~Vs~~l~-Ll~lP~~i~~~v~ 38 (93)
T PF08535_consen 17 RSWVSNHLA-LLDLPEEIKELVR 38 (93)
T ss_dssp HHHHHHHHG-GGS--HHHHHHHH
T ss_pred HHHHHHHHH-HHcCCHHHHHHHH
Confidence 468899998 5579999998877
No 235
>KOG4057|consensus
Probab=22.69 E-value=4.5e+02 Score=21.83 Aligned_cols=35 Identities=17% Similarity=0.368 Sum_probs=20.9
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 74 TKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQEK 113 (267)
Q Consensus 74 ~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el~~~ 113 (267)
+++|+.|| ++-.+++.....+-.-+..+|.+|.+.
T Consensus 32 iqeLgKEK-----~~~kn~e~qa~~F~ksit~VE~eLSaQ 66 (180)
T KOG4057|consen 32 IQELGKEK-----QIGKNMEDQANNFKKSITQVENELSAQ 66 (180)
T ss_pred HHHHhHHh-----hhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566666 333446666666666666777777664
No 236
>CHL00154 rpl29 ribosomal protein L29; Validated
Probab=22.55 E-value=2.8e+02 Score=19.57 Aligned_cols=22 Identities=5% Similarity=0.016 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHHHhHHHH
Q psy12696 60 KKETLAEIQKYFDKTKEYGDDK 81 (267)
Q Consensus 60 ~~~~~~~I~~~~~~~~~lsdEK 81 (267)
....+..+...+.+++-+..||
T Consensus 42 n~~~ir~~RrdIARikTil~ek 63 (67)
T CHL00154 42 KPHLFKHKKHRLAQLLTLLSSR 63 (67)
T ss_pred ChHHHHHHHHHHHHHHHHHHHH
Confidence 3356666777777776666555
No 237
>PF12773 DZR: Double zinc ribbon
Probab=22.54 E-value=76 Score=20.38 Aligned_cols=22 Identities=18% Similarity=0.365 Sum_probs=11.6
Q ss_pred CCcee-ecCCCCC---CCcccccCCC
Q psy12696 213 EPTYC-VCQQVSY---GEMIGCDNPD 234 (267)
Q Consensus 213 ~~~~C-~C~~~~~---~~mi~Cd~~~ 234 (267)
+..|| .|+.+-. ..++.|-.|.
T Consensus 11 ~~~fC~~CG~~l~~~~~~~~~C~~Cg 36 (50)
T PF12773_consen 11 DAKFCPHCGTPLPPPDQSKKICPNCG 36 (50)
T ss_pred cccCChhhcCChhhccCCCCCCcCCc
Confidence 35566 6665533 3355566643
No 238
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=22.40 E-value=6.2e+02 Score=23.36 Aligned_cols=20 Identities=25% Similarity=0.268 Sum_probs=9.7
Q ss_pred hhcchHHHHHhHHHHHHHHH
Q psy12696 13 LDSLPIELQRNFTLMRELDS 32 (267)
Q Consensus 13 ie~LP~El~r~l~~irelD~ 32 (267)
++.|-..|.+++..|+.=+.
T Consensus 142 legLk~~L~~~~~~l~~D~~ 161 (312)
T smart00787 142 LEGLKEGLDENLEGLKEDYK 161 (312)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 44444555555555544333
No 239
>KOG4484|consensus
Probab=22.36 E-value=4.9e+02 Score=22.10 Aligned_cols=29 Identities=38% Similarity=0.649 Sum_probs=17.0
Q ss_pred HHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHH
Q psy12696 6 LEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTI 41 (267)
Q Consensus 6 Ledfld~ie~LP~El~r~l~~irelD~~~~~~~~~i 41 (267)
+|-+|-- ++||.+|+- ++...++++..++
T Consensus 36 ~eRlLkk-~~LP~~Vr~------e~er~L~~Lk~ql 64 (199)
T KOG4484|consen 36 LERLLKK-KDLPPEVRE------ELERKLQDLKKQL 64 (199)
T ss_pred HHHHHhh-ccCCHHHHH------HHHHHHHHHHHHH
Confidence 3445543 789999873 4444555555544
No 240
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=22.34 E-value=76 Score=29.38 Aligned_cols=8 Identities=25% Similarity=0.671 Sum_probs=5.4
Q ss_pred eeCcCCcC
Q psy12696 255 WYCPKCTS 262 (267)
Q Consensus 255 w~C~~C~~ 262 (267)
-.|..|..
T Consensus 253 e~C~~C~~ 260 (309)
T PRK03564 253 ESCGDCGT 260 (309)
T ss_pred eecccccc
Confidence 56888853
No 241
>PF13758 Prefoldin_3: Prefoldin subunit
Probab=22.31 E-value=3.7e+02 Score=20.66 Aligned_cols=84 Identities=12% Similarity=0.251 Sum_probs=45.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHH-------HHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q psy12696 23 NFTLMRELDSRAQDVMKTIDRVA-------EDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKY 95 (267)
Q Consensus 23 ~l~~irelD~~~~~~~~~i~~~~-------~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~h 95 (267)
.|.--+--|+.|..+..+|...- ..|+.-...+... .-.-.+|...+..-. --..=++|+.++|+|.
T Consensus 3 sL~hWq~w~aEYe~LKEEi~~l~~~~~~~~e~l~~i~r~f~g~--lv~~kEi~~ilG~~~----~i~Rt~~Qvv~~l~RR 76 (99)
T PF13758_consen 3 SLYHWQTWEAEYEGLKEEIEALPEDDDATREDLLRIRRDFGGS--LVTEKEIKEILGEGQ----GITRTREQVVDVLSRR 76 (99)
T ss_pred hHHHHHHHHHHHHHHHHHHHhccccCCCCHHHHHHHHHhcCcc--cccHHHHHHHhCCCC----CCCcCHHHHHHHHHHH
Confidence 34445667888888888887652 2232222111100 000112222222211 1112357888888888
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy12696 96 IRKLDTDLARFEQEIQE 112 (267)
Q Consensus 96 irrLD~dl~~~e~el~~ 112 (267)
|-.+...+..|+..+..
