Query 037252
Match_columns 138
No_of_seqs 67 out of 69
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 10:19:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037252.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037252hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4299 PHD Zn-finger protein 98.7 2.4E-09 5.3E-14 98.5 1.2 54 40-97 253-311 (613)
2 smart00249 PHD PHD zinc finger 98.6 3.7E-08 8.1E-13 58.5 3.2 45 42-88 1-47 (47)
3 PF00628 PHD: PHD-finger; Int 98.5 2.6E-08 5.5E-13 62.5 1.2 47 42-90 1-50 (51)
4 KOG0383 Predicted helicase [Ge 98.3 2.8E-07 6.1E-12 86.2 1.4 55 35-93 42-96 (696)
5 COG5141 PHD zinc finger-contai 98.0 2.4E-06 5.1E-11 78.6 2.5 70 18-92 172-244 (669)
6 KOG1973 Chromatin remodeling p 98.0 3.2E-06 6.8E-11 70.5 1.9 46 42-92 223-269 (274)
7 cd04718 BAH_plant_2 BAH, or Br 97.8 4.2E-06 9.1E-11 65.7 -0.1 35 65-99 1-35 (148)
8 KOG0955 PHD finger protein BR1 97.7 2.2E-05 4.7E-10 76.5 2.6 76 16-95 195-273 (1051)
9 KOG1244 Predicted transcriptio 97.5 4.8E-05 1E-09 65.9 2.0 49 39-89 280-329 (336)
10 PF13831 PHD_2: PHD-finger; PD 97.2 7E-05 1.5E-09 45.9 -0.2 34 53-89 3-36 (36)
11 KOG0825 PHD Zn-finger protein 97.2 0.00033 7.2E-09 67.6 4.1 67 37-109 212-280 (1134)
12 COG5034 TNG2 Chromatin remodel 97.2 0.00019 4.2E-09 61.1 2.0 57 28-89 207-268 (271)
13 KOG0956 PHD finger protein AF1 96.7 0.00078 1.7E-08 64.2 1.7 47 42-90 7-56 (900)
14 KOG1245 Chromatin remodeling c 96.6 0.00047 1E-08 69.0 -0.5 55 37-93 1105-1160(1404)
15 KOG4443 Putative transcription 96.4 0.0015 3.3E-08 61.5 1.7 50 41-92 69-119 (694)
16 KOG1512 PHD Zn-finger protein 96.3 0.0019 4.1E-08 56.7 1.7 46 40-89 314-361 (381)
17 KOG4323 Polycomb-like PHD Zn-f 95.4 0.0056 1.2E-07 55.6 0.9 63 36-101 165-234 (464)
18 KOG0957 PHD finger protein [Ge 95.3 0.0067 1.5E-07 56.6 1.0 47 40-88 544-595 (707)
19 PF13771 zf-HC5HC2H: PHD-like 95.0 0.0097 2.1E-07 40.7 0.8 47 40-88 36-86 (90)
20 KOG1473 Nucleosome remodeling 94.8 0.018 3.9E-07 57.6 2.4 81 7-91 302-391 (1414)
21 KOG0954 PHD finger protein [Ge 94.6 0.017 3.6E-07 55.7 1.6 49 39-91 270-321 (893)
22 PF15446 zf-PHD-like: PHD/FYVE 94.3 0.023 4.9E-07 46.1 1.5 28 43-74 2-35 (175)
23 KOG1473 Nucleosome remodeling 94.0 0.015 3.2E-07 58.2 -0.0 58 32-92 420-480 (1414)
24 PF13832 zf-HC5HC2H_2: PHD-zin 92.1 0.066 1.4E-06 38.0 1.0 33 39-73 54-87 (110)
25 KOG0956 PHD finger protein AF1 90.6 0.11 2.3E-06 50.2 1.0 53 40-92 117-181 (900)
26 KOG4299 PHD Zn-finger protein 90.0 0.21 4.6E-06 47.0 2.4 50 32-89 41-90 (613)
27 KOG0383 Predicted helicase [Ge 89.0 0.082 1.8E-06 50.3 -1.1 51 37-91 503-554 (696)
28 PHA02862 5L protein; Provision 88.9 0.11 2.4E-06 41.5 -0.3 53 40-94 2-54 (156)
29 KOG1246 DNA-binding protein ju 87.3 0.5 1.1E-05 45.3 3.0 55 35-91 150-204 (904)
30 KOG0957 PHD finger protein [Ge 87.3 0.53 1.1E-05 44.4 3.0 51 40-92 119-180 (707)
31 KOG1081 Transcription factor N 82.2 1.3 2.8E-05 40.1 3.1 43 29-73 78-126 (463)
32 KOG3612 PHD Zn-finger protein 82.2 1.3 2.7E-05 41.8 3.1 47 41-91 61-108 (588)
33 PHA02825 LAP/PHD finger-like p 81.9 0.47 1E-05 38.2 0.2 57 37-95 5-61 (162)
34 smart00744 RINGv The RING-vari 80.1 0.45 9.7E-06 30.5 -0.4 46 42-89 1-49 (49)
35 PF11793 FANCL_C: FANCL C-term 80.1 0.26 5.5E-06 33.6 -1.6 54 41-94 3-67 (70)
36 KOG1734 Predicted RING-contain 79.7 1.1 2.4E-05 39.3 1.7 62 29-92 213-280 (328)
37 PF00130 C1_1: Phorbol esters/ 76.7 2 4.3E-05 26.7 1.8 39 34-74 5-46 (53)
38 KOG4628 Predicted E3 ubiquitin 76.2 1.4 3E-05 39.1 1.4 42 41-90 230-275 (348)
39 PF07649 C1_3: C1-like domain; 75.7 1 2.2E-05 25.9 0.2 28 42-71 2-30 (30)
40 PF08746 zf-RING-like: RING-li 74.5 0.8 1.7E-05 28.7 -0.4 32 55-88 12-43 (43)
41 PF03107 C1_2: C1 domain; Int 73.4 3.3 7.1E-05 23.9 2.0 28 42-71 2-30 (30)
42 PF13901 DUF4206: Domain of un 71.2 3.4 7.5E-05 33.1 2.4 41 41-92 153-199 (202)
43 KOG4443 Putative transcription 66.3 1.6 3.6E-05 41.8 -0.4 54 38-93 16-73 (694)
44 KOG1829 Uncharacterized conser 66.1 1.7 3.6E-05 40.9 -0.5 33 53-94 530-562 (580)
45 cd00029 C1 Protein kinase C co 64.6 4.5 9.7E-05 24.2 1.4 33 39-73 10-45 (50)
46 PF14446 Prok-RING_1: Prokaryo 64.4 4 8.7E-05 27.5 1.3 31 40-72 5-37 (54)
47 KOG3005 GIY-YIG type nuclease 63.5 4.4 9.6E-05 35.1 1.7 52 39-90 184-240 (276)
48 smart00547 ZnF_RBZ Zinc finger 62.5 4 8.6E-05 22.3 0.8 15 81-95 1-15 (26)
49 smart00109 C1 Protein kinase C 61.0 3.5 7.5E-05 24.4 0.4 33 39-73 10-44 (49)
50 cd00162 RING RING-finger (Real 59.4 2 4.3E-05 24.2 -0.8 42 43-90 2-43 (45)
51 PF13639 zf-RING_2: Ring finge 58.8 1.6 3.4E-05 26.4 -1.4 42 41-89 1-44 (44)
52 KOG1609 Protein involved in mR 57.7 4.4 9.6E-05 32.6 0.7 54 40-95 78-136 (323)
53 PF12678 zf-rbx1: RING-H2 zinc 57.2 1.7 3.6E-05 29.6 -1.6 25 61-89 49-73 (73)
54 COG2824 PhnA Uncharacterized Z 55.0 4.7 0.0001 30.8 0.4 23 75-97 13-35 (112)
55 smart00184 RING Ring finger. E 54.5 2 4.3E-05 23.3 -1.3 25 61-88 15-39 (39)
56 PF00641 zf-RanBP: Zn-finger i 52.2 6.1 0.00013 22.4 0.5 15 80-94 2-16 (30)
57 cd00350 rubredoxin_like Rubred 51.9 12 0.00027 21.9 1.8 24 70-93 4-28 (33)
58 PF12861 zf-Apc11: Anaphase-pr 48.7 5.5 0.00012 29.0 -0.1 47 42-92 34-81 (85)
59 PF10497 zf-4CXXC_R1: Zinc-fin 48.1 11 0.00023 27.8 1.3 55 38-92 5-71 (105)
60 PF12906 RINGv: RING-variant d 47.1 2.2 4.8E-05 27.1 -2.1 44 43-88 1-47 (47)
61 smart00451 ZnF_U1 U1-like zinc 46.4 26 0.00056 19.6 2.5 13 81-93 2-14 (35)
62 cd06962 NR_DBD_FXR DNA-binding 44.0 22 0.00047 25.0 2.4 53 41-95 2-66 (84)
63 PF06677 Auto_anti-p27: Sjogre 43.4 15 0.00033 23.1 1.3 20 69-89 22-41 (41)
64 PF04071 zf-like: Cysteine-ric 42.8 83 0.0018 22.8 5.2 64 46-114 17-83 (86)
65 PF06827 zf-FPG_IleRS: Zinc fi 41.7 5.6 0.00012 22.6 -0.8 15 75-89 14-28 (30)
66 PRK00420 hypothetical protein; 39.2 44 0.00095 25.3 3.5 29 61-96 25-54 (112)
67 PF13248 zf-ribbon_3: zinc-rib 39.1 18 0.00039 20.2 1.1 21 69-90 4-24 (26)
68 PF11287 DUF3088: Protein of u 37.7 15 0.00033 27.9 0.8 36 82-117 21-64 (112)
69 KOG0802 E3 ubiquitin ligase [P 37.6 5.6 0.00012 36.2 -1.9 42 40-90 291-338 (543)
70 COG0266 Nei Formamidopyrimidin 37.4 19 0.00041 31.0 1.4 15 75-89 258-272 (273)
71 PF10235 Cript: Microtubule-as 36.7 18 0.00039 26.5 1.0 26 68-93 45-70 (90)
72 cd03019 DsbA_DsbA DsbA family, 36.7 13 0.00028 27.1 0.2 21 73-93 15-35 (178)
73 PF12773 DZR: Double zinc ribb 34.9 34 0.00074 20.9 1.9 11 78-88 39-49 (50)
74 cd02972 DsbA_family DsbA famil 34.5 13 0.00027 23.5 -0.1 14 81-94 5-18 (98)
75 cd03023 DsbA_Com1_like DsbA fa 33.2 14 0.00031 25.8 -0.0 17 75-91 7-23 (154)
76 PF13240 zinc_ribbon_2: zinc-r 32.0 29 0.00062 19.2 1.1 18 72-90 4-21 (23)
77 cd07160 NR_DBD_LXR DNA-binding 31.6 51 0.0011 24.1 2.7 55 39-95 17-83 (101)
78 PRK14559 putative protein seri 31.0 40 0.00087 32.1 2.6 50 42-94 3-53 (645)
79 PF08285 DPM3: Dolichol-phosph 30.9 64 0.0014 23.4 3.1 20 94-113 67-86 (91)
80 KOG2114 Vacuolar assembly/sort 30.7 49 0.0011 33.1 3.2 43 38-90 838-880 (933)
81 PRK10445 endonuclease VIII; Pr 30.4 30 0.00065 28.7 1.5 34 42-89 227-262 (263)
82 TIGR00570 cdk7 CDK-activating 29.9 35 0.00077 29.9 1.9 46 38-91 1-52 (309)
83 PF02318 FYVE_2: FYVE-type zin 29.5 18 0.00038 26.6 -0.0 51 39-94 53-106 (118)
84 KOG1244 Predicted transcriptio 29.2 14 0.0003 32.7 -0.7 49 40-90 224-283 (336)
85 PF00412 LIM: LIM domain; Int 29.1 13 0.00029 22.8 -0.6 28 64-91 20-56 (58)
86 KOG1493 Anaphase-promoting com 29.1 17 0.00037 26.6 -0.2 43 41-93 32-81 (84)
87 PF14260 zf-C4pol: C4-type zin 29.0 1.7E+02 0.0038 19.2 4.8 44 70-114 1-44 (73)
88 COG4391 Uncharacterized protei 29.0 39 0.00084 23.5 1.6 14 77-90 43-56 (62)
89 cd07158 NR_DBD_Ppar_like The D 28.1 37 0.00079 22.9 1.4 51 43-95 1-64 (73)
90 PF05407 Peptidase_C27: Rubell 28.1 49 0.0011 26.2 2.2 30 84-113 66-95 (166)
91 KOG3408 U1-like Zn-finger-cont 28.0 65 0.0014 25.3 2.8 39 75-113 50-88 (129)
92 PF13462 Thioredoxin_4: Thiore 27.9 15 0.00032 26.2 -0.6 18 74-91 13-30 (162)
93 COG1773 Rubredoxin [Energy pro 27.5 27 0.00059 23.6 0.6 14 79-92 33-46 (55)
94 PF12171 zf-C2H2_jaz: Zinc-fin 27.2 36 0.00077 18.6 1.0 14 82-95 1-14 (27)
95 PF13920 zf-C3HC4_3: Zinc fing 26.8 7.6 0.00016 24.0 -2.1 44 39-91 1-46 (50)
96 TIGR00686 phnA alkylphosphonat 26.5 25 0.00055 26.8 0.4 23 74-96 11-33 (109)
97 PRK14873 primosome assembly pr 26.4 54 0.0012 31.1 2.6 43 40-92 383-432 (665)
98 PF10186 Atg14: UV radiation r 25.9 1.1E+02 0.0025 24.2 4.0 15 78-92 7-21 (302)
99 PF07227 DUF1423: Protein of u 25.9 76 0.0017 29.4 3.3 55 37-93 125-194 (446)
100 PF14410 GH-E: HNH/ENDO VII su 25.9 56 0.0012 22.5 1.9 39 78-116 1-51 (70)
101 PF10367 Vps39_2: Vacuolar sor 25.1 62 0.0014 21.9 2.1 34 37-72 75-108 (109)
102 PLN02638 cellulose synthase A 25.0 83 0.0018 32.1 3.6 49 35-89 12-66 (1079)
103 PF00301 Rubredoxin: Rubredoxi 25.0 39 0.00084 21.8 1.0 14 80-93 32-45 (47)
104 cd00730 rubredoxin Rubredoxin; 25.0 58 0.0013 21.2 1.8 14 80-93 32-45 (50)
105 smart00531 TFIIE Transcription 24.5 36 0.00077 25.8 0.9 15 78-92 119-133 (147)
106 PF02891 zf-MIZ: MIZ/SP-RING z 24.5 31 0.00067 22.1 0.4 22 67-89 23-48 (50)
107 PF01323 DSBA: DSBA-like thior 24.3 38 0.00082 24.9 0.9 13 81-93 6-18 (193)
108 PF12760 Zn_Tnp_IS1595: Transp 23.9 38 0.00081 21.0 0.7 12 79-91 16-27 (46)
109 KOG4218 Nuclear hormone recept 23.7 45 0.00097 30.6 1.5 55 39-95 14-80 (475)
110 COG5415 Predicted integral mem 23.7 44 0.00096 28.6 1.3 58 30-93 164-225 (251)
111 PRK10220 hypothetical protein; 23.7 32 0.00069 26.3 0.4 23 74-96 12-34 (111)
112 smart00399 ZnF_C4 c4 zinc fing 23.3 65 0.0014 21.4 1.9 51 42-94 1-63 (70)
113 cd07168 NR_DBD_DHR4_like DNA-b 23.2 60 0.0013 23.0 1.8 53 41-95 7-71 (90)
114 cd06958 NR_DBD_COUP_TF DNA-bin 23.0 53 0.0011 22.3 1.4 51 43-95 1-63 (73)
115 PF10276 zf-CHCC: Zinc-finger 23.0 44 0.00095 21.0 0.9 15 76-90 22-37 (40)
116 cd07162 NR_DBD_PXR DNA-binding 22.5 47 0.001 23.3 1.1 52 42-95 1-64 (87)
117 PF09889 DUF2116: Uncharacteri 22.3 94 0.002 21.0 2.5 23 67-90 3-26 (59)
118 KOG2932 E3 ubiquitin ligase in 22.2 1.1E+02 0.0024 27.8 3.5 77 40-127 90-182 (389)
119 PRK14973 DNA topoisomerase I; 22.2 67 0.0015 31.9 2.4 54 41-96 589-671 (936)
120 cd06965 NR_DBD_Ppar DNA-bindin 22.0 52 0.0011 23.0 1.2 50 43-95 2-63 (84)
121 COG5141 PHD zinc finger-contai 21.6 39 0.00084 32.3 0.7 51 38-89 301-360 (669)
122 cd03025 DsbA_FrnE_like DsbA fa 21.5 59 0.0013 24.0 1.5 13 82-94 8-20 (193)
123 KOG0129 Predicted RNA-binding 21.4 37 0.00079 32.0 0.4 41 37-95 452-495 (520)
124 PF12855 Ecl1: Life-span regul 21.2 33 0.00072 21.9 0.1 19 40-58 6-27 (43)
125 PRK01103 formamidopyrimidine/5 20.5 46 0.00099 27.6 0.8 15 76-90 259-273 (274)
126 PF03854 zf-P11: P-11 zinc fin 20.3 25 0.00053 23.6 -0.7 44 42-94 4-47 (50)
127 PF02977 CarbpepA_inh: Carboxy 20.3 72 0.0016 21.0 1.5 15 76-90 15-29 (46)
128 COG1645 Uncharacterized Zn-fin 20.2 50 0.0011 25.8 0.9 20 75-94 37-56 (131)
129 PHA02929 N1R/p28-like protein; 20.2 27 0.00058 29.4 -0.6 48 39-92 173-226 (238)
130 PF05502 Dynactin_p62: Dynacti 20.1 53 0.0012 30.0 1.2 36 53-95 4-39 (483)
131 PF14047 DCR: Dppa2/4 conserve 20.1 45 0.00098 23.4 0.6 28 63-92 38-65 (66)
132 KOG3456 NADH:ubiquinone oxidor 20.1 81 0.0018 24.4 2.0 45 40-92 70-114 (120)
No 1
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.75 E-value=2.4e-09 Score=98.48 Aligned_cols=54 Identities=31% Similarity=0.704 Sum_probs=47.2
Q ss_pred cccccccccCCCccE---EecCCCCCcccccccccCCC--CccCCCCCccccccchhhhhhHH
Q 037252 40 EEPCIKCNRQRDENL---LVCSQSGCPISVHENCLSCG--VKFDDVGNFYCPYCWYKCELMRT 97 (138)
Q Consensus 40 ~d~C~~C~~~G~e~L---L~Cd~~gCp~s~H~~Cl~~~--~~~dd~G~fyCP~C~yk~a~~~~ 97 (138)
+++|-.|+..|. . ++|| +||.+||..||.+| +.-.|.|.||||.|.++-.....
