Query 025899
Match_columns 246
No_of_seqs 213 out of 1298
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 10:49:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025899.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025899hhsearch_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 6.4E-40 1.4E-44 279.3 18.5 229 3-238 6-269 (271)
2 KOG1973 Chromatin remodeling p 100.0 3.8E-35 8.2E-40 260.1 13.6 238 2-244 8-273 (274)
3 PF12998 ING: Inhibitor of gro 99.9 2E-25 4.4E-30 170.6 9.9 103 2-111 1-105 (105)
4 PF00628 PHD: PHD-finger; Int 98.9 2.1E-10 4.6E-15 76.2 0.7 44 192-238 1-50 (51)
5 smart00249 PHD PHD zinc finger 98.8 5.2E-09 1.1E-13 67.3 3.1 42 192-236 1-47 (47)
6 KOG1512 PHD Zn-finger protein 97.9 3.8E-06 8.3E-11 73.9 1.4 44 193-239 317-363 (381)
7 KOG4323 Polycomb-like PHD Zn-f 97.7 1.1E-05 2.5E-10 75.7 1.2 49 190-241 171-226 (464)
8 KOG4299 PHD Zn-finger protein 97.7 1.4E-05 3.1E-10 76.9 1.1 46 191-239 254-305 (613)
9 KOG0825 PHD Zn-finger protein 97.6 4.5E-05 9.8E-10 75.1 3.0 49 188-238 213-265 (1134)
10 KOG0954 PHD finger protein [Ge 97.4 5.5E-05 1.2E-09 74.0 1.7 49 186-237 267-319 (893)
11 PF13831 PHD_2: PHD-finger; PD 97.4 1.8E-05 3.9E-10 48.8 -1.1 34 201-237 2-36 (36)
12 KOG0956 PHD finger protein AF1 97.4 6.6E-05 1.4E-09 73.0 2.0 48 190-238 6-56 (900)
13 KOG1244 Predicted transcriptio 97.4 5.3E-05 1.2E-09 66.4 1.1 51 189-242 280-334 (336)
14 KOG0383 Predicted helicase [Ge 97.4 7.5E-05 1.6E-09 73.8 1.6 50 190-244 47-99 (696)
15 KOG1245 Chromatin remodeling c 97.1 8.2E-05 1.8E-09 78.9 -1.0 49 190-241 1108-1160(1404)
16 KOG0955 PHD finger protein BR1 96.6 0.0016 3.4E-08 67.2 3.1 50 190-242 220-272 (1051)
17 KOG1632 Uncharacterized PHD Zn 96.5 0.001 2.3E-08 61.2 1.4 48 190-240 60-114 (345)
18 COG5141 PHD zinc finger-contai 95.8 0.004 8.7E-08 58.9 1.2 44 191-237 194-241 (669)
19 KOG0957 PHD finger protein [Ge 95.1 0.027 6E-07 53.5 4.3 53 183-238 112-178 (707)
20 KOG0957 PHD finger protein [Ge 95.0 1.1 2.3E-05 43.1 14.6 44 191-237 545-596 (707)
21 KOG2752 Uncharacterized conser 93.7 0.035 7.5E-07 49.9 1.7 31 189-222 127-165 (345)
22 KOG1844 PHD Zn-finger proteins 93.4 0.041 8.9E-07 52.9 1.8 49 189-240 85-136 (508)
23 KOG1632 Uncharacterized PHD Zn 92.2 0.02 4.3E-07 52.8 -2.1 51 185-238 234-294 (345)
24 PF13771 zf-HC5HC2H: PHD-like 90.6 0.14 2.9E-06 37.5 1.4 31 190-222 36-67 (90)
25 PF08702 Fib_alpha: Fibrinogen 90.1 8.7 0.00019 31.0 11.9 40 74-113 93-132 (146)
26 PF13832 zf-HC5HC2H_2: PHD-zin 89.5 0.15 3.3E-06 38.7 0.9 31 190-222 55-86 (110)
27 COG1382 GimC Prefoldin, chaper 86.3 14 0.00031 28.9 15.2 107 11-118 1-110 (119)
28 PF13341 RAG2_PHD: RAG2 PHD do 83.3 0.62 1.3E-05 32.8 1.2 32 202-235 29-67 (78)
29 KOG4443 Putative transcription 83.3 0.66 1.4E-05 45.7 1.8 47 190-239 68-118 (694)
30 PF07227 DUF1423: Protein of u 81.3 1.1 2.5E-05 42.3 2.5 43 194-239 133-192 (446)
31 PF10497 zf-4CXXC_R1: Zinc-fin 80.5 1.2 2.6E-05 34.1 2.0 52 186-238 3-69 (105)
32 KOG1473 Nucleosome remodeling 78.5 1.3 2.8E-05 46.4 2.0 42 191-237 345-389 (1414)
33 TIGR02338 gimC_beta prefoldin, 77.0 30 0.00065 26.3 13.8 45 73-117 62-106 (110)
34 PRK09343 prefoldin subunit bet 76.2 34 0.00075 26.5 14.2 104 12-117 3-110 (121)
35 KOG0994 Extracellular matrix g 73.7 54 0.0012 35.2 11.9 28 10-37 1512-1539(1758)
36 PF04012 PspA_IM30: PspA/IM30 71.3 63 0.0014 27.4 15.3 32 84-115 97-128 (221)
37 PF09755 DUF2046: Uncharacteri 70.6 85 0.0019 28.6 13.7 47 71-117 150-203 (310)
38 PF03194 LUC7: LUC7 N_terminus 70.1 20 0.00044 31.6 7.3 46 64-113 124-170 (254)
39 PF04100 Vps53_N: Vps53-like, 70.0 97 0.0021 29.0 12.5 89 10-114 19-107 (383)
40 KOG4443 Putative transcription 70.0 1.3 2.9E-05 43.7 -0.3 48 190-240 18-72 (694)
41 KOG4552 Vitamin-D-receptor int 67.7 81 0.0017 27.2 11.0 41 75-116 58-98 (272)
42 PF05103 DivIVA: DivIVA protei 64.0 4.2 9.1E-05 31.5 1.6 34 4-40 23-56 (131)
43 PF13639 zf-RING_2: Ring finge 63.1 1.2 2.5E-05 28.0 -1.5 37 194-237 5-44 (44)
44 PF13901 DUF4206: Domain of un 62.4 6.4 0.00014 33.5 2.5 44 190-243 152-202 (202)
45 COG5415 Predicted integral mem 61.5 5.5 0.00012 34.2 1.9 32 204-240 193-224 (251)
46 PF03234 CDC37_N: Cdc37 N term 61.0 98 0.0021 25.9 9.7 108 6-116 43-155 (177)
47 PF09755 DUF2046: Uncharacteri 60.2 1.4E+02 0.003 27.3 12.6 35 74-108 110-151 (310)
48 smart00744 RINGv The RING-vari 59.8 2 4.4E-05 28.0 -0.8 23 214-236 26-48 (49)
49 PF04668 Tsg: Twisted gastrula 59.7 3.4 7.3E-05 32.9 0.3 27 211-237 100-131 (132)
50 KOG1493 Anaphase-promoting com 59.5 3 6.6E-05 30.0 0.0 48 192-239 22-79 (84)
51 TIGR00634 recN DNA repair prot 57.7 91 0.002 30.6 9.9 10 6-15 291-300 (563)
52 PF00038 Filament: Intermediat 57.6 1.4E+02 0.003 26.5 11.9 86 14-99 163-252 (312)
53 KOG4360 Uncharacterized coiled 56.7 2E+02 0.0044 28.2 12.1 78 22-112 204-281 (596)
54 COG5194 APC11 Component of SCF 55.2 2.7 5.9E-05 30.5 -0.8 44 192-239 22-79 (88)
55 PF08946 Osmo_CC: Osmosensory 55.1 16 0.00035 23.5 2.8 26 88-113 8-33 (46)
56 COG3416 Uncharacterized protei 55.1 98 0.0021 26.7 8.3 69 42-113 8-76 (233)
57 KOG4299 PHD Zn-finger protein 54.4 8 0.00017 38.1 1.9 44 190-238 47-94 (613)
58 PRK14127 cell division protein 54.1 55 0.0012 25.2 6.1 39 4-45 28-66 (109)
59 PHA02414 hypothetical protein 53.8 94 0.002 23.4 9.3 77 28-113 2-78 (111)
60 PF11781 RRN7: RNA polymerase 53.1 9.4 0.0002 23.3 1.4 24 204-237 9-32 (36)
61 KOG4460 Nuclear pore complex, 52.2 1.4E+02 0.003 29.6 9.7 33 3-35 571-604 (741)
62 PF04949 Transcrip_act: Transc 51.4 1.3E+02 0.0029 24.5 10.1 28 72-99 114-141 (159)
63 COG1842 PspA Phage shock prote 51.1 1.6E+02 0.0036 25.4 15.9 39 76-114 97-135 (225)
64 PF10367 Vps39_2: Vacuolar sor 50.8 12 0.00027 27.5 2.1 29 190-221 78-107 (109)
65 PF05781 MRVI1: MRVI1 protein; 50.0 2.6E+02 0.0056 27.5 11.2 27 90-116 290-316 (538)
66 KOG1829 Uncharacterized conser 49.7 4.2 9.1E-05 40.0 -0.8 46 190-243 511-563 (580)
67 KOG0804 Cytoplasmic Zn-finger 49.1 2.5E+02 0.0055 27.0 13.6 9 100-108 436-444 (493)
68 KOG1512 PHD Zn-finger protein 48.0 6.3 0.00014 35.4 0.1 33 202-237 278-315 (381)
69 KOG2846 Predicted membrane pro 47.9 11 0.00024 34.5 1.6 38 203-245 220-257 (328)
70 PF04111 APG6: Autophagy prote 47.3 2.2E+02 0.0048 25.8 12.5 20 16-35 43-62 (314)
71 PF07496 zf-CW: CW-type Zinc F 47.3 9 0.00019 25.0 0.7 28 203-235 3-34 (50)
72 KOG2932 E3 ubiquitin ligase in 47.0 8.3 0.00018 35.1 0.7 39 191-239 91-132 (389)
73 KOG0996 Structural maintenance 46.9 2.3E+02 0.0049 30.7 10.9 46 70-115 885-930 (1293)
74 KOG0129 Predicted RNA-binding 46.7 6.9 0.00015 37.7 0.2 27 216-245 471-497 (520)
75 PF11793 FANCL_C: FANCL C-term 46.6 5.1 0.00011 28.1 -0.6 48 191-239 3-64 (70)
76 PF11690 DUF3287: Protein of u 46.6 52 0.0011 25.3 4.9 42 71-112 43-85 (109)
77 PF02891 zf-MIZ: MIZ/SP-RING z 45.4 2.8 6.2E-05 27.5 -1.9 22 217-238 23-49 (50)
78 PRK09841 cryptic autophosphory 45.0 3.5E+02 0.0076 27.5 14.9 55 3-62 249-303 (726)
79 KOG4796 RNA polymerase II elon 44.8 3.2E+02 0.007 27.0 10.9 86 16-114 508-596 (604)
80 PF07649 C1_3: C1-like domain; 44.1 5.1 0.00011 23.1 -0.7 26 193-221 3-30 (30)
81 KOG1244 Predicted transcriptio 43.2 7.8 0.00017 34.6 -0.0 45 190-237 224-282 (336)
82 PF00641 zf-RanBP: Zn-finger i 42.5 16 0.00035 20.9 1.3 14 228-241 2-15 (30)
83 cd04476 RPA1_DBD_C RPA1_DBD_C: 42.3 16 0.00034 29.6 1.7 26 214-239 31-60 (166)
84 PF12678 zf-rbx1: RING-H2 zinc 41.6 7.6 0.00016 27.4 -0.3 22 211-237 50-73 (73)
85 KOG3579 Predicted E3 ubiquitin 41.5 29 0.00062 31.3 3.2 52 182-235 260-316 (352)
86 KOG4628 Predicted E3 ubiquitin 41.1 27 0.00058 32.4 3.1 46 191-242 231-279 (348)
87 PF00130 C1_1: Phorbol esters/ 40.6 25 0.00053 22.6 2.1 34 189-225 10-47 (53)
88 COG3599 DivIVA Cell division i 39.9 2.4E+02 0.0053 24.2 13.4 39 3-44 27-65 (212)
89 TIGR03185 DNA_S_dndD DNA sulfu 39.7 3.9E+02 0.0085 26.7 11.4 36 4-39 378-414 (650)
90 PRK11637 AmiB activator; Provi 39.5 3.3E+02 0.0071 25.6 11.7 30 85-114 89-118 (428)
91 PHA02562 46 endonuclease subun 39.5 3.6E+02 0.0077 26.0 12.4 98 19-117 170-273 (562)
92 KOG2626 Histone H3 (Lys4) meth 39.5 38 0.00082 33.0 3.9 47 190-239 20-76 (544)
93 PRK10626 hypothetical protein; 39.3 1.3E+02 0.0028 26.4 6.9 35 65-99 73-107 (239)
94 PRK15365 type III secretion sy 38.8 1.7E+02 0.0037 22.1 10.3 22 20-41 6-27 (107)
95 smart00547 ZnF_RBZ Zinc finger 38.5 16 0.00034 20.0 0.8 12 229-240 1-12 (26)
96 PF11101 DUF2884: Protein of u 38.0 2.4E+02 0.0052 24.3 8.4 53 65-117 51-110 (229)
97 PHA02862 5L protein; Provision 36.4 12 0.00027 30.2 0.1 26 214-239 26-51 (156)
98 PF05130 FlgN: FlgN protein; 36.3 1.9E+02 0.004 21.8 7.9 10 96-105 110-119 (143)
99 KOG3047 Predicted transcriptio 36.0 2.2E+02 0.0049 22.7 10.1 42 75-116 102-143 (157)
100 KOG0977 Nuclear envelope prote 35.8 4.5E+02 0.0097 26.0 11.9 42 4-45 143-184 (546)
101 PF10737 GerPC: Spore germinat 35.7 1.3E+02 0.0028 25.1 6.1 36 13-48 95-136 (176)
102 PHA02825 LAP/PHD finger-like p 35.7 18 0.00039 29.7 1.0 48 189-239 7-57 (162)
103 PF04216 FdhE: Protein involve 35.6 12 0.00026 33.5 -0.1 27 189-217 171-209 (290)
104 PRK06798 fliD flagellar cappin 35.2 2E+02 0.0044 27.4 8.2 48 3-50 366-413 (440)
105 COG5034 TNG2 Chromatin remodel 35.0 3.3E+02 0.0071 24.3 10.3 42 65-107 61-102 (271)
106 KOG1671 Ubiquinol cytochrome c 34.3 20 0.00044 30.5 1.1 21 217-237 155-177 (210)
107 PRK08032 fliD flagellar cappin 34.1 2.6E+02 0.0057 26.7 8.8 48 3-50 393-440 (462)
108 KOG3053 Uncharacterized conser 34.0 20 0.00043 31.8 1.0 47 190-239 20-80 (293)
109 cd00890 Prefoldin Prefoldin is 33.9 2.1E+02 0.0045 21.6 6.9 45 73-117 82-126 (129)
110 KOG2129 Uncharacterized conser 33.8 4.4E+02 0.0095 25.3 10.8 18 14-31 130-147 (552)
111 PF07106 TBPIP: Tat binding pr 33.4 2.6E+02 0.0056 22.6 8.7 14 100-113 146-159 (169)
112 PF12718 Tropomyosin_1: Tropom 33.4 2.5E+02 0.0054 22.4 12.6 31 82-112 98-128 (143)
113 cd00632 Prefoldin_beta Prefold 33.2 2E+02 0.0044 21.3 12.7 46 72-117 57-102 (105)
114 PRK14143 heat shock protein Gr 33.2 3.3E+02 0.0072 23.8 11.0 17 70-86 102-118 (238)
115 PF05010 TACC: Transforming ac 32.9 3.1E+02 0.0068 23.4 13.0 42 72-116 130-171 (207)
116 PF12861 zf-Apc11: Anaphase-pr 32.8 17 0.00038 26.7 0.4 28 211-240 52-81 (85)
117 KOG0612 Rho-associated, coiled 32.4 6.2E+02 0.013 27.7 11.4 26 11-36 436-461 (1317)
118 COG0497 RecN ATPase involved i 32.3 4.3E+02 0.0094 26.2 9.9 10 189-198 485-494 (557)
119 TIGR00606 rad50 rad50. This fa 31.4 7E+02 0.015 27.3 12.3 29 88-116 1064-1092(1311)
120 PF08432 Vfa1: AAA-ATPase Vps4 31.3 29 0.00063 29.0 1.6 31 190-225 13-45 (182)
121 PF04849 HAP1_N: HAP1 N-termin 31.1 4.1E+02 0.009 24.2 12.4 48 65-113 236-283 (306)
122 TIGR00414 serS seryl-tRNA synt 30.9 4.6E+02 0.01 24.7 10.0 24 21-44 28-51 (418)
123 PF10168 Nup88: Nuclear pore c 30.8 6E+02 0.013 26.0 12.0 21 5-25 550-570 (717)
124 PF08746 zf-RING-like: RING-li 30.4 12 0.00025 23.7 -0.8 30 204-236 12-43 (43)
125 PF07011 DUF1313: Protein of u 30.2 1.6E+02 0.0035 21.7 5.0 25 13-37 39-63 (87)
126 KOG1734 Predicted RING-contain 30.2 20 0.00044 32.0 0.5 56 182-240 216-280 (328)
127 PF00645 zf-PARP: Poly(ADP-rib 29.9 12 0.00026 26.6 -0.8 9 214-222 39-47 (82)
128 PF00038 Filament: Intermediat 29.9 3.9E+02 0.0085 23.6 9.9 30 9-38 209-238 (312)
129 PF02403 Seryl_tRNA_N: Seryl-t 29.9 2.3E+02 0.005 20.9 8.5 24 21-44 27-50 (108)
130 PHA03158 hypothetical protein; 29.1 1.3E+02 0.0028 25.7 5.0 36 78-113 227-268 (273)
131 cd04772 HTH_TioE_rpt1 First He 28.6 76 0.0017 23.5 3.3 23 92-114 76-98 (99)
132 PHA02682 ORF080 virion core pr 28.3 2.3E+02 0.005 24.3 6.4 52 10-61 209-263 (280)
133 COG3937 Uncharacterized conser 27.8 2.8E+02 0.0061 21.3 9.3 58 55-115 35-106 (108)
134 KOG0018 Structural maintenance 27.1 8.2E+02 0.018 26.4 13.6 47 6-52 715-761 (1141)
135 PRK14011 prefoldin subunit alp 26.8 1.8E+02 0.0039 23.4 5.4 46 72-117 82-127 (144)
136 PRK14140 heat shock protein Gr 26.4 4E+02 0.0086 22.5 11.1 63 23-99 37-99 (191)
137 PF12906 RINGv: RING-variant d 26.3 7.4 0.00016 25.1 -2.2 9 214-222 25-33 (47)
138 KOG2629 Peroxisomal membrane a 26.2 5E+02 0.011 23.6 10.6 20 96-115 172-191 (300)
139 PF08400 phage_tail_N: Prophag 26.2 2.3E+02 0.005 22.6 5.8 33 4-36 86-120 (134)
140 COG5460 Uncharacterized conser 26.1 1.9E+02 0.004 20.9 4.6 29 84-115 9-37 (82)
141 cd07599 BAR_Rvs167p The Bin/Am 25.8 4E+02 0.0087 22.4 11.4 23 80-102 151-173 (216)
142 COG4396 Mu-like prophage host- 25.6 3.6E+02 0.0078 21.8 7.6 23 16-38 18-40 (170)
143 PF10481 CENP-F_N: Cenp-F N-te 25.6 5E+02 0.011 23.4 11.7 28 91-118 101-128 (307)
144 KOG4721 Serine/threonine prote 25.4 7.3E+02 0.016 25.3 10.4 52 65-116 409-466 (904)
145 PF09849 DUF2076: Uncharacteri 25.3 4.7E+02 0.01 23.0 8.5 24 92-115 48-71 (247)
146 PF00412 LIM: LIM domain; Int 25.3 35 0.00075 22.0 0.8 39 194-237 3-54 (58)
147 PF03107 C1_2: C1 domain; Int 25.3 68 0.0015 18.3 2.0 26 193-221 3-30 (30)
148 PF10058 DUF2296: Predicted in 25.2 45 0.00097 22.2 1.3 29 205-238 24-52 (54)
149 PTZ00007 (NAP-L) nucleosome as 24.9 2.3E+02 0.0051 26.1 6.4 32 10-41 31-62 (337)
150 cd02338 ZZ_PCMF_like Zinc fing 24.8 43 0.00094 21.6 1.2 31 204-238 1-32 (49)
151 TIGR02977 phageshock_pspA phag 24.5 4.4E+02 0.0095 22.4 15.3 22 94-115 108-129 (219)
152 PF07342 DUF1474: Protein of u 24.4 1.4E+02 0.0029 22.6 3.9 40 75-116 47-86 (100)
153 PRK13723 conjugal transfer pil 24.4 6.5E+02 0.014 24.3 10.5 44 65-109 393-436 (451)
154 PF06008 Laminin_I: Laminin Do 24.2 4.8E+02 0.01 22.7 12.4 106 9-114 123-235 (264)
155 KOG4215 Hepatocyte nuclear fac 24.1 54 0.0012 30.7 2.1 25 189-216 18-46 (432)
156 PRK14154 heat shock protein Gr 24.0 4.6E+02 0.01 22.5 10.4 30 68-99 85-114 (208)
157 KOG1011 Neurotransmitter relea 24.0 4.4E+02 0.0095 27.0 8.3 97 13-112 856-954 (1283)
158 PF10158 LOH1CR12: Tumour supp 23.8 3.7E+02 0.008 21.2 10.9 16 24-39 57-72 (131)
159 PRK03564 formate dehydrogenase 23.7 62 0.0013 29.5 2.4 27 189-217 186-224 (309)
160 KOG1246 DNA-binding protein ju 23.6 62 0.0014 33.8 2.7 47 190-239 155-204 (904)
161 TIGR01562 FdhE formate dehydro 23.5 54 0.0012 29.8 2.0 27 189-217 183-222 (305)
162 KOG0956 PHD finger protein AF1 23.3 47 0.001 33.6 1.6 54 183-237 111-178 (900)
163 COG0466 Lon ATP-dependent Lon 23.2 7.1E+02 0.015 25.7 9.7 31 4-34 166-196 (782)
164 PRK10698 phage shock protein P 23.1 4.8E+02 0.01 22.3 15.3 12 4-16 15-26 (222)
165 PF11855 DUF3375: Protein of u 22.9 6.9E+02 0.015 24.1 10.2 33 4-36 180-212 (478)
166 KOG3277 Uncharacterized conser 22.9 52 0.0011 27.0 1.5 26 193-220 82-127 (165)
167 PF06464 DMAP_binding: DMAP1-b 22.9 1.9E+02 0.004 22.1 4.6 21 11-34 2-22 (111)
168 cd07596 BAR_SNX The Bin/Amphip 22.6 4.2E+02 0.0092 21.5 14.5 32 3-34 94-125 (218)
169 KOG0955 PHD finger protein BR1 22.6 36 0.00079 36.0 0.7 30 191-221 330-360 (1051)
170 cd00584 Prefoldin_alpha Prefol 22.5 3.5E+02 0.0077 20.6 6.9 44 74-117 83-126 (129)
171 COG1645 Uncharacterized Zn-fin 22.5 53 0.0011 26.1 1.5 11 227-237 41-51 (131)
172 PF00301 Rubredoxin: Rubredoxi 22.5 50 0.0011 21.4 1.1 12 228-239 32-43 (47)
173 cd00162 RING RING-finger (Real 22.2 18 0.00039 21.5 -1.0 26 211-238 18-43 (45)
174 KOG1473 Nucleosome remodeling 22.2 17 0.00036 38.6 -1.7 46 191-240 429-480 (1414)
175 PF07964 Red1: Rec10 / Red1; 22.2 5.7E+02 0.012 26.1 8.9 45 5-52 625-670 (706)
176 PF08274 PhnA_Zn_Ribbon: PhnA 22.0 36 0.00078 19.9 0.3 13 201-215 17-29 (30)
177 KOG0971 Microtubule-associated 21.7 1E+03 0.022 25.5 13.3 39 80-118 320-358 (1243)
178 PF00906 Hepatitis_core: Hepat 21.7 15 0.00033 30.3 -1.7 13 6-18 10-22 (187)
179 PF02996 Prefoldin: Prefoldin 21.6 3.5E+02 0.0075 20.1 6.3 41 76-116 75-115 (120)
180 COG0723 QcrA Rieske Fe-S prote 21.6 58 0.0013 26.7 1.7 18 217-234 110-129 (177)
181 KOG0964 Structural maintenance 21.6 1E+03 0.022 25.6 13.6 24 93-116 749-772 (1200)
182 PRK11677 hypothetical protein; 21.5 4.2E+02 0.0091 21.1 7.2 27 24-50 30-56 (134)
183 PF12773 DZR: Double zinc ribb 21.2 87 0.0019 19.8 2.1 19 190-208 12-34 (50)
184 PRK10807 paraquat-inducible pr 21.1 8E+02 0.017 24.1 12.9 20 3-24 421-440 (547)
185 PRK11546 zraP zinc resistance 21.0 4.5E+02 0.0097 21.2 10.3 35 11-45 41-76 (143)
186 PF14257 DUF4349: Domain of un 20.8 4.6E+02 0.01 22.7 7.4 11 4-14 107-117 (262)
187 PF14260 zf-C4pol: C4-type zin 20.7 43 0.00092 23.2 0.6 21 191-212 46-67 (73)
188 TIGR03017 EpsF chain length de 20.7 6.9E+02 0.015 23.2 13.5 54 3-61 153-206 (444)
189 COG4575 ElaB Uncharacterized c 20.7 3.9E+02 0.0085 20.4 8.8 43 55-98 30-73 (104)
190 PF08535 KorB: KorB domain; I 20.3 2.2E+02 0.0047 20.6 4.4 21 2-23 18-38 (93)
191 PF02370 M: M protein repeat; 20.2 1.6E+02 0.0034 15.9 2.5 15 102-116 4-18 (21)
192 COG2433 Uncharacterized conser 20.2 9E+02 0.02 24.4 11.5 84 11-118 410-493 (652)
193 PF06160 EzrA: Septation ring 20.2 8.3E+02 0.018 24.0 13.0 41 70-110 171-212 (560)
194 KOG1937 Uncharacterized conser 20.0 8.1E+02 0.018 23.8 11.2 25 89-114 387-411 (521)
No 1
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=100.00 E-value=6.4e-40 Score=279.27 Aligned_cols=229 Identities=29% Similarity=0.482 Sum_probs=157.3
Q ss_pred cHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHHHHHHHHHHHHHH
Q 025899 3 FLDEFQANLESLPNILQKKYALLRDLDKSLQEIQRQNEQRCEQEIEDLMREIRAGNITPNTSLIRFSDDALDEQKHSIRI 82 (246)
Q Consensus 3 yLe~fle~l~~LP~El~r~l~~IreLD~~~~~~~~~~~~~~~~~l~~~~k~~~~gs~~~~~~~~~l~~~I~~~~~~~~~l 82 (246)
.|+||++.|+|+|.|+.+.|++|.++|.++.++++.+.+... ++...+ ++|+++..+.+..|.+.|++.+-.+..+
T Consensus 6 ~Lnd~~d~l~n~P~et~~~~t~l~~iD~k~~d~~k~l~q~~s-i~k~~~---~~~~~t~~e~ed~l~k~i~Ell~~a~~~ 81 (271)
T COG5034 6 GLNDITDHLANVPSETDIRFTELSEIDAKVCDIIKNLRQMIS-ILKKII---DLDSQTYEEVEDGLLKEIRELLLKAIYI 81 (271)
T ss_pred HHHHHHHHHHhCChhhhhhhhhhhhhhHHHHHHHHHHHHHHH-HHHHHh---hcccCccccchhHHHHHHHHHHHHHHHH
Confidence 589999999999999999999999999999999999998888 544433 6899999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HhhccccccccCCCCCCC--CCC------CC--CCCCCCCCCC
Q 025899 83 ADEKVALAVQAYDLVDTHIQQLDQYLKNFDEE-----LRRERDSVATTASPAPSL--DGS------TK--SGRSSEGGRG 147 (246)
Q Consensus 83 ~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~e-----L~~e~~~~~~~~~~~~~~--~~~------~~--~~~~~~~~~~ 147 (246)
+.+|+.||+.+.-++++|+++||..+++...+ ++..............+. ..+ .. .|+..+ ..
