Query 024980
Match_columns 259
No_of_seqs 191 out of 1174
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 09:00:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024980.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024980hhsearch_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 1.7E-38 3.7E-43 274.5 18.6 241 5-255 2-270 (271)
2 KOG1973 Chromatin remodeling p 100.0 5.3E-35 1.1E-39 262.8 14.4 244 4-258 4-271 (274)
3 PF12998 ING: Inhibitor of gro 99.9 2.6E-24 5.7E-29 166.5 12.1 104 8-118 1-105 (105)
4 PF00628 PHD: PHD-finger; Int 98.9 2.2E-10 4.9E-15 77.2 0.6 46 205-254 1-50 (51)
5 smart00249 PHD PHD zinc finger 98.7 7.4E-09 1.6E-13 67.4 2.7 44 205-252 1-47 (47)
6 PF13831 PHD_2: PHD-finger; PD 97.6 1.3E-05 2.8E-10 50.3 -0.3 35 214-253 2-36 (36)
7 KOG4323 Polycomb-like PHD Zn-f 97.5 3.2E-05 7E-10 73.8 1.1 51 203-257 171-226 (464)
8 KOG0954 PHD finger protein [Ge 97.4 5.8E-05 1.2E-09 74.9 1.0 52 197-254 265-320 (893)
9 KOG1512 PHD Zn-finger protein 97.2 0.0001 2.2E-09 66.0 0.5 42 207-254 319-362 (381)
10 KOG0956 PHD finger protein AF1 97.2 0.00017 3.7E-09 71.2 1.6 50 203-256 6-58 (900)
11 KOG4299 PHD Zn-finger protein 97.1 0.00019 4.1E-09 70.3 1.3 51 203-257 253-307 (613)
12 KOG1632 Uncharacterized PHD Zn 96.9 0.00037 8E-09 65.0 1.3 48 203-254 60-112 (345)
13 KOG0825 PHD Zn-finger protein 96.6 0.0011 2.4E-08 66.5 2.4 51 201-256 213-267 (1134)
14 KOG0955 PHD finger protein BR1 96.3 0.0031 6.7E-08 66.0 3.3 51 200-256 217-270 (1051)
15 KOG0383 Predicted helicase [Ge 95.4 0.0065 1.4E-07 61.2 1.5 52 198-255 43-94 (696)
16 COG5141 PHD zinc finger-contai 95.3 0.0052 1.1E-07 59.0 0.3 44 205-254 195-242 (669)
17 KOG1245 Chromatin remodeling c 95.2 0.0041 8.9E-08 67.3 -0.7 48 203-256 1108-1159(1404)
18 KOG0957 PHD finger protein [Ge 95.1 0.022 4.7E-07 54.9 3.9 46 204-253 121-177 (707)
19 KOG1244 Predicted transcriptio 94.8 0.011 2.4E-07 52.9 0.8 49 203-257 281-333 (336)
20 KOG0957 PHD finger protein [Ge 94.2 1.8 3.9E-05 42.2 14.2 45 204-252 545-595 (707)
21 KOG1632 Uncharacterized PHD Zn 93.4 0.012 2.7E-07 54.9 -1.7 53 198-254 234-294 (345)
22 KOG2752 Uncharacterized conser 92.7 0.048 1E-06 49.8 1.1 30 202-235 127-164 (345)
23 KOG1844 PHD Zn-finger proteins 92.4 0.069 1.5E-06 52.0 1.8 52 201-257 84-137 (508)
24 PF13771 zf-HC5HC2H: PHD-like 89.4 0.2 4.3E-06 37.1 1.5 30 204-236 37-67 (90)
25 PF13832 zf-HC5HC2H_2: PHD-zin 87.0 0.32 7E-06 37.4 1.3 31 202-235 55-85 (110)
26 PF13341 RAG2_PHD: RAG2 PHD do 86.0 0.22 4.9E-06 35.6 -0.1 35 215-252 29-68 (78)
27 PF07227 DUF1423: Protein of u 80.9 1.2 2.6E-05 42.8 2.6 49 205-257 131-194 (446)
28 PRK15365 type III secretion sy 79.7 22 0.00048 27.2 8.5 83 26-118 6-92 (107)
29 PF08746 zf-RING-like: RING-li 79.3 0.38 8.3E-06 31.1 -0.9 39 208-252 4-43 (43)
30 PF10497 zf-4CXXC_R1: Zinc-fin 75.3 2 4.4E-05 33.3 1.9 53 200-254 4-69 (105)
31 PF01396 zf-C4_Topoisom: Topoi 68.7 2.6 5.7E-05 26.6 1.0 19 213-231 18-37 (39)
32 KOG0994 Extracellular matrix g 65.8 76 0.0017 34.6 11.2 35 85-119 1570-1604(1758)
33 PF03148 Tektin: Tektin family 63.9 1.3E+02 0.0029 28.4 12.1 109 10-119 253-365 (384)
34 TIGR00634 recN DNA repair prot 62.3 53 0.0012 32.6 9.3 103 6-118 285-398 (563)
35 PHA02825 LAP/PHD finger-like p 60.5 3.7 8E-05 34.2 0.6 47 203-254 8-56 (162)
36 KOG1493 Anaphase-promoting com 59.2 3.8 8.2E-05 30.0 0.4 49 205-256 22-80 (84)
37 PF03194 LUC7: LUC7 N_terminus 58.8 76 0.0016 28.4 8.8 74 28-109 89-163 (254)
38 COG1382 GimC Prefoldin, chaper 58.7 91 0.002 24.8 13.6 107 17-124 1-109 (119)
39 PF10146 zf-C4H2: Zinc finger- 58.4 95 0.002 27.4 9.2 25 215-255 193-217 (230)
40 PF05781 MRVI1: MRVI1 protein; 57.8 1.7E+02 0.0037 29.1 11.6 27 97-123 290-316 (538)
41 PF10046 BLOC1_2: Biogenesis o 57.5 41 0.00089 25.5 6.0 46 7-52 44-89 (99)
42 KOG1512 PHD Zn-finger protein 56.1 2.5 5.4E-05 38.5 -1.1 49 201-253 259-315 (381)
43 KOG4460 Nuclear pore complex, 55.5 1.3E+02 0.0029 30.1 10.3 35 7-41 569-604 (741)
44 PF04668 Tsg: Twisted gastrula 54.8 4.7 0.0001 32.6 0.4 28 224-252 100-130 (132)
45 PRK10869 recombination and rep 54.0 1.8E+02 0.0039 29.0 11.4 105 8-118 282-393 (553)
46 KOG4443 Putative transcription 52.9 3.7 8.1E-05 41.2 -0.6 39 214-256 33-72 (694)
47 COG5415 Predicted integral mem 52.4 8.8 0.00019 33.5 1.6 33 217-257 193-225 (251)
48 PF10168 Nup88: Nuclear pore c 50.7 2.3E+02 0.0051 29.3 11.8 25 9-33 548-572 (717)
49 KOG1473 Nucleosome remodeling 49.1 12 0.00026 40.1 2.3 43 205-253 346-389 (1414)
50 PF08203 RNA_polI_A14: Yeast R 48.8 31 0.00067 25.2 3.8 52 4-56 16-72 (76)
51 PF12861 zf-Apc11: Anaphase-pr 48.1 8.8 0.00019 28.7 0.9 23 230-255 56-80 (85)
52 PF12678 zf-rbx1: RING-H2 zinc 48.1 3.9 8.5E-05 29.3 -1.0 43 205-253 22-73 (73)
53 PF09755 DUF2046: Uncharacteri 47.2 2.4E+02 0.0051 26.2 13.4 42 78-119 150-191 (310)
54 PF12718 Tropomyosin_1: Tropom 46.5 1.6E+02 0.0034 23.9 11.8 37 86-122 95-131 (143)
55 PRK09343 prefoldin subunit bet 46.4 1.4E+02 0.0031 23.4 9.1 98 18-123 3-109 (121)
56 COG5194 APC11 Component of SCF 46.2 5.8 0.00012 29.3 -0.3 45 206-255 23-79 (88)
57 PF11690 DUF3287: Protein of u 45.9 75 0.0016 24.8 5.8 46 74-119 39-85 (109)
58 KOG1244 Predicted transcriptio 45.8 4.7 0.0001 36.5 -1.0 47 203-253 224-282 (336)
59 PF04111 APG6: Autophagy prote 45.7 2.5E+02 0.0053 25.9 12.5 28 20-47 41-68 (314)
60 PRK11637 AmiB activator; Provi 44.0 2.9E+02 0.0063 26.3 12.1 19 22-40 47-65 (428)
61 PF11932 DUF3450: Protein of u 43.6 2.3E+02 0.0049 24.9 10.5 24 83-106 90-113 (251)
62 PF10796 Anti-adapt_IraP: Sigm 43.3 1.4E+02 0.003 22.4 8.1 77 24-111 5-81 (87)
63 PF14319 Zn_Tnp_IS91: Transpos 43.0 20 0.00043 27.9 2.2 37 207-255 32-69 (111)
64 PF07649 C1_3: C1-like domain; 42.4 6.8 0.00015 23.0 -0.4 25 207-235 5-30 (30)
65 KOG4443 Putative transcription 42.2 15 0.00033 37.1 1.8 36 214-255 81-118 (694)
66 KOG4628 Predicted E3 ubiquitin 41.7 17 0.00038 34.0 2.0 45 204-255 231-276 (348)
67 PRK14127 cell division protein 41.3 89 0.0019 24.4 5.6 37 10-49 28-64 (109)
68 PF04100 Vps53_N: Vps53-like, 41.1 3.2E+02 0.0069 25.9 12.6 89 15-120 18-106 (383)
69 COG0497 RecN ATPase involved i 39.7 2E+02 0.0044 28.8 9.1 106 6-118 281-394 (557)
70 PF00645 zf-PARP: Poly(ADP-rib 38.9 9.2 0.0002 27.7 -0.2 10 228-237 39-48 (82)
71 KOG1655 Protein involved in va 38.0 88 0.0019 27.1 5.5 31 95-125 22-52 (218)
72 KOG1671 Ubiquinol cytochrome c 37.2 17 0.00037 31.4 1.1 22 231-253 155-177 (210)
73 PF08702 Fib_alpha: Fibrinogen 37.1 2.3E+02 0.005 23.1 13.7 43 78-120 90-132 (146)
74 smart00744 RINGv The RING-vari 36.2 5.4 0.00012 26.4 -1.7 28 224-253 21-49 (49)
75 PF06160 EzrA: Septation ring 36.0 4.5E+02 0.0098 26.2 12.6 43 74-116 168-211 (560)
76 PTZ00396 Casein kinase II subu 35.3 28 0.0006 31.2 2.2 20 235-254 136-156 (251)
77 PF00130 C1_1: Phorbol esters/ 35.2 36 0.00078 22.1 2.3 35 202-240 10-48 (53)
78 KOG0996 Structural maintenance 34.4 6.1E+02 0.013 28.0 11.9 44 77-120 885-928 (1293)
79 KOG2932 E3 ubiquitin ligase in 34.3 18 0.00039 33.5 0.8 39 203-254 90-131 (389)
80 cd00632 Prefoldin_beta Prefold 33.5 2.1E+02 0.0046 21.6 12.2 98 12-124 3-102 (105)
81 PRK04778 septation ring format 33.3 4.7E+02 0.01 26.1 10.7 47 72-118 170-217 (569)
82 COG1579 Zn-ribbon protein, pos 33.2 3.5E+02 0.0076 24.1 10.8 32 21-52 2-33 (239)
83 cd04476 RPA1_DBD_C RPA1_DBD_C: 32.7 28 0.0006 28.6 1.7 28 228-255 31-60 (166)
84 KOG0971 Microtubule-associated 31.5 6.9E+02 0.015 27.0 13.2 53 75-127 305-360 (1243)
85 PF09755 DUF2046: Uncharacteri 31.3 4.3E+02 0.0093 24.5 12.8 36 80-115 109-151 (310)
86 PF13901 DUF4206: Domain of un 31.3 30 0.00065 29.7 1.7 31 215-258 171-201 (202)
87 PF11101 DUF2884: Protein of u 31.2 3.6E+02 0.0078 23.6 8.5 53 71-123 50-109 (229)
88 KOG1510 RNA polymerase II holo 31.1 2.9E+02 0.0063 22.5 8.2 31 16-46 75-108 (139)
89 KOG3612 PHD Zn-finger protein 31.1 52 0.0011 32.7 3.4 48 201-254 58-107 (588)
90 PRK11546 zraP zinc resistance 31.0 3E+02 0.0064 22.6 11.0 32 17-48 41-73 (143)
91 PF03234 CDC37_N: Cdc37 N term 30.7 3.3E+02 0.0072 23.0 8.5 108 11-123 42-155 (177)
92 KOG2626 Histone H3 (Lys4) meth 30.5 33 0.00072 33.9 2.0 51 201-255 18-76 (544)
93 PF07496 zf-CW: CW-type Zinc F 30.1 28 0.00061 23.0 1.1 31 216-251 3-34 (50)
94 PHA02862 5L protein; Provision 29.9 14 0.0003 30.4 -0.6 27 227-255 25-51 (156)
95 cd00890 Prefoldin Prefoldin is 29.7 2.5E+02 0.0055 21.4 6.7 43 81-123 83-125 (129)
96 PHA02562 46 endonuclease subun 29.4 5.4E+02 0.012 25.0 13.4 27 20-46 297-323 (562)
97 PF09726 Macoilin: Transmembra 29.0 6.7E+02 0.014 26.0 11.3 99 19-124 457-563 (697)
98 PHA02562 46 endonuclease subun 28.3 5.6E+02 0.012 24.9 13.8 31 73-103 216-246 (562)
99 KOG4451 Uncharacterized conser 28.3 4.3E+02 0.0093 23.6 9.0 41 8-48 50-90 (286)
100 PF10367 Vps39_2: Vacuolar sor 27.9 47 0.001 24.6 2.1 26 205-235 80-107 (109)
101 KOG2685 Cystoskeletal protein 27.9 5.6E+02 0.012 24.8 11.6 104 11-117 281-390 (421)
102 PF15233 SYCE1: Synaptonemal c 27.9 3.3E+02 0.0071 22.0 7.6 15 82-96 39-53 (134)
103 PF08946 Osmo_CC: Osmosensory 27.5 77 0.0017 20.8 2.7 26 95-120 8-33 (46)
104 PF09986 DUF2225: Uncharacteri 27.4 49 0.0011 28.7 2.4 42 203-253 5-55 (214)
105 PRK10626 hypothetical protein; 27.4 2.7E+02 0.0059 24.8 7.0 46 72-117 73-129 (239)
106 PF00641 zf-RanBP: Zn-finger i 27.3 32 0.00069 20.0 0.8 12 244-255 2-13 (30)
107 PF12999 PRKCSH-like: Glucosid 27.3 3.9E+02 0.0084 22.7 7.8 41 79-119 133-173 (176)
108 COG2433 Uncharacterized conser 26.8 7E+02 0.015 25.5 11.6 30 19-48 412-441 (652)
109 PF13851 GAS: Growth-arrest sp 26.7 4.1E+02 0.0089 22.8 14.1 91 24-120 22-114 (201)
110 PRK14811 formamidopyrimidine-D 26.6 37 0.00081 30.5 1.5 15 243-257 252-266 (269)
111 cd07591 BAR_Rvs161p The Bin/Am 26.5 4.2E+02 0.0092 23.0 8.1 22 88-109 147-168 (224)
112 KOG1941 Acetylcholine receptor 26.5 5.7 0.00012 37.7 -3.8 47 201-253 363-412 (518)
113 PF15353 HECA: Headcase protei 26.5 22 0.00048 27.6 0.0 20 216-235 30-49 (107)
114 TIGR02338 gimC_beta prefoldin, 25.8 3E+02 0.0066 20.9 11.9 42 81-122 63-104 (110)
115 PRK11637 AmiB activator; Provi 25.6 5.9E+02 0.013 24.2 11.1 23 23-45 69-91 (428)
116 PF00261 Tropomyosin: Tropomyo 25.1 4.6E+02 0.01 22.8 14.7 44 80-123 171-214 (237)
117 PF11793 FANCL_C: FANCL C-term 25.1 32 0.00069 24.4 0.7 47 207-255 7-64 (70)
118 COG5185 HEC1 Protein involved 25.0 6.9E+02 0.015 24.8 10.0 23 10-32 266-288 (622)
119 PF14446 Prok-RING_1: Prokaryo 24.9 46 0.001 22.7 1.4 29 203-235 5-36 (54)
120 PF05384 DegS: Sensor protein 24.8 4.1E+02 0.0088 22.1 13.9 104 10-121 15-127 (159)
121 PF10146 zf-C4H2: Zinc finger- 24.8 4.9E+02 0.011 23.0 12.3 25 22-46 18-42 (230)
122 KOG0612 Rho-associated, coiled 24.7 6.9E+02 0.015 27.7 10.4 26 17-42 436-461 (1317)
123 PF05130 FlgN: FlgN protein; 24.4 3.2E+02 0.0069 20.7 9.1 18 98-115 105-122 (143)
124 KOG4796 RNA polymerase II elon 24.4 7.4E+02 0.016 24.9 11.4 86 22-121 508-596 (604)
125 PF06008 Laminin_I: Laminin Do 24.3 4.9E+02 0.011 22.9 10.4 107 15-121 123-235 (264)
126 PF01214 CK_II_beta: Casein ki 24.1 37 0.00081 28.9 1.0 20 235-254 115-135 (184)
127 PRK01103 formamidopyrimidine/5 24.0 41 0.0009 30.2 1.3 13 243-255 262-274 (274)
128 KOG2196 Nuclear porin [Nuclear 23.7 5.4E+02 0.012 23.1 12.4 37 87-123 166-202 (254)
129 PF12095 DUF3571: Protein of u 22.9 77 0.0017 23.5 2.3 35 4-42 27-61 (83)
130 PF10979 DUF2786: Protein of u 22.9 1.8E+02 0.0038 18.7 3.8 32 76-107 4-38 (43)
131 smart00547 ZnF_RBZ Zinc finger 22.9 36 0.00077 18.9 0.4 10 245-254 1-10 (26)
132 cd07588 BAR_Amphiphysin The Bi 22.5 5.1E+02 0.011 22.4 8.4 20 89-108 143-162 (211)
133 PRK14127 cell division protein 22.5 1.9E+02 0.0042 22.5 4.6 43 5-47 27-69 (109)
134 PF00616 RasGAP: GTPase-activa 22.5 1.1E+02 0.0024 25.4 3.6 33 6-38 106-138 (197)
135 KOG4360 Uncharacterized coiled 22.3 8E+02 0.017 24.6 12.4 46 73-119 236-281 (596)
136 PF15619 Lebercilin: Ciliary p 21.9 5.1E+02 0.011 22.1 13.3 37 10-46 49-85 (194)
137 KOG1029 Endocytic adaptor prot 21.9 6.1E+02 0.013 26.9 9.0 24 18-41 440-463 (1118)
138 COG0266 Nei Formamidopyrimidin 21.8 36 0.00078 30.9 0.5 12 243-254 262-273 (273)
139 KOG3970 Predicted E3 ubiquitin 21.5 59 0.0013 28.8 1.7 44 206-255 53-103 (299)
140 PF05769 DUF837: Protein of un 21.3 5.1E+02 0.011 21.9 11.5 99 17-121 5-103 (181)
141 PRK14011 prefoldin subunit alp 21.2 2.5E+02 0.0053 22.9 5.2 43 81-123 84-126 (144)
142 PF02996 Prefoldin: Prefoldin 21.0 3.7E+02 0.0081 20.3 6.4 38 85-122 77-114 (120)
143 COG0723 QcrA Rieske Fe-S prote 21.0 59 0.0013 27.0 1.6 23 223-250 107-129 (177)
144 PF13922 PHD_3: PHD domain of 20.9 29 0.00063 24.6 -0.2 28 203-237 33-60 (69)
145 PF11781 RRN7: RNA polymerase 20.3 87 0.0019 19.3 1.8 26 216-254 8-33 (36)
146 cd04772 HTH_TioE_rpt1 First He 20.3 1.5E+02 0.0031 22.3 3.5 24 98-121 75-98 (99)
147 KOG3799 Rab3 effector RIM1 and 20.2 43 0.00093 27.3 0.6 49 203-255 66-116 (169)
148 PRK13267 archaemetzincin-like 20.0 23 0.00049 30.1 -1.1 13 244-256 161-173 (179)
No 1
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=100.00 E-value=1.7e-38 Score=274.54 Aligned_cols=241 Identities=25% Similarity=0.412 Sum_probs=151.0
Q ss_pred chhhHHHHHHHHhhCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCchHHHHHHHHHHHHHHH
Q 024980 5 RTGVYVDDYLEYASTLPAELQRLLNTIRELDERSHSMINQTRQQTKYCLGLASQGNKKGNGNEEDEAIEKMRKEIEVNQD 84 (259)
Q Consensus 5 ~~~~yLedfle~ie~LP~El~r~l~~IreLD~~~~~~~~~l~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~ 84 (259)
.....|+||+|.|+|+|.|+.+.|++|.++|.++.++++.+.+.....+...+.++ +...+..+.+.+.|++.+-
T Consensus 2 d~~~~Lnd~~d~l~n~P~et~~~~t~l~~iD~k~~d~~k~l~q~~si~k~~~~~~~-----~t~~e~ed~l~k~i~Ell~ 76 (271)
T COG5034 2 DLFPGLNDITDHLANVPSETDIRFTELSEIDAKVCDIIKNLRQMISILKKIIDLDS-----QTYEEVEDGLLKEIRELLL 76 (271)
T ss_pred chhHHHHHHHHHHHhCChhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhhccc-----CccccchhHHHHHHHHHHH
Confidence 34567999999999999999999999999999999999988775442222222222 2334456788899999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHhhCCCC----CCCCC-CCCCCC---CcccccccCCC
Q 024980 85 NALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNFAED-----LKQEGKIP----ADEPA-ILPPLP---IIPKIEKRKPF 151 (259)
Q Consensus 85 ~~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~~~-----L~~~~~~~----~~~~~-~~~~~~---~~~~~~~~~~~ 151 (259)
.++.+..+|+.||+.+..+++||+++||..+++.... ++..+... ....+ .....+ ..+.+. ..+
T Consensus 77 ~a~~~~~~~~~l~d~~~~l~~Rh~~~~d~~~a~~~h~~~~~~ie~~~~~~s~~~~~~~ss~a~~ss~~~~saass--qgs 154 (271)
T COG5034 77 KAIYIQKEKSDLADRAEKLLRRHRKLLDDRIAKRPHEKVAARIENCHDAVSRLERNSYSSAARRSSGEHRSAASS--QGS 154 (271)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHhhhhhhhhhhhhhhhhhhhhhhccccchhhhcccccccccccc--ccc
Confidence 9999999999999999999999999999988764332 22211110 00000 000000 000000 000
Q ss_pred CCCCCCccccccCCcc-----cccccccccCCCC-CCCC-------CccCCCCCCC--CCCCCCCCCcceecCCCCCCCc
Q 024980 152 YGTPQPKRLDFRDRDW-----DRERDRDFELMPP-PGSQ-------KREFTTPMDV--DQPIDPNEPTYCVCHQVSFGDM 216 (259)
Q Consensus 152 ~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~-~~~~-------~~~~~~~~~~--~~~~~~~~~~~C~C~~~~~g~m 216 (259)
.-++..+|.+...... .+.+...++..++ .... .-...++.+. ..+...++++||+|++|+||+|
T Consensus 155 ~~t~~~~R~n~~~~k~~~p~~~S~r~~~~t~~sp~v~~t~t~v~e~~~~~s~~~~~vss~d~se~e~lYCfCqqvSyGqM 234 (271)
T COG5034 155 RHTKLKKRKNIHNLKRRSPELSSKREVSFTLESPSVPDTATRVKEGNNGGSTKSRGVSSEDNSEGEELYCFCQQVSYGQM 234 (271)
T ss_pred cCchhHHHHhhcccccCCcchhhhccCCccCCCCCcccchhhhhcccCCCCccccCcCccccccCceeEEEecccccccc
Confidence 0011111111100000 0011111111000 0000 0000111111 1234567899999999999999
Q ss_pred cccCCCCCCCCceeecccCCCCCCCCCCCceeccccccc
Q 024980 217 IACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCRLL 255 (259)
Q Consensus 217 i~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~~~ 255 (259)
|+|||++|+ +||||+.||||..+| +|+||||+|...