T Consensus 253 ~~fCsaCn~~~~--F~~~i~CD--~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k~~in~~ 311 (613)
T KOG4299|consen 253 EDFCSACNGSGL--FNDIICCD--GCPRSFHQTCLEPPLEPENIPPGSWFCPECKIKSVINPK 311 (613)
T ss_pred HHHHHHhCCccc--cccceeec--CCchHHHHhhcCCCCCcccCCCCccccCCCeeeeecccc
Confidence 679999999999 6 9999 89999999999998 55579999999999988655443
No 2
>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 PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=98.54 E-value=2.6e-08 Score=62.50 Aligned_cols=47 Identities=28% Similarity=0.706 Sum_probs=37.1
Q ss_pred cccccccCCC-ccEEecCCCCCcccccccccCCCCcc--CCCCCccccccch
Q 037252 42 PCIKCNRQRD-ENLLVCSQSGCPISVHENCLSCGVKF--DDVGNFYCPYCWY 90 (138)
Q Consensus 42 ~C~~C~~~G~-e~LL~Cd~~gCp~s~H~~Cl~~~~~~--dd~G~fyCP~C~y 90 (138)
+|.+|+..+. +.+|.|+ +|...||..|++++... .+.+.|+||.|.-
T Consensus 1 ~C~vC~~~~~~~~~i~C~--~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCD--SCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBS--TTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcC--CCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 4778888333 3599999 99999999999987652 3456999999963
No 4
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=98.27 E-value=2.8e-07 Score=86.18 Aligned_cols=55 Identities=35% Similarity=0.718 Sum_probs=49.6
Q ss_pred CCCcccccccccccCCCccEEecCCCCCcccccccccCCCCccCCCCCccccccchhhh
Q 037252 35 VDFLEEEPCIKCNRQRDENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKCE 93 (138)
Q Consensus 35 ~~~~~~d~C~~C~~~G~e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~a 93 (138)
-++-+++.|.+|..+|. ||+|+ +||.+||..|++.++.-.|.|+|.||.|..+.-
T Consensus 42 ~~~~~~e~c~ic~~~g~--~l~c~--tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~~p~~ 96 (696)
T KOG0383|consen 42 WDDAEQEACRICADGGE--LLWCD--TCPASFHASCLGPPLTPQPNGEFICPRCFCPKN 96 (696)
T ss_pred cchhhhhhhhhhcCCCc--EEEec--cccHHHHHHccCCCCCcCCccceeeeeeccCCC
Confidence 45778999999999999 99999 999999999999988888999999999965544
No 5
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=98.04 E-value=2.4e-06 Score=78.57 Aligned_cols=70 Identities=24% Similarity=0.583 Sum_probs=53.5
Q ss_pred hhhcccCCCCCCCCCCcCCCcccccccccccCCC---ccEEecCCCCCcccccccccCCCCccCCCCCccccccchhh
Q 037252 18 IHIENHGGSGRSGDFTDVDFLEEEPCIKCNRQRD---ENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKC 92 (138)
Q Consensus 18 ~~~~~h~~s~~~~~~~~~~~~~~d~C~~C~~~G~---e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~ 92 (138)
+|+|+|--+---+-.++.+ .=++.|.+|..... +.+++|| ||-++||.+|-| ..|.|+|.|+|-.|.|..
T Consensus 172 f~~e~~lp~k~vepi~~~d-~~d~~C~~c~~t~~eN~naiVfCd--gC~i~VHq~CYG--I~f~peG~WlCrkCi~~~ 244 (669)
T COG5141 172 FFFEHGLPDKHVEPIEPSD-EFDDICTKCTSTHNENSNAIVFCD--GCEICVHQSCYG--IQFLPEGFWLCRKCIYGE 244 (669)
T ss_pred HhhhccCccccccccCCch-hhhhhhHhccccccCCcceEEEec--Ccchhhhhhccc--ceecCcchhhhhhhcccc
Confidence 5666666554222223322 22689999998776 4799999 999999999999 899999999999998753
No 6
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.97 E-value=3.2e-06 Score=70.52 Aligned_cols=46 Identities=28% Similarity=0.673 Sum_probs=39.4
Q ss_pred cccccccCCCccEEecCCCCCc-ccccccccCCCCccCCCCCccccccchhh
Q 037252 42 PCIKCNRQRDENLLVCSQSGCP-ISVHENCLSCGVKFDDVGNFYCPYCWYKC 92 (138)
Q Consensus 42 ~C~~C~~~G~e~LL~Cd~~gCp-~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~ 92 (138)
+|- |...|+ -+-||..+|| -=||..|+| +...|.|.||||.|.-..
T Consensus 223 ~Cn-qvsyg~--Mi~CDn~~C~~eWFH~~CVG--L~~~PkgkWyC~~C~~~~ 269 (274)
T KOG1973|consen 223 ICN-QVSYGK--MIGCDNPGCPIEWFHFTCVG--LKTKPKGKWYCPRCKAEN 269 (274)
T ss_pred Eec-cccccc--ccccCCCCCCcceEEEeccc--cccCCCCcccchhhhhhh
Confidence 444 667777 9999999999 779999999 889999999999997543
No 7
>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=97.81 E-value=4.2e-06 Score=65.73 Aligned_cols=35 Identities=23% Similarity=0.399 Sum_probs=30.2
Q ss_pred cccccccCCCCccCCCCCccccccchhhhhhHHHH
Q 037252 65 SVHENCLSCGVKFDDVGNFYCPYCWYKCELMRTKE 99 (138)
Q Consensus 65 s~H~~Cl~~~~~~dd~G~fyCP~C~yk~a~~~~~e 99 (138)
.||..||.+|++-.|+|+|+||.|..+.....+..
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~~~~~~~ 35 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEVEKSGQSAMP 35 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcCCCCCCcccc
Confidence 48999999999999999999999998776655543
No 8
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=97.68 E-value=2.2e-05 Score=76.49 Aligned_cols=76 Identities=22% Similarity=0.434 Sum_probs=58.6
Q ss_pred cchhhcccCCCCCCCCCCcCCCcccccccccccCCC---ccEEecCCCCCcccccccccCCCCccCCCCCccccccchhh
Q 037252 16 IGIHIENHGGSGRSGDFTDVDFLEEEPCIKCNRQRD---ENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKC 92 (138)
Q Consensus 16 ~~~~~~~h~~s~~~~~~~~~~~~~~d~C~~C~~~G~---e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~ 92 (138)
..+-.|.||-+--.++..+.+..++..|-+|.++-- .-+|.|| +|-++||..|.| .+++|+|.|+|-.|.+..
T Consensus 195 dr~eke~~f~~~e~~~~~~~~~~~D~~C~iC~~~~~~n~n~ivfCD--~Cnl~VHq~Cyg--i~~ipeg~WlCr~Cl~s~ 270 (1051)
T KOG0955|consen 195 DRLEKESYFKNYELGDPKDALLEEDAVCCICLDGECQNSNVIVFCD--GCNLAVHQECYG--IPFIPEGQWLCRRCLQSP 270 (1051)
T ss_pred hhHHHHHHhhhhhccCCCccccCCCccceeecccccCCCceEEEcC--CCcchhhhhccC--CCCCCCCcEeehhhccCc
Confidence 333444455555444555566667889999988754 3689999 999999999999 889999999999999877
Q ss_pred hhh
Q 037252 93 ELM 95 (138)
Q Consensus 93 a~~ 95 (138)
+..
T Consensus 271 ~~~ 273 (1051)
T KOG0955|consen 271 QRP 273 (1051)
T ss_pred Ccc
Confidence 653
No 9
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=97.50 E-value=4.8e-05 Score=65.91 Aligned_cols=49 Identities=29% Similarity=0.618 Sum_probs=41.2
Q ss_pred ccccccccccCCC-ccEEecCCCCCcccccccccCCCCccCCCCCccccccc
Q 037252 39 EEEPCIKCNRQRD-ENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCW 89 (138)
Q Consensus 39 ~~d~C~~C~~~G~-e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~ 89 (138)
+=-.|.+|+-+.+ +.||+|| .|-+.||-.||.+|+...|+|-|.|-.|.
T Consensus 280 eck~csicgtsenddqllfcd--dcdrgyhmyclsppm~eppegswsc~KOG 329 (336)
T KOG1244|consen 280 ECKYCSICGTSENDDQLLFCD--DCDRGYHMYCLSPPMVEPPEGSWSCHLCL 329 (336)
T ss_pred ecceeccccCcCCCceeEeec--ccCCceeeEecCCCcCCCCCCchhHHHHH
Confidence 3446777765433 3499999 99999999999999999999999999996
No 10
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=97.21 E-value=7e-05 Score=45.92 Aligned_cols=34 Identities=29% Similarity=0.764 Sum_probs=18.2
Q ss_pred cEEecCCCCCcccccccccCCCCccCCCCCccccccc
Q 037252 53 NLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCW 89 (138)
Q Consensus 53 ~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~ 89 (138)
.||.|+ +|.++||.+|-|.... .+..+|+|-.|.
T Consensus 3 ~ll~C~--~C~v~VH~~CYGv~~~-~~~~~W~C~~C~ 36 (36)
T PF13831_consen 3 PLLFCD--NCNVAVHQSCYGVSEV-PDGDDWLCDRCE 36 (36)
T ss_dssp EEEE-S--SS--EEEHHHHT-SS---SS-----HHH-
T ss_pred ceEEeC--CCCCcCChhhCCcccC-CCCCcEECCcCC
Confidence 399999 9999999999996433 333379998873
No 11
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.21 E-value=0.00033 Score=67.64 Aligned_cols=67 Identities=25% Similarity=0.484 Sum_probs=52.3
Q ss_pred CcccccccccccCCC-ccEEecCCCCCccc-ccccccCCCCccCCCCCccccccchhhhhhHHHHHHHHHHHHHH
Q 037252 37 FLEEEPCIKCNRQRD-ENLLVCSQSGCPIS-VHENCLSCGVKFDDVGNFYCPYCWYKCELMRTKELRKKAKETKK 109 (138)
Q Consensus 37 ~~~~d~C~~C~~~G~-e~LL~Cd~~gCp~s-~H~~Cl~~~~~~dd~G~fyCP~C~yk~a~~~~~e~kk~a~~AkK 109 (138)
..+.--|..|..... |-||.|+ +|-.. ||..||.+.+.-.|.+.|||+-|..- .+.+.+..+..|-.
T Consensus 212 ~~E~~~C~IC~~~DpEdVLLLCD--sCN~~~YH~YCLDPdl~eiP~~eWYC~NC~dL----~~~eh~~~~~~~~~ 280 (1134)
T KOG0825|consen 212 SQEEVKCDICTVHDPEDVLLLCD--SCNKVYYHVYCLDPDLSESPVNEWYCTNCSLL----EITEHKDFTLKTEE 280 (1134)
T ss_pred ccccccceeeccCChHHhheeec--ccccceeeccccCcccccccccceecCcchhh----hhhhhhHHHHHHHH
Confidence 344568999999887 5799999 99999 99999998777789999999999853 34444554444444
No 12
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.18 E-value=0.00019 Score=61.14 Aligned_cols=57 Identities=28% Similarity=0.637 Sum_probs=43.4
Q ss_pred CCCCCCcCC--CcccccccccccC--CCccEEecCCCCCccc-ccccccCCCCccCCCCCccccccc
Q 037252 28 RSGDFTDVD--FLEEEPCIKCNRQ--RDENLLVCSQSGCPIS-VHENCLSCGVKFDDVGNFYCPYCW 89 (138)
Q Consensus 28 ~~~~~~~~~--~~~~d~C~~C~~~--G~e~LL~Cd~~gCp~s-~H~~Cl~~~~~~dd~G~fyCP~C~ 89 (138)
.+.+.++.+ -.++-+| .|... |+ .+-||+..|++- ||..|+| +.-.|.|-||||.|.