T Consensus 77 iDYV~~Ni~tleKql~~ 93 (99)
T PF13758_consen 77 IDYVQQNIETLEKQLEA 93 (99)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 88888888888876654
No 242
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=22.20 E-value=2.2e+02 Score=18.17 Aligned_cols=15 Identities=7% Similarity=0.115 Sum_probs=5.7
Q ss_pred HHHHHHHHHHHHHHH
Q psy12696 80 DKVQLAIQTYEMVDK 94 (267)
Q Consensus 80 EKv~LA~~a~dlVd~ 94 (267)
|--.-...+..|+.+
T Consensus 23 EA~~A~~kAq~Lm~k 37 (43)
T PF10979_consen 23 EAEAALAKAQRLMAK 37 (43)
T ss_pred HHHHHHHHHHHHHHH
Confidence 333333334444433
No 243
>KOG4674|consensus
Probab=22.06 E-value=1.1e+03 Score=27.50 Aligned_cols=108 Identities=9% Similarity=0.219 Sum_probs=0.0
Q ss_pred HHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH-HHHhcCC---CChhHH--HHHHHHHHHHHHHHHHhHH
Q psy12696 6 LEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAED-YLDNMKH---YSKDKK--KETLAEIQKYFDKTKEYGD 79 (267)
Q Consensus 6 Ledfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~-~~k~~~~---~~~~~~--~~~~~~I~~~~~~~~~lsd 79 (267)
+..+-+.|..|=.++...-..|..|+....-+...+-..-.. +++.+.+ .++.++ ...+++++..|..+..-..
T Consensus 574 ~~~a~e~i~~L~~~l~e~~~~i~sLl~erd~y~e~l~~~e~~~~~k~nss~~~~t~~~~~~e~~l~qLe~~le~~~~E~~ 653 (1822)
T KOG4674|consen 574 INEASEKIAELEKELEEQEQRIESLLTERDMYKELLAELEDSHQLKPNSSALDQTEAPRAKEKRLRQLENELESYKKEKR 653 (1822)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccCCCCchhhcccccchhHHHHHHHHHHHHHHHHHHHH
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 80 DKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQEK 113 (267)
Q Consensus 80 EKv~LA~~a~dlVd~hirrLD~dl~~~e~el~~~ 113 (267)
+.+.+.+..++-+..-+.-|-.++.++.......
T Consensus 654 ~~~~~l~e~~~~l~~ev~~ir~~l~k~~~~~~fA 687 (1822)
T KOG4674|consen 654 ENLKKLQEDFDSLQKEVTAIRSQLEKLKNELNLA 687 (1822)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
No 244
>PF10046 BLOC1_2: Biogenesis of lysosome-related organelles complex-1 subunit 2 ; InterPro: IPR019269 This entry represents a family of proteins that play a role in cellular proliferation, as well as in the biogenesis of specialised organelles of the endosomal-lysosomal system [].
Probab=22.05 E-value=3.5e+02 Score=20.33 Aligned_cols=27 Identities=22% Similarity=0.416 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 79 DDKVQLAIQTYEMVDKYIRKLDTDLAR 105 (267)
Q Consensus 79 dEKv~LA~~a~dlVd~hirrLD~dl~~ 105 (267)
++.|.--..+.+.||.++++|+..++.
T Consensus 72 e~~V~~LE~~v~~LD~ysk~LE~k~k~ 98 (99)
T PF10046_consen 72 EEQVTELEQTVYELDEYSKELESKFKK 98 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 445666666777777777777766653
No 245
>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.
Probab=22.01 E-value=8.4e+02 Score=24.72 Aligned_cols=37 Identities=24% Similarity=0.309 Sum_probs=23.9
Q ss_pred HHHHHHHHhh-cchHHHHHhHHHHHHHHHHHHHHHHHH
Q psy12696 5 YLEQYLDSLD-SLPIELQRNFTLMRELDSRAQDVMKTI 41 (267)
Q Consensus 5 yLedfld~ie-~LP~El~r~l~~irelD~~~~~~~~~i 41 (267)
.++++++.+. .....+...+..+.++..+..++..+|
T Consensus 377 ~~~~~~~~~~~~~~~~~~~~~~~~~~~e~el~~l~~~l 414 (650)
T TIGR03185 377 QLEVLIQQVKRELQDAKSQLLKELRELEEELAEVDKKI 414 (650)
T ss_pred HHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555666655 466667777777777777776666655
No 246
>KOG3540|consensus
Probab=22.01 E-value=6.2e+02 Score=25.18 Aligned_cols=98 Identities=19% Similarity=0.239 Sum_probs=60.9
Q ss_pred HHHHHHHHhhcchHHHHHhHHHHHHH-HHHHHHHHHHHHHHHHHHHHhcCCCChhH-------HHHHHHHHHHHHHHHHH
Q psy12696 5 YLEQYLDSLDSLPIELQRNFTLMREL-DSRAQDVMKTIDRVAEDYLDNMKHYSKDK-------KKETLAEIQKYFDKTKE 76 (267)
Q Consensus 5 yLedfld~ie~LP~El~r~l~~irel-D~~~~~~~~~i~~~~~~~~k~~~~~~~~~-------~~~~~~~I~~~~~~~~~ 76 (267)
-||+|+..|..-|.-=.|.|.-+|.. -+.-.+.+..|....+-.. .++.. -...|+-|...+...+.
T Consensus 331 Ale~ylaALqa~pprp~~Vl~aLkrYvRAEqKdr~HTlrhyqHv~~-----vDpkkAaqmk~qV~thLrvIeeR~NqsLs 405 (615)
T KOG3540|consen 331 ALENYLAALQADPPRPHRVLQALKRYVRAEQKDRMHTLRHYQHVLA-----VDPKKAAQMKSQVMTHLRVIEERINQSLS 405 (615)
T ss_pred HHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-----cChHHHHHHHHHHHHHHHHHHHHhcchhH
Confidence 58899999999888888888777653 3333344444443332221 12211 11345667777777888
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 77 YGDDKVQLAIQTYEMVDKYIRKLDTDLARFE 107 (267)
Q Consensus 77 lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e 107 (267)
|...==++|+.+.+-|+--|..=+.+...|.