T Consensus 235 VaCDn~nCk-rEWFH~~CVGLk~pP--KG~WYC~eCk~~ 270 (271)
T COG5034 235 VACDNANCK-REWFHLECVGLKEPP--KGKWYCPECKKA 270 (271)
T ss_pred eecCCCCCc-hhheeccccccCCCC--CCcEeCHHhHhc
Confidence 999999999 999999999999999 999999999864
No 2
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=100.00 E-value=5.3e-35 Score=262.79 Aligned_cols=244 Identities=28% Similarity=0.505 Sum_probs=149.2
Q ss_pred cchhhHHHHHHHH----hhCChHHHHHHHHHHHHHHHH--HHHHHHHHH--HHHHHHHhhhcCCCCCCCCCCchHHHHHH
Q 024980 4 ARTGVYVDDYLEY----ASTLPAELQRLLNTIRELDER--SHSMINQTR--QQTKYCLGLASQGNKKGNGNEEDEAIEKM 75 (259)
Q Consensus 4 ~~~~~yLedfle~----ie~LP~El~r~l~~IreLD~~--~~~~~~~l~--~~~k~~~~~~~~~~~~~~~~~~~~~~~~~ 75 (259)
.-.+.+++++++. +.+||..++++|..|.++|.. ..+...++. ....|+....+. ...+.....
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~l~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~--------~~~~~~~~~ 75 (274)
T KOG1973|consen 4 LDQAILIEEVDDDIDMAVQNLPRNLQHNFDVIEDIDIFGRSENQKKELDLKVAVEYMSKGRSQ--------LSKPQKDPL 75 (274)
T ss_pred cchhhhhhhcccccccccccCCccchhHHHHHhhhhccchhHHHHhhhhhhhhhccccccccc--------cCccccchh
Confidence 3456788888888 999999999999999999994 455545443 223344332210 111233466
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC-CCCCCCCCCCCCCCCc-ccccccCC---
Q 024980 76 RKEIEVNQDNALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNFAEDLKQEG-KIPADEPAILPPLPII-PKIEKRKP--- 150 (259)
Q Consensus 76 ~~~I~~~~~~~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~~~L~~~~-~~~~~~~~~~~~~~~~-~~~~~~~~--- 150 (259)
...|++.+....++++||+++|.+++++|.+|+++++..++.|+.++.... .............+.. +...+.+.
T Consensus 76 ~~~~~~~~~~~~~~~~ek~~~~~~~~e~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~ 155 (274)
T KOG1973|consen 76 LEAIRSALRKCKELSDEKVQIAMQTVELIPKHIGRLETALKSFEVELELAKAESSSKRSSSLKSAKKKEREVFKEKKESK 155 (274)
T ss_pred HHHHHHHHhhhhhhhhHHHHHHHHHHHhhHhhhcchhHHHHhcccchhhhhhhcccccccchhccCccccccccchhhcC
Confidence 778999999999999999999999999999999999999997776654332 1111100000000000 00000000
Q ss_pred --CCCCCCCcc------ccccCCcccccccccccCCCCCCCCC-ccC--CCCCCCCCCCCCCCCcceecCCCCCCCcccc
Q 024980 151 --FYGTPQPKR------LDFRDRDWDRERDRDFELMPPPGSQK-REF--TTPMDVDQPIDPNEPTYCVCHQVSFGDMIAC 219 (259)
Q Consensus 151 --~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~--~~~~~~~~~~~~~~~~~C~C~~~~~g~mi~C 219 (259)
....++... .........+++...+..+....+.. ... ....+.+...++++++||+|++++||+||+|
T Consensus 156 ~~~~~~~s~~~~~~~~~~~~~~~~~~rekk~~v~~~~~~~t~~~~~s~~~~~~~~~~~~d~~e~~yC~Cnqvsyg~Mi~C 235 (274)
T KOG1973|consen 156 QGSSEKPSSVDKAKKGSKVNRRPCGAREKKRKVVEAKKEKTPKNKSSRPAESMESEEAVDPDEPTYCICNQVSYGKMIGC 235 (274)
T ss_pred CCCCCCcccccccccccccccccchhhhhhhhhccccccccccCCCCCcccccccccccCCCCCEEEEeccccccccccc
Confidence 000000000 00000000011110000000000000 000 0112335678999999999999999999999
Q ss_pred CCCCCCCCceeecccCCCCCCCCCCCceeccccccccCC
Q 024980 220 DNENCQGGEWFHYACVGLTPETRFKGKWYCPTCRLLPQC 258 (259)
Q Consensus 220 d~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~~~~~~ 258 (259)
||++|+ |+||||.||||+.+| +|+||||.|+....+
T Consensus 236 Dn~~C~-~eWFH~~CVGL~~~P--kgkWyC~~C~~~~~~ 271 (274)
T KOG1973|consen 236 DNPGCP-IEWFHFTCVGLKTKP--KGKWYCPRCKAENKK 271 (274)
T ss_pred CCCCCC-cceEEEeccccccCC--CCcccchhhhhhhhc
Confidence 999999 999999999999999 999999999976543
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=99.92 E-value=2.6e-24 Score=166.52 Aligned_cols=104 Identities=43% Similarity=0.681 Sum_probs=87.8
Q ss_pred hHHHHHHHHhhCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHhhhcCCCCCCCCCCchHHHHHHHHHHHHHHHHH
Q 024980 8 VYVDDYLEYASTLPAELQRLLNTIRELDERSHSMINQTRQQTK-YCLGLASQGNKKGNGNEEDEAIEKMRKEIEVNQDNA 86 (259)
Q Consensus 8 ~yLedfle~ie~LP~El~r~l~~IreLD~~~~~~~~~l~~~~k-~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~ 86 (259)
+|||+|++++++||.||+|+|++||+||.+++++..++++... |+....+. +.. .+....+..+|+..+.++
T Consensus 1 ~~le~f~d~~~~LP~el~r~l~~irelD~~~~~~~~~~~~~~~~~~~~~~~~------~~~-~~~~~~~~~~I~~~~~~~ 73 (105)
T PF12998_consen 1 TYLEDFLDSLENLPAELQRNLTLIRELDAKSQDLLEELDQQIQKFIKNHGSP------SLS-PEKRRELLKEIQEEYERA 73 (105)
T ss_dssp HHHHHHHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTS--------S--HHHHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHChHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhcccc------cCC-hHHHHHHHHHHHHHHHHH
Confidence 6999999999999999999999999999999999999988765 54333221 112 236678899999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 87 LSLCTEKVLLARQAYDIIDSHIKRLDEDLNNF 118 (259)
Q Consensus 87 ~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~ 118 (259)
+.+++|||.||+++|++|++|++|||.++++|
T Consensus 74 ~~l~deKv~lA~~~~d~v~~hi~rLD~dl~~f 105 (105)
T PF12998_consen 74 LELSDEKVALAQQAYDLVDRHIRRLDQDLKKF 105 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHCT---
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 99999999999999999999999999999876
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=98.93 E-value=2.2e-10 Score=77.17 Aligned_cols=46 Identities=52% Similarity=1.325 Sum_probs=38.1
Q ss_pred ce-ecCCCC-CCCccccCCCCCCCCceeecccCCCCCCCC--CCCceecccccc
Q 024980 205 YC-VCHQVS-FGDMIACDNENCQGGEWFHYACVGLTPETR--FKGKWYCPTCRL 254 (259)
Q Consensus 205 ~C-~C~~~~-~g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~--~~~~w~C~~C~~ 254 (259)
|| +|+++. .++||.|| .|. .|||..|+|++..+. ..+.|+|+.|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~--~C~--~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCD--SCN--RWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBS--TTS--CEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcC--CCC--hhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 68 899965 46999999 899 999999999987731 245999999975
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 PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=97.58 E-value=1.3e-05 Score=50.27 Aligned_cols=35 Identities=29% Similarity=0.848 Sum_probs=19.7
Q ss_pred CCccccCCCCCCCCceeecccCCCCCCCCCCCceeccccc
Q 024980 214 GDMIACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCR 253 (259)
Q Consensus 214 g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~ 253 (259)
..||.|+ .|. -++|.+|.|+...+. .+.|+|..|+
T Consensus 2 n~ll~C~--~C~--v~VH~~CYGv~~~~~-~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCD--NCN--VAVHQSCYGVSEVPD-GDDWLCDRCE 36 (36)
T ss_dssp CEEEE-S--SS----EEEHHHHT-SS--S-S-----HHH-
T ss_pred CceEEeC--CCC--CcCChhhCCcccCCC-CCcEECCcCC
Confidence 4689999 899 889999999999983 2279999884
No 7
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=97.50 E-value=3.2e-05 Score=73.81 Aligned_cols=51 Identities=27% Similarity=0.753 Sum_probs=38.0
Q ss_pred CcceecCCCCC-CCccccCCCCCCCCceeecccCCCCCCC--C--CCCceeccccccccC
Q 024980 203 PTYCVCHQVSF-GDMIACDNENCQGGEWFHYACVGLTPET--R--FKGKWYCPTCRLLPQ 257 (259)
Q Consensus 203 ~~~C~C~~~~~-g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~--~--~~~~w~C~~C~~~~~ 257 (259)
--||+|.++.. ..||+|+ .|. .|||-.|.--...+ + ....|||-.|...+.
T Consensus 171 c~vC~~g~~~~~NrmlqC~--~C~--~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~ 226 (464)
T KOG4323|consen 171 CSVCYCGGPGAGNRMLQCD--KCR--QWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPK 226 (464)
T ss_pred eeeeecCCcCccceeeeec--ccc--cHHHHHhccCCCCHhhccCccceEeehhhccchh
Confidence 56777777753 3899999 899 99999998633332 1 356999999986543
No 8
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=97.37 E-value=5.8e-05 Score=74.92 Aligned_cols=52 Identities=37% Similarity=0.869 Sum_probs=44.6
Q ss_pred CCCCCCCcce-ecCCCCC---CCccccCCCCCCCCceeecccCCCCCCCCCCCceecccccc
Q 024980 197 PIDPNEPTYC-VCHQVSF---GDMIACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCRL 254 (259)
Q Consensus 197 ~~~~~~~~~C-~C~~~~~---g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~~ 254 (259)
.+.-++.+.| +|+.+.. .+||.|| .|. .-+|..|.||.+.| .|.|.|..|.-
T Consensus 265 gie~dedviCDvCrspD~e~~neMVfCd--~Cn--~cVHqaCyGIle~p--~gpWlCr~Cal 320 (893)
T KOG0954|consen 265 GIEYDEDVICDVCRSPDSEEANEMVFCD--KCN--ICVHQACYGILEVP--EGPWLCRTCAL 320 (893)
T ss_pred eeeccccceeceecCCCccccceeEEec--cch--hHHHHhhhceeecC--CCCeeehhccc
Confidence 4555688899 8999964 4899999 899 67999999999999 89999999863
No 9
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.20 E-value=0.0001 Score=66.05 Aligned_cols=42 Identities=33% Similarity=0.827 Sum_probs=36.9
Q ss_pred ecCCCCC-CCccccCCCCCCCCceeecccCCCCCCCCCCCceecc-cccc
Q 024980 207 VCHQVSF-GDMIACDNENCQGGEWFHYACVGLTPETRFKGKWYCP-TCRL 254 (259)
Q Consensus 207 ~C~~~~~-g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~-~C~~ 254 (259)
+|++|.- .+|+.|| .|. .=||.-||||...| .|.|.|. .|..
T Consensus 319 IC~~P~~E~E~~FCD--~CD--RG~HT~CVGL~~lP--~G~WICD~~C~~ 362 (381)
T KOG1512|consen 319 ICLGPVIESEHLFCD--VCD--RGPHTLCVGLQDLP--RGEWICDMRCRE 362 (381)
T ss_pred ccCCcccchheeccc--ccc--CCCCcccccccccc--CccchhhhHHHH
Confidence 7888874 6999999 999 55999999999999 9999998 5753
No 10
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=97.15 E-value=0.00017 Score=71.22 Aligned_cols=50 Identities=30% Similarity=0.828 Sum_probs=42.3
Q ss_pred CcceecCCCC-C--CCccccCCCCCCCCceeecccCCCCCCCCCCCceecccccccc
Q 024980 203 PTYCVCHQVS-F--GDMIACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCRLLP 256 (259)
Q Consensus 203 ~~~C~C~~~~-~--g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~~~~ 256 (259)
.-+|+|-..- + ..+|-||+..|. .-+|..|.||...| .|.|||..|..+.
T Consensus 6 GGCCVCSDErGWaeNPLVYCDG~nCs--VAVHQaCYGIvqVP--tGpWfCrKCesqe 58 (900)
T KOG0956|consen 6 GGCCVCSDERGWAENPLVYCDGHNCS--VAVHQACYGIVQVP--TGPWFCRKCESQE 58 (900)
T ss_pred cceeeecCcCCCccCceeeecCCCce--eeeehhcceeEecC--CCchhhhhhhhhh
Confidence 3579996553 3 479999999999 77999999999999 9999999997543
No 11
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.09 E-value=0.00019 Score=70.30 Aligned_cols=51 Identities=33% Similarity=0.978 Sum_probs=38.0
Q ss_pred Ccce-ecCCCC-CCCccccCCCCCCCCceeecccCCCCCCCC--CCCceeccccccccC
Q 024980 203 PTYC-VCHQVS-FGDMIACDNENCQGGEWFHYACVGLTPETR--FKGKWYCPTCRLLPQ 257 (259)
Q Consensus 203 ~~~C-~C~~~~-~g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~--~~~~w~C~~C~~~~~ 257 (259)
..|| .|++.. |...|+|| .|+ --||+.|+.-+-.+. ..|.|||++|.-...
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD--~Cp--~sFH~~CLePPl~~eniP~g~W~C~ec~~k~~ 307 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCD--GCP--RSFHQTCLEPPLEPENIPPGSWFCPECKIKSV 307 (613)
T ss_pred HHHHHHhCCccccccceeec--CCc--hHHHHhhcCCCCCcccCCCCccccCCCeeeee
Confidence 3499 698874 56779999 799 779999986432221 389999999975543
No 12
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=96.89 E-value=0.00037 Score=65.02 Aligned_cols=48 Identities=29% Similarity=0.720 Sum_probs=41.2
Q ss_pred CcceecCCCCCC--CccccCCCCCCCCceeeccc--CCCCCCCC-CCCceecccccc
Q 024980 203 PTYCVCHQVSFG--DMIACDNENCQGGEWFHYAC--VGLTPETR-FKGKWYCPTCRL 254 (259)
Q Consensus 203 ~~~C~C~~~~~g--~mi~Cd~~~C~~~~wfH~~C--vgl~~~~~-~~~~w~C~~C~~ 254 (259)
..||.|..+... .|++|| .|. .|||..| ||++...+ ....|+|..|..
T Consensus 60 ~~~~~~~~~~~p~~~~~~cd--~C~--~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~ 112 (345)
T KOG1632|consen 60 QRYCKCYKPCDPDDLMEQCD--LCE--DWYHGECWEVGTAEKEAPKEDPKVCDECKE 112 (345)
T ss_pred hchhhcccccCchhhhhccc--ccc--ccccccccccCchhhcCCccccccccccch
Confidence 449999999765 899999 999 9999999 99987764 477999999974
No 13
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.62 E-value=0.0011 Score=66.51 Aligned_cols=51 Identities=27% Similarity=0.821 Sum_probs=40.7
Q ss_pred CCCcce-ecCCCCC-CCccccCCCCCCCCceeecccCCC--CCCCCCCCceecccccccc
Q 024980 201 NEPTYC-VCHQVSF-GDMIACDNENCQGGEWFHYACVGL--TPETRFKGKWYCPTCRLLP 256 (259)
Q Consensus 201 ~~~~~C-~C~~~~~-g~mi~Cd~~~C~~~~wfH~~Cvgl--~~~~~~~~~w~C~~C~~~~ 256 (259)
.+..-| +|..+.- .-||.|| .|. ...||.-|+.. .+.| .+.|||+.|.-+.
T Consensus 213 ~E~~~C~IC~~~DpEdVLLLCD--sCN-~~~YH~YCLDPdl~eiP--~~eWYC~NC~dL~ 267 (1134)
T KOG0825|consen 213 QEEVKCDICTVHDPEDVLLLCD--SCN-KVYYHVYCLDPDLSESP--VNEWYCTNCSLLE 267 (1134)
T ss_pred cccccceeeccCChHHhheeec--ccc-cceeeccccCccccccc--ccceecCcchhhh
Confidence 455667 7888765 4799999 999 77899999985 4467 8899999998553
No 14
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=96.27 E-value=0.0031 Score=66.02 Aligned_cols=51 Identities=25% Similarity=0.722 Sum_probs=42.1
Q ss_pred CCCCcceecCCCC-C--CCccccCCCCCCCCceeecccCCCCCCCCCCCceecccccccc
Q 024980 200 PNEPTYCVCHQVS-F--GDMIACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCRLLP 256 (259)
Q Consensus 200 ~~~~~~C~C~~~~-~--g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~~~~ 256 (259)
+++..+|||...- . ...|.|| .|. --+|..|+|+...| .|.|+|..|....
T Consensus 217 ~~D~~C~iC~~~~~~n~n~ivfCD--~Cn--l~VHq~Cygi~~ip--eg~WlCr~Cl~s~ 270 (1051)
T KOG0955|consen 217 EEDAVCCICLDGECQNSNVIVFCD--GCN--LAVHQECYGIPFIP--EGQWLCRRCLQSP 270 (1051)
T ss_pred CCCccceeecccccCCCceEEEcC--CCc--chhhhhccCCCCCC--CCcEeehhhccCc
Confidence 3457888998764 2 5789999 899 45999999999999 9999999997543
No 15
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=95.44 E-value=0.0065 Score=61.23 Aligned_cols=52 Identities=27% Similarity=0.696 Sum_probs=37.9
Q ss_pred CCCCCCcceecCCCCCCCccccCCCCCCCCceeecccCCCCCCCCCCCceeccccccc
Q 024980 198 IDPNEPTYCVCHQVSFGDMIACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCRLL 255 (259)
Q Consensus 198 ~~~~~~~~C~C~~~~~g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~~~ 255 (259)
.+.+..-.|+|... |+.|.|| .|+ .|||..|.|..-.+...+.|.|+.|..-
T Consensus 43 ~~~~~e~c~ic~~~--g~~l~c~--tC~--~s~h~~cl~~pl~~~p~~~~~c~Rc~~p 94 (696)
T KOG0383|consen 43 DDAEQEACRICADG--GELLWCD--TCP--ASFHASCLGPPLTPQPNGEFICPRCFCP 94 (696)
T ss_pred chhhhhhhhhhcCC--CcEEEec--ccc--HHHHHHccCCCCCcCCccceeeeeeccC
Confidence 34444444578654 7889999 999 9999999986655532556999999543
No 16
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=95.31 E-value=0.0052 Score=58.99 Aligned_cols=44 Identities=27% Similarity=0.774 Sum_probs=37.0
Q ss_pred ce-ecCCCCC---CCccccCCCCCCCCceeecccCCCCCCCCCCCceecccccc
Q 024980 205 YC-VCHQVSF---GDMIACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCRL 254 (259)
Q Consensus 205 ~C-~C~~~~~---g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~~ 254 (259)
.| +|..... .-.|.|| +|. | -.|.+|.|+...| .|.|+|..|.-
T Consensus 195 ~C~~c~~t~~eN~naiVfCd--gC~-i-~VHq~CYGI~f~p--eG~WlCrkCi~ 242 (669)
T COG5141 195 ICTKCTSTHNENSNAIVFCD--GCE-I-CVHQSCYGIQFLP--EGFWLCRKCIY 242 (669)
T ss_pred hhHhccccccCCcceEEEec--Ccc-h-hhhhhcccceecC--cchhhhhhhcc
Confidence 45 6877764 4689999 799 4 5899999999999 99999999964
No 17
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=95.24 E-value=0.0041 Score=67.27 Aligned_cols=48 Identities=35% Similarity=0.917 Sum_probs=38.6
Q ss_pred Ccce-ecCCCCCC-CccccCCCCCCCCceeecccCC--CCCCCCCCCceecccccccc
Q 024980 203 PTYC-VCHQVSFG-DMIACDNENCQGGEWFHYACVG--LTPETRFKGKWYCPTCRLLP 256 (259)
Q Consensus 203 ~~~C-~C~~~~~g-~mi~Cd~~~C~~~~wfH~~Cvg--l~~~~~~~~~w~C~~C~~~~ 256 (259)
...| +|+..... .|+-|+ .|. .|||+-|+- +...| .+.|+||.|+...