T Consensus 207 ~~~~vss~d~se~e~lYC-fCqqvSyGq--MVaCDn~nCkrEWFH~~CVG--Lk~pPKG~WYC~eCk 268 (271)
T COG5034 207 KSRGVSSEDNSEGEELYC-FCQQVSYGQ--MVACDNANCKREWFHLECVG--LKEPPKGKWYCPECK 268 (271)
T ss_pred cccCcCccccccCceeEE-Eeccccccc--ceecCCCCCchhheeccccc--cCCCCCCcEeCHHhH
Confidence 444444444 2334455 46654 77 999999999996 7999999 888999999999996
No 13
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=96.67 E-value=0.00078 Score=64.24 Aligned_cols=47 Identities=28% Similarity=0.755 Sum_probs=39.2
Q ss_pred cccccccCCC--c-cEEecCCCCCcccccccccCCCCccCCCCCccccccch
Q 037252 42 PCIKCNRQRD--E-NLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWY 90 (138)
Q Consensus 42 ~C~~C~~~G~--e-~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~y 90 (138)
-|.+|.+.-- | -|+.|||-.|.++||.-|-+ ..-.|.|.|||-.|.-
T Consensus 7 GCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYG--IvqVPtGpWfCrKCes 56 (900)
T KOG0956|consen 7 GCCVCSDERGWAENPLVYCDGHNCSVAVHQACYG--IVQVPTGPWFCRKCES 56 (900)
T ss_pred ceeeecCcCCCccCceeeecCCCceeeeehhcce--eEecCCCchhhhhhhh
Confidence 4778865432 2 49999999999999999999 6678999999999963
No 14
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=96.58 E-value=0.00047 Score=69.03 Aligned_cols=55 Identities=25% Similarity=0.595 Sum_probs=48.8
Q ss_pred CcccccccccccCCC-ccEEecCCCCCcccccccccCCCCccCCCCCccccccchhhh
Q 037252 37 FLEEEPCIKCNRQRD-ENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKCE 93 (138)
Q Consensus 37 ~~~~d~C~~C~~~G~-e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~a 93 (138)
....-+|-+|...++ +.++.|+ +|--.||..|+-+-+...+.|+|+||.|.-.+-
T Consensus 1105 s~~~~~c~~cr~k~~~~~m~lc~--~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1105 SAVNALCKVCRRKKQDEKMLLCD--ECLSGFHLFCLRPALSSVPPGDWMCPSCRKEHR 1160 (1404)
T ss_pred ccchhhhhhhhhcccchhhhhhH--hhhhhHHHHhhhhhhccCCcCCccCCccchhhh
Confidence 344669999999988 5999999 999999999999999999999999999985553
No 15
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=96.39 E-value=0.0015 Score=61.51 Aligned_cols=50 Identities=24% Similarity=0.497 Sum_probs=44.2
Q ss_pred ccccccccCCC-ccEEecCCCCCcccccccccCCCCccCCCCCccccccchhh
Q 037252 41 EPCIKCNRQRD-ENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKC 92 (138)
Q Consensus 41 d~C~~C~~~G~-e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~ 92 (138)
-.|..|+..|+ .+++.|+ +|-++||-.|+.++..-.++|-|+||.|.-=+
T Consensus 69 rvCe~c~~~gD~~kf~~Ck--~cDvsyh~yc~~P~~~~v~sg~~~ckk~~~c~ 119 (694)
T KOG4443|consen 69 RVCEACGTTGDPKKFLLCK--RCDVSYHCYCQKPPNDKVPSGPWLCKKCTRCR 119 (694)
T ss_pred eeeeeccccCCcccccccc--cccccccccccCCccccccCcccccHHHHhhh
Confidence 46888888777 5899999 99999999999999999999999999987433
No 16
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.31 E-value=0.0019 Score=56.70 Aligned_cols=46 Identities=24% Similarity=0.463 Sum_probs=40.5
Q ss_pred cccccccccCCC-ccEEecCCCCCcccccccccCCCCccCCCCCcccc-ccc
Q 037252 40 EEPCIKCNRQRD-ENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCP-YCW 89 (138)
Q Consensus 40 ~d~C~~C~~~G~-e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP-~C~ 89 (138)
=.+|+.|++.-. +..|+|| .|-+.||.-|+| +.-.|.|.|.|- ||.
T Consensus 314 C~lC~IC~~P~~E~E~~FCD--~CDRG~HT~CVG--L~~lP~G~WICD~~C~ 361 (381)
T KOG1512|consen 314 CELCRICLGPVIESEHLFCD--VCDRGPHTLCVG--LQDLPRGEWICDMRCR 361 (381)
T ss_pred cHhhhccCCcccchheeccc--cccCCCCccccc--cccccCccchhhhHHH
Confidence 458999998876 4899999 999999999999 888999999997 564
No 17
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=95.42 E-value=0.0056 Score=55.65 Aligned_cols=63 Identities=21% Similarity=0.381 Sum_probs=49.6
Q ss_pred CCcccccccccccCCC---ccEEecCCCCCcccccccccCCCCc----cCCCCCccccccchhhhhhHHHHHH
Q 037252 36 DFLEEEPCIKCNRQRD---ENLLVCSQSGCPISVHENCLSCGVK----FDDVGNFYCPYCWYKCELMRTKELR 101 (138)
Q Consensus 36 ~~~~~d~C~~C~~~G~---e~LL~Cd~~gCp~s~H~~Cl~~~~~----~dd~G~fyCP~C~yk~a~~~~~e~k 101 (138)
...|.. |.+|.-+|. .++|.|+ +|---||.-|.-+..+ -|+...|||-.|.+.....+..+++
T Consensus 165 ~~~n~q-c~vC~~g~~~~~NrmlqC~--~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~~~r~t~~ 234 (464)
T KOG4323|consen 165 HKVNLQ-CSVCYCGGPGAGNRMLQCD--KCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPKKVPRLTLR 234 (464)
T ss_pred ccccce-eeeeecCCcCccceeeeec--ccccHHHHHhccCCCCHhhccCccceEeehhhccchhhccccccc
Confidence 344444 999986654 3899999 9999999999986433 2688999999999998877766666
No 18
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=95.28 E-value=0.0067 Score=56.59 Aligned_cols=47 Identities=28% Similarity=0.559 Sum_probs=42.6
Q ss_pred cccccccccCCC-ccEEecCCCCCcccccccccCCCCccCCCCC----cccccc
Q 037252 40 EEPCIKCNRQRD-ENLLVCSQSGCPISVHENCLSCGVKFDDVGN----FYCPYC 88 (138)
Q Consensus 40 ~d~C~~C~~~G~-e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~----fyCP~C 88 (138)
...|.+|++.-+ -.|+.|| +|-+.||.-||++|++-.|..+ |.|..|
T Consensus 544 ~ysCgiCkks~dQHll~~CD--tC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsEC 595 (707)
T KOG0957|consen 544 NYSCGICKKSTDQHLLTQCD--TCHLHYHLGCLSPPLTRLPKKNKNFGWQCSEC 595 (707)
T ss_pred ceeeeeeccchhhHHHhhcc--hhhceeeccccCCccccCcccccCcceeeccc
Confidence 578999999876 4789999 9999999999999998888877 999999
No 19
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=94.96 E-value=0.0097 Score=40.71 Aligned_cols=47 Identities=26% Similarity=0.590 Sum_probs=35.9
Q ss_pred cccccccccC-CCccEEecCCCCCcccccccccCCCCcc---CCCCCcccccc
Q 037252 40 EEPCIKCNRQ-RDENLLVCSQSGCPISVHENCLSCGVKF---DDVGNFYCPYC 88 (138)
Q Consensus 40 ~d~C~~C~~~-G~e~LL~Cd~~gCp~s~H~~Cl~~~~~~---dd~G~fyCP~C 88 (138)
...|..|++. |- .+.|...+|..+||..|.-...-+ ++...++-.||
T Consensus 36 ~~~C~~C~~~~Ga--~i~C~~~~C~~~fH~~CA~~~~~~~~~~~~~~~~~~~C 86 (90)
T PF13771_consen 36 KLKCSICKKKGGA--CIGCSHPGCSRSFHVPCARKAGCFIEFDEDNGKFRIFC 86 (90)
T ss_pred CCCCcCCCCCCCe--EEEEeCCCCCcEEChHHHccCCeEEEEccCCCceEEEC
Confidence 4689999999 99 999999999999999998853322 22334555555
No 20
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=94.78 E-value=0.018 Score=57.59 Aligned_cols=81 Identities=19% Similarity=0.282 Sum_probs=61.4
Q ss_pred eecccccCccchhhcc-cCCCC---CC-----CCCCcCCCcccccccccccCCCccEEecCCCCCcccccccccCCCCcc
Q 037252 7 VASAYNDDEIGIHIEN-HGGSG---RS-----GDFTDVDFLEEEPCIKCNRQRDENLLVCSQSGCPISVHENCLSCGVKF 77 (138)
Q Consensus 7 ~~~~~~~~~~~~~~~~-h~~s~---~~-----~~~~~~~~~~~d~C~~C~~~G~e~LL~Cd~~gCp~s~H~~Cl~~~~~~ 77 (138)
|-.+|-.--|...++- ||++- ++ +=++.+...=+|.|..|.+.|. ||||- +||+.||-+|+-.|.--
T Consensus 302 ~~~eY~~~pv~~klkILQ~L~Dq~l~~~s~R~e~~se~~~~~ddhcrf~~d~~~--~lc~E--t~prvvhlEcv~hP~~~ 377 (1414)
T KOG1473|consen 302 VEDEYPYRPVSNKLKILQFLCDQFLTVNSLRDEIDSEGEIEYDDHCRFCHDLGD--LLCCE--TCPRVVHLECVFHPRFA 377 (1414)
T ss_pred ccccccccchhhhHHHHHHHHHHHHHHHHHHHHHhcccceeecccccccCcccc--eeecc--cCCceEEeeecCCcccc
Confidence 3345555555555555 66655 11 2245555666899999999999 99999 99999999999987777
Q ss_pred CCCCCccccccchh
Q 037252 78 DDVGNFYCPYCWYK 91 (138)
Q Consensus 78 dd~G~fyCP~C~yk 91 (138)
.++..|-|-.|.+-
T Consensus 378 ~~s~~~e~evc~~h 391 (1414)
T KOG1473|consen 378 VPSAFWECEVCNIH 391 (1414)
T ss_pred CCCccchhhhhhhh
Confidence 89999999999743
No 21
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=94.59 E-value=0.017 Score=55.72 Aligned_cols=49 Identities=24% Similarity=0.617 Sum_probs=42.0
Q ss_pred ccccccccccCCC---ccEEecCCCCCcccccccccCCCCccCCCCCccccccchh
Q 037252 39 EEEPCIKCNRQRD---ENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYK 91 (138)
Q Consensus 39 ~~d~C~~C~~~G~---e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk 91 (138)
|+-+|-+|..+.- ..+++|| .|-+.||..|.| ..-+|+|.|.|--|...
T Consensus 270 edviCDvCrspD~e~~neMVfCd--~Cn~cVHqaCyG--Ile~p~gpWlCr~Calg 321 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCD--KCNICVHQACYG--ILEVPEGPWLCRTCALG 321 (893)
T ss_pred ccceeceecCCCccccceeEEec--cchhHHHHhhhc--eeecCCCCeeehhcccc
Confidence 6778999988722 1699999 999999999999 77789999999999864
No 22
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=94.26 E-value=0.023 Score=46.14 Aligned_cols=28 Identities=36% Similarity=0.865 Sum_probs=23.4
Q ss_pred ccccc------cCCCccEEecCCCCCcccccccccCCC
Q 037252 43 CIKCN------RQRDENLLVCSQSGCPISVHENCLSCG 74 (138)
Q Consensus 43 C~~C~------~~G~e~LL~Cd~~gCp~s~H~~Cl~~~ 74 (138)
|-.|. ..|+ |+.|- ||..|||..|||+-
T Consensus 2 C~~C~~~g~~~~kG~--Lv~CQ--GCs~sYHk~CLG~R 35 (175)
T PF15446_consen 2 CDTCGYEGDDRNKGP--LVYCQ--GCSSSYHKACLGPR 35 (175)
T ss_pred cccccCCCCCccCCC--eEEcC--ccChHHHhhhcCCc
Confidence 67775 3466 99999 99999999999963
No 23
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=94.03 E-value=0.015 Score=58.21 Aligned_cols=58 Identities=16% Similarity=0.071 Sum_probs=49.3
Q ss_pred CCcCCCcccccccccccCCCccEEecCCCCCcccccc-cccC--CCCccCCCCCccccccchhh
Q 037252 32 FTDVDFLEEEPCIKCNRQRDENLLVCSQSGCPISVHE-NCLS--CGVKFDDVGNFYCPYCWYKC 92 (138)
Q Consensus 32 ~~~~~~~~~d~C~~C~~~G~e~LL~Cd~~gCp~s~H~-~Cl~--~~~~~dd~G~fyCP~C~yk~ 92 (138)
.++-=|++.+-|++|++++. +|+|. ++||..||. .||+ .--.+.+.|-|+||.|..++
T Consensus 420 ~gr~ywfi~rrl~Ie~~det--~l~yy-sT~pqly~ll~cLd~~~~e~~L~d~i~~~~ee~~rq 480 (1414)
T KOG1473|consen 420 YGRKYWFISRRLRIEGMDET--LLWYY-STCPQLYHLLRCLDRTYVEMYLCDGIWERREEIIRQ 480 (1414)
T ss_pred cccchhceeeeeEEecCCCc--EEEEe-cCcHHHHHHHHHhchHHHHHhhccchhhhHHHHHHh
Confidence 44445999999999999999 99999 349999999 9999 44566799999999998765
No 24
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=92.12 E-value=0.066 Score=38.04 Aligned_cols=33 Identities=24% Similarity=0.630 Sum_probs=28.9
Q ss_pred ccccccccccC-CCccEEecCCCCCcccccccccCC
Q 037252 39 EEEPCIKCNRQ-RDENLLVCSQSGCPISVHENCLSC 73 (138)
Q Consensus 39 ~~d~C~~C~~~-G~e~LL~Cd~~gCp~s~H~~Cl~~ 73 (138)
....|..|+.. |- ++.|+..+|..+||..|.-.
T Consensus 54 ~~~~C~iC~~~~G~--~i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 54 FKLKCSICGKSGGA--CIKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred cCCcCcCCCCCCce--eEEcCCCCCCcCCCHHHHHH
Confidence 35799999995 77 99999888999999999864
No 25
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=90.60 E-value=0.11 Score=50.22 Aligned_cols=53 Identities=32% Similarity=0.820 Sum_probs=43.1
Q ss_pred cccccccccCCCc------cEEecCCCCCcccccccccCC-CCccCCCCC-----ccccccchhh
Q 037252 40 EEPCIKCNRQRDE------NLLVCSQSGCPISVHENCLSC-GVKFDDVGN-----FYCPYCWYKC 92 (138)
Q Consensus 40 ~d~C~~C~~~G~e------~LL~Cd~~gCp~s~H~~Cl~~-~~~~dd~G~-----fyCP~C~yk~ 92 (138)
.-.|++|+..|.+ --+-|...+|-.+||.+|.-. .+-.+++|+ -||-||.|-.
T Consensus 117 nKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~Hf 181 (900)
T KOG0956|consen 117 NKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKYHF 181 (900)
T ss_pred cceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccccceechhHHHHH
Confidence 4589999999764 368899999999999999876 466677766 4999999854
No 26
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=90.04 E-value=0.21 Score=47.04 Aligned_cols=50 Identities=22% Similarity=0.298 Sum_probs=38.4
Q ss_pred CCcCCCcccccccccccCCCccEEecCCCCCcccccccccCCCCccCCCCCccccccc
Q 037252 32 FTDVDFLEEEPCIKCNRQRDENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCW 89 (138)
Q Consensus 32 ~~~~~~~~~d~C~~C~~~G~e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~ 89 (138)
..+..| -..|-.|..+|+ +|+|+ .||.+||..|.+..+. +.-.++|-.|.