T Consensus 406 lL~~~P~vaqeirdev~ell~~e~~~~de~~ 436 (615)
T KOG3540|consen 406 LLYDVPAVAQEIRDEVDELLQVEDSHDDEFS 436 (615)
T ss_pred HHhcChHHHHHHHHHHHHHHhhhhcChhhhc
Confidence 8888778888888888776655554444444
No 247
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=21.97 E-value=52 Score=21.61 Aligned_cols=31 Identities=16% Similarity=0.414 Sum_probs=20.1
Q ss_pred ccccCCC-CCCcceecccCccCCCCCCceeCcCCcC
Q psy12696 228 IGCDNPD-CPIEWFHFACVSLTTKPKGKWYCPKCTS 262 (267)
Q Consensus 228 i~Cd~~~-c~~~wfH~~Cv~l~~~p~~~w~C~~C~~ 262 (267)
|.|+.|. .|+.++.+.|+.= .+--+|..|-.
T Consensus 1 i~C~~C~~~~i~g~R~~C~~C----~d~dlC~~Cf~ 32 (49)
T cd02338 1 VSCDGCGKSNFTGRRYKCLIC----YDYDLCADCYD 32 (49)
T ss_pred CCCCCCcCCCcEEeeEEeCCC----CCCccchhHHh
Confidence 5688877 6777777777742 23456777743
No 248
>KOG4721|consensus
Probab=21.96 E-value=9e+02 Score=25.04 Aligned_cols=37 Identities=22% Similarity=0.284 Sum_probs=26.6
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHH
Q psy12696 76 EYGDDKVQLAIQTYEMVDKYIRKLDT---DLARFEQEIQE 112 (267)
Q Consensus 76 ~lsdEKv~LA~~a~dlVd~hirrLD~---dl~~~e~el~~ 112 (267)
+.=+.|++-++++|+-|...+-+|+. +|..-|..++.
T Consensus 428 ~~YE~KLertN~ly~eLs~cm~qLelkEkElaerEq~l~r 467 (904)
T KOG4721|consen 428 EHYERKLERTNNLYMELSACMLQLELKEKELAEREQALER 467 (904)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34468999999999999999988874 34444444443
No 249
>COG5293 Predicted ATPase [General function prediction only]
Probab=21.93 E-value=7.9e+02 Score=24.36 Aligned_cols=51 Identities=16% Similarity=0.160 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 62 ETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQE 112 (267)
Q Consensus 62 ~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el~~ 112 (267)
+-+++.....+.+..+..|=++++...|+-+..+..-...-...|...+..
T Consensus 403 e~l~k~~~~~~~i~~lkhe~l~~~~r~y~e~q~q~~~~~~~~~lF~~~~r~ 453 (591)
T COG5293 403 EPLRKLHALDQYIGTLKHECLDLEERIYTEVQQQCSLFASIGRLFKEMIRE 453 (591)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334555666677777888888899999998888866444444555554444
No 250
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.69 E-value=56 Score=29.42 Aligned_cols=15 Identities=33% Similarity=0.992 Sum_probs=11.7
Q ss_pred CCCceeCcCCcCccc
Q psy12696 251 PKGKWYCPKCTSDRK 265 (267)
Q Consensus 251 p~~~w~C~~C~~~~~ 265 (267)
..+.||||.|.....
T Consensus 252 gR~ty~Cp~CQ~~~~ 266 (269)
T PRK14811 252 GRGTHFCPQCQPLRP 266 (269)
T ss_pred CCCcEECCCCcCCCC
Confidence 467899999987543
No 251
>PF08400 phage_tail_N: Prophage tail fibre N-terminal; InterPro: IPR013609 This entry represents the N terminus of phage 933W tail fibre protein. The characteristics of the protein distribution suggest prophage matches.
Probab=21.62 E-value=2.8e+02 Score=22.43 Aligned_cols=34 Identities=24% Similarity=0.370 Sum_probs=23.4
Q ss_pred HHHHHHHHh--hcchHHHHHhHHHHHHHHHHHHHHH
Q psy12696 5 YLEQYLDSL--DSLPIELQRNFTLMRELDSRAQDVM 38 (267)
Q Consensus 5 yLedfld~i--e~LP~El~r~l~~irelD~~~~~~~ 38 (267)
-|++||..+ ..|+.|+...|.+|...=.+..+..