T Consensus 1108 ~~~c~~cr~k~~~~~m~lc~--~c~--~~~h~~C~rp~~~~~~--~~dW~C~~c~~e~ 1159 (1404)
T KOG1245|consen 1108 NALCKVCRRKKQDEKMLLCD--ECL--SGFHLFCLRPALSSVP--PGDWMCPSCRKEH 1159 (1404)
T ss_pred hhhhhhhhhcccchhhhhhH--hhh--hhHHHHhhhhhhccCC--cCCccCCccchhh
Confidence 4556 78777644 899999 999 999999976 45555 8999999998754
No 18
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=95.12 E-value=0.022 Score=54.94 Aligned_cols=46 Identities=33% Similarity=0.899 Sum_probs=34.3
Q ss_pred cceec-CC--CCCCCccccCCCCCCCCceeecccCCCCCC---C--C---CCCceeccccc
Q 024980 204 TYCVC-HQ--VSFGDMIACDNENCQGGEWFHYACVGLTPE---T--R---FKGKWYCPTCR 253 (259)
Q Consensus 204 ~~C~C-~~--~~~g~mi~Cd~~~C~~~~wfH~~Cvgl~~~---~--~---~~~~w~C~~C~ 253 (259)
.+|+| ++ +.-|++|+|| .|. |. +|-+|.|+... | . ....|||..|.
T Consensus 121 iCcVClg~rs~da~ei~qCd--~CG-i~-VHEgCYGv~dn~si~s~~s~~stepWfCeaC~ 177 (707)
T KOG0957|consen 121 ICCVCLGQRSVDAGEILQCD--KCG-IN-VHEGCYGVLDNVSIPSGSSDCSTEPWFCEACL 177 (707)
T ss_pred EEEEeecCccccccceeecc--ccC-ce-ecccccccccccccCCCCccCCCCchhhhhHh
Confidence 67799 22 3358999999 799 54 89999998732 1 1 34689999986
No 19
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=94.77 E-value=0.011 Score=52.89 Aligned_cols=49 Identities=24% Similarity=0.773 Sum_probs=37.8
Q ss_pred Ccce-ecCCCCC-CCccccCCCCCCCCceeecccCC--CCCCCCCCCceeccccccccC
Q 024980 203 PTYC-VCHQVSF-GDMIACDNENCQGGEWFHYACVG--LTPETRFKGKWYCPTCRLLPQ 257 (259)
Q Consensus 203 ~~~C-~C~~~~~-g~mi~Cd~~~C~~~~wfH~~Cvg--l~~~~~~~~~w~C~~C~~~~~ 257 (259)
-.|| +|+-..+ ..++.|| +|. .=||+=|+. +.++| .|.|-|--|...++
T Consensus 281 ck~csicgtsenddqllfcd--dcd--rgyhmyclsppm~epp--egswsc~KOG~~~~ 333 (336)
T KOG1244|consen 281 CKYCSICGTSENDDQLLFCD--DCD--RGYHMYCLSPPMVEPP--EGSWSCHLCLEELK 333 (336)
T ss_pred cceeccccCcCCCceeEeec--ccC--CceeeEecCCCcCCCC--CCchhHHHHHHHHh
Confidence 4566 6766654 4799999 999 559999997 55666 99999999976543
No 20
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=94.21 E-value=1.8 Score=42.24 Aligned_cols=45 Identities=27% Similarity=0.746 Sum_probs=35.0
Q ss_pred cce-ecCCCCC-CCccccCCCCCCCCceeecccCC--CCCCCC--CCCceecccc
Q 024980 204 TYC-VCHQVSF-GDMIACDNENCQGGEWFHYACVG--LTPETR--FKGKWYCPTC 252 (259)
Q Consensus 204 ~~C-~C~~~~~-g~mi~Cd~~~C~~~~wfH~~Cvg--l~~~~~--~~~~w~C~~C 252 (259)
.-| +|.+... -.++.|| .|. --||..|+. |+..|. ..--|.|.+|
T Consensus 545 ysCgiCkks~dQHll~~CD--tC~--lhYHlGCL~PPLTR~Pkk~kn~gWqCsEC 595 (707)
T KOG0957|consen 545 YSCGICKKSTDQHLLTQCD--TCH--LHYHLGCLSPPLTRLPKKNKNFGWQCSEC 595 (707)
T ss_pred eeeeeeccchhhHHHhhcc--hhh--ceeeccccCCccccCcccccCcceeeccc
Confidence 346 7877654 4789999 999 669999997 788784 2346999999
No 21
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=93.40 E-value=0.012 Score=54.90 Aligned_cols=53 Identities=26% Similarity=0.588 Sum_probs=40.5
Q ss_pred CCCCCCcceecCCCCC---CCccccCCCCCCCCceeecccCCCCCCCC-CCCc----eecccccc
Q 024980 198 IDPNEPTYCVCHQVSF---GDMIACDNENCQGGEWFHYACVGLTPETR-FKGK----WYCPTCRL 254 (259)
Q Consensus 198 ~~~~~~~~C~C~~~~~---g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~-~~~~----w~C~~C~~ 254 (259)
.++.+..+|.+.+..+ -.||+|+ .|. .|||..||.+...++ .... ++|+.|..
T Consensus 234 ~~~~~~~~~~~cg~~~~~~~~~~~~~--~~e--~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~ 294 (345)
T KOG1632|consen 234 APDYSKLICDPCGLSDANKKFEICCD--LCE--SWFHGDCVQIFEARKRLNEIRNEVYKCPHCTV 294 (345)
T ss_pred ccccccccccccCcchHHHHHHHHHH--HHH--HHhcccccccccchhhhhhhhccceecCceee
Confidence 4455568886555443 3699999 999 999999999999885 2334 99999975
No 22
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=92.68 E-value=0.048 Score=49.77 Aligned_cols=30 Identities=33% Similarity=1.044 Sum_probs=25.6
Q ss_pred CCcceecCCCCC-------CCccccCCCCCCCCceee-cccC
Q 024980 202 EPTYCVCHQVSF-------GDMIACDNENCQGGEWFH-YACV 235 (259)
Q Consensus 202 ~~~~C~C~~~~~-------g~mi~Cd~~~C~~~~wfH-~~Cv 235 (259)
+..||.|..++. |.|++|- .|+ .||| -.|.
T Consensus 127 qG~~C~Cd~~Ypdp~~~~e~~m~QC~--iCE--DWFHce~c~ 164 (345)
T KOG2752|consen 127 QGLFCKCDTPYPDPVRTEEGEMLQCV--ICE--DWFHCEGCM 164 (345)
T ss_pred cceeEEecCCCCCccccccceeeeEE--ecc--chhcccccC
Confidence 379999999864 5899999 999 9999 6664
No 23
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=92.38 E-value=0.069 Score=52.02 Aligned_cols=52 Identities=33% Similarity=0.666 Sum_probs=43.1
Q ss_pred CCCcceecCCCC--CCCccccCCCCCCCCceeecccCCCCCCCCCCCceeccccccccC
Q 024980 201 NEPTYCVCHQVS--FGDMIACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCRLLPQ 257 (259)
Q Consensus 201 ~~~~~C~C~~~~--~g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~~~~~ 257 (259)
....-|+|+... .|.||+|+ .|+ .|-|.-|+|....-. ..+|.|..|.....
T Consensus 84 ~~~~~c~c~~~~~~~g~~i~c~--~c~--~Wqh~~C~g~~~~~~-p~~y~c~~c~~~~~ 137 (508)
T KOG1844|consen 84 REISRCDCGLEDDMEGLMIQCD--WCG--RWQHKICCGSFKSTK-PDKYVCEICTPRNK 137 (508)
T ss_pred CcccccccccccCCCceeeCCc--ccC--cccCceeeeecCCCC-chhceeeeeccccc
Confidence 457789998774 57999999 999 999999999877662 47999999986543
No 24
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=89.41 E-value=0.2 Score=37.07 Aligned_cols=30 Identities=30% Similarity=0.805 Sum_probs=25.1
Q ss_pred cce-ecCCCCCCCccccCCCCCCCCceeecccCC
Q 024980 204 TYC-VCHQVSFGDMIACDNENCQGGEWFHYACVG 236 (259)
Q Consensus 204 ~~C-~C~~~~~g~mi~Cd~~~C~~~~wfH~~Cvg 236 (259)
..| +|+++ .|-.|.|..+.|. .+||+.|.-
T Consensus 37 ~~C~~C~~~-~Ga~i~C~~~~C~--~~fH~~CA~ 67 (90)
T PF13771_consen 37 LKCSICKKK-GGACIGCSHPGCS--RSFHVPCAR 67 (90)
T ss_pred CCCcCCCCC-CCeEEEEeCCCCC--cEEChHHHc
Confidence 345 78877 6889999999999 999999953
No 25
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=87.00 E-value=0.32 Score=37.44 Aligned_cols=31 Identities=26% Similarity=0.638 Sum_probs=25.7
Q ss_pred CCcceecCCCCCCCccccCCCCCCCCceeecccC
Q 024980 202 EPTYCVCHQVSFGDMIACDNENCQGGEWFHYACV 235 (259)
Q Consensus 202 ~~~~C~C~~~~~g~mi~Cd~~~C~~~~wfH~~Cv 235 (259)
....++|++. .|-.|.|.+++|. .+||..|.
T Consensus 55 ~~~C~iC~~~-~G~~i~C~~~~C~--~~fH~~CA 85 (110)
T PF13832_consen 55 KLKCSICGKS-GGACIKCSHPGCS--TAFHPTCA 85 (110)
T ss_pred CCcCcCCCCC-CceeEEcCCCCCC--cCCCHHHH
Confidence 3444589887 6889999998999 99999994
No 26
>PF13341 RAG2_PHD: RAG2 PHD domain; PDB: 2JWO_A 2V86_B 2V85_B 2V87_A 2V83_C 2V89_A 2V88_A.
Probab=85.96 E-value=0.22 Score=35.57 Aligned_cols=35 Identities=29% Similarity=0.739 Sum_probs=21.0
Q ss_pred CccccCCCCCCCCceeecccCCCCCCC-----CCCCceecccc
Q 024980 215 DMIACDNENCQGGEWFHYACVGLTPET-----RFKGKWYCPTC 252 (259)
Q Consensus 215 ~mi~Cd~~~C~~~~wfH~~Cvgl~~~~-----~~~~~w~C~~C 252 (259)
-||.|.+. . .-|.|..|+.|++.- ....++||.+=
T Consensus 29 AMI~cs~~--~-GHWvhaqCm~LsE~~L~~LSq~n~KYfC~dH 68 (78)
T PF13341_consen 29 AMIFCSRG--G-GHWVHAQCMDLSETMLIQLSQENTKYFCNDH 68 (78)
T ss_dssp -EEEE-ST--T--EEEETGGGT--HHHHHHHHHSSS-B--TTT
T ss_pred eEEEEeCC--C-ceEeEeecccchHHHHHHHccCCceEEEhhh
Confidence 59999974 5 799999999998763 14679999753
No 27
>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=80.90 E-value=1.2 Score=42.76 Aligned_cols=49 Identities=24% Similarity=0.733 Sum_probs=33.9
Q ss_pred ceecCCCCC---C-CccccCCCCCCCCceeecccC--------CCCCCCC---CCCceeccccccccC
Q 024980 205 YCVCHQVSF---G-DMIACDNENCQGGEWFHYACV--------GLTPETR---FKGKWYCPTCRLLPQ 257 (259)
Q Consensus 205 ~C~C~~~~~---g-~mi~Cd~~~C~~~~wfH~~Cv--------gl~~~~~---~~~~w~C~~C~~~~~ 257 (259)
.|+|++-.+ + .+|.|| .|. -|-|..|. |.+.... ..+.|+|..|-...+
T Consensus 131 C~iC~kfD~~~n~~~Wi~Cd--~Cg--H~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~se 194 (446)
T PF07227_consen 131 CCICSKFDDNKNTCSWIGCD--VCG--HWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTSE 194 (446)
T ss_pred ccccCCcccCCCCeeEEecc--CCC--ceehhhhhcccccccCCccCCCCCccCceEEEccCCCChhh
Confidence 347877643 2 699999 999 99999992 3222211 356899999976543
No 28
>PRK15365 type III secretion system chaperone SseA; Provisional
Probab=79.68 E-value=22 Score=27.20 Aligned_cols=83 Identities=11% Similarity=0.105 Sum_probs=46.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH---HHHHHHhhhcCCCCCCCCCCchHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHH
Q 024980 26 RLLNTIRELDERSHSMINQTRQ---QTKYCLGLASQGNKKGNGNEEDEAIEKMRKEIEVNQDNAL-SLCTEKVLLARQAY 101 (259)
Q Consensus 26 r~l~~IreLD~~~~~~~~~l~~---~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~-~lsdEKv~LA~q~~ 101 (259)
-.|+++++|..+|..+...++. .+.++....+. +. ..++...+...++...|-.-. .+..||.. +.
T Consensus 6 ~~~~~l~DL~~rYs~L~s~lkKfkq~q~~I~q~L~e---RA---~~d~kaRE~l~rLd~aFP~G~~~~~qE~~k----~m 75 (107)
T PRK15365 6 AAFSEYRDLEQSYMQLNHCLKKFHQIRAKVSQQLAE---RA---ESPKKSRETESILHNLFPQGVAGVNQEAEK----DL 75 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---Hh---cCCHHHHHHHHHHHHHCcchhhHHhHHHHH----HH
Confidence 3588999999999887666544 33333111111 11 112233344455555554443 56778744 44
Q ss_pred HHHHHHHHHHHHHHHHH
Q 024980 102 DIIDSHIKRLDEDLNNF 118 (259)
Q Consensus 102 dlVdrhirrLD~dl~~~ 118 (259)
.-|....++|+..|+++
T Consensus 76 ~~i~~~FKQLEt~LKnl 92 (107)
T PRK15365 76 KKIVSLFKQLEVRLKQL 92 (107)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 45557778888777643
No 29
>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=79.30 E-value=0.38 Score=31.13 Aligned_cols=39 Identities=26% Similarity=0.690 Sum_probs=17.5
Q ss_pred cCCCC-CCCccccCCCCCCCCceeecccCCCCCCCCCCCceecccc
Q 024980 208 CHQVS-FGDMIACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTC 252 (259)
Q Consensus 208 C~~~~-~g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C 252 (259)
|+..- .| +.|.|++|. +. +|..|+.--... ...--||.|
T Consensus 4 C~~iv~~G--~~C~~~~C~-~r-~H~~C~~~y~r~--~~~~~CP~C 43 (43)
T PF08746_consen 4 CKEIVTQG--QRCSNRDCN-VR-LHDDCFKKYFRH--RSNPKCPNC 43 (43)
T ss_dssp T-SB-SSS--EE-SS--S---E-E-HHHHHHHTTT---SS-B-TTT
T ss_pred cchhHeee--ccCCCCccC-ch-HHHHHHHHHHhc--CCCCCCcCC
Confidence 44443 35 679999999 66 599998633333 212278877
No 30
>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=75.33 E-value=2 Score=33.27 Aligned_cols=53 Identities=25% Similarity=0.533 Sum_probs=33.7
Q ss_pred CCCCcce-ecCCCCCCCcccc----CCCCC---CCCceeecccCCCCCC----C-CCCCceecccccc
Q 024980 200 PNEPTYC-VCHQVSFGDMIAC----DNENC---QGGEWFHYACVGLTPE----T-RFKGKWYCPTCRL 254 (259)
Q Consensus 200 ~~~~~~C-~C~~~~~g~mi~C----d~~~C---~~~~wfH~~Cvgl~~~----~-~~~~~w~C~~C~~ 254 (259)
.....+| .|++...+..+.| .+..| . .=|=+.|+-.... . ....+|.||.|+.
T Consensus 4 ~~~g~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~--~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 4 SVNGKTCHQCRQKTLDFKTICTGHWKNSSCRGCR--GKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred CCCCCCchhhcCCCCCCceEcCCCCCCCCCccCc--ceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 3446678 6888777766677 55577 6 3366777432111 1 1367999999985
No 31
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=68.72 E-value=2.6 Score=26.56 Aligned_cols=19 Identities=26% Similarity=0.567 Sum_probs=16.5
Q ss_pred CCCccccCC-CCCCCCceee
Q 024980 213 FGDMIACDN-ENCQGGEWFH 231 (259)
Q Consensus 213 ~g~mi~Cd~-~~C~~~~wfH 231 (259)
+|.+++|.| |.|.+++|++
T Consensus 18 ~g~F~~Cs~yP~C~~~~~~~ 37 (39)
T PF01396_consen 18 KGKFLGCSNYPECKYTEPLP 37 (39)
T ss_pred CCCEEECCCCCCcCCeEeCC
Confidence 578999999 8999888865
No 32
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=65.83 E-value=76 Score=34.63 Aligned_cols=35 Identities=20% Similarity=0.074 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 85 NALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNFA 119 (259)
Q Consensus 85 ~~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~ 119 (259)
++++.+++--..|+.+..-.++-|+...+.|.+.+
T Consensus 1570 eaL~~Ad~Aq~~a~~ai~~a~~~~~~a~~~l~kv~ 1604 (1758)
T KOG0994|consen 1570 EALEEADVAQGEAQDAIQGADRDIRLAQQLLAKVQ 1604 (1758)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence 33444444444444444444444444444444433
No 33
>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=63.93 E-value=1.3e+02 Score=28.40 Aligned_cols=109 Identities=15% Similarity=0.151 Sum_probs=68.8
Q ss_pred HHHHHHHhhCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--h--cCCCCCCCCCCchHHHHHHHHHHHHHHHH
Q 024980 10 VDDYLEYASTLPAELQRLLNTIRELDERSHSMINQTRQQTKYCLGL--A--SQGNKKGNGNEEDEAIEKMRKEIEVNQDN 85 (259)
Q Consensus 10 Ledfle~ie~LP~El~r~l~~IreLD~~~~~~~~~l~~~~k~~~~~--~--~~~~~~~~~~~~~~~~~~~~~~I~~~~~~ 85 (259)
+.+..+....|-..+...+.+|.++...+..+...+......++-. + ....+.+..+-.++....+..++ ..+..
T Consensus 253 i~et~~ak~~Le~ql~~~~~ei~~~e~~i~~L~~ai~~k~~~lkvaqTRL~~R~~RP~vElcrD~~q~~L~~Ev-~~l~~ 331 (384)
T PF03148_consen 253 IHETQEAKNELEWQLKKTLQEIAEMEKNIEDLEKAIRDKEGPLKVAQTRLENRTQRPNVELCRDPPQYGLIEEV-KELRE 331 (384)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhHhcCCchHHHHhhHHHHHHHHH-HHHHH
Confidence 4555566667777888888888888888888877776554433211 0 00011111111111222444554 34456
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 86 ALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNFA 119 (259)
Q Consensus 86 ~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~ 119 (259)
.+.--.+|+.-|...+..+.++..+|+.||..-.
T Consensus 332 ~i~~L~~~L~~a~~~l~~L~~~~~~Le~di~~K~ 365 (384)
T PF03148_consen 332 SIEALQEKLDEAEASLQKLERTRLRLEEDIAVKN 365 (384)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6667788999999999999999999999997543
No 34
>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=62.26 E-value=53 Score=32.62 Aligned_cols=103 Identities=17% Similarity=0.269 Sum_probs=49.7
Q ss_pred hhhHHHHHHHHhhCCh---HHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHhhhcCCCCCCCCCCchHHHHHHHHH
Q 024980 6 TGVYVDDYLEYASTLP---AELQRLLNTIRELDERSHSMINQTRQQ----TKYCLGLASQGNKKGNGNEEDEAIEKMRKE 78 (259)
Q Consensus 6 ~~~yLedfle~ie~LP---~El~r~l~~IreLD~~~~~~~~~l~~~----~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (259)
.+.-|.+|++.++.=| .+++..+..++.|-.++..-..++-+. .+.+..... .....+.+..+
T Consensus 285 ~~~~l~~~~~~l~~dp~~L~ele~RL~~l~~LkrKyg~s~e~l~~~~~~l~~eL~~l~~----------~~~~le~L~~e 354 (563)
T TIGR00634 285 ATRELQNYLDELEFDPERLNEIEERLAQIKRLKRKYGASVEEVLEYAEKIKEELDQLDD----------SDESLEALEEE 354 (563)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhC----------CHHHHHHHHHH
Confidence 4555777777777777 445555555555555554222222221 111111100 00112223333
Q ss_pred HHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 79 IEVNQ----DNALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNF 118 (259)
Q Consensus 79 I~~~~----~~~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~ 118 (259)
+.... ..+..|+......|..+-..|..+++.|...-..|
T Consensus 355 l~~l~~~l~~~a~~Ls~~R~~~a~~l~~~v~~~l~~L~m~~~~f 398 (563)
T TIGR00634 355 VDKLEEELDKAAVALSLIRRKAAERLAKRVEQELKALAMEKAEF 398 (563)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcEE
Confidence 33222 34456666666667777777777777766443333
No 35
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=60.48 E-value=3.7 Score=34.22 Aligned_cols=47 Identities=19% Similarity=0.401 Sum_probs=25.1
Q ss_pred Ccce-ecCCCCCCCccccCCCCCCC-CceeecccCCCCCCCCCCCceecccccc
Q 024980 203 PTYC-VCHQVSFGDMIACDNENCQG-GEWFHYACVGLTPETRFKGKWYCPTCRL 254 (259)
Q Consensus 203 ~~~C-~C~~~~~g~mi~Cd~~~C~~-~~wfH~~Cvgl~~~~~~~~~w~C~~C~~ 254 (259)
...| +|+......---|. |.| ..|.|.+|+.-=-.. .+...|+.|..