T Consensus 82 ~~~~~~l~d~~~~l~~Rh~~~~d~~~a~~~h~~~~~~ie~~~~~~s~~~~~~~ss~a~~ss~~~~saassqgs~~t--~~ 159 (271)
T COG5034 82 QKEKSDLADRAEKLLRRHRKLLDDRIAKRPHEKVAARIENCHDAVSRLERNSYSSAARRSSGEHRSAASSQGSRHT--KL 159 (271)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhHHHhhhhhhhhhhhhhhhhhhhhhhccccchhhhccccccccccccccccCc--hh
Confidence 99999999999999999999999998776543 221111110000000000 000 00 011000 00
Q ss_pred CCcc-h---hhhhHHHHH----------------HHHhhhhhcCCCCCCCCCCCCCCCCCCCCceeeeCCCCCCCceecC
Q 025899 148 GRKK-T---RLATAAAAA----------------AAAVTEAAATPVANPTGMELDLPVDPNEPTYCVCNQVSYGEMVACD 207 (246)
Q Consensus 148 ~~k~-~---~~~~~~~~~----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~C~~~~~g~mi~Cd 207 (246)
.+++ . ...++..++ .+.+.++.. ....+...-+......++++||+|++++||+||+||
T Consensus 160 ~~R~n~~~~k~~~p~~~S~r~~~~t~~sp~v~~t~t~v~e~~~-~~s~~~~~vss~d~se~e~lYCfCqqvSyGqMVaCD 238 (271)
T COG5034 160 KKRKNIHNLKRRSPELSSKREVSFTLESPSVPDTATRVKEGNN-GGSTKSRGVSSEDNSEGEELYCFCQQVSYGQMVACD 238 (271)
T ss_pred HHHHhhcccccCCcchhhhccCCccCCCCCcccchhhhhcccC-CCCccccCcCccccccCceeEEEecccccccceecC
Confidence 0000 0 000010000 001111110 011111112223334678999999999999999999
Q ss_pred CCCCCCcceecccCCCCccCCCceeCcCCcc
Q 025899 208 NPNCKIEWFHFGCVGLKEQPKGKWYCPDCAA 238 (246)
Q Consensus 208 ~~~C~~~wfH~~Cv~l~~~~~~~w~C~~C~~ 238 (246)
|.||+++|||+.||||..+|+|+|||+.|..
T Consensus 239 n~nCkrEWFH~~CVGLk~pPKG~WYC~eCk~ 269 (271)
T COG5034 239 NANCKREWFHLECVGLKEPPKGKWYCPECKK 269 (271)
T ss_pred CCCCchhheeccccccCCCCCCcEeCHHhHh
Confidence 9999999999999999999999999999975
No 2
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=100.00 E-value=3.8e-35 Score=260.12 Aligned_cols=238 Identities=30% Similarity=0.599 Sum_probs=146.9
Q ss_pred CcHHHHHHH----hhcccHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHHHHHHH
Q 025899 2 SFLDEFQAN----LESLPNILQKKYALLRDLDKSL--QEIQRQNEQRCEQEIEDLMREIRAGNITPNTSLIRFSDDALDE 75 (246)
Q Consensus 2 ~yLe~fle~----l~~LP~El~r~l~~IreLD~~~--~~~~~~~~~~~~~~l~~~~k~~~~gs~~~~~~~~~l~~~I~~~ 75 (246)
++++++++. +.+||..++++|..|.++|... .+...++.. .....+.+ ...+.........+...|+..
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~f~~l~~~~~~~~~~~~~~e~~~---~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~ 82 (274)
T KOG1973|consen 8 ILIEEVDDDIDMAVQNLPRNLQHNFDVIEDIDIFGRSENQKKELDL---KVAVEYMS--KGRSQLSKPQKDPLLEAIRSA 82 (274)
T ss_pred hhhhhcccccccccccCCccchhHHHHHhhhhccchhHHHHhhhhh---hhhhcccc--ccccccCccccchhHHHHHHH
Confidence 466777777 9999999999999999999964 443333321 11111221 222211122233444678899
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc-ccccccCCCC-CCCCC------C--CCCCC--CCC
Q 025899 76 QKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELRRER-DSVATTASPA-PSLDG------S--TKSGR--SSE 143 (246)
Q Consensus 76 ~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~eL~~e~-~~~~~~~~~~-~~~~~------~--~~~~~--~~~ 143 (246)
+..+.+++|||+++|.++++++.+||+++|..++.|+.++.... ......+... ..... . ..+.+ .+.
T Consensus 83 ~~~~~~~~~ek~~~~~~~~e~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~ 162 (274)
T KOG1973|consen 83 LRKCKELSDEKVQIAMQTVELIPKHIGRLETALKSFEVELELAKAESSSKRSSSLKSAKKKEREVFKEKKESKQGSSEKP 162 (274)
T ss_pred HhhhhhhhhHHHHHHHHHHHhhHhhhcchhHHHHhcccchhhhhhhcccccccchhccCccccccccchhhcCCCCCCCc
Confidence 99999999999999999999999999999999998888765431 1110000000 00000 0 00000 000
Q ss_pred CCCCCCcchhhh--hHH--HHHHHHhh-hh---hcCCCCC--CCCCCCCCCCCCCCCceeeeCCCCCCCceecCCCCCCC
Q 025899 144 GGRGGRKKTRLA--TAA--AAAAAAVT-EA---AATPVAN--PTGMELDLPVDPNEPTYCVCNQVSYGEMVACDNPNCKI 213 (246)
Q Consensus 144 ~~~~~~k~~~~~--~~~--~~~~~~~~-~~---~~~~~~~--~~~~~~~~~~~~~~~~~C~C~~~~~g~mi~Cd~~~C~~ 213 (246)
+.....++.... .+. ......+. .. ......+ ......+...++++++||+|++++||+||+|||.+|+|
T Consensus 163 s~~~~~~~~~~~~~~~~~~rekk~~v~~~~~~~t~~~~~s~~~~~~~~~~~~d~~e~~yC~Cnqvsyg~Mi~CDn~~C~~ 242 (274)
T KOG1973|consen 163 SSVDKAKKGSKVNRRPCGAREKKRKVVEAKKEKTPKNKSSRPAESMESEEAVDPDEPTYCICNQVSYGKMIGCDNPGCPI 242 (274)
T ss_pred ccccccccccccccccchhhhhhhhhccccccccccCCCCCcccccccccccCCCCCEEEEecccccccccccCCCCCCc
Confidence 000011100000 000 00000000 00 0001111 22355678889999999999999999999999999999
Q ss_pred cceecccCCCCccCCCceeCcCCccccccCC
Q 025899 214 EWFHFGCVGLKEQPKGKWYCPDCAALKNRRK 244 (246)
Q Consensus 214 ~wfH~~Cv~l~~~~~~~w~C~~C~~~~~~~~ 244 (246)
+||||.||||+.+|+|+||||.|.....+.+
T Consensus 243 eWFH~~CVGL~~~PkgkWyC~~C~~~~~~~~ 273 (274)
T KOG1973|consen 243 EWFHFTCVGLKTKPKGKWYCPRCKAENKKKG 273 (274)
T ss_pred ceEEEeccccccCCCCcccchhhhhhhhccC
Confidence 9999999999999999999999998776543
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=99.93 E-value=2e-25 Score=170.60 Aligned_cols=103 Identities=39% Similarity=0.666 Sum_probs=89.3
Q ss_pred CcHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCC--CCCCchhhHHHHHHHHHHHHH
Q 025899 2 SFLDEFQANLESLPNILQKKYALLRDLDKSLQEIQRQNEQRCEQEIEDLMREIRAGN--ITPNTSLIRFSDDALDEQKHS 79 (246)
Q Consensus 2 ~yLe~fle~l~~LP~El~r~l~~IreLD~~~~~~~~~~~~~~~~~l~~~~k~~~~gs--~~~~~~~~~l~~~I~~~~~~~ 79 (246)
+|||+|+++|++||.||+|+|++||+||.++++++.++++....++. ..++ ++++ ....+..+|+..+.++
T Consensus 1 ~~le~f~d~~~~LP~el~r~l~~irelD~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~-~~~~~~~~I~~~~~~~ 73 (105)
T PF12998_consen 1 TYLEDFLDSLENLPAELQRNLTLIRELDAKSQDLLEELDQQIQKFIK------NHGSPSLSPE-KRRELLKEIQEEYERA 73 (105)
T ss_dssp HHHHHHHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT------CTTS--S-HH-HHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHChHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHh------hcccccCChH-HHHHHHHHHHHHHHHH
Confidence 69999999999999999999999999999999999999988887655 3444 5555 5555667999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 80 IRIADEKVALAVQAYDLVDTHIQQLDQYLKNF 111 (246)
Q Consensus 80 ~~l~dEKv~LA~q~~dlVd~hirrLD~dl~kf 111 (246)
+.+++|||.||+++|++|++|++|||+++++|
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 99999999999999999999999999999987
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=2.1e-10 Score=76.25 Aligned_cols=44 Identities=52% Similarity=1.476 Sum_probs=36.5
Q ss_pred ee-eeCCCC-CCCceecCCCCCCCcceecccCCCCcc----CCCceeCcCCcc
Q 025899 192 YC-VCNQVS-YGEMVACDNPNCKIEWFHFGCVGLKEQ----PKGKWYCPDCAA 238 (246)
Q Consensus 192 ~C-~C~~~~-~g~mi~Cd~~~C~~~wfH~~Cv~l~~~----~~~~w~C~~C~~ 238 (246)
|| +|++.. .+.||.||. |. .|||..|++++.. +.+.|+|+.|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~~--C~-~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDS--CN-RWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBST--TS-CEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCC--CC-hhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 68 999854 378999999 77 9999999998864 356999999974
No 5
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.91 E-value=3.8e-06 Score=73.88 Aligned_cols=44 Identities=34% Similarity=0.801 Sum_probs=37.9
Q ss_pred e-eeCCCCC-CCceecCCCCCCCcceecccCCCCccCCCceeCc-CCccc
Q 025899 193 C-VCNQVSY-GEMVACDNPNCKIEWFHFGCVGLKEQPKGKWYCP-DCAAL 239 (246)
Q Consensus 193 C-~C~~~~~-g~mi~Cd~~~C~~~wfH~~Cv~l~~~~~~~w~C~-~C~~~ 239 (246)
| +|++|.- .+|+.||-|| ..||..||||...|.|.|+|. .|...
T Consensus 317 C~IC~~P~~E~E~~FCD~CD---RG~HT~CVGL~~lP~G~WICD~~C~~~ 363 (381)
T KOG1512|consen 317 CRICLGPVIESEHLFCDVCD---RGPHTLCVGLQDLPRGEWICDMRCREA 363 (381)
T ss_pred hhccCCcccchheecccccc---CCCCccccccccccCccchhhhHHHHh
Confidence 5 8998864 6899999955 889999999999999999998 57543
No 7
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=97.71 E-value=1.1e-05 Score=75.75 Aligned_cols=49 Identities=27% Similarity=0.830 Sum_probs=35.8
Q ss_pred CceeeeCCCC-CCCceecCCCCCCCcceecccCC--C----CccCCCceeCcCCccccc
Q 025899 190 PTYCVCNQVS-YGEMVACDNPNCKIEWFHFGCVG--L----KEQPKGKWYCPDCAALKN 241 (246)
Q Consensus 190 ~~~C~C~~~~-~g~mi~Cd~~~C~~~wfH~~Cv~--l----~~~~~~~w~C~~C~~~~~ 241 (246)
..||.|+++. +..||+|+. |. .|||..|.- + -..+...|||..|...++
T Consensus 171 c~vC~~g~~~~~NrmlqC~~--C~-~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~ 226 (464)
T KOG4323|consen 171 CSVCYCGGPGAGNRMLQCDK--CR-QWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPK 226 (464)
T ss_pred eeeeecCCcCccceeeeecc--cc-cHHHHHhccCCCCHhhccCccceEeehhhccchh
Confidence 4456666653 237999999 66 999999976 1 124578999999986654
No 8
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.66 E-value=1.4e-05 Score=76.92 Aligned_cols=46 Identities=33% Similarity=1.087 Sum_probs=36.6
Q ss_pred cee-eeCCCC-CCCceecCCCCCCCcceecccCCCC----ccCCCceeCcCCccc
Q 025899 191 TYC-VCNQVS-YGEMVACDNPNCKIEWFHFGCVGLK----EQPKGKWYCPDCAAL 239 (246)
Q Consensus 191 ~~C-~C~~~~-~g~mi~Cd~~~C~~~wfH~~Cv~l~----~~~~~~w~C~~C~~~ 239 (246)
.|| .|++.. |-+.|+||. || .-||+.|+.-+ ..|.|.|||+.|...
T Consensus 254 ~fCsaCn~~~~F~~~i~CD~--Cp-~sFH~~CLePPl~~eniP~g~W~C~ec~~k 305 (613)
T KOG4299|consen 254 DFCSACNGSGLFNDIICCDG--CP-RSFHQTCLEPPLEPENIPPGSWFCPECKIK 305 (613)
T ss_pred HHHHHhCCccccccceeecC--Cc-hHHHHhhcCCCCCcccCCCCccccCCCeee
Confidence 499 999873 344599999 88 78999998733 368999999999653
No 9
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.56 E-value=4.5e-05 Score=75.06 Aligned_cols=49 Identities=31% Similarity=0.928 Sum_probs=39.3
Q ss_pred CCCcee-eeCCCCC-CCceecCCCCCCCcceecccCC--CCccCCCceeCcCCcc
Q 025899 188 NEPTYC-VCNQVSY-GEMVACDNPNCKIEWFHFGCVG--LKEQPKGKWYCPDCAA 238 (246)
Q Consensus 188 ~~~~~C-~C~~~~~-g~mi~Cd~~~C~~~wfH~~Cv~--l~~~~~~~w~C~~C~~ 238 (246)
.+..-| +|...+- ..||.||. |-...||.+|+. |.+.|.+.|||+.|.-
T Consensus 213 ~E~~~C~IC~~~DpEdVLLLCDs--CN~~~YH~YCLDPdl~eiP~~eWYC~NC~d 265 (1134)
T KOG0825|consen 213 QEEVKCDICTVHDPEDVLLLCDS--CNKVYYHVYCLDPDLSESPVNEWYCTNCSL 265 (1134)
T ss_pred cccccceeeccCChHHhheeecc--cccceeeccccCcccccccccceecCcchh
Confidence 456678 9998765 45999999 554559999998 5668999999999964
No 10
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=97.43 E-value=5.5e-05 Score=74.01 Aligned_cols=49 Identities=39% Similarity=0.853 Sum_probs=41.4
Q ss_pred CCCCCcee-eeCCCCC---CCceecCCCCCCCcceecccCCCCccCCCceeCcCCc
Q 025899 186 DPNEPTYC-VCNQVSY---GEMVACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCA 237 (246)
Q Consensus 186 ~~~~~~~C-~C~~~~~---g~mi~Cd~~~C~~~wfH~~Cv~l~~~~~~~w~C~~C~ 237 (246)
.-+|.+.| ||+.++. .+||.||+| . --.|..|.||...|.|.|+|..|.
T Consensus 267 e~dedviCDvCrspD~e~~neMVfCd~C--n-~cVHqaCyGIle~p~gpWlCr~Ca 319 (893)
T KOG0954|consen 267 EYDEDVICDVCRSPDSEEANEMVFCDKC--N-ICVHQACYGILEVPEGPWLCRTCA 319 (893)
T ss_pred eccccceeceecCCCccccceeEEeccc--h-hHHHHhhhceeecCCCCeeehhcc
Confidence 33478999 9998853 479999995 4 568999999999999999999885
No 11
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=97.42 E-value=1.8e-05 Score=48.85 Aligned_cols=34 Identities=38% Similarity=1.031 Sum_probs=20.0
Q ss_pred CCceecCCCCCCCcceecccCCCCccCCC-ceeCcCCc
Q 025899 201 GEMVACDNPNCKIEWFHFGCVGLKEQPKG-KWYCPDCA 237 (246)
Q Consensus 201 g~mi~Cd~~~C~~~wfH~~Cv~l~~~~~~-~w~C~~C~ 237 (246)
..||.|++ |. -++|.+|.|+...|.+ .|+|..|.
T Consensus 2 n~ll~C~~--C~-v~VH~~CYGv~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDN--CN-VAVHQSCYGVSEVPDGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SS--S---EEEHHHHT-SS--SS-----HHH-
T ss_pred CceEEeCC--CC-CcCChhhCCcccCCCCCcEECCcCC
Confidence 46899999 66 7899999999998866 89998874
No 12
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=97.42 E-value=6.6e-05 Score=72.99 Aligned_cols=48 Identities=33% Similarity=0.943 Sum_probs=41.1
Q ss_pred CceeeeCCC-CC--CCceecCCCCCCCcceecccCCCCccCCCceeCcCCcc
Q 025899 190 PTYCVCNQV-SY--GEMVACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCAA 238 (246)
Q Consensus 190 ~~~C~C~~~-~~--g~mi~Cd~~~C~~~wfH~~Cv~l~~~~~~~w~C~~C~~ 238 (246)
.-+|||..- .| ..+|.||+-+|. -..|..|.||..+|.|.|||..|..
T Consensus 6 GGCCVCSDErGWaeNPLVYCDG~nCs-VAVHQaCYGIvqVPtGpWfCrKCes 56 (900)
T KOG0956|consen 6 GGCCVCSDERGWAENPLVYCDGHNCS-VAVHQACYGIVQVPTGPWFCRKCES 56 (900)
T ss_pred cceeeecCcCCCccCceeeecCCCce-eeeehhcceeEecCCCchhhhhhhh
Confidence 457899754 34 358999999999 8899999999999999999999964
No 13
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=97.41 E-value=5.3e-05 Score=66.35 Aligned_cols=51 Identities=27% Similarity=0.774 Sum_probs=41.4
Q ss_pred CCcee-eeCCCCC-CCceecCCCCCCCcceecccCC--CCccCCCceeCcCCcccccc
Q 025899 189 EPTYC-VCNQVSY-GEMVACDNPNCKIEWFHFGCVG--LKEQPKGKWYCPDCAALKNR 242 (246)
Q Consensus 189 ~~~~C-~C~~~~~-g~mi~Cd~~~C~~~wfH~~Cv~--l~~~~~~~w~C~~C~~~~~~ 242 (246)
|-.|| +|+...+ .+++.||.|| .-||..|+. +..+|.|.|.|.-|...-+.
T Consensus 280 eck~csicgtsenddqllfcddcd---rgyhmyclsppm~eppegswsc~KOG~~~~e 334 (336)
T KOG1244|consen 280 ECKYCSICGTSENDDQLLFCDDCD---RGYHMYCLSPPMVEPPEGSWSCHLCLEELKE 334 (336)
T ss_pred ecceeccccCcCCCceeEeecccC---CceeeEecCCCcCCCCCCchhHHHHHHHHhh
Confidence 45678 8987765 5789999955 889999998 77788999999999876544
No 14
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.36 E-value=7.5e-05 Score=73.83 Aligned_cols=50 Identities=42% Similarity=0.983 Sum_probs=39.8
Q ss_pred Ccee-eeCCCCCCCceecCCCCCCCcceecccCC--CCccCCCceeCcCCccccccCC
Q 025899 190 PTYC-VCNQVSYGEMVACDNPNCKIEWFHFGCVG--LKEQPKGKWYCPDCAALKNRRK 244 (246)
Q Consensus 190 ~~~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cv~--l~~~~~~~w~C~~C~~~~~~~~ 244 (246)
.-+| +|... |..|+||. |+ .|||..|.+ ++..|.+.|.|+.|.....++|
T Consensus 47 ~e~c~ic~~~--g~~l~c~t--C~-~s~h~~cl~~pl~~~p~~~~~c~Rc~~p~~~~k 99 (696)
T KOG0383|consen 47 QEACRICADG--GELLWCDT--CP-ASFHASCLGPPLTPQPNGEFICPRCFCPKNAGK 99 (696)
T ss_pred hhhhhhhcCC--CcEEEecc--cc-HHHHHHccCCCCCcCCccceeeeeeccCCCccc
Confidence 4455 99877 99999999 99 999999998 4556667799999966655444
No 15
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=97.11 E-value=8.2e-05 Score=78.86 Aligned_cols=49 Identities=35% Similarity=0.916 Sum_probs=41.4
Q ss_pred Ccee-eeCCCCCC-CceecCCCCCCCcceecccCC--CCccCCCceeCcCCccccc
Q 025899 190 PTYC-VCNQVSYG-EMVACDNPNCKIEWFHFGCVG--LKEQPKGKWYCPDCAALKN 241 (246)
Q Consensus 190 ~~~C-~C~~~~~g-~mi~Cd~~~C~~~wfH~~Cv~--l~~~~~~~w~C~~C~~~~~ 241 (246)
...| +|...... .|+.|+. |- .|||+.|+. +...|.+.|+||.|+..+.
T Consensus 1108 ~~~c~~cr~k~~~~~m~lc~~--c~-~~~h~~C~rp~~~~~~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1108 NALCKVCRRKKQDEKMLLCDE--CL-SGFHLFCLRPALSSVPPGDWMCPSCRKEHR 1160 (1404)
T ss_pred hhhhhhhhhcccchhhhhhHh--hh-hhHHHHhhhhhhccCCcCCccCCccchhhh
Confidence 5678 99877543 7999999 55 999999987 7778999999999998874
No 16
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=96.55 E-value=0.0016 Score=67.15 Aligned_cols=50 Identities=30% Similarity=0.767 Sum_probs=40.1
Q ss_pred CceeeeCCCCC---CCceecCCCCCCCcceecccCCCCccCCCceeCcCCcccccc
Q 025899 190 PTYCVCNQVSY---GEMVACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCAALKNR 242 (246)
Q Consensus 190 ~~~C~C~~~~~---g~mi~Cd~~~C~~~wfH~~Cv~l~~~~~~~w~C~~C~~~~~~ 242 (246)
..+|||....- ...|.||. |. --+|..|+|+...|.|.|+|-.|...+.+
T Consensus 220 ~~C~iC~~~~~~n~n~ivfCD~--Cn-l~VHq~Cygi~~ipeg~WlCr~Cl~s~~~ 272 (1051)
T KOG0955|consen 220 AVCCICLDGECQNSNVIVFCDG--CN-LAVHQECYGIPFIPEGQWLCRRCLQSPQR 272 (1051)
T ss_pred ccceeecccccCCCceEEEcCC--Cc-chhhhhccCCCCCCCCcEeehhhccCcCc
Confidence 44559987642 46899999 55 67999999999999999999999766543
No 17
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=96.51 E-value=0.001 Score=61.16 Aligned_cols=48 Identities=31% Similarity=0.789 Sum_probs=39.9
Q ss_pred CceeeeCCCCCC--CceecCCCCCCCcceeccc--CCCCc---cCCCceeCcCCcccc
Q 025899 190 PTYCVCNQVSYG--EMVACDNPNCKIEWFHFGC--VGLKE---QPKGKWYCPDCAALK 240 (246)
Q Consensus 190 ~~~C~C~~~~~g--~mi~Cd~~~C~~~wfH~~C--v~l~~---~~~~~w~C~~C~~~~ 240 (246)
..||.|..+... .|+.|+. |. .|||..| ||++. .+...|+|..|....
T Consensus 60 ~~~~~~~~~~~p~~~~~~cd~--C~-~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~ 114 (345)
T KOG1632|consen 60 QRYCKCYKPCDPDDLMEQCDL--CE-DWYHGECWEVGTAEKEAPKEDPKVCDECKEAQ 114 (345)
T ss_pred hchhhcccccCchhhhhcccc--cc-ccccccccccCchhhcCCccccccccccchhh
Confidence 348999888664 7999999 88 9999999 99877 347899999997654
No 18
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=95.75 E-value=0.004 Score=58.87 Aligned_cols=44 Identities=30% Similarity=0.776 Sum_probs=36.5
Q ss_pred cee-eeCCCCC---CCceecCCCCCCCcceecccCCCCccCCCceeCcCCc
Q 025899 191 TYC-VCNQVSY---GEMVACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCA 237 (246)
Q Consensus 191 ~~C-~C~~~~~---g~mi~Cd~~~C~~~wfH~~Cv~l~~~~~~~w~C~~C~ 237 (246)
..| +|..... ...|.||+| . --.|.+|.|+.-.|.|+|+|-.|.
T Consensus 194 ~~C~~c~~t~~eN~naiVfCdgC--~-i~VHq~CYGI~f~peG~WlCrkCi 241 (669)
T COG5141 194 DICTKCTSTHNENSNAIVFCDGC--E-ICVHQSCYGIQFLPEGFWLCRKCI 241 (669)
T ss_pred hhhHhccccccCCcceEEEecCc--c-hhhhhhcccceecCcchhhhhhhc
Confidence 357 8987754 357999995 4 568999999999999999999995
No 19
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=95.07 E-value=0.027 Score=53.52 Aligned_cols=53 Identities=34% Similarity=0.871 Sum_probs=35.7
Q ss_pred CCCCCCCC-ceeeeCC-C--CCCCceecCCCCCCCcceecccCCCCc---cC-------CCceeCcCCcc
Q 025899 183 LPVDPNEP-TYCVCNQ-V--SYGEMVACDNPNCKIEWFHFGCVGLKE---QP-------KGKWYCPDCAA 238 (246)
Q Consensus 183 ~~~~~~~~-~~C~C~~-~--~~g~mi~Cd~~~C~~~wfH~~Cv~l~~---~~-------~~~w~C~~C~~ 238 (246)
.+..|-.. .+|||-. - ..|+.|+||+ |. --.|-+|.|+.. .| ...|||..|..