T Consensus 41 ~~~~k~--~ts~~~~~~~gn--~~~~~--~~~~s~h~~~~~~~~s--p~~~~~~~~~~ 90 (613)
T KOG4299|consen 41 RRSGKA--ATSCGICKSGGN--LLCCD--HCPASFHLECDKPPLS--PDLKGSEINCS 90 (613)
T ss_pred ccccch--hhhcchhhhcCC--ccccc--cCccccchhccCcccC--ccccccccccc
Confidence 344444 889999999999 99999 9999999999996544 55445544444
No 27
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=88.95 E-value=0.082 Score=50.26 Aligned_cols=51 Identities=18% Similarity=0.240 Sum_probs=47.3
Q ss_pred CcccccccccccCCCccEEecCCCCCcccccccccCC-CCccCCCCCccccccchh
Q 037252 37 FLEEEPCIKCNRQRDENLLVCSQSGCPISVHENCLSC-GVKFDDVGNFYCPYCWYK 91 (138)
Q Consensus 37 ~~~~d~C~~C~~~G~e~LL~Cd~~gCp~s~H~~Cl~~-~~~~dd~G~fyCP~C~yk 91 (138)
.+.++.|-.|.+.++ +|.|. .|+..+|..|+.+ |++..+-|.|-||.|+-+
T Consensus 503 ~~~d~~~~~~~~~l~--~l~~p--~~lrr~k~d~l~~~P~Kte~i~~~~~~~~Q~~ 554 (696)
T KOG0383|consen 503 EFHDISCEEQIKKLH--LLLCP--HMLRRLKLDVLKPMPLKTELIGRVELSPCQKK 554 (696)
T ss_pred hcchhhHHHHHHhhc--cccCc--hhhhhhhhhhccCCCccceeEEEEecCHHHHH
Confidence 556789999999999 99999 9999999999998 999999999999999843
No 28
>PHA02862 5L protein; Provisional
Probab=88.91 E-value=0.11 Score=41.54 Aligned_cols=53 Identities=23% Similarity=0.350 Sum_probs=43.7
Q ss_pred cccccccccCCCccEEecCCCCCcccccccccCCCCccCCCCCccccccchhhhh
Q 037252 40 EEPCIKCNRQRDENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKCEL 94 (138)
Q Consensus 40 ~d~C~~C~~~G~e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~a~ 94 (138)
.+.|+.|...+++.+-+|-=+|=-.-+|.+||.. =...++.-+||.|.++...
T Consensus 2 ~diCWIC~~~~~e~~~PC~C~GS~K~VHq~CL~~--WIn~S~k~~CeLCkteY~I 54 (156)
T PHA02862 2 SDICWICNDVCDERNNFCGCNEEYKVVHIKCMQL--WINYSKKKECNLCKTKYNI 54 (156)
T ss_pred CCEEEEecCcCCCCcccccccCcchhHHHHHHHH--HHhcCCCcCccCCCCeEEE
Confidence 4789999999987778877557788999999984 3357889999999987765
No 29
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=87.33 E-value=0.5 Score=45.26 Aligned_cols=55 Identities=31% Similarity=0.726 Sum_probs=49.1
Q ss_pred CCCcccccccccccCCCccEEecCCCCCcccccccccCCCCccCCCCCccccccchh
Q 037252 35 VDFLEEEPCIKCNRQRDENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYK 91 (138)
Q Consensus 35 ~~~~~~d~C~~C~~~G~e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk 91 (138)
........|..|.++..+.++.|+ +|--++|..|...+++..+.|+|.||.|...
T Consensus 150 ~~~~~~~~~~~~~k~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 204 (904)
T KOG1246|consen 150 VEFIDYPQCNTCSKGKEEKLLLCD--SCDDSYHTYCLRPPLTRVPDGDWRCPKCIPT 204 (904)
T ss_pred cccccchhhhccccCCCccceecc--cccCcccccccCCCCCcCCcCcccCCccccc
Confidence 456677899999999976666888 9999999999999999999999999999866
No 30
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=87.30 E-value=0.53 Score=44.41 Aligned_cols=51 Identities=29% Similarity=0.647 Sum_probs=36.5
Q ss_pred cccccccccCCC---ccEEecCCCCCcccccccccCCC-----CccCC---CCCccccccchhh
Q 037252 40 EEPCIKCNRQRD---ENLLVCSQSGCPISVHENCLSCG-----VKFDD---VGNFYCPYCWYKC 92 (138)
Q Consensus 40 ~d~C~~C~~~G~---e~LL~Cd~~gCp~s~H~~Cl~~~-----~~~dd---~G~fyCP~C~yk~ 92 (138)
-.+|-+|-..-. ..+|.|+ .|-+.||..|-|.. +.... ..-|||--|.|-.
T Consensus 119 ~~iCcVClg~rs~da~ei~qCd--~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~Gv 180 (707)
T KOG0957|consen 119 AVICCVCLGQRSVDAGEILQCD--KCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYGV 180 (707)
T ss_pred ceEEEEeecCccccccceeecc--ccCceecccccccccccccCCCCccCCCCchhhhhHhcCC
Confidence 348999964322 1499999 99999999999964 22222 2679998887754
No 31
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=82.24 E-value=1.3 Score=40.11 Aligned_cols=43 Identities=19% Similarity=0.392 Sum_probs=35.3
Q ss_pred CCCCCcCCCcccccccccccCCCccEEecC------CCCCcccccccccCC
Q 037252 29 SGDFTDVDFLEEEPCIKCNRQRDENLLVCS------QSGCPISVHENCLSC 73 (138)
Q Consensus 29 ~~~~~~~~~~~~d~C~~C~~~G~e~LL~Cd------~~gCp~s~H~~Cl~~ 73 (138)
..+.....-++.+.|-+|.++|. |+.|+ -.+||.++|..|...
T Consensus 78 ~~~~~~~~~~~~~~c~vc~~ggs--~v~~~s~~~~~~r~c~~~~~~~c~~~ 126 (463)
T KOG1081|consen 78 EPGSRRHPKIEPSECFVCFKGGS--LVTCKSRIQAPHRKCKPAQLEKCSKR 126 (463)
T ss_pred CCCchhccCCCcchhccccCCCc--cceeccccccccccCcCccCcccccC
Confidence 34455566778899999999999 99999 788888888888775
No 32
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=82.23 E-value=1.3 Score=41.77 Aligned_cols=47 Identities=26% Similarity=0.325 Sum_probs=39.3
Q ss_pred ccccccccCCCccEEecCCCCCcccccccccCCCCcc-CCCCCccccccchh
Q 037252 41 EPCIKCNRQRDENLLVCSQSGCPISVHENCLSCGVKF-DDVGNFYCPYCWYK 91 (138)
Q Consensus 41 d~C~~C~~~G~e~LL~Cd~~gCp~s~H~~Cl~~~~~~-dd~G~fyCP~C~yk 91 (138)
-+|-.|..+|. +|.|+ .|-++||..|+.+.... +-+--|-||.|.--
T Consensus 61 ~~cfechlpg~--vl~c~--vc~Rs~h~~c~sp~~q~r~~s~p~~~p~p~s~ 108 (588)
T KOG3612|consen 61 PFCFECHLPGA--VLKCI--VCHRSFHENCQSPDPQKRNYSVPSDKPQPYSF 108 (588)
T ss_pred cccccccCCcc--eeeee--hhhccccccccCcchhhccccccccCCccccc
Confidence 38999999999 99999 99999999999975544 35567889988643
No 33
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=81.86 E-value=0.47 Score=38.18 Aligned_cols=57 Identities=21% Similarity=0.318 Sum_probs=41.9
Q ss_pred CcccccccccccCCCccEEecCCCCCcccccccccCCCCccCCCCCccccccchhhhhh
Q 037252 37 FLEEEPCIKCNRQRDENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKCELM 95 (138)
Q Consensus 37 ~~~~d~C~~C~~~G~e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~a~~ 95 (138)
+..+..|+.|..+++...-+|.=.|=--.+|.+|+. .=.+.+++-.||.|.++....
T Consensus 5 s~~~~~CRIC~~~~~~~~~PC~CkGs~k~VH~sCL~--rWi~~s~~~~CeiC~~~Y~i~ 61 (162)
T PHA02825 5 SLMDKCCWICKDEYDVVTNYCNCKNENKIVHKECLE--EWINTSKNKSCKICNGPYNIK 61 (162)
T ss_pred CCCCCeeEecCCCCCCccCCcccCCCchHHHHHHHH--HHHhcCCCCcccccCCeEEEE
Confidence 445789999998886434456533556688999998 344567999999998876654
No 34
>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=80.14 E-value=0.45 Score=30.49 Aligned_cols=46 Identities=28% Similarity=0.556 Sum_probs=29.0
Q ss_pred ccccccc---CCCccEEecCCCCCcccccccccCCCCccCCCCCccccccc
Q 037252 42 PCIKCNR---QRDENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCW 89 (138)
Q Consensus 42 ~C~~C~~---~G~e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~ 89 (138)
+|+.|.. +++.-+.+|.=.|--.-||.+||. .=+..++.-.||.|.
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~--~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLE--RWINESGNKTCEICK 49 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHH--HHHHHcCCCcCCCCC
Confidence 4788886 333244566522334679999998 334455566899883
No 35
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=80.10 E-value=0.26 Score=33.61 Aligned_cols=54 Identities=24% Similarity=0.304 Sum_probs=20.7
Q ss_pred ccccccccC----CCccEEecCCCCCcccccccccCCCCccCC-------CCCccccccchhhhh
Q 037252 41 EPCIKCNRQ----RDENLLVCSQSGCPISVHENCLSCGVKFDD-------VGNFYCPYCWYKCEL 94 (138)
Q Consensus 41 d~C~~C~~~----G~e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd-------~G~fyCP~C~yk~a~ 94 (138)
..|.+|-.. ++.-.+.|+...|...||..||..-....+ .-..-||+|.-+...
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW 67 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence 457777643 322358999999999999999984211111 122349999865443
No 36
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.67 E-value=1.1 Score=39.34 Aligned_cols=62 Identities=24% Similarity=0.368 Sum_probs=37.5
Q ss_pred CCCCCcCCCcccccccccccCCCccE-----E-ecCCCCCcccccccccCCCCccCCCCCccccccchhh
Q 037252 29 SGDFTDVDFLEEEPCIKCNRQRDENL-----L-VCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKC 92 (138)
Q Consensus 29 ~~~~~~~~~~~~d~C~~C~~~G~e~L-----L-~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~ 92 (138)
|++=-|..-.++..|.+|++.=+..+ + .=-.-+|.-+||.-|+.- =..-..--.||||.-+.
T Consensus 213 s~~glPtkhl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrG--WcivGKkqtCPYCKekV 280 (328)
T KOG1734|consen 213 SPSGLPTKHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRG--WCIVGKKQTCPYCKEKV 280 (328)
T ss_pred CCCCCCCCCCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhh--heeecCCCCCchHHHHh
Confidence 34445667888999999997654111 0 000014669999999872 12222334799997544
No 37
>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=76.70 E-value=2 Score=26.71 Aligned_cols=39 Identities=26% Similarity=0.462 Sum_probs=26.8
Q ss_pred cCCCcccccccccccCC---CccEEecCCCCCcccccccccCCC
Q 037252 34 DVDFLEEEPCIKCNRQR---DENLLVCSQSGCPISVHENCLSCG 74 (138)
Q Consensus 34 ~~~~~~~d~C~~C~~~G---~e~LL~Cd~~gCp~s~H~~Cl~~~ 74 (138)
+..+..-..|.+|++.= ...=+.|. .|-+.+|.+|+..-
T Consensus 5 ~~~~~~~~~C~~C~~~i~g~~~~g~~C~--~C~~~~H~~C~~~~ 46 (53)
T PF00130_consen 5 PTTFSKPTYCDVCGKFIWGLGKQGYRCS--WCGLVCHKKCLSKV 46 (53)
T ss_dssp EEESSSTEB-TTSSSBECSSSSCEEEET--TTT-EEETTGGCTS
T ss_pred EccCCCCCCCcccCcccCCCCCCeEEEC--CCCChHhhhhhhhc
Confidence 33445567899998643 11378999 99999999999853
No 38
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.22 E-value=1.4 Score=39.05 Aligned_cols=42 Identities=26% Similarity=0.683 Sum_probs=31.9
Q ss_pred ccccccccCCCc----cEEecCCCCCcccccccccCCCCccCCCCCccccccch
Q 037252 41 EPCIKCNRQRDE----NLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWY 90 (138)
Q Consensus 41 d~C~~C~~~G~e----~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~y 90 (138)
+.|.+|-++=.+ ++|+|+ -.||..|+.+=+. .- .-+||.|.-
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~-----H~FH~~CIDpWL~--~~-r~~CPvCK~ 275 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCS-----HKFHVNCIDPWLT--QT-RTFCPVCKR 275 (348)
T ss_pred ceEEEeecccccCCeeeEecCC-----CchhhccchhhHh--hc-CccCCCCCC
Confidence 499999876542 778888 9999999995433 22 568999975
No 39
>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=75.68 E-value=1 Score=25.85 Aligned_cols=28 Identities=32% Similarity=0.792 Sum_probs=12.7
Q ss_pred cccccccCCCc-cEEecCCCCCccccccccc
Q 037252 42 PCIKCNRQRDE-NLLVCSQSGCPISVHENCL 71 (138)
Q Consensus 42 ~C~~C~~~G~e-~LL~Cd~~gCp~s~H~~Cl 71 (138)
.|..|++.+.. -...|. .|-..+|.+|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~--~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCS--ECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-T--TT-----HHHH
T ss_pred cCCcCCCcCCCCceEECc--cCCCccChhcC
Confidence 47889988864 689999 99999999884
No 40
>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=74.50 E-value=0.8 Score=28.75 Aligned_cols=32 Identities=31% Similarity=0.826 Sum_probs=16.0
Q ss_pred EecCCCCCcccccccccCCCCccCCCCCcccccc
Q 037252 55 LVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYC 88 (138)
Q Consensus 55 L~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C 88 (138)
+.|+..+|+..+|..|+. .-+-...+--||.|
T Consensus 12 ~~C~~~~C~~r~H~~C~~--~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 12 QRCSNRDCNVRLHDDCFK--KYFRHRSNPKCPNC 43 (43)
T ss_dssp EE-SS--S--EE-HHHHH--HHTTT-SS-B-TTT
T ss_pred ccCCCCccCchHHHHHHH--HHHhcCCCCCCcCC
Confidence 378888999999999998 23333333378877
No 41
>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=73.44 E-value=3.3 Score=23.90 Aligned_cols=28 Identities=32% Similarity=0.687 Sum_probs=23.2
Q ss_pred cccccccCCCcc-EEecCCCCCccccccccc
Q 037252 42 PCIKCNRQRDEN-LLVCSQSGCPISVHENCL 71 (138)
Q Consensus 42 ~C~~C~~~G~e~-LL~Cd~~gCp~s~H~~Cl 71 (138)
.|-+|++..+.. .-.|+ .|...+|.+|.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~--~c~f~lh~~Ca 30 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCS--ECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCcCCCEeEEeC--CCCCeEcCccC
Confidence 478888888755 78898 99999999985
No 42
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=71.19 E-value=3.4 Score=33.11 Aligned_cols=41 Identities=24% Similarity=0.566 Sum_probs=30.6
Q ss_pred ccccccccCCC------ccEEecCCCCCcccccccccCCCCccCCCCCccccccchhh
Q 037252 41 EPCIKCNRQRD------ENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKC 92 (138)
Q Consensus 41 d~C~~C~~~G~------e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~ 92 (138)
.+|-.|+.++- ++...|. .|-..||.+|+.. --||.|.-.+
T Consensus 153 fiCe~C~~~~~IfPF~~~~~~~C~--~C~~v~H~~C~~~---------~~CpkC~R~~ 199 (202)
T PF13901_consen 153 FICEICNSDDIIFPFQIDTTVRCP--KCKSVFHKSCFRK---------KSCPKCARRQ 199 (202)
T ss_pred CCCccCCCCCCCCCCCCCCeeeCC--cCccccchhhcCC---------CCCCCcHhHh
Confidence 46777776532 2678999 9999999999993 1299998543
No 43
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=66.28 E-value=1.6 Score=41.76 Aligned_cols=54 Identities=24% Similarity=0.476 Sum_probs=41.2
Q ss_pred cccccccccccCCCc---cEEecCCCCCcccccccccCCCCcc-CCCCCccccccchhhh
Q 037252 38 LEEEPCIKCNRQRDE---NLLVCSQSGCPISVHENCLSCGVKF-DDVGNFYCPYCWYKCE 93 (138)
Q Consensus 38 ~~~d~C~~C~~~G~e---~LL~Cd~~gCp~s~H~~Cl~~~~~~-dd~G~fyCP~C~yk~a 93 (138)
.....|.+|+..|.. +||.|. .|-.-||..|+..-..- +=.+-|-||-|..-.+
T Consensus 16 ~~~~mc~l~~s~G~~~ag~m~ac~--~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~ 73 (694)
T KOG4443|consen 16 IVCLMCPLCGSSGKGRAGRLLACS--DCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEA 73 (694)
T ss_pred hhhhhhhhhccccccccCcchhhh--hhcccCCcchhhHHHhHHHhcCCcccCCceeeee
Confidence 346789999999883 599999 99999999999853332 2234499999975443
No 44
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=66.06 E-value=1.7 Score=40.93 Aligned_cols=33 Identities=30% Similarity=0.586 Sum_probs=26.0
Q ss_pred cEEecCCCCCcccccccccCCCCccCCCCCccccccchhhhh
Q 037252 53 NLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKCEL 94 (138)
Q Consensus 53 ~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~a~ 94 (138)
+.-.|+ +|-..||.+|+...... ||.|...+..