T Consensus 8 ~~~CRIC~~~~~~~~~PC~---CkGs~k~VH~sCL~rWi~~--s~~~~CeiC~~ 56 (162)
T PHA02825 8 DKCCWICKDEYDVVTNYCN---CKNENKIVHKECLEEWINT--SKNKSCKICNG 56 (162)
T ss_pred CCeeEecCCCCCCccCCcc---cCCCchHHHHHHHHHHHhc--CCCCcccccCC
Confidence 4557 67666432211244 542 458888887522222 44566777754
No 36
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=59.19 E-value=3.8 Score=30.00 Aligned_cols=49 Identities=27% Similarity=0.611 Sum_probs=33.5
Q ss_pred ce-ecCCCCCCCccccC--CCCCCCCce------eecccCCC-CCCCCCCCceecccccccc
Q 024980 205 YC-VCHQVSFGDMIACD--NENCQGGEW------FHYACVGL-TPETRFKGKWYCPTCRLLP 256 (259)
Q Consensus 205 ~C-~C~~~~~g~mi~Cd--~~~C~~~~w------fH~~Cvgl-~~~~~~~~~w~C~~C~~~~ 256 (259)
.| +|+.+..|--=.|. +|+|+ +.| ||..|+-- -..| ...-.||-|+..-
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCP-Lv~G~C~h~fh~hCI~~wl~~~--tsq~~CPmcRq~~ 80 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCP-LVWGYCLHAFHAHCILKWLNTP--TSQGQCPMCRQTW 80 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCc-cHHHHHHHHHHHHHHHHHhcCc--cccccCCcchhee
Confidence 46 89999887433444 57899 888 99999741 1223 3357899998753
No 37
>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=58.80 E-value=76 Score=28.39 Aligned_cols=74 Identities=20% Similarity=0.196 Sum_probs=46.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHH
Q 024980 28 LNTIRELDERSHSMINQTRQQTKYCLGLASQGNKKGNGNEEDEAIEKMRKEIEVNQDNALSLCTE-KVLLARQAYDIIDS 106 (259)
Q Consensus 28 l~~IreLD~~~~~~~~~l~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~~lsdE-Kv~LA~q~~dlVdr 106 (259)
-..|++.|.++......+........ ..........+..+-.+|...+.++-.|+.+ +|.-|+.+...|+.
T Consensus 89 ~~~i~d~drrI~~~k~RL~~~~~~~~--------~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~ 160 (254)
T PF03194_consen 89 QRLIRDCDRRIERAKERLEQTQEEQA--------KEADEEKAEKIDELDEKIGELLKEAEELGEEGDVDEAQKLMEEVEK 160 (254)
T ss_pred HHHHHHHHHHHHHHHHHHHhCccccc--------cchhhhHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34677777777666555543221100 0000001234567778899999999999988 99999998877775
Q ss_pred HHH
Q 024980 107 HIK 109 (259)
Q Consensus 107 hir 109 (259)
--.
T Consensus 161 Lk~ 163 (254)
T PF03194_consen 161 LKE 163 (254)
T ss_pred HHH
Confidence 433
No 38
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=58.70 E-value=91 Score=24.76 Aligned_cols=107 Identities=17% Similarity=0.254 Sum_probs=58.5
Q ss_pred hhCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCchHHHHHH--HHHHHHHHHHHHHHHHHHH
Q 024980 17 ASTLPAELQRLLNTIRELDERSHSMINQTRQQTKYCLGLASQGNKKGNGNEEDEAIEKM--RKEIEVNQDNALSLCTEKV 94 (259)
Q Consensus 17 ie~LP~El~r~l~~IreLD~~~~~~~~~l~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~--~~~I~~~~~~~~~lsdEKv 94 (259)
+.+||.++++.+.....|-.+.+.+..+..+...-+.+....- .--.-++++...-+. ..-|......+..=-++++
T Consensus 1 ~~~lpp~~q~~l~q~QqLq~ql~~~~~qk~~le~qL~E~~~al-~Ele~l~eD~~vYk~VG~llvk~~k~~~~~eL~er~ 79 (119)
T COG1382 1 MEQLPPEVQAQLAQLQQLQQQLQKVILQKQQLEAQLKEIEKAL-EELEKLDEDAPVYKKVGNLLVKVSKEEAVDELEERK 79 (119)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHhcCCcccHHHHHhhhHHhhhhHHHHHHHHHHHH
Confidence 3689999999999999998888877555444322221110000 000001111111000 0123445566666667776
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024980 95 LLARQAYDIIDSHIKRLDEDLNNFAEDLKQ 124 (259)
Q Consensus 95 ~LA~q~~dlVdrhirrLD~dl~~~~~~L~~ 124 (259)
..-.-=...+++..++|+..++++...|..
T Consensus 80 E~Le~ri~tLekQe~~l~e~l~eLq~~i~~ 109 (119)
T COG1382 80 ETLELRIKTLEKQEEKLQERLEELQSEIQK 109 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 666666666777777777777777666543
No 39
>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=58.38 E-value=95 Score=27.44 Aligned_cols=25 Identities=28% Similarity=0.793 Sum_probs=16.2
Q ss_pred CccccCCCCCCCCceeecccCCCCCCCCCCCceeccccccc
Q 024980 215 DMIACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCRLL 255 (259)
Q Consensus 215 ~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~~~ 255 (259)
.|=.|. .|. .-.|- ..| .||-|..+
T Consensus 193 PMK~C~--sC~--qqIHR------NAP------iCPlCK~K 217 (230)
T PF10146_consen 193 PMKTCQ--SCH--QQIHR------NAP------ICPLCKAK 217 (230)
T ss_pred CcchhH--hHH--HHHhc------CCC------CCcccccc
Confidence 488888 787 65563 234 48888654
No 40
>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=57.82 E-value=1.7e+02 Score=29.12 Aligned_cols=27 Identities=15% Similarity=0.308 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 97 ARQAYDIIDSHIKRLDEDLNNFAEDLK 123 (259)
Q Consensus 97 A~q~~dlVdrhirrLD~dl~~~~~~L~ 123 (259)
...+.+++..|+..|..-+++.-++|+
T Consensus 290 ~SkAvevM~qhvenLkr~~~kehaeL~ 316 (538)
T PF05781_consen 290 VSKAVEVMIQHVENLKRMYEKEHAELE 316 (538)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346677777787777766666555544
No 41
>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=57.53 E-value=41 Score=25.50 Aligned_cols=46 Identities=20% Similarity=0.268 Sum_probs=28.4
Q ss_pred hhHHHHHHHHhhCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 7 GVYVDDYLEYASTLPAELQRLLNTIRELDERSHSMINQTRQQTKYC 52 (259)
Q Consensus 7 ~~yLedfle~ie~LP~El~r~l~~IreLD~~~~~~~~~l~~~~k~~ 52 (259)
+.=|..+++.+...=.+|+..+..|-++|.++..+..-+...-.|.
T Consensus 44 ~~~l~~~~~~l~~k~~~l~~~l~~Id~Ie~~V~~LE~~v~~LD~ys 89 (99)
T PF10046_consen 44 AAGLEKNLEDLNQKYEELQPYLQQIDQIEEQVTELEQTVYELDEYS 89 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3345666666666667777777777777777766644444443343
No 42
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=56.09 E-value=2.5 Score=38.45 Aligned_cols=49 Identities=29% Similarity=0.506 Sum_probs=35.2
Q ss_pred CCCcceecCCCCC-----CCccccCCCCCCCCceeecccCCCCCCCC---CCCceeccccc
Q 024980 201 NEPTYCVCHQVSF-----GDMIACDNENCQGGEWFHYACVGLTPETR---FKGKWYCPTCR 253 (259)
Q Consensus 201 ~~~~~C~C~~~~~-----g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~---~~~~w~C~~C~ 253 (259)
++-..|+=.+.+. ..||.|. .|. .-+|..||.++..-+ ..-.|-|..|+
T Consensus 259 ~~~~~~~~~~~~~~~~r~~S~I~C~--~C~--~~~HP~Ci~M~~elv~~~KTY~W~C~~C~ 315 (381)
T KOG1512|consen 259 NERKHFWDIQTNIIQSRRNSWIVCK--PCA--TRPHPYCVAMIPELVGQYKTYFWKCSSCE 315 (381)
T ss_pred hhhhhhhcchhhhhhhhhccceeec--ccc--cCCCCcchhcCHHHHhHHhhcchhhcccH
Confidence 3445666555543 3799999 899 458999999887753 34478888875
No 43
>KOG4460 consensus Nuclear pore complex, Nup88/rNup84 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=55.45 E-value=1.3e+02 Score=30.11 Aligned_cols=35 Identities=14% Similarity=0.335 Sum_probs=28.1
Q ss_pred hhHHHHHHHHhhCChHHHHHHHHHHHH-HHHHHHHH
Q 024980 7 GVYVDDYLEYASTLPAELQRLLNTIRE-LDERSHSM 41 (259)
Q Consensus 7 ~~yLedfle~ie~LP~El~r~l~~Ire-LD~~~~~~ 41 (259)
-.|-|+||..-+-.-.||+|....|.. +|.+.|++
T Consensus 569 ~vfrEqYi~~~dlV~~e~qrH~~~l~~~k~~QlQ~l 604 (741)
T KOG4460|consen 569 QVFREQYILKQDLVKEEIQRHVKLLCDQKKKQLQDL 604 (741)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999999988865 45666665
No 44
>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=54.85 E-value=4.7 Score=32.58 Aligned_cols=28 Identities=32% Similarity=0.587 Sum_probs=14.9
Q ss_pred CCCCceeeccc---CCCCCCCCCCCceecccc
Q 024980 224 CQGGEWFHYAC---VGLTPETRFKGKWYCPTC 252 (259)
Q Consensus 224 C~~~~wfH~~C---vgl~~~~~~~~~w~C~~C 252 (259)
=. |.|||..| ||-+=..-....--|..|
T Consensus 100 ss-YRWFHdgCCECVG~~CinYGinesrC~~C 130 (132)
T PF04668_consen 100 SS-YRWFHDGCCECVGPTCINYGINESRCSNC 130 (132)
T ss_pred cc-ceeeccchhhccCchhhhccCCcHhHhcC
Confidence 35 99999955 764322211223345555
No 45
>PRK10869 recombination and repair protein; Provisional
Probab=54.04 E-value=1.8e+02 Score=29.00 Aligned_cols=105 Identities=19% Similarity=0.254 Sum_probs=52.2
Q ss_pred hHHHHHHHHhhCCh---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCchHHHHHHHHHHHH---
Q 024980 8 VYVDDYLEYASTLP---AELQRLLNTIRELDERSHSMINQTRQQTKYCLGLASQGNKKGNGNEEDEAIEKMRKEIEV--- 81 (259)
Q Consensus 8 ~yLedfle~ie~LP---~El~r~l~~IreLD~~~~~~~~~l~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~--- 81 (259)
.-|.+|++.++.=| .++...|..|+.|-.+|..-..++-...+.+....+.- . .-......+..++..
T Consensus 282 ~~l~~~~~~~~~dp~~l~~ie~Rl~~l~~L~rKyg~~~~~~~~~~~~l~~eL~~L--~----~~e~~l~~Le~e~~~l~~ 355 (553)
T PRK10869 282 DELRHYLDRLDLDPNRLAELEQRLSKQISLARKHHVSPEELPQHHQQLLEEQQQL--D----DQEDDLETLALAVEKHHQ 355 (553)
T ss_pred HHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHh--h----CCHHHHHHHHHHHHHHHH
Confidence 34556777776667 45666666777777776633333322111111000000 0 001112233333333
Q ss_pred -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 82 -NQDNALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNF 118 (259)
Q Consensus 82 -~~~~~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~ 118 (259)
....+.+|+.....-|..+-..|..+++.|...-..|
T Consensus 356 ~l~~~A~~LS~~R~~aA~~l~~~v~~~L~~L~m~~a~f 393 (553)
T PRK10869 356 QALETAQKLHQSRQRYAKELAQLITESMHELSMPHGKF 393 (553)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCcEE
Confidence 2245566666677777777777777777776544443
No 46
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=52.86 E-value=3.7 Score=41.23 Aligned_cols=39 Identities=33% Similarity=0.930 Sum_probs=29.4
Q ss_pred CCccccCCCCCCCCceeecccCCCCCCCC-CCCceecccccccc
Q 024980 214 GDMIACDNENCQGGEWFHYACVGLTPETR-FKGKWYCPTCRLLP 256 (259)
Q Consensus 214 g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~-~~~~w~C~~C~~~~ 256 (259)
|.|+.|. +|. .-||..||.+-..-+ ..+-|-||.|+.=.
T Consensus 33 g~m~ac~--~c~--~~yH~~cvt~~~~~~~l~~gWrC~~crvCe 72 (694)
T KOG4443|consen 33 GRLLACS--DCG--QKYHPYCVTSWAQHAVLSGGWRCPSCRVCE 72 (694)
T ss_pred Ccchhhh--hhc--ccCCcchhhHHHhHHHhcCCcccCCceeee
Confidence 6899999 899 889999998544432 23349999998543
No 47
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=52.38 E-value=8.8 Score=33.48 Aligned_cols=33 Identities=21% Similarity=0.577 Sum_probs=26.7
Q ss_pred cccCCCCCCCCceeecccCCCCCCCCCCCceeccccccccC
Q 024980 217 IACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCRLLPQ 257 (259)
Q Consensus 217 i~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~~~~~ 257 (259)
+=|. .|. .|..|+.+.+.| ...|+||.|....|
T Consensus 193 lIC~--~C~----hhngl~~~~ek~--~~efiC~~Cn~~n~ 225 (251)
T COG5415 193 LICP--QCH----HHNGLYRLAEKP--IIEFICPHCNHKND 225 (251)
T ss_pred hccc--ccc----cccccccccccc--chheecccchhhcC
Confidence 4466 687 599999999888 77999999987654
No 48
>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=50.72 E-value=2.3e+02 Score=29.31 Aligned_cols=25 Identities=20% Similarity=0.434 Sum_probs=14.6
Q ss_pred HHHHHHHHhhCChHHHHHHHHHHHH
Q 024980 9 YVDDYLEYASTLPAELQRLLNTIRE 33 (259)
Q Consensus 9 yLedfle~ie~LP~El~r~l~~Ire 33 (259)
+-|+|++..+-.=.+|++.+.+++.
T Consensus 548 lreeYi~~~~~ar~ei~~rv~~Lk~ 572 (717)
T PF10168_consen 548 LREEYIEKQDLAREEIQRRVKLLKQ 572 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566666666556666666554443
No 49
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=49.13 E-value=12 Score=40.12 Aligned_cols=43 Identities=30% Similarity=0.824 Sum_probs=32.7
Q ss_pred ce-ecCCCCCCCccccCCCCCCCCceeecccCCCCCCCCCCCceeccccc
Q 024980 205 YC-VCHQVSFGDMIACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCR 253 (259)
Q Consensus 205 ~C-~C~~~~~g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~ 253 (259)
.| +|+.- |..+||+ .|+ .-+|..||...........|-|.-|.
T Consensus 346 hcrf~~d~--~~~lc~E--t~p--rvvhlEcv~hP~~~~~s~~~e~evc~ 389 (1414)
T KOG1473|consen 346 HCRFCHDL--GDLLCCE--TCP--RVVHLECVFHPRFAVPSAFWECEVCN 389 (1414)
T ss_pred cccccCcc--cceeecc--cCC--ceEEeeecCCccccCCCccchhhhhh
Confidence 35 66654 7889999 799 66899999865543347789999886
No 50
>PF08203 RNA_polI_A14: Yeast RNA polymerase I subunit RPA14; InterPro: IPR013239 Saccharomyces cerevisiae RNA polymerase I (Pol I) is a complex consisting of 14 subunits. Subunit RPA14 forms part of a Pol I subcomplex consisting of RPA14 and and RPA43. The RPA14 and RPA43 heterodimer is proposed to play a role in the recruitment of Pol I to the promoter []. ; PDB: 2RF4_F.
Probab=48.82 E-value=31 Score=25.21 Aligned_cols=52 Identities=13% Similarity=0.209 Sum_probs=27.9
Q ss_pred cchhhHHHHHHHHhhCCh-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024980 4 ARTGVYVDDYLEYASTLP-----AELQRLLNTIRELDERSHSMINQTRQQTKYCLGLA 56 (259)
Q Consensus 4 ~~~~~yLedfle~ie~LP-----~El~r~l~~IreLD~~~~~~~~~l~~~~k~~~~~~ 56 (259)
.|+..||+.||+..|.+- .+.. ....+-..|......+.+++..+..+++++
T Consensus 16 ~ea~~fL~~FI~~~E~~~~~~~~~~~~-~~~t~~s~~t~~ss~LSQLKRiQRdlrGLP 72 (76)
T PF08203_consen 16 DEAEQFLTEFIDEKESIASNLTNSEDN-SAGTGLSSDTGLSSVLSQLKRIQRDLRGLP 72 (76)
T ss_dssp HHHHHHHHHHHHHHHSS--------------------TTHHHHHHHHHHHHHHHHHS-
T ss_pred HHHHHHHHHHHHHHHHHhccccccccc-cccccccCCCccHHHHHHHHHHHHhhCCCC
Confidence 457789999999999981 1111 113344455555566677776676666653
No 51
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=48.12 E-value=8.8 Score=28.67 Aligned_cols=23 Identities=39% Similarity=0.844 Sum_probs=15.8
Q ss_pred eecccCC--CCCCCCCCCceeccccccc
Q 024980 230 FHYACVG--LTPETRFKGKWYCPTCRLL 255 (259)
Q Consensus 230 fH~~Cvg--l~~~~~~~~~w~C~~C~~~ 255 (259)
||..|+- +... ..+-.||-||..
T Consensus 56 FH~hCI~kWl~~~---~~~~~CPmCR~~ 80 (85)
T PF12861_consen 56 FHMHCILKWLSTQ---SSKGQCPMCRQP 80 (85)
T ss_pred HHHHHHHHHHccc---cCCCCCCCcCCe
Confidence 9999975 3332 234589999975
No 52
>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=48.11 E-value=3.9 Score=29.31 Aligned_cols=43 Identities=26% Similarity=0.655 Sum_probs=23.1
Q ss_pred ceecCCCCCCCccccCC--C-------CCCCCceeecccCCCCCCCCCCCceeccccc
Q 024980 205 YCVCHQVSFGDMIACDN--E-------NCQGGEWFHYACVGLTPETRFKGKWYCPTCR 253 (259)
Q Consensus 205 ~C~C~~~~~g~mi~Cd~--~-------~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~ 253 (259)
..||..+..+.-+.|+. + .|. =-||+.|+.-=- .....||.|+
T Consensus 22 C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~--H~FH~~Ci~~Wl----~~~~~CP~CR 73 (73)
T PF12678_consen 22 CAICREPLEDPCPECQAPQDECPIVWGPCG--HIFHFHCISQWL----KQNNTCPLCR 73 (73)
T ss_dssp ETTTTSBTTSTTCCHHHCTTTS-EEEETTS--EEEEHHHHHHHH----TTSSB-TTSS
T ss_pred ccccChhhhChhhhhcCCccccceEecccC--CCEEHHHHHHHH----hcCCcCCCCC
Confidence 34788876443333331 1 355 349999984111 1123899986
No 53
>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=47.25 E-value=2.4e+02 Score=26.17 Aligned_cols=42 Identities=21% Similarity=0.227 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 78 EIEVNQDNALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNFA 119 (259)
Q Consensus 78 ~I~~~~~~~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~ 119 (259)
++.........|..|||.|=+++-.-=+--+++|...+.++.
T Consensus 150 e~~~~q~~le~Lr~EKVdlEn~LE~EQE~lvN~L~Kqm~~l~ 191 (310)
T PF09755_consen 150 EKSAKQEELERLRREKVDLENTLEQEQEALVNRLWKQMDKLE 191 (310)
T ss_pred HHHHhHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444556789999999888765433333344444443433
No 54
>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=46.54 E-value=1.6e+02 Score=23.91 Aligned_cols=37 Identities=22% Similarity=0.311 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 86 ALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNFAEDL 122 (259)
Q Consensus 86 ~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~~~L 122 (259)
-+.-..+|+.-|....+-++|.++.|+.....++.-+
T Consensus 95 ~L~e~~ekl~e~d~~ae~~eRkv~~le~~~~~~E~k~ 131 (143)
T PF12718_consen 95 KLKETTEKLREADVKAEHFERKVKALEQERDQWEEKY 131 (143)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHhhHHHHHHHH
Confidence 3566777777777777778888888887776665543
No 55
>PRK09343 prefoldin subunit beta; Provisional
Probab=46.35 E-value=1.4e+02 Score=23.38 Aligned_cols=98 Identities=18% Similarity=0.254 Sum_probs=48.9
Q ss_pred hCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHhhhcCCCCCCCCCCchHHHHH--HHHHHHHHHHHHHH
Q 024980 18 STLPAELQRLLNTIRELDERSHSMINQTRQQTK-------YCLGLASQGNKKGNGNEEDEAIEK--MRKEIEVNQDNALS 88 (259)
Q Consensus 18 e~LP~El~r~l~~IreLD~~~~~~~~~l~~~~k-------~~~~~~~~~~~~~~~~~~~~~~~~--~~~~I~~~~~~~~~ 88 (259)
.+||.+|+..+..+..+-.+++.+..+...... -+.++... +++...=+ -.--|......+..
T Consensus 3 ~~~~~~~q~~~~~~q~lq~~l~~~~~q~~~le~q~~e~~~~~~EL~~L--------~~d~~VYk~VG~vlv~qd~~e~~~ 74 (121)
T PRK09343 3 ENIPPEVQAQLAQLQQLQQQLERLLQQKSQIDLELREINKALEELEKL--------PDDTPIYKIVGNLLVKVDKTKVEK 74 (121)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC--------CCcchhHHHhhHHHhhccHHHHHH
Confidence 367777777777777777776665554443221 11122111 00000000 00123444555555
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 89 LCTEKVLLARQAYDIIDSHIKRLDEDLNNFAEDLK 123 (259)
Q Consensus 89 lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~~~L~ 123 (259)
--++++.....-..-+++....|...+.+.+..|.
T Consensus 75 ~l~~r~E~ie~~ik~lekq~~~l~~~l~e~q~~l~ 109 (121)
T PRK09343 75 ELKERKELLELRSRTLEKQEKKLREKLKELQAKIN 109 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55666665555555566666666666665555443
No 56
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=46.20 E-value=5.8 Score=29.31 Aligned_cols=45 Identities=29% Similarity=0.655 Sum_probs=30.8
Q ss_pred e-ecCCCCCCCccccCC-----CCCCCCce------eecccCCCCCCCCCCCceeccccccc
Q 024980 206 C-VCHQVSFGDMIACDN-----ENCQGGEW------FHYACVGLTPETRFKGKWYCPTCRLL 255 (259)
Q Consensus 206 C-~C~~~~~g~mi~Cd~-----~~C~~~~w------fH~~Cvgl~~~~~~~~~w~C~~C~~~ 255 (259)
| +|+-...|.-+.|-+ +.|+ +.| ||+.|+.-= - ..+-.||-|+..
T Consensus 23 CaICRnhim~~C~eCq~~~~~~~eC~-v~wG~CnHaFH~HCI~rW--L--~Tk~~CPld~q~ 79 (88)
T COG5194 23 CAICRNHIMGTCPECQFGMTPGDECP-VVWGVCNHAFHDHCIYRW--L--DTKGVCPLDRQT 79 (88)
T ss_pred hhhhhccccCcCcccccCCCCCCcce-EEEEecchHHHHHHHHHH--H--hhCCCCCCCCce
Confidence 6 788887777777764 6788 888 999998411 1 224567777643
No 57
>PF11690 DUF3287: Protein of unknown function (DUF3287); InterPro: IPR021704 This eukaryotic family of proteins has no known function.
