Query 025663
Match_columns 249
No_of_seqs 278 out of 1358
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 08:11:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025663.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025663hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1244 Predicted transcriptio 99.1 1.3E-11 2.8E-16 109.3 1.8 51 59-109 281-331 (336)
2 PF00628 PHD: PHD-finger; Int 99.1 1.2E-11 2.6E-16 83.6 0.8 48 61-108 1-50 (51)
3 COG5034 TNG2 Chromatin remodel 99.1 4.9E-11 1.1E-15 104.7 4.3 48 58-109 220-270 (271)
4 KOG1973 Chromatin remodeling p 98.9 3.2E-10 6.9E-15 102.4 2.6 48 58-109 218-268 (274)
5 smart00249 PHD PHD zinc finger 98.9 1.1E-09 2.4E-14 71.4 3.1 46 61-106 1-47 (47)
6 KOG0825 PHD Zn-finger protein 98.9 5.9E-10 1.3E-14 110.2 2.3 54 56-109 212-266 (1134)
7 KOG4299 PHD Zn-finger protein 98.9 6E-10 1.3E-14 108.2 1.7 51 59-109 253-305 (613)
8 KOG1512 PHD Zn-finger protein 98.7 4.7E-09 1E-13 93.8 1.7 48 59-108 314-362 (381)
9 KOG1083 Putative transcription 98.5 2.1E-07 4.5E-12 94.9 6.4 77 150-249 1111-1187(1306)
10 cd04718 BAH_plant_2 BAH, or Br 98.4 1.6E-07 3.6E-12 77.1 2.9 29 83-111 1-29 (148)
11 KOG0955 PHD finger protein BR1 98.3 3.1E-07 6.8E-12 95.1 2.6 52 56-109 216-269 (1051)
12 KOG0954 PHD finger protein [Ge 98.3 2.6E-07 5.7E-12 91.4 1.2 51 57-109 269-321 (893)
13 KOG1245 Chromatin remodeling c 98.2 3.3E-07 7.2E-12 97.9 -0.6 55 56-110 1105-1159(1404)
14 COG5141 PHD zinc finger-contai 98.1 1.1E-06 2.4E-11 83.7 1.5 53 55-109 189-243 (669)
15 KOG0383 Predicted helicase [Ge 98.0 1.7E-06 3.6E-11 86.6 1.7 52 56-110 44-95 (696)
16 KOG0957 PHD finger protein [Ge 98.0 1.4E-06 2.9E-11 83.3 0.9 50 59-108 544-597 (707)
17 KOG4323 Polycomb-like PHD Zn-f 98.0 2.4E-06 5.1E-11 81.7 1.0 51 59-109 168-224 (464)
18 KOG4443 Putative transcription 97.9 5E-06 1.1E-10 81.7 2.0 52 58-109 67-118 (694)
19 KOG0956 PHD finger protein AF1 97.8 6.6E-06 1.4E-10 81.2 1.3 48 60-109 6-57 (900)
20 PF13831 PHD_2: PHD-finger; PD 97.8 4.1E-06 8.9E-11 52.9 -0.8 34 72-107 2-36 (36)
21 KOG1246 DNA-binding protein ju 97.7 2E-05 4.4E-10 81.8 3.5 140 58-209 154-308 (904)
22 KOG1473 Nucleosome remodeling 96.1 0.0037 8E-08 65.2 2.9 48 59-109 344-391 (1414)
23 KOG0957 PHD finger protein [Ge 95.2 0.011 2.4E-07 57.2 2.0 50 60-109 120-179 (707)
24 PF15446 zf-PHD-like: PHD/FYVE 94.1 0.022 4.9E-07 47.8 1.2 49 61-109 1-60 (175)
25 PF14446 Prok-RING_1: Prokaryo 92.5 0.069 1.5E-06 36.7 1.4 35 57-91 3-38 (54)
26 KOG1512 PHD Zn-finger protein 92.3 0.058 1.3E-06 49.0 1.1 76 59-134 258-342 (381)
27 KOG4628 Predicted E3 ubiquitin 91.7 0.12 2.6E-06 48.4 2.4 47 60-109 230-276 (348)
28 KOG4443 Putative transcription 91.4 0.1 2.2E-06 52.1 1.6 76 59-134 18-104 (694)
29 PF11793 FANCL_C: FANCL C-term 91.0 0.022 4.8E-07 41.1 -2.5 51 59-109 2-64 (70)
30 KOG0383 Predicted helicase [Ge 89.8 0.23 4.9E-06 50.5 2.6 54 79-132 1-58 (696)
31 KOG1632 Uncharacterized PHD Zn 89.3 0.28 6E-06 46.0 2.7 48 61-109 62-113 (345)
32 PF13639 zf-RING_2: Ring finge 88.7 0.035 7.6E-07 35.9 -2.7 43 61-107 2-44 (44)
33 KOG4299 PHD Zn-finger protein 88.1 0.32 7E-06 48.4 2.3 48 59-109 47-95 (613)
34 PF12861 zf-Apc11: Anaphase-pr 86.6 0.27 5.8E-06 36.9 0.6 46 62-109 35-80 (85)
35 PF07649 C1_3: C1-like domain; 84.5 0.31 6.7E-06 29.0 0.1 29 61-89 2-30 (30)
36 PF13901 DUF4206: Domain of un 83.8 0.79 1.7E-05 39.6 2.3 41 59-108 152-197 (202)
37 PF13832 zf-HC5HC2H_2: PHD-zin 80.5 0.8 1.7E-05 35.2 1.1 30 59-90 55-86 (110)
38 PF07227 DUF1423: Protein of u 78.9 1.3 2.8E-05 42.7 2.1 51 59-109 128-192 (446)
39 KOG1844 PHD Zn-finger proteins 77.1 1.4 3E-05 42.9 1.8 49 59-109 86-135 (508)
40 KOG1952 Transcription factor N 76.7 0.98 2.1E-05 46.6 0.6 51 58-108 190-244 (950)
41 PF12678 zf-rbx1: RING-H2 zinc 76.5 0.79 1.7E-05 33.1 -0.1 45 59-107 19-73 (73)
42 KOG1473 Nucleosome remodeling 75.9 0.42 9.1E-06 50.6 -2.2 50 57-109 426-479 (1414)
43 KOG3612 PHD Zn-finger protein 75.5 3.9 8.5E-05 40.4 4.3 53 53-109 54-108 (588)
44 PF13771 zf-HC5HC2H: PHD-like 73.6 1.7 3.6E-05 32.1 1.0 30 59-90 36-67 (90)
45 COG1773 Rubredoxin [Energy pro 73.5 2.3 5E-05 29.3 1.6 21 88-109 25-45 (55)
46 PF07496 zf-CW: CW-type Zinc F 69.4 2.2 4.8E-05 28.5 0.8 32 74-106 3-35 (50)
47 KOG1734 Predicted RING-contain 68.9 1.4 2.9E-05 40.0 -0.4 52 56-109 221-279 (328)
48 cd00162 RING RING-finger (Real 68.5 1.4 3.1E-05 27.0 -0.3 42 62-108 2-43 (45)
49 PF00130 C1_1: Phorbol esters/ 66.3 4.6 9.9E-05 26.7 1.9 32 59-90 11-44 (53)
50 KOG1632 Uncharacterized PHD Zn 65.9 0.99 2.1E-05 42.3 -2.0 54 56-109 236-295 (345)
51 KOG1244 Predicted transcriptio 64.0 2.8 6.1E-05 38.1 0.6 76 56-131 221-306 (336)
52 KOG2752 Uncharacterized conser 63.0 4 8.8E-05 37.7 1.4 31 59-90 128-165 (345)
53 KOG1829 Uncharacterized conser 61.9 2.1 4.7E-05 42.7 -0.6 45 57-108 509-558 (580)
54 PF10497 zf-4CXXC_R1: Zinc-fin 60.8 3.7 8E-05 31.9 0.7 49 59-108 7-69 (105)
55 PHA02929 N1R/p28-like protein; 60.5 4 8.6E-05 36.4 0.9 48 58-109 173-225 (238)
56 PF00301 Rubredoxin: Rubredoxi 59.7 6.1 0.00013 26.3 1.5 14 95-109 30-43 (47)
57 KOG3053 Uncharacterized conser 57.8 1.8 3.8E-05 39.0 -1.7 56 54-109 15-80 (293)
58 smart00184 RING Ring finger. E 55.9 2.6 5.5E-05 24.8 -0.8 39 62-106 1-39 (39)
59 PF10367 Vps39_2: Vacuolar sor 55.4 7.7 0.00017 29.0 1.7 31 59-90 78-108 (109)
60 PHA02825 LAP/PHD finger-like p 55.3 4.2 9.1E-05 34.0 0.2 51 57-109 6-57 (162)
61 KOG4323 Polycomb-like PHD Zn-f 54.7 9.7 0.00021 37.1 2.6 52 56-109 80-133 (464)
62 KOG2932 E3 ubiquitin ligase in 53.1 7.8 0.00017 35.9 1.5 35 72-109 87-132 (389)
63 PF15446 zf-PHD-like: PHD/FYVE 52.8 35 0.00076 28.9 5.3 22 72-93 122-143 (175)
64 PHA02862 5L protein; Provision 51.8 4.4 9.5E-05 33.5 -0.2 48 59-109 2-51 (156)
65 PF03107 C1_2: C1 domain; Int 50.7 12 0.00026 22.1 1.6 29 61-89 2-30 (30)
66 cd00029 C1 Protein kinase C co 50.2 8.4 0.00018 24.7 1.0 32 59-90 11-44 (50)
67 KOG0956 PHD finger protein AF1 49.0 7.6 0.00017 39.6 0.9 79 59-137 117-210 (900)
68 PLN03208 E3 ubiquitin-protein 47.9 6.3 0.00014 34.0 0.1 49 58-109 17-77 (193)
69 PRK03564 formate dehydrogenase 46.5 24 0.00051 32.7 3.6 40 58-109 186-235 (309)
70 smart00109 C1 Protein kinase C 46.3 7.4 0.00016 24.7 0.2 32 59-90 11-43 (49)
71 KOG1081 Transcription factor N 45.9 15 0.00033 35.8 2.4 31 56-89 86-116 (463)
72 cd00730 rubredoxin Rubredoxin; 44.7 14 0.00031 24.8 1.4 14 95-109 30-43 (50)
73 PF12773 DZR: Double zinc ribb 43.7 23 0.00051 23.0 2.4 9 100-108 29-37 (50)
74 PRK14559 putative protein seri 43.4 22 0.00047 36.3 3.1 48 60-109 2-50 (645)
75 cd00350 rubredoxin_like Rubred 42.6 19 0.00041 21.8 1.7 11 99-109 16-26 (33)
76 PF14445 Prok-RING_2: Prokaryo 42.3 2.4 5.3E-05 28.7 -2.5 42 59-107 7-48 (57)
77 PF08746 zf-RING-like: RING-li 42.1 7.4 0.00016 25.2 -0.3 41 62-106 1-43 (43)
78 PF06937 EURL: EURL protein; 41.9 13 0.00027 33.8 1.1 22 59-80 15-36 (285)
79 smart00744 RINGv The RING-vari 41.6 6 0.00013 26.3 -0.8 44 61-106 1-48 (49)
80 KOG3799 Rab3 effector RIM1 and 41.5 9.8 0.00021 31.1 0.3 53 57-109 63-116 (169)
81 TIGR01562 FdhE formate dehydro 39.5 36 0.00079 31.4 3.7 41 57-109 182-233 (305)
82 COG1948 MUS81 ERCC4-type nucle 39.5 26 0.00056 31.6 2.7 27 221-247 82-108 (254)
83 KOG0317 Predicted E3 ubiquitin 39.4 9.8 0.00021 34.8 -0.0 50 56-112 236-285 (293)
84 PF04216 FdhE: Protein involve 39.4 13 0.00028 33.7 0.7 42 56-109 169-220 (290)
85 KOG3970 Predicted E3 ubiquitin 39.3 9.7 0.00021 33.8 -0.1 50 59-109 50-103 (299)
86 COG5175 MOT2 Transcriptional r 39.3 7.1 0.00015 36.6 -0.9 49 57-109 12-62 (480)
87 COG5574 PEX10 RING-finger-cont 38.3 10 0.00022 34.3 -0.1 51 57-112 213-263 (271)
88 PF14044 NETI: NETI protein 38.2 18 0.00039 25.1 1.1 21 221-241 4-25 (57)
89 PF05191 ADK_lid: Adenylate ki 38.0 23 0.00049 22.1 1.5 28 75-108 2-29 (36)
90 PF05502 Dynactin_p62: Dynacti 37.7 17 0.00037 35.7 1.3 8 101-108 53-60 (483)
91 PLN02189 cellulose synthase 35.5 25 0.00054 37.6 2.2 50 57-109 32-85 (1040)
92 PLN02400 cellulose synthase 35.2 28 0.00061 37.4 2.5 49 58-109 35-87 (1085)
93 PF00641 zf-RanBP: Zn-finger i 34.2 15 0.00032 21.5 0.2 12 98-109 2-13 (30)
94 PF12906 RINGv: RING-variant d 34.2 5.5 0.00012 26.3 -1.9 43 62-106 1-47 (47)
95 smart00547 ZnF_RBZ Zinc finger 34.0 20 0.00043 20.1 0.7 11 99-109 1-11 (26)
96 PLN02436 cellulose synthase A 33.8 28 0.0006 37.4 2.2 49 58-109 35-87 (1094)
97 PF13922 PHD_3: PHD domain of 33.5 11 0.00023 27.0 -0.6 21 72-92 41-61 (69)
98 PF09416 UPF1_Zn_bind: RNA hel 33.2 21 0.00046 29.7 1.0 23 61-84 2-24 (152)
99 KOG1705 Uncharacterized conser 32.3 23 0.0005 27.0 1.0 49 59-108 27-77 (110)
100 PF12554 MOZART1: Mitotic-spin 32.2 42 0.00091 22.5 2.1 21 221-241 18-38 (48)
101 PF14569 zf-UDP: Zinc-binding 31.6 6.3 0.00014 29.1 -2.0 49 57-108 7-59 (80)
102 PF13411 MerR_1: MerR HTH fami 31.6 50 0.0011 22.5 2.6 27 212-238 31-57 (69)
103 PF10080 DUF2318: Predicted me 31.5 23 0.00049 27.5 0.9 32 59-90 35-68 (102)
104 PLN02638 cellulose synthase A 31.3 30 0.00066 37.2 2.0 49 58-109 16-68 (1079)
105 PLN02195 cellulose synthase A 29.6 35 0.00076 36.3 2.1 49 58-109 5-57 (977)
106 PF14787 zf-CCHC_5: GAG-polypr 28.6 29 0.00063 21.8 0.8 12 76-87 4-15 (36)
107 TIGR00595 priA primosomal prot 28.1 38 0.00082 33.3 2.0 43 59-109 213-262 (505)
108 PHA02926 zinc finger-like prot 27.9 18 0.00039 32.1 -0.3 52 58-109 169-228 (242)
109 PF13041 PPR_2: PPR repeat fam 27.7 59 0.0013 20.7 2.3 19 223-241 19-37 (50)
110 TIGR03831 YgiT_finger YgiT-typ 27.7 20 0.00043 22.6 -0.0 10 100-109 32-41 (46)
111 PLN02915 cellulose synthase A 27.5 47 0.001 35.7 2.6 49 58-109 14-66 (1044)
112 KOG3268 Predicted E3 ubiquitin 27.2 15 0.00032 31.6 -0.9 50 60-109 166-226 (234)
113 cd04764 HTH_MlrA-like_sg1 Heli 27.1 69 0.0015 21.9 2.7 27 212-238 31-57 (67)
114 PF08274 PhnA_Zn_Ribbon: PhnA 27.0 36 0.00078 20.5 1.0 21 61-81 4-26 (30)
115 PRK00420 hypothetical protein; 27.0 35 0.00076 26.9 1.3 17 93-109 33-49 (112)
116 COG5415 Predicted integral mem 26.7 33 0.00073 30.1 1.2 35 72-110 190-224 (251)
117 PRK11595 DNA utilization prote 26.7 30 0.00065 30.1 0.9 49 60-109 6-57 (227)
118 PRK14873 primosome assembly pr 26.0 48 0.001 33.9 2.4 42 59-109 383-431 (665)
119 KOG1395 Tryptophan synthase be 25.2 85 0.0019 30.0 3.6 49 191-242 368-417 (477)
120 PF12926 MOZART2: Mitotic-spin 24.7 53 0.0012 24.8 1.8 27 205-231 9-35 (88)
121 KOG0225 Pyruvate dehydrogenase 23.9 1E+02 0.0022 29.2 3.8 39 196-247 247-285 (394)
122 COG5243 HRD1 HRD ubiquitin lig 23.5 17 0.00037 34.6 -1.2 47 56-109 284-343 (491)
123 KOG2114 Vacuolar assembly/sort 23.4 35 0.00075 35.8 0.8 39 60-108 841-880 (933)
124 PRK04023 DNA polymerase II lar 23.1 72 0.0016 34.3 3.0 24 56-82 623-646 (1121)
125 KOG4218 Nuclear hormone recept 23.1 40 0.00087 31.9 1.0 53 57-109 13-76 (475)
126 PF07875 Coat_F: Coat F domain 23.0 59 0.0013 22.4 1.7 26 216-241 37-62 (64)
127 PRK11827 hypothetical protein; 22.7 57 0.0012 22.9 1.5 27 59-85 8-37 (60)
128 PF11080 DUF2622: Protein of u 21.9 1.7E+02 0.0037 22.5 4.1 65 176-245 22-86 (96)
129 TIGR01206 lysW lysine biosynth 21.7 66 0.0014 22.0 1.6 32 61-92 4-40 (54)
130 PF04810 zf-Sec23_Sec24: Sec23 21.6 34 0.00073 21.6 0.2 32 74-109 2-33 (40)
131 PF05553 DUF761: Cotton fibre 21.6 85 0.0018 19.9 2.0 16 222-237 23-38 (38)
132 KOG3896 Dynactin, subunit p62 21.5 65 0.0014 30.4 2.1 41 64-109 14-54 (449)
133 PF00645 zf-PARP: Poly(ADP-rib 21.5 22 0.00048 25.7 -0.8 35 59-93 7-50 (82)
134 PF13913 zf-C2HC_2: zinc-finge 21.5 40 0.00086 19.1 0.5 14 73-86 1-14 (25)
135 KOG4718 Non-SMC (structural ma 21.4 25 0.00054 30.9 -0.6 50 57-109 179-228 (235)
136 TIGR00756 PPR pentatricopeptid 20.9 1E+02 0.0023 17.0 2.3 17 224-240 17-33 (35)
137 PF05715 zf-piccolo: Piccolo Z 20.9 45 0.00098 23.4 0.7 11 99-109 48-58 (61)
138 PRK05580 primosome assembly pr 20.8 62 0.0013 33.1 2.0 44 58-109 380-430 (679)
139 COG5540 RING-finger-containing 20.3 48 0.001 30.8 1.0 48 59-109 323-370 (374)
No 1
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=99.14 E-value=1.3e-11 Score=109.28 Aligned_cols=51 Identities=43% Similarity=1.058 Sum_probs=48.1
Q ss_pred cccccccccccCCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 59 DVGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
..+|.+|+..++.+++|+||.|+++||++||.||+.+.|+|.|.|-.|...