T Consensus 530 ~~~rC~--~C~avfH~~C~~r~s~~-------CPrC~R~q~r 562 (580)
T KOG1829|consen 530 NTRRCS--TCLAVFHKKCLRRKSPC-------CPRCERRQKR 562 (580)
T ss_pred cceeHH--HHHHHHHHHHHhccCCC-------CCchHHHHHH
Confidence 456799 99999999999965432 9999866544
No 45
>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=64.60 E-value=4.5 Score=24.24 Aligned_cols=33 Identities=24% Similarity=0.498 Sum_probs=24.5
Q ss_pred ccccccccccCCC---ccEEecCCCCCcccccccccCC
Q 037252 39 EEEPCIKCNRQRD---ENLLVCSQSGCPISVHENCLSC 73 (138)
Q Consensus 39 ~~d~C~~C~~~G~---e~LL~Cd~~gCp~s~H~~Cl~~ 73 (138)
....|..|++.=. ..=+.|+ .|-+.+|.+|...
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~~C~--~C~~~~H~~C~~~ 45 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQGLRCS--WCKVKCHKKCADK 45 (50)
T ss_pred CCCChhhcchhhhccccceeEcC--CCCCchhhhhhcc
Confidence 4567888865321 1267899 9999999999874
No 46
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=64.44 E-value=4 Score=27.47 Aligned_cols=31 Identities=23% Similarity=0.729 Sum_probs=25.1
Q ss_pred cccccccccCC--CccEEecCCCCCcccccccccC
Q 037252 40 EEPCIKCNRQR--DENLLVCSQSGCPISVHENCLS 72 (138)
Q Consensus 40 ~d~C~~C~~~G--~e~LL~Cd~~gCp~s~H~~Cl~ 72 (138)
.-.|..|++.= ++-+++|. .|-..||..|-.
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp--~CgapyHR~C~~ 37 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCP--ECGAPYHRDCWE 37 (54)
T ss_pred CccChhhCCcccCCCCEEECC--CCCCcccHHHHh
Confidence 35799998754 23499999 999999999974
No 47
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=63.53 E-value=4.4 Score=35.12 Aligned_cols=52 Identities=27% Similarity=0.412 Sum_probs=38.4
Q ss_pred ccccccccccCCCccEEecCCCCCcccccccccCCCCccCCCCCcc-----ccccch
Q 037252 39 EEEPCIKCNRQRDENLLVCSQSGCPISVHENCLSCGVKFDDVGNFY-----CPYCWY 90 (138)
Q Consensus 39 ~~d~C~~C~~~G~e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fy-----CP~C~y 90 (138)
+..+|.++-..-++.++.|-..+|+.-.|.+||+....-+..|+-+ ||.|--
T Consensus 184 ~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~ 240 (276)
T KOG3005|consen 184 ECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEK 240 (276)
T ss_pred hhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhc
Confidence 4556666653333589999999999999999999744445666654 999974
No 48
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=62.54 E-value=4 Score=22.27 Aligned_cols=15 Identities=27% Similarity=0.652 Sum_probs=11.7
Q ss_pred CCccccccchhhhhh
Q 037252 81 GNFYCPYCWYKCELM 95 (138)
Q Consensus 81 G~fyCP~C~yk~a~~ 95 (138)
|+|.||.|.+.....
T Consensus 1 g~W~C~~C~~~N~~~ 15 (26)
T smart00547 1 GDWECPACTFLNFAS 15 (26)
T ss_pred CcccCCCCCCcChhh
Confidence 689999998766553
No 49
>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=61.01 E-value=3.5 Score=24.40 Aligned_cols=33 Identities=24% Similarity=0.534 Sum_probs=24.2
Q ss_pred ccccccccccCCCc--cEEecCCCCCcccccccccCC
Q 037252 39 EEEPCIKCNRQRDE--NLLVCSQSGCPISVHENCLSC 73 (138)
Q Consensus 39 ~~d~C~~C~~~G~e--~LL~Cd~~gCp~s~H~~Cl~~ 73 (138)
....|.+|++.=.. .=+.|. .|.+.+|.+|+..
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~--~C~~~~H~~C~~~ 44 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCS--WCKVKCHKKCAEK 44 (49)
T ss_pred CCCCccccccccCcCCCCcCCC--CCCchHHHHHHhh
Confidence 34679999654321 147899 9999999999874
No 50
>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=59.42 E-value=2 Score=24.23 Aligned_cols=42 Identities=24% Similarity=0.483 Sum_probs=25.7
Q ss_pred ccccccCCCccEEecCCCCCcccccccccCCCCccCCCCCccccccch
Q 037252 43 CIKCNRQRDENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWY 90 (138)
Q Consensus 43 C~~C~~~G~e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~y 90 (138)
|.+|...-. ..+.-. .|--.||..|+..-.. .+...||.|..
T Consensus 2 C~iC~~~~~-~~~~~~--~C~H~~c~~C~~~~~~---~~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEFR-EPVVLL--PCGHVFCRSCIDKWLK---SGKNTCPLCRT 43 (45)
T ss_pred CCcCchhhh-CceEec--CCCChhcHHHHHHHHH---hCcCCCCCCCC
Confidence 555655541 133333 4778899999874322 26778999964
No 51
>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=58.79 E-value=1.6 Score=26.40 Aligned_cols=42 Identities=26% Similarity=0.590 Sum_probs=25.2
Q ss_pred ccccccccCCC--ccEEecCCCCCcccccccccCCCCccCCCCCccccccc
Q 037252 41 EPCIKCNRQRD--ENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCW 89 (138)
Q Consensus 41 d~C~~C~~~G~--e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~ 89 (138)
|.|.+|-.+=+ +.+.... |--.||.+|+..-+.. ...||+|.
T Consensus 1 d~C~IC~~~~~~~~~~~~l~---C~H~fh~~Ci~~~~~~----~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLP---CGHVFHRSCIKEWLKR----NNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEET---TSEEEEHHHHHHHHHH----SSB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEcc---CCCeeCHHHHHHHHHh----CCcCCccC
Confidence 45666665432 2344443 8899999999853332 23999983
No 52
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=57.73 E-value=4.4 Score=32.61 Aligned_cols=54 Identities=28% Similarity=0.457 Sum_probs=43.2
Q ss_pred cccccccccCCCc-----cEEecCCCCCcccccccccCCCCccCCCCCccccccchhhhhh
Q 037252 40 EEPCIKCNRQRDE-----NLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKCELM 95 (138)
Q Consensus 40 ~d~C~~C~~~G~e-----~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~a~~ 95 (138)
+..|+.|...+.+ -+..|+-.|=+..+|..|+. .=+..+|+..|..|+......
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~--~W~~~~~~~~CeiC~~~~~~~ 136 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLE--KWFSIKGNITCEICKSFFINV 136 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHH--hhhccccCeeeecccccceec
Confidence 5799999997753 26778766778889999999 455689999999999866654
No 53
>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=57.24 E-value=1.7 Score=29.62 Aligned_cols=25 Identities=32% Similarity=0.619 Sum_probs=16.4
Q ss_pred CCcccccccccCCCCccCCCCCccccccc
Q 037252 61 GCPISVHENCLSCGVKFDDVGNFYCPYCW 89 (138)
Q Consensus 61 gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~ 89 (138)
.|...||..|+..=+... .-||.|.
T Consensus 49 ~C~H~FH~~Ci~~Wl~~~----~~CP~CR 73 (73)
T PF12678_consen 49 PCGHIFHFHCISQWLKQN----NTCPLCR 73 (73)
T ss_dssp TTSEEEEHHHHHHHHTTS----SB-TTSS
T ss_pred ccCCCEEHHHHHHHHhcC----CcCCCCC
Confidence 577999999997432221 2899883
No 54
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=55.01 E-value=4.7 Score=30.83 Aligned_cols=23 Identities=22% Similarity=0.522 Sum_probs=18.6
Q ss_pred CccCCCCCccccccchhhhhhHH
Q 037252 75 VKFDDVGNFYCPYCWYKCELMRT 97 (138)
Q Consensus 75 ~~~dd~G~fyCP~C~yk~a~~~~ 97 (138)
-.|++.+.|+||.|++...-.+.
T Consensus 13 ytYed~~~~~cpec~~ew~~~~~ 35 (112)
T COG2824 13 YTYEDGGQLICPECAHEWNENEA 35 (112)
T ss_pred eEEecCceEeCchhccccccccc
Confidence 46789999999999998775443
No 55
>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=54.51 E-value=2 Score=23.28 Aligned_cols=25 Identities=32% Similarity=0.724 Sum_probs=15.8
Q ss_pred CCcccccccccCCCCccCCCCCcccccc
Q 037252 61 GCPISVHENCLSCGVKFDDVGNFYCPYC 88 (138)
Q Consensus 61 gCp~s~H~~Cl~~~~~~dd~G~fyCP~C 88 (138)
.|--.||..|+..-.. .+..-||.|
T Consensus 15 ~C~H~~c~~C~~~~~~---~~~~~CP~C 39 (39)
T smart00184 15 PCGHTFCRSCIRKWLK---SGNNTCPIC 39 (39)
T ss_pred cCCChHHHHHHHHHHH---hCcCCCCCC
Confidence 3557788888873222 455668876
No 56
>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=52.23 E-value=6.1 Score=22.45 Aligned_cols=15 Identities=27% Similarity=0.751 Sum_probs=12.2
Q ss_pred CCCccccccchhhhh
Q 037252 80 VGNFYCPYCWYKCEL 94 (138)
Q Consensus 80 ~G~fyCP~C~yk~a~ 94 (138)
.|+|.|+.|.+....
T Consensus 2 ~g~W~C~~C~~~N~~ 16 (30)
T PF00641_consen 2 EGDWKCPSCTFMNPA 16 (30)
T ss_dssp SSSEEETTTTEEEES
T ss_pred CcCccCCCCcCCchH
Confidence 589999999987654
No 57
>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=51.92 E-value=12 Score=21.89 Aligned_cols=24 Identities=29% Similarity=0.775 Sum_probs=15.3
Q ss_pred ccCCCCccCCC-CCccccccchhhh
Q 037252 70 CLSCGVKFDDV-GNFYCPYCWYKCE 93 (138)
Q Consensus 70 Cl~~~~~~dd~-G~fyCP~C~yk~a 93 (138)
|....-.+++. .+|.||.|-..+.
T Consensus 4 C~~CGy~y~~~~~~~~CP~Cg~~~~ 28 (33)
T cd00350 4 CPVCGYIYDGEEAPWVCPVCGAPKD 28 (33)
T ss_pred CCCCCCEECCCcCCCcCcCCCCcHH
Confidence 34444444443 8999999976543
No 58
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=48.71 E-value=5.5 Score=28.95 Aligned_cols=47 Identities=21% Similarity=0.437 Sum_probs=30.4
Q ss_pred cccccccCCCc-cEEecCCCCCcccccccccCCCCccCCCCCccccccchhh
Q 037252 42 PCIKCNRQRDE-NLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKC 92 (138)
Q Consensus 42 ~C~~C~~~G~e-~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~ 92 (138)
-|..|...|++ -|+.+ .|.-.||..|+.-=+... +.+-.||.|.-..
T Consensus 34 ~Cp~Ck~Pgd~Cplv~g---~C~H~FH~hCI~kWl~~~-~~~~~CPmCR~~w 81 (85)
T PF12861_consen 34 CCPDCKFPGDDCPLVWG---KCSHNFHMHCILKWLSTQ-SSKGQCPMCRQPW 81 (85)
T ss_pred CCCCccCCCCCCceeec---cCccHHHHHHHHHHHccc-cCCCCCCCcCCee
Confidence 35556667764 34433 388899999987544433 4466999997543
No 59
>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=48.15 E-value=11 Score=27.77 Aligned_cols=55 Identities=22% Similarity=0.529 Sum_probs=33.3
Q ss_pred cccccccccccCCCccEEec----CCCCC---cccccccccCCC-----CccCCCCCccccccchhh
Q 037252 38 LEEEPCIKCNRQRDENLLVC----SQSGC---PISVHENCLSCG-----VKFDDVGNFYCPYCWYKC 92 (138)
Q Consensus 38 ~~~d~C~~C~~~G~e~LL~C----d~~gC---p~s~H~~Cl~~~-----~~~dd~G~fyCP~C~yk~ 92 (138)
.+-..|..|...-.+....| ....| ...|=..||.-. ....+.++|-||.|.-..
T Consensus 5 ~~g~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~CrgiC 71 (105)
T PF10497_consen 5 VNGKTCHQCRQKTLDFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGIC 71 (105)
T ss_pred CCCCCchhhcCCCCCCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCCee
Confidence 34456777776433335666 22266 888877887621 112357899999987533
No 60
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=47.08 E-value=2.2 Score=27.05 Aligned_cols=44 Identities=30% Similarity=0.612 Sum_probs=23.1
Q ss_pred ccccccCCCc-c--EEecCCCCCcccccccccCCCCccCCCCCcccccc
Q 037252 43 CIKCNRQRDE-N--LLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYC 88 (138)
Q Consensus 43 C~~C~~~G~e-~--LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C 88 (138)
|+.|..+..+ . +.+|.=.|=-.-+|.+||.. =+..+++..|+.|
T Consensus 1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~--W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLER--WIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHH--HHHHHT-SB-TTT
T ss_pred CeEeCCcCCCCCceecccccCCCcchhHHHHHHH--HHHhcCCCcCCCC
Confidence 5667666552 2 45665223334899999983 2233566667765
No 61
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=46.39 E-value=26 Score=19.63 Aligned_cols=13 Identities=38% Similarity=0.991 Sum_probs=10.7
Q ss_pred CCccccccchhhh
Q 037252 81 GNFYCPYCWYKCE 93 (138)
Q Consensus 81 G~fyCP~C~yk~a 93 (138)
|.|||.+|-....
T Consensus 2 ~~~~C~~C~~~~~ 14 (35)
T smart00451 2 GGFYCKLCNVTFT 14 (35)
T ss_pred cCeEccccCCccC
Confidence 6899999987665
No 62
>cd06962 NR_DBD_FXR DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. FXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. FXR is a member of the nuclear receptor family of ligand activated transcription factors. Bile acids are endogenous ligands for FXRs. Upon binding of a ligand, FXR binds to FXR response element (FXRE), which is an inverted repeat of TGACCT spaced by one nucleotide, either as a monomer or as a heterodimer with retinoid X receptor (RXR), to regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, FXR has a central well conserved
Probab=44.03 E-value=22 Score=25.04 Aligned_cols=53 Identities=23% Similarity=0.417 Sum_probs=34.5
Q ss_pred ccccccccCCCc---cEEecCCCCCccccccccc--------CCC-CccCCCCCccccccchhhhhh
Q 037252 41 EPCIKCNRQRDE---NLLVCSQSGCPISVHENCL--------SCG-VKFDDVGNFYCPYCWYKCELM 95 (138)
Q Consensus 41 d~C~~C~~~G~e---~LL~Cd~~gCp~s~H~~Cl--------~~~-~~~dd~G~fyCP~C~yk~a~~ 95 (138)
+.|.+|+..... +++.|. +|-.=|...=. ... -..+..+.+.|++|-+++-.+
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~--aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~ 66 (84)
T cd06962 2 ELCVVCGDKASGYHYNALTCE--GCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKE 66 (84)
T ss_pred CCCeecCCcCcceEECcceee--cceeeeeeeeccCCceecCCCCcCccCccccccCccchhhHHHH
Confidence 569999875542 788899 88766654332 111 112345678899999988664
No 63
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=43.43 E-value=15 Score=23.13 Aligned_cols=20 Identities=30% Similarity=0.717 Sum_probs=13.1
Q ss_pred cccCCCCccCCCCCccccccc
Q 037252 69 NCLSCGVKFDDVGNFYCPYCW 89 (138)
Q Consensus 69 ~Cl~~~~~~dd~G~fyCP~C~ 89 (138)
.| +.|+--+..|.-|||.|.