Probab=45.89 E-value=75 Score=24.83 Aligned_cols=46 Identities=15% Similarity=0.322 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Q 024980 74 KMRKEIEVNQDNALSLCTEKVLLARQAYDI-IDSHIKRLDEDLNNFA 119 (259)
Q Consensus 74 ~~~~~I~~~~~~~~~lsdEKv~LA~q~~dl-VdrhirrLD~dl~~~~ 119 (259)
+...-|...-.+-+++.+|+-.|...+.+| |+|-++.|+++-..-+
T Consensus 39 ea~~F~~kV~~qH~~~~~e~r~L~kKi~~l~veRkmr~Les~p~~W~ 85 (109)
T PF11690_consen 39 EAYDFIDKVVDQHQRYCDERRKLRKKIQDLRVERKMRALESHPFDWE 85 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCChHHHH
Confidence 344455656666788999999999999997 9999999998876543
No 58
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=45.75 E-value=4.7 Score=36.50 Aligned_cols=47 Identities=26% Similarity=0.720 Sum_probs=34.8
Q ss_pred Ccce-ecCCCC-----C---CCccccCCCCCCCCceeecccCCCCCCC--C-CCCceeccccc
Q 024980 203 PTYC-VCHQVS-----F---GDMIACDNENCQGGEWFHYACVGLTPET--R-FKGKWYCPTCR 253 (259)
Q Consensus 203 ~~~C-~C~~~~-----~---g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~--~-~~~~w~C~~C~ 253 (259)
..|| ||=.-+ . .++|.|. +|. .-=|.+|+-.|... + ..-.|.|-+|.
T Consensus 224 n~YCDFclgdsr~nkkt~~peelvscs--dcg--rsghpsclqft~nm~~avk~yrwqcieck 282 (336)
T KOG1244|consen 224 NPYCDFCLGDSRENKKTGMPEELVSCS--DCG--RSGHPSCLQFTANMIAAVKTYRWQCIECK 282 (336)
T ss_pred CcccceeccccccccccCCchhhcchh--hcC--CCCCcchhhhhHHHHHHHHhheeeeeecc
Confidence 4688 784443 2 3799999 999 56799999887764 1 35589998885
No 59
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=45.66 E-value=2.5e+02 Score=25.90 Aligned_cols=28 Identities=7% Similarity=0.356 Sum_probs=12.6
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 20 LPAELQRLLNTIRELDERSHSMINQTRQ 47 (259)
Q Consensus 20 LP~El~r~l~~IreLD~~~~~~~~~l~~ 47 (259)
.+.++.....++..|...-.++..++.+
T Consensus 41 ~~~~~~~~~~el~~le~Ee~~l~~eL~~ 68 (314)
T PF04111_consen 41 SEEDIEELEEELEKLEQEEEELLQELEE 68 (314)
T ss_dssp -HH--HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555555555555555444443
No 60
>PRK11637 AmiB activator; Provisional
Probab=44.01 E-value=2.9e+02 Score=26.29 Aligned_cols=19 Identities=11% Similarity=0.237 Sum_probs=7.6
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 024980 22 AELQRLLNTIRELDERSHS 40 (259)
Q Consensus 22 ~El~r~l~~IreLD~~~~~ 40 (259)
.++...-..|.++.....+
T Consensus 47 ~~l~~l~~qi~~~~~~i~~ 65 (428)
T PRK11637 47 DQLKSIQQDIAAKEKSVRQ 65 (428)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3333344444444443333
No 61
>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=43.57 E-value=2.3e+02 Score=24.91 Aligned_cols=24 Identities=13% Similarity=0.119 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 83 QDNALSLCTEKVLLARQAYDIIDS 106 (259)
Q Consensus 83 ~~~~~~lsdEKv~LA~q~~dlVdr 106 (259)
-.....+..-+-.|.-.++.||+.
T Consensus 90 ~~qi~~~~~~~~~l~p~m~~m~~~ 113 (251)
T PF11932_consen 90 EQQIEQIEETRQELVPLMEQMIDE 113 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333344444444444444444443
No 62
>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=43.28 E-value=1.4e+02 Score=22.37 Aligned_cols=77 Identities=16% Similarity=0.187 Sum_probs=48.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 24 LQRLLNTIRELDERSHSMINQTRQQTKYCLGLASQGNKKGNGNEEDEAIEKMRKEIEVNQDNALSLCTEKVLLARQAYDI 103 (259)
Q Consensus 24 l~r~l~~IreLD~~~~~~~~~l~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~q~~dl 103 (259)
+...|-.|-++|....++..+++.+.-.+..+-.. . +....+++...|...+..+..-+++=.. .-.++
T Consensus 5 i~~lL~KlA~~e~esKeL~AqVEAleivitALL~~-------l-~~~~~~~~i~~I~~Ai~~a~~~~~~~~~---sd~eL 73 (87)
T PF10796_consen 5 IAELLAKLAEKEAESKELTAQVEALEIVITALLRT-------L-DQGGRQEMIESIEKAIEDASPSSDVPLK---SDAEL 73 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------h-CcchHHHHHHHHHHHHHHhcccCCccch---HHHHH
Confidence 55678889999999999999998765433222111 0 1124567888888888877766554322 13455
Q ss_pred HHHHHHHH
Q 024980 104 IDSHIKRL 111 (259)
Q Consensus 104 VdrhirrL 111 (259)
+.+|+++|
T Consensus 74 L~~~~~~L 81 (87)
T PF10796_consen 74 LLQYVKKL 81 (87)
T ss_pred HHHHHHHH
Confidence 55666555
No 63
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=43.03 E-value=20 Score=27.91 Aligned_cols=37 Identities=22% Similarity=0.722 Sum_probs=25.4
Q ss_pred ecCCCCCC-CccccCCCCCCCCceeecccCCCCCCCCCCCceeccccccc
Q 024980 207 VCHQVSFG-DMIACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCRLL 255 (259)
Q Consensus 207 ~C~~~~~g-~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~~~ 255 (259)
-|+....| ....|+ +|.+...+.+||= .. +||.|...
T Consensus 32 ~Crt~~~G~~~~~C~--~Cg~~~~~~~SCk---------~R-~CP~C~~~ 69 (111)
T PF14319_consen 32 ACRTEALGFHRYRCE--DCGHEKIVYNSCK---------NR-HCPSCQAK 69 (111)
T ss_pred hcCCccCCcceeecC--CCCceEEecCccc---------Cc-CCCCCCCh
Confidence 37777776 566799 7995555556774 23 89999754
No 64
>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=42.42 E-value=6.8 Score=22.95 Aligned_cols=25 Identities=24% Similarity=0.513 Sum_probs=11.1
Q ss_pred ecCCCCCC-CccccCCCCCCCCceeecccC
Q 024980 207 VCHQVSFG-DMIACDNENCQGGEWFHYACV 235 (259)
Q Consensus 207 ~C~~~~~g-~mi~Cd~~~C~~~~wfH~~Cv 235 (259)
.|+.+.++ .+-.|. .|. -++|..|+
T Consensus 5 ~C~~~~~~~~~Y~C~--~Cd--f~lH~~Ca 30 (30)
T PF07649_consen 5 ACGKPIDGGWFYRCS--ECD--FDLHEECA 30 (30)
T ss_dssp TTS----S--EEE-T--TT-------HHHH
T ss_pred cCCCcCCCCceEECc--cCC--CccChhcC
Confidence 57888777 677898 899 66899885
No 65
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=42.18 E-value=15 Score=37.07 Aligned_cols=36 Identities=22% Similarity=0.675 Sum_probs=26.4
Q ss_pred CCccccCCCCCCCCceeecccCC--CCCCCCCCCceeccccccc
Q 024980 214 GDMIACDNENCQGGEWFHYACVG--LTPETRFKGKWYCPTCRLL 255 (259)
Q Consensus 214 g~mi~Cd~~~C~~~~wfH~~Cvg--l~~~~~~~~~w~C~~C~~~ 255 (259)
+.+..|+ .|. .-||.-|.- ++..+ .|.|+|+.|...
T Consensus 81 ~kf~~Ck--~cD--vsyh~yc~~P~~~~v~--sg~~~ckk~~~c 118 (694)
T KOG4443|consen 81 KKFLLCK--RCD--VSYHCYCQKPPNDKVP--SGPWLCKKCTRC 118 (694)
T ss_pred ccccccc--ccc--ccccccccCCcccccc--CcccccHHHHhh
Confidence 4566788 899 568988875 34444 899999988643
No 66
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.67 E-value=17 Score=34.05 Aligned_cols=45 Identities=24% Similarity=0.566 Sum_probs=28.5
Q ss_pred cceecCCCC-CCCccccCCCCCCCCceeecccCCCCCCCCCCCceeccccccc
Q 024980 204 TYCVCHQVS-FGDMIACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCRLL 255 (259)
Q Consensus 204 ~~C~C~~~~-~g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~~~ 255 (259)
++|||-.-+ .|+-|.=- -|. .. ||..||.-=-. ...-+||-|+..
T Consensus 231 ~CaIClEdY~~GdklRiL--PC~-H~-FH~~CIDpWL~---~~r~~CPvCK~d 276 (348)
T KOG4628|consen 231 TCAICLEDYEKGDKLRIL--PCS-HK-FHVNCIDPWLT---QTRTFCPVCKRD 276 (348)
T ss_pred eEEEeecccccCCeeeEe--cCC-Cc-hhhccchhhHh---hcCccCCCCCCc
Confidence 667997765 46655544 466 34 99999931111 114589999864
No 67
>PRK14127 cell division protein GpsB; Provisional
Probab=41.34 E-value=89 Score=24.38 Aligned_cols=37 Identities=22% Similarity=0.373 Sum_probs=18.8
Q ss_pred HHHHHHHhhCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 10 VDDYLEYASTLPAELQRLLNTIRELDERSHSMINQTRQQT 49 (259)
Q Consensus 10 Ledfle~ie~LP~El~r~l~~IreLD~~~~~~~~~l~~~~ 49 (259)
+++||+.|.. ++.....++.+|-.+...+..++.+..
T Consensus 28 VD~FLd~V~~---dye~l~~e~~~Lk~e~~~l~~~l~e~~ 64 (109)
T PRK14127 28 VDKFLDDVIK---DYEAFQKEIEELQQENARLKAQVDELT 64 (109)
T ss_pred HHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555554432 455555555555555555555554433
No 68
>PF04100 Vps53_N: Vps53-like, N-terminal ; InterPro: IPR007234 Vps53 complexes with Vps52 and Vps54 to form a multi-subunit complex involved in regulating membrane trafficking events [].
Probab=41.08 E-value=3.2e+02 Score=25.89 Aligned_cols=89 Identities=24% Similarity=0.325 Sum_probs=46.7
Q ss_pred HHhhCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 15 EYASTLPAELQRLLNTIRELDERSHSMINQTRQQTKYCLGLASQGNKKGNGNEEDEAIEKMRKEIEVNQDNALSLCTEKV 94 (259)
Q Consensus 15 e~ie~LP~El~r~l~~IreLD~~~~~~~~~l~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv 94 (259)
+++++||.-+.+.-..|++||....+..++... ... .+ .. ........|.+.+.++.++ .+|-
T Consensus 18 ~SL~~ld~~i~~l~~~i~~ld~eI~~~v~~q~~-------~~~----~~---~~--~l~~a~~~i~~L~~~i~~i-k~kA 80 (383)
T PF04100_consen 18 QSLSNLDELIAKLRKEIRELDEEIKELVREQSS-------SGQ----DA---EE--DLEEAQEAIQELFEKISEI-KSKA 80 (383)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhh-------ccc----cc---cc--cHHHHHHHHHHHHHHHHHH-HHHH
Confidence 567778888888888888888777655332210 000 00 00 1111222333333333332 2344
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 95 LLARQAYDIIDSHIKRLDEDLNNFAE 120 (259)
Q Consensus 95 ~LA~q~~dlVdrhirrLD~dl~~~~~ 120 (259)
.-++++..-|.+-|++||..-.++..
T Consensus 81 ~~sE~~V~~it~dIk~LD~AKrNLT~ 106 (383)
T PF04100_consen 81 EESEQMVQEITRDIKQLDNAKRNLTQ 106 (383)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44567777777888888866555443
No 69
>COG0497 RecN ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=39.69 E-value=2e+02 Score=28.84 Aligned_cols=106 Identities=17% Similarity=0.212 Sum_probs=49.7
Q ss_pred hhhHHHHHHHHhhCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh----hhcCCCCCCCCCCchHHHHHHHHHHHH
Q 024980 6 TGVYVDDYLEYASTLPAELQRLLNTIRELDERSHSMINQTRQQTKYCLG----LASQGNKKGNGNEEDEAIEKMRKEIEV 81 (259)
Q Consensus 6 ~~~yLedfle~ie~LP~El~r~l~~IreLD~~~~~~~~~l~~~~k~~~~----~~~~~~~~~~~~~~~~~~~~~~~~I~~ 81 (259)
+..-|.+|++.++-=|.+|....+.|..|..-...+...++....|... +.+. . ........+..++..
T Consensus 281 a~~el~~~~~~le~Dp~~L~~ve~Rl~~L~~l~RKY~~~~~~l~~~~~~~~~el~~L---~----~~~~~~~~Le~~~~~ 353 (557)
T COG0497 281 ASEELRAYLDELEFDPNRLEEVEERLFALKSLARKYGVTIEDLLEYLDKIKEELAQL---D----NSEESLEALEKEVKK 353 (557)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHh---h----hhhhHHHHHHHHHHH
Confidence 4445677777777777777776666655554333332222221111110 0000 0 001112223333332
Q ss_pred HH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 82 NQ----DNALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNF 118 (259)
Q Consensus 82 ~~----~~~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~ 118 (259)
.+ ..|..|+......|..+-..|...++.|-..-..|
T Consensus 354 l~~~~~~~A~~Ls~~R~~~A~~L~~~v~~eL~~L~Me~a~F 394 (557)
T COG0497 354 LKAELLEAAEALSAIRKKAAKELEKEVTAELKALAMEKARF 394 (557)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCceE
Confidence 22 34566666666666666666666666655444433
No 70
>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=38.87 E-value=9.2 Score=27.67 Aligned_cols=10 Identities=30% Similarity=1.152 Sum_probs=8.6
Q ss_pred ceeecccCCC
Q 024980 228 EWFHYACVGL 237 (259)
Q Consensus 228 ~wfH~~Cvgl 237 (259)
.|||+.|+-.
T Consensus 39 ~W~H~~C~~~ 48 (82)
T PF00645_consen 39 KWYHWDCFFK 48 (82)
T ss_dssp EEEEHHHHHH
T ss_pred ceECcccccc
Confidence 9999999753
No 71
>KOG1655 consensus Protein involved in vacuolar protein sorting [Intracellular trafficking, secretion, and vesicular transport]
Probab=38.03 E-value=88 Score=27.12 Aligned_cols=31 Identities=19% Similarity=0.427 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024980 95 LLARQAYDIIDSHIKRLDEDLNNFAEDLKQE 125 (259)
Q Consensus 95 ~LA~q~~dlVdrhirrLD~dl~~~~~~L~~~ 125 (259)
.-.++.-+.|++.|.+||.+|.+|...+...
T Consensus 22 ~~v~~r~dSve~KIskLDaeL~k~~~Qi~k~ 52 (218)
T KOG1655|consen 22 DSVNKRSDSVEKKISKLDAELCKYKDQIKKT 52 (218)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHHHHHHHHhc
Confidence 3346677889999999999999999877544
No 72
>KOG1671 consensus Ubiquinol cytochrome c reductase, subunit RIP1 [Energy production and conversion]
Probab=37.18 E-value=17 Score=31.43 Aligned_cols=22 Identities=32% Similarity=0.736 Sum_probs=15.2
Q ss_pred ecccCCCCCCCCCCCceecc-ccc
Q 024980 231 HYACVGLTPETRFKGKWYCP-TCR 253 (259)
Q Consensus 231 H~~Cvgl~~~~~~~~~w~C~-~C~ 253 (259)
|+.||-+...- +.|.|||| .|.
T Consensus 155 hLGCVp~~~AG-d~gg~~CPCHGS 177 (210)
T KOG1671|consen 155 HLGCVPIANAG-DYGGYYCPCHGS 177 (210)
T ss_pred ccccccccccc-ccCceecccccc
Confidence 88999554332 47899999 443
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=37.10 E-value=2.3e+02 Score=23.10 Aligned_cols=43 Identities=12% Similarity=0.146 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 78 EIEVNQDNALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNFAE 120 (259)
Q Consensus 78 ~I~~~~~~~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~~ 120 (259)
.|...++...--...-|..-+.++......|.+|+.++..+.+
T Consensus 90 ~~~~~~e~~i~~~~~~I~~Lq~~~~~~~~ki~~Le~~i~~~~~ 132 (146)
T PF08702_consen 90 MIIYILETKIINQPSNIRVLQNILRSNRQKIQRLEQDIDQQER 132 (146)
T ss_dssp HHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334555666667777888889999999999999999976543
No 74
>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=36.20 E-value=5.4 Score=26.40 Aligned_cols=28 Identities=25% Similarity=0.674 Sum_probs=17.0
Q ss_pred CCC-CceeecccCCCCCCCCCCCceeccccc
Q 024980 224 CQG-GEWFHYACVGLTPETRFKGKWYCPTCR 253 (259)
Q Consensus 224 C~~-~~wfH~~Cvgl~~~~~~~~~w~C~~C~ 253 (259)
|.| ..|||.+|+--=-.. .++..||.|.
T Consensus 21 C~G~~~~vH~~Cl~~W~~~--~~~~~C~iC~ 49 (49)
T smart00744 21 CKGSLKYVHQECLERWINE--SGNKTCEICK 49 (49)
T ss_pred cCCchhHHHHHHHHHHHHH--cCCCcCCCCC
Confidence 652 369999998521112 3345888873
No 75
>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=35.96 E-value=4.5e+02 Score=26.18 Aligned_cols=43 Identities=21% Similarity=0.238 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 74 KMRKEIEVNQDNALSLCTE-KVLLARQAYDIIDSHIKRLDEDLN 116 (259)
Q Consensus 74 ~~~~~I~~~~~~~~~lsdE-Kv~LA~q~~dlVdrhirrLD~dl~ 116 (259)
..+..|...|....++... =..=|..++.-+..++..|...+.
T Consensus 168 ~~L~~ie~~F~~f~~lt~~GD~~~A~eil~~l~~~~~~l~~~~e 211 (560)
T PF06160_consen 168 KQLENIEEEFSEFEELTENGDYLEAREILEKLKEETDELEEIME 211 (560)
T ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444444443332 233344444444444444444443
No 76
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=35.34 E-value=28 Score=31.22 Aligned_cols=20 Identities=35% Similarity=0.801 Sum_probs=16.2
Q ss_pred CCCCCCCC-CCCceecccccc
Q 024980 235 VGLTPETR-FKGKWYCPTCRL 254 (259)
Q Consensus 235 vgl~~~~~-~~~~w~C~~C~~ 254 (259)
||++..+. ..-+.|||.|..
T Consensus 136 vGlSd~~g~~~VKlyCP~C~D 156 (251)
T PTZ00396 136 IGLSDVLKTSRVKVYCPRCQE 156 (251)
T ss_pred cccCCCcCcCceeEeCCCchh
Confidence 78888885 556999999974
No 77
>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=35.16 E-value=36 Score=22.15 Aligned_cols=35 Identities=31% Similarity=0.737 Sum_probs=24.7
Q ss_pred CCcce-ecCCCCC---CCccccCCCCCCCCceeecccCCCCCC
Q 024980 202 EPTYC-VCHQVSF---GDMIACDNENCQGGEWFHYACVGLTPE 240 (259)
Q Consensus 202 ~~~~C-~C~~~~~---g~mi~Cd~~~C~~~~wfH~~Cvgl~~~ 240 (259)
.+.+| +|+..-+ ..-+.|. .|. .-+|-.|+.....
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~--~C~--~~~H~~C~~~~~~ 48 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCS--WCG--LVCHKKCLSKVPP 48 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEET--TTT---EEETTGGCTSSS
T ss_pred CCCCCcccCcccCCCCCCeEEEC--CCC--ChHhhhhhhhcCC
Confidence 46788 7888763 4677899 899 5699999865443
No 78
>KOG0996 consensus Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]
Probab=34.43 E-value=6.1e+02 Score=28.02 Aligned_cols=44 Identities=18% Similarity=0.305 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 77 KEIEVNQDNALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNFAE 120 (259)
Q Consensus 77 ~~I~~~~~~~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~~ 120 (259)
.+|......+..+.++|++.-..=.+-|...|..|.+++.++..
T Consensus 885 ~~i~~lq~~i~~i~~e~~q~qk~kv~~~~~~~~~l~~~i~k~~~ 928 (1293)
T KOG0996|consen 885 ARIKELQNKIDEIGGEKVQAQKDKVEKINEQLDKLEADIAKLTV 928 (1293)
T ss_pred HHHHHHHHHHHHhhchhhHHhHHHHHHHHHHHHHHHHHHHHhHH
Confidence 45666666777777777777666666666666666666666544
No 79
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=34.26 E-value=18 Score=33.45 Aligned_cols=39 Identities=28% Similarity=0.717 Sum_probs=25.1
Q ss_pred Ccce-ecCCCC--CCCccccCCCCCCCCceeecccCCCCCCCCCCCceecccccc
Q 024980 203 PTYC-VCHQVS--FGDMIACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCRL 254 (259)
Q Consensus 203 ~~~C-~C~~~~--~g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~~ 254 (259)
.-+| -|.-+- ||.||-|+ --|=+.|.-... .-.||.|..
T Consensus 90 VHfCd~Cd~PI~IYGRmIPCk-------HvFCl~CAr~~~------dK~Cp~C~d 131 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIYGRMIPCK-------HVFCLECARSDS------DKICPLCDD 131 (389)
T ss_pred eEeecccCCcceeeecccccc-------hhhhhhhhhcCc------cccCcCccc
Confidence 4566 477764 89999999 226677764333 336777753
No 80
>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=33.50 E-value=2.1e+02 Score=21.57 Aligned_cols=98 Identities=15% Similarity=0.224 Sum_probs=55.1
Q ss_pred HHHHHhhCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCchHHHHHHH--HHHHHHHHHHHHH
Q 024980 12 DYLEYASTLPAELQRLLNTIRELDERSHSMINQTRQQTKYCLGLASQGNKKGNGNEEDEAIEKMR--KEIEVNQDNALSL 89 (259)
Q Consensus 12 dfle~ie~LP~El~r~l~~IreLD~~~~~~~~~l~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~--~~I~~~~~~~~~l 89 (259)
+.+..+..|-.+++.....++.|+....+...-++... .+. +....-... .-|......+...