T Consensus 281 ck~csicgtsenddqllfcddcdrgyhmyclsppm~eppegswsc~KOG~~ 331 (336)
T KOG1244|consen 281 CKYCSICGTSENDDQLLFCDDCDRGYHMYCLSPPMVEPPEGSWSCHLCLEE 331 (336)
T ss_pred cceeccccCcCCCceeEeecccCCceeeEecCCCcCCCCCCchhHHHHHHH
Confidence 578999999999999999999999999999999999999999999999853
No 2
>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=99.13 E-value=1.2e-11 Score=83.61 Aligned_cols=48 Identities=31% Similarity=1.010 Sum_probs=42.2
Q ss_pred cccccccccCCCCceeecccCCcccccccCCcCC--CCCCCCccCccccc
Q 025663 61 GCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVV--RVPIGTWLCPKCSG 108 (249)
Q Consensus 61 ~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~--~~p~g~W~Cp~C~~ 108 (249)
+|.+|++.+..+.||.||.|+.|||..|++|++. ..+.+.|+|+.|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 5889999888899999999999999999999877 44456899999974
No 3
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=99.11 E-value=4.9e-11 Score=104.72 Aligned_cols=48 Identities=29% Similarity=0.906 Sum_probs=41.9
Q ss_pred ccccccccccccCCCCceeec--ccCC-cccccccCCcCCCCCCCCccCcccccC
Q 025663 58 GDVGCEQCGSGERAEELLLCD--KCDK-GFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 58 ~~~~C~vC~~~~~~~~~l~CD--~C~~-~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
+..|| -|++. ..|+||.|| .|.+ |||+.|++ |...|+|.|||+.|...
T Consensus 220 e~lYC-fCqqv-SyGqMVaCDn~nCkrEWFH~~CVG--Lk~pPKG~WYC~eCk~~ 270 (271)
T COG5034 220 EELYC-FCQQV-SYGQMVACDNANCKREWFHLECVG--LKEPPKGKWYCPECKKA 270 (271)
T ss_pred ceeEE-Eeccc-ccccceecCCCCCchhheeccccc--cCCCCCCcEeCHHhHhc
Confidence 34556 89987 679999999 4998 99999999 99999999999999753
No 4
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=98.95 E-value=3.2e-10 Score=102.40 Aligned_cols=48 Identities=29% Similarity=0.872 Sum_probs=41.0
Q ss_pred ccccccccccccCCCCceeecc--cC-CcccccccCCcCCCCCCCCccCcccccC
Q 025663 58 GDVGCEQCGSGERAEELLLCDK--CD-KGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 58 ~~~~C~vC~~~~~~~~~l~CD~--C~-~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
+..|| +|.+ ...|+||.||. |+ .|||+.|++ |...|.|.|||+.|...
T Consensus 218 e~~yC-~Cnq-vsyg~Mi~CDn~~C~~eWFH~~CVG--L~~~PkgkWyC~~C~~~ 268 (274)
T KOG1973|consen 218 EPTYC-ICNQ-VSYGKMIGCDNPGCPIEWFHFTCVG--LKTKPKGKWYCPRCKAE 268 (274)
T ss_pred CCEEE-Eecc-cccccccccCCCCCCcceEEEeccc--cccCCCCcccchhhhhh
Confidence 34566 6664 36799999997 99 699999999 99999999999999875
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 KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.89 E-value=5.9e-10 Score=110.21 Aligned_cols=54 Identities=35% Similarity=0.882 Sum_probs=49.5
Q ss_pred ccccccccccccccCCCCceeecccCCc-ccccccCCcCCCCCCCCccCcccccC
Q 025663 56 DYGDVGCEQCGSGERAEELLLCDKCDKG-FHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 56 ~~~~~~C~vC~~~~~~~~~l~CD~C~~~-fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
..+..-|.+|...+..+.||+||.|+.+ ||++||+|+|.++|.+.|||++|.-.
T Consensus 212 ~~E~~~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~dL 266 (1134)
T KOG0825|consen 212 SQEEVKCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSLL 266 (1134)
T ss_pred ccccccceeeccCChHHhheeecccccceeeccccCcccccccccceecCcchhh
Confidence 3446789999999988999999999998 99999999999999999999999864
No 7
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.87 E-value=6e-10 Score=108.24 Aligned_cols=51 Identities=31% Similarity=0.945 Sum_probs=45.6
Q ss_pred cccccccccccCCCCceeecccCCcccccccCCcCC--CCCCCCccCcccccC
Q 025663 59 DVGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVV--RVPIGTWLCPKCSGQ 109 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~--~~p~g~W~Cp~C~~~ 109 (249)
+++|..|++.+....+|+||+|++.||+.|+.||+. .+|.|.|||+.|...
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k 305 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKIK 305 (613)
T ss_pred HHHHHHhCCccccccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCeee
Confidence 469999999976677799999999999999999954 599999999999875
No 8
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.70 E-value=4.7e-09 Score=93.79 Aligned_cols=48 Identities=33% Similarity=0.807 Sum_probs=43.9
Q ss_pred cccccccccccCCCCceeecccCCcccccccCCcCCCCCCCCccCc-cccc
Q 025663 59 DVGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCP-KCSG 108 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp-~C~~ 108 (249)
...|.+|+++.-.+++++||.|+++||.+|++ |..+|.|.|+|- .|..
T Consensus 314 C~lC~IC~~P~~E~E~~FCD~CDRG~HT~CVG--L~~lP~G~WICD~~C~~ 362 (381)
T KOG1512|consen 314 CELCRICLGPVIESEHLFCDVCDRGPHTLCVG--LQDLPRGEWICDMRCRE 362 (381)
T ss_pred cHhhhccCCcccchheeccccccCCCCccccc--cccccCccchhhhHHHH
Confidence 46799999999899999999999999999999 999999999998 4654
No 9
>KOG1083 consensus Putative transcription factor ASH1/LIN-59 [Transcription]
Probab=98.48 E-value=2.1e-07 Score=94.94 Aligned_cols=77 Identities=16% Similarity=0.049 Sum_probs=66.6
Q ss_pred chhhHHHhhhccCCCCCCccHHHHHHhhhhhHHHhhhcccccCCCCCCCCCCCCCCCChhhhhcccccccChhcHHHHHH
Q 025663 150 ASLVLQKKRRRLLPFTPSEDRSQRLSQMGSLAHALTALQMEFSDDLTYMPGMAPRSANQAEFEEGGMQVLSKEDTETLEQ 229 (249)
Q Consensus 150 ~~~~~~kk~r~~lp~vps~d~~~~~~~~a~l~~a~~~~~~~~s~~l~y~p~~a~~~~n~~~~e~~g~~~~~~~d~~~~~~ 229 (249)
-.+...++.+++++ || +.|+++|++|+.++.+.+..+++.+.|.+|+++.++ .|. .+
T Consensus 1111 ~~~~tk~~~~kk~~-vp----k~R~~~~~dL~~~~~A~n~~~~c~kg~~~g~~~cld---------------~d~---c~ 1167 (1306)
T KOG1083|consen 1111 MWNYTKILLTKKNL-VP----KIRINVYKDLQRLSKAGNNTCKCRKGRPRKQKTCLD---------------PDS---CS 1167 (1306)
T ss_pred HHHhhhhhcccccc-ch----HHHHHHHHhhhhhhhccCccccccCCCCCCCccccC---------------chh---hh
Confidence 34466777777777 55 899999999999999999999999999999998887 222 78
Q ss_pred HHHHHhcCCCCCeEEEeccC
Q 025663 230 CRAMCKRGECPPLVVRQMAR 249 (249)
Q Consensus 230 ~~~~~~~g~~~~~~v~~~~~ 249 (249)
|++|+++|+||||+|+||++
T Consensus 1168 nqrm~r~e~cp~L~v~~gp~ 1187 (1306)
T KOG1083|consen 1168 NQRMQRHEECPPLEVFRGPK 1187 (1306)
T ss_pred hHHhhhhccCCCcceeccCC
Confidence 89999999999999999974
No 10
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=98.40 E-value=1.6e-07 Score=77.09 Aligned_cols=29 Identities=48% Similarity=1.212 Sum_probs=26.6
Q ss_pred cccccccCCcCCCCCCCCccCcccccCCc
Q 025663 83 GFHMKCLRPIVVRVPIGTWLCPKCSGQRR 111 (249)
Q Consensus 83 ~fH~~Cl~P~l~~~p~g~W~Cp~C~~~~~ 111 (249)
+||+.||+|||..+|+|+|+||.|...+.
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~ 29 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEVEKS 29 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcCCCC
Confidence 69999999999999999999999997633
No 11
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=98.29 E-value=3.1e-07 Score=95.08 Aligned_cols=52 Identities=31% Similarity=0.759 Sum_probs=46.3
Q ss_pred ccccccccccccccCC--CCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 56 DYGDVGCEQCGSGERA--EELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 56 ~~~~~~C~vC~~~~~~--~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
.+.+.+|.+|..++.. +.+|+||.|+..+|+.|++ +..+|+|.|+|..|...
T Consensus 216 ~~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cyg--i~~ipeg~WlCr~Cl~s 269 (1051)
T KOG0955|consen 216 LEEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYG--IPFIPEGQWLCRRCLQS 269 (1051)
T ss_pred cCCCccceeecccccCCCceEEEcCCCcchhhhhccC--CCCCCCCcEeehhhccC
Confidence 3557899999998754 8999999999999999999 66799999999999865
No 12
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=98.26 E-value=2.6e-07 Score=91.38 Aligned_cols=51 Identities=39% Similarity=0.921 Sum_probs=45.6
Q ss_pred ccccccccccccc--CCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 57 YGDVGCEQCGSGE--RAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 57 ~~~~~C~vC~~~~--~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
+++.+|.+|..++ ..++||+||.|+...|+.|++ +.++|.|.|+|..|.-.
T Consensus 269 dedviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyG--Ile~p~gpWlCr~Calg 321 (893)
T KOG0954|consen 269 DEDVICDVCRSPDSEEANEMVFCDKCNICVHQACYG--ILEVPEGPWLCRTCALG 321 (893)
T ss_pred cccceeceecCCCccccceeEEeccchhHHHHhhhc--eeecCCCCeeehhcccc
Confidence 3678999999986 458999999999999999999 89999999999999754
No 13
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=98.16 E-value=3.3e-07 Score=97.89 Aligned_cols=55 Identities=40% Similarity=1.009 Sum_probs=50.7
Q ss_pred ccccccccccccccCCCCceeecccCCcccccccCCcCCCCCCCCccCcccccCC
Q 025663 56 DYGDVGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQR 110 (249)
Q Consensus 56 ~~~~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~~ 110 (249)
......|.+|........|+.||.|..+||++|+.|.+..+|.|+|+|+.|...+
T Consensus 1105 s~~~~~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~ 1159 (1404)
T KOG1245|consen 1105 SAVNALCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKEH 1159 (1404)
T ss_pred ccchhhhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchhh
Confidence 3446889999999888899999999999999999999999999999999999875
No 14
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=98.09 E-value=1.1e-06 Score=83.70 Aligned_cols=53 Identities=32% Similarity=0.725 Sum_probs=45.5
Q ss_pred cccccccccccccccC--CCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 55 GDYGDVGCEQCGSGER--AEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 55 ~~~~~~~C~vC~~~~~--~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
+++=++.|.+|...+. .+.+++||+|+...|+.|++ +..+|+|.|+|..|.-.
T Consensus 189 ~d~~d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYG--I~f~peG~WlCrkCi~~ 243 (669)
T COG5141 189 SDEFDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYG--IQFLPEGFWLCRKCIYG 243 (669)
T ss_pred chhhhhhhHhccccccCCcceEEEecCcchhhhhhccc--ceecCcchhhhhhhccc
Confidence 3444789999998763 47899999999999999999 77899999999999854
No 15
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=98.04 E-value=1.7e-06 Score=86.63 Aligned_cols=52 Identities=38% Similarity=0.945 Sum_probs=46.8
Q ss_pred ccccccccccccccCCCCceeecccCCcccccccCCcCCCCCCCCccCcccccCC
Q 025663 56 DYGDVGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQR 110 (249)
Q Consensus 56 ~~~~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~~ 110 (249)
+.+...|.+|..+ +++|+||.|..+||.+|+++++...|.+.|.|+.|....
T Consensus 44 ~~~~e~c~ic~~~---g~~l~c~tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~~p~ 95 (696)
T KOG0383|consen 44 DAEQEACRICADG---GELLWCDTCPASFHASCLGPPLTPQPNGEFICPRCFCPK 95 (696)
T ss_pred hhhhhhhhhhcCC---CcEEEeccccHHHHHHccCCCCCcCCccceeeeeeccCC
Confidence 4556889999998 999999999999999999999999999999999995543
No 16
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=98.03 E-value=1.4e-06 Score=83.30 Aligned_cols=50 Identities=30% Similarity=0.835 Sum_probs=45.3
Q ss_pred cccccccccccCCCCceeecccCCcccccccCCcCCCCCCC----CccCccccc
Q 025663 59 DVGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIG----TWLCPKCSG 108 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g----~W~Cp~C~~ 108 (249)
...|.+|.+..+...++.||.|...||+.||.|||+.+|+. .|.|..|.+
T Consensus 544 ~ysCgiCkks~dQHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECdk 597 (707)
T KOG0957|consen 544 NYSCGICKKSTDQHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECDK 597 (707)
T ss_pred ceeeeeeccchhhHHHhhcchhhceeeccccCCccccCcccccCcceeeccccc
Confidence 46799999998888999999999999999999999999986 399999944
No 17
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=97.96 E-value=2.4e-06 Score=81.69 Aligned_cols=51 Identities=29% Similarity=0.854 Sum_probs=41.2
Q ss_pred ccccccccccc--CCCCceeecccCCcccccccCCcCCC----CCCCCccCcccccC
Q 025663 59 DVGCEQCGSGE--RAEELLLCDKCDKGFHMKCLRPIVVR----VPIGTWLCPKCSGQ 109 (249)
Q Consensus 59 ~~~C~vC~~~~--~~~~~l~CD~C~~~fH~~Cl~P~l~~----~p~g~W~Cp~C~~~ 109 (249)
+..|.+|+.+. ..+.||+|+.|..|||..|+.|++.. -+...|||..|...
T Consensus 168 n~qc~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~ 224 (464)
T KOG4323|consen 168 NLQCSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRG 224 (464)
T ss_pred cceeeeeecCCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccc
Confidence 34488888654 44699999999999999999998764 34557999999865
No 18
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=97.89 E-value=5e-06 Score=81.67 Aligned_cols=52 Identities=38% Similarity=0.945 Sum_probs=47.7
Q ss_pred ccccccccccccCCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 58 GDVGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 58 ~~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
...+|..|+...++..+++|+.|+-.||.+|..|++..++.|.|+|+.|...