T Consensus 112 ~~Sapkk~~iCcVClg~rs~da~ei~qCd~--CG-i~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~ 178 (707)
T KOG0957|consen 112 TPSAPKKAVICCVCLGQRSVDAGEILQCDK--CG-INVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLY 178 (707)
T ss_pred ccCccccceEEEEeecCccccccceeeccc--cC-ceecccccccccccccCCCCccCCCCchhhhhHhc
Confidence 33344444 4569943 2 3489999999 66 448999999663 12 36799998853
No 20
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=95.03 E-value=1.1 Score=43.09 Aligned_cols=44 Identities=32% Similarity=0.977 Sum_probs=34.1
Q ss_pred cee-eeCCCCC-CCceecCCCCCCCcceecccCC--CCccCCC----ceeCcCCc
Q 025899 191 TYC-VCNQVSY-GEMVACDNPNCKIEWFHFGCVG--LKEQPKG----KWYCPDCA 237 (246)
Q Consensus 191 ~~C-~C~~~~~-g~mi~Cd~~~C~~~wfH~~Cv~--l~~~~~~----~w~C~~C~ 237 (246)
.-| ||.+... --.++||- |. --||+.|+. |+..|+. -|.|..|-
T Consensus 545 ysCgiCkks~dQHll~~CDt--C~-lhYHlGCL~PPLTR~Pkk~kn~gWqCsECd 596 (707)
T KOG0957|consen 545 YSCGICKKSTDQHLLTQCDT--CH-LHYHLGCLSPPLTRLPKKNKNFGWQCSECD 596 (707)
T ss_pred eeeeeeccchhhHHHhhcch--hh-ceeeccccCCccccCcccccCcceeecccc
Confidence 348 9987643 34789999 66 679999998 8887754 49999993
No 21
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=93.68 E-value=0.035 Score=49.94 Aligned_cols=31 Identities=39% Similarity=1.073 Sum_probs=25.0
Q ss_pred CCceeeeCCCCC-------CCceecCCCCCCCccee-cccCC
Q 025899 189 EPTYCVCNQVSY-------GEMVACDNPNCKIEWFH-FGCVG 222 (246)
Q Consensus 189 ~~~~C~C~~~~~-------g~mi~Cd~~~C~~~wfH-~~Cv~ 222 (246)
+..||.|..+.. |.|++|-. |+ .||| -.|..
T Consensus 127 qG~~C~Cd~~Ypdp~~~~e~~m~QC~i--CE-DWFHce~c~~ 165 (345)
T KOG2752|consen 127 QGLFCKCDTPYPDPVRTEEGEMLQCVI--CE-DWFHCEGCMQ 165 (345)
T ss_pred cceeEEecCCCCCccccccceeeeEEe--cc-chhcccccCc
Confidence 578999998754 56999999 88 9999 66644
No 22
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=93.38 E-value=0.041 Score=52.92 Aligned_cols=49 Identities=31% Similarity=0.666 Sum_probs=39.9
Q ss_pred CCceeeeCCC-C-CCCceecCCCCCCCcceecccCCCCccC-CCceeCcCCcccc
Q 025899 189 EPTYCVCNQV-S-YGEMVACDNPNCKIEWFHFGCVGLKEQP-KGKWYCPDCAALK 240 (246)
Q Consensus 189 ~~~~C~C~~~-~-~g~mi~Cd~~~C~~~wfH~~Cv~l~~~~-~~~w~C~~C~~~~ 240 (246)
....|+|+.. . .|.||+|+. |+ .|-|..|+|....- +..|.|..|....
T Consensus 85 ~~~~c~c~~~~~~~g~~i~c~~--c~-~Wqh~~C~g~~~~~~p~~y~c~~c~~~~ 136 (508)
T KOG1844|consen 85 EISRCDCGLEDDMEGLMIQCDW--CG-RWQHKICCGSFKSTKPDKYVCEICTPRN 136 (508)
T ss_pred cccccccccccCCCceeeCCcc--cC-cccCceeeeecCCCCchhceeeeecccc
Confidence 4667999865 3 578999999 88 99999999966543 5899999997654
No 23
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=92.17 E-value=0.02 Score=52.77 Aligned_cols=51 Identities=27% Similarity=0.686 Sum_probs=37.5
Q ss_pred CCCCCCcee-eeCCCCC--CCceecCCCCCCCcceecccCCCCccC---CC----ceeCcCCcc
Q 025899 185 VDPNEPTYC-VCNQVSY--GEMVACDNPNCKIEWFHFGCVGLKEQP---KG----KWYCPDCAA 238 (246)
Q Consensus 185 ~~~~~~~~C-~C~~~~~--g~mi~Cd~~~C~~~wfH~~Cv~l~~~~---~~----~w~C~~C~~ 238 (246)
.++.+..+| .|+..+. -.||+|+. |. .|||..||.+...+ .. .|+|++|..
T Consensus 234 ~~~~~~~~~~~cg~~~~~~~~~~~~~~--~e-~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~ 294 (345)
T KOG1632|consen 234 APDYSKLICDPCGLSDANKKFEICCDL--CE-SWFHGDCVQIFEARKRLNEIRNEVYKCPHCTV 294 (345)
T ss_pred ccccccccccccCcchHHHHHHHHHHH--HH-HHhcccccccccchhhhhhhhccceecCceee
Confidence 344455677 6665432 35899999 77 99999999988865 23 499999975
No 24
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=90.62 E-value=0.14 Score=37.46 Aligned_cols=31 Identities=29% Similarity=0.860 Sum_probs=26.3
Q ss_pred Ccee-eeCCCCCCCceecCCCCCCCcceecccCC
Q 025899 190 PTYC-VCNQVSYGEMVACDNPNCKIEWFHFGCVG 222 (246)
Q Consensus 190 ~~~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cv~ 222 (246)
...| +|+++ .|-.|.|...+|. .+||+.|.-
T Consensus 36 ~~~C~~C~~~-~Ga~i~C~~~~C~-~~fH~~CA~ 67 (90)
T PF13771_consen 36 KLKCSICKKK-GGACIGCSHPGCS-RSFHVPCAR 67 (90)
T ss_pred CCCCcCCCCC-CCeEEEEeCCCCC-cEEChHHHc
Confidence 3467 99876 6889999999999 999999965
No 25
>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=90.15 E-value=8.7 Score=31.04 Aligned_cols=40 Identities=13% Similarity=0.080 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 74 DEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDE 113 (246)
Q Consensus 74 ~~~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~ 113 (246)
-.++....-...-|..-+.+++-....|.+|++++..++.
T Consensus 93 ~~~e~~i~~~~~~I~~Lq~~~~~~~~ki~~Le~~i~~~~~ 132 (146)
T PF08702_consen 93 YILETKIINQPSNIRVLQNILRSNRQKIQRLEQDIDQQER 132 (146)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566667777788888888888899999999988875
No 26
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=89.51 E-value=0.15 Score=38.73 Aligned_cols=31 Identities=29% Similarity=0.808 Sum_probs=25.9
Q ss_pred Ccee-eeCCCCCCCceecCCCCCCCcceecccCC
Q 025899 190 PTYC-VCNQVSYGEMVACDNPNCKIEWFHFGCVG 222 (246)
Q Consensus 190 ~~~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cv~ 222 (246)
...| +|++. .|..|.|...+|. .+||..|.-
T Consensus 55 ~~~C~iC~~~-~G~~i~C~~~~C~-~~fH~~CA~ 86 (110)
T PF13832_consen 55 KLKCSICGKS-GGACIKCSHPGCS-TAFHPTCAR 86 (110)
T ss_pred CCcCcCCCCC-CceeEEcCCCCCC-cCCCHHHHH
Confidence 3456 99976 5889999998999 999999953
No 27
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=86.30 E-value=14 Score=28.87 Aligned_cols=107 Identities=15% Similarity=0.276 Sum_probs=68.3
Q ss_pred hhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-hhCCCCCCchhhHHHH--HHHHHHHHHHHHHHHHH
Q 025899 11 LESLPNILQKKYALLRDLDKSLQEIQRQNEQRCEQEIEDLMREI-RAGNITPNTSLIRFSD--DALDEQKHSIRIADEKV 87 (246)
Q Consensus 11 l~~LP~El~r~l~~IreLD~~~~~~~~~~~~~~~~~l~~~~k~~-~~gs~~~~~~~~~l~~--~I~~~~~~~~~l~dEKv 87 (246)
+.+||.+++..+.....|-.+++.+..+..+.... +....+++ .-..+..+...-+..- -|......+.+--++++
T Consensus 1 ~~~lpp~~q~~l~q~QqLq~ql~~~~~qk~~le~q-L~E~~~al~Ele~l~eD~~vYk~VG~llvk~~k~~~~~eL~er~ 79 (119)
T COG1382 1 MEQLPPEVQAQLAQLQQLQQQLQKVILQKQQLEAQ-LKEIEKALEELEKLDEDAPVYKKVGNLLVKVSKEEAVDELEERK 79 (119)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcCCcccHHHHHhhhHHhhhhHHHHHHHHHHHH
Confidence 36899999999999999999999877766554443 33333322 1123333322222111 13344556666667777
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 025899 88 ALAVQAYDLVDTHIQQLDQYLKNFDEELRRE 118 (246)
Q Consensus 88 ~LA~q~~dlVd~hirrLD~dl~kfe~eL~~e 118 (246)
+.-.-=...+.+..++|+..++.+...|...
T Consensus 80 E~Le~ri~tLekQe~~l~e~l~eLq~~i~~~ 110 (119)
T COG1382 80 ETLELRIKTLEKQEEKLQERLEELQSEIQKA 110 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7777777777788888888888888777653
No 28
>PF13341 RAG2_PHD: RAG2 PHD domain; PDB: 2JWO_A 2V86_B 2V85_B 2V87_A 2V83_C 2V89_A 2V88_A.
Probab=83.32 E-value=0.62 Score=32.81 Aligned_cols=32 Identities=31% Similarity=0.785 Sum_probs=19.5
Q ss_pred CceecCCCCCCCcceecccCCCCcc-------CCCceeCcC
Q 025899 202 EMVACDNPNCKIEWFHFGCVGLKEQ-------PKGKWYCPD 235 (246)
Q Consensus 202 ~mi~Cd~~~C~~~wfH~~Cv~l~~~-------~~~~w~C~~ 235 (246)
-||.|.+. ...|.|-.|..|++. ...+|||..
T Consensus 29 AMI~cs~~--~GHWvhaqCm~LsE~~L~~LSq~n~KYfC~d 67 (78)
T PF13341_consen 29 AMIFCSRG--GGHWVHAQCMDLSETMLIQLSQENTKYFCND 67 (78)
T ss_dssp -EEEE-ST--T-EEEETGGGT--HHHHHHHHHSSS-B--TT
T ss_pred eEEEEeCC--CceEeEeecccchHHHHHHHccCCceEEEhh
Confidence 49999985 348999999999883 357899975
No 29
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=83.32 E-value=0.66 Score=45.72 Aligned_cols=47 Identities=21% Similarity=0.615 Sum_probs=34.2
Q ss_pred Ccee-eeCCC-CCCCceecCCCCCCCcceecccCC--CCccCCCceeCcCCccc
Q 025899 190 PTYC-VCNQV-SYGEMVACDNPNCKIEWFHFGCVG--LKEQPKGKWYCPDCAAL 239 (246)
Q Consensus 190 ~~~C-~C~~~-~~g~mi~Cd~~~C~~~wfH~~Cv~--l~~~~~~~w~C~~C~~~ 239 (246)
-+.| .|+.. +......|+.|| .-||..|.. +...+.|.|+|+.|...
T Consensus 68 crvCe~c~~~gD~~kf~~Ck~cD---vsyh~yc~~P~~~~v~sg~~~ckk~~~c 118 (694)
T KOG4443|consen 68 CRVCEACGTTGDPKKFLLCKRCD---VSYHCYCQKPPNDKVPSGPWLCKKCTRC 118 (694)
T ss_pred ceeeeeccccCCccccccccccc---ccccccccCCccccccCcccccHHHHhh
Confidence 4556 66643 224567899966 679999987 66688999999988643
No 30
>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=81.26 E-value=1.1 Score=42.35 Aligned_cols=43 Identities=23% Similarity=0.741 Sum_probs=30.4
Q ss_pred eeCCCCC--C--CceecCCCCCCCcceecccC--------CCCc-c----CCCceeCcCCccc
Q 025899 194 VCNQVSY--G--EMVACDNPNCKIEWFHFGCV--------GLKE-Q----PKGKWYCPDCAAL 239 (246)
Q Consensus 194 ~C~~~~~--g--~mi~Cd~~~C~~~wfH~~Cv--------~l~~-~----~~~~w~C~~C~~~ 239 (246)
+|++.++ + -.|.||. |. .|-|..|. |.+. . ..+.|+|..|-..
T Consensus 133 iC~kfD~~~n~~~Wi~Cd~--Cg-H~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~ 192 (446)
T PF07227_consen 133 ICSKFDDNKNTCSWIGCDV--CG-HWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKT 192 (446)
T ss_pred ccCCcccCCCCeeEEeccC--CC-ceehhhhhcccccccCCccCCCCCccCceEEEccCCCCh
Confidence 8887644 2 3799998 77 99999993 2111 1 2458999999653
No 31
>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=80.54 E-value=1.2 Score=34.06 Aligned_cols=52 Identities=27% Similarity=0.654 Sum_probs=32.4
Q ss_pred CCCCCcee-eeCCCCCCCceec----CCCCC---CCcceecccCC----CC---ccCCCceeCcCCcc
Q 025899 186 DPNEPTYC-VCNQVSYGEMVAC----DNPNC---KIEWFHFGCVG----LK---EQPKGKWYCPDCAA 238 (246)
Q Consensus 186 ~~~~~~~C-~C~~~~~g~mi~C----d~~~C---~~~wfH~~Cv~----l~---~~~~~~w~C~~C~~ 238 (246)
|+.....| .|++...+..+.| .+..| . .=|=..|+- .. ......|.||.|+.
T Consensus 3 d~~~g~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~-~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 3 DSVNGKTCHQCRQKTLDFKTICTGHWKNSSCRGCR-GKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred cCCCCCCchhhcCCCCCCceEcCCCCCCCCCccCc-ceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 44556788 9988776666677 23335 5 335556643 11 12467899999975
No 32
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=78.48 E-value=1.3 Score=46.38 Aligned_cols=42 Identities=29% Similarity=0.859 Sum_probs=35.5
Q ss_pred cee-eeCCCCCCCceecCCCCCCCcceecccCC--CCccCCCceeCcCCc
Q 025899 191 TYC-VCNQVSYGEMVACDNPNCKIEWFHFGCVG--LKEQPKGKWYCPDCA 237 (246)
Q Consensus 191 ~~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cv~--l~~~~~~~w~C~~C~ 237 (246)
-.| ||+.. |+.+||.+ || .-+|+.||. +-..|...|-|.-|.
T Consensus 345 dhcrf~~d~--~~~lc~Et--~p-rvvhlEcv~hP~~~~~s~~~e~evc~ 389 (1414)
T KOG1473|consen 345 DHCRFCHDL--GDLLCCET--CP-RVVHLECVFHPRFAVPSAFWECEVCN 389 (1414)
T ss_pred ccccccCcc--cceeeccc--CC-ceEEeeecCCccccCCCccchhhhhh
Confidence 367 99887 89999999 99 889999998 444788899999886
No 33
>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=77.00 E-value=30 Score=26.26 Aligned_cols=45 Identities=16% Similarity=0.238 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025899 73 LDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELRR 117 (246)
Q Consensus 73 ~~~~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~eL~~ 117 (246)
......++.--.+++........-+++.+..|...+..++..|..
T Consensus 62 ~~~~~e~~~~l~~r~e~ie~~i~~lek~~~~l~~~l~e~q~~l~~ 106 (110)
T TIGR02338 62 KTDKEEAIQELKEKKETLELRVKTLQRQEERLREQLKELQEKIQE 106 (110)
T ss_pred eecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555666666666666677777777777777777777766653
No 34
>PRK09343 prefoldin subunit beta; Provisional
Probab=76.15 E-value=34 Score=26.54 Aligned_cols=104 Identities=15% Similarity=0.206 Sum_probs=61.5
Q ss_pred hcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHhhhCCCCCCchhhHHHH--HHHHHHHHHHHHHHHHH
Q 025899 12 ESLPNILQKKYALLRDLDKSLQEIQRQNEQRCEQEIED--LMREIRAGNITPNTSLIRFSD--DALDEQKHSIRIADEKV 87 (246)
Q Consensus 12 ~~LP~El~r~l~~IreLD~~~~~~~~~~~~~~~~~l~~--~~k~~~~gs~~~~~~~~~l~~--~I~~~~~~~~~l~dEKv 87 (246)
.+||.+|+..+..++.+-..++.+..+.......+-+. ... .-..+.++...-+..- -|......+..--.+++
T Consensus 3 ~~~~~~~q~~~~~~q~lq~~l~~~~~q~~~le~q~~e~~~~~~--EL~~L~~d~~VYk~VG~vlv~qd~~e~~~~l~~r~ 80 (121)
T PRK09343 3 ENIPPEVQAQLAQLQQLQQQLERLLQQKSQIDLELREINKALE--ELEKLPDDTPIYKIVGNLLVKVDKTKVEKELKERK 80 (121)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHcCCCcchhHHHhhHHHhhccHHHHHHHHHHHH
Confidence 47999999999999999888887766665544442221 111 1223444333222111 23445566666666676
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025899 88 ALAVQAYDLVDTHIQQLDQYLKNFDEELRR 117 (246)
Q Consensus 88 ~LA~q~~dlVd~hirrLD~dl~kfe~eL~~ 117 (246)
.....-..-+++....|...+..++..|..
T Consensus 81 E~ie~~ik~lekq~~~l~~~l~e~q~~l~~ 110 (121)
T PRK09343 81 ELLELRSRTLEKQEKKLREKLKELQAKINE 110 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 666666666666666666666666665543
No 35
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=73.74 E-value=54 Score=35.23 Aligned_cols=28 Identities=21% Similarity=0.357 Sum_probs=17.2
Q ss_pred HhhcccHHHHHHHHHHHHHHHHHHHHHH
Q 025899 10 NLESLPNILQKKYALLRDLDKSLQEIQR 37 (246)
Q Consensus 10 ~l~~LP~El~r~l~~IreLD~~~~~~~~ 37 (246)
.|.+|-.+|++.+..|..+|..+++..-
T Consensus 1512 qi~~L~~~I~e~v~sL~nVd~IL~~T~~ 1539 (1758)
T KOG0994|consen 1512 QIQQLTGEIQERVASLPNVDAILSRTKG 1539 (1758)
T ss_pred HHHHHHHHHHHHHHhcccHHHHHHhhhh
Confidence 4555666666666666666766665433
No 36
>PF04012 PspA_IM30: PspA/IM30 family; InterPro: IPR007157 This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma54-containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator [].
Probab=71.25 E-value=63 Score=27.36 Aligned_cols=32 Identities=19% Similarity=0.414 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 84 DEKVALAVQAYDLVDTHIQQLDQYLKNFDEEL 115 (246)
Q Consensus 84 dEKv~LA~q~~dlVd~hirrLD~dl~kfe~eL 115 (246)
.+.+.-..+.++....++.+|...+..++..+
T Consensus 97 e~~~~~l~~~~~~~~~~~~~l~~~l~~l~~kl 128 (221)
T PF04012_consen 97 EEQAERLEQQLDQAEAQVEKLKEQLEELEAKL 128 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444455555666666666666665555543
No 37
>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=70.56 E-value=85 Score=28.61 Aligned_cols=47 Identities=19% Similarity=0.258 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHhh
Q 025899 71 DALDEQKHSIRIADEKVALAVQAY-------DLVDTHIQQLDQYLKNFDEELRR 117 (246)
Q Consensus 71 ~I~~~~~~~~~l~dEKv~LA~q~~-------dlVd~hirrLD~dl~kfe~eL~~ 117 (246)
++.........|..|||.|=+++= ..+.+.+-+|..+-..|+..|.+
T Consensus 150 e~~~~q~~le~Lr~EKVdlEn~LE~EQE~lvN~L~Kqm~~l~~eKr~Lq~~l~~ 203 (310)
T PF09755_consen 150 EKSAKQEELERLRREKVDLENTLEQEQEALVNRLWKQMDKLEAEKRRLQEKLEQ 203 (310)
T ss_pred HHHHhHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 333334455689999999887653 34444555555555555554443
No 38
>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=70.06 E-value=20 Score=31.58 Aligned_cols=46 Identities=13% Similarity=0.202 Sum_probs=35.0
Q ss_pred hhhHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 64 SLIRFSDDALDEQKHSIRIADE-KVALAVQAYDLVDTHIQQLDQYLKNFDE 113 (246)
Q Consensus 64 ~~~~l~~~I~~~~~~~~~l~dE-Kv~LA~q~~dlVd~hirrLD~dl~kfe~ 113 (246)
.+..+..+|...+.++-.|+.+ +|.-|+.+...|+. |-...+.++.
T Consensus 124 ~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~----Lk~ek~~le~ 170 (254)
T PF03194_consen 124 KIDELDEKIGELLKEAEELGEEGDVDEAQKLMEEVEK----LKEEKEELEK 170 (254)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH----HHHHHHHHHh
Confidence 4567778899999999999998 99999988887775 4444444444
No 39
>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=70.02 E-value=97 Score=29.00 Aligned_cols=89 Identities=20% Similarity=0.303 Sum_probs=48.9
Q ss_pred HhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 10 NLESLPNILQKKYALLRDLDKSLQEIQRQNEQRCEQEIEDLMREIRAGNITPNTSLIRFSDDALDEQKHSIRIADEKVAL 89 (246)
Q Consensus 10 ~l~~LP~El~r~l~~IreLD~~~~~~~~~~~~~~~~~l~~~~k~~~~gs~~~~~~~~~l~~~I~~~~~~~~~l~dEKv~L 89 (246)
+|++||.-+.+.=..|++||..+.+..+... ..|.- .....+.....|.+.+.++.++ .+|-+-
T Consensus 19 SL~~ld~~i~~l~~~i~~ld~eI~~~v~~q~--------------~~~~~-~~~~l~~a~~~i~~L~~~i~~i-k~kA~~ 82 (383)
T PF04100_consen 19 SLSNLDELIAKLRKEIRELDEEIKELVREQS--------------SSGQD-AEEDLEEAQEAIQELFEKISEI-KSKAEE 82 (383)
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHh--------------hcccc-ccccHHHHHHHHHHHHHHHHHH-HHHHHH
Confidence 5566666666666666666666554333211 11211 1122333334444444444333 345567
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 90 AVQAYDLVDTHIQQLDQYLKNFDEE 114 (246)
Q Consensus 90 A~q~~dlVd~hirrLD~dl~kfe~e 114 (246)
+.+++.-|.+-|++||.--.++-..
T Consensus 83 sE~~V~~it~dIk~LD~AKrNLT~S 107 (383)
T PF04100_consen 83 SEQMVQEITRDIKQLDNAKRNLTQS 107 (383)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7788888889999999776666543
No 40
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=70.00 E-value=1.3 Score=43.68 Aligned_cols=48 Identities=31% Similarity=0.798 Sum_probs=33.5
Q ss_pred Ccee-eeCCCC---CCCceecCCCCCCCcceecccCCCCcc---CCCceeCcCCcccc
Q 025899 190 PTYC-VCNQVS---YGEMVACDNPNCKIEWFHFGCVGLKEQ---PKGKWYCPDCAALK 240 (246)
Q Consensus 190 ~~~C-~C~~~~---~g~mi~Cd~~~C~~~wfH~~Cv~l~~~---~~~~w~C~~C~~~~ 240 (246)
...| +|.... .|.|+.|.+ |. .-||..||.+-.. -.+-|-||.|+.-.
T Consensus 18 ~~mc~l~~s~G~~~ag~m~ac~~--c~-~~yH~~cvt~~~~~~~l~~gWrC~~crvCe 72 (694)
T KOG4443|consen 18 CLMCPLCGSSGKGRAGRLLACSD--CG-QKYHPYCVTSWAQHAVLSGGWRCPSCRVCE 72 (694)
T ss_pred hhhhhhhccccccccCcchhhhh--hc-ccCCcchhhHHHhHHHhcCCcccCCceeee
Confidence 3446 676442 367999999 77 8899999994432 13449999997543
No 41
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=67.71 E-value=81 Score=27.22 Aligned_cols=41 Identities=20% Similarity=0.400 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025899 75 EQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELR 116 (246)
Q Consensus 75 ~~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~eL~ 116 (246)
.++..++++-|- +-..++.+.++.|+.+=|.+|.+|+..|+
T Consensus 58 ef~~llkla~eq-~k~e~~m~~Lea~VEkrD~~IQqLqk~LK 98 (272)
T KOG4552|consen 58 EFKTLLKLAPEQ-QKREQLMRTLEAHVEKRDEVIQQLQKNLK 98 (272)
T ss_pred HHHHHHHHhHhH-HHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence 344455554443 22346666777888888888888776654
No 42
>PF05103 DivIVA: DivIVA protein; InterPro: IPR007793 The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate minicells []. Inactivation of divIVA produces a minicell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype []. These proteins appear to contain coiled-coils.; PDB: 2WUK_C 2WUJ_A.
Probab=64.02 E-value=4.2 Score=31.49 Aligned_cols=34 Identities=26% Similarity=0.392 Sum_probs=22.0
Q ss_pred HHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 4 LDEFQANLESLPNILQKKYALLRDLDKSLQEIQRQNE 40 (246)
Q Consensus 4 Le~fle~l~~LP~El~r~l~~IreLD~~~~~~~~~~~ 40 (246)
|++||+.|. .++.....++.+|..++.++..++.
T Consensus 23 VD~fl~~l~---~~~~~l~~e~~~L~~~~~~l~~~l~ 56 (131)
T PF05103_consen 23 VDDFLDELA---EELERLQRENAELKEEIEELQAQLE 56 (131)
T ss_dssp HHHHHHHHH---HHHHHHHHHHHHHHHHHHCCCCT--
T ss_pred HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 577777776 6777777777777776665544443
No 43
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=63.05 E-value=1.2 Score=28.03 Aligned_cols=37 Identities=35% Similarity=0.652 Sum_probs=21.5
Q ss_pred eeCCCC-CCCceecCCCCCCCcceecccCC--CCccCCCceeCcCCc
Q 025899 194 VCNQVS-YGEMVACDNPNCKIEWFHFGCVG--LKEQPKGKWYCPDCA 237 (246)
Q Consensus 194 ~C~~~~-~g~mi~Cd~~~C~~~wfH~~Cv~--l~~~~~~~w~C~~C~ 237 (246)
||...- .++.+.--. |. -.||..|+. +.. ...||.|+
T Consensus 5 IC~~~~~~~~~~~~l~--C~-H~fh~~Ci~~~~~~----~~~CP~CR 44 (44)
T PF13639_consen 5 ICLEEFEDGEKVVKLP--CG-HVFHRSCIKEWLKR----NNSCPVCR 44 (44)
T ss_dssp TTTCBHHTTSCEEEET--TS-EEEEHHHHHHHHHH----SSB-TTTH
T ss_pred CCChhhcCCCeEEEcc--CC-CeeCHHHHHHHHHh----CCcCCccC
Confidence 676553 244333333 66 899999986 322 24888885
No 44
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=62.40 E-value=6.4 Score=33.46 Aligned_cols=44 Identities=34% Similarity=0.818 Sum_probs=30.9
Q ss_pred Ccee-eeCCCC--C----CCceecCCCCCCCcceecccCCCCccCCCceeCcCCccccccC
Q 025899 190 PTYC-VCNQVS--Y----GEMVACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCAALKNRR 243 (246)
Q Consensus 190 ~~~C-~C~~~~--~----g~mi~Cd~~~C~~~wfH~~Cv~l~~~~~~~w~C~~C~~~~~~~ 243 (246)
...| +|+... | ...+.|.. |. .-||-.|..- -.||.|.+...|+
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~~--C~-~v~H~~C~~~-------~~CpkC~R~~~r~ 202 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCPK--CK-SVFHKSCFRK-------KSCPKCARRQKRK 202 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCCc--Cc-cccchhhcCC-------CCCCCcHhHhccC
Confidence 3578 887652 2 24678999 77 7899999972 2299998766543
No 45
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=61.53 E-value=5.5 Score=34.17 Aligned_cols=32 Identities=31% Similarity=0.758 Sum_probs=26.1
Q ss_pred eecCCCCCCCcceecccCCCCccCCCceeCcCCcccc
Q 025899 204 VACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCAALK 240 (246)
Q Consensus 204 i~Cd~~~C~~~wfH~~Cv~l~~~~~~~w~C~~C~~~~ 240 (246)
+-|.. |. .|..|+.+.+.|...|+||.|-...