T Consensus 3 ~~~~~~q~l~~~~~~l~~~~~~l~~~~~E~~~v~~EL~----~l~-----------~d~~vy~~VG~vfv~~~~~ea~~~ 67 (105)
T cd00632 3 EQLAQLQQLQQQLQAYIVQRQKVEAQLNENKKALEELE----KLA-----------DDAEVYKLVGNVLVKQEKEEARTE 67 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----cCC-----------CcchHHHHhhhHHhhccHHHHHHH
Confidence 34444555556666666666666666665433332221 110 000000000 1244555667777
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024980 90 CTEKVLLARQAYDIIDSHIKRLDEDLNNFAEDLKQ 124 (259)
Q Consensus 90 sdEKv~LA~q~~dlVdrhirrLD~dl~~~~~~L~~ 124 (259)
-++++.......+-++..+..|...+..++..|.+
T Consensus 68 Le~~~e~le~~i~~l~~~~~~l~~~~~elk~~l~~ 102 (105)
T cd00632 68 LKERLETIELRIKRLERQEEDLQEKLKELQEKIQQ 102 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77777777777778888888888888877776653
No 81
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=33.28 E-value=4.7e+02 Score=26.10 Aligned_cols=47 Identities=17% Similarity=0.300 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 72 IEKMRKEIEVNQDNALSLCT-EKVLLARQAYDIIDSHIKRLDEDLNNF 118 (259)
Q Consensus 72 ~~~~~~~I~~~~~~~~~lsd-EKv~LA~q~~dlVdrhirrLD~dl~~~ 118 (259)
.+..+..|...|.....+-. --..=|..+++-+..|+..|...+...
T Consensus 170 le~~l~~~e~~f~~f~~l~~~Gd~~~A~e~l~~l~~~~~~l~~~~~~i 217 (569)
T PRK04778 170 LEKQLENLEEEFSQFVELTESGDYVEAREILDQLEEELAALEQIMEEI 217 (569)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555555544422 123345555666666666666655543
No 82
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=33.16 E-value=3.5e+02 Score=24.07 Aligned_cols=32 Identities=16% Similarity=0.117 Sum_probs=20.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 21 PAELQRLLNTIRELDERSHSMINQTRQQTKYC 52 (259)
Q Consensus 21 P~El~r~l~~IreLD~~~~~~~~~l~~~~k~~ 52 (259)
+......|-.|..||.....+...+....+++
T Consensus 2 m~~~~~~L~~iq~lD~e~~rl~~~~~~~~~~l 33 (239)
T COG1579 2 MNNNLKSLLAIQKLDLEKDRLEPRIKEIRKAL 33 (239)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHhhhhhHHHH
Confidence 34455677778888888877766655444433
No 83
>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=32.69 E-value=28 Score=28.59 Aligned_cols=28 Identities=25% Similarity=0.660 Sum_probs=16.4
Q ss_pred ceeecccCCCCCCC-C-CCCceeccccccc
Q 024980 228 EWFHYACVGLTPET-R-FKGKWYCPTCRLL 255 (259)
Q Consensus 228 ~wfH~~Cvgl~~~~-~-~~~~w~C~~C~~~ 255 (259)
.||..+|-+=...- . ..+.|+|+.|...
T Consensus 31 ~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~ 60 (166)
T cd04476 31 NWWYPACPGCNKKVVEEGNGTYRCEKCNKS 60 (166)
T ss_pred CeEEccccccCcccEeCCCCcEECCCCCCc
Confidence 46666665322211 1 1379999999754
No 84
>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=31.55 E-value=6.9e+02 Score=26.96 Aligned_cols=53 Identities=13% Similarity=0.265 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Q 024980 75 MRKEIEVNQDNA---LSLCTEKVLLARQAYDIIDSHIKRLDEDLNNFAEDLKQEGK 127 (259)
Q Consensus 75 ~~~~I~~~~~~~---~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~~~L~~~~~ 127 (259)
.+..+.+.++.+ +++++|+..--++=+++..-.+..|+.||+-++++.++.|.
T Consensus 305 emad~ad~iEmaTldKEmAEERaesLQ~eve~lkEr~deletdlEILKaEmeekG~ 360 (1243)
T KOG0971|consen 305 EMADTADAIEMATLDKEMAEERAESLQQEVEALKERVDELETDLEILKAEMEEKGS 360 (1243)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 334455444433 78899998888888899999999999999999888877764
No 85
>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=31.30 E-value=4.3e+02 Score=24.50 Aligned_cols=36 Identities=25% Similarity=0.299 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH----HHH---HHHHHHHHHH
Q 024980 80 EVNQDNALSLCTEKVLLARQAYD----IID---SHIKRLDEDL 115 (259)
Q Consensus 80 ~~~~~~~~~lsdEKv~LA~q~~d----lVd---rhirrLD~dl 115 (259)
.....+..+|.+||+.|.+++-. +|+ +.|.+|..+.
T Consensus 109 n~L~rkl~qLr~EK~~lE~~Le~EqE~~V~kL~k~i~~Le~e~ 151 (310)
T PF09755_consen 109 NDLSRKLNQLRQEKVELENQLEQEQEYLVNKLQKKIERLEKEK 151 (310)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 34567889999999999998763 344 5555555443
No 86
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=31.26 E-value=30 Score=29.75 Aligned_cols=31 Identities=26% Similarity=0.712 Sum_probs=23.4
Q ss_pred CccccCCCCCCCCceeecccCCCCCCCCCCCceeccccccccCC
Q 024980 215 DMIACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCRLLPQC 258 (259)
Q Consensus 215 ~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~~~~~~ 258 (259)
..+.|+ .|. .-||-.|.. . -.||.|.+...+
T Consensus 171 ~~~~C~--~C~--~v~H~~C~~----~-----~~CpkC~R~~~r 201 (202)
T PF13901_consen 171 TTVRCP--KCK--SVFHKSCFR----K-----KSCPKCARRQKR 201 (202)
T ss_pred CeeeCC--cCc--cccchhhcC----C-----CCCCCcHhHhcc
Confidence 567899 899 779999995 1 129999876543
No 87
>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=31.18 E-value=3.6e+02 Score=23.56 Aligned_cols=53 Identities=17% Similarity=0.329 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH
Q 024980 71 AIEKMRKEIEVNQDNALSLCTEKVLLARQAYDIID-------SHIKRLDEDLNNFAEDLK 123 (259)
Q Consensus 71 ~~~~~~~~I~~~~~~~~~lsdEKv~LA~q~~dlVd-------rhirrLD~dl~~~~~~L~ 123 (259)
....+...|+...=++..++.+.|.||..+++.|- .-..+|..-+..|...+.
T Consensus 50 ~l~~Y~~~lr~~lP~~~~~a~d~l~la~~ald~V~~~~~g~~~~~~~l~~l~~~l~~~~~ 109 (229)
T PF11101_consen 50 ALQQYQQGLRQQLPWVVQLASDGLELARDALDEVATSLLGDSNARDRLKQLMDQLKQQVD 109 (229)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHH
Confidence 34567778899999999999999999999998873 444556666666555543
No 88
>KOG1510 consensus RNA polymerase II holoenzyme and mediator subcomplex, subunit SURB7/SRB7 [Transcription]
Probab=31.15 E-value=2.9e+02 Score=22.47 Aligned_cols=31 Identities=23% Similarity=0.400 Sum_probs=17.3
Q ss_pred HhhCChHH---HHHHHHHHHHHHHHHHHHHHHHH
Q 024980 16 YASTLPAE---LQRLLNTIRELDERSHSMINQTR 46 (259)
Q Consensus 16 ~ie~LP~E---l~r~l~~IreLD~~~~~~~~~l~ 46 (259)
.|++||.+ -...+..|..|+.+..+...++.
T Consensus 75 LIdsLP~~~~~~e~Ql~~i~kLq~en~e~~~el~ 108 (139)
T KOG1510|consen 75 LIDSLPGEEGSAEAQLEKIKKLQEENEEVALELE 108 (139)
T ss_pred HHHhCCCcccCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566655 44556666666666655544443
No 89
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=31.13 E-value=52 Score=32.66 Aligned_cols=48 Identities=25% Similarity=0.540 Sum_probs=35.3
Q ss_pred CCCccee-cCCCCCCCccccCCCCCCCCceeecccCCCCCCC-CCCCceecccccc
Q 024980 201 NEPTYCV-CHQVSFGDMIACDNENCQGGEWFHYACVGLTPET-RFKGKWYCPTCRL 254 (259)
Q Consensus 201 ~~~~~C~-C~~~~~g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~-~~~~~w~C~~C~~ 254 (259)
|-.+||+ |+.+ |..+-|+ .|. .=||..|..-.... .....|.||.|+.
T Consensus 58 N~d~~cfechlp--g~vl~c~--vc~--Rs~h~~c~sp~~q~r~~s~p~~~p~p~s 107 (588)
T KOG3612|consen 58 NIDPFCFECHLP--GAVLKCI--VCH--RSFHENCQSPDPQKRNYSVPSDKPQPYS 107 (588)
T ss_pred CCCcccccccCC--cceeeee--hhh--ccccccccCcchhhccccccccCCcccc
Confidence 4578896 8877 7778899 899 77999998543332 1345799998864
No 90
>PRK11546 zraP zinc resistance protein; Provisional
Probab=31.03 E-value=3e+02 Score=22.56 Aligned_cols=32 Identities=19% Similarity=0.251 Sum_probs=20.4
Q ss_pred hhCChHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Q 024980 17 ASTLPAELQRLLNTIR-ELDERSHSMINQTRQQ 48 (259)
Q Consensus 17 ie~LP~El~r~l~~Ir-eLD~~~~~~~~~l~~~ 48 (259)
..+|+.|=+-.+..|+ +-..+..+++.++-..
T Consensus 41 ~~~LT~EQQa~~q~I~~~f~~~t~~LRqqL~aK 73 (143)
T PRK11546 41 AAPLTTEQQAAWQKIHNDFYAQTSALRQQLVSK 73 (143)
T ss_pred cccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4578999887776664 3445555666665443
No 91
>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=30.74 E-value=3.3e+02 Score=23.03 Aligned_cols=108 Identities=12% Similarity=0.134 Sum_probs=54.4
Q ss_pred HHHHHHhhCChHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHhhhcCCCC--CCCCCCchHHHHHHHHHHHHHHH
Q 024980 11 DDYLEYASTLPAELQRLLNTIRELDERSHSMINQT----RQQTKYCLGLASQGNK--KGNGNEEDEAIEKMRKEIEVNQD 84 (259)
Q Consensus 11 edfle~ie~LP~El~r~l~~IreLD~~~~~~~~~l----~~~~k~~~~~~~~~~~--~~~~~~~~~~~~~~~~~I~~~~~ 84 (259)
+++-..++.|-.+..-+-.++.+++..+..+...- ....+.+......... ..+.....+.... -|...+.
T Consensus 42 ~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~~~~~~~~~~e~~~~~~~~~~~p~y~~---Mi~~L~~ 118 (177)
T PF03234_consen 42 EERKQEIEELKYERKINEKLLKRIQKLLSALDKEEEADKQEVMESLNEPFDKKEKPGVENKDPEQPTYDE---MIEDLLD 118 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccchHHHHHHHHhcccccccccccccCCCCCCCHHH---HHHHHHH
Confidence 45555666666666666666666666665543321 1111122111100000 0001111222233 3445555
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 85 NALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNFAEDLK 123 (259)
Q Consensus 85 ~~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~~~L~ 123 (259)
.+..-.+++- ...+...|..|..+|+...+.....|+
T Consensus 119 qvk~~~de~~--~~~~~~~l~~H~~kl~~~~ke~~~kLe 155 (177)
T PF03234_consen 119 QVKKEPDEKS--GKAELEELQEHRAKLEKEQKELKKKLE 155 (177)
T ss_pred HHhcccCccc--HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5555555544 778888889999888877766655544
No 92
>KOG2626 consensus Histone H3 (Lys4) methyltransferase complex, subunit CPS60/ASH2/BRE2 [Chromatin structure and dynamics; Transcription]
Probab=30.53 E-value=33 Score=33.88 Aligned_cols=51 Identities=20% Similarity=0.458 Sum_probs=34.7
Q ss_pred CCCcceecCCCCC--CCccccCCCCCCCCceeecccCCCCC-----CCC-CCCceeccccccc
Q 024980 201 NEPTYCVCHQVSF--GDMIACDNENCQGGEWFHYACVGLTP-----ETR-FKGKWYCPTCRLL 255 (259)
Q Consensus 201 ~~~~~C~C~~~~~--g~mi~Cd~~~C~~~~wfH~~Cvgl~~-----~~~-~~~~w~C~~C~~~ 255 (259)
-..++|+|..... -.-++|. .|. .|||..|.-... .|- ..-.|.|..|...
T Consensus 18 ~~~~~~y~e~~r~l~~~elqcs--~cl--k~~~~~~~~~~~~~~s~~pf~t~y~fvc~~c~~~ 76 (544)
T KOG2626|consen 18 KQATVCYCEGERNLGIVELQCS--TCL--KWFHLPTLEAFHLIKSSLPFMTSYEFVCKECTPS 76 (544)
T ss_pred cCccccccccccccCceeeEee--ecc--cccccccccccccccccCCcccceeEEeccccCc
Confidence 3478899988764 3678999 899 999975543221 121 2347889999754
No 93
>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=30.08 E-value=28 Score=22.97 Aligned_cols=31 Identities=26% Similarity=0.864 Sum_probs=15.6
Q ss_pred ccccCCCCCCCCceeecccCCCCCCCC-CCCceeccc
Q 024980 216 MIACDNENCQGGEWFHYACVGLTPETR-FKGKWYCPT 251 (259)
Q Consensus 216 mi~Cd~~~C~~~~wfH~~Cvgl~~~~~-~~~~w~C~~ 251 (259)
.|+|| .|. .|=... .++..... ..+.|||..
T Consensus 3 WVQCd--~C~--KWR~lp-~~~~~~~~~~~d~W~C~~ 34 (50)
T PF07496_consen 3 WVQCD--SCL--KWRRLP-EEVDPIREELPDPWYCSM 34 (50)
T ss_dssp EEE-T--TT----EEEE--CCHHCTSCCSSTT--GGG
T ss_pred EEECC--CCC--ceeeCC-hhhCcccccCCCeEEcCC
Confidence 58999 899 998776 55443211 133999986
No 94
>PHA02862 5L protein; Provisional
Probab=29.85 E-value=14 Score=30.41 Aligned_cols=27 Identities=22% Similarity=0.307 Sum_probs=18.6
Q ss_pred CceeecccCCCCCCCCCCCceeccccccc
Q 024980 227 GEWFHYACVGLTPETRFKGKWYCPTCRLL 255 (259)
Q Consensus 227 ~~wfH~~Cvgl~~~~~~~~~w~C~~C~~~ 255 (259)
+.|.|.+|+..=-.+ .++-+|+.|...
T Consensus 25 ~K~VHq~CL~~WIn~--S~k~~CeLCkte 51 (156)
T PHA02862 25 YKVVHIKCMQLWINY--SKKKECNLCKTK 51 (156)
T ss_pred chhHHHHHHHHHHhc--CCCcCccCCCCe
Confidence 488999997632233 557789988754
No 95
>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=29.65 E-value=2.5e+02 Score=21.40 Aligned_cols=43 Identities=9% Similarity=0.381 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 81 VNQDNALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNFAEDLK 123 (259)
Q Consensus 81 ~~~~~~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~~~L~ 123 (259)
..+.+|.+.-++|+...+...+-+++.+..+...+..+...+.
T Consensus 83 ~~~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~~l~ 125 (129)
T cd00890 83 KSLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQEELQ 125 (129)
T ss_pred ecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445778888999999999999999999999988888877654
No 96
>PHA02562 46 endonuclease subunit; Provisional
Probab=29.42 E-value=5.4e+02 Score=25.04 Aligned_cols=27 Identities=11% Similarity=0.283 Sum_probs=14.7
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 20 LPAELQRLLNTIRELDERSHSMINQTR 46 (259)
Q Consensus 20 LP~El~r~l~~IreLD~~~~~~~~~l~ 46 (259)
+|..+...-..|.+|..++..+...+.
T Consensus 297 ~~~~~~~l~d~i~~l~~~l~~l~~~i~ 323 (562)
T PHA02562 297 GPDRITKIKDKLKELQHSLEKLDTAID 323 (562)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355555555566666555555544443
No 97
>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=28.97 E-value=6.7e+02 Score=25.96 Aligned_cols=99 Identities=17% Similarity=0.232 Sum_probs=0.0
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
Q 024980 19 TLPAELQRLLNTIRELDERSHSMINQTRQQTKYCLGLASQGNKKGNGNEEDEAIEKMRKEIEVNQDNALSLCTEKVLLA- 97 (259)
Q Consensus 19 ~LP~El~r~l~~IreLD~~~~~~~~~l~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA- 97 (259)
.|-.||+..=.+.-+|..+++++....++-...+..+-.+ +.+.-......+.-...-.++..-.+++-+-+
T Consensus 457 ~lk~eL~qlr~ene~Lq~Kl~~L~~aRq~DKq~l~~LEkr-------L~eE~~~R~~lEkQL~eErk~r~~ee~~aar~~ 529 (697)
T PF09726_consen 457 SLKSELSQLRQENEQLQNKLQNLVQARQQDKQSLQQLEKR-------LAEERRQRASLEKQLQEERKARKEEEEKAARAL 529 (697)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhcc
Q ss_pred -------HHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024980 98 -------RQAYDIIDSHIKRLDEDLNNFAEDLKQ 124 (259)
Q Consensus 98 -------~q~~dlVdrhirrLD~dl~~~~~~L~~ 124 (259)
+..-+..-.+.+.||.++.+++.+|..
T Consensus 530 ~~~~~~r~e~~e~~r~r~~~lE~E~~~lr~elk~ 563 (697)
T PF09726_consen 530 AQAQATRQECAESCRQRRRQLESELKKLRRELKQ 563 (697)
T ss_pred ccchhccchhHHHHHHHHHHHHHHHHHHHHHHHH
No 98
>PHA02562 46 endonuclease subunit; Provisional
Probab=28.29 E-value=5.6e+02 Score=24.91 Aligned_cols=31 Identities=10% Similarity=0.142 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 73 EKMRKEIEVNQDNALSLCTEKVLLARQAYDI 103 (259)
Q Consensus 73 ~~~~~~I~~~~~~~~~lsdEKv~LA~q~~dl 103 (259)
..+..++.....++..+..+.-.+-..+.++
T Consensus 216 ~~l~~e~~~l~~~~~~l~~~l~~l~~~i~~l 246 (562)
T PHA02562 216 ARKQNKYDELVEEAKTIKAEIEELTDELLNL 246 (562)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444455555555555555555555555555
No 99
>KOG4451 consensus Uncharacterized conserved protein (tumor-associated antigen HCA127 in humans) [Function unknown]
Probab=28.28 E-value=4.3e+02 Score=23.55 Aligned_cols=41 Identities=20% Similarity=0.221 Sum_probs=31.0
Q ss_pred hHHHHHHHHhhCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 8 VYVDDYLEYASTLPAELQRLLNTIRELDERSHSMINQTRQQ 48 (259)
Q Consensus 8 ~yLedfle~ie~LP~El~r~l~~IreLD~~~~~~~~~l~~~ 48 (259)
.-||+|-..++.|=.|=.-.+++||++-.-..++...+++.
T Consensus 50 ~~leey~~em~~lL~ekm~Hveelr~iHadiN~men~ikq~ 90 (286)
T KOG4451|consen 50 ENLEEYELEMGVLLLEKMGHVEELREIHADINEMENDIKQV 90 (286)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Confidence 35788888888888887777888888888887776666543
No 100
>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=27.89 E-value=47 Score=24.61 Aligned_cols=26 Identities=27% Similarity=0.692 Sum_probs=16.2
Q ss_pred ce-ecCCCCC-CCccccCCCCCCCCceeecccC
Q 024980 205 YC-VCHQVSF-GDMIACDNENCQGGEWFHYACV 235 (259)
Q Consensus 205 ~C-~C~~~~~-g~mi~Cd~~~C~~~~wfH~~Cv 235 (259)
.| +|+++-. +.++-.- |. .-||++|.
T Consensus 80 ~C~vC~k~l~~~~f~~~p---~~--~v~H~~C~ 107 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFP---CG--HVVHYSCI 107 (109)
T ss_pred CccCcCCcCCCceEEEeC---CC--eEEecccc
Confidence 36 8998865 3333333 33 44899997
No 101
>KOG2685 consensus Cystoskeletal protein Tektin [Cytoskeleton]
Probab=27.89 E-value=5.6e+02 Score=24.75 Aligned_cols=104 Identities=15% Similarity=0.188 Sum_probs=59.0
Q ss_pred HHHHHHhhCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------hhhcCCCCCCCCCCchHHHHHHHHHHHHHHH
Q 024980 11 DDYLEYASTLPAELQRLLNTIRELDERSHSMINQTRQQTKYCL------GLASQGNKKGNGNEEDEAIEKMRKEIEVNQD 84 (259)
Q Consensus 11 edfle~ie~LP~El~r~l~~IreLD~~~~~~~~~l~~~~k~~~------~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~ 84 (259)
.+.-+-...|-..+...+.+|.+.+.....+...|....-.++ +.+. .+.+-.+=-+.+--.+..++.. +.