T Consensus 67 ~crvCe~c~~~gD~~kf~~Ck~cDvsyh~yc~~P~~~~v~sg~~~ckk~~~c 118 (694)
T KOG4443|consen 67 SCRVCEACGTTGDPKKFLLCKRCDVSYHCYCQKPPNDKVPSGPWLCKKCTRC 118 (694)
T ss_pred CceeeeeccccCCcccccccccccccccccccCCccccccCcccccHHHHhh
Confidence 3578999998889999999999999999999999999999999999988653
No 19
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=97.81 E-value=6.6e-06 Score=81.16 Aligned_cols=48 Identities=38% Similarity=0.964 Sum_probs=41.4
Q ss_pred cccccccccc--CCCCceeecc--cCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 60 VGCEQCGSGE--RAEELLLCDK--CDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 60 ~~C~vC~~~~--~~~~~l~CD~--C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
.-|.||.+.. .++.||.||+ |.-+.|+.|++ +..+|.|.|||..|..+
T Consensus 6 GGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYG--IvqVPtGpWfCrKCesq 57 (900)
T KOG0956|consen 6 GGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYG--IVQVPTGPWFCRKCESQ 57 (900)
T ss_pred cceeeecCcCCCccCceeeecCCCceeeeehhcce--eEecCCCchhhhhhhhh
Confidence 3488998854 3579999994 99999999999 88999999999999765
No 20
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=97.75 E-value=4.1e-06 Score=52.95 Aligned_cols=34 Identities=44% Similarity=1.132 Sum_probs=20.4
Q ss_pred CCceeecccCCcccccccCCcCCCCCCC-CccCcccc
Q 025663 72 EELLLCDKCDKGFHMKCLRPIVVRVPIG-TWLCPKCS 107 (249)
Q Consensus 72 ~~~l~CD~C~~~fH~~Cl~P~l~~~p~g-~W~Cp~C~ 107 (249)
++||.|+.|....|..|++ +..++.+ +|+|..|.
T Consensus 2 n~ll~C~~C~v~VH~~CYG--v~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYG--VSEVPDGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT---SS--SS-----HHH-
T ss_pred CceEEeCCCCCcCChhhCC--cccCCCCCcEECCcCC
Confidence 5799999999999999999 6666666 79998884
No 21
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=97.73 E-value=2e-05 Score=81.84 Aligned_cols=140 Identities=24% Similarity=0.389 Sum_probs=91.8
Q ss_pred ccccccccccccCCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC-----CcccccCc---c-eeeceecccC
Q 025663 58 GDVGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ-----RRVRSFSQ---R-KIIDFFKIKK 128 (249)
Q Consensus 58 ~~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~-----~~~~~~~~---~-~~~~~~~~~k 128 (249)
+...|..|..+... .++.|+.|...||..|..|++..++.+.|.|+.|... ....+|.+ . ....|.....
T Consensus 154 ~~~~~~~~~k~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gf~~~~~~yt~~~f~~~~~ 232 (904)
T KOG1246|consen 154 DYPQCNTCSKGKEE-KLLLCDSCDDSYHTYCLRPPLTRVPDGDWRCPKCIPTPESKPNYKFGFEQGSREYTLPKFEEYAD 232 (904)
T ss_pred cchhhhccccCCCc-cceecccccCcccccccCCCCCcCCcCcccCCcccccccCCcccccCcCCCCCccccchhhhHhh
Confidence 35679999998766 4459999999999999999999999999999999876 22223331 1 1111111111
Q ss_pred CCccccccCCCchhhhhhhccchhh--HHHhhhccCCCCCCccHHHHHHhhhhhHHHhhhcccccCCCCCCCC----CCC
Q 025663 129 PNLTEEKCDSPQDTRKRRRRSASLV--LQKKRRRLLPFTPSEDRSQRLSQMGSLAHALTALQMEFSDDLTYMP----GMA 202 (249)
Q Consensus 129 ~~~~~~~~~~~~~~~kkrrr~~~~~--~~kk~r~~lp~vps~d~~~~~~~~a~l~~a~~~~~~~~s~~l~y~p----~~a 202 (249)
... . .....+.+.. ....++.+|..+.+....+.++|++++.+...++|++.++.-+-.. .|+
T Consensus 233 ~~~-~----------~~~~~~~~~~~~~~~vE~e~w~~v~~~~~~~~~~~g~d~~~~~~~s~~~~~~~~~~~~~~~~~y~ 301 (904)
T KOG1246|consen 233 NFK-K----------DYFPKSKNSPDSTEDVEKEFWRLVASNLESVEVLYGADLSTKEFGSGFPKSASGPLLGSEAEKYS 301 (904)
T ss_pred hhh-c----------cccccccCCCCchHHHHHHHHHhhcccccceeeeeccchhhccccccccccCCCCCCCcchhhhc
Confidence 100 0 0001111111 2345778888899998888999999999999999998776544442 455
Q ss_pred CCCCChh
Q 025663 203 PRSANQA 209 (249)
Q Consensus 203 ~~~~n~~ 209 (249)
-++||+.
T Consensus 302 ~s~wnL~ 308 (904)
T KOG1246|consen 302 NSGWNLN 308 (904)
T ss_pred cCccccc
Confidence 5555443
No 22
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=96.12 E-value=0.0037 Score=65.20 Aligned_cols=48 Identities=29% Similarity=0.695 Sum_probs=44.3
Q ss_pred cccccccccccCCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 59 DVGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
++.|.+|... +.++||..|++.||+.|+.||...+|+..|-|--|...
T Consensus 344 ddhcrf~~d~---~~~lc~Et~prvvhlEcv~hP~~~~~s~~~e~evc~~h 391 (1414)
T KOG1473|consen 344 DDHCRFCHDL---GDLLCCETCPRVVHLECVFHPRFAVPSAFWECEVCNIH 391 (1414)
T ss_pred cccccccCcc---cceeecccCCceEEeeecCCccccCCCccchhhhhhhh
Confidence 6789999988 89999999999999999999999999999999999743
No 23
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=95.17 E-value=0.011 Score=57.22 Aligned_cols=50 Identities=36% Similarity=0.759 Sum_probs=38.7
Q ss_pred cccccccccc--CCCCceeecccCCcccccccCCcC-CCCCCC-------CccCcccccC
Q 025663 60 VGCEQCGSGE--RAEELLLCDKCDKGFHMKCLRPIV-VRVPIG-------TWLCPKCSGQ 109 (249)
Q Consensus 60 ~~C~vC~~~~--~~~~~l~CD~C~~~fH~~Cl~P~l-~~~p~g-------~W~Cp~C~~~ 109 (249)
.+|.||-... +.+++|.||.|+...|-.|++.-- ..+|.+ .|||--|...
T Consensus 120 ~iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~G 179 (707)
T KOG0957|consen 120 VICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYG 179 (707)
T ss_pred eEEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHhcC
Confidence 4899998753 668999999999999999999531 124433 6999988764
No 24
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=94.10 E-value=0.022 Score=47.83 Aligned_cols=49 Identities=31% Similarity=0.767 Sum_probs=36.2
Q ss_pred ccccccc---ccCCCCceeecccCCcccccccCCcCCC------CCCCC--ccCcccccC
Q 025663 61 GCEQCGS---GERAEELLLCDKCDKGFHMKCLRPIVVR------VPIGT--WLCPKCSGQ 109 (249)
Q Consensus 61 ~C~vC~~---~~~~~~~l~CD~C~~~fH~~Cl~P~l~~------~p~g~--W~Cp~C~~~ 109 (249)
.|.+|+. ...-|.||+|-+|...||..|+++-... +-.+. -.|..|+.-
T Consensus 1 ~C~~C~~~g~~~~kG~Lv~CQGCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~ 60 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGPLVYCQGCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGI 60 (175)
T ss_pred CcccccCCCCCccCCCeEEcCccChHHHhhhcCCccccceeeEEEcCCceEEechhhcCh
Confidence 4888854 3356899999999999999999986542 22233 578888753
No 25
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=92.51 E-value=0.069 Score=36.72 Aligned_cols=35 Identities=23% Similarity=0.788 Sum_probs=29.7
Q ss_pred ccccccccccccc-CCCCceeecccCCcccccccCC
Q 025663 57 YGDVGCEQCGSGE-RAEELLLCDKCDKGFHMKCLRP 91 (249)
Q Consensus 57 ~~~~~C~vC~~~~-~~~~~l~CD~C~~~fH~~Cl~P 91 (249)
+....|.+|+..- +.+++|.|..|...||-.|+..
T Consensus 3 ~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred ccCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 3457899999976 4689999999999999999963
No 26
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=92.28 E-value=0.058 Score=48.97 Aligned_cols=76 Identities=14% Similarity=0.152 Sum_probs=54.0
Q ss_pred ccccccccccc------CCCCceeecccCCcccccccCCcCCC---CCCCCccCcccccCCcccccCcceeeceecccCC
Q 025663 59 DVGCEQCGSGE------RAEELLLCDKCDKGFHMKCLRPIVVR---VPIGTWLCPKCSGQRRVRSFSQRKIIDFFKIKKP 129 (249)
Q Consensus 59 ~~~C~vC~~~~------~~~~~l~CD~C~~~fH~~Cl~P~l~~---~p~g~W~Cp~C~~~~~~~~~~~~~~~~~~~~~k~ 129 (249)
...|.+|..+. ..+.||+|..|...+|.+|+.-+..- +-...|.|..|.--..--+-.....+-|+++|..
T Consensus 258 ~~~~~~~~~~~~~~~~~r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~IC~~P~~E~E~~FCD~CDR 337 (381)
T KOG1512|consen 258 RNERKHFWDIQTNIIQSRRNSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCELCRICLGPVIESEHLFCDVCDR 337 (381)
T ss_pred hhhhhhhhcchhhhhhhhhccceeecccccCCCCcchhcCHHHHhHHhhcchhhcccHhhhccCCcccchheeccccccC
Confidence 46788887753 34689999999999999999854322 3345799999975433322235566789999988
Q ss_pred Ccccc
Q 025663 130 NLTEE 134 (249)
Q Consensus 130 ~~~~~ 134 (249)
+.+..
T Consensus 338 G~HT~ 342 (381)
T KOG1512|consen 338 GPHTL 342 (381)
T ss_pred CCCcc
Confidence 77654
No 27
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.67 E-value=0.12 Score=48.37 Aligned_cols=47 Identities=23% Similarity=0.592 Sum_probs=38.9
Q ss_pred ccccccccccCCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 60 VGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 60 ~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
+.|.+|......|+.|.==-|.-.||..|++|+|..- .=+||-|...
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~---r~~CPvCK~d 276 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT---RTFCPVCKRD 276 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc---CccCCCCCCc
Confidence 6999999998777777667799999999999997654 2379999864
No 28
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=91.36 E-value=0.1 Score=52.15 Aligned_cols=76 Identities=25% Similarity=0.562 Sum_probs=51.0
Q ss_pred ccccccccccc--CCCCceeecccCCcccccccCCcCCCC-CCCCccCcccccCCc------ccccC--cceeeceeccc
Q 025663 59 DVGCEQCGSGE--RAEELLLCDKCDKGFHMKCLRPIVVRV-PIGTWLCPKCSGQRR------VRSFS--QRKIIDFFKIK 127 (249)
Q Consensus 59 ~~~C~vC~~~~--~~~~~l~CD~C~~~fH~~Cl~P~l~~~-p~g~W~Cp~C~~~~~------~~~~~--~~~~~~~~~~~ 127 (249)
...|.+|+..+ ..+.|+.|..|..-||.+|+...+... -.+-|-|+.|+.... +..|. ..-+..|.-+|
T Consensus 18 ~~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~~~gD~~kf~~Ck~cDvsyh~yc 97 (694)
T KOG4443|consen 18 CLMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACGTTGDPKKFLLCKRCDVSYHCYC 97 (694)
T ss_pred hhhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeeeeccccCCcccccccccccccccccc
Confidence 46688888754 567899999999999999999766543 234599999986422 33343 34455555555
Q ss_pred CCCcccc
Q 025663 128 KPNLTEE 134 (249)
Q Consensus 128 k~~~~~~ 134 (249)
.......
T Consensus 98 ~~P~~~~ 104 (694)
T KOG4443|consen 98 QKPPNDK 104 (694)
T ss_pred cCCcccc
Confidence 5444433
No 29
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=90.96 E-value=0.022 Score=41.08 Aligned_cols=51 Identities=27% Similarity=0.582 Sum_probs=21.8
Q ss_pred cccccccccccC-CC--Cceeec--ccCCcccccccCCcCCCCCCC-------CccCcccccC
Q 025663 59 DVGCEQCGSGER-AE--ELLLCD--KCDKGFHMKCLRPIVVRVPIG-------TWLCPKCSGQ 109 (249)
Q Consensus 59 ~~~C~vC~~~~~-~~--~~l~CD--~C~~~fH~~Cl~P~l~~~p~g-------~W~Cp~C~~~ 109 (249)
+..|.||..... .+ ..+.|+ .|...||..||--.+...+.. .+-||.|...
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~ 64 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSP 64 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCe
Confidence 356999998643 33 457998 899999999998554332221 3679999864
No 30
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=89.78 E-value=0.23 Score=50.51 Aligned_cols=54 Identities=19% Similarity=0.307 Sum_probs=42.9
Q ss_pred ccCCcccccccCCcCCCCCCCCccCcccccCCc----ccccCcceeeceecccCCCcc
Q 025663 79 KCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQRR----VRSFSQRKIIDFFKIKKPNLT 132 (249)
Q Consensus 79 ~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~~~----~~~~~~~~~~~~~~~~k~~~~ 132 (249)
.|.+.||..|+.|.+...|+++|.|+.|..... .........++++++|.++++
T Consensus 1 ~~~r~~~~~~~~p~~~~~~~~~~k~~~~e~~~~~~~~~~~~~~~~~~e~c~ic~~~g~ 58 (696)
T KOG0383|consen 1 TCPRAYHRVCLDPKLKEEPEMDPKCPGCESSSAQVEAKDDDWDDAEQEACRICADGGE 58 (696)
T ss_pred CCCcccCcCCCCcccccCCcCCccCcchhhcccccccccCCcchhhhhhhhhhcCCCc
Confidence 489999999999999999999999999975411 111235778999999999854
No 31
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=89.34 E-value=0.28 Score=46.01 Aligned_cols=48 Identities=21% Similarity=0.549 Sum_probs=38.4
Q ss_pred cccccccccCCC-CceeecccCCcccccc--cCCcCCCCCC-CCccCcccccC
Q 025663 61 GCEQCGSGERAE-ELLLCDKCDKGFHMKC--LRPIVVRVPI-GTWLCPKCSGQ 109 (249)
Q Consensus 61 ~C~vC~~~~~~~-~~l~CD~C~~~fH~~C--l~P~l~~~p~-g~W~Cp~C~~~ 109 (249)
+| .|....++. .|+.||.|..|||..| ++.+....|. ..|+|..|...
T Consensus 62 ~~-~~~~~~~p~~~~~~cd~C~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~ 113 (345)
T KOG1632|consen 62 YC-KCYKPCDPDDLMEQCDLCEDWYHGECWEVGTAEKEAPKEDPKVCDECKEA 113 (345)
T ss_pred hh-hcccccCchhhhhccccccccccccccccCchhhcCCccccccccccchh
Confidence 44 666666554 8999999999999999 9977766554 47999999865
No 32
>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=88.70 E-value=0.035 Score=35.89 Aligned_cols=43 Identities=26% Similarity=0.532 Sum_probs=29.6
Q ss_pred cccccccccCCCCceeecccCCcccccccCCcCCCCCCCCccCcccc
Q 025663 61 GCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCS 107 (249)
Q Consensus 61 ~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~ 107 (249)
.|.+|...-..++.+.--.|+-.||..|+...+... ..||.|+
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~----~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN----NSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS----SB-TTTH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC----CcCCccC
Confidence 588999876444444333499999999999766542 3788884
No 33
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=88.10 E-value=0.32 Score=48.36 Aligned_cols=48 Identities=31% Similarity=0.771 Sum_probs=40.4
Q ss_pred cccccccccccCCCCceeecccCCcccccccCCcCCC-CCCCCccCcccccC
Q 025663 59 DVGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVR-VPIGTWLCPKCSGQ 109 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~-~p~g~W~Cp~C~~~ 109 (249)
...|.+|.++ +.+++|+.|+..||+.|.++.+.. .+.+.|.|..|...
T Consensus 47 ~ts~~~~~~~---gn~~~~~~~~~s~h~~~~~~~~sp~~~~~~~~~~~~~~~ 95 (613)
T KOG4299|consen 47 ATSCGICKSG---GNLLCCDHCPASFHLECDKPPLSPDLKGSEINCSRCPKG 95 (613)
T ss_pred hhhcchhhhc---CCccccccCccccchhccCcccCcccccccccccCCCcc
Confidence 4679999998 899999999999999999998874 33347999999763
No 34
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=86.55 E-value=0.27 Score=36.94 Aligned_cols=46 Identities=26% Similarity=0.595 Sum_probs=29.8
Q ss_pred ccccccccCCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 62 CEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 62 C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
|..|.-+++.-.++.+ .|.-.||+.|+.-.+.... .+=.||-|+..
T Consensus 35 Cp~Ck~Pgd~Cplv~g-~C~H~FH~hCI~kWl~~~~-~~~~CPmCR~~ 80 (85)
T PF12861_consen 35 CPDCKFPGDDCPLVWG-KCSHNFHMHCILKWLSTQS-SKGQCPMCRQP 80 (85)
T ss_pred CCCccCCCCCCceeec-cCccHHHHHHHHHHHcccc-CCCCCCCcCCe
Confidence 3334444333344443 4999999999998877642 23489999864
No 35
>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=84.46 E-value=0.31 Score=29.04 Aligned_cols=29 Identities=28% Similarity=0.753 Sum_probs=12.5
Q ss_pred cccccccccCCCCceeecccCCccccccc
Q 025663 61 GCEQCGSGERAEELLLCDKCDKGFHMKCL 89 (249)
Q Consensus 61 ~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl 89 (249)
.|.+|+.....+..-.|..|+-..|..|.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhcC
Confidence 58899998655466799999999999884
No 36
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=83.76 E-value=0.79 Score=39.62 Aligned_cols=41 Identities=37% Similarity=0.876 Sum_probs=32.1
Q ss_pred ccccccccccc-----CCCCceeecccCCcccccccCCcCCCCCCCCccCccccc
Q 025663 59 DVGCEQCGSGE-----RAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSG 108 (249)
Q Consensus 59 ~~~C~vC~~~~-----~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~ 108 (249)
..+|++|...+ ..+..+.|..|...||..|... =.||.|..