T Consensus 193 lIC~~--C~---hhngl~~~~ek~~~efiC~~Cn~~n 224 (251)
T COG5415 193 LICPQ--CH---HHNGLYRLAEKPIIEFICPHCNHKN 224 (251)
T ss_pred hcccc--cc---ccccccccccccchheecccchhhc
Confidence 45666 55 6999999999998899999996554
No 46
>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=61.01 E-value=98 Score=25.87 Aligned_cols=108 Identities=19% Similarity=0.240 Sum_probs=56.1
Q ss_pred HHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh-----hCCCCCCchhhHHHHHHHHHHHHHH
Q 025899 6 EFQANLESLPNILQKKYALLRDLDKSLQEIQRQNEQRCEQEIEDLMREIR-----AGNITPNTSLIRFSDDALDEQKHSI 80 (246)
Q Consensus 6 ~fle~l~~LP~El~r~l~~IreLD~~~~~~~~~~~~~~~~~l~~~~k~~~-----~gs~~~~~~~~~l~~~I~~~~~~~~ 80 (246)
++-..++.|-.+..-+-.++.+++..+..+... .......+........ .+...+.+....+...|...+..+.
T Consensus 43 ~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~v~~~~~~~~~~~e~~~~~~~~~~~p~y~~Mi~~L~~qvk 121 (177)
T PF03234_consen 43 ERKQEIEELKYERKINEKLLKRIQKLLSALDKE-EEADKQEVMESLNEPFDKKEKPGVENKDPEQPTYDEMIEDLLDQVK 121 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc-ccchHHHHHHHHhcccccccccccccCCCCCCCHHHHHHHHHHHHh
Confidence 344455555566666666666666655543332 1111111111111000 0112222333344445666666676
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025899 81 RIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELR 116 (246)
Q Consensus 81 ~l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~eL~ 116 (246)
..-|++- ...+...|..|..+|+...+.....|.
T Consensus 122 ~~~de~~--~~~~~~~l~~H~~kl~~~~ke~~~kLe 155 (177)
T PF03234_consen 122 KEPDEKS--GKAELEELQEHRAKLEKEQKELKKKLE 155 (177)
T ss_pred cccCccc--HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5555554 778888899999998877766665543
No 47
>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=60.17 E-value=1.4e+02 Score=27.29 Aligned_cols=35 Identities=23% Similarity=0.275 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHH
Q 025899 74 DEQKHSIRIADEKVALAVQAYD-------LVDTHIQQLDQYL 108 (246)
Q Consensus 74 ~~~~~~~~l~dEKv~LA~q~~d-------lVd~hirrLD~dl 108 (246)
....+..++.+||+.|.+++-. -+-+.|.+|..+.
T Consensus 110 ~L~rkl~qLr~EK~~lE~~Le~EqE~~V~kL~k~i~~Le~e~ 151 (310)
T PF09755_consen 110 DLSRKLNQLRQEKVELENQLEQEQEYLVNKLQKKIERLEKEK 151 (310)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 4456788999999999988763 3335555555444
No 48
>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=59.78 E-value=2 Score=28.00 Aligned_cols=23 Identities=22% Similarity=0.481 Sum_probs=14.3
Q ss_pred cceecccCCCCccCCCceeCcCC
Q 025899 214 EWFHFGCVGLKEQPKGKWYCPDC 236 (246)
Q Consensus 214 ~wfH~~Cv~l~~~~~~~w~C~~C 236 (246)
.|||.+|+.-=-...+.-.||.|
T Consensus 26 ~~vH~~Cl~~W~~~~~~~~C~iC 48 (49)
T smart00744 26 KYVHQECLERWINESGNKTCEIC 48 (49)
T ss_pred hHHHHHHHHHHHHHcCCCcCCCC
Confidence 69999998621112233478877
No 49
>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=59.74 E-value=3.4 Score=32.88 Aligned_cols=27 Identities=33% Similarity=0.777 Sum_probs=15.1
Q ss_pred CCCcceeccc---CCCCccC--CCceeCcCCc
Q 025899 211 CKIEWFHFGC---VGLKEQP--KGKWYCPDCA 237 (246)
Q Consensus 211 C~~~wfH~~C---v~l~~~~--~~~w~C~~C~ 237 (246)
-.|+|||-.| ||-+-.. ...-.|..|.
T Consensus 100 ssYRWFHdgCCECVG~~CinYGinesrC~~Cp 131 (132)
T PF04668_consen 100 SSYRWFHDGCCECVGPTCINYGINESRCSNCP 131 (132)
T ss_pred ccceeeccchhhccCchhhhccCCcHhHhcCC
Confidence 3489999966 6633322 2334455553
No 50
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=59.50 E-value=3 Score=30.00 Aligned_cols=48 Identities=27% Similarity=0.719 Sum_probs=31.6
Q ss_pred ee-eeCCCCCCCceecC--CCCCCCcc------eecccCC-CCccCCCceeCcCCccc
Q 025899 192 YC-VCNQVSYGEMVACD--NPNCKIEW------FHFGCVG-LKEQPKGKWYCPDCAAL 239 (246)
Q Consensus 192 ~C-~C~~~~~g~mi~Cd--~~~C~~~w------fH~~Cv~-l~~~~~~~w~C~~C~~~ 239 (246)
.| +|+.+.+|-=-.|- ++|||+-| ||.-|+- --..|...-.||-|+..
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~ 79 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQT 79 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchhe
Confidence 67 99988777444443 33688655 8888865 22234456789999864
No 51
>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=57.69 E-value=91 Score=30.57 Aligned_cols=10 Identities=30% Similarity=0.448 Sum_probs=3.9
Q ss_pred HHHHHhhccc
Q 025899 6 EFQANLESLP 15 (246)
Q Consensus 6 ~fle~l~~LP 15 (246)
+|++.++.=|
T Consensus 291 ~~~~~l~~dp 300 (563)
T TIGR00634 291 NYLDELEFDP 300 (563)
T ss_pred HHHHhCCCCH
Confidence 3344443334
No 52
>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope. They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....
Probab=57.57 E-value=1.4e+02 Score=26.53 Aligned_cols=86 Identities=13% Similarity=0.159 Sum_probs=47.8
Q ss_pred ccHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCC--CC-CCchhhHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 14 LPNILQKKYALLR-DLDKSLQEIQRQNEQRCEQEIEDLMREIRAGN--IT-PNTSLIRFSDDALDEQKHSIRIADEKVAL 89 (246)
Q Consensus 14 LP~El~r~l~~Ir-eLD~~~~~~~~~~~~~~~~~l~~~~k~~~~gs--~~-~~~~~~~l~~~I~~~~~~~~~l~dEKv~L 89 (246)
-..+|...|..|| +.|..+.....+++..+...+..+........ +. .......+...|......+..+...+-.|
T Consensus 163 ~~~dL~~~L~eiR~~ye~~~~~~~~e~e~~y~~k~~~l~~~~~~~~~~~~~~~~E~~~~r~~~~~l~~el~~l~~~~~~L 242 (312)
T PF00038_consen 163 RSSDLSAALREIRAQYEEIAQKNREELEEWYQSKLEELRQQSEKSSEELESAKEELKELRRQIQSLQAELESLRAKNASL 242 (312)
T ss_dssp ----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccchhhhhhHHHHHHHHHhhhhhhhhhhcccccccccccccccccccchhHhHHHHHHhhhhHhhhhhhccccchhhh
Confidence 3567888888887 55777777777777666665555443211110 00 00112334445666666667777778788
Q ss_pred HHHHHHHHHH
Q 025899 90 AVQAYDLVDT 99 (246)
Q Consensus 90 A~q~~dlVd~ 99 (246)
-.++.++-..
T Consensus 243 e~~l~~le~~ 252 (312)
T PF00038_consen 243 ERQLRELEQR 252 (312)
T ss_dssp HHHHHHHHHH
T ss_pred hhhHHHHHHH
Confidence 8777776543
No 53
>KOG4360 consensus Uncharacterized coiled coil protein [Function unknown]
Probab=56.74 E-value=2e+02 Score=28.16 Aligned_cols=78 Identities=18% Similarity=0.177 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 22 YALLRDLDKSLQEIQRQNEQRCEQEIEDLMREIRAGNITPNTSLIRFSDDALDEQKHSIRIADEKVALAVQAYDLVDTHI 101 (246)
Q Consensus 22 l~~IreLD~~~~~~~~~~~~~~~~~l~~~~k~~~~gs~~~~~~~~~l~~~I~~~~~~~~~l~dEKv~LA~q~~dlVd~hi 101 (246)
+.++|++..++..+..+++.+++++.... ....++-.+|-+...+++.+.-||-.+...+...+|.|
T Consensus 204 ~KelrdtN~q~~s~~eel~~kt~el~~q~------------Ee~skLlsql~d~qkk~k~~~~Ekeel~~~Lq~~~da~- 270 (596)
T KOG4360|consen 204 VKELRDTNTQARSGQEELQSKTKELSRQQ------------EENSKLLSQLVDLQKKIKYLRHEKEELDEHLQAYKDAQ- 270 (596)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhhH-
Confidence 34555555555555555555555432211 11234445677777888888888888888888888876
Q ss_pred HHHHHHHHHHH
Q 025899 102 QQLDQYLKNFD 112 (246)
Q Consensus 102 rrLD~dl~kfe 112 (246)
+.|..+++.++
T Consensus 271 ~ql~aE~~Ele 281 (596)
T KOG4360|consen 271 RQLTAELEELE 281 (596)
T ss_pred HHHHHHHHHHH
Confidence 34544444443
No 54
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=55.23 E-value=2.7 Score=30.49 Aligned_cols=44 Identities=30% Similarity=0.694 Sum_probs=26.8
Q ss_pred ee-eeCCCCCCCceecCC-----CCCCCcc------eecccCC--CCccCCCceeCcCCccc
Q 025899 192 YC-VCNQVSYGEMVACDN-----PNCKIEW------FHFGCVG--LKEQPKGKWYCPDCAAL 239 (246)
Q Consensus 192 ~C-~C~~~~~g~mi~Cd~-----~~C~~~w------fH~~Cv~--l~~~~~~~w~C~~C~~~ 239 (246)
.| +|+-...|.-+.|-. .+|+..| ||+.|+. |.. +-.||-++..
T Consensus 22 ~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T----k~~CPld~q~ 79 (88)
T COG5194 22 VCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT----KGVCPLDRQT 79 (88)
T ss_pred hhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh----CCCCCCCCce
Confidence 35 777665555555543 2466544 9999986 444 4567777643
No 55
>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=55.13 E-value=16 Score=23.53 Aligned_cols=26 Identities=19% Similarity=0.516 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 88 ALAVQAYDLVDTHIQQLDQYLKNFDE 113 (246)
Q Consensus 88 ~LA~q~~dlVd~hirrLD~dl~kfe~ 113 (246)
.|-+..||.|+..|..+|..++.|++
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 56678899999999999999988885
No 56
>COG3416 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.12 E-value=98 Score=26.69 Aligned_cols=69 Identities=16% Similarity=0.183 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHhhhCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 42 RCEQEIEDLMREIRAGNITPNTSLIRFSDDALDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDE 113 (246)
Q Consensus 42 ~~~~~l~~~~k~~~~gs~~~~~~~~~l~~~I~~~~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~ 113 (246)
+.+.+++.+++ .+.-.+++..+.+..+..+.+=.+-=|--+-|-|-.+++.-.+.||++|++.++.++.
T Consensus 8 lle~lf~rlk~---a~~~~rD~~Ae~lI~~~~~~qP~a~Y~laQ~vliqE~ALk~a~~~i~eLe~ri~~lq~ 76 (233)
T COG3416 8 LLENLFHRLKK---AEANERDPQAEALIAEAVAKQPDAAYYLAQRVLIQEQALKKASTQIKELEKRIAILQA 76 (233)
T ss_pred HHHHHHHHHhh---cccCCCChHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34455555543 2333455555555444333332233333445666677777777888888888877776
No 57
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=54.45 E-value=8 Score=38.14 Aligned_cols=44 Identities=30% Similarity=0.806 Sum_probs=32.7
Q ss_pred Ccee-eeCCCCCCCceecCCCCCCCcceecccCCCCccC---CCceeCcCCcc
Q 025899 190 PTYC-VCNQVSYGEMVACDNPNCKIEWFHFGCVGLKEQP---KGKWYCPDCAA 238 (246)
Q Consensus 190 ~~~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cv~l~~~~---~~~w~C~~C~~ 238 (246)
.+.| +|.+. |...+|+. |+ .-||..|.+....| ...|.|..|..
T Consensus 47 ~ts~~~~~~~--gn~~~~~~--~~-~s~h~~~~~~~~sp~~~~~~~~~~~~~~ 94 (613)
T KOG4299|consen 47 ATSCGICKSG--GNLLCCDH--CP-ASFHLECDKPPLSPDLKGSEINCSRCPK 94 (613)
T ss_pred hhhcchhhhc--CCcccccc--Cc-cccchhccCcccCcccccccccccCCCc
Confidence 4556 77766 77889999 88 89999999955545 45667776654
No 58
>PRK14127 cell division protein GpsB; Provisional
Probab=54.14 E-value=55 Score=25.19 Aligned_cols=39 Identities=13% Similarity=0.204 Sum_probs=27.9
Q ss_pred HHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 4 LDEFQANLESLPNILQKKYALLRDLDKSLQEIQRQNEQRCEQ 45 (246)
Q Consensus 4 Le~fle~l~~LP~El~r~l~~IreLD~~~~~~~~~~~~~~~~ 45 (246)
+++||+.|. .++.....++.+|-.+...+..++.+...+
T Consensus 28 VD~FLd~V~---~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~ 66 (109)
T PRK14127 28 VDKFLDDVI---KDYEAFQKEIEELQQENARLKAQVDELTKQ 66 (109)
T ss_pred HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 678888777 677777888888877777766666554443
No 59
>PHA02414 hypothetical protein
Probab=53.76 E-value=94 Score=23.44 Aligned_cols=77 Identities=18% Similarity=0.282 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 28 LDKSLQEIQRQNEQRCEQEIEDLMREIRAGNITPNTSLIRFSDDALDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQY 107 (246)
Q Consensus 28 LD~~~~~~~~~~~~~~~~~l~~~~k~~~~gs~~~~~~~~~l~~~I~~~~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~d 107 (246)
.|..++++..+++...++ ++.|.++.......+...+ +++..+.---|.-+++-..-+.-|--+|.|||..
T Consensus 2 ~D~~in~Lv~~v~~ledK--------iQ~Gelt~kgdn~eL~~av-~ELRdivvslDKd~Av~sEKqshi~yQi~~Lee~ 72 (111)
T PHA02414 2 MDKEINNLVSQVETLEDK--------IQEGELTDKGDNKELEVAV-AELRDIVVSLDKDVAVNSEKQSHIYYQIERLEEK 72 (111)
T ss_pred cchHHHHHHHHHHHHHHH--------HhcCccccCCchHHHHHHH-HHHHHHHHHhhhHhhhhHHHhhHHHHHHHHHHHH
Confidence 466677777666654443 2567776544333332222 2222333333333343333355555677888888
Q ss_pred HHHHHH
Q 025899 108 LKNFDE 113 (246)
Q Consensus 108 l~kfe~ 113 (246)
+..|+.
T Consensus 73 i~aL~~ 78 (111)
T PHA02414 73 ISALAE 78 (111)
T ss_pred HHHHHh
Confidence 887774
No 60
>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=53.07 E-value=9.4 Score=23.29 Aligned_cols=24 Identities=33% Similarity=1.009 Sum_probs=16.4
Q ss_pred eecCCCCCCCcceecccCCCCccCCCceeCcCCc
Q 025899 204 VACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCA 237 (246)
Q Consensus 204 i~Cd~~~C~~~wfH~~Cv~l~~~~~~~w~C~~C~ 237 (246)
+.|.. |.-.||. ...|.|||..|-
T Consensus 9 ~~C~~--C~~~~~~--------~~dG~~yC~~cG 32 (36)
T PF11781_consen 9 EPCPV--CGSRWFY--------SDDGFYYCDRCG 32 (36)
T ss_pred CcCCC--CCCeEeE--------ccCCEEEhhhCc
Confidence 45777 6645664 446899998883
No 61
>KOG4460 consensus Nuclear pore complex, Nup88/rNup84 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=52.20 E-value=1.4e+02 Score=29.63 Aligned_cols=33 Identities=24% Similarity=0.427 Sum_probs=25.6
Q ss_pred cHHHHHHHhhcccHHHHHHHHHHHH-HHHHHHHH
Q 025899 3 FLDEFQANLESLPNILQKKYALLRD-LDKSLQEI 35 (246)
Q Consensus 3 yLe~fle~l~~LP~El~r~l~~Ire-LD~~~~~~ 35 (246)
|-|+||..-+-+-.||+|+...|.. .|.+.|++
T Consensus 571 frEqYi~~~dlV~~e~qrH~~~l~~~k~~QlQ~l 604 (741)
T KOG4460|consen 571 FREQYILKQDLVKEEIQRHVKLLCDQKKKQLQDL 604 (741)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4589999999999999999988865 45555553
No 62
>PF04949 Transcrip_act: Transcriptional activator; InterPro: IPR007033 Golgins are a family of coiled-coil proteins associated with the Golgi apparatus necessary for tethering events in membrane fusion and as structural supports for Golgi cisternae []. This entry represents proteins annotated as RAB6-interacting golgins.
Probab=51.39 E-value=1.3e+02 Score=24.45 Aligned_cols=28 Identities=18% Similarity=0.139 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 72 ALDEQKHSIRIADEKVALAVQAYDLVDT 99 (246)
Q Consensus 72 I~~~~~~~~~l~dEKv~LA~q~~dlVd~ 99 (246)
....+...-+..+||.+|+..+.+||..
T Consensus 114 ykealea~nEknkeK~~Lv~~L~eLv~e 141 (159)
T PF04949_consen 114 YKEALEAFNEKNKEKAQLVTRLMELVSE 141 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344555568899999999999999986
No 63
>COG1842 PspA Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]
Probab=51.12 E-value=1.6e+02 Score=25.45 Aligned_cols=39 Identities=8% Similarity=0.196 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 76 QKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEE 114 (246)
Q Consensus 76 ~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~e 114 (246)
|......-+.=+..+....+-|...+.+|+..|..|+..
T Consensus 97 le~~~~~~~~~~~~~~~~~~~l~~~~~~Le~Ki~e~~~~ 135 (225)
T COG1842 97 LEDLAKALEAELQQAEEQVEKLKKQLAALEQKIAELRAK 135 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444445556677777777888888888888888764
No 64
>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=50.81 E-value=12 Score=27.49 Aligned_cols=29 Identities=24% Similarity=0.605 Sum_probs=17.6
Q ss_pred Ccee-eeCCCCCCCceecCCCCCCCcceecccC
Q 025899 190 PTYC-VCNQVSYGEMVACDNPNCKIEWFHFGCV 221 (246)
Q Consensus 190 ~~~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cv 221 (246)
...| +|+++-....+.--. |. .-||+.|.
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p--~~-~v~H~~C~ 107 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFP--CG-HVVHYSCI 107 (109)
T ss_pred CCCccCcCCcCCCceEEEeC--CC-eEEecccc
Confidence 3458 999885433222222 22 67999997
No 65
>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=49.97 E-value=2.6e+02 Score=27.55 Aligned_cols=27 Identities=19% Similarity=0.347 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025899 90 AVQAYDLVDTHIQQLDQYLKNFDEELR 116 (246)
Q Consensus 90 A~q~~dlVd~hirrLD~dl~kfe~eL~ 116 (246)
...+.+++..|+..|..-.++..+||.
T Consensus 290 ~SkAvevM~qhvenLkr~~~kehaeL~ 316 (538)
T PF05781_consen 290 VSKAVEVMIQHVENLKRMYEKEHAELE 316 (538)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 347778888888888877777776654
No 66
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=49.65 E-value=4.2 Score=40.04 Aligned_cols=46 Identities=28% Similarity=0.703 Sum_probs=30.8
Q ss_pred Ccee-eeCCCC--C----CCceecCCCCCCCcceecccCCCCccCCCceeCcCCccccccC
Q 025899 190 PTYC-VCNQVS--Y----GEMVACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCAALKNRR 243 (246)
Q Consensus 190 ~~~C-~C~~~~--~----g~mi~Cd~~~C~~~wfH~~Cv~l~~~~~~~w~C~~C~~~~~~~ 243 (246)
...| +|+... | ..-.-|+. |. .|||-.|......- ||.|.+-.+|+
T Consensus 511 gfiCe~Cq~~~iiyPF~~~~~~rC~~--C~-avfH~~C~~r~s~~-----CPrC~R~q~r~ 563 (580)
T KOG1829|consen 511 GFICELCQHNDIIYPFETRNTRRCST--CL-AVFHKKCLRRKSPC-----CPRCERRQKRA 563 (580)
T ss_pred eeeeeeccCCCcccccccccceeHHH--HH-HHHHHHHHhccCCC-----CCchHHHHHHh
Confidence 3456 774432 2 22467888 77 99999998755543 99998765543
No 67
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=49.10 E-value=2.5e+02 Score=27.03 Aligned_cols=9 Identities=33% Similarity=0.534 Sum_probs=3.4
Q ss_pred HHHHHHHHH
Q 025899 100 HIQQLDQYL 108 (246)
Q Consensus 100 hirrLD~dl 108 (246)
.|.-|...|
T Consensus 436 ~I~dLqEQl 444 (493)
T KOG0804|consen 436 KITDLQEQL 444 (493)
T ss_pred HHHHHHHHH
Confidence 333343333
No 68
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=47.98 E-value=6.3 Score=35.41 Aligned_cols=33 Identities=24% Similarity=0.635 Sum_probs=26.0
Q ss_pred CceecCCCCCCCcceecccCCCCcc-----CCCceeCcCCc
Q 025899 202 EMVACDNPNCKIEWFHFGCVGLKEQ-----PKGKWYCPDCA 237 (246)
Q Consensus 202 ~mi~Cd~~~C~~~wfH~~Cv~l~~~-----~~~~w~C~~C~ 237 (246)
.||+|.. |. .-+|.+||.++.. ..-.|.|..|.
T Consensus 278 S~I~C~~--C~-~~~HP~Ci~M~~elv~~~KTY~W~C~~C~ 315 (381)
T KOG1512|consen 278 SWIVCKP--CA-TRPHPYCVAMIPELVGQYKTYFWKCSSCE 315 (381)
T ss_pred cceeecc--cc-cCCCCcchhcCHHHHhHHhhcchhhcccH
Confidence 5999999 77 6799999997763 23468888884
No 69
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=47.94 E-value=11 Score=34.45 Aligned_cols=38 Identities=29% Similarity=0.620 Sum_probs=29.2
Q ss_pred ceecCCCCCCCcceecccCCCCccCCCceeCcCCccccccCCC
Q 025899 203 MVACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCAALKNRRKG 245 (246)
Q Consensus 203 mi~Cd~~~C~~~wfH~~Cv~l~~~~~~~w~C~~C~~~~~~~~~ 245 (246)
-+=|.+ |. .|-.|+...+-+.-.|+|++|...+..+|.
T Consensus 220 ALIC~~--C~---~HNGla~~ee~~yi~F~C~~Cn~LN~~~k~ 257 (328)
T KOG2846|consen 220 ALICSQ--CH---HHNGLARKEEYEYITFRCPHCNALNPAKKS 257 (328)
T ss_pred hhcchh--hc---cccCcCChhhcCceEEECccccccCCCcCC
Confidence 355777 76 699999887777778999999877766553
No 70
>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=47.33 E-value=2.2e+02 Score=25.84 Aligned_cols=20 Identities=15% Similarity=0.232 Sum_probs=7.2
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 025899 16 NILQKKYALLRDLDKSLQEI 35 (246)
Q Consensus 16 ~El~r~l~~IreLD~~~~~~ 35 (246)
.++.....+|..|...-.++
T Consensus 43 ~~~~~~~~el~~le~Ee~~l 62 (314)
T PF04111_consen 43 EDIEELEEELEKLEQEEEEL 62 (314)
T ss_dssp H--HHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHH
Confidence 33444444444444433333
No 71
>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=47.29 E-value=9 Score=25.00 Aligned_cols=28 Identities=32% Similarity=0.921 Sum_probs=14.1
Q ss_pred ceecCCCCCCCcceecccCCCCc----cCCCceeCcC
Q 025899 203 MVACDNPNCKIEWFHFGCVGLKE----QPKGKWYCPD 235 (246)
Q Consensus 203 mi~Cd~~~C~~~wfH~~Cv~l~~----~~~~~w~C~~ 235 (246)
-|+||. |. .|=.+. .++.. .| +.|||..
T Consensus 3 WVQCd~--C~-KWR~lp-~~~~~~~~~~~-d~W~C~~ 34 (50)
T PF07496_consen 3 WVQCDS--CL-KWRRLP-EEVDPIREELP-DPWYCSM 34 (50)
T ss_dssp EEE-TT--T---EEEE--CCHHCTSCCSS-TT--GGG
T ss_pred EEECCC--CC-ceeeCC-hhhCcccccCC-CeEEcCC
Confidence 489998 77 997766 44322 33 3999986
No 72
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=47.02 E-value=8.3 Score=35.07 Aligned_cols=39 Identities=28% Similarity=0.779 Sum_probs=26.0
Q ss_pred cee-eeCCC--CCCCceecCCCCCCCcceecccCCCCccCCCceeCcCCccc
Q 025899 191 TYC-VCNQV--SYGEMVACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCAAL 239 (246)
Q Consensus 191 ~~C-~C~~~--~~g~mi~Cd~~~C~~~wfH~~Cv~l~~~~~~~w~C~~C~~~ 239 (246)
.+| -|..+ -||.||-|+. -|=+.|..+.. +-.|+.|...