T Consensus 281 ~etqdar~kL~~ql~k~leEi~~~e~~I~~le~airdK~~pLKVAqTRle~Rt--~RPnvELCrD~AQ~~L~~EV~~-l~ 357 (421)
T KOG2685|consen 281 RETQDARNKLEWQLAKTLEEIADAENNIEALERAIRDKEGPLKVAQTRLENRT--YRPNVELCRDQAQYRLVDEVHE-LD 357 (421)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccccHHHHHHHHHHcc--cCCchHHHHhHHHHHHHHHHHH-HH
Confidence 3444555666677777788888777777766666644322111 1111 0111000001111223333322 23
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 85 NALSLCTEKVLLARQAYDIIDSHIKRLDEDLNN 117 (259)
Q Consensus 85 ~~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~ 117 (259)
....--.+|+.-|+..+.++.+|-.+|+.||+-
T Consensus 358 ~t~~~L~~kL~eA~~~l~~L~~~~~rLe~di~~ 390 (421)
T KOG2685|consen 358 DTVAALKEKLDEAEDSLKLLVNHRARLERDIAI 390 (421)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555688999999999999999999999964
No 102
>PF15233 SYCE1: Synaptonemal complex central element protein 1
Probab=27.89 E-value=3.3e+02 Score=22.03 Aligned_cols=15 Identities=47% Similarity=0.240 Sum_probs=6.9
Q ss_pred HHHHHHHHHHHHHHH
Q 024980 82 NQDNALSLCTEKVLL 96 (259)
Q Consensus 82 ~~~~~~~lsdEKv~L 96 (259)
...+...|..|||.|
T Consensus 39 L~~ELDsL~~EkvhL 53 (134)
T PF15233_consen 39 LQRELDSLNGEKVHL 53 (134)
T ss_pred HHHHHHHHhhhHHHH
Confidence 334444455555444
No 103
>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=27.48 E-value=77 Score=20.79 Aligned_cols=26 Identities=27% Similarity=0.538 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 95 LLARQAYDIIDSHIKRLDEDLNNFAE 120 (259)
Q Consensus 95 ~LA~q~~dlVdrhirrLD~dl~~~~~ 120 (259)
.|-+..||-|+..|..+|..++.+++
T Consensus 8 elLqe~~d~IEqkiedid~qIaeLe~ 33 (46)
T PF08946_consen 8 ELLQEHYDNIEQKIEDIDEQIAELEA 33 (46)
T ss_dssp -------THHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhHHHhHHHHHHHHHHHHH
Confidence 35567788888888888888876654
No 104
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=27.42 E-value=49 Score=28.69 Aligned_cols=42 Identities=29% Similarity=0.586 Sum_probs=26.1
Q ss_pred Ccce-ecCCCC--------CCCccccCCCCCCCCceeecccCCCCCCCCCCCceeccccc
Q 024980 203 PTYC-VCHQVS--------FGDMIACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCR 253 (259)
Q Consensus 203 ~~~C-~C~~~~--------~g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~ 253 (259)
..-| +|+... .+-++.=|.|.|+.| . |+.+-. =..|.||.|-
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y-----~--~vnP~~--Y~V~vCP~Cg 55 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRY-----K--GVNPLF--YEVWVCPHCG 55 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCCCcccc-----C--CCCCee--eeEEECCCCC
Confidence 4557 677652 235777888889822 1 233333 5689999994
No 105
>PRK10626 hypothetical protein; Provisional
Probab=27.40 E-value=2.7e+02 Score=24.78 Aligned_cols=46 Identities=15% Similarity=0.171 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHH
Q 024980 72 IEKMRKEIEVNQDNALSLCTEKVLLARQAYDIID-----------SHIKRLDEDLNN 117 (259)
Q Consensus 72 ~~~~~~~I~~~~~~~~~lsdEKv~LA~q~~dlVd-----------rhirrLD~dl~~ 117 (259)
..++...|+..+=++.+++.+.|.+|.+++|.|- .++..|+.++++
T Consensus 73 ~~~Yq~~lr~~lP~i~~~a~~~l~~A~~alD~Vi~~~~G~~snvr~rl~~l~~~l~~ 129 (239)
T PRK10626 73 AKDYQAALRQDLPWIDEGAKSRLEKARVALDKVIVQELGESSNVRNRLTKLDAQLKQ 129 (239)
T ss_pred HHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHHhccCccchHHHHHHHHHHHHHH
Confidence 4567778888888999999999999999999864 355666666543
No 106
>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=27.29 E-value=32 Score=19.96 Aligned_cols=12 Identities=42% Similarity=1.583 Sum_probs=9.5
Q ss_pred CCceeccccccc
Q 024980 244 KGKWYCPTCRLL 255 (259)
Q Consensus 244 ~~~w~C~~C~~~ 255 (259)
.|.|.|+.|.-.
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 579999999743
No 107
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=27.29 E-value=3.9e+02 Score=22.68 Aligned_cols=41 Identities=12% Similarity=0.215 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 79 IEVNQDNALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNFA 119 (259)
Q Consensus 79 I~~~~~~~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~ 119 (259)
..+.+....++..+=++-|....+-+.+.+..|+.+|...+
T Consensus 133 ~~~~~~~G~~~r~~~i~~a~~~~~e~~~~l~~l~~ei~~~~ 173 (176)
T PF12999_consen 133 EEEIYKEGLKIRQELIEEAKKKREELEKKLEELEKEIQAAK 173 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 33444455555555555566666666666677776666543
No 108
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=26.83 E-value=7e+02 Score=25.48 Aligned_cols=30 Identities=13% Similarity=0.203 Sum_probs=14.6
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 19 TLPAELQRLLNTIRELDERSHSMINQTRQQ 48 (259)
Q Consensus 19 ~LP~El~r~l~~IreLD~~~~~~~~~l~~~ 48 (259)
..+-|+.-....|+.++.+...+..++..+
T Consensus 412 ~e~~ei~~~~~~i~~~~~~ve~l~~e~~~L 441 (652)
T COG2433 412 EERREITVYEKRIKKLEETVERLEEENSEL 441 (652)
T ss_pred ccccchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444555555555555555544444433
No 109
>PF13851 GAS: Growth-arrest specific micro-tubule binding
Probab=26.67 E-value=4.1e+02 Score=22.75 Aligned_cols=91 Identities=16% Similarity=0.211 Sum_probs=51.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHH
Q 024980 24 LQRLLNTIRELDERSHSMINQTRQQTKYCLGLASQGNKKGNGNEEDEAIEKMRKEIEVNQDNALSLCTEKVLLAR--QAY 101 (259)
Q Consensus 24 l~r~l~~IreLD~~~~~~~~~l~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~LA~--q~~ 101 (259)
..-+|.+|+.|-.++.++........+.+.+..+.. + .+.+ .......++.........+..+|..|++ .-+
T Consensus 22 T~~NL~lIksLKeei~emkk~e~~~~k~m~ei~~eN--~--~L~e--pL~~a~~e~~eL~k~L~~y~kdK~~L~~~k~rl 95 (201)
T PF13851_consen 22 TLNNLELIKSLKEEIAEMKKKEERNEKLMAEISQEN--K--RLSE--PLKKAEEEVEELRKQLKNYEKDKQSLQNLKARL 95 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--H--HHhH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456778888887777776655544444332221110 0 0011 1234455566666777778888887765 344
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 024980 102 DIIDSHIKRLDEDLNNFAE 120 (259)
Q Consensus 102 dlVdrhirrLD~dl~~~~~ 120 (259)
..+++.++.|..+..-++.
T Consensus 96 ~~~ek~l~~Lk~e~evL~q 114 (201)
T PF13851_consen 96 KELEKELKDLKWEHEVLEQ 114 (201)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 5566777777766554443
No 110
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=26.59 E-value=37 Score=30.52 Aligned_cols=15 Identities=33% Similarity=0.915 Sum_probs=12.6
Q ss_pred CCCceeccccccccC
Q 024980 243 FKGKWYCPTCRLLPQ 257 (259)
Q Consensus 243 ~~~~w~C~~C~~~~~ 257 (259)
..+.||||.|....+
T Consensus 252 gR~ty~Cp~CQ~~~~ 266 (269)
T PRK14811 252 GRGTHFCPQCQPLRP 266 (269)
T ss_pred CCCcEECCCCcCCCC
Confidence 478999999998765
No 111
>cd07591 BAR_Rvs161p The Bin/Amphiphysin/Rvs (BAR) domain of Saccharomyces cerevisiae Reduced viability upon starvation protein 161 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 161 (Rvs161p) and Schizosaccharomyces pombe Hob3 (homolog of Bin3). S. cerevisiae Rvs161p plays a role in regulating cell polarity, actin cytoskeleton polarization, vesicle trafficking, endocytosis, bud formation, and the mating response. It forms a heterodimer with another BAR domain protein Rvs167p. 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. S. pombe Hob3 is important in regulating filamentous actin localization an
Probab=26.51 E-value=4.2e+02 Score=23.03 Aligned_cols=22 Identities=14% Similarity=0.388 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 024980 88 SLCTEKVLLARQAYDIIDSHIK 109 (259)
Q Consensus 88 ~lsdEKv~LA~q~~dlVdrhir 109 (259)
.-++++++.|...|+.++.+++
T Consensus 147 ~kae~el~~a~~~Ye~lN~~Lk 168 (224)
T cd07591 147 PRAEKELDEAKEVYETLNDQLK 168 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3477778888888888877765
No 112
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=26.46 E-value=5.7 Score=37.75 Aligned_cols=47 Identities=28% Similarity=0.654 Sum_probs=29.0
Q ss_pred CCCcce-ecCCCCC--CCccccCCCCCCCCceeecccCCCCCCCCCCCceeccccc
Q 024980 201 NEPTYC-VCHQVSF--GDMIACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCR 253 (259)
Q Consensus 201 ~~~~~C-~C~~~~~--g~mi~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~ 253 (259)
.-.+|| +|++-.. .+=++-- -|.|| ||..|+----.. .+.--||.|+
T Consensus 363 e~~L~Cg~CGe~~Glk~e~LqAL--pCsHI--fH~rCl~e~L~~--n~~rsCP~Cr 412 (518)
T KOG1941|consen 363 ETELYCGLCGESIGLKNERLQAL--PCSHI--FHLRCLQEILEN--NGTRSCPNCR 412 (518)
T ss_pred HHhhhhhhhhhhhcCCccccccc--chhHH--HHHHHHHHHHHh--CCCCCCccHH
Confidence 347899 7877532 2333333 46655 999998511123 5567899998
No 113
>PF15353 HECA: Headcase protein family homologue
Probab=26.45 E-value=22 Score=27.60 Aligned_cols=20 Identities=35% Similarity=0.979 Sum_probs=17.4
Q ss_pred ccccCCCCCCCCceeecccC
Q 024980 216 MIACDNENCQGGEWFHYACV 235 (259)
Q Consensus 216 mi~Cd~~~C~~~~wfH~~Cv 235 (259)
=|.|.|+.|+.-.|.|..|+
T Consensus 30 kv~Cnne~Cp~~~~MH~~CF 49 (107)
T PF15353_consen 30 KVICNNESCPFGQYMHRECF 49 (107)
T ss_pred EEEeCCCCCCCCCchHHHHH
Confidence 45799999998899999996
No 114
>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=25.78 E-value=3e+02 Score=20.94 Aligned_cols=42 Identities=19% Similarity=0.286 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 81 VNQDNALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNFAEDL 122 (259)
Q Consensus 81 ~~~~~~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~~~L 122 (259)
.....+..--++++........-+++.+..|...+...+..|
T Consensus 63 ~~~~e~~~~l~~r~e~ie~~i~~lek~~~~l~~~l~e~q~~l 104 (110)
T TIGR02338 63 TDKEEAIQELKEKKETLELRVKTLQRQEERLREQLKELQEKI 104 (110)
T ss_pred ecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455555555555555566666666666666666655544
No 115
>PRK11637 AmiB activator; Provisional
Probab=25.57 E-value=5.9e+02 Score=24.20 Aligned_cols=23 Identities=13% Similarity=0.202 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 024980 23 ELQRLLNTIRELDERSHSMINQT 45 (259)
Q Consensus 23 El~r~l~~IreLD~~~~~~~~~l 45 (259)
++......|..++.++..+..++
T Consensus 69 ~~~~~~~~l~~l~~qi~~~~~~i 91 (428)
T PRK11637 69 QRASLLAQLKKQEEAISQASRKL 91 (428)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33334444444444444433333
No 116
>PF00261 Tropomyosin: Tropomyosin; 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 [].; PDB: 2EFR_A 2Z5H_C 2Z5I_D 2D3E_B 2EFS_D 3U59_B 1C1G_C 1IHQ_A 3AZD_B 1MV4_B ....
Probab=25.09 E-value=4.6e+02 Score=22.82 Aligned_cols=44 Identities=16% Similarity=0.365 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 80 EVNQDNALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNFAEDLK 123 (259)
Q Consensus 80 ~~~~~~~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~~~L~ 123 (259)
...|..-+..-.+++.-|..-++...+.+.+|+..+..++.+|.
T Consensus 171 e~~~e~~i~~L~~~lkeaE~Rae~aE~~v~~Le~~id~le~eL~ 214 (237)
T PF00261_consen 171 EDEYEEKIRDLEEKLKEAENRAEFAERRVKKLEKEIDRLEDELE 214 (237)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555556677778888888888888888888888888877765
No 117
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=25.09 E-value=32 Score=24.38 Aligned_cols=47 Identities=23% Similarity=0.494 Sum_probs=18.1
Q ss_pred ecCCCC--CC--CccccCCCCCCCCceeecccCCC-----CCCCC--CCCceeccccccc
Q 024980 207 VCHQVS--FG--DMIACDNENCQGGEWFHYACVGL-----TPETR--FKGKWYCPTCRLL 255 (259)
Q Consensus 207 ~C~~~~--~g--~mi~Cd~~~C~~~~wfH~~Cvgl-----~~~~~--~~~~w~C~~C~~~ 255 (259)
||...- .+ .-+.|+|+.|. -=||..|+-- ..... ..-.+-||.|...
T Consensus 7 IC~~~~~~~~~~p~~~C~n~~C~--~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~ 64 (70)
T PF11793_consen 7 ICYSYRLDDGEIPDVVCPNPSCG--KKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSP 64 (70)
T ss_dssp SS--SS-TT-----B--S-TT------B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SE
T ss_pred cCCcEecCCCCcCceEcCCcccC--CHHHHHHHHHHHHHcccCCeeecccccCCcCCCCe
Confidence 665542 23 35889999999 5599999641 11110 1235679999854
No 118
>COG5185 HEC1 Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning]
Probab=25.00 E-value=6.9e+02 Score=24.81 Aligned_cols=23 Identities=17% Similarity=0.127 Sum_probs=14.1
Q ss_pred HHHHHHHhhCChHHHHHHHHHHH
Q 024980 10 VDDYLEYASTLPAELQRLLNTIR 32 (259)
Q Consensus 10 Ledfle~ie~LP~El~r~l~~Ir 32 (259)
..+....+++|..+..+....|.
T Consensus 266 ~~~i~~~i~~lk~~n~~l~e~i~ 288 (622)
T COG5185 266 VHIINTDIANLKTQNDNLYEKIQ 288 (622)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445567777777766665543
No 119
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=24.94 E-value=46 Score=22.67 Aligned_cols=29 Identities=28% Similarity=0.669 Sum_probs=23.0
Q ss_pred Ccce-ecCCCC--CCCccccCCCCCCCCceeecccC
Q 024980 203 PTYC-VCHQVS--FGDMIACDNENCQGGEWFHYACV 235 (259)
Q Consensus 203 ~~~C-~C~~~~--~g~mi~Cd~~~C~~~~wfH~~Cv 235 (259)
..-| +|+.+. .++.|.|. .|. .=||.+|.
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp--~Cg--apyHR~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCP--ECG--APYHRDCW 36 (54)
T ss_pred CccChhhCCcccCCCCEEECC--CCC--CcccHHHH
Confidence 3446 688876 46899999 999 77999997
No 120
>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=24.78 E-value=4.1e+02 Score=22.09 Aligned_cols=104 Identities=15% Similarity=0.227 Sum_probs=61.0
Q ss_pred HHHHHHHhhCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC---CCCCCCCCCchHHHHHHHHHHHHHHHHH
Q 024980 10 VDDYLEYASTLPAELQRLLNTIRELDERSHSMINQTRQQTKYCLGLASQ---GNKKGNGNEEDEAIEKMRKEIEVNQDNA 86 (259)
Q Consensus 10 Ledfle~ie~LP~El~r~l~~IreLD~~~~~~~~~l~~~~k~~~~~~~~---~~~~~~~~~~~~~~~~~~~~I~~~~~~~ 86 (259)
-++.++..++-=.|+.+.-.++.++-..+.+...+++.+..-....+.. -++. ... ---..|...|..|
T Consensus 15 K~qIf~I~E~~R~E~~~l~~EL~evk~~v~~~I~evD~Le~~er~aR~rL~eVS~~---f~~-----ysE~dik~AYe~A 86 (159)
T PF05384_consen 15 KEQIFEIAEQARQEYERLRKELEEVKEEVSEVIEEVDKLEKRERQARQRLAEVSRN---FDR-----YSEEDIKEAYEEA 86 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh---hcc-----cCHHHHHHHHHHH
Confidence 3556666667777777888888888888888777777655422211110 0000 000 0124688888888
Q ss_pred HHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHH
Q 024980 87 LSLCTEKVLLARQA------YDIIDSHIKRLDEDLNNFAED 121 (259)
Q Consensus 87 ~~lsdEKv~LA~q~------~dlVdrhirrLD~dl~~~~~~ 121 (259)
..++-+...+-++- .|-+++.+++|..-+++-+..
T Consensus 87 ~~lQ~~L~~~re~E~qLr~rRD~LErrl~~l~~tierAE~l 127 (159)
T PF05384_consen 87 HELQVRLAMLREREKQLRERRDELERRLRNLEETIERAENL 127 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77776665554444 445666777777666655443
No 121
>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=24.76 E-value=4.9e+02 Score=22.96 Aligned_cols=25 Identities=4% Similarity=0.117 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 22 AELQRLLNTIRELDERSHSMINQTR 46 (259)
Q Consensus 22 ~El~r~l~~IreLD~~~~~~~~~l~ 46 (259)
++|...+..++..+..+.++..+++
T Consensus 18 ~~i~~e~~~~e~ee~~L~e~~kE~~ 42 (230)
T PF10146_consen 18 NEILQEVESLENEEKCLEEYRKEME 42 (230)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444444444443
No 122
>KOG0612 consensus Rho-associated, coiled-coil containing protein kinase [Signal transduction mechanisms]
Probab=24.68 E-value=6.9e+02 Score=27.69 Aligned_cols=26 Identities=19% Similarity=0.296 Sum_probs=18.7
Q ss_pred hhCChHHHHHHHHHHHHHHHHHHHHH
Q 024980 17 ASTLPAELQRLLNTIRELDERSHSMI 42 (259)
Q Consensus 17 ie~LP~El~r~l~~IreLD~~~~~~~ 42 (259)
+.-|+..+...+..++.+|.+++...
T Consensus 436 ~~~le~~l~~~~~~~~~~~~~~~~~~ 461 (1317)
T KOG0612|consen 436 LQILEQSLVNEMQEKEKLDEKCQAVA 461 (1317)
T ss_pred hhhcccchhhHHHHhhhHHHHHHHHh
Confidence 34456667888888888888887653
No 123
>PF05130 FlgN: FlgN protein; InterPro: IPR007809 Flagella synthesis protein FlgN is an export chaperone involved in flagellar synthesis []. This entry represents a FlgN-like domain, consisting of a 4 long helices bundle, where the last helix is shorter than the three others.; GO: 0009296 flagellum assembly, 0019861 flagellum; PDB: 2FUP_A 3OPC_A.
Probab=24.42 E-value=3.2e+02 Score=20.74 Aligned_cols=18 Identities=6% Similarity=0.255 Sum_probs=7.3
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 024980 98 RQAYDIIDSHIKRLDEDL 115 (259)
Q Consensus 98 ~q~~dlVdrhirrLD~dl 115 (259)
.....+|..++..++.-+
T Consensus 105 ~~N~~ll~~~~~~~~~~l 122 (143)
T PF05130_consen 105 ERNQQLLEQALEFVQQLL 122 (143)
T ss_dssp HHHHHHHHHCCHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 333344444444444333
No 124
>KOG4796 consensus RNA polymerase II elongation factor [Transcription]
Probab=24.41 E-value=7.4e+02 Score=24.94 Aligned_cols=86 Identities=17% Similarity=0.266 Sum_probs=49.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCchHHHHHHHHHHHHHHHHHH---HHHHHHHHHHH
Q 024980 22 AELQRLLNTIRELDERSHSMINQTRQQTKYCLGLASQGNKKGNGNEEDEAIEKMRKEIEVNQDNAL---SLCTEKVLLAR 98 (259)
Q Consensus 22 ~El~r~l~~IreLD~~~~~~~~~l~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~---~lsdEKv~LA~ 98 (259)
.+|.--+.+.|+|-.++.....+..++...+.....+++ +..+.+..+|...|++.. .+.+||
T Consensus 508 ~dF~~eY~EYreLharve~vs~rF~~Lea~L~srls~gS---------~ey~~i~~qI~qEYeki~~dp~y~eeK----- 573 (604)
T KOG4796|consen 508 KDFEAEYDEYRELHARVETVSRRFRQLEAQLKSRLSPGS---------PEYKQIEKQILQEYEKIRKDPNYMEEK----- 573 (604)
T ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCC---------CcHHHHHHHHHHHHHHhhcCccHHHHH-----
Confidence 355666777777777777666655555444443333322 134567778999888875 355666
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 024980 99 QAYDIIDSHIKRLDEDLNNFAED 121 (259)
Q Consensus 99 q~~dlVdrhirrLD~dl~~~~~~ 121 (259)
+=.+.+-..++.|..-|..|+..
T Consensus 574 ~RceYLhsKLaHIK~lI~efDk~ 596 (604)
T KOG4796|consen 574 QRCEYLHSKLAHIKTLIGEFDKQ 596 (604)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 33344444444455555556553
No 125
>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=24.33 E-value=4.9e+02 Score=22.91 Aligned_cols=107 Identities=18% Similarity=0.194 Sum_probs=0.0
Q ss_pred HHhhCChHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCch-HHHHHHHHHHHHHHHHHHHHHH
Q 024980 15 EYASTLPAELQRLLNTI--RELDERSHSMINQTRQQTKYCLGLASQGNKKGNGNEED-EAIEKMRKEIEVNQDNALSLCT 91 (259)
Q Consensus 15 e~ie~LP~El~r~l~~I--reLD~~~~~~~~~l~~~~k~~~~~~~~~~~~~~~~~~~-~~~~~~~~~I~~~~~~~~~lsd 91 (259)
..+...=.|.++.|.+| |.+....+.+-.++..-...+....+...+....+... +.+...+.+....+..+..+-+
T Consensus 123 ~~l~~~l~ea~~mL~emr~r~f~~~~~~Ae~El~~A~~LL~~v~~~~~~~~~~~~~l~~~i~~~L~~~~~kL~Dl~~~l~ 202 (264)
T PF06008_consen 123 EDLQRALAEAQRMLEEMRKRDFTPQRQNAEDELKEAEDLLSRVQKWFQKPQQENESLAEAIRDDLNDYNAKLQDLRDLLN 202 (264)
T ss_pred HHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHHHHHHHHhhHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_pred H---HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 92 E---KVLLARQAYDIIDSHIKRLDEDLNNFAED 121 (259)
Q Consensus 92 E---Kv~LA~q~~dlVdrhirrLD~dl~~~~~~ 121 (259)
+ ++.-|..+...+...+..+......+...