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~---------~~CpkC~R 197 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK---------KSCPKCAR 197 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC---------CCCCCcHh
Confidence 46788998754 3357789999999999999882 13999975
No 37
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=80.50 E-value=0.8 Score=35.22 Aligned_cols=30 Identities=30% Similarity=0.882 Sum_probs=26.5
Q ss_pred cccccccccccCCCCceeecc--cCCcccccccC
Q 025663 59 DVGCEQCGSGERAEELLLCDK--CDKGFHMKCLR 90 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l~CD~--C~~~fH~~Cl~ 90 (249)
...|.+|+.. .|..+.|.. |..+||..|..
T Consensus 55 ~~~C~iC~~~--~G~~i~C~~~~C~~~fH~~CA~ 86 (110)
T PF13832_consen 55 KLKCSICGKS--GGACIKCSHPGCSTAFHPTCAR 86 (110)
T ss_pred CCcCcCCCCC--CceeEEcCCCCCCcCCCHHHHH
Confidence 5789999996 488999987 99999999976
No 38
>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=78.89 E-value=1.3 Score=42.73 Aligned_cols=51 Identities=20% Similarity=0.381 Sum_probs=35.4
Q ss_pred ccccccccccc---CCCCceeecccCCcccccccCCc--------CCC---CCCCCccCcccccC
Q 025663 59 DVGCEQCGSGE---RAEELLLCDKCDKGFHMKCLRPI--------VVR---VPIGTWLCPKCSGQ 109 (249)
Q Consensus 59 ~~~C~vC~~~~---~~~~~l~CD~C~~~fH~~Cl~P~--------l~~---~p~g~W~Cp~C~~~ 109 (249)
...|.+|.+-+ ++--.|.||.|.-|-|..|.--. ... ..++.++|..|-..
T Consensus 128 ~C~C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~ 192 (446)
T PF07227_consen 128 RCMCCICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKT 192 (446)
T ss_pred cCCccccCCcccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCCh
Confidence 34577787754 44578899999999999996521 111 12347999999765
No 39
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=77.15 E-value=1.4 Score=42.87 Aligned_cols=49 Identities=22% Similarity=0.605 Sum_probs=39.8
Q ss_pred cccccccccccC-CCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 59 DVGCEQCGSGER-AEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 59 ~~~C~vC~~~~~-~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
...| +|+..++ .+.|+.|+.|..|-|..|++..-...| ..+.|..|...
T Consensus 86 ~~~c-~c~~~~~~~g~~i~c~~c~~Wqh~~C~g~~~~~~p-~~y~c~~c~~~ 135 (508)
T KOG1844|consen 86 ISRC-DCGLEDDMEGLMIQCDWCGRWQHKICCGSFKSTKP-DKYVCEICTPR 135 (508)
T ss_pred cccc-ccccccCCCceeeCCcccCcccCceeeeecCCCCc-hhceeeeeccc
Confidence 4556 8888888 899999999999999999996544443 46889999864
No 40
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=76.75 E-value=0.98 Score=46.62 Aligned_cols=51 Identities=24% Similarity=0.672 Sum_probs=38.9
Q ss_pred cccccccccccc-CCCCceeecccCCcccccccCCcCCCCC-C--CCccCccccc
Q 025663 58 GDVGCEQCGSGE-RAEELLLCDKCDKGFHMKCLRPIVVRVP-I--GTWLCPKCSG 108 (249)
Q Consensus 58 ~~~~C~vC~~~~-~~~~~l~CD~C~~~fH~~Cl~P~l~~~p-~--g~W~Cp~C~~ 108 (249)
+-..|.||.... ....++.|..|...||+.|..-+-.... . ..|-||.|..
T Consensus 190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs 244 (950)
T KOG1952|consen 190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS 244 (950)
T ss_pred CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence 356799999865 4478899999999999999886543311 1 2599999984
No 41
>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=76.52 E-value=0.79 Score=33.10 Aligned_cols=45 Identities=24% Similarity=0.574 Sum_probs=28.5
Q ss_pred cccccccccccC----------CCCceeecccCCcccccccCCcCCCCCCCCccCcccc
Q 025663 59 DVGCEQCGSGER----------AEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCS 107 (249)
Q Consensus 59 ~~~C~vC~~~~~----------~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~ 107 (249)
++.|.+|...-. .+-.+.=..|+-.||..|+...+... ..||.|+
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~----~~CP~CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN----NTCPLCR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS----SB-TTSS
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC----CcCCCCC
Confidence 344999988541 12233334699999999998766433 3799885
No 42
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=75.89 E-value=0.42 Score=50.59 Aligned_cols=50 Identities=20% Similarity=0.303 Sum_probs=40.8
Q ss_pred cccccccccccccCCCCceeecc-cCCcccc-cccC--CcCCCCCCCCccCcccccC
Q 025663 57 YGDVGCEQCGSGERAEELLLCDK-CDKGFHM-KCLR--PIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 57 ~~~~~C~vC~~~~~~~~~l~CD~-C~~~fH~-~Cl~--P~l~~~p~g~W~Cp~C~~~ 109 (249)
.....|.+|+.. +.+++|+. |+..||+ .|++ -.-..++++-|+|+.|...
T Consensus 426 fi~rrl~Ie~~d---et~l~yysT~pqly~ll~cLd~~~~e~~L~d~i~~~~ee~~r 479 (1414)
T KOG1473|consen 426 FISRRLRIEGMD---ETLLWYYSTCPQLYHLLRCLDRTYVEMYLCDGIWERREEIIR 479 (1414)
T ss_pred ceeeeeEEecCC---CcEEEEecCcHHHHHHHHHhchHHHHHhhccchhhhHHHHHH
Confidence 335679999976 88899987 9999999 9999 3334588899999999864
No 43
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=75.53 E-value=3.9 Score=40.38 Aligned_cols=53 Identities=21% Similarity=0.214 Sum_probs=40.9
Q ss_pred cccccccccccccccccCCCCceeecccCCcccccccCCcCCCCCC--CCccCcccccC
Q 025663 53 ERGDYGDVGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPI--GTWLCPKCSGQ 109 (249)
Q Consensus 53 ~~~~~~~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~--g~W~Cp~C~~~ 109 (249)
......+.+|.-|.-. +..+.|+.|-+.||..|..|--. .+. ..|.|+.|...
T Consensus 54 ~~~~N~d~~cfechlp---g~vl~c~vc~Rs~h~~c~sp~~q-~r~~s~p~~~p~p~s~ 108 (588)
T KOG3612|consen 54 LPSSNIDPFCFECHLP---GAVLKCIVCHRSFHENCQSPDPQ-KRNYSVPSDKPQPYSF 108 (588)
T ss_pred ccccCCCcccccccCC---cceeeeehhhccccccccCcchh-hccccccccCCccccc
Confidence 3344557899999988 99999999999999999997532 222 35999988753
No 44
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=73.56 E-value=1.7 Score=32.07 Aligned_cols=30 Identities=27% Similarity=0.800 Sum_probs=25.7
Q ss_pred cccccccccccCCCCceeec--ccCCcccccccC
Q 025663 59 DVGCEQCGSGERAEELLLCD--KCDKGFHMKCLR 90 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l~CD--~C~~~fH~~Cl~ 90 (249)
...|.+|+.. .|..|.|. .|...||..|..
T Consensus 36 ~~~C~~C~~~--~Ga~i~C~~~~C~~~fH~~CA~ 67 (90)
T PF13771_consen 36 KLKCSICKKK--GGACIGCSHPGCSRSFHVPCAR 67 (90)
T ss_pred CCCCcCCCCC--CCeEEEEeCCCCCcEEChHHHc
Confidence 4689999976 37899997 599999999987
No 45
>COG1773 Rubredoxin [Energy production and conversion]
Probab=73.54 E-value=2.3 Score=29.33 Aligned_cols=21 Identities=24% Similarity=0.669 Sum_probs=13.7
Q ss_pred ccCCcCCCCCCCCccCcccccC
Q 025663 88 CLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 88 Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
|-+.+...+|. +|.||.|-..
T Consensus 25 ~pgT~fedlPd-~w~CP~Cg~~ 45 (55)
T COG1773 25 APGTPFEDLPD-DWVCPECGVG 45 (55)
T ss_pred CCCCchhhCCC-ccCCCCCCCC
Confidence 33333455665 7999999863
No 46
>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=69.42 E-value=2.2 Score=28.52 Aligned_cols=32 Identities=28% Similarity=0.597 Sum_probs=16.7
Q ss_pred ceeecccCCccccc-ccCCcCCCCCCCCccCccc
Q 025663 74 LLLCDKCDKGFHMK-CLRPIVVRVPIGTWLCPKC 106 (249)
Q Consensus 74 ~l~CD~C~~~fH~~-Cl~P~l~~~p~g~W~Cp~C 106 (249)
-|.||.|.+|-.+. .+......+|. .|+|..-
T Consensus 3 WVQCd~C~KWR~lp~~~~~~~~~~~d-~W~C~~n 35 (50)
T PF07496_consen 3 WVQCDSCLKWRRLPEEVDPIREELPD-PWYCSMN 35 (50)
T ss_dssp EEE-TTT--EEEE-CCHHCTSCCSST-T--GGGS
T ss_pred EEECCCCCceeeCChhhCcccccCCC-eEEcCCC
Confidence 58999999988875 22222244666 8999874
No 47
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.90 E-value=1.4 Score=40.05 Aligned_cols=52 Identities=23% Similarity=0.496 Sum_probs=33.3
Q ss_pred ccccccccccccccCCCC----ce---eecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 56 DYGDVGCEQCGSGERAEE----LL---LCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 56 ~~~~~~C~vC~~~~~~~~----~l---~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
..++.+|.+|++.-+.+. +| .==.|+-.||-+|....- +-...-.||.|.++
T Consensus 221 hl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWc--ivGKkqtCPYCKek 279 (328)
T KOG1734|consen 221 HLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWC--IVGKKQTCPYCKEK 279 (328)
T ss_pred CCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhhe--eecCCCCCchHHHH
Confidence 355789999998642211 11 112699999999987431 11124589999875
No 48
>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=68.52 E-value=1.4 Score=27.05 Aligned_cols=42 Identities=24% Similarity=0.512 Sum_probs=28.9
Q ss_pred ccccccccCCCCceeecccCCcccccccCCcCCCCCCCCccCccccc
Q 025663 62 CEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSG 108 (249)
Q Consensus 62 C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~ 108 (249)
|.+|.... ...+.-..|.-.||..|+...+.. +...||.|..
T Consensus 2 C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~---~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEF--REPVVLLPCGHVFCRSCIDKWLKS---GKNTCPLCRT 43 (45)
T ss_pred CCcCchhh--hCceEecCCCChhcHHHHHHHHHh---CcCCCCCCCC
Confidence 67777653 344445568889999999855443 4567998864
No 49
>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=66.31 E-value=4.6 Score=26.70 Aligned_cols=32 Identities=28% Similarity=0.521 Sum_probs=25.7
Q ss_pred ccccccccccc--CCCCceeecccCCcccccccC
Q 025663 59 DVGCEQCGSGE--RAEELLLCDKCDKGFHMKCLR 90 (249)
Q Consensus 59 ~~~C~vC~~~~--~~~~~l~CD~C~~~fH~~Cl~ 90 (249)
...|.+|+..- ...+-+.|..|....|..|+.
T Consensus 11 ~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~ 44 (53)
T PF00130_consen 11 PTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLS 44 (53)
T ss_dssp TEB-TTSSSBECSSSSCEEEETTTT-EEETTGGC
T ss_pred CCCCcccCcccCCCCCCeEEECCCCChHhhhhhh
Confidence 46899999875 457888999999999999987
No 50
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=65.88 E-value=0.99 Score=42.33 Aligned_cols=54 Identities=28% Similarity=0.735 Sum_probs=38.6
Q ss_pred ccccccccccccccCC-CCceeecccCCcccccccCCcCCCCCCC-C----ccCcccccC
Q 025663 56 DYGDVGCEQCGSGERA-EELLLCDKCDKGFHMKCLRPIVVRVPIG-T----WLCPKCSGQ 109 (249)
Q Consensus 56 ~~~~~~C~vC~~~~~~-~~~l~CD~C~~~fH~~Cl~P~l~~~p~g-~----W~Cp~C~~~ 109 (249)
+.+..+|..|+..+.. ..+++|+.|..|||..|+.+........ . .+|+.|...
T Consensus 236 ~~~~~~~~~cg~~~~~~~~~~~~~~~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~~ 295 (345)
T KOG1632|consen 236 DYSKLICDPCGLSDANKKFEICCDLCESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTVL 295 (345)
T ss_pred ccccccccccCcchHHHHHHHHHHHHHHHhcccccccccchhhhhhhhccceecCceeec
Confidence 3445788889986533 5778999999999999999543321111 3 899999874
No 51
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=63.95 E-value=2.8 Score=38.07 Aligned_cols=76 Identities=20% Similarity=0.347 Sum_probs=49.9
Q ss_pred cccccccccccccc-------CCCCceeecccCCcccccccCCcC---CCCCCCCccCcccccCCcccccCcceeeceec
Q 025663 56 DYGDVGCEQCGSGE-------RAEELLLCDKCDKGFHMKCLRPIV---VRVPIGTWLCPKCSGQRRVRSFSQRKIIDFFK 125 (249)
Q Consensus 56 ~~~~~~C~vC~~~~-------~~~~~l~CD~C~~~fH~~Cl~P~l---~~~p~g~W~Cp~C~~~~~~~~~~~~~~~~~~~ 125 (249)
.....+|..|-... -+.++|.|..|++.=|.+||.-.. ..+-...|.|-.|..-..--...+.-..-|+.
T Consensus 221 a~Pn~YCDFclgdsr~nkkt~~peelvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~csicgtsenddqllfcd 300 (336)
T KOG1244|consen 221 AQPNPYCDFCLGDSRENKKTGMPEELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTSENDDQLLFCD 300 (336)
T ss_pred ccCCcccceeccccccccccCCchhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCcCCCceeEeec
Confidence 34467899997643 357999999999999999998321 13445689999997643322222344455565
Q ss_pred ccCCCc
Q 025663 126 IKKPNL 131 (249)
Q Consensus 126 ~~k~~~ 131 (249)
-|..+-
T Consensus 301 dcdrgy 306 (336)
T KOG1244|consen 301 DCDRGY 306 (336)
T ss_pred ccCCce
Confidence 555543
No 52
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=63.05 E-value=4 Score=37.72 Aligned_cols=31 Identities=29% Similarity=0.733 Sum_probs=24.3
Q ss_pred cccccccccccCC------CCceeecccCCccc-ccccC
Q 025663 59 DVGCEQCGSGERA------EELLLCDKCDKGFH-MKCLR 90 (249)
Q Consensus 59 ~~~C~vC~~~~~~------~~~l~CD~C~~~fH-~~Cl~ 90 (249)
..+| .|...+++ +.|+.|-.|+-||| ..|+.
T Consensus 128 G~~C-~Cd~~Ypdp~~~~e~~m~QC~iCEDWFHce~c~~ 165 (345)
T KOG2752|consen 128 GLFC-KCDTPYPDPVRTEEGEMLQCVICEDWFHCEGCMQ 165 (345)
T ss_pred ceeE-EecCCCCCccccccceeeeEEeccchhcccccCc
Confidence 3556 78776533 79999999999999 77776
No 53
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=61.91 E-value=2.1 Score=42.69 Aligned_cols=45 Identities=31% Similarity=0.671 Sum_probs=31.3
Q ss_pred ccccccccccccc-----CCCCceeecccCCcccccccCCcCCCCCCCCccCccccc
Q 025663 57 YGDVGCEQCGSGE-----RAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSG 108 (249)
Q Consensus 57 ~~~~~C~vC~~~~-----~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~ 108 (249)
....+|.+|...+ ......-|+.|..+||..|+.- ..-.||.|..
T Consensus 509 ~~gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r-------~s~~CPrC~R 558 (580)
T KOG1829|consen 509 GKGFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRR-------KSPCCPRCER 558 (580)
T ss_pred cCeeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhc-------cCCCCCchHH
Confidence 3356788885543 1345567999999999999882 1223999975
No 54
>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=60.79 E-value=3.7 Score=31.93 Aligned_cols=49 Identities=31% Similarity=0.672 Sum_probs=32.7
Q ss_pred cccccccccccCCCCceee------ccc---CCcccccccCCcCC-----CCCCCCccCccccc
Q 025663 59 DVGCEQCGSGERAEELLLC------DKC---DKGFHMKCLRPIVV-----RVPIGTWLCPKCSG 108 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l~C------D~C---~~~fH~~Cl~P~l~-----~~p~g~W~Cp~C~~ 108 (249)
...|..|.+... +..+.| ..| ...|=..||.-.-. .+..++|.||.|+.
T Consensus 7 g~~CHqCrqKt~-~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 7 GKTCHQCRQKTL-DFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred CCCchhhcCCCC-CCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 567999998643 444567 566 66777777653222 23456899999985
No 55
>PHA02929 N1R/p28-like protein; Provisional
Probab=60.47 E-value=4 Score=36.39 Aligned_cols=48 Identities=21% Similarity=0.482 Sum_probs=33.1
Q ss_pred ccccccccccccCCCC-----ceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 58 GDVGCEQCGSGERAEE-----LLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 58 ~~~~C~vC~~~~~~~~-----~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
.+..|.+|...-...+ +..=..|.-.||..|+...+...+ .||.|+..