T Consensus 22 ~C-~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 22 DC-GTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred CC-CCeeEEecCCCEECCCCC
Confidence 46 333333578899999983
No 64
>PF04071 zf-like: Cysteine-rich small domain; InterPro: IPR007212 This is a probable metal-binding domain. It is found in a probable precorrin-3B C17-methyltransferase from Methanobacterium thermoautotrophicum, that catalyses the methylation of C-17 in precorrin-3B to form precorrin-4.
Probab=42.81 E-value=83 Score=22.84 Aligned_cols=64 Identities=22% Similarity=0.429 Sum_probs=49.2
Q ss_pred cccCCCccEEecCCCCCcccc-cccccCCCCccCCCC--CccccccchhhhhhHHHHHHHHHHHHHHHHHhh
Q 037252 46 CNRQRDENLLVCSQSGCPISV-HENCLSCGVKFDDVG--NFYCPYCWYKCELMRTKELRKKAKETKKQLACF 114 (138)
Q Consensus 46 C~~~G~e~LL~Cd~~gCp~s~-H~~Cl~~~~~~dd~G--~fyCP~C~yk~a~~~~~e~kk~a~~AkK~L~~F 114 (138)
|...|| +=|.|- ||+-. -..|+|. ......| -|-|.-|......+-|....+..++.-+++.+.
T Consensus 17 CH~~~q-nClFCy---CPlY~c~d~~~G~-~~~~~~G~~vw~C~~C~~~H~~e~~~~i~~~~~~~~~~~k~~ 83 (86)
T PF04071_consen 17 CHFEGQ-NCLFCY---CPLYPCGDECGGN-FIYTKNGSKVWDCSDCTLPHRPENYDYIIRKLKEIIEELKKL 83 (86)
T ss_pred CcCCCC-CcceEe---CCcccccCCCCcc-EEEcCCCCeeeECccCCCccCHHHHHHHHHHHHHHHHHHHHh
Confidence 335555 578887 99974 6899974 3445667 999999999999999988888877777776653
No 65
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=41.67 E-value=5.6 Score=22.62 Aligned_cols=15 Identities=20% Similarity=0.786 Sum_probs=10.4
Q ss_pred CccCCCCCccccccc
Q 037252 75 VKFDDVGNFYCPYCW 89 (138)
Q Consensus 75 ~~~dd~G~fyCP~C~ 89 (138)
........+|||.|+
T Consensus 14 ~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 14 IGINGRSTYLCPRCQ 28 (30)
T ss_dssp EEETTEEEEE-TTTC
T ss_pred eEecCCCCeECcCCc
Confidence 344677889999996
No 66
>PRK00420 hypothetical protein; Validated
Probab=39.24 E-value=44 Score=25.26 Aligned_cols=29 Identities=24% Similarity=0.479 Sum_probs=19.7
Q ss_pred CCcccccccccCCCCccC-CCCCccccccchhhhhhH
Q 037252 61 GCPISVHENCLSCGVKFD-DVGNFYCPYCWYKCELMR 96 (138)
Q Consensus 61 gCp~s~H~~Cl~~~~~~d-d~G~fyCP~C~yk~a~~~ 96 (138)
.||. |-. +-|. ..|.-|||.|--...++.
T Consensus 25 ~CP~-----Cg~--pLf~lk~g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 25 HCPV-----CGL--PLFELKDGEVVCPVHGKVYIVKS 54 (112)
T ss_pred CCCC-----CCC--cceecCCCceECCCCCCeeeecc
Confidence 5665 554 3443 899999999986655543
No 67
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=39.09 E-value=18 Score=20.17 Aligned_cols=21 Identities=33% Similarity=0.714 Sum_probs=14.1
Q ss_pred cccCCCCccCCCCCccccccch
Q 037252 69 NCLSCGVKFDDVGNFYCPYCWY 90 (138)
Q Consensus 69 ~Cl~~~~~~dd~G~fyCP~C~y 90 (138)
.|-..+. ..+.+.-|||+|-.
T Consensus 4 ~Cp~Cg~-~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 4 FCPNCGA-EIDPDAKFCPNCGA 24 (26)
T ss_pred CCcccCC-cCCcccccChhhCC
Confidence 3444544 46778889999964
No 68
>PF11287 DUF3088: Protein of unknown function (DUF3088); InterPro: IPR021439 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=37.69 E-value=15 Score=27.94 Aligned_cols=36 Identities=22% Similarity=0.515 Sum_probs=20.4
Q ss_pred Cccccccchhhhh-hHHHHHHHH-------HHHHHHHHHhhhcc
Q 037252 82 NFYCPYCWYKCEL-MRTKELRKK-------AKETKKQLACFIDS 117 (138)
Q Consensus 82 ~fyCP~C~yk~a~-~~~~e~kk~-------a~~AkK~L~~Fl~~ 117 (138)
.||||.|..---. ..+..++.. ...-|+++.+.|+.
T Consensus 21 ~f~Cp~c~~iEGlLa~~P~l~~~ldV~rV~f~RPR~~vi~llGE 64 (112)
T PF11287_consen 21 RFYCPHCAAIEGLLASFPDLRERLDVRRVDFPRPRQAVIALLGE 64 (112)
T ss_pred eEECCchHHHHhHHhhChhhhhcccEEEeCCCCchHHHHHHhCh
Confidence 3999999854322 223333332 23456777777775
No 69
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=37.64 E-value=5.6 Score=36.17 Aligned_cols=42 Identities=29% Similarity=0.601 Sum_probs=33.0
Q ss_pred cccccccccCCCc------cEEecCCCCCcccccccccCCCCccCCCCCccccccch
Q 037252 40 EEPCIKCNRQRDE------NLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWY 90 (138)
Q Consensus 40 ~d~C~~C~~~G~e------~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~y 90 (138)
.+.|++|...... ++|.|. ..||..|+..=..- +-.||.|..
T Consensus 291 ~~~C~IC~e~l~~~~~~~~~rL~C~-----Hifh~~CL~~W~er----~qtCP~CR~ 338 (543)
T KOG0802|consen 291 DELCIICLEELHSGHNITPKRLPCG-----HIFHDSCLRSWFER----QQTCPTCRT 338 (543)
T ss_pred CCeeeeechhhccccccccceeecc-----cchHHHHHHHHHHH----hCcCCcchh
Confidence 7899999988763 578887 89999999842221 678999986
No 70
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=37.36 E-value=19 Score=30.99 Aligned_cols=15 Identities=40% Similarity=1.088 Sum_probs=12.9
Q ss_pred CccCCCCCccccccc
Q 037252 75 VKFDDVGNFYCPYCW 89 (138)
Q Consensus 75 ~~~dd~G~fyCP~C~ 89 (138)
..+...+.||||.|+
T Consensus 258 ~~~~gR~t~~CP~CQ 272 (273)
T COG0266 258 IKLGGRSTFYCPVCQ 272 (273)
T ss_pred EEEcCCcCEeCCCCC
Confidence 466799999999997
No 71
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=36.74 E-value=18 Score=26.53 Aligned_cols=26 Identities=35% Similarity=0.735 Sum_probs=18.8
Q ss_pred ccccCCCCccCCCCCccccccchhhh
Q 037252 68 ENCLSCGVKFDDVGNFYCPYCWYKCE 93 (138)
Q Consensus 68 ~~Cl~~~~~~dd~G~fyCP~C~yk~a 93 (138)
.+|.-+...+...|.-||+.|+|++-
T Consensus 45 ~~C~~CK~~v~q~g~~YCq~CAYkkG 70 (90)
T PF10235_consen 45 SKCKICKTKVHQPGAKYCQTCAYKKG 70 (90)
T ss_pred ccccccccccccCCCccChhhhcccC
Confidence 35555555666678889999999864
No 72
>cd03019 DsbA_DsbA DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol oxidant known, due to the unusual stability of the thiolate anion form of the first cysteine in the CXXC motif. The highly unstable oxidized form of DsbA directly donates disulfide bonds to reduced proteins secreted into the bacterial periplasm. This rapid and unidirectional process helps to catalyze the folding of newly-synthesized polypeptides. To regain catalytic activity, reduced DsbA is then reoxidized by the membrane protein DsbB, which generates its disulfides from oxidized quinones, which in turn are reoxidized by the electron transport chain.
Probab=36.72 E-value=13 Score=27.10 Aligned_cols=21 Identities=14% Similarity=0.263 Sum_probs=15.1
Q ss_pred CCCccCCCCCccccccchhhh
Q 037252 73 CGVKFDDVGNFYCPYCWYKCE 93 (138)
Q Consensus 73 ~~~~~dd~G~fyCP~C~yk~a 93 (138)
.++++..-.||.||+|+.-..
T Consensus 15 ~~~~i~~f~D~~Cp~C~~~~~ 35 (178)
T cd03019 15 GKPEVIEFFSYGCPHCYNFEP 35 (178)
T ss_pred CCcEEEEEECCCCcchhhhhH
Confidence 345566778999999985443
No 73
>PF12773 DZR: Double zinc ribbon
Probab=34.92 E-value=34 Score=20.95 Aligned_cols=11 Identities=27% Similarity=0.933 Sum_probs=6.5
Q ss_pred CCCCCcccccc
Q 037252 78 DDVGNFYCPYC 88 (138)
Q Consensus 78 dd~G~fyCP~C 88 (138)
.+.+.-|||.|
T Consensus 39 ~~~~~~fC~~C 49 (50)
T PF12773_consen 39 NPPNAKFCPNC 49 (50)
T ss_pred CcCCcCccCcc
Confidence 45556666665
No 74
>cd02972 DsbA_family DsbA family; consists of DsbA and DsbA-like proteins, including DsbC, DsbG, glutathione (GSH) S-transferase kappa (GSTK), 2-hydroxychromene-2-carboxylate (HCCA) isomerase, an oxidoreductase (FrnE) presumed to be involved in frenolicin biosynthesis, a 27-kDa outer membrane protein, and similar proteins. Members of this family contain a redox active CXXC motif (except GSTK and HCCA isomerase) imbedded in a TRX fold, and an alpha helical insert of about 75 residues (shorter in DsbC and DsbG) relative to TRX. DsbA is involved in the oxidative protein folding pathway in prokaryotes, catalyzing disulfide bond formation of proteins secreted into the bacterial periplasm. DsbC and DsbG function as protein disulfide isomerases and chaperones to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins.
Probab=34.45 E-value=13 Score=23.51 Aligned_cols=14 Identities=29% Similarity=0.622 Sum_probs=9.8
Q ss_pred CCccccccchhhhh
Q 037252 81 GNFYCPYCWYKCEL 94 (138)
Q Consensus 81 G~fyCP~C~yk~a~ 94 (138)
.|+.||+|+.-...
T Consensus 5 ~d~~Cp~C~~~~~~ 18 (98)
T cd02972 5 FDPLCPYCYLFEPE 18 (98)
T ss_pred ECCCCHhHHhhhHH
Confidence 36789999865443
No 75
>cd03023 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
Probab=33.24 E-value=14 Score=25.78 Aligned_cols=17 Identities=24% Similarity=0.522 Sum_probs=12.6
Q ss_pred CccCCCCCccccccchh
Q 037252 75 VKFDDVGNFYCPYCWYK 91 (138)
Q Consensus 75 ~~~dd~G~fyCP~C~yk 91 (138)
+.+..-.|+.||+|+.-
T Consensus 7 ~~i~~f~D~~Cp~C~~~ 23 (154)
T cd03023 7 VTIVEFFDYNCGYCKKL 23 (154)
T ss_pred EEEEEEECCCChhHHHh
Confidence 44556679999999854
No 76
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=32.00 E-value=29 Score=19.17 Aligned_cols=18 Identities=28% Similarity=0.851 Sum_probs=9.9
Q ss_pred CCCCccCCCCCccccccch
Q 037252 72 SCGVKFDDVGNFYCPYCWY 90 (138)
Q Consensus 72 ~~~~~~dd~G~fyCP~C~y 90 (138)
.....+. .+.-|||+|-.
T Consensus 4 ~CG~~~~-~~~~fC~~CG~ 21 (23)
T PF13240_consen 4 NCGAEIE-DDAKFCPNCGT 21 (23)
T ss_pred ccCCCCC-CcCcchhhhCC
Confidence 3334444 34556888854
No 77
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=31.65 E-value=51 Score=24.14 Aligned_cols=55 Identities=22% Similarity=0.416 Sum_probs=36.4
Q ss_pred ccccccccccCCCc---cEEecCCCCCcccccccccC--------CC-CccCCCCCccccccchhhhhh
Q 037252 39 EEEPCIKCNRQRDE---NLLVCSQSGCPISVHENCLS--------CG-VKFDDVGNFYCPYCWYKCELM 95 (138)
Q Consensus 39 ~~d~C~~C~~~G~e---~LL~Cd~~gCp~s~H~~Cl~--------~~-~~~dd~G~fyCP~C~yk~a~~ 95 (138)
....|.+|+..... +++.|. +|-.=|...-.. .. =..+..+...|++|-+++-.+
T Consensus 17 ~~~~C~VCg~~a~g~hyGv~sC~--aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~ 83 (101)
T cd07160 17 GNEVCSVCGDKASGFHYNVLSCE--GCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCRE 83 (101)
T ss_pred CCCCCeecCCcCcceEECcceeh--hhhhhhhhcccccCccccCCCCccccCCcccccCccchhHHHHH
Confidence 45689999986553 889999 998766554332 11 111345567899998887654
No 78
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=31.05 E-value=40 Score=32.05 Aligned_cols=50 Identities=28% Similarity=0.630 Sum_probs=30.8
Q ss_pred cccccccCCCccEEecCCCCCcccc-cccccCCCCccCCCCCccccccchhhhh
Q 037252 42 PCIKCNRQRDENLLVCSQSGCPISV-HENCLSCGVKFDDVGNFYCPYCWYKCEL 94 (138)
Q Consensus 42 ~C~~C~~~G~e~LL~Cd~~gCp~s~-H~~Cl~~~~~~dd~G~fyCP~C~yk~a~ 94 (138)
.|..|+..-.++--+|. .|=.++ |..|-.++.. .+.|.-|||.|-.+-..
T Consensus 3 ~Cp~Cg~~n~~~akFC~--~CG~~l~~~~Cp~CG~~-~~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQ--KCGTSLTHKPCPQCGTE-VPVDEAHCPNCGAETGT 53 (645)
T ss_pred cCCCCCCcCCCCCcccc--ccCCCCCCCcCCCCCCC-CCcccccccccCCcccc
Confidence 45555554444445555 554442 3667777644 67788899999876443
No 79
>PF08285 DPM3: Dolichol-phosphate mannosyltransferase subunit 3 (DPM3); InterPro: IPR013174 This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex [].