T Consensus 91 HfCd~Cd~PI~IYGRmIPCkH------vFCl~CAr~~~----dK~Cp~C~d~ 132 (389)
T KOG2932|consen 91 HFCDRCDFPIAIYGRMIPCKH------VFCLECARSDS----DKICPLCDDR 132 (389)
T ss_pred EeecccCCcceeeecccccch------hhhhhhhhcCc----cccCcCcccH
Confidence 356 78777 4799999764 46667765554 4567777543
No 73
>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=46.91 E-value=2.3e+02 Score=30.65 Aligned_cols=46 Identities=13% Similarity=0.206 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 70 DDALDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEEL 115 (246)
Q Consensus 70 ~~I~~~~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~eL 115 (246)
.+|...+..+..++.+|++.-..-.+-|...|..|.+++.++..-+
T Consensus 885 ~~i~~lq~~i~~i~~e~~q~qk~kv~~~~~~~~~l~~~i~k~~~~i 930 (1293)
T KOG0996|consen 885 ARIKELQNKIDEIGGEKVQAQKDKVEKINEQLDKLEADIAKLTVAI 930 (1293)
T ss_pred HHHHHHHHHHHHhhchhhHHhHHHHHHHHHHHHHHHHHHHHhHHHH
Confidence 3455556666677777777766666666666666666666666543
No 74
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=46.73 E-value=6.9 Score=37.73 Aligned_cols=27 Identities=26% Similarity=0.477 Sum_probs=17.4
Q ss_pred eecccCCCCccCCCceeCcCCccccccCCC
Q 025899 216 FHFGCVGLKEQPKGKWYCPDCAALKNRRKG 245 (246)
Q Consensus 216 fH~~Cv~l~~~~~~~w~C~~C~~~~~~~~~ 245 (246)
-+|.|-.++-- .|||+.|......+.+
T Consensus 471 aPfFC~n~~C~---QYYCe~CWa~~HS~~~ 497 (520)
T KOG0129|consen 471 APFFCRNATCF---QYYCESCWAKIHSGPG 497 (520)
T ss_pred CCcccCCccHH---hhhchHHHHHhhcCCc
Confidence 34556555543 5999999877655543
No 75
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=46.65 E-value=5.1 Score=28.12 Aligned_cols=48 Identities=31% Similarity=0.667 Sum_probs=18.6
Q ss_pred cee-eeCCCC--CCC--ceecCCCCCCCcceecccCC--CC---ccC----CCceeCcCCccc
Q 025899 191 TYC-VCNQVS--YGE--MVACDNPNCKIEWFHFGCVG--LK---EQP----KGKWYCPDCAAL 239 (246)
Q Consensus 191 ~~C-~C~~~~--~g~--mi~Cd~~~C~~~wfH~~Cv~--l~---~~~----~~~w~C~~C~~~ 239 (246)
..| ||...- .++ -+.|++..|. .-||..|+- +. ... .-.+-||.|...
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~-~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~ 64 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCG-KKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSP 64 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT-----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SE
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccC-CHHHHHHHHHHHHHcccCCeeecccccCCcCCCCe
Confidence 345 776542 232 4889988888 779999986 11 111 234679999765
No 76
>PF11690 DUF3287: Protein of unknown function (DUF3287); InterPro: IPR021704 This eukaryotic family of proteins has no known function.
Probab=46.57 E-value=52 Score=25.30 Aligned_cols=42 Identities=19% Similarity=0.222 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Q 025899 71 DALDEQKHSIRIADEKVALAVQAYDL-VDTHIQQLDQYLKNFD 112 (246)
Q Consensus 71 ~I~~~~~~~~~l~dEKv~LA~q~~dl-Vd~hirrLD~dl~kfe 112 (246)
-|.+.-.+-+.+.+|+-.|...+.+| |++-++.|+++-..-+
T Consensus 43 F~~kV~~qH~~~~~e~r~L~kKi~~l~veRkmr~Les~p~~W~ 85 (109)
T PF11690_consen 43 FIDKVVDQHQRYCDERRKLRKKIQDLRVERKMRALESHPFDWE 85 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCChHHHH
Confidence 34455556788999999999999997 9999999988876655
No 77
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=45.43 E-value=2.8 Score=27.46 Aligned_cols=22 Identities=41% Similarity=0.996 Sum_probs=9.7
Q ss_pred ecccCCCCc-----cCCCceeCcCCcc
Q 025899 217 HFGCVGLKE-----QPKGKWYCPDCAA 238 (246)
Q Consensus 217 H~~Cv~l~~-----~~~~~w~C~~C~~ 238 (246)
|+.|..+.. ...+.|.||.|..
T Consensus 23 H~~CFDl~~fl~~~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 23 HLQCFDLESFLESNQRTPKWKCPICNK 49 (50)
T ss_dssp SS--EEHHHHHHHHHHS---B-TTT--
T ss_pred ccceECHHHHHHHhhccCCeECcCCcC
Confidence 888877644 2246699999974
No 78
>PRK09841 cryptic autophosphorylating protein tyrosine kinase Etk; Provisional
Probab=44.99 E-value=3.5e+02 Score=27.47 Aligned_cols=55 Identities=13% Similarity=0.231 Sum_probs=35.8
Q ss_pred cHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCC
Q 025899 3 FLDEFQANLESLPNILQKKYALLRDLDKSLQEIQRQNEQRCEQEIEDLMREIRAGNITPN 62 (246)
Q Consensus 3 yLe~fle~l~~LP~El~r~l~~IreLD~~~~~~~~~~~~~~~~~l~~~~k~~~~gs~~~~ 62 (246)
+.+.|++. ++-.-.......+.-|+.++.++..++++.... +..|++ ++|.+...
T Consensus 249 la~~Yi~~--~l~~k~~~a~~a~~fL~~qL~~l~~~L~~aE~~-l~~fr~--~~~~~d~~ 303 (726)
T PRK09841 249 IANNYLQQ--NIARQAAQDSQSLEFLQRQLPEVRSELDQAEEK-LNVYRQ--QRDSVDLN 303 (726)
T ss_pred HHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHH--HcCCCCCC
Confidence 34556643 333445556667888999999988888776655 556766 67766543
No 79
>KOG4796 consensus RNA polymerase II elongation factor [Transcription]
Probab=44.84 E-value=3.2e+02 Score=26.99 Aligned_cols=86 Identities=16% Similarity=0.316 Sum_probs=59.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHHHHHHHHHHHH---HHHHHHHHHHHH
Q 025899 16 NILQKKYALLRDLDKSLQEIQRQNEQRCEQEIEDLMREIRAGNITPNTSLIRFSDDALDEQKHSI---RIADEKVALAVQ 92 (246)
Q Consensus 16 ~El~r~l~~IreLD~~~~~~~~~~~~~~~~~l~~~~k~~~~gs~~~~~~~~~l~~~I~~~~~~~~---~l~dEKv~LA~q 92 (246)
.+|.--..+.|+|-.++..+.++..++..++.- .+..| .+..+.+.++|..+|++.. .+.+|| +
T Consensus 508 ~dF~~eY~EYreLharve~vs~rF~~Lea~L~s----rls~g----S~ey~~i~~qI~qEYeki~~dp~y~eeK-----~ 574 (604)
T KOG4796|consen 508 KDFEAEYDEYRELHARVETVSRRFRQLEAQLKS----RLSPG----SPEYKQIEKQILQEYEKIRKDPNYMEEK-----Q 574 (604)
T ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHh----ccCCC----CCcHHHHHHHHHHHHHHhhcCccHHHHH-----H
Confidence 456667788888888888877777665555321 11333 2446778889999998886 566666 6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 025899 93 AYDLVDTHIQQLDQYLKNFDEE 114 (246)
Q Consensus 93 ~~dlVd~hirrLD~dl~kfe~e 114 (246)
=++.+-..+..|..-|..|+..
T Consensus 575 RceYLhsKLaHIK~lI~efDk~ 596 (604)
T KOG4796|consen 575 RCEYLHSKLAHIKTLIGEFDKQ 596 (604)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh
Confidence 6777777777777778888763
No 80
>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=44.08 E-value=5.1 Score=23.12 Aligned_cols=26 Identities=27% Similarity=0.661 Sum_probs=10.1
Q ss_pred e-eeCCCCCC-CceecCCCCCCCcceecccC
Q 025899 193 C-VCNQVSYG-EMVACDNPNCKIEWFHFGCV 221 (246)
Q Consensus 193 C-~C~~~~~g-~mi~Cd~~~C~~~wfH~~Cv 221 (246)
| +|+.+.++ .+-.|.. |. -++|..|+
T Consensus 3 C~~C~~~~~~~~~Y~C~~--Cd-f~lH~~Ca 30 (30)
T PF07649_consen 3 CDACGKPIDGGWFYRCSE--CD-FDLHEECA 30 (30)
T ss_dssp -TTTS----S--EEE-TT--T------HHHH
T ss_pred CCcCCCcCCCCceEECcc--CC-CccChhcC
Confidence 5 78877666 5667888 55 67888774
No 81
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=43.22 E-value=7.8 Score=34.59 Aligned_cols=45 Identities=29% Similarity=0.753 Sum_probs=32.8
Q ss_pred Ccee-eeCCCC--C------CCceecCCCCCCCcceecccCCCCcc-----CCCceeCcCCc
Q 025899 190 PTYC-VCNQVS--Y------GEMVACDNPNCKIEWFHFGCVGLKEQ-----PKGKWYCPDCA 237 (246)
Q Consensus 190 ~~~C-~C~~~~--~------g~mi~Cd~~~C~~~wfH~~Cv~l~~~-----~~~~w~C~~C~ 237 (246)
..|| +|-+.+ + .++|.|.. |. .--|.+|+-.+.. ..-.|.|-.|.
T Consensus 224 n~YCDFclgdsr~nkkt~~peelvscsd--cg-rsghpsclqft~nm~~avk~yrwqcieck 282 (336)
T KOG1244|consen 224 NPYCDFCLGDSRENKKTGMPEELVSCSD--CG-RSGHPSCLQFTANMIAAVKTYRWQCIECK 282 (336)
T ss_pred CcccceeccccccccccCCchhhcchhh--cC-CCCCcchhhhhHHHHHHHHhheeeeeecc
Confidence 3589 996543 1 25799998 77 7789999987663 34579888885
No 82
>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=42.52 E-value=16 Score=20.91 Aligned_cols=14 Identities=36% Similarity=1.248 Sum_probs=9.7
Q ss_pred CCceeCcCCccccc
Q 025899 228 KGKWYCPDCAALKN 241 (246)
Q Consensus 228 ~~~w~C~~C~~~~~ 241 (246)
.|.|.|+.|...+.
T Consensus 2 ~g~W~C~~C~~~N~ 15 (30)
T PF00641_consen 2 EGDWKCPSCTFMNP 15 (30)
T ss_dssp SSSEEETTTTEEEE
T ss_pred CcCccCCCCcCCch
Confidence 46788888875543
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=42.26 E-value=16 Score=29.64 Aligned_cols=26 Identities=27% Similarity=0.811 Sum_probs=18.1
Q ss_pred cceecccCC----CCccCCCceeCcCCccc
Q 025899 214 EWFHFGCVG----LKEQPKGKWYCPDCAAL 239 (246)
Q Consensus 214 ~wfH~~Cv~----l~~~~~~~w~C~~C~~~ 239 (246)
.||..+|.. +...+.+.|+|+.|-..
T Consensus 31 ~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~ 60 (166)
T cd04476 31 NWWYPACPGCNKKVVEEGNGTYRCEKCNKS 60 (166)
T ss_pred CeEEccccccCcccEeCCCCcEECCCCCCc
Confidence 477777765 33334479999999764
No 84
>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=41.56 E-value=7.6 Score=27.38 Aligned_cols=22 Identities=45% Similarity=1.100 Sum_probs=15.0
Q ss_pred CCCcceecccCC--CCccCCCceeCcCCc
Q 025899 211 CKIEWFHFGCVG--LKEQPKGKWYCPDCA 237 (246)
Q Consensus 211 C~~~wfH~~Cv~--l~~~~~~~w~C~~C~ 237 (246)
|. -.||+.|+. |... ..||.|+
T Consensus 50 C~-H~FH~~Ci~~Wl~~~----~~CP~CR 73 (73)
T PF12678_consen 50 CG-HIFHFHCISQWLKQN----NTCPLCR 73 (73)
T ss_dssp TS-EEEEHHHHHHHHTTS----SB-TTSS
T ss_pred cC-CCEEHHHHHHHHhcC----CcCCCCC
Confidence 65 679999986 4333 3899885
No 85
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.52 E-value=29 Score=31.30 Aligned_cols=52 Identities=31% Similarity=0.721 Sum_probs=34.8
Q ss_pred CCCCCCCCCcee-eeCCC-CCCCceecCCCCCCCcceecccCC--CCcc-CCCceeCcC
Q 025899 182 DLPVDPNEPTYC-VCNQV-SYGEMVACDNPNCKIEWFHFGCVG--LKEQ-PKGKWYCPD 235 (246)
Q Consensus 182 ~~~~~~~~~~~C-~C~~~-~~g~mi~Cd~~~C~~~wfH~~Cv~--l~~~-~~~~w~C~~ 235 (246)
+...-++.++.| +|+.- .+-.+|+|-. -++.=|-|.|-. |... ..+..|||.
T Consensus 260 ~s~~A~~apLcCTLC~ERLEDTHFVQCPS--Vp~HKFCFPCSResIK~Qg~sgevYCPS 316 (352)
T KOG3579|consen 260 DSGAAPSAPLCCTLCHERLEDTHFVQCPS--VPSHKFCFPCSRESIKQQGASGEVYCPS 316 (352)
T ss_pred ccccCCCCceeehhhhhhhccCceeecCC--CcccceecccCHHHHHhhcCCCceeCCC
Confidence 344556678888 99855 4567899877 554456677765 3332 468999994
No 86
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.10 E-value=27 Score=32.36 Aligned_cols=46 Identities=24% Similarity=0.577 Sum_probs=29.8
Q ss_pred ceeeeCCCC-CCCceecCCCCCCCcceecccCC--CCccCCCceeCcCCcccccc
Q 025899 191 TYCVCNQVS-YGEMVACDNPNCKIEWFHFGCVG--LKEQPKGKWYCPDCAALKNR 242 (246)
Q Consensus 191 ~~C~C~~~~-~g~mi~Cd~~~C~~~wfH~~Cv~--l~~~~~~~w~C~~C~~~~~~ 242 (246)
++|||-... .|+-+.==. |. .-||..||. |+.. .-+||-|...-.+
T Consensus 231 ~CaIClEdY~~GdklRiLP--C~-H~FH~~CIDpWL~~~---r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 231 TCAICLEDYEKGDKLRILP--CS-HKFHVNCIDPWLTQT---RTFCPVCKRDIRT 279 (348)
T ss_pred eEEEeecccccCCeeeEec--CC-CchhhccchhhHhhc---CccCCCCCCcCCC
Confidence 455998653 376554444 55 459999996 3332 3589999876443
No 87
>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=40.56 E-value=25 Score=22.62 Aligned_cols=34 Identities=29% Similarity=0.675 Sum_probs=24.5
Q ss_pred CCcee-eeCCCCC---CCceecCCCCCCCcceecccCCCCc
Q 025899 189 EPTYC-VCNQVSY---GEMVACDNPNCKIEWFHFGCVGLKE 225 (246)
Q Consensus 189 ~~~~C-~C~~~~~---g~mi~Cd~~~C~~~wfH~~Cv~l~~ 225 (246)
.+.+| +|+..-+ ...+.|.. |. --+|-.|+....
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~--C~-~~~H~~C~~~~~ 47 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSW--CG-LVCHKKCLSKVP 47 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETT--TT--EEETTGGCTSS
T ss_pred CCCCCcccCcccCCCCCCeEEECC--CC-ChHhhhhhhhcC
Confidence 46788 9998763 45788999 77 779999987443
No 88
>COG3599 DivIVA Cell division initiation protein [Cell division and chromosome partitioning]
Probab=39.92 E-value=2.4e+02 Score=24.21 Aligned_cols=39 Identities=15% Similarity=0.298 Sum_probs=22.4
Q ss_pred cHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 3 FLDEFQANLESLPNILQKKYALLRDLDKSLQEIQRQNEQRCE 44 (246)
Q Consensus 3 yLe~fle~l~~LP~El~r~l~~IreLD~~~~~~~~~~~~~~~ 44 (246)
.|++|||.|. .++-..+.++++|-.+..++..++.....
T Consensus 27 EVdeFLD~V~---~dye~~l~e~~~l~~~i~~L~~~l~~~~~ 65 (212)
T COG3599 27 EVDEFLDDVI---DDYEQLLDENEDLEDEIDELKEELKEAAD 65 (212)
T ss_pred HHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 4566776665 55555556666666665555555544433
No 89
>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.
Probab=39.75 E-value=3.9e+02 Score=26.67 Aligned_cols=36 Identities=19% Similarity=0.375 Sum_probs=18.0
Q ss_pred HHHHHHHhh-cccHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 4 LDEFQANLE-SLPNILQKKYALLRDLDKSLQEIQRQN 39 (246)
Q Consensus 4 Le~fle~l~-~LP~El~r~l~~IreLD~~~~~~~~~~ 39 (246)
++++++.+. .....+...+..+.++...+.++.+++
T Consensus 378 ~~~~~~~~~~~~~~~~~~~~~~~~~~e~el~~l~~~l 414 (650)
T TIGR03185 378 LEVLIQQVKRELQDAKSQLLKELRELEEELAEVDKKI 414 (650)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444 344555555555555555555544444
No 90
>PRK11637 AmiB activator; Provisional
Probab=39.53 E-value=3.3e+02 Score=25.59 Aligned_cols=30 Identities=10% Similarity=0.338 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 85 EKVALAVQAYDLVDTHIQQLDQYLKNFDEE 114 (246)
Q Consensus 85 EKv~LA~q~~dlVd~hirrLD~dl~kfe~e 114 (246)
+++.-.++-...++..|..|+.+|..++.+
T Consensus 89 ~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~ 118 (428)
T PRK11637 89 RKLRETQNTLNQLNKQIDELNASIAKLEQQ 118 (428)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333334444444444444444444444433
No 91
>PHA02562 46 endonuclease subunit; Provisional
Probab=39.51 E-value=3.6e+02 Score=25.98 Aligned_cols=98 Identities=12% Similarity=0.194 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--
Q 025899 19 QKKYALLRDLDKSLQEIQRQNEQRCEQEIEDLMREIRAGNITPNTSLIRFSDDALDEQKHSIRIADEKVALAVQAYDL-- 96 (246)
Q Consensus 19 ~r~l~~IreLD~~~~~~~~~~~~~~~~~l~~~~k~~~~gs~~~~~~~~~l~~~I~~~~~~~~~l~dEKv~LA~q~~dl-- 96 (246)
...-..++++..+...+..++.....+ +..+...+..-........+.+.+++......+..+..+.-.+-..+.++
T Consensus 170 ~~~k~~~~e~~~~i~~l~~~i~~l~~~-i~~~~~~i~~~~~~~~~~i~~l~~e~~~l~~~~~~l~~~l~~l~~~i~~l~~ 248 (562)
T PHA02562 170 KLNKDKIRELNQQIQTLDMKIDHIQQQ-IKTYNKNIEEQRKKNGENIARKQNKYDELVEEAKTIKAEIEELTDELLNLVM 248 (562)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q ss_pred ----HHHHHHHHHHHHHHHHHHHhh
Q 025899 97 ----VDTHIQQLDQYLKNFDEELRR 117 (246)
Q Consensus 97 ----Vd~hirrLD~dl~kfe~eL~~ 117 (246)
++..+..|...+...+.++..
T Consensus 249 ~i~~~~~~L~~l~~~~~~~~~~l~~ 273 (562)
T PHA02562 249 DIEDPSAALNKLNTAAAKIKSKIEQ 273 (562)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHH
No 92
>KOG2626 consensus Histone H3 (Lys4) methyltransferase complex, subunit CPS60/ASH2/BRE2 [Chromatin structure and dynamics; Transcription]
Probab=39.48 E-value=38 Score=33.01 Aligned_cols=47 Identities=23% Similarity=0.639 Sum_probs=33.1
Q ss_pred CceeeeCCCCC--CCceecCCCCCCCcceecccCCCCc-----cC---CCceeCcCCccc
Q 025899 190 PTYCVCNQVSY--GEMVACDNPNCKIEWFHFGCVGLKE-----QP---KGKWYCPDCAAL 239 (246)
Q Consensus 190 ~~~C~C~~~~~--g~mi~Cd~~~C~~~wfH~~Cv~l~~-----~~---~~~w~C~~C~~~ 239 (246)
.++|+|..... -.-++|.. |. .|||..|+-... .| .-.+.|..|...
T Consensus 20 ~~~~y~e~~r~l~~~elqcs~--cl-k~~~~~~~~~~~~~~s~~pf~t~y~fvc~~c~~~ 76 (544)
T KOG2626|consen 20 ATVCYCEGERNLGIVELQCST--CL-KWFHLPTLEAFHLIKSSLPFMTSYEFVCKECTPS 76 (544)
T ss_pred ccccccccccccCceeeEeee--cc-cccccccccccccccccCCcccceeEEeccccCc
Confidence 67899987654 35689999 77 999986643222 22 347889999765
No 93
>PRK10626 hypothetical protein; Provisional
Probab=39.26 E-value=1.3e+02 Score=26.44 Aligned_cols=35 Identities=14% Similarity=-0.020 Sum_probs=29.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 65 LIRFSDDALDEQKHSIRIADEKVALAVQAYDLVDT 99 (246)
Q Consensus 65 ~~~l~~~I~~~~~~~~~l~dEKv~LA~q~~dlVd~ 99 (246)
..+++..|...+=++.+++.+.+.+|.+++|.|--
T Consensus 73 ~~~Yq~~lr~~lP~i~~~a~~~l~~A~~alD~Vi~ 107 (239)
T PRK10626 73 AKDYQAALRQDLPWIDEGAKSRLEKARVALDKVIV 107 (239)
T ss_pred HHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677788888889999999999999999998754
No 94
>PRK15365 type III secretion system chaperone SseA; Provisional
Probab=38.79 E-value=1.7e+02 Score=22.10 Aligned_cols=22 Identities=18% Similarity=0.372 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 025899 20 KKYALLRDLDKSLQEIQRQNEQ 41 (246)
Q Consensus 20 r~l~~IreLD~~~~~~~~~~~~ 41 (246)
-.|+++++|..++..+...+..
T Consensus 6 ~~~~~l~DL~~rYs~L~s~lkK 27 (107)
T PRK15365 6 AAFSEYRDLEQSYMQLNHCLKK 27 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3578999999998876665544
No 95
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=38.50 E-value=16 Score=20.04 Aligned_cols=12 Identities=50% Similarity=1.442 Sum_probs=8.1
Q ss_pred CceeCcCCcccc
Q 025899 229 GKWYCPDCAALK 240 (246)
Q Consensus 229 ~~w~C~~C~~~~ 240 (246)
++|.|+.|.-.+
T Consensus 1 g~W~C~~C~~~N 12 (26)
T smart00547 1 GDWECPACTFLN 12 (26)
T ss_pred CcccCCCCCCcC
Confidence 468888885443
No 96
>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=37.96 E-value=2.4e+02 Score=24.31 Aligned_cols=53 Identities=19% Similarity=0.344 Sum_probs=40.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHhh
Q 025899 65 LIRFSDDALDEQKHSIRIADEKVALAVQAYDLVD-------THIQQLDQYLKNFDEELRR 117 (246)
Q Consensus 65 ~~~l~~~I~~~~~~~~~l~dEKv~LA~q~~dlVd-------~hirrLD~dl~kfe~eL~~ 117 (246)
...++..|...+=.+..++.+.+.||..+++-|- ..-.+|.+-+..|...+..
T Consensus 51 l~~Y~~~lr~~lP~~~~~a~d~l~la~~ald~V~~~~~g~~~~~~~l~~l~~~l~~~~~~ 110 (229)
T PF11101_consen 51 LQQYQQGLRQQLPWVVQLASDGLELARDALDEVATSLLGDSNARDRLKQLMDQLKQQVDR 110 (229)
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHH
Confidence 4566778888888999999999999999999874 3445566666666665544
No 97
>PHA02862 5L protein; Provisional
Probab=36.38 E-value=12 Score=30.24 Aligned_cols=26 Identities=23% Similarity=0.313 Sum_probs=19.4
Q ss_pred cceecccCCCCccCCCceeCcCCccc
Q 025899 214 EWFHFGCVGLKEQPKGKWYCPDCAAL 239 (246)
Q Consensus 214 ~wfH~~Cv~l~~~~~~~w~C~~C~~~ 239 (246)
.|.|.+|+..=-.+.++-+|+.|..+
T Consensus 26 K~VHq~CL~~WIn~S~k~~CeLCkte 51 (156)
T PHA02862 26 KVVHIKCMQLWINYSKKKECNLCKTK 51 (156)
T ss_pred hhHHHHHHHHHHhcCCCcCccCCCCe
Confidence 89999998732245567899999654
No 98
>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=36.29 E-value=1.9e+02 Score=21.81 Aligned_cols=10 Identities=10% Similarity=0.411 Sum_probs=3.6
Q ss_pred HHHHHHHHHH
Q 025899 96 LVDTHIQQLD 105 (246)
Q Consensus 96 lVd~hirrLD 105 (246)
+|..++..++
T Consensus 110 ll~~~~~~~~ 119 (143)
T PF05130_consen 110 LLEQALEFVQ 119 (143)
T ss_dssp HHHHCCHHHH
T ss_pred HHHHHHHHHH
Confidence 3333333333
No 99
>KOG3047 consensus Predicted transcriptional regulator UXT [Transcription]
Probab=36.02 E-value=2.2e+02 Score=22.65 Aligned_cols=42 Identities=12% Similarity=0.199 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025899 75 EQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELR 116 (246)
Q Consensus 75 ~~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~eL~ 116 (246)
.+..|+...|.|..+-..+.+-+.+-.-+|.++|--+-+-+.
T Consensus 102 kLadAiKf~DRK~dlLkel~ekLqKdsmkiKa~ihMLLagl~ 143 (157)
T KOG3047|consen 102 KLADAIKFCDRKMDLLKELMEKLQKDSMKIKADIHMLLAGLD 143 (157)
T ss_pred hHHHHHHHHHHhHHHHHHHHHHHHHhHHHHHHHHHHHHHhhh
Confidence 456788999999999999999998888888888877776543
No 100
>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]
Probab=35.77 E-value=4.5e+02 Score=26.03 Aligned_cols=42 Identities=19% Similarity=0.383 Sum_probs=32.6
Q ss_pred HHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 4 LDEFQANLESLPNILQKKYALLRDLDKSLQEIQRQNEQRCEQ 45 (246)
Q Consensus 4 Le~fle~l~~LP~El~r~l~~IreLD~~~~~~~~~~~~~~~~ 45 (246)
+.+|+..+.+|-.|+......|+.++.....+.++.......
T Consensus 143 ~~~~~~~l~~leAe~~~~krr~~~le~e~~~Lk~en~rl~~~ 184 (546)
T KOG0977|consen 143 LDDYLSRLSELEAEINTLKRRIKALEDELKRLKAENSRLREE 184 (546)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHH
Confidence 456778888888888888888888888888877777665555
No 101
>PF10737 GerPC: Spore germination protein GerPC; InterPro: IPR019673 GerPC is required for the formation of functionally normal spores. The gerP locus encodes a number of proteins which are thought to be involved in the establishment of normal spore coat structure and/or permeability, which allows the access of germinants to their receptor [].
Probab=35.68 E-value=1.3e+02 Score=25.14 Aligned_cols=36 Identities=25% Similarity=0.307 Sum_probs=19.2
Q ss_pred cccHHHHHHHHHH-HHHHHHHH-----HHHHHHHHHHHHHHH
Q 025899 13 SLPNILQKKYALL-RDLDKSLQ-----EIQRQNEQRCEQEIE 48 (246)
Q Consensus 13 ~LP~El~r~l~~I-reLD~~~~-----~~~~~~~~~~~~~l~ 48 (246)
.+|..|.+.-... +.||..+. ++.+++.++...|+.