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~----tCPlCR~~ 225 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKN----TCPVCRTP 225 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCC----CCCCCCCE
Confidence 4578999998632211 123347888999999997765432 69999864
No 56
>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=59.72 E-value=6.1 Score=26.30 Aligned_cols=14 Identities=36% Similarity=1.210 Sum_probs=8.1
Q ss_pred CCCCCCccCcccccC
Q 025663 95 RVPIGTWLCPKCSGQ 109 (249)
Q Consensus 95 ~~p~g~W~Cp~C~~~ 109 (249)
.+|+ +|.||.|...
T Consensus 30 ~Lp~-~w~CP~C~a~ 43 (47)
T PF00301_consen 30 DLPD-DWVCPVCGAP 43 (47)
T ss_dssp GS-T-T-B-TTTSSB
T ss_pred HCCC-CCcCcCCCCc
Confidence 3544 7999999865
No 57
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=57.81 E-value=1.8 Score=38.99 Aligned_cols=56 Identities=23% Similarity=0.430 Sum_probs=40.3
Q ss_pred ccccccccccccccccCCCCc---e---eecccCCcccccccCCcCCCCCCC----CccCcccccC
Q 025663 54 RGDYGDVGCEQCGSGERAEEL---L---LCDKCDKGFHMKCLRPIVVRVPIG----TWLCPKCSGQ 109 (249)
Q Consensus 54 ~~~~~~~~C~vC~~~~~~~~~---l---~CD~C~~~fH~~Cl~P~l~~~p~g----~W~Cp~C~~~ 109 (249)
++.+.+..|.+|..++.++.. + .|-+-.+|.|+.|+--.+++.--| .=.|+.|..+
T Consensus 15 ~~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTE 80 (293)
T KOG3053|consen 15 DNQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTE 80 (293)
T ss_pred CccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcch
Confidence 444557899999998754432 2 567888999999998776653222 4689999865
No 58
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=55.87 E-value=2.6 Score=24.81 Aligned_cols=39 Identities=26% Similarity=0.562 Sum_probs=23.2
Q ss_pred ccccccccCCCCceeecccCCcccccccCCcCCCCCCCCccCccc
Q 025663 62 CEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKC 106 (249)
Q Consensus 62 C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C 106 (249)
|.+|... .....--.|.-.||..|+...+. .+...||.|
T Consensus 1 C~iC~~~---~~~~~~~~C~H~~c~~C~~~~~~---~~~~~CP~C 39 (39)
T smart00184 1 CPICLEE---LKDPVVLPCGHTFCRSCIRKWLK---SGNNTCPIC 39 (39)
T ss_pred CCcCccC---CCCcEEecCCChHHHHHHHHHHH---hCcCCCCCC
Confidence 5667665 23333346888899999875443 233446665
No 59
>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=55.39 E-value=7.7 Score=29.04 Aligned_cols=31 Identities=19% Similarity=0.568 Sum_probs=21.7
Q ss_pred cccccccccccCCCCceeecccCCcccccccC
Q 025663 59 DVGCEQCGSGERAEELLLCDKCDKGFHMKCLR 90 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~ 90 (249)
+..|.+|++.-..+..+. --|+..||..|..
T Consensus 78 ~~~C~vC~k~l~~~~f~~-~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVV-FPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEEE-eCCCeEEeccccc
Confidence 567999999764443332 3456899999974
No 60
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=55.34 E-value=4.2 Score=34.05 Aligned_cols=51 Identities=22% Similarity=0.345 Sum_probs=35.3
Q ss_pred cccccccccccccCCCCce-eecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 57 YGDVGCEQCGSGERAEELL-LCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 57 ~~~~~C~vC~~~~~~~~~l-~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
..+..|.+|..+++...-. .|.+--++.|..|+.-++.. .+...|+.|..+
T Consensus 6 ~~~~~CRIC~~~~~~~~~PC~CkGs~k~VH~sCL~rWi~~--s~~~~CeiC~~~ 57 (162)
T PHA02825 6 LMDKCCWICKDEYDVVTNYCNCKNENKIVHKECLEEWINT--SKNKSCKICNGP 57 (162)
T ss_pred CCCCeeEecCCCCCCccCCcccCCCchHHHHHHHHHHHhc--CCCCcccccCCe
Confidence 4467899999875432221 23445568999999977664 367889999865
No 61
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=54.73 E-value=9.7 Score=37.10 Aligned_cols=52 Identities=17% Similarity=0.362 Sum_probs=39.6
Q ss_pred cccccccccccccc--CCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 56 DYGDVGCEQCGSGE--RAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 56 ~~~~~~C~vC~~~~--~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
...+..|.+|.... .+.+++.|+.|..+||..|..|..... +.|.+..|+..
T Consensus 80 ~~~e~~~nv~~s~~~~p~~e~~~~~r~~~~~~q~~~i~~~~~~--~~~~~~~c~~~ 133 (464)
T KOG4323|consen 80 PSSELNPNVLTSETVLPENEKVICGRCKSGYHQGCNIPRFPSL--DIGESTECVFP 133 (464)
T ss_pred CccccCCcccccccccCchhhhhhhhhccCcccccCccCcCcC--Ccccccccccc
Confidence 34467788988754 346788999999999999999764433 46889988764
No 62
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=53.07 E-value=7.8 Score=35.95 Aligned_cols=35 Identities=29% Similarity=0.638 Sum_probs=20.1
Q ss_pred CCce-eecccCCc----------ccccccCCcCCCCCCCCccCcccccC
Q 025663 72 EELL-LCDKCDKG----------FHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 72 ~~~l-~CD~C~~~----------fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
+.+| +||.|+.- -|.+||.=... +.+-+|+.|...
T Consensus 87 ~p~VHfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~---~~dK~Cp~C~d~ 132 (389)
T KOG2932|consen 87 GPRVHFCDRCDFPIAIYGRMIPCKHVFCLECARS---DSDKICPLCDDR 132 (389)
T ss_pred CcceEeecccCCcceeeecccccchhhhhhhhhc---CccccCcCcccH
Confidence 4433 67777642 27777763221 224589999753
No 63
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=52.79 E-value=35 Score=28.92 Aligned_cols=22 Identities=27% Similarity=0.723 Sum_probs=18.2
Q ss_pred CCceeecccCCcccccccCCcC
Q 025663 72 EELLLCDKCDKGFHMKCLRPIV 93 (249)
Q Consensus 72 ~~~l~CD~C~~~fH~~Cl~P~l 93 (249)
+.|.-|..|.++||+.-|-++-
T Consensus 122 nVLFRC~~C~RawH~~HLP~~~ 143 (175)
T PF15446_consen 122 NVLFRCTSCHRAWHFEHLPPPS 143 (175)
T ss_pred heEEecCCccceeehhhCCCCc
Confidence 4566899999999999988753
No 64
>PHA02862 5L protein; Provisional
Probab=51.81 E-value=4.4 Score=33.48 Aligned_cols=48 Identities=19% Similarity=0.260 Sum_probs=34.7
Q ss_pred cccccccccccCCCCce--eecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 59 DVGCEQCGSGERAEELL--LCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l--~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
++.|.+|...++.+ .- .|-+-.+|.|..|+.-.+.. .+.=.|+.|..+
T Consensus 2 ~diCWIC~~~~~e~-~~PC~C~GS~K~VHq~CL~~WIn~--S~k~~CeLCkte 51 (156)
T PHA02862 2 SDICWICNDVCDER-NNFCGCNEEYKVVHIKCMQLWINY--SKKKECNLCKTK 51 (156)
T ss_pred CCEEEEecCcCCCC-cccccccCcchhHHHHHHHHHHhc--CCCcCccCCCCe
Confidence 35799999986433 23 45567889999999977743 345689999865
No 65
>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=50.70 E-value=12 Score=22.14 Aligned_cols=29 Identities=21% Similarity=0.559 Sum_probs=21.5
Q ss_pred cccccccccCCCCceeecccCCccccccc
Q 025663 61 GCEQCGSGERAEELLLCDKCDKGFHMKCL 89 (249)
Q Consensus 61 ~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl 89 (249)
.|.+|++..++...=.|+.|.-..|..|.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCCeEcCccC
Confidence 58899876433326689999999998884
No 66
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=50.19 E-value=8.4 Score=24.70 Aligned_cols=32 Identities=25% Similarity=0.511 Sum_probs=26.0
Q ss_pred cccccccccccCC--CCceeecccCCcccccccC
Q 025663 59 DVGCEQCGSGERA--EELLLCDKCDKGFHMKCLR 90 (249)
Q Consensus 59 ~~~C~vC~~~~~~--~~~l~CD~C~~~fH~~Cl~ 90 (249)
...|.+|+..-.. ..-+.|+.|....|..|..
T Consensus 11 ~~~C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~ 44 (50)
T cd00029 11 PTFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCAD 44 (50)
T ss_pred CCChhhcchhhhccccceeEcCCCCCchhhhhhc
Confidence 4579999886543 4777899999999999976
No 67
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=48.96 E-value=7.6 Score=39.58 Aligned_cols=79 Identities=15% Similarity=0.405 Sum_probs=46.0
Q ss_pred cccccccccccCC-----CCceeec--ccCCcccccccCCc-CCCCCCC-----CccCcccccC-CcccccC-cceeece
Q 025663 59 DVGCEQCGSGERA-----EELLLCD--KCDKGFHMKCLRPI-VVRVPIG-----TWLCPKCSGQ-RRVRSFS-QRKIIDF 123 (249)
Q Consensus 59 ~~~C~vC~~~~~~-----~~~l~CD--~C~~~fH~~Cl~P~-l~~~p~g-----~W~Cp~C~~~-~~~~~~~-~~~~~~~ 123 (249)
...|.||...+++ |.-+.|- .|.+.||..|..-. |-...+| --||-.|... .+.+.-+ ...|-.|
T Consensus 117 nKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~HfsKlkk~~~~k~ipsy 196 (900)
T KOG0956|consen 117 NKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKYHFSKLKKSPAIKVIPSY 196 (900)
T ss_pred cceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccccceechhHHHHHHHhhcCCCcccCCCC
Confidence 5789999987543 4566674 69999999998732 1111121 2589999753 1111111 2334466
Q ss_pred ecccCCCccccccC
Q 025663 124 FKIKKPNLTEEKCD 137 (249)
Q Consensus 124 ~~~~k~~~~~~~~~ 137 (249)
.+++.+.......+
T Consensus 197 ~~s~s~s~s~q~~s 210 (900)
T KOG0956|consen 197 KPSQSASPSVQQLS 210 (900)
T ss_pred ccccccCCchhhhh
Confidence 66666665555444
No 68
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=47.91 E-value=6.3 Score=34.04 Aligned_cols=49 Identities=22% Similarity=0.508 Sum_probs=32.2
Q ss_pred ccccccccccccCCCCceeecccCCcccccccCCcCCCC------------CCCCccCcccccC
Q 025663 58 GDVGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRV------------PIGTWLCPKCSGQ 109 (249)
Q Consensus 58 ~~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~------------p~g~W~Cp~C~~~ 109 (249)
++..|.+|...-. +.. .-.|.-.|++.|+..++..- ..+...||.|...
T Consensus 17 ~~~~CpICld~~~-dPV--vT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~ 77 (193)
T PLN03208 17 GDFDCNICLDQVR-DPV--VTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSD 77 (193)
T ss_pred CccCCccCCCcCC-CcE--EcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCc
Confidence 4578999998632 222 24688899999987543210 1235789999875
No 69
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=46.46 E-value=24 Score=32.71 Aligned_cols=40 Identities=25% Similarity=0.627 Sum_probs=29.5
Q ss_pred cccccccccccc----------CCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 58 GDVGCEQCGSGE----------RAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 58 ~~~~C~vC~~~~----------~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
...+|.+||..- .....+.|..|.-.||+.=+ .|+.|-..
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~------------~C~~Cg~~ 235 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRV------------KCSNCEQS 235 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCc------------cCCCCCCC
Confidence 568999999852 23477899999998886532 48889754
No 70
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=46.27 E-value=7.4 Score=24.69 Aligned_cols=32 Identities=25% Similarity=0.492 Sum_probs=25.6
Q ss_pred cccccccccccCCC-CceeecccCCcccccccC
Q 025663 59 DVGCEQCGSGERAE-ELLLCDKCDKGFHMKCLR 90 (249)
Q Consensus 59 ~~~C~vC~~~~~~~-~~l~CD~C~~~fH~~Cl~ 90 (249)
..+|.+|++.-... +.+.|..|....|..|..
T Consensus 11 ~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~ 43 (49)
T smart00109 11 PTKCCVCRKSIWGSFQGLRCSWCKVKCHKKCAE 43 (49)
T ss_pred CCCccccccccCcCCCCcCCCCCCchHHHHHHh
Confidence 46799999875432 478899999999999977
No 71
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=45.94 E-value=15 Score=35.79 Aligned_cols=31 Identities=26% Similarity=0.439 Sum_probs=21.9
Q ss_pred ccccccccccccccCCCCceeecccCCccccccc
Q 025663 56 DYGDVGCEQCGSGERAEELLLCDKCDKGFHMKCL 89 (249)
Q Consensus 56 ~~~~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl 89 (249)
..+...|.+|..+ +.+++|+.|...+|-.|.
T Consensus 86 ~~~~~~c~vc~~g---gs~v~~~s~~~~~~r~c~ 116 (463)
T KOG1081|consen 86 KIEPSECFVCFKG---GSLVTCKSRIQAPHRKCK 116 (463)
T ss_pred CCCcchhccccCC---CccceeccccccccccCc
Confidence 4456889999998 889999954444444443
No 72
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=44.71 E-value=14 Score=24.83 Aligned_cols=14 Identities=36% Similarity=1.191 Sum_probs=10.5
Q ss_pred CCCCCCccCcccccC
Q 025663 95 RVPIGTWLCPKCSGQ 109 (249)
Q Consensus 95 ~~p~g~W~Cp~C~~~ 109 (249)
.+|. +|.||.|...
T Consensus 30 ~Lp~-~w~CP~C~a~ 43 (50)
T cd00730 30 DLPD-DWVCPVCGAG 43 (50)
T ss_pred HCCC-CCCCCCCCCc
Confidence 3554 7999999865
No 73
>PF12773 DZR: Double zinc ribbon
Probab=43.66 E-value=23 Score=23.00 Aligned_cols=9 Identities=33% Similarity=1.173 Sum_probs=5.0
Q ss_pred CccCccccc
Q 025663 100 TWLCPKCSG 108 (249)
Q Consensus 100 ~W~Cp~C~~ 108 (249)
.++|+.|-.
T Consensus 29 ~~~C~~Cg~ 37 (50)
T PF12773_consen 29 KKICPNCGA 37 (50)
T ss_pred CCCCcCCcC
Confidence 456666654
No 74
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=43.43 E-value=22 Score=36.27 Aligned_cols=48 Identities=27% Similarity=0.673 Sum_probs=32.0
Q ss_pred ccccccccccCCCCceeecccCCcc-cccccCCcCCCCCCCCccCcccccC
Q 025663 60 VGCEQCGSGERAEELLLCDKCDKGF-HMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 60 ~~C~vC~~~~~~~~~l~CD~C~~~f-H~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
..|..|+.. .+....+|..|+... |..|-.-. ..+|.+.=||+.|-..
T Consensus 2 ~~Cp~Cg~~-n~~~akFC~~CG~~l~~~~Cp~CG-~~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 2 LICPQCQFE-NPNNNRFCQKCGTSLTHKPCPQCG-TEVPVDEAHCPNCGAE 50 (645)
T ss_pred CcCCCCCCc-CCCCCccccccCCCCCCCcCCCCC-CCCCcccccccccCCc
Confidence 368888876 445666888887753 35565432 3466777799999654
No 75
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=42.64 E-value=19 Score=21.75 Aligned_cols=11 Identities=36% Similarity=1.398 Sum_probs=8.8
Q ss_pred CCccCcccccC
Q 025663 99 GTWLCPKCSGQ 109 (249)
Q Consensus 99 g~W~Cp~C~~~ 109 (249)
..|.||.|-..
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 47999999754
No 76
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=42.34 E-value=2.4 Score=28.75 Aligned_cols=42 Identities=24% Similarity=0.571 Sum_probs=30.6
Q ss_pred cccccccccccCCCCceeecccCCcccccccCCcCCCCCCCCccCcccc
Q 025663 59 DVGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCS 107 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~ 107 (249)
...|..|.......++-.|..|++|---.|+. +.-+.|..|-
T Consensus 7 ry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~-------deYY~CksC~ 48 (57)
T PF14445_consen 7 RYSCDLCNSSHPISELRQCVLCGRWACNSCWQ-------DEYYTCKSCN 48 (57)
T ss_pred hHhHHhhcccCcHHHHHHHhhhchhhhhhhhh-------hhHhHHHhhh
Confidence 45788999887777888899998877777766 3335566664
No 77
>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=42.07 E-value=7.4 Score=25.22 Aligned_cols=41 Identities=24% Similarity=0.651 Sum_probs=19.2
Q ss_pred ccccccccCCCCceeec--ccCCcccccccCCcCCCCCCCCccCccc
Q 025663 62 CEQCGSGERAEELLLCD--KCDKGFHMKCLRPIVVRVPIGTWLCPKC 106 (249)
Q Consensus 62 C~vC~~~~~~~~~l~CD--~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C 106 (249)
|.+|.+-- -.-+.|. .|...+|..|+.--+..... . .||.|
T Consensus 1 C~~C~~iv--~~G~~C~~~~C~~r~H~~C~~~y~r~~~~-~-~CP~C 43 (43)
T PF08746_consen 1 CEACKEIV--TQGQRCSNRDCNVRLHDDCFKKYFRHRSN-P-KCPNC 43 (43)
T ss_dssp -TTT-SB---SSSEE-SS--S--EE-HHHHHHHTTT-SS---B-TTT
T ss_pred CcccchhH--eeeccCCCCccCchHHHHHHHHHHhcCCC-C-CCcCC
Confidence 45566532 3445787 69999999998854443332 1 68876
No 78
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation [].