Probab=30.86 E-value=64 Score=23.36 Aligned_cols=20 Identities=40% Similarity=0.390 Sum_probs=17.8
Q ss_pred hhHHHHHHHHHHHHHHHHHh
Q 037252 94 LMRTKELRKKAKETKKQLAC 113 (138)
Q Consensus 94 ~~~~~e~kk~a~~AkK~L~~ 113 (138)
-+.++++++...+||+.|.+
T Consensus 67 peA~~eL~~eI~eAK~dLr~ 86 (91)
T PF08285_consen 67 PEAAKELQKEIKEAKADLRK 86 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 36899999999999999875
No 80
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.73 E-value=49 Score=33.11 Aligned_cols=43 Identities=28% Similarity=0.523 Sum_probs=31.2
Q ss_pred cccccccccccCCCccEEecCCCCCcccccccccCCCCccCCCCCccccccch
Q 037252 38 LEEEPCIKCNRQRDENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWY 90 (138)
Q Consensus 38 ~~~d~C~~C~~~G~e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~y 90 (138)
+..-.|-.|+..=+ | +=--=.|--+||..|++ .+.+-||.|.-
T Consensus 838 ~q~skCs~C~~~Ld--l-P~VhF~CgHsyHqhC~e-------~~~~~CP~C~~ 880 (933)
T KOG2114|consen 838 FQVSKCSACEGTLD--L-PFVHFLCGHSYHQHCLE-------DKEDKCPKCLP 880 (933)
T ss_pred eeeeeecccCCccc--c-ceeeeecccHHHHHhhc-------cCcccCCccch
Confidence 33457888887776 3 11112577999999999 67889999985
No 81
>PRK10445 endonuclease VIII; Provisional
Probab=30.36 E-value=30 Score=28.73 Aligned_cols=34 Identities=18% Similarity=0.453 Sum_probs=23.6
Q ss_pred cccccccCCCccEEecCCCCCcccccccccCC--CCccCCCCCccccccc
Q 037252 42 PCIKCNRQRDENLLVCSQSGCPISVHENCLSC--GVKFDDVGNFYCPYCW 89 (138)
Q Consensus 42 ~C~~C~~~G~e~LL~Cd~~gCp~s~H~~Cl~~--~~~~dd~G~fyCP~C~ 89 (138)
..++.+..|+ .||. |-.. ...+...+.||||.|+
T Consensus 227 ~~~Vy~r~g~---------~Cp~-----Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 227 RFKVFHRDGE---------ACER-----CGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred eEEEeCCCCC---------CCCC-----CCCEeEEEEECCCCcEECCCCc
Confidence 4567777777 5664 4332 3445689999999996
No 82
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.88 E-value=35 Score=29.92 Aligned_cols=46 Identities=28% Similarity=0.618 Sum_probs=28.5
Q ss_pred cccccccccccCCC---c-cEEe--cCCCCCcccccccccCCCCccCCCCCccccccchh
Q 037252 38 LEEEPCIKCNRQRD---E-NLLV--CSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYK 91 (138)
Q Consensus 38 ~~~d~C~~C~~~G~---e-~LL~--Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk 91 (138)
++++.|..|..+-- + +|+. |. |.-|-.+-..+-..|...||.|...
T Consensus 1 md~~~CP~Ck~~~y~np~~kl~i~~CG--------H~~C~sCv~~l~~~~~~~CP~C~~~ 52 (309)
T TIGR00570 1 MDDQGCPRCKTTKYRNPSLKLMVNVCG--------HTLCESCVDLLFVRGSGSCPECDTP 52 (309)
T ss_pred CCCCCCCcCCCCCccCcccccccCCCC--------CcccHHHHHHHhcCCCCCCCCCCCc
Confidence 35678999998532 1 2342 44 6666555444445677799999543
No 83
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=29.55 E-value=18 Score=26.55 Aligned_cols=51 Identities=24% Similarity=0.459 Sum_probs=32.7
Q ss_pred ccccccccccC-CC--ccEEecCCCCCcccccccccCCCCccCCCCCccccccchhhhh
Q 037252 39 EEEPCIKCNRQ-RD--ENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKCEL 94 (138)
Q Consensus 39 ~~d~C~~C~~~-G~--e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~a~ 94 (138)
++..|+.|... |- ..=..|. .|...+=.+|-.. ....+.|.|..|...+..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~--~C~~~VC~~C~~~---~~~~~~WlC~vC~k~rel 106 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCV--DCKHRVCKKCGVY---SKKEPIWLCKVCQKQREL 106 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEET--TTTEEEETTSEEE---TSSSCCEEEHHHHHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCC--cCCccccCccCCc---CCCCCCEEChhhHHHHHH
Confidence 56789999874 22 0024677 7877776666653 456889999999865443
No 84
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=29.18 E-value=14 Score=32.72 Aligned_cols=49 Identities=29% Similarity=0.531 Sum_probs=36.2
Q ss_pred cccccccc-------cCCC-ccEEecCCCCCcccccccccCCCCccC---CCCCccccccch
Q 037252 40 EEPCIKCN-------RQRD-ENLLVCSQSGCPISVHENCLSCGVKFD---DVGNFYCPYCWY 90 (138)
Q Consensus 40 ~d~C~~C~-------~~G~-e~LL~Cd~~gCp~s~H~~Cl~~~~~~d---d~G~fyCP~C~y 90 (138)
..+|--|- +.|. |.|+-|+ .|-+|=|.+||-+.+... -.=+|-|-.|.|
T Consensus 224 n~YCDFclgdsr~nkkt~~peelvscs--dcgrsghpsclqft~nm~~avk~yrwqcieck~ 283 (336)
T KOG1244|consen 224 NPYCDFCLGDSRENKKTGMPEELVSCS--DCGRSGHPSCLQFTANMIAAVKTYRWQCIECKY 283 (336)
T ss_pred CcccceeccccccccccCCchhhcchh--hcCCCCCcchhhhhHHHHHHHHhheeeeeecce
Confidence 45677773 3344 6799999 999999999999765442 455788877765
No 85
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=29.14 E-value=13 Score=22.79 Aligned_cols=28 Identities=32% Similarity=0.790 Sum_probs=18.2
Q ss_pred ccccccccCC---------CCccCCCCCccccccchh
Q 037252 64 ISVHENCLSC---------GVKFDDVGNFYCPYCWYK 91 (138)
Q Consensus 64 ~s~H~~Cl~~---------~~~~dd~G~fyCP~C~yk 91 (138)
..||..|+.. +.-+.-.|..||..|..+
T Consensus 20 ~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~ 56 (58)
T PF00412_consen 20 KFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQK 56 (58)
T ss_dssp EEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHH
T ss_pred cEEEccccccCCCCCccCCCeeEeECCEEECHHHHhh
Confidence 4688888763 112345678888888754
No 86
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=29.10 E-value=17 Score=26.56 Aligned_cols=43 Identities=23% Similarity=0.612 Sum_probs=28.8
Q ss_pred ccccccccCCCccEEecCCCCCcc-------cccccccCCCCccCCCCCccccccchhhh
Q 037252 41 EPCIKCNRQRDENLLVCSQSGCPI-------SVHENCLSCGVKFDDVGNFYCPYCWYKCE 93 (138)
Q Consensus 41 d~C~~C~~~G~e~LL~Cd~~gCp~-------s~H~~Cl~~~~~~dd~G~fyCP~C~yk~a 93 (138)
--|..|+-.|+ .||+ +||.-|+---+. .+..+-.||.|.-..+
T Consensus 32 g~Cp~Ck~PgD---------dCPLv~G~C~h~fh~hCI~~wl~-~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 32 GCCPDCKLPGD---------DCPLVWGYCLHAFHAHCILKWLN-TPTSQGQCPMCRQTWQ 81 (84)
T ss_pred CcCCCCcCCCC---------CCccHHHHHHHHHHHHHHHHHhc-CccccccCCcchheeE
Confidence 35667777777 7886 688888863222 3556678999975443
No 87
>PF14260 zf-C4pol: C4-type zinc-finger of DNA polymerase delta
Probab=28.95 E-value=1.7e+02 Score=19.19 Aligned_cols=44 Identities=20% Similarity=0.431 Sum_probs=26.3
Q ss_pred ccCCCCccCCCCCccccccchhhhhhHHHHHHHHHHHHHHHHHhh
Q 037252 70 CLSCGVKFDDVGNFYCPYCWYKCELMRTKELRKKAKETKKQLACF 114 (138)
Q Consensus 70 Cl~~~~~~dd~G~fyCP~C~yk~a~~~~~e~kk~a~~AkK~L~~F 114 (138)
|+.............|+.|....+...+ .+..+...+.+.+...
T Consensus 1 C~~C~~~~~~~~~~lC~~C~~~~~~~~~-~l~~~~~~~E~~~~~l 44 (73)
T PF14260_consen 1 CLVCGAKTQEGESPLCSNCRSDPQQTIY-NLLSRLRELERRFNEL 44 (73)
T ss_pred CCCCCCcCCCCCCCcCcccCcChHHHHH-HHHHHHHHHHHHHHHH
Confidence 4444444444446999999976665555 5555555555555543
No 88
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.95 E-value=39 Score=23.50 Aligned_cols=14 Identities=43% Similarity=1.051 Sum_probs=11.6
Q ss_pred cCCCCCccccccch
Q 037252 77 FDDVGNFYCPYCWY 90 (138)
Q Consensus 77 ~dd~G~fyCP~C~y 90 (138)
..++|.--||||.-
T Consensus 43 mg~~gev~CPYC~t 56 (62)
T COG4391 43 MGDEGEVVCPYCST 56 (62)
T ss_pred cCCCCcEecCcccc
Confidence 35899999999974
No 89
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=28.08 E-value=37 Score=22.92 Aligned_cols=51 Identities=25% Similarity=0.599 Sum_probs=28.4
Q ss_pred ccccccCCCc---cEEecCCCCCcccccc---------cccCCC-CccCCCCCccccccchhhhhh
Q 037252 43 CIKCNRQRDE---NLLVCSQSGCPISVHE---------NCLSCG-VKFDDVGNFYCPYCWYKCELM 95 (138)
Q Consensus 43 C~~C~~~G~e---~LL~Cd~~gCp~s~H~---------~Cl~~~-~~~dd~G~fyCP~C~yk~a~~ 95 (138)
|.+|+..... +++.|. +|-.=|.. .|.... -..+..+...|++|.+++-.+
T Consensus 1 C~VCg~~~~g~hyGv~~C~--aC~~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~ 64 (73)
T cd07158 1 CKVCGDKASGFHYGVHSCE--GCKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLS 64 (73)
T ss_pred CcccCccCcceEECcchhh--HHHHHHhhhhcCCCCcccCCCCCCcCCCccccccCccchhhhhhH
Confidence 5566654442 566777 66543322 333211 112356678899999887543
No 90
>PF05407 Peptidase_C27: Rubella virus endopeptidase; InterPro: IPR008738 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C27 (clan CA). The type example is the rubella virus endopeptidase (Rubella virus), which is required for processing of the rubella virus replication protein.; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity
Probab=28.07 E-value=49 Score=26.24 Aligned_cols=30 Identities=23% Similarity=0.337 Sum_probs=22.6
Q ss_pred cccccchhhhhhHHHHHHHHHHHHHHHHHh
Q 037252 84 YCPYCWYKCELMRTKELRKKAKETKKQLAC 113 (138)
Q Consensus 84 yCP~C~yk~a~~~~~e~kk~a~~AkK~L~~ 113 (138)
-||.|.|-++..+.+....-+.+..+--.+
T Consensus 66 gcprcaygralsearthedfaalsqrwsas 95 (166)
T PF05407_consen 66 GCPRCAYGRALSEARTHEDFAALSQRWSAS 95 (166)
T ss_pred CCchhhhhhhhhhhhhhHHHHHHHHHhhhh
Confidence 399999999999888887777665544333
No 91
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=27.97 E-value=65 Score=25.28 Aligned_cols=39 Identities=21% Similarity=0.257 Sum_probs=26.8
Q ss_pred CccCCCCCccccccchhhhhhHHHHHHHHHHHHHHHHHh
Q 037252 75 VKFDDVGNFYCPYCWYKCELMRTKELRKKAKETKKQLAC 113 (138)
Q Consensus 75 ~~~dd~G~fyCP~C~yk~a~~~~~e~kk~a~~AkK~L~~ 113 (138)
+.+...|+|||-.|.--...+.....-.+.-.=|+.|..
T Consensus 50 ~dlPG~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~ 88 (129)
T KOG3408|consen 50 PDLPGGGQFYCIECARYFIDAKALKTHFKTKVHKRRVKE 88 (129)
T ss_pred CCCCCCceeehhhhhhhhcchHHHHHHHhccHHHHHHHh
Confidence 455688999999998766666666555555555555544
No 92
>PF13462 Thioredoxin_4: Thioredoxin; PDB: 3FEU_A 3HZ8_A 3DVW_A 3A3T_E 3GMF_A 1Z6M_A 3GYK_C 3BCK_A 3BD2_A 3BCI_A ....
Probab=27.93 E-value=15 Score=26.23 Aligned_cols=18 Identities=22% Similarity=0.486 Sum_probs=12.4
Q ss_pred CCccCCCCCccccccchh
Q 037252 74 GVKFDDVGNFYCPYCWYK 91 (138)
Q Consensus 74 ~~~~dd~G~fyCP~C~yk 91 (138)
++.+..-.+|+||+|..-
T Consensus 13 ~~~v~~f~d~~Cp~C~~~ 30 (162)
T PF13462_consen 13 PITVTEFFDFQCPHCAKF 30 (162)
T ss_dssp SEEEEEEE-TTSHHHHHH
T ss_pred CeEEEEEECCCCHhHHHH
Confidence 345566789999999854
No 93
>COG1773 Rubredoxin [Energy production and conversion]
Probab=27.54 E-value=27 Score=23.58 Aligned_cols=14 Identities=21% Similarity=0.427 Sum_probs=10.9
Q ss_pred CCCCccccccchhh
Q 037252 79 DVGNFYCPYCWYKC 92 (138)
Q Consensus 79 d~G~fyCP~C~yk~ 92 (138)
=.-+|+||.|-..+
T Consensus 33 lPd~w~CP~Cg~~K 46 (55)
T COG1773 33 LPDDWVCPECGVGK 46 (55)
T ss_pred CCCccCCCCCCCCH
Confidence 35689999998654
No 94
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=27.18 E-value=36 Score=18.58 Aligned_cols=14 Identities=29% Similarity=0.513 Sum_probs=9.3
Q ss_pred Cccccccchhhhhh
Q 037252 82 NFYCPYCWYKCELM 95 (138)
Q Consensus 82 ~fyCP~C~yk~a~~ 95 (138)
+|||+.|-.....+
T Consensus 1 q~~C~~C~k~f~~~ 14 (27)
T PF12171_consen 1 QFYCDACDKYFSSE 14 (27)
T ss_dssp -CBBTTTTBBBSSH
T ss_pred CCCcccCCCCcCCH
Confidence 58999998655443
No 95
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=26.77 E-value=7.6 Score=24.01 Aligned_cols=44 Identities=30% Similarity=0.542 Sum_probs=23.8
Q ss_pred ccccccccccCCCc-cEEecCCCCCccc-ccccccCCCCccCCCCCccccccchh
Q 037252 39 EEEPCIKCNRQRDE-NLLVCSQSGCPIS-VHENCLSCGVKFDDVGNFYCPYCWYK 91 (138)
Q Consensus 39 ~~d~C~~C~~~G~e-~LL~Cd~~gCp~s-~H~~Cl~~~~~~dd~G~fyCP~C~yk 91 (138)
++..|.+|...-.+ -++.|. -. |-..|+..-.. ....||+|.-+
T Consensus 1 ~~~~C~iC~~~~~~~~~~pCg-----H~~~C~~C~~~~~~----~~~~CP~Cr~~ 46 (50)
T PF13920_consen 1 EDEECPICFENPRDVVLLPCG-----HLCFCEECAERLLK----RKKKCPICRQP 46 (50)
T ss_dssp -HSB-TTTSSSBSSEEEETTC-----EEEEEHHHHHHHHH----TTSBBTTTTBB
T ss_pred CcCCCccCCccCCceEEeCCC-----ChHHHHHHhHHhcc----cCCCCCcCChh
Confidence 35778888876543 344554 22 33344442211 77789998643
No 96
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=26.46 E-value=25 Score=26.76 Aligned_cols=23 Identities=22% Similarity=0.556 Sum_probs=19.2
Q ss_pred CCccCCCCCccccccchhhhhhH
Q 037252 74 GVKFDDVGNFYCPYCWYKCELMR 96 (138)
Q Consensus 74 ~~~~dd~G~fyCP~C~yk~a~~~ 96 (138)
.-.|.+...|.||.|.|.++...