T Consensus 95 e~p~~l~~~e~~~~~~ld~~y~~~IieDIrKQl~~RI~~Ylq 136 (176)
T PF10737_consen 95 EAPQRLEQLEQQYNVPLDDSYRSFIIEDIRKQLPQRIQFYLQ 136 (176)
T ss_pred HHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHhHHHHHHHHh
Confidence 4555555554443 23455444 456666666666555
No 102
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=35.67 E-value=18 Score=29.71 Aligned_cols=48 Identities=19% Similarity=0.333 Sum_probs=29.3
Q ss_pred CCcee-eeCCCCCCCceecCCCCCC--CcceecccCCCCccCCCceeCcCCccc
Q 025899 189 EPTYC-VCNQVSYGEMVACDNPNCK--IEWFHFGCVGLKEQPKGKWYCPDCAAL 239 (246)
Q Consensus 189 ~~~~C-~C~~~~~g~mi~Cd~~~C~--~~wfH~~Cv~l~~~~~~~w~C~~C~~~ 239 (246)
....| +|..... ..+ .-|.|. ..|.|-+|+..=....+...|+.|..+
T Consensus 7 ~~~~CRIC~~~~~-~~~--~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~ 57 (162)
T PHA02825 7 MDKCCWICKDEYD-VVT--NYCNCKNENKIVHKECLEEWINTSKNKSCKICNGP 57 (162)
T ss_pred CCCeeEecCCCCC-Ccc--CCcccCCCchHHHHHHHHHHHhcCCCCcccccCCe
Confidence 35578 8976643 222 233344 369999998733334467788888543
No 103
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=35.57 E-value=12 Score=33.47 Aligned_cols=27 Identities=33% Similarity=0.902 Sum_probs=13.4
Q ss_pred CCcee-eeCCCCC----------C-CceecCCCCCCCccee
Q 025899 189 EPTYC-VCNQVSY----------G-EMVACDNPNCKIEWFH 217 (246)
Q Consensus 189 ~~~~C-~C~~~~~----------g-~mi~Cd~~~C~~~wfH 217 (246)
...|| ||+.... | .++.|.- |..+|-+
T Consensus 171 ~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~--C~t~W~~ 209 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRGGEREGKRYLHCSL--CGTEWRF 209 (290)
T ss_dssp T-SS-TTT---EEEEEEE------EEEEEETT--T--EEE-
T ss_pred cCCcCCCCCCcCceEEEecCCCCccEEEEcCC--CCCeeee
Confidence 35799 9998631 2 3788999 8888954
No 104
>PRK06798 fliD flagellar capping protein; Validated
Probab=35.18 E-value=2e+02 Score=27.39 Aligned_cols=48 Identities=17% Similarity=0.219 Sum_probs=28.3
Q ss_pred cHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 3 FLDEFQANLESLPNILQKKYALLRDLDKSLQEIQRQNEQRCEQEIEDL 50 (246)
Q Consensus 3 yLe~fle~l~~LP~El~r~l~~IreLD~~~~~~~~~~~~~~~~~l~~~ 50 (246)
||+.|+..-..|.......=..|+.++.+...+-++++.+.+.+...|
T Consensus 366 ~l~~~~~~~G~i~~r~~~l~~~i~~l~~~~~~~e~rl~~~e~~l~~qf 413 (440)
T PRK06798 366 SLDKIFGDEGIIGERSKSIDNRVSKLDLKITDIDTQNKQKQDNIVDKY 413 (440)
T ss_pred HHHhhhCCCceeehhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555444456666666666666666666666666655555554444
No 105
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=34.96 E-value=3.3e+02 Score=24.25 Aligned_cols=42 Identities=12% Similarity=-0.063 Sum_probs=37.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 65 LIRFSDDALDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQY 107 (246)
Q Consensus 65 ~~~l~~~I~~~~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~d 107 (246)
.+.. ..|.+.+++.+..++.|...+.++.+.++.-|+|++.-
T Consensus 61 ~e~e-d~l~k~i~Ell~~a~~~~~~~~~l~d~~~~l~~Rh~~~ 102 (271)
T COG5034 61 EEVE-DGLLKEIRELLLKAIYIQKEKSDLADRAEKLLRRHRKL 102 (271)
T ss_pred ccch-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3444 57999999999999999999999999999999999883
No 106
>KOG1671 consensus Ubiquinol cytochrome c reductase, subunit RIP1 [Energy production and conversion]
Probab=34.33 E-value=20 Score=30.51 Aligned_cols=21 Identities=38% Similarity=1.004 Sum_probs=15.7
Q ss_pred ecccCCCCccC-CCceeCc-CCc
Q 025899 217 HFGCVGLKEQP-KGKWYCP-DCA 237 (246)
Q Consensus 217 H~~Cv~l~~~~-~~~w~C~-~C~ 237 (246)
|+.||-+.... -|.|||| +|.
T Consensus 155 hLGCVp~~~AGd~gg~~CPCHGS 177 (210)
T KOG1671|consen 155 HLGCVPIANAGDYGGYYCPCHGS 177 (210)
T ss_pred cccccccccccccCceecccccc
Confidence 89999876654 5789999 443
No 107
>PRK08032 fliD flagellar capping protein; Reviewed
Probab=34.08 E-value=2.6e+02 Score=26.73 Aligned_cols=48 Identities=8% Similarity=0.095 Sum_probs=25.2
Q ss_pred cHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 3 FLDEFQANLESLPNILQKKYALLRDLDKSLQEIQRQNEQRCEQEIEDL 50 (246)
Q Consensus 3 yLe~fle~l~~LP~El~r~l~~IreLD~~~~~~~~~~~~~~~~~l~~~ 50 (246)
||+.|+..-.-|.......=..|+.|+.+...+-++++...+++...|
T Consensus 393 ~l~~~~~~~G~l~~~~~~l~~~i~~l~~~i~~~~~rl~~~e~rl~~qF 440 (462)
T PRK08032 393 NLKSWLSTTGIIKTATDGVNKTLKKLTKQYNAVSDSIDATIARYKAQF 440 (462)
T ss_pred HHHHHHcCCccchhHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555444444444444555666666666665555555555544433
No 108
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.99 E-value=20 Score=31.81 Aligned_cols=47 Identities=23% Similarity=0.681 Sum_probs=30.3
Q ss_pred Ccee-eeCCCCC--CC--c---eecCCCCCCCcceecccCC--CCc----cCCCceeCcCCccc
Q 025899 190 PTYC-VCNQVSY--GE--M---VACDNPNCKIEWFHFGCVG--LKE----QPKGKWYCPDCAAL 239 (246)
Q Consensus 190 ~~~C-~C~~~~~--g~--m---i~Cd~~~C~~~wfH~~Cv~--l~~----~~~~~w~C~~C~~~ 239 (246)
+.+| +|=..+. +. . -.|-+.+ .|.|-+|+- +.+ .+...-.||.|..+
T Consensus 20 eR~CWiCF~TdeDn~~a~WV~PCrCRGt~---KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTE 80 (293)
T KOG3053|consen 20 ERCCWICFATDEDNRLAAWVHPCRCRGTT---KWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTE 80 (293)
T ss_pred ceeEEEEeccCcccchhhhcccccccCcc---HHHHHHHHHHHHhHHhcCCCCceeechhhcch
Confidence 5688 8965532 21 2 2355544 999999987 333 24567899999654
No 109
>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=33.92 E-value=2.1e+02 Score=21.62 Aligned_cols=45 Identities=11% Similarity=0.320 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025899 73 LDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELRR 117 (246)
Q Consensus 73 ~~~~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~eL~~ 117 (246)
...+..+.++-++|+...+...+-+++.+..+...+..+...+..
T Consensus 82 e~~~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~~l~~ 126 (129)
T cd00890 82 EKSLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQEELQQ 126 (129)
T ss_pred EecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355667888999999999999999999999999999988877654
No 110
>KOG2129 consensus Uncharacterized conserved protein H4 [Function unknown]
Probab=33.77 E-value=4.4e+02 Score=25.32 Aligned_cols=18 Identities=33% Similarity=0.344 Sum_probs=11.5
Q ss_pred ccHHHHHHHHHHHHHHHH
Q 025899 14 LPNILQKKYALLRDLDKS 31 (246)
Q Consensus 14 LP~El~r~l~~IreLD~~ 31 (246)
|-++|-|.|..+|.-...
T Consensus 130 lTn~Lsrkl~qLr~ek~~ 147 (552)
T KOG2129|consen 130 LTNPLSRKLKQLRHEKLP 147 (552)
T ss_pred ccCchhHHHHHHHhhhcc
Confidence 456777777777743333
No 111
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=33.42 E-value=2.6e+02 Score=22.60 Aligned_cols=14 Identities=14% Similarity=0.370 Sum_probs=6.6
Q ss_pred HHHHHHHHHHHHHH
Q 025899 100 HIQQLDQYLKNFDE 113 (246)
Q Consensus 100 hirrLD~dl~kfe~ 113 (246)
.+.+++....++..
T Consensus 146 e~~~~~~~~~~~~k 159 (169)
T PF07106_consen 146 EKEKLEKEYKKWRK 159 (169)
T ss_pred HHHHHHHHHHHHHH
Confidence 44444444444443
No 112
>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=33.35 E-value=2.5e+02 Score=22.40 Aligned_cols=31 Identities=16% Similarity=0.205 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 82 IADEKVALAVQAYDLVDTHIQQLDQYLKNFD 112 (246)
Q Consensus 82 l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe 112 (246)
-..+|+.-|....+-+++.+..|+.....++
T Consensus 98 e~~ekl~e~d~~ae~~eRkv~~le~~~~~~E 128 (143)
T PF12718_consen 98 ETTEKLREADVKAEHFERKVKALEQERDQWE 128 (143)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHhhHHHHH
Confidence 3334444444444444444444444443333
No 113
>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=33.19 E-value=2e+02 Score=21.32 Aligned_cols=46 Identities=13% Similarity=0.232 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025899 72 ALDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELRR 117 (246)
Q Consensus 72 I~~~~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~eL~~ 117 (246)
|......+...-++++........-++..+..|...+..+...|..
T Consensus 57 v~~~~~ea~~~Le~~~e~le~~i~~l~~~~~~l~~~~~elk~~l~~ 102 (105)
T cd00632 57 VKQEKEEARTELKERLETIELRIKRLERQEEDLQEKLKELQEKIQQ 102 (105)
T ss_pred hhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566777777777777778888888888888888888877653
No 114
>PRK14143 heat shock protein GrpE; Provisional
Probab=33.19 E-value=3.3e+02 Score=23.80 Aligned_cols=17 Identities=12% Similarity=-0.099 Sum_probs=6.9
Q ss_pred HHHHHHHHHHHHHHHHH
Q 025899 70 DDALDEQKHSIRIADEK 86 (246)
Q Consensus 70 ~~I~~~~~~~~~l~dEK 86 (246)
++..++...+..++-++
T Consensus 102 KR~~kE~e~~~~~a~~~ 118 (238)
T PRK14143 102 KRTSREQEDLRLQLKCN 118 (238)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33334444444444333
No 115
>PF05010 TACC: Transforming acidic coiled-coil-containing protein (TACC); InterPro: IPR007707 This family contains the proteins TACC 1, 2 and 3, found concentrated in the centrosomes of eukaryotes which may play a conserved role in organising centrosomal microtubules. The human TACC proteins have been linked to cancer and TACC2 has been identified as a possible tumour suppressor (AZU-1) [].
Probab=32.95 E-value=3.1e+02 Score=23.43 Aligned_cols=42 Identities=17% Similarity=0.121 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025899 72 ALDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELR 116 (246)
Q Consensus 72 I~~~~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~eL~ 116 (246)
....|.....-+.+|+..|+.-++-|-+ ...+++..|.+.|+
T Consensus 130 ~eqry~aLK~hAeekL~~ANeei~~v~~---~~~~e~~aLqa~lk 171 (207)
T PF05010_consen 130 EEQRYQALKAHAEEKLEKANEEIAQVRS---KHQAELLALQASLK 171 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HhHHHHHHHHHHHH
Confidence 3445667778889999999988876665 55555555555443
No 116
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=32.76 E-value=17 Score=26.67 Aligned_cols=28 Identities=36% Similarity=0.685 Sum_probs=19.2
Q ss_pred CCCcceecccCC--CCccCCCceeCcCCcccc
Q 025899 211 CKIEWFHFGCVG--LKEQPKGKWYCPDCAALK 240 (246)
Q Consensus 211 C~~~wfH~~Cv~--l~~~~~~~w~C~~C~~~~ 240 (246)
|. .-||..|+- |... ..+=.||-|+..=
T Consensus 52 C~-H~FH~hCI~kWl~~~-~~~~~CPmCR~~w 81 (85)
T PF12861_consen 52 CS-HNFHMHCILKWLSTQ-SSKGQCPMCRQPW 81 (85)
T ss_pred Cc-cHHHHHHHHHHHccc-cCCCCCCCcCCee
Confidence 44 569999976 5443 2345999998753
No 117
>KOG0612 consensus Rho-associated, coiled-coil containing protein kinase [Signal transduction mechanisms]
Probab=32.43 E-value=6.2e+02 Score=27.69 Aligned_cols=26 Identities=23% Similarity=0.265 Sum_probs=18.9
Q ss_pred hhcccHHHHHHHHHHHHHHHHHHHHH
Q 025899 11 LESLPNILQKKYALLRDLDKSLQEIQ 36 (246)
Q Consensus 11 l~~LP~El~r~l~~IreLD~~~~~~~ 36 (246)
+.-|+..+...+.+++.+|.+++.+.
T Consensus 436 ~~~le~~l~~~~~~~~~~~~~~~~~~ 461 (1317)
T KOG0612|consen 436 LQILEQSLVNEMQEKEKLDEKCQAVA 461 (1317)
T ss_pred hhhcccchhhHHHHhhhHHHHHHHHh
Confidence 44566667788888888888887643
No 118
>COG0497 RecN ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=32.29 E-value=4.3e+02 Score=26.20 Aligned_cols=10 Identities=20% Similarity=0.414 Sum_probs=6.7
Q ss_pred CCceeeeCCC
Q 025899 189 EPTYCVCNQV 198 (246)
Q Consensus 189 ~~~~C~C~~~ 198 (246)
..+.||=+.|
T Consensus 485 ~QVl~VTHlP 494 (557)
T COG0497 485 HQVLCVTHLP 494 (557)
T ss_pred ceEEEEecHH
Confidence 4667777766
No 119
>TIGR00606 rad50 rad50. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.38 E-value=7e+02 Score=27.33 Aligned_cols=29 Identities=24% Similarity=0.291 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025899 88 ALAVQAYDLVDTHIQQLDQYLKNFDEELR 116 (246)
Q Consensus 88 ~LA~q~~dlVd~hirrLD~dl~kfe~eL~ 116 (246)
.........+...+++|+.++..+..+|.
T Consensus 1064 ~~l~~~~a~l~g~~k~le~qi~~l~~eL~ 1092 (1311)
T TIGR00606 1064 DLIKRNHVLALGRQKGYEKEIKHFKKELR 1092 (1311)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 33333444455677888888888888874
No 120
>PF08432 Vfa1: AAA-ATPase Vps4-associated protein 1; InterPro: IPR013640 This is a family of fungal proteins of unknown function.
Probab=31.32 E-value=29 Score=28.95 Aligned_cols=31 Identities=29% Similarity=0.635 Sum_probs=21.4
Q ss_pred Ccee-eeCCCCCCCceecCCCCCCCcceecccCC-CCc
Q 025899 190 PTYC-VCNQVSYGEMVACDNPNCKIEWFHFGCVG-LKE 225 (246)
Q Consensus 190 ~~~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cv~-l~~ 225 (246)
.--| ||..|+..-+|.=++. .||| .|-+ |..
T Consensus 13 ~k~C~IC~KpsttVL~t~~~~----DfFY-~C~~HL~D 45 (182)
T PF08432_consen 13 AKACFICYKPSTTVLITPDNK----DFFY-VCPSHLKD 45 (182)
T ss_pred CCceeEecCCCceEEecCCCC----CeEE-eCcccccC
Confidence 4568 9999987777754443 6886 7865 543
No 121
>PF04849 HAP1_N: HAP1 N-terminal conserved region; InterPro: IPR006933 This family is defined by an N-terminal conserved region found in several huntingtin-associated protein 1 (HAP1) homologues. HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner. However, its possible role in the pathogenesis of Huntingtons disease is unclear. This family also includes a similar N-terminal conserved region from hypothetical protein products of ALS2CR3 genes found in the human juvenile amyotrophic lateral sclerosis critical region 2q33-2q34 [].
Probab=31.07 E-value=4.1e+02 Score=24.22 Aligned_cols=48 Identities=17% Similarity=0.239 Sum_probs=35.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 65 LIRFSDDALDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDE 113 (246)
Q Consensus 65 ~~~l~~~I~~~~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~ 113 (246)
+..+..+|.+...+++.++-|+-.|.+++...-+.|-. |-.++..|..
T Consensus 236 It~LlsqivdlQ~r~k~~~~EnEeL~q~L~~ske~Q~~-L~aEL~elqd 283 (306)
T PF04849_consen 236 ITSLLSQIVDLQQRCKQLAAENEELQQHLQASKESQRQ-LQAELQELQD 283 (306)
T ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH-HHHHHHHHHH
Confidence 34555677777788888999998888888888777654 7777766664
No 122
>TIGR00414 serS seryl-tRNA synthetase. This model represents the seryl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. The seryl-tRNA synthetases of two archaeal species, Methanococcus jannaschii and Methanobacterium thermoautotrophicum, differ considerably and are included in a different model.
Probab=30.88 E-value=4.6e+02 Score=24.74 Aligned_cols=24 Identities=17% Similarity=0.144 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 21 KYALLRDLDKSLQEIQRQNEQRCE 44 (246)
Q Consensus 21 ~l~~IreLD~~~~~~~~~~~~~~~ 44 (246)
.+..|-.+|.+..++..+++....
T Consensus 28 ~vd~i~~ld~~~r~~~~~~~~l~~ 51 (418)
T TIGR00414 28 DLEKLIALDDERKKLLSEIEELQA 51 (418)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356677777777766666655443
No 123
>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=30.75 E-value=6e+02 Score=26.01 Aligned_cols=21 Identities=19% Similarity=0.363 Sum_probs=9.9
Q ss_pred HHHHHHhhcccHHHHHHHHHH
Q 025899 5 DEFQANLESLPNILQKKYALL 25 (246)
Q Consensus 5 e~fle~l~~LP~El~r~l~~I 25 (246)
|+|++..+-.=.+|++++..+
T Consensus 550 eeYi~~~~~ar~ei~~rv~~L 570 (717)
T PF10168_consen 550 EEYIEKQDLAREEIQRRVKLL 570 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 445554444444555544433
No 124
>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=30.44 E-value=12 Score=23.73 Aligned_cols=30 Identities=27% Similarity=0.871 Sum_probs=14.0
Q ss_pred eecCCCCCCCcceecccCC--CCccCCCceeCcCC
Q 025899 204 VACDNPNCKIEWFHFGCVG--LKEQPKGKWYCPDC 236 (246)
Q Consensus 204 i~Cd~~~C~~~wfH~~Cv~--l~~~~~~~w~C~~C 236 (246)
+.|.+.+|... +|..|+. +..... -.||.|
T Consensus 12 ~~C~~~~C~~r-~H~~C~~~y~r~~~~--~~CP~C 43 (43)
T PF08746_consen 12 QRCSNRDCNVR-LHDDCFKKYFRHRSN--PKCPNC 43 (43)
T ss_dssp EE-SS--S--E-E-HHHHHHHTTT-SS---B-TTT
T ss_pred ccCCCCccCch-HHHHHHHHHHhcCCC--CCCcCC
Confidence 57888779944 6999987 333221 278877
No 125
>PF07011 DUF1313: Protein of unknown function (DUF1313); InterPro: IPR009741 This family consists of several hypothetical plant proteins of around 100 residues in length. The function of this family is unknown.
Probab=30.18 E-value=1.6e+02 Score=21.66 Aligned_cols=25 Identities=20% Similarity=0.555 Sum_probs=20.4
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHH
Q 025899 13 SLPNILQKKYALLRDLDKSLQEIQR 37 (246)
Q Consensus 13 ~LP~El~r~l~~IreLD~~~~~~~~ 37 (246)
-.|.-|.|++.+||||..-+...+.
T Consensus 39 r~PdnL~RNV~LIrELN~NI~rVv~ 63 (87)
T PF07011_consen 39 RIPDNLSRNVGLIRELNGNISRVVD 63 (87)
T ss_pred cCCchhhHhHHHHHHHHhhHHHHHH
Confidence 4799999999999999987666443
No 126
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.17 E-value=20 Score=32.02 Aligned_cols=56 Identities=25% Similarity=0.334 Sum_probs=31.4
Q ss_pred CCCCCCCCCcee-eeCCCCCC-C----ce---ecCCCCCCCcceecccCCCCccCCCceeCcCCcccc
Q 025899 182 DLPVDPNEPTYC-VCNQVSYG-E----MV---ACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCAALK 240 (246)
Q Consensus 182 ~~~~~~~~~~~C-~C~~~~~g-~----mi---~Cd~~~C~~~wfH~~Cv~l~~~~~~~w~C~~C~~~~ 240 (246)
..|..-++...| +|++.-.. . .| -=-. |. .-||-.|+.-=-.-.++=+||.|..+-
T Consensus 216 glPtkhl~d~vCaVCg~~~~~s~~eegvienty~Ls--Cn-HvFHEfCIrGWcivGKkqtCPYCKekV 280 (328)
T KOG1734|consen 216 GLPTKHLSDSVCAVCGQQIDVSVDEEGVIENTYKLS--CN-HVFHEFCIRGWCIVGKKQTCPYCKEKV 280 (328)
T ss_pred CCCCCCCCcchhHhhcchheeecchhhhhhhheeee--cc-cchHHHhhhhheeecCCCCCchHHHHh
Confidence 344455666778 99876321 1 11 1112 44 569999976222223456899997653
No 127
>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=29.93 E-value=12 Score=26.63 Aligned_cols=9 Identities=33% Similarity=1.353 Sum_probs=8.1
Q ss_pred cceecccCC
Q 025899 214 EWFHFGCVG 222 (246)
Q Consensus 214 ~wfH~~Cv~ 222 (246)
.|||+.|+.
T Consensus 39 ~W~H~~C~~ 47 (82)
T PF00645_consen 39 KWYHWDCFF 47 (82)
T ss_dssp EEEEHHHHH
T ss_pred ceECccccc
Confidence 899999976
No 128
>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope. They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....
Probab=29.92 E-value=3.9e+02 Score=23.59 Aligned_cols=30 Identities=20% Similarity=0.316 Sum_probs=16.1
Q ss_pred HHhhcccHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 9 ANLESLPNILQKKYALLRDLDKSLQEIQRQ 38 (246)
Q Consensus 9 e~l~~LP~El~r~l~~IreLD~~~~~~~~~ 38 (246)
..+..+..|+.+.-..|..|...+..+...
T Consensus 209 ~~~~~~~~E~~~~r~~~~~l~~el~~l~~~ 238 (312)
T PF00038_consen 209 EELESAKEELKELRRQIQSLQAELESLRAK 238 (312)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cccchhHhHHHHHHhhhhHhhhhhhccccc
Confidence 344455556655555565555555554433
No 129
>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....
Probab=29.88 E-value=2.3e+02 Score=20.93 Aligned_cols=24 Identities=21% Similarity=0.270 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 21 KYALLRDLDKSLQEIQRQNEQRCE 44 (246)
Q Consensus 21 ~l~~IreLD~~~~~~~~~~~~~~~ 44 (246)
.+..|.+||.+...+..+++....
T Consensus 27 ~vd~i~~ld~~~r~l~~~~e~lr~ 50 (108)
T PF02403_consen 27 DVDEIIELDQERRELQQELEELRA 50 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456667777777766666654433
No 130
>PHA03158 hypothetical protein; Provisional
Probab=29.14 E-value=1.3e+02 Score=25.69 Aligned_cols=36 Identities=22% Similarity=0.390 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHH
Q 025899 78 HSIRIADEKVALAVQAYDLVDT------HIQQLDQYLKNFDE 113 (246)
Q Consensus 78 ~~~~l~dEKv~LA~q~~dlVd~------hirrLD~dl~kfe~ 113 (246)
.|+.-+.||..|.+|++..-.+ |++.|+.+|+.++.
T Consensus 227 WCv~t~~EK~~~~kQllka~kkc~~~s~~~~~leeei~elek 268 (273)
T PHA03158 227 WCIKTAKEKAAILKQLLKAAKKCCKNSEHEKELEEEIEELEK 268 (273)
T ss_pred cEeecHHHhHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHH
Confidence 3467789999999998877654 77778777777765
No 131
>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=28.57 E-value=76 Score=23.48 Aligned_cols=23 Identities=35% Similarity=0.528 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 025899 92 QAYDLVDTHIQQLDQYLKNFDEE 114 (246)
Q Consensus 92 q~~dlVd~hirrLD~dl~kfe~e 114 (246)
.+.++++.|+..|+..++.++.+
T Consensus 76 ~~~~ll~~~~~~l~~~i~~L~~~ 98 (99)
T cd04772 76 SALALVDAAHALLQRYRQQLDQE 98 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 67899999999999999998865
No 132
>PHA02682 ORF080 virion core protein; Provisional
Probab=28.28 E-value=2.3e+02 Score=24.31 Aligned_cols=52 Identities=21% Similarity=0.306 Sum_probs=36.4
Q ss_pred HhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHhhhCCCCC
Q 025899 10 NLESLPNILQKKYALLRDLDKSLQEIQRQNEQRCEQ---EIEDLMREIRAGNITP 61 (246)
Q Consensus 10 ~l~~LP~El~r~l~~IreLD~~~~~~~~~~~~~~~~---~l~~~~k~~~~gs~~~ 61 (246)
+-+++--||..+-..+|+|......+.++|++.... .++++++.+.+|.+..
T Consensus 209 ~k~~ikkeladiadsvrdl~aeS~~LtrDIE~AKstTq~AIdDLRrLl~~~~v~~ 263 (280)
T PHA02682 209 DKDLIKKELADIADSVRDLNAESLSLTRDIENAKSTTQAAIDDLRRLLTGGGVAR 263 (280)
T ss_pred hHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHhhHHHHHHHHHHHHhcCCccc
Confidence 345667888888899999999999999988865443 3555555545554443
No 133
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=27.81 E-value=2.8e+02 Score=21.26 Aligned_cols=58 Identities=19% Similarity=0.443 Sum_probs=30.6
Q ss_pred hhCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHH
Q 025899 55 RAGNITPNTSLIRFSDDALDEQKHSIRIADEKVALAVQAYDLVDT--------------HIQQLDQYLKNFDEEL 115 (246)
Q Consensus 55 ~~gs~~~~~~~~~l~~~I~~~~~~~~~l~dEKv~LA~q~~dlVd~--------------hirrLD~dl~kfe~eL 115 (246)
..|.++++.. .+|..++.+..+......++| +-.++-++++. .|.+|+..+..++.++
T Consensus 35 kkGeln~eEa-k~~vddl~~q~k~~~~e~e~K--~~r~i~~ml~~~~~~r~~~~~~l~~rvd~Lerqv~~Lenk~ 106 (108)
T COG3937 35 KKGELNAEEA-KRFVDDLLRQAKEAQGELEEK--IPRKIEEMLSDLEVARQSEMDELTERVDALERQVADLENKL 106 (108)
T ss_pred HcCCCCHHHH-HHHHHHHHHHHHHHhhhHHHh--hhHHHHHHHhhccccccchHHHHHHHHHHHHHHHHHHHHHh
Confidence 3577765432 334445555555666666666 34444444443 4455555555555443
No 134
>KOG0018 consensus Structural maintenance of chromosome protein 1 (sister chromatid cohesion complex Cohesin, subunit SMC1) [Cell cycle control, cell division, chromosome partitioning]
Probab=27.14 E-value=8.2e+02 Score=26.39 Aligned_cols=47 Identities=6% Similarity=0.201 Sum_probs=29.2
Q ss_pred HHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 6 EFQANLESLPNILQKKYALLRDLDKSLQEIQRQNEQRCEQEIEDLMR 52 (246)
Q Consensus 6 ~fle~l~~LP~El~r~l~~IreLD~~~~~~~~~~~~~~~~~l~~~~k 52 (246)
.+.+-++.++.++--....|+.......++..++.+..+..+..|-+
T Consensus 715 ~~~~~i~~~~p~i~~i~r~l~~~e~~~~~L~~~~n~ved~if~~f~~ 761 (1141)
T KOG0018|consen 715 RTESEIDEFGPEISEIKRKLQNREGEMKELEERMNKVEDRIFKGFCR 761 (1141)
T ss_pred HHHHHHHhhCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 34445566677666666666666666666666666666665555544
No 135
>PRK14011 prefoldin subunit alpha; Provisional
Probab=26.81 E-value=1.8e+02 Score=23.37 Aligned_cols=46 Identities=13% Similarity=0.153 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025899 72 ALDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELRR 117 (246)
Q Consensus 72 I~~~~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~eL~~ 117 (246)
+......|+++-+.|+.......+.+...|..+...+..+..+|+.