Probab=41.95 E-value=13 Score=33.79 Aligned_cols=22 Identities=36% Similarity=0.788 Sum_probs=19.9
Q ss_pred cccccccccccCCCCceeeccc
Q 025663 59 DVGCEQCGSGERAEELLLCDKC 80 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l~CD~C 80 (249)
+.+|.||..+.+.+.+.+|..|
T Consensus 15 dniCsVCkl~Td~~tLsfChiC 36 (285)
T PF06937_consen 15 DNICSVCKLGTDTETLSFCHIC 36 (285)
T ss_pred Cceeeeeeecccccceeeccee
Confidence 5789999999888999999888
No 79
>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=41.65 E-value=6 Score=26.32 Aligned_cols=44 Identities=23% Similarity=0.450 Sum_probs=25.6
Q ss_pred cccccccccCCCC-ce-eec--ccCCcccccccCCcCCCCCCCCccCccc
Q 025663 61 GCEQCGSGERAEE-LL-LCD--KCDKGFHMKCLRPIVVRVPIGTWLCPKC 106 (249)
Q Consensus 61 ~C~vC~~~~~~~~-~l-~CD--~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C 106 (249)
+|.+|....++++ ++ -|. +--+++|..|+...+.... ...|+-|
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~--~~~C~iC 48 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESG--NKTCEIC 48 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcC--CCcCCCC
Confidence 4788887333333 33 232 2236899999997654432 2367766
No 80
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=41.55 E-value=9.8 Score=31.12 Aligned_cols=53 Identities=23% Similarity=0.487 Sum_probs=36.2
Q ss_pred ccccccccccccc-CCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 57 YGDVGCEQCGSGE-RAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 57 ~~~~~C~vC~~~~-~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
.++..|.+|.... .+|---.|..|..-|--.|-+-.....-+-.|.|..|...
T Consensus 63 ~ddatC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrsNKv~wvcnlc~k~ 116 (169)
T KOG3799|consen 63 GDDATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRSNKVMWVCNLCRKQ 116 (169)
T ss_pred CcCcchhhhhhcccccccCcccchhhhhHHHhcCCeeeeccCceEEeccCCcHH
Confidence 4568899999874 2344446888888887788773322222346999999875
No 81
>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=39.52 E-value=36 Score=31.44 Aligned_cols=41 Identities=24% Similarity=0.578 Sum_probs=29.8
Q ss_pred ccccccccccccc-----------CCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 57 YGDVGCEQCGSGE-----------RAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 57 ~~~~~C~vC~~~~-----------~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
++..+|.+||..- .....+.|..|.-.||+.=+ .|+.|-..
T Consensus 182 ~~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~------------~C~~Cg~~ 233 (305)
T TIGR01562 182 ESRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRV------------KCSHCEES 233 (305)
T ss_pred CCCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCc------------cCCCCCCC
Confidence 3456999999842 22368899999998886532 49999764
No 82
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=39.52 E-value=26 Score=31.58 Aligned_cols=27 Identities=30% Similarity=0.272 Sum_probs=24.1
Q ss_pred hhcHHHHHHHHHHHhcCCCCCeEEEec
Q 025663 221 KEDTETLEQCRAMCKRGECPPLVVRQM 247 (249)
Q Consensus 221 ~~d~~~~~~~~~~~~~g~~~~~~v~~~ 247 (249)
--|--.|+||++|.+.|+.|-|+|++|
T Consensus 82 i~dgRlfeQ~~rL~~~y~rpvliVegd 108 (254)
T COG1948 82 IIDGRLFEQAKRLKKSYERPVLIVEGD 108 (254)
T ss_pred HhcchHHHHHHHHHhcCCccEEEEEcc
Confidence 345578999999999999999999998
No 83
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=39.45 E-value=9.8 Score=34.78 Aligned_cols=50 Identities=16% Similarity=0.321 Sum_probs=37.1
Q ss_pred ccccccccccccccCCCCceeecccCCcccccccCCcCCCCCCCCccCcccccCCcc
Q 025663 56 DYGDVGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQRRV 112 (249)
Q Consensus 56 ~~~~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~~~~ 112 (249)
..+..-|.+|-.. -.-.-|--|+--|-++|+.-+..+.++ ||.|+....+
T Consensus 236 ~~a~~kC~LCLe~---~~~pSaTpCGHiFCWsCI~~w~~ek~e----CPlCR~~~~p 285 (293)
T KOG0317|consen 236 PEATRKCSLCLEN---RSNPSATPCGHIFCWSCILEWCSEKAE----CPLCREKFQP 285 (293)
T ss_pred CCCCCceEEEecC---CCCCCcCcCcchHHHHHHHHHHccccC----CCcccccCCC
Confidence 3456789999986 334457778888999999877666655 9999976433
No 84
>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=39.44 E-value=13 Score=33.73 Aligned_cols=42 Identities=24% Similarity=0.593 Sum_probs=20.0
Q ss_pred cccccccccccccc-------C---CCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 56 DYGDVGCEQCGSGE-------R---AEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 56 ~~~~~~C~vC~~~~-------~---~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
.+...+|.+||..- . +...+.|..|...||+.= ..||.|-..
T Consensus 169 ~w~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R------------~~Cp~Cg~~ 220 (290)
T PF04216_consen 169 GWQRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVR------------IKCPYCGNT 220 (290)
T ss_dssp -TT-SS-TTT---EEEEEEE------EEEEEETTT--EEE--T------------TS-TTT---
T ss_pred CccCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecC------------CCCcCCCCC
Confidence 44568999999842 1 237889999999888542 359999765
No 85
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.32 E-value=9.7 Score=33.82 Aligned_cols=50 Identities=26% Similarity=0.578 Sum_probs=32.3
Q ss_pred cccccccccccCCCCceeecccCCcccccccCCcCCCCCCC----CccCcccccC
Q 025663 59 DVGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIG----TWLCPKCSGQ 109 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g----~W~Cp~C~~~ 109 (249)
+.-|..|+..-..++.+- =.|.-.||+.|++-.....|.. .+.||.|...
T Consensus 50 ~pNC~LC~t~La~gdt~R-LvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~e 103 (299)
T KOG3970|consen 50 NPNCRLCNTPLASGDTTR-LVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQE 103 (299)
T ss_pred CCCCceeCCccccCccee-ehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCc
Confidence 456888887633333221 1478899999999554444432 4899999875
No 86
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=39.28 E-value=7.1 Score=36.64 Aligned_cols=49 Identities=18% Similarity=0.416 Sum_probs=25.8
Q ss_pred cccccccccccccCC--CCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 57 YGDVGCEQCGSGERA--EELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 57 ~~~~~C~vC~~~~~~--~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
+++++|..|...-+. ....-| -|+...-.+|+.-.-..+ .--||-|+..
T Consensus 12 deed~cplcie~mditdknf~pc-~cgy~ic~fc~~~irq~l---ngrcpacrr~ 62 (480)
T COG5175 12 DEEDYCPLCIEPMDITDKNFFPC-PCGYQICQFCYNNIRQNL---NGRCPACRRK 62 (480)
T ss_pred cccccCcccccccccccCCcccC-CcccHHHHHHHHHHHhhc---cCCChHhhhh
Confidence 445679999976322 122222 233333457776332222 2369999865
No 87
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.32 E-value=10 Score=34.31 Aligned_cols=51 Identities=24% Similarity=0.458 Sum_probs=36.1
Q ss_pred cccccccccccccCCCCceeecccCCcccccccCCcCCCCCCCCccCcccccCCcc
Q 025663 57 YGDVGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQRRV 112 (249)
Q Consensus 57 ~~~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~~~~ 112 (249)
..+.-|.+|... -+-..|-.|+-.|-+.|+...+... .-=+||.|+.+-.+
T Consensus 213 ~~d~kC~lC~e~---~~~ps~t~CgHlFC~~Cl~~~~t~~--k~~~CplCRak~~p 263 (271)
T COG5574 213 LADYKCFLCLEE---PEVPSCTPCGHLFCLSCLLISWTKK--KYEFCPLCRAKVYP 263 (271)
T ss_pred ccccceeeeecc---cCCcccccccchhhHHHHHHHHHhh--ccccCchhhhhccc
Confidence 346779999987 5677899999999999988522211 12379999976333
No 88
>PF14044 NETI: NETI protein
Probab=38.18 E-value=18 Score=25.10 Aligned_cols=21 Identities=38% Similarity=0.624 Sum_probs=16.3
Q ss_pred hhcHHHHHHH-HHHHhcCCCCC
Q 025663 221 KEDTETLEQC-RAMCKRGECPP 241 (249)
Q Consensus 221 ~~d~~~~~~~-~~~~~~g~~~~ 241 (249)
-++.||+..| .+|.++|++|-
T Consensus 4 V~enETI~~CL~RM~~eGY~Pv 25 (57)
T PF14044_consen 4 VEENETISDCLARMKKEGYMPV 25 (57)
T ss_pred ccCCCcHHHHHHHHHHcCCCce
Confidence 3577899888 46888999883
No 89
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=37.99 E-value=23 Score=22.11 Aligned_cols=28 Identities=29% Similarity=0.796 Sum_probs=18.8
Q ss_pred eeecccCCcccccccCCcCCCCCCCCccCccccc
Q 025663 75 LLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSG 108 (249)
Q Consensus 75 l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~ 108 (249)
..|..|...||..= ..|..+..|..|-.
T Consensus 2 r~C~~Cg~~Yh~~~------~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 2 RICPKCGRIYHIEF------NPPKVEGVCDNCGG 29 (36)
T ss_dssp EEETTTTEEEETTT------B--SSTTBCTTTTE
T ss_pred cCcCCCCCcccccc------CCCCCCCccCCCCC
Confidence 36888999999543 23455778988864
No 90
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=37.69 E-value=17 Score=35.67 Aligned_cols=8 Identities=38% Similarity=1.070 Sum_probs=5.1
Q ss_pred ccCccccc
Q 025663 101 WLCPKCSG 108 (249)
Q Consensus 101 W~Cp~C~~ 108 (249)
|.||.|..
T Consensus 53 f~CP~C~~ 60 (483)
T PF05502_consen 53 FDCPICFS 60 (483)
T ss_pred ccCCCCCC
Confidence 66777754
No 91
>PLN02189 cellulose synthase
Probab=35.49 E-value=25 Score=37.62 Aligned_cols=50 Identities=24% Similarity=0.580 Sum_probs=38.8
Q ss_pred cccccccccccc----cCCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 57 YGDVGCEQCGSG----ERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 57 ~~~~~C~vC~~~----~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
.+..+|.+|+.. .+....+.|..|.-..--.|+. -+..+|.=.||.|...
T Consensus 32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cye---yer~eg~q~CpqCkt~ 85 (1040)
T PLN02189 32 LDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYE---YERREGTQNCPQCKTR 85 (1040)
T ss_pred ccCccccccccccCcCCCCCEEEeeccCCCccccchhh---hhhhcCCccCcccCCc
Confidence 345699999985 3456778999998888888986 3455778899999864
No 92
>PLN02400 cellulose synthase
Probab=35.20 E-value=28 Score=37.41 Aligned_cols=49 Identities=22% Similarity=0.588 Sum_probs=37.8
Q ss_pred cccccccccccc----CCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 58 GDVGCEQCGSGE----RAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 58 ~~~~C~vC~~~~----~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
+..+|++|+..- +.+..+.|..|.-..--.|+. -+.-+|.=.||.|...
T Consensus 35 ~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYE---YERkeGnq~CPQCkTr 87 (1085)
T PLN02400 35 NGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYE---YERKDGTQCCPQCKTR 87 (1085)
T ss_pred CCceeeecccccCcCCCCCEEEEEccCCCccccchhh---eecccCCccCcccCCc
Confidence 456999999852 456788999998877778886 3455778899999864
No 93
>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=34.25 E-value=15 Score=21.55 Aligned_cols=12 Identities=42% Similarity=1.165 Sum_probs=9.9
Q ss_pred CCCccCcccccC
Q 025663 98 IGTWLCPKCSGQ 109 (249)
Q Consensus 98 ~g~W~Cp~C~~~ 109 (249)
.|+|.|+.|...
T Consensus 2 ~g~W~C~~C~~~ 13 (30)
T PF00641_consen 2 EGDWKCPSCTFM 13 (30)
T ss_dssp SSSEEETTTTEE
T ss_pred CcCccCCCCcCC
Confidence 578999999764
No 94
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=34.22 E-value=5.5 Score=26.26 Aligned_cols=43 Identities=33% Similarity=0.675 Sum_probs=23.4
Q ss_pred ccccccccCCCC-ce-ee--cccCCcccccccCCcCCCCCCCCccCccc
Q 025663 62 CEQCGSGERAEE-LL-LC--DKCDKGFHMKCLRPIVVRVPIGTWLCPKC 106 (249)
Q Consensus 62 C~vC~~~~~~~~-~l-~C--D~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C 106 (249)
|.+|..++..+. ++ -| .+--++.|..|+.-.+.. .+...|+.|
T Consensus 1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~--~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRE--SGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHH--HT-SB-TTT
T ss_pred CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHh--cCCCcCCCC
Confidence 678888765544 44 33 233348999999855443 233445544
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=33.96 E-value=20 Score=20.10 Aligned_cols=11 Identities=45% Similarity=1.298 Sum_probs=8.7
Q ss_pred CCccCcccccC
Q 025663 99 GTWLCPKCSGQ 109 (249)
Q Consensus 99 g~W~Cp~C~~~ 109 (249)
|+|.|+.|...
T Consensus 1 g~W~C~~C~~~ 11 (26)
T smart00547 1 GDWECPACTFL 11 (26)
T ss_pred CcccCCCCCCc
Confidence 57999999653
No 96
>PLN02436 cellulose synthase A
Probab=33.80 E-value=28 Score=37.45 Aligned_cols=49 Identities=22% Similarity=0.608 Sum_probs=38.2
Q ss_pred cccccccccccc----CCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 58 GDVGCEQCGSGE----RAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 58 ~~~~C~vC~~~~----~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
+..+|++|+..- +.+..+.|..|.-..--.|+. -+..+|.=.||.|...
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cye---yer~eg~~~Cpqckt~ 87 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYE---YERREGNQACPQCKTR 87 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCccccchhh---hhhhcCCccCcccCCc
Confidence 346999999852 456778999999888888986 3455677899999865
No 97
>PF13922 PHD_3: PHD domain of transcriptional enhancer, Asx
Probab=33.50 E-value=11 Score=26.99 Aligned_cols=21 Identities=24% Similarity=0.773 Sum_probs=19.1
Q ss_pred CCceeecccCCcccccccCCc
Q 025663 72 EELLLCDKCDKGFHMKCLRPI 92 (249)
Q Consensus 72 ~~~l~CD~C~~~fH~~Cl~P~ 92 (249)
..||.|-.|+..-|-.|++|.
T Consensus 41 kAMi~Cq~CGAFCHDDCIgps 61 (69)
T PF13922_consen 41 KAMIMCQGCGAFCHDDCIGPS 61 (69)
T ss_pred HHHHHHhhccchhccccccHH
Confidence 579999999999999999974
No 98
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=33.17 E-value=21 Score=29.69 Aligned_cols=23 Identities=30% Similarity=0.834 Sum_probs=15.8
Q ss_pred cccccccccCCCCceeecccCCcc
Q 025663 61 GCEQCGSGERAEELLLCDKCDKGF 84 (249)
Q Consensus 61 ~C~vC~~~~~~~~~l~CD~C~~~f 84 (249)
.|..|+.. ++.-++.|..|++||
T Consensus 2 aC~YCG~~-~p~~vv~C~~c~kWF 24 (152)
T PF09416_consen 2 ACAYCGIH-DPSCVVKCNTCNKWF 24 (152)
T ss_dssp S-TTT-----CCCEEEETTTTEEE
T ss_pred CccccCCC-CcccEeEcCCCCcEe
Confidence 47788854 568899999999999
No 99
>KOG1705 consensus Uncharacterized conserved protein, contains CXXC motifs [Function unknown]
Probab=32.28 E-value=23 Score=27.02 Aligned_cols=49 Identities=29% Similarity=0.641 Sum_probs=32.5
Q ss_pred cccccccccccCCCCce-eecccCC-cccccccCCcCCCCCCCCccCccccc
Q 025663 59 DVGCEQCGSGERAEELL-LCDKCDK-GFHMKCLRPIVVRVPIGTWLCPKCSG 108 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l-~CD~C~~-~fH~~Cl~P~l~~~p~g~W~Cp~C~~ 108 (249)
+..|.+|..--.+-.++ +||.|.. .|.-.|+.=.+..+ ..-+||..|..