T Consensus 85 TLN~fL~~~~e~dl~Pevlk~fe~m~~~a~~~a~~a 120 (134)
T PF08400_consen 85 TLNDFLTAPDEDDLRPEVLKRFEEMVAQAARSAEAA 120 (134)
T ss_pred cHHHHhhccccccCCHHHHHHHHHHHHHHHHHHHHH
Confidence 488999754 6799999988887776544433333
No 252
>PF07195 FliD_C: Flagellar hook-associated protein 2 C-terminus; InterPro: IPR010809 The flagellar hook-associated protein 2 (HAP2 or FliD) forms the distal end of the flagella, and plays a role in mucin specific adhesion of the bacteria []. This alignment covers the C-terminal region of the flagellar hook-associated protein 2.; GO: 0007155 cell adhesion, 0009288 bacterial-type flagellum
Probab=21.61 E-value=4.3e+02 Score=23.03 Aligned_cols=46 Identities=20% Similarity=0.362 Sum_probs=24.6
Q ss_pred HHHHHHHHh-hcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 5 YLEQYLDSL-DSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLD 50 (267)
Q Consensus 5 yLedfld~i-e~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k 50 (267)
||+.|+..- ..|.....-.=..|+.++.+...+...++.....|.+
T Consensus 179 ~l~~~~~~~~G~i~~~~~~l~~~~~~~~~~i~~~~~rl~~~~~~l~~ 225 (239)
T PF07195_consen 179 YLDSYTGSSTGSITSRIDSLNSQIKSLDKQIEDLEERLESKEERLRK 225 (239)
T ss_pred HHHHHhCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444444 4445555555556666666666665555555555443
No 253
>PRK05683 flgK flagellar hook-associated protein FlgK; Validated
Probab=21.55 E-value=8.6e+02 Score=25.07 Aligned_cols=34 Identities=9% Similarity=0.162 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHhHHHHHHHH---HHHHHHHHHHHH
Q psy12696 64 LAEIQKYFDKTKEYGDDKVQLA---IQTYEMVDKYIR 97 (267)
Q Consensus 64 ~~~I~~~~~~~~~lsdEKv~LA---~~a~dlVd~hir 97 (267)
..+|...++++-+|-.+=..+. ....||+|++=+
T Consensus 165 V~~IN~l~~qIA~LN~qI~~~~~~G~~~NdLlDqRD~ 201 (676)
T PRK05683 165 TDQVNNLTTSIASYNKQIAQASASGATPNDLLDARDE 201 (676)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCCchHhHHHHHH
Confidence 3445555555544433322211 125566666433
No 254
>cd07681 F-BAR_PACSIN3 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Protein kinase C and Casein kinase Substrate in Neurons 3 (PACSIN3). F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Protein kinase C and Casein kinase Substrate in Neurons (PACSIN) proteins, also called Synaptic dynamin-associated proteins (Syndapins), act as regulators of cytoskeletal and membrane dynamics. Vetebrates harbor three isoforms with distinct expression patterns and specific functions. PACSIN 3 or Syndapin III is expressed ubiquitously and regulates glucose uptake in adipocytes through its role in GLUT1 trafficking. It also modulates the subcellular localization and stimulus-specific function of the cation channel TRPV4. PACSIN 3 contains an N-terminal F-BAR domain and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to
Probab=21.54 E-value=6e+02 Score=22.85 Aligned_cols=38 Identities=5% Similarity=0.143 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Q psy12696 60 KKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIR 97 (267)
Q Consensus 60 ~~~~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd~hir 97 (267)
+......+...++.++++-.|.|..--.++.-|.+|+.
T Consensus 202 ~~~w~e~m~~~~d~~Q~~EeeRi~flK~~L~~~~~~l~ 239 (258)
T cd07681 202 NPRYMEDMEQAFEICQEAERKRLCFFKEMLLDLHQHLD 239 (258)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44566677777777777777777777777777777763
No 255
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=21.49 E-value=42 Score=19.42 Aligned_cols=13 Identities=23% Similarity=1.022 Sum_probs=8.6
Q ss_pred CCCCceeCcCCcC
Q psy12696 250 KPKGKWYCPKCTS 262 (267)
Q Consensus 250 ~p~~~w~C~~C~~ 262 (267)
.....+||+.|..
T Consensus 17 ~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 17 NGRSTYLCPRCQK 29 (30)
T ss_dssp TTEEEEE-TTTCC
T ss_pred cCCCCeECcCCcC
Confidence 3456799999974
No 256
>PF13376 OmdA: Bacteriocin-protection, YdeI or OmpD-Associated
Probab=21.48 E-value=2.7e+02 Score=18.90 Aligned_cols=51 Identities=12% Similarity=0.270 Sum_probs=29.9
Q ss_pred cchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHH
Q psy12696 15 SLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEI 67 (267)
Q Consensus 15 ~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I 67 (267)
.+|.||..-|..-.+.-.-...+-......+-.|+...+ +++.|.+.+.++
T Consensus 5 ~vP~dl~~aL~~~p~a~~~f~~l~~~~rr~~i~wi~~AK--~~etR~kRi~~~ 55 (63)
T PF13376_consen 5 EVPEDLEAALEANPEAKEFFESLTPSYRREYIRWINSAK--TEETRAKRIAKL 55 (63)
T ss_pred CCCHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHcC--CHHHHHHHHHHH
Confidence 367787777766666666666666655666666665444 344444444333
No 257
>PF05769 DUF837: Protein of unknown function (DUF837); InterPro: IPR008555 This family consists of several eukaryotic proteins of unknown function. One of the family members (O02197 from SWISSPROT) is a circulating cathodic antigen (CCA) found in Schistosoma mansoni (Blood fluke) [].
Probab=21.46 E-value=5e+02 Score=21.95 Aligned_cols=95 Identities=7% Similarity=0.206 Sum_probs=53.9
Q ss_pred HhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q psy12696 12 SLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNM------KHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLA 85 (267)
Q Consensus 12 ~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~------~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA 85 (267)
+|+.|-.+-++....+++.|..+..+..+....-..+.... ..+....+...-..|...-.++.+|..|--
T Consensus 4 ti~~il~dak~L~~rL~~~d~~ad~Ll~qa~~l~~~i~sm~~y~eei~~l~~~~~~~~~~~l~~En~qi~~Lq~EN~--- 80 (181)
T PF05769_consen 4 TIEQILADAKRLVERLKDHDNAADSLLSQAEALNKQIESMRQYQEEIQELNELSKNRPRAGLQQENRQIRQLQQENR--- 80 (181)
T ss_pred cHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHhhHHHHHHHHHHH---
Confidence 36677788899999999999999988887654433332110 000000000000224444455566666653
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 86 IQTYEMVDKYIRKLDTDLARFEQEI 110 (267)
Q Consensus 86 ~~a~dlVd~hirrLD~dl~~~e~el 110 (267)
.+..+|+-|-.-|+.-+.+|..-.
T Consensus 81 -eL~~~leEhq~alelIM~KyReq~ 104 (181)
T PF05769_consen 81 -ELRQSLEEHQSALELIMSKYREQM 104 (181)
T ss_pred -HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445566777777777777776443
No 258
>PF11855 DUF3375: Protein of unknown function (DUF3375); InterPro: IPR021804 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 479 to 499 amino acids in length.