T Consensus 82 VEk~~~eA~~~~~~ri~~l~~~~~~l~~~i~~~~~~~~~l~~~L~~ 127 (144)
T PRK14011 82 LEKDVSEVIEDFKKSVEELDKTKKEGNKKIEELNKEITKLRKELEK 127 (144)
T ss_pred EEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456678899999999999999999999999999999999887765
No 136
>PRK14140 heat shock protein GrpE; Provisional
Probab=26.40 E-value=4e+02 Score=22.51 Aligned_cols=63 Identities=13% Similarity=0.183 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 23 ALLRDLDKSLQEIQRQNEQRCEQEIEDLMREIRAGNITPNTSLIRFSDDALDEQKHSIRIADEKVALAVQAYDLVDT 99 (246)
Q Consensus 23 ~~IreLD~~~~~~~~~~~~~~~~~l~~~~k~~~~gs~~~~~~~~~l~~~I~~~~~~~~~l~dEKv~LA~q~~dlVd~ 99 (246)
++|-+++.++..+..++....+.++.... ..+.++++..++...+..++-++ ++..++..+|.
T Consensus 37 ~~~~~l~~~i~~l~~ei~elkd~~lR~~A------------e~eN~rkR~~rE~~~~~~~a~~~--~~~~LLpvlDn 99 (191)
T PRK14140 37 ELLDEEQAKIAELEAKLDELEERYLRLQA------------DFENYKRRIQKENEAAEKYRAQS--LASDLLPALDN 99 (191)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHH
Confidence 34455555555555555544444332111 13344455555555565555554 34445555554
No 137
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=26.28 E-value=7.4 Score=25.07 Aligned_cols=9 Identities=22% Similarity=0.781 Sum_probs=7.5
Q ss_pred cceecccCC
Q 025899 214 EWFHFGCVG 222 (246)
Q Consensus 214 ~wfH~~Cv~ 222 (246)
.|.|..|+-
T Consensus 25 ~~vH~~CL~ 33 (47)
T PF12906_consen 25 KYVHRSCLE 33 (47)
T ss_dssp GSEECCHHH
T ss_pred chhHHHHHH
Confidence 689999975
No 138
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=26.24 E-value=5e+02 Score=23.57 Aligned_cols=20 Identities=10% Similarity=0.325 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 025899 96 LVDTHIQQLDQYLKNFDEEL 115 (246)
Q Consensus 96 lVd~hirrLD~dl~kfe~eL 115 (246)
.+++.|++|+.++.....++
T Consensus 172 ~~s~~~~k~esei~~Ik~lv 191 (300)
T KOG2629|consen 172 QLSRNIEKLESEINTIKQLV 191 (300)
T ss_pred HhhhhHHHHHHHHHHHHHHH
Confidence 34455566666655555443
No 139
>PF08400 phage_tail_N: Prophage tail fibre N-terminal; InterPro: IPR013609 This entry represents the N terminus of phage 933W tail fibre protein. The characteristics of the protein distribution suggest prophage matches.
Probab=26.16 E-value=2.3e+02 Score=22.58 Aligned_cols=33 Identities=15% Similarity=0.216 Sum_probs=24.2
Q ss_pred HHHHHHH--hhcccHHHHHHHHHHHHHHHHHHHHH
Q 025899 4 LDEFQAN--LESLPNILQKKYALLRDLDKSLQEIQ 36 (246)
Q Consensus 4 Le~fle~--l~~LP~El~r~l~~IreLD~~~~~~~ 36 (246)
|++||.. -..|+.|+...|.+|...=.+..+..
T Consensus 86 LN~fL~~~~e~dl~Pevlk~fe~m~~~a~~~a~~a 120 (134)
T PF08400_consen 86 LNDFLTAPDEDDLRPEVLKRFEEMVAQAARSAEAA 120 (134)
T ss_pred HHHHhhccccccCCHHHHHHHHHHHHHHHHHHHHH
Confidence 8899974 36899999999988876655544433
No 140
>COG5460 Uncharacterized conserved protein [Function unknown]
Probab=26.09 E-value=1.9e+02 Score=20.92 Aligned_cols=29 Identities=28% Similarity=0.446 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 84 DEKVALAVQAYDLVDTHIQQLDQYLKNFDEEL 115 (246)
Q Consensus 84 dEKv~LA~q~~dlVd~hirrLD~dl~kfe~eL 115 (246)
++|-.|+..+.+.+.+ .+|.++.+|.+++
T Consensus 9 ~~~a~lv~~i~dYL~~---E~~~evg~~~Ae~ 37 (82)
T COG5460 9 QEKAALVTRIRDYLTR---ETETEVGKFDAEF 37 (82)
T ss_pred HHHHHHHHHHHHHHHH---HHHHHHHHhhHHH
Confidence 5677888888887776 7888888888874
No 141
>cd07599 BAR_Rvs167p The Bin/Amphiphysin/Rvs (BAR) domain of Saccharomyces cerevisiae Reduced viability upon starvation protein 167 and similar proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of fungal proteins with similarity to Saccharomyces cerevisiae Reduced viability upon starvation protein 167 (Rvs167p) and Schizosaccharomyces pombe Hob1 (homolog of Bin1). S. cerevisiae Rvs167p plays a role in regulation of the actin cytoskeleton, endocytosis, and sporulation. It forms a heterodimer with another BAR domain protein Rvs161p. Rvs161p and Rvs167p share common functions but are not interchangeable. Their BAR domains cannot be replaced with each other and the overexpression of one cannot suppress the mutant phenotypes of the other. Rvs167p also interacts with the GTPase activating protein (GAP) Gyp5p, which is involved in ER to Golgi vesicle trafficking. BAR domains fo
Probab=25.79 E-value=4e+02 Score=22.36 Aligned_cols=23 Identities=13% Similarity=0.323 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 025899 80 IRIADEKVALAVQAYDLVDTHIQ 102 (246)
Q Consensus 80 ~~l~dEKv~LA~q~~dlVd~hir 102 (246)
+.-++++...|...|+.++.+++
T Consensus 151 l~kae~~l~~a~~~y~~lN~~Lk 173 (216)
T cd07599 151 LAKLERKLEEAKEEYEALNELLK 173 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34457888889999998888554
No 142
>COG4396 Mu-like prophage host-nuclease inhibitor protein Gam [General function prediction only]
Probab=25.62 E-value=3.6e+02 Score=21.78 Aligned_cols=23 Identities=9% Similarity=0.254 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 025899 16 NILQKKYALLRDLDKSLQEIQRQ 38 (246)
Q Consensus 16 ~El~r~l~~IreLD~~~~~~~~~ 38 (246)
.|+++.+..|.+|......+-.+
T Consensus 18 eeV~~~Ir~iGDlqRE~~RLeTe 40 (170)
T COG4396 18 EEVTAFIRQIGDLQREVKRLETE 40 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 35667777777766655544333
No 143
>PF10481 CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR018463 Mitosin or centromere-associated protein-F (Cenp-F) is found bound across the centromere as one of the proteins of the outer layer of the kinetochore []. Most of the kinetochore/centromere functions appear to depend upon binding of the C-terminal part of the molecule, whereas the N-terminal part, here, may be a cytoplasmic player in controlling the function of microtubules and dynein [].
Probab=25.61 E-value=5e+02 Score=23.42 Aligned_cols=28 Identities=29% Similarity=0.394 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 025899 91 VQAYDLVDTHIQQLDQYLKNFDEELRRE 118 (246)
Q Consensus 91 ~q~~dlVd~hirrLD~dl~kfe~eL~~e 118 (246)
..-+.--.+.|.+|+++++.+..+|+..
T Consensus 101 EgQl~s~Kkqie~Leqelkr~KsELErs 128 (307)
T PF10481_consen 101 EGQLNSCKKQIEKLEQELKRCKSELERS 128 (307)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444568889999999999998764
No 144
>KOG4721 consensus Serine/threonine protein kinase, contains leucine zipper domain [Signal transduction mechanisms]
Probab=25.42 E-value=7.3e+02 Score=25.27 Aligned_cols=52 Identities=17% Similarity=0.240 Sum_probs=36.4
Q ss_pred hhHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHh
Q 025899 65 LIRFSDDALDEQKHSIRI---ADEKVALAVQAYDLVDTHIQQLD---QYLKNFDEELR 116 (246)
Q Consensus 65 ~~~l~~~I~~~~~~~~~l---~dEKv~LA~q~~dlVd~hirrLD---~dl~kfe~eL~ 116 (246)
++.|..+-.+++.+++++ =+.|++-++++|+-+...+-+|+ .+|..-|..|+
T Consensus 409 eeelirrR~eelrHa~DIR~~YE~KLertN~ly~eLs~cm~qLelkEkElaerEq~l~ 466 (904)
T KOG4721|consen 409 EEELIRRRREELRHALDIREHYERKLERTNNLYMELSACMLQLELKEKELAEREQALE 466 (904)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444445666777654 46899999999999999998885 45555555454
No 145
>PF09849 DUF2076: Uncharacterized protein conserved in bacteria (DUF2076); InterPro: IPR018648 This family of hypothetical prokaryotic proteins has no known function but includes putative perimplasmic ligand-binding sensor proteins.
Probab=25.32 E-value=4.7e+02 Score=23.01 Aligned_cols=24 Identities=13% Similarity=0.289 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 92 QAYDLVDTHIQQLDQYLKNFDEEL 115 (246)
Q Consensus 92 q~~dlVd~hirrLD~dl~kfe~eL 115 (246)
|+.-+.+.-|+++...|+.|+..|
T Consensus 48 Q~vlvQE~AL~~a~~ri~eLe~ql 71 (247)
T PF09849_consen 48 QTVLVQEQALKQAQARIQELEAQL 71 (247)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444455666777777777777765
No 146
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=25.29 E-value=35 Score=22.05 Aligned_cols=39 Identities=36% Similarity=0.798 Sum_probs=21.3
Q ss_pred eeCCCCCC-Cce-ecCCCCCCCcceecccCC-------CCcc----CCCceeCcCCc
Q 025899 194 VCNQVSYG-EMV-ACDNPNCKIEWFHFGCVG-------LKEQ----PKGKWYCPDCA 237 (246)
Q Consensus 194 ~C~~~~~g-~mi-~Cd~~~C~~~wfH~~Cv~-------l~~~----~~~~w~C~~C~ 237 (246)
.|+++-.+ +++ .-.+ ..||..|.. |... ..+..||..|-
T Consensus 3 ~C~~~I~~~~~~~~~~~-----~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~ 54 (58)
T PF00412_consen 3 RCGKPIYGTEIVIKAMG-----KFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCY 54 (58)
T ss_dssp TTSSBESSSSEEEEETT-----EEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHH
T ss_pred CCCCCccCcEEEEEeCC-----cEEEccccccCCCCCccCCCeeEeECCEEECHHHH
Confidence 46665433 333 3444 567888854 2222 15678887764
No 147
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=25.27 E-value=68 Score=18.34 Aligned_cols=26 Identities=31% Similarity=0.733 Sum_probs=18.7
Q ss_pred e-eeCCCCCCC-ceecCCCCCCCcceecccC
Q 025899 193 C-VCNQVSYGE-MVACDNPNCKIEWFHFGCV 221 (246)
Q Consensus 193 C-~C~~~~~g~-mi~Cd~~~C~~~wfH~~Cv 221 (246)
| +|++...|. +-.|+. |. --+|..|+
T Consensus 3 C~~C~~~~~~~~~Y~C~~--c~-f~lh~~Ca 30 (30)
T PF03107_consen 3 CDVCRRKIDGFYFYHCSE--CC-FTLHVRCA 30 (30)
T ss_pred CCCCCCCcCCCEeEEeCC--CC-CeEcCccC
Confidence 6 788877777 777876 55 45787774
No 148
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=25.20 E-value=45 Score=22.23 Aligned_cols=29 Identities=31% Similarity=0.629 Sum_probs=18.0
Q ss_pred ecCCCCCCCcceecccCCCCccCCCceeCcCCcc
Q 025899 205 ACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCAA 238 (246)
Q Consensus 205 ~Cd~~~C~~~wfH~~Cv~l~~~~~~~w~C~~C~~ 238 (246)
=|.+ |. .|..++.-.....-.|.|+.|-.
T Consensus 24 IC~~--C~---~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 24 ICSK--CF---SHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred ECcc--cc---hhhcccccccCCceEEEcCCCCC
Confidence 3666 55 57776642222334899999964
No 149
>PTZ00007 (NAP-L) nucleosome assembly protein -L; Provisional
Probab=24.91 E-value=2.3e+02 Score=26.14 Aligned_cols=32 Identities=16% Similarity=0.273 Sum_probs=25.5
Q ss_pred HhhcccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 10 NLESLPNILQKKYALLRDLDKSLQEIQRQNEQ 41 (246)
Q Consensus 10 ~l~~LP~El~r~l~~IreLD~~~~~~~~~~~~ 41 (246)
.|..||..+++.+..|+.|..++..+-.+...
T Consensus 31 ~i~~Lp~~~~~rv~aL~~lQ~e~~~le~ef~~ 62 (337)
T PTZ00007 31 KLSHLTDEQRETLKKLQLLQKEFDDLEVEYNA 62 (337)
T ss_pred hhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999988887776555443
No 150
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=24.78 E-value=43 Score=21.63 Aligned_cols=31 Identities=23% Similarity=0.443 Sum_probs=17.7
Q ss_pred eecCCCC-CCCcceecccCCCCccCCCceeCcCCcc
Q 025899 204 VACDNPN-CKIEWFHFGCVGLKEQPKGKWYCPDCAA 238 (246)
Q Consensus 204 i~Cd~~~-C~~~wfH~~Cv~l~~~~~~~w~C~~C~~ 238 (246)
|.||.|. .++.++.+.|+.= .+--+|..|..
T Consensus 1 i~C~~C~~~~i~g~R~~C~~C----~d~dlC~~Cf~ 32 (49)
T cd02338 1 VSCDGCGKSNFTGRRYKCLIC----YDYDLCADCYD 32 (49)
T ss_pred CCCCCCcCCCcEEeeEEeCCC----CCCccchhHHh
Confidence 4567754 4555666666632 23456777754
No 151
>TIGR02977 phageshock_pspA phage shock protein A. Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by PFAM model pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects.
Probab=24.47 E-value=4.4e+02 Score=22.35 Aligned_cols=22 Identities=14% Similarity=0.356 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 025899 94 YDLVDTHIQQLDQYLKNFDEEL 115 (246)
Q Consensus 94 ~dlVd~hirrLD~dl~kfe~eL 115 (246)
++-+...+..|...|..|+..+
T Consensus 108 ~~~~~~~v~~l~~~l~~L~~ki 129 (219)
T TIGR02977 108 LAAVEETLAKLQEDIAKLQAKL 129 (219)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4445555555555555555443
No 152
>PF07342 DUF1474: Protein of unknown function (DUF1474); InterPro: IPR009942 This entry is represented by Bacteriophage PT1028, Orf16. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial proteins of around 100 residues in length. Members of this family seem to be found exclusively in Staphylococcus aureus. The function of this family is unknown.
Probab=24.41 E-value=1.4e+02 Score=22.60 Aligned_cols=40 Identities=18% Similarity=0.417 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025899 75 EQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELR 116 (246)
Q Consensus 75 ~~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~eL~ 116 (246)
.+.....+..-.|+. .|+.||+--+++++|.-|++|.+ ++
T Consensus 47 ~~~~g~~YhEhRI~n-~Q~~dL~~~Ylkefd~li~kF~e-iE 86 (100)
T PF07342_consen 47 IINHGYSYHEHRIQN-TQTIDLMHMYLKEFDELIEKFKE-IE 86 (100)
T ss_pred HHHHHHHHHHHHHhH-HHHHHHHHHHHHHHHHHHHHHHH-HH
Confidence 344566677777665 47889999999999999999995 44
No 153
>PRK13723 conjugal transfer pilus assembly protein TraH; Provisional
Probab=24.40 E-value=6.5e+02 Score=24.28 Aligned_cols=44 Identities=14% Similarity=0.202 Sum_probs=28.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 65 LIRFSDDALDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLK 109 (246)
Q Consensus 65 ~~~l~~~I~~~~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~dl~ 109 (246)
..++.+.|...-..+..+..+= ..-+.+..+|++|++.+++.+.
T Consensus 393 ~~~~~~~l~~a~~~~~~~~~~~-~~~~~~~~~i~~~~~~~eqq~~ 436 (451)
T PRK13723 393 MDHLRENLNQAQRQIAAFQSQV-QVQQDALLVVDRQMSYMRQQLS 436 (451)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555444444444443 3338888899999999998764
No 154
>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=24.19 E-value=4.8e+02 Score=22.69 Aligned_cols=106 Identities=16% Similarity=0.177 Sum_probs=0.0
Q ss_pred HHhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchh-hHHHHHH------HHHHHHHHH
Q 025899 9 ANLESLPNILQKKYALLRDLDKSLQEIQRQNEQRCEQEIEDLMREIRAGNITPNTSL-IRFSDDA------LDEQKHSIR 81 (246)
Q Consensus 9 e~l~~LP~El~r~l~~IreLD~~~~~~~~~~~~~~~~~l~~~~k~~~~gs~~~~~~~-~~l~~~I------~~~~~~~~~ 81 (246)
.++...=.|+++.|.+||..|...+.-..+.+-...+.+-.-++..=......+... +.+...| ...+..++.
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 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 82 IADEKVALAVQAYDLVDTHIQQLDQYLKNFDEE 114 (246)
Q Consensus 82 l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~e 114 (246)
-+.+++.-|..+...+...++.+......+...
T Consensus 203 eA~~~~~ea~~ln~~n~~~l~~~~~k~~~l~~~ 235 (264)
T PF06008_consen 203 EAQNKTREAEDLNRANQKNLEDLEKKKQELSEQ 235 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 155
>KOG4215 consensus Hepatocyte nuclear factor 4 and similar steroid hormone receptors [Transcription]
Probab=24.07 E-value=54 Score=30.65 Aligned_cols=25 Identities=32% Similarity=1.075 Sum_probs=18.5
Q ss_pred CCcee-eeCCCCCCC---ceecCCCCCCCcce
Q 025899 189 EPTYC-VCNQVSYGE---MVACDNPNCKIEWF 216 (246)
Q Consensus 189 ~~~~C-~C~~~~~g~---mi~Cd~~~C~~~wf 216 (246)
...+| ||+....|- .|.||+ |+ .+|
T Consensus 18 ~~~~CaICGDkaTGKHYGA~SCdG--CK-GFF 46 (432)
T KOG4215|consen 18 VAEFCAICGDKATGKHYGAISCDG--CK-GFF 46 (432)
T ss_pred ccchhheeCCcccccccceeecCc--ch-HHH
Confidence 35678 999876652 689999 88 544
No 156
>PRK14154 heat shock protein GrpE; Provisional
Probab=24.01 E-value=4.6e+02 Score=22.46 Aligned_cols=30 Identities=13% Similarity=0.258 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 68 FSDDALDEQKHSIRIADEKVALAVQAYDLVDT 99 (246)
Q Consensus 68 l~~~I~~~~~~~~~l~dEKv~LA~q~~dlVd~ 99 (246)
+++++.++...+..++-++ ++..++..+|.
T Consensus 85 yRKR~~kE~e~~~~~a~e~--~~~~LLpVlDn 114 (208)
T PRK14154 85 LRKRIEREKADIIKFGSKQ--LITDLLPVADS 114 (208)
T ss_pred HHHHHHHHHHHHHHHHHHH--HHHHHhhHHhH
Confidence 3444445555555555544 33444554444
No 157
>KOG1011 consensus Neurotransmitter release regulator, UNC-13 [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=24.00 E-value=4.4e+02 Score=26.98 Aligned_cols=97 Identities=15% Similarity=0.190 Sum_probs=55.9
Q ss_pred cccHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 13 SLPNILQKKYALL--RDLDKSLQEIQRQNEQRCEQEIEDLMREIRAGNITPNTSLIRFSDDALDEQKHSIRIADEKVALA 90 (246)
Q Consensus 13 ~LP~El~r~l~~I--reLD~~~~~~~~~~~~~~~~~l~~~~k~~~~gs~~~~~~~~~l~~~I~~~~~~~~~l~dEKv~LA 90 (246)
.|-..|-..|..| .|||..+.+++++++...+..++.+... =..++.+.. ..-..++-..+..+..-+..|-..|
T Consensus 856 qlrvqlekmfeamggkeld~ea~d~lk~lqvkln~vldels~~-f~tsfqphi--~e~v~qmg~il~qvkgt~~a~~sva 932 (1283)
T KOG1011|consen 856 QLRVQLEKMFEAMGGKELDEEAGDVLKELQVKLNSVLDELSAV-FVTSFQPHI--HECVIQMGDILVQVKGTGLAKTSVA 932 (1283)
T ss_pred HHHHHHHHHHHHhcchhhhHHHHHHHHHHHHHHHHHHHHHHHH-HHhhcCccH--HHHHHHHHHHHhhhcccccchhhcc
Confidence 3334445555555 4799999999999888888777766431 112444432 2222244455555666666666666
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 025899 91 VQAYDLVDTHIQQLDQYLKNFD 112 (246)
Q Consensus 91 ~q~~dlVd~hirrLD~dl~kfe 112 (246)
+.+-..+.--+.-||..|-.|.
T Consensus 933 ~dad~vl~plmdlldgnlt~fa 954 (1283)
T KOG1011|consen 933 QDADAVLEPLMDLLDGNLTLFA 954 (1283)
T ss_pred cchHHHHHHHHHHHhchHHHHH
Confidence 6655555555555555554444
No 158
>PF10158 LOH1CR12: Tumour suppressor protein; InterPro: IPR018780 This entry represents a region of 130 amino acids that is the most conserved part of some hypothetical proteins involved in loss of heterozygosity, and thus, tumour suppression []. The exact function of these proteins is not known.
Probab=23.79 E-value=3.7e+02 Score=21.23 Aligned_cols=16 Identities=13% Similarity=0.443 Sum_probs=6.5
Q ss_pred HHHHHHHHHHHHHHHH
Q 025899 24 LLRDLDKSLQEIQRQN 39 (246)
Q Consensus 24 ~IreLD~~~~~~~~~~ 39 (246)
.|++.|.....+...+
T Consensus 57 riKevd~~~~~l~~~~ 72 (131)
T PF10158_consen 57 RIKEVDQEIAKLLQQM 72 (131)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3444444444433333
No 159
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=23.71 E-value=62 Score=29.51 Aligned_cols=27 Identities=30% Similarity=0.973 Sum_probs=18.4
Q ss_pred CCcee-eeCCCCC----------C-CceecCCCCCCCccee
Q 025899 189 EPTYC-VCNQVSY----------G-EMVACDNPNCKIEWFH 217 (246)
Q Consensus 189 ~~~~C-~C~~~~~----------g-~mi~Cd~~~C~~~wfH 217 (246)
...+| ||+.... | ..+.|.- |..+|.+
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~Csl--C~teW~~ 224 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNL--CESEWHV 224 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCC--CCCcccc
Confidence 35789 9987631 2 2677888 7778844
No 160
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=23.63 E-value=62 Score=33.76 Aligned_cols=47 Identities=30% Similarity=0.880 Sum_probs=34.7
Q ss_pred Ccee-eeCCCCCCCceecCCCCCCCcceecccCC--CCccCCCceeCcCCccc
Q 025899 190 PTYC-VCNQVSYGEMVACDNPNCKIEWFHFGCVG--LKEQPKGKWYCPDCAAL 239 (246)
Q Consensus 190 ~~~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cv~--l~~~~~~~w~C~~C~~~ 239 (246)
...| .|.+.....++.|+. |. .=+|..|.. ++..+.+.|.|+.|...
T Consensus 155 ~~~~~~~~k~~~~~~~~~~~--~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 204 (904)
T KOG1246|consen 155 YPQCNTCSKGKEEKLLLCDS--CD-DSYHTYCLRPPLTRVPDGDWRCPKCIPT 204 (904)
T ss_pred chhhhccccCCCccceeccc--cc-CcccccccCCCCCcCCcCcccCCccccc
Confidence 3346 777664334558998 55 779999987 55578999999999765
No 161
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=23.53 E-value=54 Score=29.83 Aligned_cols=27 Identities=30% Similarity=0.835 Sum_probs=18.5
Q ss_pred CCcee-eeCCCCC-----------C-CceecCCCCCCCccee
Q 025899 189 EPTYC-VCNQVSY-----------G-EMVACDNPNCKIEWFH 217 (246)
Q Consensus 189 ~~~~C-~C~~~~~-----------g-~mi~Cd~~~C~~~wfH 217 (246)
...+| ||+.... | .++.|.- |..+|.+
T Consensus 183 ~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~Csl--C~teW~~ 222 (305)
T TIGR01562 183 SRTLCPACGSPPVASMVRQGGKETGLRYLSCSL--CATEWHY 222 (305)
T ss_pred CCCcCCCCCChhhhhhhcccCCCCCceEEEcCC--CCCcccc
Confidence 35699 9987631 1 2788998 7778844
No 162
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=23.29 E-value=47 Score=33.58 Aligned_cols=54 Identities=31% Similarity=0.706 Sum_probs=34.7
Q ss_pred CCCCCCCCceeeeCCCC------CCCceecCCCCCCCcceecccC---CCCccC-----CCceeCcCCc
Q 025899 183 LPVDPNEPTYCVCNQVS------YGEMVACDNPNCKIEWFHFGCV---GLKEQP-----KGKWYCPDCA 237 (246)
Q Consensus 183 ~~~~~~~~~~C~C~~~~------~g~mi~Cd~~~C~~~wfH~~Cv---~l~~~~-----~~~w~C~~C~ 237 (246)
.|.|-.+.++.||+... -|--+.|..-+|. ..||..|. ||--.. +..-||-.|.
T Consensus 111 VP~dRfnKtCYIC~E~GrpnkA~~GACMtCNKs~Ck-qaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk 178 (900)
T KOG0956|consen 111 VPHDRFNKTCYICNEEGRPNKAAKGACMTCNKSGCK-QAFHVTCAQRAGLLCEEEGNISDNVKYCGYCK 178 (900)
T ss_pred CchhhhcceeeeecccCCccccccccceecccccch-hhhhhhHhhhhccceeccccccccceechhHH
Confidence 44444444444997652 1545678777899 99999994 433222 3467999995
No 163
>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]
Probab=23.16 E-value=7.1e+02 Score=25.73 Aligned_cols=31 Identities=16% Similarity=0.066 Sum_probs=15.8
Q ss_pred HHHHHHHhhcccHHHHHHHHHHHHHHHHHHH
Q 025899 4 LDEFQANLESLPNILQKKYALLRDLDKSLQE 34 (246)
Q Consensus 4 Le~fle~l~~LP~El~r~l~~IreLD~~~~~ 34 (246)
|-||+.+.-+++.+.+..+-++..+-.++..