T Consensus 203 eA~~~~~ea~~ln~~n~~~l~~~~~k~~~l~~~ 235 (264)
T PF06008_consen 203 EAQNKTREAEDLNRANQKNLEDLEKKKQELSEQ 235 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 126
>PF01214 CK_II_beta: Casein kinase II regulatory subunit; InterPro: IPR000704 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Casein kinase, a ubiquitous, well-conserved protein kinase involved in cell metabolism and differentiation, is characterised by its preference for Ser or Thr in acidic stretches of amino acids. The enzyme is a tetramer of 2 alpha- and 2 beta-subunits [, ]. However, some species (e.g., mammals) possess 2 related forms of the alpha-subunit (alpha and alpha'), while others (e.g., fungi) possess 2 related beta-subunits (beta and beta') []. The alpha-subunit is the catalytic unit and contains regions characteristic of serine/threonine protein kinases. The beta-subunit is believed to be regulatory, possessing an N-terminal auto-phosphorylation site, an internal acidic domain, and a potential metal-binding motif []. The beta subunit is a highly conserved protein of about 25kDa that contains, in its central section, a cysteine-rich motif, CX(n)C, that could be involved in binding a metal such as zinc []. The mammalian beta-subunit gene promoter shares common features with those of other mammalian protein kinases and is closely related to the promoter of the regulatory subunit of cAMP-dependent protein kinase [].; GO: 0019887 protein kinase regulator activity, 0005956 protein kinase CK2 complex; PDB: 2R6M_B 1RQF_K 1DS5_G 1QF8_B 3EED_A 4DGL_A 1JWH_D.
Probab=24.07 E-value=37 Score=28.91 Aligned_cols=20 Identities=35% Similarity=0.782 Sum_probs=14.7
Q ss_pred CCCCCCCC-CCCceecccccc
Q 024980 235 VGLTPETR-FKGKWYCPTCRL 254 (259)
Q Consensus 235 vgl~~~~~-~~~~w~C~~C~~ 254 (259)
||++..|. ..-+.|||.|..
T Consensus 115 iGlsd~~g~~~vKlyCP~C~d 135 (184)
T PF01214_consen 115 IGLSDTPGESTVKLYCPRCKD 135 (184)
T ss_dssp EBS-SSTTS-BBEEEETTTTE
T ss_pred ccCCCCCCccceeEECCCCcc
Confidence 88888874 456999999974
No 127
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=24.02 E-value=41 Score=30.21 Aligned_cols=13 Identities=23% Similarity=0.879 Sum_probs=10.8
Q ss_pred CCCceeccccccc
Q 024980 243 FKGKWYCPTCRLL 255 (259)
Q Consensus 243 ~~~~w~C~~C~~~ 255 (259)
..+.||||.|..+
T Consensus 262 gR~t~~CP~CQ~~ 274 (274)
T PRK01103 262 GRSTFFCPRCQKR 274 (274)
T ss_pred CCCcEECcCCCCc
Confidence 4789999999853
No 128
>KOG2196 consensus Nuclear porin [Nuclear structure]
Probab=23.70 E-value=5.4e+02 Score=23.09 Aligned_cols=37 Identities=32% Similarity=0.384 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 87 LSLCTEKVLLARQAYDIIDSHIKRLDEDLNNFAEDLK 123 (259)
Q Consensus 87 ~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~~~L~ 123 (259)
..-.|++-.-+-++.+-||-.+++|+.||...-..|-
T Consensus 166 ~~~~D~eR~qty~~a~nidsqLk~l~~dL~~ii~~lN 202 (254)
T KOG2196|consen 166 LSRADVEREQTYKMAENIDSQLKRLSEDLKQIIKSLN 202 (254)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 4445666666677778899999999999987655543
No 129
>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=22.91 E-value=77 Score=23.54 Aligned_cols=35 Identities=14% Similarity=0.394 Sum_probs=23.7
Q ss_pred cchhhHHHHHHHHhhCChHHHHHHHHHHHHHHHHHHHHH
Q 024980 4 ARTGVYVDDYLEYASTLPAELQRLLNTIRELDERSHSMI 42 (259)
Q Consensus 4 ~~~~~yLedfle~ie~LP~El~r~l~~IreLD~~~~~~~ 42 (259)
+|+-.+|.+++...++||.+|++.- .+|.+++.++
T Consensus 27 ~Ell~~Lk~~L~~~~~LP~dL~~~~----s~~~qa~~Ll 61 (83)
T PF12095_consen 27 EELLEKLKEWLQNQDDLPPDLAKFS----SVEEQAQYLL 61 (83)
T ss_dssp HHHHHHHHHHHHHTTTS-HHHHH-------HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCCHHHHhCC----CHHHHHHHHH
Confidence 3466789999999999999998754 4566665553
No 130
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=22.91 E-value=1.8e+02 Score=18.66 Aligned_cols=32 Identities=16% Similarity=-0.052 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHH--HHH-HHHHHHHHHHHHHHHH
Q 024980 76 RKEIEVNQDNALS--LCT-EKVLLARQAYDIIDSH 107 (259)
Q Consensus 76 ~~~I~~~~~~~~~--lsd-EKv~LA~q~~dlVdrh 107 (259)
+.+|+..+..+.. ..+ |.-.-...+..|+.+|
T Consensus 4 l~kI~kLLalA~~~~~~~~EA~~A~~kAq~Lm~ky 38 (43)
T PF10979_consen 4 LEKIRKLLALAESTGSNEHEAEAALAKAQRLMAKY 38 (43)
T ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHHHh
Confidence 3344444444443 222 3333334444444443
No 131
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=22.88 E-value=36 Score=18.86 Aligned_cols=10 Identities=50% Similarity=1.717 Sum_probs=8.0
Q ss_pred Cceecccccc
Q 024980 245 GKWYCPTCRL 254 (259)
Q Consensus 245 ~~w~C~~C~~ 254 (259)
+.|.|+.|.-
T Consensus 1 g~W~C~~C~~ 10 (26)
T smart00547 1 GDWECPACTF 10 (26)
T ss_pred CcccCCCCCC
Confidence 5799999964
No 132
>cd07588 BAR_Amphiphysin The Bin/Amphiphysin/Rvs (BAR) domain of Amphiphysins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Amphiphysins function primarily in endocytosis and other membrane remodeling events. They contain an N-terminal BAR domain with an additional N-terminal amphipathic helix (an N-BAR), a variable central domain, and a C-terminal SH3 domain. This subfamily is composed of different isoforms of amphiphysin and Bridging integrator 2 (Bin2). Amphiphysin I proteins, enriched in the brain and nervous system, contain domains that bind clathrin, Adaptor Protein complex 2 (AP2), dynamin and synaptojanin. They function in synaptic vesicle endocytosis. Some amphiphysin II isoforms, also called Bridging integrator 1 (Bin1), are localized in many different tissues and may function in intracellular vesicle trafficking. In skeletal muscle, Bin1 plays a role in the organization and maintenance of th
Probab=22.54 E-value=5.1e+02 Score=22.43 Aligned_cols=20 Identities=15% Similarity=0.433 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 024980 89 LCTEKVLLARQAYDIIDSHI 108 (259)
Q Consensus 89 lsdEKv~LA~q~~dlVdrhi 108 (259)
-++++++.|.+.|+.+...+
T Consensus 143 kae~el~~Ak~~Ye~lN~~L 162 (211)
T cd07588 143 KAEEELQQAKKVYEELNTEL 162 (211)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 47788889999998776544
No 133
>PRK14127 cell division protein GpsB; Provisional
Probab=22.54 E-value=1.9e+02 Score=22.50 Aligned_cols=43 Identities=14% Similarity=0.260 Sum_probs=36.6
Q ss_pred chhhHHHHHHHHhhCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 5 RTGVYVDDYLEYASTLPAELQRLLNTIRELDERSHSMINQTRQ 47 (259)
Q Consensus 5 ~~~~yLedfle~ie~LP~El~r~l~~IreLD~~~~~~~~~l~~ 47 (259)
|.-.||++-++.++.|=.|+.+.-.+++.|..++.++..++..
T Consensus 27 EVD~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~~~ 69 (109)
T PRK14127 27 EVDKFLDDVIKDYEAFQKEIEELQQENARLKAQVDELTKQVSV 69 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 4557899999999999999999999999999999888877753
No 134
>PF00616 RasGAP: GTPase-activator protein for Ras-like GTPase; InterPro: IPR001936 Ras proteins are membrane-associated molecular switches that bind GTP and GDP and slowly hydrolyze GTP to GDP []. This intrinsic GTPase activity of ras is stimulated by a family of proteins collectively known as 'GAP' or GTPase-activating proteins [, ]. As it is the GTP bound form of ras which is active, these proteins are said to be down-regulators of ras. The Ras GTPase-activating proteins are quite large (from 765 residues for sar1 to 3079 residues for IRA2) but share only a limited (about 250 residues) region of sequence similarity, referred to as the 'catalytic domain' or rasGAP domain. Note: There are distinctly different GAPs for the rap and rho/rac subfamilies of ras-like proteins (reviewed in reference []) that do not share sequence similarity with ras GAPs.; GO: 0005096 GTPase activator activity, 0051056 regulation of small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3BXJ_B 1WQ1_G 1WER_A 1NF1_A 3FAY_A.
Probab=22.52 E-value=1.1e+02 Score=25.36 Aligned_cols=33 Identities=18% Similarity=0.344 Sum_probs=26.4
Q ss_pred hhhHHHHHHHHhhCChHHHHHHHHHHHHHHHHH
Q 024980 6 TGVYVDDYLEYASTLPAELQRLLNTIRELDERS 38 (259)
Q Consensus 6 ~~~yLedfle~ie~LP~El~r~l~~IreLD~~~ 38 (259)
+..+++..++++..+|..|+..+..|++.=.+.
T Consensus 106 ~~~~~~~i~~s~~~~P~~lr~i~~~i~~~~~~~ 138 (197)
T PF00616_consen 106 CESFLDAIISSIDQIPPSLRYICKQIYEAVEKK 138 (197)
T ss_dssp HHHHHHHHHGGGGGS-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHh
Confidence 456788888999999999999999999875443
No 135
>KOG4360 consensus Uncharacterized coiled coil protein [Function unknown]
Probab=22.31 E-value=8e+02 Score=24.57 Aligned_cols=46 Identities=20% Similarity=0.209 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 73 EKMRKEIEVNQDNALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNFA 119 (259)
Q Consensus 73 ~~~~~~I~~~~~~~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~ 119 (259)
-++..+|-+...+++.++-||-.+-..+..+.|.| +.|..+++.++
T Consensus 236 skLlsql~d~qkk~k~~~~Ekeel~~~Lq~~~da~-~ql~aE~~Ele 281 (596)
T KOG4360|consen 236 SKLLSQLVDLQKKIKYLRHEKEELDEHLQAYKDAQ-RQLTAELEELE 281 (596)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhhH-HHHHHHHHHHH
Confidence 46777888888888888888888888888887777 44555554443
No 136
>PF15619 Lebercilin: Ciliary protein causing Leber congenital amaurosis disease
Probab=21.94 E-value=5.1e+02 Score=22.15 Aligned_cols=37 Identities=32% Similarity=0.427 Sum_probs=29.4
Q ss_pred HHHHHHHhhCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 10 VDDYLEYASTLPAELQRLLNTIRELDERSHSMINQTR 46 (259)
Q Consensus 10 Ledfle~ie~LP~El~r~l~~IreLD~~~~~~~~~l~ 46 (259)
|..|-+.=..||.=|++.-.+||.|-.++........
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 6778888889999999999999998888776554443
No 137
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=21.91 E-value=6.1e+02 Score=26.85 Aligned_cols=24 Identities=21% Similarity=0.340 Sum_probs=13.6
Q ss_pred hCChHHHHHHHHHHHHHHHHHHHH
Q 024980 18 STLPAELQRLLNTIRELDERSHSM 41 (259)
Q Consensus 18 e~LP~El~r~l~~IreLD~~~~~~ 41 (259)
.+|-.||.-.-..+.+|+.++++.
T Consensus 440 ~ql~~eletLn~k~qqls~kl~Dv 463 (1118)
T KOG1029|consen 440 KQLQQELETLNFKLQQLSGKLQDV 463 (1118)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhhh
Confidence 345555555555566666666654
No 138
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=21.81 E-value=36 Score=30.93 Aligned_cols=12 Identities=33% Similarity=1.093 Sum_probs=10.3
Q ss_pred CCCceecccccc
Q 024980 243 FKGKWYCPTCRL 254 (259)
Q Consensus 243 ~~~~w~C~~C~~ 254 (259)
..+.||||.|..
T Consensus 262 gR~t~~CP~CQ~ 273 (273)
T COG0266 262 GRSTFYCPVCQK 273 (273)
T ss_pred CCcCEeCCCCCC
Confidence 588999999973
No 139
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.54 E-value=59 Score=28.80 Aligned_cols=44 Identities=27% Similarity=0.693 Sum_probs=29.1
Q ss_pred e-ecCCCC-CCCccccCCCCCCCCceeecccCCC-----CCCCCCCCceeccccccc
Q 024980 206 C-VCHQVS-FGDMIACDNENCQGGEWFHYACVGL-----TPETRFKGKWYCPTCRLL 255 (259)
Q Consensus 206 C-~C~~~~-~g~mi~Cd~~~C~~~~wfH~~Cvgl-----~~~~~~~~~w~C~~C~~~ 255 (259)
| .|+-+- .|+-|.-- |- .-||+.|+.- ....+ ..-+.||-|...
T Consensus 53 C~LC~t~La~gdt~RLv---Cy--hlfHW~ClneraA~lPanTA-PaGyqCP~Cs~e 103 (299)
T KOG3970|consen 53 CRLCNTPLASGDTTRLV---CY--HLFHWKCLNERAANLPANTA-PAGYQCPCCSQE 103 (299)
T ss_pred CceeCCccccCcceeeh---hh--hhHHHHHhhHHHhhCCCcCC-CCcccCCCCCCc
Confidence 6 688875 56655433 65 6699999763 22222 447999999754
No 140
>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=21.33 E-value=5.1e+02 Score=21.91 Aligned_cols=99 Identities=14% Similarity=0.247 Sum_probs=56.8
Q ss_pred hhCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 17 ASTLPAELQRLLNTIRELDERSHSMINQTRQQTKYCLGLASQGNKKGNGNEEDEAIEKMRKEIEVNQDNALSLCTEKVLL 96 (259)
Q Consensus 17 ie~LP~El~r~l~~IreLD~~~~~~~~~l~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~~lsdEKv~L 96 (259)
|+.|-.+-++....+++.|..+..++.+.....+-+....+- ..--..+ .......-...|...-....+|+.|-
T Consensus 5 i~~il~dak~L~~rL~~~d~~ad~Ll~qa~~l~~~i~sm~~y-~eei~~l-~~~~~~~~~~~l~~En~qi~~Lq~EN--- 79 (181)
T PF05769_consen 5 IEQILADAKRLVERLKDHDNAADSLLSQAEALNKQIESMRQY-QEEIQEL-NELSKNRPRAGLQQENRQIRQLQQEN--- 79 (181)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHH-HHHhhcccchhHHHhhHHHHHHHHHH---
Confidence 566777888999999999998888877765544322211100 0000000 00000000023444455567777776
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 97 ARQAYDIIDSHIKRLDEDLNNFAED 121 (259)
Q Consensus 97 A~q~~dlVdrhirrLD~dl~~~~~~ 121 (259)
..+...|+.|-.-|+.-+.||...
T Consensus 80 -~eL~~~leEhq~alelIM~KyReq 103 (181)
T PF05769_consen 80 -RELRQSLEEHQSALELIMSKYREQ 103 (181)
T ss_pred -HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355667788888888888888764
No 141
>PRK14011 prefoldin subunit alpha; Provisional
Probab=21.22 E-value=2.5e+02 Score=22.95 Aligned_cols=43 Identities=9% Similarity=0.180 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 81 VNQDNALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNFAEDLK 123 (259)
Q Consensus 81 ~~~~~~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~~~L~ 123 (259)
....+|++.-+.|+.......+.++..|.++...+..+..+|+
T Consensus 84 k~~~eA~~~~~~ri~~l~~~~~~l~~~i~~~~~~~~~l~~~L~ 126 (144)
T PRK14011 84 KDVSEVIEDFKKSVEELDKTKKEGNKKIEELNKEITKLRKELE 126 (144)
T ss_pred ecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445666777777777777777777777777777777666554
No 142
>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=21.02 E-value=3.7e+02 Score=20.26 Aligned_cols=38 Identities=8% Similarity=0.326 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 85 NALSLCTEKVLLARQAYDIIDSHIKRLDEDLNNFAEDL 122 (259)
Q Consensus 85 ~~~~lsdEKv~LA~q~~dlVdrhirrLD~dl~~~~~~L 122 (259)
+|.++-+.|+...+...+-+...++.+...+..+...+
T Consensus 77 eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~~~~~l 114 (120)
T PF02996_consen 77 EAIEFLKKRIKELEEQLEKLEKELAELQAQIEQLEQTL 114 (120)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55556666666666666666666666666665555443
No 143
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=20.95 E-value=59 Score=27.04 Aligned_cols=23 Identities=26% Similarity=0.716 Sum_probs=15.7
Q ss_pred CCCCCceeecccCCCCCCCCCCCceecc
Q 024980 223 NCQGGEWFHYACVGLTPETRFKGKWYCP 250 (259)
Q Consensus 223 ~C~~~~wfH~~Cvgl~~~~~~~~~w~C~ 250 (259)
-|. |+.|.-.-......+.|+||
T Consensus 107 iCt-----HlGC~~~~~~~~~~~~~~CP 129 (177)
T COG0723 107 ICT-----HLGCTVPWNNAGAEGGFFCP 129 (177)
T ss_pred ecc-----CCCCccCcccCCCCCeEEcc
Confidence 677 88887655311227899998
No 144
>PF13922 PHD_3: PHD domain of transcriptional enhancer, Asx
Probab=20.85 E-value=29 Score=24.61 Aligned_cols=28 Identities=32% Similarity=0.876 Sum_probs=23.1
Q ss_pred CcceecCCCCCCCccccCCCCCCCCceeecccCCC
Q 024980 203 PTYCVCHQVSFGDMIACDNENCQGGEWFHYACVGL 237 (259)
Q Consensus 203 ~~~C~C~~~~~g~mi~Cd~~~C~~~~wfH~~Cvgl 237 (259)
+.-|.|+-. -||-|- .|. .+-|..|+|-
T Consensus 33 ~~~C~C~Lk---AMi~Cq--~CG--AFCHDDCIgp 60 (69)
T PF13922_consen 33 SNKCACSLK---AMIMCQ--GCG--AFCHDDCIGP 60 (69)
T ss_pred ccccccchH---HHHHHh--hcc--chhccccccH
Confidence 455888765 599999 899 8899999973
No 145
>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=20.29 E-value=87 Score=19.31 Aligned_cols=26 Identities=31% Similarity=0.889 Sum_probs=17.5
Q ss_pred ccccCCCCCCCCceeecccCCCCCCCCCCCceecccccc
Q 024980 216 MIACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCRL 254 (259)
Q Consensus 216 mi~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~~ 254 (259)
-+.|. .|. -.||. .. .|.|||..|=.
T Consensus 8 ~~~C~--~C~-~~~~~--------~~--dG~~yC~~cG~ 33 (36)
T PF11781_consen 8 NEPCP--VCG-SRWFY--------SD--DGFYYCDRCGH 33 (36)
T ss_pred CCcCC--CCC-CeEeE--------cc--CCEEEhhhCce
Confidence 35688 688 34653 23 88999988843
No 146
>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=20.27 E-value=1.5e+02 Score=22.28 Aligned_cols=24 Identities=13% Similarity=0.218 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 024980 98 RQAYDIIDSHIKRLDEDLNNFAED 121 (259)
Q Consensus 98 ~q~~dlVdrhirrLD~dl~~~~~~ 121 (259)
..+.++++.|+..|+..++.++.+
T Consensus 75 ~~~~~ll~~~~~~l~~~i~~L~~~ 98 (99)
T cd04772 75 ASALALVDAAHALLQRYRQQLDQE 98 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 377899999999999999877654
No 147
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.23 E-value=43 Score=27.26 Aligned_cols=49 Identities=33% Similarity=0.659 Sum_probs=31.7
Q ss_pred CcceecCCCCCCCcc--ccCCCCCCCCceeecccCCCCCCCCCCCceeccccccc
Q 024980 203 PTYCVCHQVSFGDMI--ACDNENCQGGEWFHYACVGLTPETRFKGKWYCPTCRLL 255 (259)
Q Consensus 203 ~~~C~C~~~~~g~mi--~Cd~~~C~~~~wfH~~Cvgl~~~~~~~~~w~C~~C~~~ 255 (259)
+++=||+...|-+=| -|. .|. +. |-..|-|-.....++-.|.|..|+..
T Consensus 66 atC~IC~KTKFADG~GH~C~--YCq-~r-~CARCGGrv~lrsNKv~wvcnlc~k~ 116 (169)
T KOG3799|consen 66 ATCGICHKTKFADGCGHNCS--YCQ-TR-FCARCGGRVSLRSNKVMWVCNLCRKQ 116 (169)
T ss_pred cchhhhhhcccccccCcccc--hhh-hh-HHHhcCCeeeeccCceEEeccCCcHH
Confidence 343389988764333 377 788 43 67788774433333678999999754
No 148
>PRK13267 archaemetzincin-like protein; Reviewed
Probab=20.01 E-value=23 Score=30.05 Aligned_cols=13 Identities=23% Similarity=0.542 Sum_probs=10.6
Q ss_pred CCceecccccccc
Q 024980 244 KGKWYCPTCRLLP 256 (259)
Q Consensus 244 ~~~w~C~~C~~~~ 256 (259)
+..+|||.|..+.
T Consensus 161 k~~~lC~~C~~kL 173 (179)
T PRK13267 161 KEPNFCGSCQRKL 173 (179)
T ss_pred CCcccCHHHHHHH
Confidence 5689999998654
Done!