Probab=21.37 E-value=7.7e+02 Score=24.08 Aligned_cols=33 Identities=27% Similarity=0.371 Sum_probs=28.7
Q ss_pred HHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHH
Q psy12696 6 LEQYLDSLDSLPIELQRNFTLMRELDSRAQDVM 38 (267)
Q Consensus 6 Ledfld~ie~LP~El~r~l~~irelD~~~~~~~ 38 (267)
+.+++.....||.+|.+.=..+++||..+.+-+
T Consensus 180 ~~~i~~la~~L~~DFr~V~~~~r~l~r~lr~~i 212 (478)
T PF11855_consen 180 ARQILQLARELPADFRRVEDNFRELDRALRERI 212 (478)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567888899999999999999999999886543
No 259
>PF11985 DUF3486: Protein of unknown function (DUF3486); InterPro: IPR021874 This entry is represented by Bacteriophage Mu, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.33 E-value=4.8e+02 Score=21.67 Aligned_cols=29 Identities=17% Similarity=0.331 Sum_probs=17.2
Q ss_pred HhhcchHHHHHhHHH-HHHHHHHHHHHHHH
Q psy12696 12 SLDSLPIELQRNFTL-MRELDSRAQDVMKT 40 (267)
Q Consensus 12 ~ie~LP~El~r~l~~-irelD~~~~~~~~~ 40 (267)
.|+-||.||+.-|.. |++-.-...++..+
T Consensus 6 kId~LP~eir~~l~~~L~~~~~t~~ei~~~ 35 (180)
T PF11985_consen 6 KIDLLPPEIREWLDQMLRDGGFTQYEILAE 35 (180)
T ss_pred hHhhCCHHHHHHHHHHHHhCCCChHHHHHH
Confidence 588999999875555 44433333333333
No 260
>COG5560 UBP12 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=21.22 E-value=23 Score=35.96 Aligned_cols=13 Identities=46% Similarity=1.339 Sum_probs=10.3
Q ss_pred CCceeCcCCcCcc
Q psy12696 252 KGKWYCPKCTSDR 264 (267)
Q Consensus 252 ~~~w~C~~C~~~~ 264 (267)
.+.||||.|..-+
T Consensus 693 ~DswyCpgCkefr 705 (823)
T COG5560 693 SDSWYCPGCKEFR 705 (823)
T ss_pred cccccCCchHhhh
Confidence 5689999997654
No 261
>PF09730 BicD: Microtubule-associated protein Bicaudal-D; InterPro: IPR018477 BicD proteins consist of three coiled-coiled domains and are involved in dynein-mediated minus end-directed transport from the Golgi apparatus to the endoplasmic reticulum (ER) []. Glycogen synthase kinase-3beta (GSK-3beta) is required for the binding of BICD to dynein but not to dynactin, acting to maintain the anchoring of microtubules to the centromere []. It appears that amino-acid residues 437-617 of BicD and the kinase activity of GSK-3 are necessary for the formation of a complex between BicD and GSK-3beta in intact cells [].; GO: 0006810 transport, 0005794 Golgi apparatus
Probab=21.18 E-value=9.5e+02 Score=25.05 Aligned_cols=73 Identities=14% Similarity=0.243 Sum_probs=33.6
Q ss_pred HHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCh--hHHHHHHHHHHHHHHHHHHhHHHHH
Q psy12696 10 LDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSK--DKKKETLAEIQKYFDKTKEYGDDKV 82 (267)
Q Consensus 10 ld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~--~~~~~~~~~I~~~~~~~~~lsdEKv 82 (267)
+.-+..|-.||...-..+..+..++.+-...++..++.+......+.. .+..+.+..|+..+..+...+.|.-
T Consensus 365 v~Ev~~Lk~ELk~Lk~k~~~~~~~~~~ek~~~~~e~q~L~ekl~~lek~~re~qeri~~LE~ELr~l~~~A~E~q 439 (717)
T PF09730_consen 365 VSEVIQLKAELKALKSKYNELEERYKQEKDRLESEVQNLKEKLMSLEKSSREDQERISELEKELRALSKLAGESQ 439 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhHH
Confidence 333444555555555555555555544444443333333222111111 1123455566666666666666643
No 262
>COG3599 DivIVA Cell division initiation protein [Cell division and chromosome partitioning]
Probab=21.13 E-value=5.6e+02 Score=22.35 Aligned_cols=36 Identities=8% Similarity=0.285 Sum_probs=19.2
Q ss_pred HHHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHH
Q psy12696 5 YLEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDR 43 (267)
Q Consensus 5 yLedfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~ 43 (267)
.+++|||.|. .++-..+..+++|-.+...+..+|..
T Consensus 27 EVdeFLD~V~---~dye~~l~e~~~l~~~i~~L~~~l~~ 62 (212)
T COG3599 27 EVDEFLDDVI---DDYEQLLDENEDLEDEIDELKEELKE 62 (212)
T ss_pred HHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555665554 45555555555555555555555443
No 263
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=21.13 E-value=9.7e+02 Score=25.10 Aligned_cols=14 Identities=7% Similarity=0.302 Sum_probs=5.5
Q ss_pred HHHHHHHHHHHHHH
Q psy12696 29 ELDSRAQDVMKTID 42 (267)
Q Consensus 29 elD~~~~~~~~~i~ 42 (267)
+...++.+++..++
T Consensus 508 ~~~~~~~~li~~L~ 521 (771)
T TIGR01069 508 EFKEEINVLIEKLS 521 (771)
T ss_pred hhHHHHHHHHHHHH
Confidence 33333444444433
No 264
>TIGR02168 SMC_prok_B chromosome segregation protein SMC, common bacterial type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
Probab=21.09 E-value=1e+03 Score=25.33 Aligned_cols=105 Identities=12% Similarity=0.254 Sum_probs=0.0
Q ss_pred HHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q psy12696 6 LEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLA 85 (267)
Q Consensus 6 Ledfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA 85 (267)
+..|.+.++..=..|.|.-..|.+++.+...+..++... ..|......+..-...-...++.....+...+ ++++.-.