T Consensus 166 lad~iaa~l~~~~~~kQ~iLe~~~v~~Rlek 196 (782)
T COG0466 166 LADTIAAHLPLKLEEKQEILETLDVKERLEK 196 (782)
T ss_pred HHHHHHHhCCCCHHHHHHHHHhCCHHHHHHH
Confidence 3455555555555555555444444444443
No 164
>PRK10698 phage shock protein PspA; Provisional
Probab=23.15 E-value=4.8e+02 Score=22.34 Aligned_cols=12 Identities=17% Similarity=0.484 Sum_probs=6.1
Q ss_pred HHHHHHHhhcccH
Q 025899 4 LDEFQANLESLPN 16 (246)
Q Consensus 4 Le~fle~l~~LP~ 16 (246)
+.+.++.+++ |.
T Consensus 15 in~~ldkaED-P~ 26 (222)
T PRK10698 15 INALLEKAED-PQ 26 (222)
T ss_pred HHHHHHhhcC-HH
Confidence 4455555554 44
No 165
>PF11855 DUF3375: Protein of unknown function (DUF3375); InterPro: IPR021804 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 479 to 499 amino acids in length.
Probab=22.93 E-value=6.9e+02 Score=24.06 Aligned_cols=33 Identities=21% Similarity=0.289 Sum_probs=28.7
Q ss_pred HHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHH
Q 025899 4 LDEFQANLESLPNILQKKYALLRDLDKSLQEIQ 36 (246)
Q Consensus 4 Le~fle~l~~LP~El~r~l~~IreLD~~~~~~~ 36 (246)
+.+++.....||.+|.+.=..+|+||..+.+-+
T Consensus 180 ~~~i~~la~~L~~DFr~V~~~~r~l~r~lr~~i 212 (478)
T PF11855_consen 180 ARQILQLARELPADFRRVEDNFRELDRALRERI 212 (478)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457888999999999999999999999986533
No 166
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.89 E-value=52 Score=26.96 Aligned_cols=26 Identities=50% Similarity=1.054 Sum_probs=17.4
Q ss_pred e-eeCCCCC----------CC-ceecCCCCCC--------Ccceeccc
Q 025899 193 C-VCNQVSY----------GE-MVACDNPNCK--------IEWFHFGC 220 (246)
Q Consensus 193 C-~C~~~~~----------g~-mi~Cd~~~C~--------~~wfH~~C 220 (246)
| +|+.-+. |. .|+|.+ |. ..|||-.=
T Consensus 82 CkvCntRs~ktisk~AY~~GvVivqC~g--C~~~HliaDnL~~F~d~~ 127 (165)
T KOG3277|consen 82 CKVCNTRSTKTISKQAYEKGVVIVQCPG--CKNHHLIADNLGWFHDLK 127 (165)
T ss_pred eeccCCccccccChhhhhCceEEEECCC--Cccceeehhhhccccccc
Confidence 8 9987532 42 689999 65 36887543
No 167
>PF06464 DMAP_binding: DMAP1-binding Domain; InterPro: IPR010506 This domain binds DMAP1, a transcriptional co-repressor.; GO: 0008134 transcription factor binding, 0005634 nucleus
Probab=22.88 E-value=1.9e+02 Score=22.09 Aligned_cols=21 Identities=38% Similarity=0.578 Sum_probs=14.2
Q ss_pred hhcccHHHHHHHHHHHHHHHHHHH
Q 025899 11 LESLPNILQKKYALLRDLDKSLQE 34 (246)
Q Consensus 11 l~~LP~El~r~l~~IreLD~~~~~ 34 (246)
+..||.||+..| ++||..+.+
T Consensus 2 ~s~LP~evq~~L---~~L~~el~~ 22 (111)
T PF06464_consen 2 PSSLPPEVQNRL---QELDLELEE 22 (111)
T ss_pred cccCCHHHHHHH---HHHHHhhhc
Confidence 568999998755 456665443
No 168
>cd07596 BAR_SNX The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=22.61 E-value=4.2e+02 Score=21.50 Aligned_cols=32 Identities=16% Similarity=0.208 Sum_probs=19.9
Q ss_pred cHHHHHHHhhcccHHHHHHHHHHHHHHHHHHH
Q 025899 3 FLDEFQANLESLPNILQKKYALLRDLDKSLQE 34 (246)
Q Consensus 3 yLe~fle~l~~LP~El~r~l~~IreLD~~~~~ 34 (246)
.|.+|+..+..++.=|.+.-..+.+++.....
T Consensus 94 ~L~~y~~~~~s~k~~l~~R~~~~~~~~~~~~~ 125 (218)
T cd07596 94 PLKEYLRYCQAVKETLDDRADALLTLQSLKKD 125 (218)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35667777777777777666666666444333
No 169
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=22.56 E-value=36 Score=36.05 Aligned_cols=30 Identities=33% Similarity=0.887 Sum_probs=24.9
Q ss_pred cee-eeCCCCCCCceecCCCCCCCcceecccC
Q 025899 191 TYC-VCNQVSYGEMVACDNPNCKIEWFHFGCV 221 (246)
Q Consensus 191 ~~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cv 221 (246)
..| +|.+...|--|+|..-+|. .|||..|.
T Consensus 330 L~cy~cK~~~~gaciqcs~~~c~-~a~hvtca 360 (1051)
T KOG0955|consen 330 LTCYICKQKGLGACIQCSKANCY-TAFHVTCA 360 (1051)
T ss_pred ceeeeeccCCCCcceecchhhhh-hhhhhhhH
Confidence 446 9987767888999977898 99999993
No 170
>cd00584 Prefoldin_alpha Prefoldin alpha subunit; 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=22.52 E-value=3.5e+02 Score=20.58 Aligned_cols=44 Identities=14% Similarity=0.359 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025899 74 DEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELRR 117 (246)
Q Consensus 74 ~~~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~eL~~ 117 (246)
..+..|.++-+.|+.......+-+.+-+.+|-.++..+...+..
T Consensus 83 ~~~~eA~~~l~~r~~~l~~~~~~l~~~l~~l~~~~~~~~~~l~~ 126 (129)
T cd00584 83 KDLEEAIEFLDKKIEELTKQIEKLQKELAKLKDQINTLEAELQE 126 (129)
T ss_pred ecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45567888888999988888888888888888888888876543
No 171
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=22.52 E-value=53 Score=26.14 Aligned_cols=11 Identities=36% Similarity=1.162 Sum_probs=9.0
Q ss_pred CCCceeCcCCc
Q 025899 227 PKGKWYCPDCA 237 (246)
Q Consensus 227 ~~~~w~C~~C~ 237 (246)
..|+-|||.|-
T Consensus 41 KdG~v~CPvC~ 51 (131)
T COG1645 41 KDGEVFCPVCG 51 (131)
T ss_pred eCCeEECCCCC
Confidence 56888999986
No 172
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=22.48 E-value=50 Score=21.36 Aligned_cols=12 Identities=42% Similarity=1.149 Sum_probs=7.6
Q ss_pred CCceeCcCCccc
Q 025899 228 KGKWYCPDCAAL 239 (246)
Q Consensus 228 ~~~w~C~~C~~~ 239 (246)
.+.|.||.|...
T Consensus 32 p~~w~CP~C~a~ 43 (47)
T PF00301_consen 32 PDDWVCPVCGAP 43 (47)
T ss_dssp -TT-B-TTTSSB
T ss_pred CCCCcCcCCCCc
Confidence 578999999765
No 173
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=22.18 E-value=18 Score=21.46 Aligned_cols=26 Identities=31% Similarity=0.640 Sum_probs=15.9
Q ss_pred CCCcceecccCCCCccCCCceeCcCCcc
Q 025899 211 CKIEWFHFGCVGLKEQPKGKWYCPDCAA 238 (246)
Q Consensus 211 C~~~wfH~~Cv~l~~~~~~~w~C~~C~~ 238 (246)
|. .-||..|+..-.. .+...||.|..
T Consensus 18 C~-H~~c~~C~~~~~~-~~~~~Cp~C~~ 43 (45)
T cd00162 18 CG-HVFCRSCIDKWLK-SGKNTCPLCRT 43 (45)
T ss_pred CC-ChhcHHHHHHHHH-hCcCCCCCCCC
Confidence 44 4588888752111 14567999875
No 174
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=22.16 E-value=17 Score=38.58 Aligned_cols=46 Identities=11% Similarity=0.216 Sum_probs=34.8
Q ss_pred cee-eeCCCCCCCceecCCCCCCCcceec-ccCCCCc----cCCCceeCcCCcccc
Q 025899 191 TYC-VCNQVSYGEMVACDNPNCKIEWFHF-GCVGLKE----QPKGKWYCPDCAALK 240 (246)
Q Consensus 191 ~~C-~C~~~~~g~mi~Cd~~~C~~~wfH~-~Cv~l~~----~~~~~w~C~~C~~~~ 240 (246)
..| +|.+- +..++|++. || ..+|+ .|++-+. .+++-|+|+.|.-..
T Consensus 429 rrl~Ie~~d--et~l~yysT-~p-qly~ll~cLd~~~~e~~L~d~i~~~~ee~~rq 480 (1414)
T KOG1473|consen 429 RRLRIEGMD--ETLLWYYST-CP-QLYHLLRCLDRTYVEMYLCDGIWERREEIIRQ 480 (1414)
T ss_pred eeeEEecCC--CcEEEEecC-cH-HHHHHHHHhchHHHHHhhccchhhhHHHHHHh
Confidence 346 77754 778888874 88 89999 9999333 478999999997544
No 175
>PF07964 Red1: Rec10 / Red1; InterPro: IPR012491 Rec10 / Red1 is involved in meiotic recombination and chromosome segregation during homologous chromosome formation. This protein localises to the synaptonemal complex in Saccharomyces cerevisiae and the analogous structures (linear elements) in Schizosaccharomyces pombe []. This family is currently only found in fungi. ; GO: 0007059 chromosome segregation, 0007131 reciprocal meiotic recombination
Probab=22.15 E-value=5.7e+02 Score=26.14 Aligned_cols=45 Identities=13% Similarity=0.414 Sum_probs=33.2
Q ss_pred HHHHHHhhcccHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 5 DEFQANLESLPNILQKKYALLR-DLDKSLQEIQRQNEQRCEQEIEDLMR 52 (246)
Q Consensus 5 e~fle~l~~LP~El~r~l~~Ir-eLD~~~~~~~~~~~~~~~~~l~~~~k 52 (246)
|+-..+|.++-+||.+-++.|- ||+.+ +++++.+.+..++..+.+
T Consensus 625 eQI~~SI~~FSneL~~KI~IIN~ELNnK---I~kELSeKYQ~LF~eLQ~ 670 (706)
T PF07964_consen 625 EQIFSSISNFSNELIRKISIINEELNNK---IMKELSEKYQRLFKELQK 670 (706)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH
Confidence 5566789999999999998883 55655 666777777776666554
No 176
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=22.03 E-value=36 Score=19.94 Aligned_cols=13 Identities=46% Similarity=1.347 Sum_probs=6.4
Q ss_pred CCceecCCCCCCCcc
Q 025899 201 GEMVACDNPNCKIEW 215 (246)
Q Consensus 201 g~mi~Cd~~~C~~~w 215 (246)
|.++-|.. |.++|
T Consensus 17 ~~~~vCp~--C~~ew 29 (30)
T PF08274_consen 17 GELLVCPE--CGHEW 29 (30)
T ss_dssp SSSEEETT--TTEEE
T ss_pred CCEEeCCc--ccccC
Confidence 44444555 55454
No 177
>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=21.75 E-value=1e+03 Score=25.50 Aligned_cols=39 Identities=15% Similarity=0.312 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 025899 80 IRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELRRE 118 (246)
Q Consensus 80 ~~l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~eL~~e 118 (246)
+++++|+..--++=++.+...+..|+.||+-|.+|+...
T Consensus 320 KEmAEERaesLQ~eve~lkEr~deletdlEILKaEmeek 358 (1243)
T KOG0971|consen 320 KEMAEERAESLQQEVEALKERVDELETDLEILKAEMEEK 358 (1243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 688999999999999999999999999999999988764
No 178
>PF00906 Hepatitis_core: Hepatitis core antigen; InterPro: IPR002006 This entry represent the core domain of the viral capsid (HBcAg) from various Hepatitis B virus (HBV), which is a major human pathogen. The virus is composed of an outer envelope of host-derived lipid containing the surface proteins, and an inner protein capsid that contains genomic DNA. The capsid is composed of a single polypeptide, HBcAg, also known as the core antigen. The capsid has a 5-helical fold, where two long helices form a hairpin that dimerises into a 4-helical bundle []; this fold is unusual for icosahedral viruses. The monomer fold is stabilised by a hydrophobic core that is highly conserved among human viral variants. The capsid is assembled from dimers via interactions involving a highly conserved arginine-rich region near the C terminus. This viral capsid acts as a core antigen, the major immunodominant region lying at the tips of the alpha-helical hairpins that form spikes on the capsid surface.; GO: 0005198 structural molecule activity, 0009405 pathogenesis; PDB: 1HHH_C 2QIJ_C 3KXS_F 2G34_B 2G33_C 3OX8_F 3OXS_C 3OXR_C 1QGT_B.
Probab=21.65 E-value=15 Score=30.30 Aligned_cols=13 Identities=23% Similarity=0.125 Sum_probs=6.7
Q ss_pred HHHHHhhcccHHH
Q 025899 6 EFQANLESLPNIL 18 (246)
Q Consensus 6 ~fle~l~~LP~El 18 (246)
..+|.++-||.+|
T Consensus 10 a~veLlsflPsdF 22 (187)
T PF00906_consen 10 ASVELLSFLPSDF 22 (187)
T ss_dssp --HHHHCTS-GCG
T ss_pred ceeehhhcCcccc
Confidence 3456667777765
No 179
>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=21.62 E-value=3.5e+02 Score=20.14 Aligned_cols=41 Identities=7% Similarity=0.306 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025899 76 QKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELR 116 (246)
Q Consensus 76 ~~~~~~l~dEKv~LA~q~~dlVd~hirrLD~dl~kfe~eL~ 116 (246)
+..|.++-+.|+...+...+-+...+..+...+..++..+.
T Consensus 75 ~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~~~~~l~ 115 (120)
T PF02996_consen 75 LEEAIEFLKKRIKELEEQLEKLEKELAELQAQIEQLEQTLQ 115 (120)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44677777778887777777777777777777777776554
No 180
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=21.60 E-value=58 Score=26.71 Aligned_cols=18 Identities=33% Similarity=0.957 Sum_probs=12.8
Q ss_pred ecccCCCCc--cCCCceeCc
Q 025899 217 HFGCVGLKE--QPKGKWYCP 234 (246)
Q Consensus 217 H~~Cv~l~~--~~~~~w~C~ 234 (246)
|+.|...-. ...+.|+||
T Consensus 110 HlGC~~~~~~~~~~~~~~CP 129 (177)
T COG0723 110 HLGCTVPWNNAGAEGGFFCP 129 (177)
T ss_pred CCCCccCcccCCCCCeEEcc
Confidence 777766443 556899998
No 181
>KOG0964 consensus Structural maintenance of chromosome protein 3 (sister chromatid cohesion complex Cohesin, subunit SMC3) [Cell cycle control, cell division, chromosome partitioning]
Probab=21.55 E-value=1e+03 Score=25.58 Aligned_cols=24 Identities=21% Similarity=0.422 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q 025899 93 AYDLVDTHIQQLDQYLKNFDEELR 116 (246)
Q Consensus 93 ~~dlVd~hirrLD~dl~kfe~eL~ 116 (246)
.++.|..|+..+.+....|+++|.
T Consensus 749 ~Le~i~~~l~~~~~~~~~~e~el~ 772 (1200)
T KOG0964|consen 749 ELEEIKTSLHKLESQSNYFESELG 772 (1200)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHh
Confidence 344455566666666666666543
No 182
>PRK11677 hypothetical protein; Provisional
Probab=21.53 E-value=4.2e+02 Score=21.06 Aligned_cols=27 Identities=11% Similarity=0.154 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 24 LLRDLDKSLQEIQRQNEQRCEQEIEDL 50 (246)
Q Consensus 24 ~IreLD~~~~~~~~~~~~~~~~~l~~~ 50 (246)
..+.|..++.....++++...+...+|
T Consensus 30 ~q~~le~eLe~~k~ele~YkqeV~~HF 56 (134)
T PRK11677 30 QQQALQYELEKNKAELEEYRQELVSHF 56 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444444544444443333
No 183
>PF12773 DZR: Double zinc ribbon
Probab=21.22 E-value=87 Score=19.78 Aligned_cols=19 Identities=21% Similarity=0.523 Sum_probs=10.1
Q ss_pred Ccee-eeCCCCC---CCceecCC
Q 025899 190 PTYC-VCNQVSY---GEMVACDN 208 (246)
Q Consensus 190 ~~~C-~C~~~~~---g~mi~Cd~ 208 (246)
..|| .|+.+-. ..++.|-+
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~ 34 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPN 34 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcC
Confidence 5566 6665532 33455555
No 184
>PRK10807 paraquat-inducible protein B; Provisional
Probab=21.14 E-value=8e+02 Score=24.15 Aligned_cols=20 Identities=25% Similarity=0.243 Sum_probs=13.1
Q ss_pred cHHHHHHHhhcccHHHHHHHHH
Q 025899 3 FLDEFQANLESLPNILQKKYAL 24 (246)
Q Consensus 3 yLe~fle~l~~LP~El~r~l~~ 24 (246)
-+.+.++.+..|| |..++..
T Consensus 421 ~~~~il~kin~lp--le~i~~~ 440 (547)
T PRK10807 421 KLMEALDKINNLP--LNPMIEQ 440 (547)
T ss_pred HHHHHHHHHhcCC--HHHHHHH
Confidence 3567788888888 4444443
No 185
>PRK11546 zraP zinc resistance protein; Provisional
Probab=21.05 E-value=4.5e+02 Score=21.20 Aligned_cols=35 Identities=9% Similarity=0.097 Sum_probs=22.0
Q ss_pred hhcccHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Q 025899 11 LESLPNILQKKYALLRD-LDKSLQEIQRQNEQRCEQ 45 (246)
Q Consensus 11 l~~LP~El~r~l~~Ire-LD~~~~~~~~~~~~~~~~ 45 (246)
..+|+.|=+-.+..|++ -..+..+++.++..+..+
T Consensus 41 ~~~LT~EQQa~~q~I~~~f~~~t~~LRqqL~aKr~E 76 (143)
T PRK11546 41 AAPLTTEQQAAWQKIHNDFYAQTSALRQQLVSKRYE 76 (143)
T ss_pred cccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45788888888877653 444555666665554444
No 186
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=20.83 E-value=4.6e+02 Score=22.68 Aligned_cols=11 Identities=36% Similarity=0.646 Sum_probs=5.5
Q ss_pred HHHHHHHhhcc
Q 025899 4 LDEFQANLESL 14 (246)
Q Consensus 4 Le~fle~l~~L 14 (246)
+++|++.|..+
T Consensus 107 ~~~~l~~l~~~ 117 (262)
T PF14257_consen 107 FDSFLDELSEL 117 (262)
T ss_pred HHHHHHHHhcc
Confidence 44555555544
No 187
>PF14260 zf-C4pol: C4-type zinc-finger of DNA polymerase delta
Probab=20.74 E-value=43 Score=23.22 Aligned_cols=21 Identities=38% Similarity=0.869 Sum_probs=15.5
Q ss_pred cee-eeCCCCCCCceecCCCCCC
Q 025899 191 TYC-VCNQVSYGEMVACDNPNCK 212 (246)
Q Consensus 191 ~~C-~C~~~~~g~mi~Cd~~~C~ 212 (246)
..| .|. ++....|.|++-|||
T Consensus 46 ~iC~~C~-~~~~~~~~C~s~DCp 67 (73)
T PF14260_consen 46 TICQSCS-GSLHEEIECDSLDCP 67 (73)
T ss_pred HHHHHhc-CcCCCCCcccCCCCC
Confidence 456 676 444567899999999
No 188
>TIGR03017 EpsF chain length determinant protein EpsF. Sequences in this family of proteins are members of the chain length determinant family (pfam02706) which includes the wzc protein from E.coli. This family of proteins are homologous to the EpsF protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.
Probab=20.74 E-value=6.9e+02 Score=23.23 Aligned_cols=54 Identities=6% Similarity=0.097 Sum_probs=32.9
Q ss_pred cHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCC
Q 025899 3 FLDEFQANLESLPNILQKKYALLRDLDKSLQEIQRQNEQRCEQEIEDLMREIRAGNITP 61 (246)
Q Consensus 3 yLe~fle~l~~LP~El~r~l~~IreLD~~~~~~~~~~~~~~~~~l~~~~k~~~~gs~~~ 61 (246)
+++.|++..... -....-..+.-|+.++.++..++.+.... +..|++ ++|-+.+
T Consensus 153 ~~~~y~~~~~~~--~~~~~~~~~~fl~~ql~~~~~~l~~ae~~-l~~fr~--~~~i~~~ 206 (444)
T TIGR03017 153 FAQAYIDTNIEL--KVEPAQKAALWFVQQIAALREDLARAQSK-LSAYQQ--EKGIVSS 206 (444)
T ss_pred HHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHH--HcCCccc
Confidence 345566544422 22233346778888888888888776665 555666 6775544
No 189
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=20.65 E-value=3.9e+02 Score=20.37 Aligned_cols=43 Identities=16% Similarity=0.201 Sum_probs=21.9
Q ss_pred hhCCCCCCchhhHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Q 025899 55 RAGNITPNTSLIRFSDDALDEQKHSI-RIADEKVALAVQAYDLVD 98 (246)
Q Consensus 55 ~~gs~~~~~~~~~l~~~I~~~~~~~~-~l~dEKv~LA~q~~dlVd 98 (246)
..|+.+. .+.+.++.+|...+.++. .+++-+=.+++++.+.|+
T Consensus 30 ssg~~a~-~e~~~lR~r~~~~Lk~~r~rl~~~~d~v~~~sk~a~~ 73 (104)
T COG4575 30 SSGSLAG-DEAEELRSKAESALKEARDRLGDTGDAVVQRSKAAAD 73 (104)
T ss_pred hcccchh-hHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence 3454433 345556666777666654 344444444444444443
No 190
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=20.29 E-value=2.2e+02 Score=20.58 Aligned_cols=21 Identities=24% Similarity=0.365 Sum_probs=15.6
Q ss_pred CcHHHHHHHhhcccHHHHHHHH
Q 025899 2 SFLDEFQANLESLPNILQKKYA 23 (246)
Q Consensus 2 ~yLe~fle~l~~LP~El~r~l~ 23 (246)
+|+.+|+. +-+||.+|+..+.
T Consensus 18 s~Vs~~l~-Ll~lP~~i~~~v~ 38 (93)
T PF08535_consen 18 SWVSNHLA-LLDLPEEIKELVR 38 (93)
T ss_dssp HHHHHHHG-GGS--HHHHHHHH
T ss_pred HHHHHHHH-HHcCCHHHHHHHH
Confidence 47788888 5689999999988
No 191
>PF02370 M: M protein repeat; InterPro: IPR003345 This short repeat is found in multiple copies in bacterial M proteins. The M proteins bind to IgA and are closely associated with virulence. The M protein has been postulated to be a major group A streptococcal (GAS) virulence factor because of its contribution to the bacterial resistance to opsonophagocytosis [].; PDB: 2KK9_A.
Probab=20.20 E-value=1.6e+02 Score=15.87 Aligned_cols=15 Identities=20% Similarity=0.357 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHHHh
Q 025899 102 QQLDQYLKNFDEELR 116 (246)
Q Consensus 102 rrLD~dl~kfe~eL~ 116 (246)
+.|++++.+|+++..
T Consensus 4 k~lEa~~qkLe~e~q 18 (21)
T PF02370_consen 4 KQLEADHQKLEAEKQ 18 (21)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHh
Confidence 578888888887653
No 192
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=20.18 E-value=9e+02 Score=24.38 Aligned_cols=84 Identities=13% Similarity=0.185 Sum_probs=0.0
Q ss_pred hhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 11 LESLPNILQKKYALLRDLDKSLQEIQRQNEQRCEQEIEDLMREIRAGNITPNTSLIRFSDDALDEQKHSIRIADEKVALA 90 (246)
Q Consensus 11 l~~LP~El~r~l~~IreLD~~~~~~~~~~~~~~~~~l~~~~k~~~~gs~~~~~~~~~l~~~I~~~~~~~~~l~dEKv~LA 90 (246)
....+-|+.-....|+.++.++..+..++..+... .+.+.+.|...-.++-.+..+=
T Consensus 410 ~~~e~~ei~~~~~~i~~~~~~ve~l~~e~~~L~~~-------------------~ee~k~eie~L~~~l~~~~r~~---- 466 (652)
T COG2433 410 EEEERREITVYEKRIKKLEETVERLEEENSELKRE-------------------LEELKREIEKLESELERFRREV---- 466 (652)
T ss_pred ccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHHHHHHHHHH----
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 025899 91 VQAYDLVDTHIQQLDQYLKNFDEELRRE 118 (246)
Q Consensus 91 ~q~~dlVd~hirrLD~dl~kfe~eL~~e 118 (246)
..--.+++.++.+|..+..|+.+|..+
T Consensus 467 -~~~~~~~rei~~~~~~I~~L~~~L~e~ 493 (652)
T COG2433 467 -RDKVRKDREIRARDRRIERLEKELEEK 493 (652)
T ss_pred -HHHHhhhHHHHHHHHHHHHHHHHHHHH
No 193
>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=20.17 E-value=8.3e+02 Score=23.98 Aligned_cols=41 Identities=7% Similarity=0.191 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 70 DDALDEQKHSIRIADE-KVALAVQAYDLVDTHIQQLDQYLKN 110 (246)
Q Consensus 70 ~~I~~~~~~~~~l~dE-Kv~LA~q~~dlVd~hirrLD~dl~k 110 (246)
..|...+....++-.. =..=|..++.-+..++..|...++.
T Consensus 171 ~~ie~~F~~f~~lt~~GD~~~A~eil~~l~~~~~~l~~~~e~ 212 (560)
T PF06160_consen 171 ENIEEEFSEFEELTENGDYLEAREILEKLKEETDELEEIMED 212 (560)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555666555544443 3444556666666666666555433
No 194
>KOG1937 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.02 E-value=8.1e+02 Score=23.78 Aligned_cols=25 Identities=20% Similarity=0.300 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025899 89 LAVQAYDLVDTHIQQLDQYLKNFDEE 114 (246)
Q Consensus 89 LA~q~~dlVd~hirrLD~dl~kfe~e 114 (246)
..+.+.+ |+..||++++||.+...+
T Consensus 387 ytqrikE-i~gniRKq~~DI~Kil~e 411 (521)
T KOG1937|consen 387 YTQRIKE-IDGNIRKQEQDIVKILEE 411 (521)
T ss_pred HHHHHHH-HHhHHHHHHHHHHHHHHH
Confidence 3444444 346688888888777654
Done!