T Consensus 27 DgkC~ICDS~VRP~tlVRiC~eC~~Gs~q~~ciic~~~gV-~d~~yc~ectr 77 (110)
T KOG1705|consen 27 DGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGVGV-SDAYYCKECTR 77 (110)
T ss_pred CCcccccccccccceeeeeehhcCCccccCceEEecCCcc-cchHHHHHHHh
Confidence 46688887766666665 8999998 55656765333222 23589999874
No 100
>PF12554 MOZART1: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR022214 This family of proteins is found in eukaryotes. Proteins in this family are typically between 71 and 105 amino acids in length. There is a single completely conserved residue L that may be functionally important.
Probab=32.21 E-value=42 Score=22.47 Aligned_cols=21 Identities=38% Similarity=0.697 Sum_probs=18.0
Q ss_pred hhcHHHHHHHHHHHhcCCCCC
Q 025663 221 KEDTETLEQCRAMCKRGECPP 241 (249)
Q Consensus 221 ~~d~~~~~~~~~~~~~g~~~~ 241 (249)
.=|.|+|..|-+|+..|.-|-
T Consensus 18 gLd~etL~ici~L~e~GVnPe 38 (48)
T PF12554_consen 18 GLDRETLSICIELCENGVNPE 38 (48)
T ss_pred CCCHHHHHHHHHHHHCCCCHH
Confidence 447899999999999998774
No 101
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=31.62 E-value=6.3 Score=29.11 Aligned_cols=49 Identities=22% Similarity=0.577 Sum_probs=21.7
Q ss_pred ccccccccccccc----CCCCceeecccCCcccccccCCcCCCCCCCCccCccccc
Q 025663 57 YGDVGCEQCGSGE----RAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSG 108 (249)
Q Consensus 57 ~~~~~C~vC~~~~----~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~ 108 (249)
.+..+|.+|+..- +.+..+.|..|....--.|+.- +..+|.-.||.|..
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEY---Erkeg~q~CpqCkt 59 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEY---ERKEGNQVCPQCKT 59 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHH---HHHTS-SB-TTT--
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHH---HhhcCcccccccCC
Confidence 3457899999842 4567789999977666667652 23456778999974
No 102
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=31.57 E-value=50 Score=22.51 Aligned_cols=27 Identities=33% Similarity=0.571 Sum_probs=22.9
Q ss_pred hcccccccChhcHHHHHHHHHHHhcCC
Q 025663 212 EEGGMQVLSKEDTETLEQCRAMCKRGE 238 (249)
Q Consensus 212 e~~g~~~~~~~d~~~~~~~~~~~~~g~ 238 (249)
..+|-..++.+|++.|..++.|.+.|.
T Consensus 31 ~~~g~r~y~~~dv~~l~~i~~l~~~G~ 57 (69)
T PF13411_consen 31 DENGYRYYSEEDVERLREIKELRKQGM 57 (69)
T ss_dssp STTSSEEE-HHHHHHHHHHHHHHHTTT
T ss_pred ccCceeeccHHHHHHHHHHHHHHHCcC
Confidence 556778899999999999999999875
No 103
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=31.52 E-value=23 Score=27.45 Aligned_cols=32 Identities=25% Similarity=0.666 Sum_probs=24.2
Q ss_pred ccccccccccc--CCCCceeecccCCcccccccC
Q 025663 59 DVGCEQCGSGE--RAEELLLCDKCDKGFHMKCLR 90 (249)
Q Consensus 59 ~~~C~vC~~~~--~~~~~l~CD~C~~~fH~~Cl~ 90 (249)
-+.|.+|+... -.++.|.|-.|+..|+..=++
T Consensus 35 ~daCeiC~~~GY~q~g~~lvC~~C~~~~~~~~ig 68 (102)
T PF10080_consen 35 FDACEICGPKGYYQEGDQLVCKNCGVRFNLPTIG 68 (102)
T ss_pred EEeccccCCCceEEECCEEEEecCCCEEehhhcc
Confidence 47799996643 347888999999988875444
No 104
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=31.31 E-value=30 Score=37.15 Aligned_cols=49 Identities=27% Similarity=0.634 Sum_probs=38.2
Q ss_pred cccccccccccc----CCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 58 GDVGCEQCGSGE----RAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 58 ~~~~C~vC~~~~----~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
+..+|.+|+..- +.+..+.|..|.-..--.|+. -+..+|.=.||.|...
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYE---YEr~eG~q~CPqCktr 68 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYE---YERKDGNQSCPQCKTK 68 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEeccCCCccccchhh---hhhhcCCccCCccCCc
Confidence 356999999852 456778999998888888986 3455778899999864
No 105
>PLN02195 cellulose synthase A
Probab=29.58 E-value=35 Score=36.31 Aligned_cols=49 Identities=27% Similarity=0.710 Sum_probs=38.0
Q ss_pred cccccccccccc----CCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 58 GDVGCEQCGSGE----RAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 58 ~~~~C~vC~~~~----~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
+..+|.+|+..- +.+..+.|..|.-..--.|+. -+..+|.=-||.|...
T Consensus 5 ~~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCye---yer~eg~q~CpqCkt~ 57 (977)
T PLN02195 5 GAPICATCGEEVGVDSNGEAFVACHECSYPLCKACLE---YEIKEGRKVCLRCGGP 57 (977)
T ss_pred CCccceecccccCcCCCCCeEEEeccCCCccccchhh---hhhhcCCccCCccCCc
Confidence 346899999832 446778999999888888986 3455778899999865
No 106
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=28.65 E-value=29 Score=21.84 Aligned_cols=12 Identities=58% Similarity=1.400 Sum_probs=8.5
Q ss_pred eecccCCccccc
Q 025663 76 LCDKCDKGFHMK 87 (249)
Q Consensus 76 ~CD~C~~~fH~~ 87 (249)
+|-.|.++||+.
T Consensus 4 ~CprC~kg~Hwa 15 (36)
T PF14787_consen 4 LCPRCGKGFHWA 15 (36)
T ss_dssp C-TTTSSSCS-T
T ss_pred cCcccCCCcchh
Confidence 688899999984
No 107
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.15 E-value=38 Score=33.31 Aligned_cols=43 Identities=28% Similarity=0.705 Sum_probs=25.7
Q ss_pred cccccccccccCCCCceeecccCC--cccc-----cccCCcCCCCCCCCccCcccccC
Q 025663 59 DVGCEQCGSGERAEELLLCDKCDK--GFHM-----KCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l~CD~C~~--~fH~-----~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
...|..|+. .+.|..|+- .||. .|+-= .....-.|.||.|-..
T Consensus 213 ~~~C~~Cg~------~~~C~~C~~~l~~h~~~~~l~Ch~C--g~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 213 NLLCRSCGY------ILCCPNCDVSLTYHKKEGKLRCHYC--GYQEPIPKTCPQCGSE 262 (505)
T ss_pred eeEhhhCcC------ccCCCCCCCceEEecCCCeEEcCCC--cCcCCCCCCCCCCCCC
Confidence 457888865 467888875 5663 34431 1111225899999764
No 108
>PHA02926 zinc finger-like protein; Provisional
Probab=27.92 E-value=18 Score=32.10 Aligned_cols=52 Identities=19% Similarity=0.362 Sum_probs=32.6
Q ss_pred ccccccccccccC----CCC--ceeecccCCcccccccCCcCCCCC--CCCccCcccccC
Q 025663 58 GDVGCEQCGSGER----AEE--LLLCDKCDKGFHMKCLRPIVVRVP--IGTWLCPKCSGQ 109 (249)
Q Consensus 58 ~~~~C~vC~~~~~----~~~--~l~CD~C~~~fH~~Cl~P~l~~~p--~g~W~Cp~C~~~ 109 (249)
.+..|.+|...-. +++ .-.=+.|+-.|++.|..-+..... .....||.|+..
T Consensus 169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~ 228 (242)
T PHA02926 169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTR 228 (242)
T ss_pred CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcce
Confidence 3578999997521 111 112247888899999885544321 235789999875
No 109
>PF13041 PPR_2: PPR repeat family
Probab=27.73 E-value=59 Score=20.70 Aligned_cols=19 Identities=37% Similarity=0.396 Sum_probs=15.6
Q ss_pred cHHHHHHHHHHHhcCCCCC
Q 025663 223 DTETLEQCRAMCKRGECPP 241 (249)
Q Consensus 223 d~~~~~~~~~~~~~g~~~~ 241 (249)
--++++++++|.++|.-|=
T Consensus 19 ~~~a~~l~~~M~~~g~~P~ 37 (50)
T PF13041_consen 19 FEEALKLFKEMKKRGIKPD 37 (50)
T ss_pred HHHHHHHHHHHHHcCCCCC
Confidence 3579999999999997663
No 110
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=27.70 E-value=20 Score=22.57 Aligned_cols=10 Identities=30% Similarity=1.169 Sum_probs=7.7
Q ss_pred CccCcccccC
Q 025663 100 TWLCPKCSGQ 109 (249)
Q Consensus 100 ~W~Cp~C~~~ 109 (249)
-|+|+.|-..
T Consensus 32 ~~~C~~CGE~ 41 (46)
T TIGR03831 32 ALVCPQCGEE 41 (46)
T ss_pred ccccccCCCE
Confidence 4999999653
No 111
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=27.51 E-value=47 Score=35.66 Aligned_cols=49 Identities=20% Similarity=0.573 Sum_probs=38.2
Q ss_pred cccccccccccc----CCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 58 GDVGCEQCGSGE----RAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 58 ~~~~C~vC~~~~----~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
+..+|.+|+..- +.+..+.|..|.-..--.|+. -+..+|.=.||.|...
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cye---ye~~~g~~~cp~c~t~ 66 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYE---YERSEGNQCCPQCNTR 66 (1044)
T ss_pred CcchhhccccccCcCCCCCEEEEeccCCCccccchhh---hhhhcCCccCCccCCc
Confidence 457899999852 446778999999888888886 3455777899999864
No 112
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.19 E-value=15 Score=31.57 Aligned_cols=50 Identities=28% Similarity=0.509 Sum_probs=28.9
Q ss_pred ccccccccccCCC--Cceeec--ccCCcccccccCCcCCCCCCC-------CccCcccccC
Q 025663 60 VGCEQCGSGERAE--ELLLCD--KCDKGFHMKCLRPIVVRVPIG-------TWLCPKCSGQ 109 (249)
Q Consensus 60 ~~C~vC~~~~~~~--~~l~CD--~C~~~fH~~Cl~P~l~~~p~g-------~W~Cp~C~~~ 109 (249)
..|.+|..-.-.| .--.|| .|++.||+.|+.-+|..+-.. ---||.|...
T Consensus 166 ~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~P 226 (234)
T KOG3268|consen 166 GACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDP 226 (234)
T ss_pred hcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCc
Confidence 4455555421112 223577 599999999998665432111 1258888754
No 113
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=27.06 E-value=69 Score=21.87 Aligned_cols=27 Identities=26% Similarity=0.484 Sum_probs=23.9
Q ss_pred hcccccccChhcHHHHHHHHHHHhcCC
Q 025663 212 EEGGMQVLSKEDTETLEQCRAMCKRGE 238 (249)
Q Consensus 212 e~~g~~~~~~~d~~~~~~~~~~~~~g~ 238 (249)
..||-..++.+|++.|...+.+.+.|.
T Consensus 31 ~~~g~R~y~~~~l~~l~~i~~l~~~g~ 57 (67)
T cd04764 31 TENGRRYYTDEDIELLKKIKTLLEKGL 57 (67)
T ss_pred CCCCceeeCHHHHHHHHHHHHHHHCCC
Confidence 457778899999999999999999884
No 114
>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=26.98 E-value=36 Score=20.48 Aligned_cols=21 Identities=43% Similarity=0.974 Sum_probs=9.5
Q ss_pred ccccccccc--CCCCceeecccC
Q 025663 61 GCEQCGSGE--RAEELLLCDKCD 81 (249)
Q Consensus 61 ~C~vC~~~~--~~~~~l~CD~C~ 81 (249)
.|..|+... ..+.++.|+.|.
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp~C~ 26 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCPECG 26 (30)
T ss_dssp --TTT-----EE-SSSEEETTTT
T ss_pred CCCCCCCcceeccCCEEeCCccc
Confidence 477777653 346677777774
No 115
>PRK00420 hypothetical protein; Validated
Probab=26.97 E-value=35 Score=26.91 Aligned_cols=17 Identities=18% Similarity=0.380 Sum_probs=12.4
Q ss_pred CCCCCCCCccCcccccC
Q 025663 93 VVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 93 l~~~p~g~W~Cp~C~~~ 109 (249)
+.....|.-+||.|-..
T Consensus 33 Lf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 33 LFELKDGEVVCPVHGKV 49 (112)
T ss_pred ceecCCCceECCCCCCe
Confidence 44445788999999764
No 116
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=26.74 E-value=33 Score=30.14 Aligned_cols=35 Identities=29% Similarity=0.756 Sum_probs=23.9
Q ss_pred CCceeecccCCcccccccCCcCCCCCCCCccCcccccCC
Q 025663 72 EELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQR 110 (249)
Q Consensus 72 ~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~~ 110 (249)
-.-++|..|. +|-.|+. +.+-|..+++|++|-...
T Consensus 190 ~~alIC~~C~--hhngl~~--~~ek~~~efiC~~Cn~~n 224 (251)
T COG5415 190 FKALICPQCH--HHNGLYR--LAEKPIIEFICPHCNHKN 224 (251)
T ss_pred hhhhcccccc--ccccccc--cccccchheecccchhhc
Confidence 3456666663 4667887 455555689999998753
No 117
>PRK11595 DNA utilization protein GntX; Provisional
Probab=26.66 E-value=30 Score=30.12 Aligned_cols=49 Identities=14% Similarity=0.291 Sum_probs=26.5
Q ss_pred ccccccccccCCCCceeecccCCcccc---cccCCcCCCCCCCCccCcccccC
Q 025663 60 VGCEQCGSGERAEELLLCDKCDKGFHM---KCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 60 ~~C~vC~~~~~~~~~l~CD~C~~~fH~---~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
..|.+|+.....+...+|+.|...++. .|..=... .....-+|..|...
T Consensus 6 ~~C~~C~~~~~~~~~~lC~~C~~~l~~~~~~C~~Cg~~-~~~~~~~C~~C~~~ 57 (227)
T PRK11595 6 GLCWLCRMPLALSHWGICSVCSRALRTLKTCCPQCGLP-ATHPHLPCGRCLQK 57 (227)
T ss_pred CcCccCCCccCCCCCcccHHHHhhCCcccCcCccCCCc-CCCCCCCcHHHHcC
Confidence 369999976433444589999765553 23321100 11112358888654
No 118
>PRK14873 primosome assembly protein PriA; Provisional
Probab=25.97 E-value=48 Score=33.90 Aligned_cols=42 Identities=24% Similarity=0.737 Sum_probs=26.8
Q ss_pred cccccccccccCCCCceeecccCC--ccccc-----ccCCcCCCCCCCCccCcccccC
Q 025663 59 DVGCEQCGSGERAEELLLCDKCDK--GFHMK-----CLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l~CD~C~~--~fH~~-----Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
-..|..|+. .+.|..|+- .||.. |+-=-.. ...|.||.|-..
T Consensus 383 ~l~C~~Cg~------~~~C~~C~~~L~~h~~~~~l~Ch~CG~~---~~p~~Cp~Cgs~ 431 (665)
T PRK14873 383 SLACARCRT------PARCRHCTGPLGLPSAGGTPRCRWCGRA---APDWRCPRCGSD 431 (665)
T ss_pred eeEhhhCcC------eeECCCCCCceeEecCCCeeECCCCcCC---CcCccCCCCcCC
Confidence 457888875 567888885 66642 5431111 136999999764
No 119
>KOG1395 consensus Tryptophan synthase beta chain [Amino acid transport and metabolism]
Probab=25.20 E-value=85 Score=30.04 Aligned_cols=49 Identities=33% Similarity=0.556 Sum_probs=38.6
Q ss_pred cCCCCCCCCCCCCCCCChhhhhcccccccChhcHHHHHHHHHHHh-cCCCCCe
Q 025663 191 FSDDLTYMPGMAPRSANQAEFEEGGMQVLSKEDTETLEQCRAMCK-RGECPPL 242 (249)
Q Consensus 191 ~s~~l~y~p~~a~~~~n~~~~e~~g~~~~~~~d~~~~~~~~~~~~-~g~~~~~ 242 (249)
.|-.|.| |||+|... -.++.|=|+-++--|.|.|+-++++++ +|..|-|
T Consensus 368 IsAGLdY-pGvgPels--~~k~~grae~isitd~eclegfk~~srlEGIIPAl 417 (477)
T KOG1395|consen 368 ISAGLDY-PGVGPELS--HLKETGRAEFISITDAECLEGFKQLSRLEGIIPAL 417 (477)
T ss_pred cccCCCC-CCCChhHH--HHHhcCceeEEecChHHHHHHHHHHHHhcccccCC
Confidence 3446777 89996543 457778899999999999999999987 6877765
No 120
>PF12926 MOZART2: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR024332 The MOZART2 family of proteins (also known as FAM128 and Mitotic-spindle organizing protein 2) operate as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation. This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, the MOZART proteins, both 1 and 2, do not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBGCP nomenclature cannot be used for it. The exact function of MOZART2 is not clear [].