T Consensus 167 ~~~~~~~~~~t~~nL~r~~d~l~el~~ql~~L~~q~~~a-~~~~~~~~~~~~l~~~l~~~~~~~~~~~l~~~-~~~~~~~ 244 (1179)
T TIGR02168 167 ISKYKERRKETERKLERTRENLDRLEDILNELERQLKSL-ERQAEKAERYKELKAELRELELALLVLRLEEL-REELEEL 244 (1179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHH
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 86 IQTYEMVDKYIRKLDTDLARFEQEIQE 112 (267)
Q Consensus 86 ~~a~dlVd~hirrLD~dl~~~e~el~~ 112 (267)
..-++.+..-+..+...+..++..+..
T Consensus 245 ~~~~~~~~~~~~~~~~~~~~~~~~l~~ 271 (1179)
T TIGR02168 245 QEELKEAEEELEELTAELQELEEKLEE 271 (1179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
No 265
>COG4064 MtrG Tetrahydromethanopterin S-methyltransferase, subunit G [Coenzyme metabolism]
Probab=21.06 E-value=2.8e+02 Score=19.92 Aligned_cols=31 Identities=10% Similarity=0.164 Sum_probs=23.4
Q ss_pred hHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 17 PIELQRNFTLMRELDSRAQDVMKTIDRVAED 47 (267)
Q Consensus 17 P~El~r~l~~irelD~~~~~~~~~i~~~~~~ 47 (267)
|.|+......+-++|.++.-...++-+++.+
T Consensus 14 ~~dfne~~kRLdeieekvef~~~Ev~Qr~Gk 44 (75)
T COG4064 14 PDDFNEIHKRLDEIEEKVEFVNGEVYQRIGK 44 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence 7788888888888888888777776666554
No 266
>TIGR00606 rad50 rad50. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.99 E-value=1.2e+03 Score=26.03 Aligned_cols=23 Identities=9% Similarity=0.244 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 88 TYEMVDKYIRKLDTDLARFEQEI 110 (267)
Q Consensus 88 a~dlVd~hirrLD~dl~~~e~el 110 (267)
....+...+++|+.++..+..++
T Consensus 1069 ~~a~l~g~~k~le~qi~~l~~eL 1091 (1311)
T TIGR00606 1069 NHVLALGRQKGYEKEIKHFKKEL 1091 (1311)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444456778888888887777
No 267
>PF14992 TMCO5: TMCO5 family
Probab=20.96 E-value=4.4e+02 Score=24.10 Aligned_cols=21 Identities=5% Similarity=0.248 Sum_probs=9.0
Q ss_pred HHHHHHHHHHHhHHHHHHHHH
Q psy12696 66 EIQKYFDKTKEYGDDKVQLAI 86 (267)
Q Consensus 66 ~I~~~~~~~~~lsdEKv~LA~ 86 (267)
.+.+.|+.+..+..+-+.=+.
T Consensus 134 kve~d~~~v~~l~eDq~~~i~ 154 (280)
T PF14992_consen 134 KVEDDYQQVHQLCEDQANEIK 154 (280)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444444333333
No 268
>PRK06798 fliD flagellar capping protein; Validated
Probab=20.93 E-value=2.1e+02 Score=27.71 Aligned_cols=72 Identities=14% Similarity=0.184 Sum_probs=0.0
Q ss_pred HHHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHhHHHH
Q psy12696 5 YLEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDK 81 (267)
Q Consensus 5 yLedfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEK 81 (267)
||+.|+..--.|.......=..|+.|+.+..++-..++++.+.|.++...|. ..+.+++.....+..+-..|
T Consensus 366 ~l~~~~~~~G~i~~r~~~l~~~i~~l~~~~~~~e~rl~~~e~~l~~qf~ale-----~~ms~lnsQ~s~l~~~~~~~ 437 (440)
T PRK06798 366 SLDKIFGDEGIIGERSKSIDNRVSKLDLKITDIDTQNKQKQDNIVDKYQKLE-----STLAALDSQLKTIKAMTKQK 437 (440)
T ss_pred HHHhhhCCCceeehhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHhccc
No 269
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=20.92 E-value=63 Score=20.19 Aligned_cols=12 Identities=25% Similarity=0.863 Sum_probs=8.1
Q ss_pred CCceeCcCCcCc
Q psy12696 252 KGKWYCPKCTSD 263 (267)
Q Consensus 252 ~~~w~C~~C~~~ 263 (267)
...|.|+.|...
T Consensus 22 ~~~w~C~~C~~~ 33 (40)
T PF04810_consen 22 GKTWICNFCGTK 33 (40)
T ss_dssp TTEEEETTT--E
T ss_pred CCEEECcCCCCc
Confidence 457999999754
No 270
>PRK01917 cation-binding hemerythrin HHE family protein; Provisional
Probab=20.89 E-value=4.3e+02 Score=20.96 Aligned_cols=28 Identities=18% Similarity=0.229 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 82 VQLAIQTYEMVDKYIRKLDTDLARFEQE 109 (267)
Q Consensus 82 v~LA~~a~dlVd~hirrLD~dl~~~e~e 109 (267)
..+..-+.+.+-.||...|..+..|-..
T Consensus 100 ~~l~~~L~~Wl~~HI~~~D~~~~~~l~~ 127 (139)
T PRK01917 100 RRLVAELPEWFDQHVRTMDAMMVSHLKM 127 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3466677888999999999999888543
No 271
>PF11101 DUF2884: Protein of unknown function (DUF2884); InterPro: IPR021307 Some members in this bacterial family of proteins are annotated as YggN which currently has no known function.