Probab=24.66 E-value=53 Score=24.82 Aligned_cols=27 Identities=26% Similarity=0.304 Sum_probs=21.2
Q ss_pred CCChhhhhcccccccChhcHHHHHHHH
Q 025663 205 SANQAEFEEGGMQVLSKEDTETLEQCR 231 (249)
Q Consensus 205 ~~n~~~~e~~g~~~~~~~d~~~~~~~~ 231 (249)
..+..++-.---++|+.|+.|.|++|+
T Consensus 9 ~~~~~k~~~~rk~~Ls~eE~EL~ELa~ 35 (88)
T PF12926_consen 9 TAQVYKYSLRRKKVLSAEEVELYELAQ 35 (88)
T ss_pred hHHHHHHHHHHHhccCHHHHHHHHHHH
Confidence 455566666667999999999999986
No 121
>KOG0225 consensus Pyruvate dehydrogenase E1, alpha subunit [Energy production and conversion]
Probab=23.91 E-value=1e+02 Score=29.17 Aligned_cols=39 Identities=26% Similarity=0.537 Sum_probs=28.1
Q ss_pred CCCCCCCCCCCChhhhhcccccccChhcHHHHHHHHHHHhcCCCCCeEEEec
Q 025663 196 TYMPGMAPRSANQAEFEEGGMQVLSKEDTETLEQCRAMCKRGECPPLVVRQM 247 (249)
Q Consensus 196 ~y~p~~a~~~~n~~~~e~~g~~~~~~~d~~~~~~~~~~~~~g~~~~~~v~~~ 247 (249)
.|+||+. ++||+||-- .++.+-.+.-+.+|. .||||++|
T Consensus 247 ~yiPGl~----------VdGmdvlaV--r~a~KfA~~~~~~g~-GPilmE~~ 285 (394)
T KOG0225|consen 247 DYIPGLK----------VDGMDVLAV--REATKFAKKYALEGK-GPILMEMD 285 (394)
T ss_pred CCCCceE----------ECCcchhhH--HHHHHHHHHHHhcCC-CCEEEEEe
Confidence 5677755 889999954 456666677777776 57777776
No 122
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=23.55 E-value=17 Score=34.58 Aligned_cols=47 Identities=26% Similarity=0.583 Sum_probs=30.9
Q ss_pred ccccccccccccc-cCCC------------CceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 56 DYGDVGCEQCGSG-ERAE------------ELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 56 ~~~~~~C~vC~~~-~~~~------------~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
..+|..|.+|..+ -.++ .-+ -|+--+|+.|+.-++.. .=-||-|+..
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrL---pCGHilHl~CLknW~ER----qQTCPICr~p 343 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRL---PCGHILHLHCLKNWLER----QQTCPICRRP 343 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccc---cccceeeHHHHHHHHHh----ccCCCcccCc
Confidence 5668999999976 1111 112 37777999999855432 2369999754
No 123
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.43 E-value=35 Score=35.77 Aligned_cols=39 Identities=28% Similarity=0.670 Sum_probs=30.3
Q ss_pred ccccccccccCCCCceeec-ccCCcccccccCCcCCCCCCCCccCccccc
Q 025663 60 VGCEQCGSGERAEELLLCD-KCDKGFHMKCLRPIVVRVPIGTWLCPKCSG 108 (249)
Q Consensus 60 ~~C~vC~~~~~~~~~l~CD-~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~ 108 (249)
..|..|... =++-.-. .|.-.||+.|+. .++--||.|..
T Consensus 841 skCs~C~~~---LdlP~VhF~CgHsyHqhC~e-------~~~~~CP~C~~ 880 (933)
T KOG2114|consen 841 SKCSACEGT---LDLPFVHFLCGHSYHQHCLE-------DKEDKCPKCLP 880 (933)
T ss_pred eeecccCCc---cccceeeeecccHHHHHhhc-------cCcccCCccch
Confidence 579999876 4444443 699999999998 55678999987
No 124
>PRK04023 DNA polymerase II large subunit; Validated
Probab=23.14 E-value=72 Score=34.27 Aligned_cols=24 Identities=25% Similarity=0.620 Sum_probs=18.1
Q ss_pred ccccccccccccccCCCCceeecccCC
Q 025663 56 DYGDVGCEQCGSGERAEELLLCDKCDK 82 (249)
Q Consensus 56 ~~~~~~C~vC~~~~~~~~~l~CD~C~~ 82 (249)
+.....|..|+.. .....|..|+.
T Consensus 623 EVg~RfCpsCG~~---t~~frCP~CG~ 646 (1121)
T PRK04023 623 EIGRRKCPSCGKE---TFYRRCPFCGT 646 (1121)
T ss_pred cccCccCCCCCCc---CCcccCCCCCC
Confidence 3446789999987 56678888875
No 125
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=23.11 E-value=40 Score=31.88 Aligned_cols=53 Identities=25% Similarity=0.444 Sum_probs=33.1
Q ss_pred cccccccccccccCC--CCceeecccCCcc--------cccccCCcCCCCCCC-CccCcccccC
Q 025663 57 YGDVGCEQCGSGERA--EELLLCDKCDKGF--------HMKCLRPIVVRVPIG-TWLCPKCSGQ 109 (249)
Q Consensus 57 ~~~~~C~vC~~~~~~--~~~l~CD~C~~~f--------H~~Cl~P~l~~~p~g-~W~Cp~C~~~ 109 (249)
+.+..|.|||..-++ -.++-|..|.-.| |..|..-.--.+.+. .=-||.|+-+
T Consensus 13 dl~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQ 76 (475)
T KOG4218|consen 13 DLGELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQ 76 (475)
T ss_pred ccccccccccCccccceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhHH
Confidence 335789999985432 3688999997655 566765332223322 3568888643
No 126
>PF07875 Coat_F: Coat F domain; InterPro: IPR012851 The Coat F proteins contribute to the Bacillales spore coat. They occur multiple times in the genomes in which they are found. Bacillus subtilis endospore protein coats protect them and may play a role in their germination []. Spore coat protein F, on the outer surface of the endospore, is one of a suite of proteins that could be used to differentiate between members of the Bacillus genus [].
Probab=22.98 E-value=59 Score=22.38 Aligned_cols=26 Identities=23% Similarity=0.284 Sum_probs=21.9
Q ss_pred ccccChhcHHHHHHHHHHHhcCCCCC
Q 025663 216 MQVLSKEDTETLEQCRAMCKRGECPP 241 (249)
Q Consensus 216 ~~~~~~~d~~~~~~~~~~~~~g~~~~ 241 (249)
++.+...--..++++.-|.++|.|||
T Consensus 37 ~~~~~~~~~~~~~l~~~m~~kGwY~~ 62 (64)
T PF07875_consen 37 QQILNECQQMQYELFNYMNQKGWYQP 62 (64)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCcCC
Confidence 45676777778999999999999997
No 127
>PRK11827 hypothetical protein; Provisional
Probab=22.75 E-value=57 Score=22.86 Aligned_cols=27 Identities=19% Similarity=0.532 Sum_probs=17.2
Q ss_pred cccccccccc---cCCCCceeecccCCccc
Q 025663 59 DVGCEQCGSG---ERAEELLLCDKCDKGFH 85 (249)
Q Consensus 59 ~~~C~vC~~~---~~~~~~l~CD~C~~~fH 85 (249)
-.+|.+|+.. +...+-+.|..|...|-
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~laYP 37 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLAFP 37 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCeecc
Confidence 3568888764 12345567888877764
No 128
>PF11080 DUF2622: Protein of unknown function (DUF2622); InterPro: IPR022597 This family is conserved in the Enterobacteriaceae family. The function is not known.
Probab=21.91 E-value=1.7e+02 Score=22.49 Aligned_cols=65 Identities=20% Similarity=0.168 Sum_probs=46.4
Q ss_pred hhhhhHHHhhhcccccCCCCCCCCCCCCCCCChhhhhcccccccChhcHHHHHHHHHHHhcCCCCCeEEE
Q 025663 176 QMGSLAHALTALQMEFSDDLTYMPGMAPRSANQAEFEEGGMQVLSKEDTETLEQCRAMCKRGECPPLVVR 245 (249)
Q Consensus 176 ~~a~l~~a~~~~~~~~s~~l~y~p~~a~~~~n~~~~e~~g~~~~~~~d~~~~~~~~~~~~~g~~~~~~v~ 245 (249)
-.+.|+.+|+.-||...-...+ |-- --++.+-.|+...++++|++.+.+--.-...|..|-+-|.
T Consensus 22 d~~~L~~~lt~~GF~~tl~D~~--G~~---HeLgtntfgl~S~l~~~eV~~la~~lae~algk~p~V~V~ 86 (96)
T PF11080_consen 22 DINELNNHLTRAGFSTTLTDED--GNP---HELGTNTFGLISALSAEEVAQLARGLAESALGKTPEVEVT 86 (96)
T ss_pred HHHHHHHHHHhcCceeEEecCC--CCE---eecCCCeEEEEecCCHHHHHHHHHHHhhhhcCCCCceEEE
Confidence 3456788999998875443333 321 1234456677888999999998888777889999988775
No 129
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=21.73 E-value=66 Score=22.01 Aligned_cols=32 Identities=31% Similarity=0.851 Sum_probs=25.6
Q ss_pred ccccccccc-----CCCCceeecccCCcccccccCCc
Q 025663 61 GCEQCGSGE-----RAEELLLCDKCDKGFHMKCLRPI 92 (249)
Q Consensus 61 ~C~vC~~~~-----~~~~~l~CD~C~~~fH~~Cl~P~ 92 (249)
.|..|+... ..|+++-|..|..-|-...++|.
T Consensus 4 ~CP~CG~~iev~~~~~GeiV~Cp~CGaeleVv~~~p~ 40 (54)
T TIGR01206 4 ECPDCGAEIELENPELGELVICDECGAELEVVSLDPL 40 (54)
T ss_pred CCCCCCCEEecCCCccCCEEeCCCCCCEEEEEeCCCC
Confidence 588888742 23789999999999999888873
No 130
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=21.61 E-value=34 Score=21.63 Aligned_cols=32 Identities=22% Similarity=0.527 Sum_probs=14.8
Q ss_pred ceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 74 LLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 74 ~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
.+.|..|..-.-.+|..- .....|.|+.|...
T Consensus 2 p~rC~~C~aylNp~~~~~----~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFD----DGGKTWICNFCGTK 33 (40)
T ss_dssp S-B-TTT--BS-TTSEEE----TTTTEEEETTT--E
T ss_pred ccccCCCCCEECCcceEc----CCCCEEECcCCCCc
Confidence 456777766555555331 12236999999753
No 131
>PF05553 DUF761: Cotton fibre expressed protein; InterPro: IPR008480 This family consists of several plant proteins of unknown function. Three of the sequences from Gossypium hirsutum (Upland cotton) in this family are described as G. hirsutum fibre expressed proteins []. The remaining sequences, found in Arabidopsis thaliana, are uncharacterised.
Probab=21.56 E-value=85 Score=19.92 Aligned_cols=16 Identities=31% Similarity=0.592 Sum_probs=13.0
Q ss_pred hcHHHHHHHHHHHhcC
Q 025663 222 EDTETLEQCRAMCKRG 237 (249)
Q Consensus 222 ~d~~~~~~~~~~~~~g 237 (249)
+-.+.+..+++|+.||
T Consensus 23 qr~~S~~ry~eml~Rg 38 (38)
T PF05553_consen 23 QRQESLQRYQEMLARG 38 (38)
T ss_pred HHHHHHHHHHHHHhcC
Confidence 4457888999999987
No 132
>KOG3896 consensus Dynactin, subunit p62 [Cell motility]
Probab=21.51 E-value=65 Score=30.40 Aligned_cols=41 Identities=27% Similarity=0.618 Sum_probs=28.1
Q ss_pred ccccccCCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 64 QCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 64 vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
.|+.-..-..+++|-.|.+.--..|+. .++ ..-|||.|.+.
T Consensus 14 ~cg~~~pl~~L~FCRyC~klrc~~Cv~---hEv--dshfCp~CLEn 54 (449)
T KOG3896|consen 14 TCGKFRPLPDLVFCRYCFKLRCDDCVL---HEV--DSHFCPRCLEN 54 (449)
T ss_pred eccccccccceeeeecccccccccccc---ccc--ccccchhhccC
Confidence 566554557899999998766666655 333 24688888775
No 133
>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=21.50 E-value=22 Score=25.69 Aligned_cols=35 Identities=20% Similarity=0.350 Sum_probs=23.5
Q ss_pred cccccccccccCCCCceeec---------ccCCcccccccCCcC
Q 025663 59 DVGCEQCGSGERAEELLLCD---------KCDKGFHMKCLRPIV 93 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l~CD---------~C~~~fH~~Cl~P~l 93 (249)
...|..|+.....+++=+.- .-..|||+.|.....
T Consensus 7 Ra~Ck~C~~~I~kg~lRiG~~~~~~~~~~~~~~W~H~~C~~~~~ 50 (82)
T PF00645_consen 7 RAKCKGCKKKIAKGELRIGKIVPSPEGDGDIPKWYHWDCFFKKQ 50 (82)
T ss_dssp TEBETTTSCBE-TTSEEEEEEEEETTSSCEEEEEEEHHHHHHTT
T ss_pred CccCcccCCcCCCCCEEEEEEecccccCCCCCceECccccccch
Confidence 45788999877666666553 234689999987543
No 134
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=21.50 E-value=40 Score=19.09 Aligned_cols=14 Identities=36% Similarity=0.828 Sum_probs=9.2
Q ss_pred CceeecccCCcccc
Q 025663 73 ELLLCDKCDKGFHM 86 (249)
Q Consensus 73 ~~l~CD~C~~~fH~ 86 (249)
+|+.|..|++.|..
T Consensus 1 ~l~~C~~CgR~F~~ 14 (25)
T PF13913_consen 1 ELVPCPICGRKFNP 14 (25)
T ss_pred CCCcCCCCCCEECH
Confidence 35677777777743
No 135
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=21.38 E-value=25 Score=30.94 Aligned_cols=50 Identities=18% Similarity=0.352 Sum_probs=34.4
Q ss_pred cccccccccccccCCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 57 YGDVGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 57 ~~~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
++-..|..|..-- =+-+.|..|+..||..|..--+.+.|. =|.|.+|...
T Consensus 179 dnlk~Cn~Ch~Lv--Iqg~rCg~c~i~~h~~c~qty~q~~~~-cphc~d~w~h 228 (235)
T KOG4718|consen 179 DNLKNCNLCHCLV--IQGIRCGSCNIQYHRGCIQTYLQRRDI-CPHCGDLWTH 228 (235)
T ss_pred HHHHHHhHhHHHh--heeeccCcccchhhhHHHHHHhcccCc-CCchhcccCc
Confidence 3457799998741 244679999999999998855555332 3666666543
No 136
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=20.91 E-value=1e+02 Score=16.96 Aligned_cols=17 Identities=41% Similarity=0.573 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHhcCCCC
Q 025663 224 TETLEQCRAMCKRGECP 240 (249)
Q Consensus 224 ~~~~~~~~~~~~~g~~~ 240 (249)
-++++.+++|.+.|.-|
T Consensus 17 ~~a~~~~~~M~~~g~~p 33 (35)
T TIGR00756 17 EEALELFKEMLERGIEP 33 (35)
T ss_pred HHHHHHHHHHHHcCCCC
Confidence 46888999999998655
No 137
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=20.88 E-value=45 Score=23.38 Aligned_cols=11 Identities=45% Similarity=1.147 Sum_probs=9.2
Q ss_pred CCccCcccccC
Q 025663 99 GTWLCPKCSGQ 109 (249)
Q Consensus 99 g~W~Cp~C~~~ 109 (249)
.+|+|-.|..+
T Consensus 48 ~eWLCLnCQ~q 58 (61)
T PF05715_consen 48 KEWLCLNCQMQ 58 (61)
T ss_pred ceeeeecchhh
Confidence 47999999865
No 138
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.76 E-value=62 Score=33.07 Aligned_cols=44 Identities=25% Similarity=0.551 Sum_probs=25.9
Q ss_pred ccccccccccccCCCCceeecccCC--cccc-----cccCCcCCCCCCCCccCcccccC
Q 025663 58 GDVGCEQCGSGERAEELLLCDKCDK--GFHM-----KCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 58 ~~~~C~vC~~~~~~~~~l~CD~C~~--~fH~-----~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
....|..|+. .+.|..|+. .||. .|+-= ...-.-.|.||.|-..
T Consensus 380 ~~~~C~~Cg~------~~~C~~C~~~l~~h~~~~~l~Ch~C--g~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 380 PFLLCRDCGW------VAECPHCDASLTLHRFQRRLRCHHC--GYQEPIPKACPECGST 430 (679)
T ss_pred CceEhhhCcC------ccCCCCCCCceeEECCCCeEECCCC--cCCCCCCCCCCCCcCC
Confidence 3567888874 466877775 5663 34431 1111225899999653
No 139
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.30 E-value=48 Score=30.81 Aligned_cols=48 Identities=27% Similarity=0.532 Sum_probs=31.8
Q ss_pred cccccccccccCCCCceeecccCCcccccccCCcCCCCCCCCccCcccccC
Q 025663 59 DVGCEQCGSGERAEELLLCDKCDKGFHMKCLRPIVVRVPIGTWLCPKCSGQ 109 (249)
Q Consensus 59 ~~~C~vC~~~~~~~~~l~CD~C~~~fH~~Cl~P~l~~~p~g~W~Cp~C~~~ 109 (249)
..-|.+|...--.++-+.---|+-.||..|+.-++.. ..-.||-|...
T Consensus 323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~---y~~~CPvCrt~ 370 (374)
T COG5540 323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLG---YSNKCPVCRTA 370 (374)
T ss_pred CceEEEEhhhhcccceEEEeccCceechhHHHHHHhh---hcccCCccCCC
Confidence 3679999875322333444569999999999855432 23469999864
Done!