Probab=20.82 E-value=5.7e+02 Score=22.33 Aligned_cols=60 Identities=10% Similarity=0.225 Sum_probs=42.6
Q ss_pred CCChhHHHH---HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHH
Q psy12696 54 HYSKDKKKE---TLAEIQKYFDKTKEYGDDKVQLAIQTYEMVD-------KYIRKLDTDLARFEQEIQEK 113 (267)
Q Consensus 54 ~~~~~~~~~---~~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd-------~hirrLD~dl~~~e~el~~~ 113 (267)
.++.+++.. ....|+..+=.+..++.+.|.||..+.+.|- ..-.+|..-+..|...+...
T Consensus 42 ~L~~~Q~q~l~~Y~~~lr~~lP~~~~~a~d~l~la~~ald~V~~~~~g~~~~~~~l~~l~~~l~~~~~~~ 111 (229)
T PF11101_consen 42 SLNAEQQQALQQYQQGLRQQLPWVVQLASDGLELARDALDEVATSLLGDSNARDRLKQLMDQLKQQVDRR 111 (229)
T ss_pred cCCHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHHH
Confidence 355555542 3357899999999999999999999998874 34445666666666655553
No 272
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.77 E-value=2.7e+02 Score=20.97 Aligned_cols=24 Identities=8% Similarity=0.232 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 87 QTYEMVDKYIRKLDTDLARFEQEI 110 (267)
Q Consensus 87 ~a~dlVd~hirrLD~dl~~~e~el 110 (267)
.+..++..|+..|++.+..+...+
T Consensus 81 ~~~~~l~~~~~~l~~~i~~l~~~~ 104 (107)
T cd04777 81 YYKSFLKNKKDELEKEIEDLKKAI 104 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 367888889999998888876543
No 273
>KOG4796|consensus
Probab=20.74 E-value=8.7e+02 Score=24.45 Aligned_cols=86 Identities=17% Similarity=0.361 Sum_probs=50.6
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHH---HhHHHHHHHHHHHHHHHHH
Q psy12696 18 IELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTK---EYGDDKVQLAIQTYEMVDK 94 (267)
Q Consensus 18 ~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~~~~~~~~I~~~~~~~~---~lsdEKv~LA~~a~dlVd~ 94 (267)
.+|.--+.+.|+|-.++..+.....++-.++......-+++ -...-.+|..+|+++. .+.+|| +=++.|..
T Consensus 508 ~dF~~eY~EYreLharve~vs~rF~~Lea~L~srls~gS~e-y~~i~~qI~qEYeki~~dp~y~eeK-----~RceYLhs 581 (604)
T KOG4796|consen 508 KDFEAEYDEYRELHARVETVSRRFRQLEAQLKSRLSPGSPE-YKQIEKQILQEYEKIRKDPNYMEEK-----QRCEYLHS 581 (604)
T ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCc-HHHHHHHHHHHHHHhhcCccHHHHH-----HHHHHHHH
Confidence 45566667788887777777666554444433222222222 2345567888888887 344555 55666666
Q ss_pred HHHHHHHHHHHHHHH
Q psy12696 95 YIRKLDTDLARFEQE 109 (267)
Q Consensus 95 hirrLD~dl~~~e~e 109 (267)
.++.|-.-|..|+..
T Consensus 582 KLaHIK~lI~efDk~ 596 (604)
T KOG4796|consen 582 KLAHIKTLIGEFDKQ 596 (604)
T ss_pred HHHHHHHHHHHHHHh
Confidence 666666666666643
No 274
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=20.65 E-value=22 Score=21.40 Aligned_cols=24 Identities=33% Similarity=0.638 Sum_probs=14.9
Q ss_pred ceecccCccCCCCCCceeCcCCcCc
Q psy12696 239 WFHFACVSLTTKPKGKWYCPKCTSD 263 (267)
Q Consensus 239 wfH~~Cv~l~~~p~~~w~C~~C~~~ 263 (267)
-||..|+..... .+...||.|...
T Consensus 21 ~~c~~C~~~~~~-~~~~~Cp~C~~~ 44 (45)
T cd00162 21 VFCRSCIDKWLK-SGKNTCPLCRTP 44 (45)
T ss_pred hhcHHHHHHHHH-hCcCCCCCCCCc
Confidence 488899862111 145679999753
No 275
>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....
Probab=20.30 E-value=3.8e+02 Score=20.06 Aligned_cols=21 Identities=29% Similarity=0.607 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q psy12696 92 VDKYIRKLDTDLARFEQEIQE 112 (267)
Q Consensus 92 Vd~hirrLD~dl~~~e~el~~ 112 (267)
|...|..|+..+..++.++..
T Consensus 79 lk~~i~~le~~~~~~e~~l~~ 99 (108)
T PF02403_consen 79 LKEEIKELEEQLKELEEELNE 99 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 344466666666666665554
No 276
>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.
Probab=20.28 E-value=9.1e+02 Score=24.46 Aligned_cols=24 Identities=13% Similarity=0.231 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 79 DDKVQLAIQTYEMVDKYIRKLDTD 102 (267)
Q Consensus 79 dEKv~LA~~a~dlVd~hirrLD~d 102 (267)
...+..|+.+.++++.....|...
T Consensus 479 ~~~~~~~~~~~~~l~~~~~~l~~~ 502 (650)
T TIGR03185 479 ERAITIADKAKKTLKEFREKLLER 502 (650)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445666666666666655555544
No 277
>PRK10626 hypothetical protein; Provisional
Probab=20.27 E-value=5.4e+02 Score=22.96 Aligned_cols=40 Identities=10% Similarity=0.120 Sum_probs=31.3
Q ss_pred CCChhHHHH--H-HHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Q psy12696 54 HYSKDKKKE--T-LAEIQKYFDKTKEYGDDKVQLAIQTYEMVD 93 (267)
Q Consensus 54 ~~~~~~~~~--~-~~~I~~~~~~~~~lsdEKv~LA~~a~dlVd 93 (267)
.++..++.. . -..|+..+=++.+++.+.|.+|.++.|.|-
T Consensus 64 ~L~~~Qqq~~~~Yq~~lr~~lP~i~~~a~~~l~~A~~alD~Vi 106 (239)
T PRK10626 64 SLNAAQRQQAKDYQAALRQDLPWIDEGAKSRLEKARVALDKVI 106 (239)
T ss_pred cCCHHHHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHH
Confidence 355555552 2 256888999999999999999999999875
No 278
>PF07851 TMPIT: TMPIT-like protein; InterPro: IPR012926 A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this. ; GO: 0016021 integral to membrane
Probab=20.24 E-value=7.2e+02 Score=23.28 Aligned_cols=44 Identities=18% Similarity=0.298 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHH-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 63 TLAEIQKYFDKTKE-YGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEI 110 (267)
Q Consensus 63 ~~~~I~~~~~~~~~-lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~el 110 (267)
.+..+...++++.. ...|- ....+-++..|++...-+..+|..+
T Consensus 47 rLk~L~~sLk~~~~~~~~e~----~~~i~~L~~~Ik~r~~~l~DmEa~L 91 (330)
T PF07851_consen 47 RLKELKKSLKRCKKSLSAEE----RELIEKLEEDIKERRCQLFDMEAFL 91 (330)
T ss_pred HHHHHHHHHHHhccCCChhH----HHHHHHHHHHHHHHHhhHHHHHhhC
Confidence 34555555555543 22232 3333334444444444444444433
No 279
>KOG0995|consensus
Probab=20.14 E-value=9.1e+02 Score=24.42 Aligned_cols=103 Identities=17% Similarity=0.193 Sum_probs=64.7
Q ss_pred hHHHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhH-------HH---HHHHHHHHHHHH
Q psy12696 4 SYLEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDK-------KK---ETLAEIQKYFDK 73 (267)
Q Consensus 4 ~yLedfld~ie~LP~El~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~~~~~~~~-------~~---~~~~~I~~~~~~ 73 (267)
.|+.++.+--.++|..|.+.=.+|.+...++..+..+.+.+....-.+ .++..+ +. +.+.+|+..++.
T Consensus 280 ~y~~~~~~k~~~~~~~l~~l~~Eie~kEeE~e~lq~~~d~Lk~~Ie~Q--~iS~~dve~mn~Er~~l~r~l~~i~~~~d~ 357 (581)
T KOG0995|consen 280 AYVSQMKSKKQHMEKKLEMLKSEIEEKEEEIEKLQKENDELKKQIELQ--GISGEDVERMNLERNKLKRELNKIQSELDR 357 (581)
T ss_pred HHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 588888888889999999999999999999999988888776654332 445432 22 223344444433
Q ss_pred H-HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12696 74 T-KEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQE 109 (267)
Q Consensus 74 ~-~~lsdEKv~LA~~a~dlVd~hirrLD~dl~~~e~e 109 (267)
. ++.-+.|..+.... +-|......++.-+.++...
T Consensus 358 l~k~vw~~~l~~~~~f-~~le~~~~~~~~l~~~i~l~ 393 (581)
T KOG0995|consen 358 LSKEVWELKLEIEDFF-KELEKKFIDLNSLIRRIKLG 393 (581)
T ss_pred HHHHHHhHHHHHHHHH-HHHHHHHHHHHHHHHHHHHH
Confidence 2 24445555544443 44444466666666555544
No 280
>PRK09841 cryptic autophosphorylating protein tyrosine kinase Etk; Provisional
Probab=20.12 E-value=9.7e+02 Score=24.70 Aligned_cols=51 Identities=10% Similarity=0.171 Sum_probs=32.0
Q ss_pred HHHHHHHHhhcchHHHHHhHHHHHHHHHHHHHHHHHH---HHHHHHHHHhcCCCCh
Q psy12696 5 YLEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTI---DRVAEDYLDNMKHYSK 57 (267)
Q Consensus 5 yLedfld~ie~LP~El~r~l~~irelD~~~~~~~~~i---~~~~~~~~k~~~~~~~ 57 (267)
+.+.|++. ++-.-......-+.-|+.++..+..++ +..++.|.+.++.++.
T Consensus 249 la~~Yi~~--~l~~k~~~a~~a~~fL~~qL~~l~~~L~~aE~~l~~fr~~~~~~d~ 302 (726)
T PRK09841 249 IANNYLQQ--NIARQAAQDSQSLEFLQRQLPEVRSELDQAEEKLNVYRQQRDSVDL 302 (726)
T ss_pred HHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCC
Confidence 44445532 222334444556778888888887775 5568888887766553
No 281
>TIGR01013 2a58 Phosphate:Na+ Symporter (PNaS) Family.
Probab=20.12 E-value=7.8e+02 Score=23.66 Aligned_cols=20 Identities=15% Similarity=0.024 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q psy12696 81 KVQLAIQTYEMVDKYIRKLD 100 (267)
Q Consensus 81 Kv~LA~~a~dlVd~hirrLD 100 (267)
|..+-.-..++-++|++||.
T Consensus 413 ~~~i~~l~~~~~~~h~~rl~ 432 (456)
T TIGR01013 413 KIPFRILELFSSLLHVLQLR 432 (456)
T ss_pred ccHHHHHHHHHHHHHHHHHc
Confidence 33333333444444554443
No 282
>PF05596 Taeniidae_ag: Taeniidae antigen; InterPro: IPR008860 This family consists of several antigen proteins from Taenia and Echinococcus (tapeworm) species.
Probab=20.08 E-value=3e+02 Score=19.31 Aligned_cols=32 Identities=22% Similarity=0.355 Sum_probs=26.7
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy12696 21 QRNFTLMRELDSRAQDVMKTIDRVAEDYLDNM 52 (267)
Q Consensus 21 ~r~l~~irelD~~~~~~~~~i~~~~~~~~k~~ 52 (267)
|.+..+.+++.+-+++++..|...+.+|++..
T Consensus 30 qkIa~l~kdw~~~~~~~r~KiR~~L~ey~k~L 61 (64)
T PF05596_consen 30 QKIAQLAKDWNEICQEVRKKIRAALAEYCKGL 61 (64)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 56668889999999999999998888888753
Done!