T Consensus 11 eytY~dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 11 EYTYHDGTQLICPSCLYEWNENE 33 (109)
T ss_pred cceEecCCeeECccccccccccc
Confidence 35778999999999999887754
No 97
>PRK14873 primosome assembly protein PriA; Provisional
Probab=26.41 E-value=54 Score=31.14 Aligned_cols=43 Identities=26% Similarity=0.722 Sum_probs=31.4
Q ss_pred cccccccccCCCccEEecCCCCC--ccccccc-----ccCCCCccCCCCCccccccchhh
Q 037252 40 EEPCIKCNRQRDENLLVCSQSGC--PISVHEN-----CLSCGVKFDDVGNFYCPYCWYKC 92 (138)
Q Consensus 40 ~d~C~~C~~~G~e~LL~Cd~~gC--p~s~H~~-----Cl~~~~~~dd~G~fyCP~C~yk~ 92 (138)
--.|..|+ . .+.|. .| |+.||.. |-.+.-.. ..|.||.|--+.
T Consensus 383 ~l~C~~Cg---~--~~~C~--~C~~~L~~h~~~~~l~Ch~CG~~~---~p~~Cp~Cgs~~ 432 (665)
T PRK14873 383 SLACARCR---T--PARCR--HCTGPLGLPSAGGTPRCRWCGRAA---PDWRCPRCGSDR 432 (665)
T ss_pred eeEhhhCc---C--eeECC--CCCCceeEecCCCeeECCCCcCCC---cCccCCCCcCCc
Confidence 45777774 5 77788 77 7889965 88887542 489999997653
No 98
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=25.90 E-value=1.1e+02 Score=24.23 Aligned_cols=15 Identities=27% Similarity=0.696 Sum_probs=12.4
Q ss_pred CCCCCccccccchhh
Q 037252 78 DDVGNFYCPYCWYKC 92 (138)
Q Consensus 78 dd~G~fyCP~C~yk~ 92 (138)
.....|||+.|.-.+
T Consensus 7 ~~~~~~~C~~C~~~~ 21 (302)
T PF10186_consen 7 NSRRRFYCANCVNNR 21 (302)
T ss_pred CCCCCeECHHHHHHH
Confidence 467899999999775
No 99
>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=25.87 E-value=76 Score=29.36 Aligned_cols=55 Identities=24% Similarity=0.395 Sum_probs=36.7
Q ss_pred CcccccccccccCCC----ccEEecCCCCCcccccccccCC------CCcc-----CCCCCccccccchhhh
Q 037252 37 FLEEEPCIKCNRQRD----ENLLVCSQSGCPISVHENCLSC------GVKF-----DDVGNFYCPYCWYKCE 93 (138)
Q Consensus 37 ~~~~d~C~~C~~~G~----e~LL~Cd~~gCp~s~H~~Cl~~------~~~~-----dd~G~fyCP~C~yk~a 93 (138)
|=..=-|++|.+=.. -.-+.|| .|-.+-|..|.=. ++.. .-.+.|||..|..+-.
T Consensus 125 FC~~C~C~iC~kfD~~~n~~~Wi~Cd--~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~se 194 (446)
T PF07227_consen 125 FCRRCMCCICSKFDDNKNTCSWIGCD--VCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTSE 194 (446)
T ss_pred ccccCCccccCCcccCCCCeeEEecc--CCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChhh
Confidence 333445777766432 2789999 9999999999743 1111 1356899999976543
No 100
>PF14410 GH-E: HNH/ENDO VII superfamily nuclease with conserved GHE residues
Probab=25.86 E-value=56 Score=22.46 Aligned_cols=39 Identities=21% Similarity=0.160 Sum_probs=24.2
Q ss_pred CCCCCccccccchhh---------hhhHHHHHHHHH---HHHHHHHHhhhc
Q 037252 78 DDVGNFYCPYCWYKC---------ELMRTKELRKKA---KETKKQLACFID 116 (138)
Q Consensus 78 dd~G~fyCP~C~yk~---------a~~~~~e~kk~a---~~AkK~L~~Fl~ 116 (138)
|+.|.|+||-|++.. ..-++..+...| -..+|++.+|+.
T Consensus 1 ~~~G~~~~~~~~~~i~~~~dmgH~~~~e~~~~~~~~~~~~~t~ke~~d~~n 51 (70)
T PF14410_consen 1 DPDGKVRDPNTGYPIEGPWDMGHKPGVEYWRLVGRAEEGGITRKEFLDWYN 51 (70)
T ss_pred CCCCeEecCCCCCCCCCCCCccCchHHHHHHHHHHHHhcCCCHHHHHHHHh
Confidence 578999999999887 223444444443 234566666654
No 101
>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=25.14 E-value=62 Score=21.89 Aligned_cols=34 Identities=24% Similarity=0.554 Sum_probs=22.4
Q ss_pred CcccccccccccCCCccEEecCCCCCcccccccccC
Q 037252 37 FLEEEPCIKCNRQRDENLLVCSQSGCPISVHENCLS 72 (138)
Q Consensus 37 ~~~~d~C~~C~~~G~e~LL~Cd~~gCp~s~H~~Cl~ 72 (138)
......|.+|++.=..+...=- -|-..||..|+.
T Consensus 75 i~~~~~C~vC~k~l~~~~f~~~--p~~~v~H~~C~~ 108 (109)
T PF10367_consen 75 ITESTKCSVCGKPLGNSVFVVF--PCGHVVHYSCIK 108 (109)
T ss_pred ECCCCCccCcCCcCCCceEEEe--CCCeEEeccccc
Confidence 4556789999986442233222 344889999975
No 102
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=25.04 E-value=83 Score=32.12 Aligned_cols=49 Identities=22% Similarity=0.565 Sum_probs=37.7
Q ss_pred CCCcccccccccccC------CCccEEecCCCCCcccccccccCCCCccCCCCCccccccc
Q 037252 35 VDFLEEEPCIKCNRQ------RDENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCW 89 (138)
Q Consensus 35 ~~~~~~d~C~~C~~~------G~e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~ 89 (138)
....+--+|.+|+++ |+ --+-|. .|-.-+=..|..-. ..+|+-.||-|.
T Consensus 12 ~~~~~~qiCqICGD~vg~~~~Ge-~FVAC~--eC~FPVCrpCYEYE---r~eG~q~CPqCk 66 (1079)
T PLN02638 12 MKHGGGQVCQICGDNVGKTVDGE-PFVACD--VCAFPVCRPCYEYE---RKDGNQSCPQCK 66 (1079)
T ss_pred ccccCCceeeecccccCcCCCCC-EEEEec--cCCCccccchhhhh---hhcCCccCCccC
Confidence 344555699999987 53 457798 99888888887632 578999999997
No 103
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=25.04 E-value=39 Score=21.79 Aligned_cols=14 Identities=21% Similarity=0.551 Sum_probs=8.7
Q ss_pred CCCccccccchhhh
Q 037252 80 VGNFYCPYCWYKCE 93 (138)
Q Consensus 80 ~G~fyCP~C~yk~a 93 (138)
..+|-||.|-..+.
T Consensus 32 p~~w~CP~C~a~K~ 45 (47)
T PF00301_consen 32 PDDWVCPVCGAPKS 45 (47)
T ss_dssp -TT-B-TTTSSBGG
T ss_pred CCCCcCcCCCCccc
Confidence 56899999987653
No 104
>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=24.99 E-value=58 Score=21.17 Aligned_cols=14 Identities=21% Similarity=0.598 Sum_probs=10.8
Q ss_pred CCCccccccchhhh
Q 037252 80 VGNFYCPYCWYKCE 93 (138)
Q Consensus 80 ~G~fyCP~C~yk~a 93 (138)
..+|-||.|-..+.
T Consensus 32 p~~w~CP~C~a~K~ 45 (50)
T cd00730 32 PDDWVCPVCGAGKD 45 (50)
T ss_pred CCCCCCCCCCCcHH
Confidence 44899999986654
No 105
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=24.54 E-value=36 Score=25.79 Aligned_cols=15 Identities=40% Similarity=0.729 Sum_probs=11.9
Q ss_pred CCCCCccccccchhh
Q 037252 78 DDVGNFYCPYCWYKC 92 (138)
Q Consensus 78 dd~G~fyCP~C~yk~ 92 (138)
++.|.|.||.|-..-
T Consensus 119 d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 119 DMDGTFTCPRCGEEL 133 (147)
T ss_pred CCCCcEECCCCCCEE
Confidence 467889999997654
No 106
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=24.45 E-value=31 Score=22.06 Aligned_cols=22 Identities=27% Similarity=0.762 Sum_probs=8.6
Q ss_pred cccccCCCCcc----CCCCCccccccc
Q 037252 67 HENCLSCGVKF----DDVGNFYCPYCW 89 (138)
Q Consensus 67 H~~Cl~~~~~~----dd~G~fyCP~C~ 89 (138)
|..|+.-. .| ...+.|.||.|.
T Consensus 23 H~~CFDl~-~fl~~~~~~~~W~CPiC~ 48 (50)
T PF02891_consen 23 HLQCFDLE-SFLESNQRTPKWKCPICN 48 (50)
T ss_dssp SS--EEHH-HHHHHHHHS---B-TTT-
T ss_pred ccceECHH-HHHHHhhccCCeECcCCc
Confidence 77777621 11 245569999996
No 107
>PF01323 DSBA: DSBA-like thioredoxin domain; InterPro: IPR001853 DSBA is a sub-family of the Thioredoxin family []. The efficient and correct folding of bacterial disulphide bonded proteins in vivo is dependent upon a class of periplasmic oxidoreductase proteins called DsbA, after the Escherichia coli enzyme. The bacterial protein-folding factor DsbA is the most oxidizing of the thioredoxin family. DsbA catalyses disulphide-bond formation during the folding of secreted proteins. The extremely oxidizing nature of DsbA has been proposed to result from either domain motion or stabilising active-site interactions in the reduced form. DsbA's highly oxidizing nature is a result of hydrogen bond, electrostatic and helix-dipole interactions that favour the thiolate over the disulphide at the active site []. In the pathogenic bacterium Vibrio cholerae, the DsbA homologue (TcpG) is responsible for the folding, maturation and secretion of virulence factors. While the overall architecture of TcpG and DsbA is similar and the surface features are retained in TcpG, there are significant differences. For example, the kinked active site helix results from a three-residue loop in DsbA, but is caused by a proline in TcpG (making TcpG more similar to thioredoxin in this respect). Furthermore, the proposed peptide binding groove of TcpG is substantially shortened compared with that of DsbA due to a six-residue deletion. Also, the hydrophobic pocket of TcpG is more shallow and the acidic patch is much less extensive than that of E. coli DsbA [].; GO: 0015035 protein disulfide oxidoreductase activity; PDB: 3GL5_A 3DKS_D 3RPP_C 3RPN_B 1YZX_A 3L9V_C 2IMD_A 2IME_A 2IMF_A 2B3S_B ....
Probab=24.29 E-value=38 Score=24.93 Aligned_cols=13 Identities=31% Similarity=1.058 Sum_probs=10.0
Q ss_pred CCccccccchhhh
Q 037252 81 GNFYCPYCWYKCE 93 (138)
Q Consensus 81 G~fyCP~C~yk~a 93 (138)
-|+.||+|+....
T Consensus 6 ~D~~Cp~cy~~~~ 18 (193)
T PF01323_consen 6 FDFICPWCYLASP 18 (193)
T ss_dssp EBTTBHHHHHHHH
T ss_pred EeCCCHHHHHHHH
Confidence 3789999996554
No 108
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=23.92 E-value=38 Score=20.98 Aligned_cols=12 Identities=42% Similarity=0.874 Sum_probs=9.2
Q ss_pred CCCCccccccchh
Q 037252 79 DVGNFYCPYCWYK 91 (138)
Q Consensus 79 d~G~fyCP~C~yk 91 (138)
+.| |.||.|-.+
T Consensus 16 ~~g-~~CP~Cg~~ 27 (46)
T PF12760_consen 16 PDG-FVCPHCGST 27 (46)
T ss_pred CCC-CCCCCCCCe
Confidence 445 889999865
No 109
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=23.74 E-value=45 Score=30.65 Aligned_cols=55 Identities=24% Similarity=0.463 Sum_probs=38.8
Q ss_pred ccccccccccCCC---ccEEecCCCCCcccc--------cccccCC-CCccCCCCCccccccchhhhhh
Q 037252 39 EEEPCIKCNRQRD---ENLLVCSQSGCPISV--------HENCLSC-GVKFDDVGNFYCPYCWYKCELM 95 (138)
Q Consensus 39 ~~d~C~~C~~~G~---e~LL~Cd~~gCp~s~--------H~~Cl~~-~~~~dd~G~fyCP~C~yk~a~~ 95 (138)
..++|.+|++.-. -+||-|. +|-=-| |-.|... .-..|-.-+--||+|.+.+-..
T Consensus 14 l~ElCPVCGDkVSGYHYGLLTCE--SCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQKCLt 80 (475)
T KOG4218|consen 14 LGELCPVCGDKVSGYHYGLLTCE--SCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQKCLT 80 (475)
T ss_pred cccccccccCccccceeeeeehh--hhhhHHHHHhhcCcceecccccccccchHhhccCCchhHHHHhh
Confidence 4679999998654 2899999 886544 4456654 2234556677899999887653
No 110
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=23.74 E-value=44 Score=28.61 Aligned_cols=58 Identities=16% Similarity=0.327 Sum_probs=31.1
Q ss_pred CCCCcCCCcccccccccccCC----CccEEecCCCCCcccccccccCCCCccCCCCCccccccchhhh
Q 037252 30 GDFTDVDFLEEEPCIKCNRQR----DENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKCE 93 (138)
Q Consensus 30 ~~~~~~~~~~~d~C~~C~~~G----~e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~a 93 (138)
.-..+..|++.-+=+.=+..- .-.-|+|. -|- .|..|.. +.--|.-.|+||.|-...-
T Consensus 164 ~~~~~~~w~D~V~~vl~G~ne~~~~~~~alIC~--~C~--hhngl~~--~~ek~~~efiC~~Cn~~n~ 225 (251)
T COG5415 164 KKEDSDAWFDKVISVLAGGNELDLSPFKALICP--QCH--HHNGLYR--LAEKPIIEFICPHCNHKND 225 (251)
T ss_pred CcccchHHHHHHHHHHhCCCccccCchhhhccc--ccc--ccccccc--cccccchheecccchhhcC
Confidence 336666677654444332221 11346666 442 3444554 3334555999999987663
No 111
>PRK10220 hypothetical protein; Provisional
Probab=23.66 E-value=32 Score=26.33 Aligned_cols=23 Identities=22% Similarity=0.525 Sum_probs=19.3
Q ss_pred CCccCCCCCccccccchhhhhhH
Q 037252 74 GVKFDDVGNFYCPYCWYKCELMR 96 (138)
Q Consensus 74 ~~~~dd~G~fyCP~C~yk~a~~~ 96 (138)
.-.|.+...|.||.|.+.+..++
T Consensus 12 eytY~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 12 EYTYEDNGMYICPECAHEWNDAE 34 (111)
T ss_pred cceEcCCCeEECCcccCcCCccc
Confidence 35778999999999999887764
No 112
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=23.34 E-value=65 Score=21.40 Aligned_cols=51 Identities=18% Similarity=0.386 Sum_probs=29.9
Q ss_pred cccccccCCCc---cEEecCCCCCccccccc--------ccCCC-CccCCCCCccccccchhhhh
Q 037252 42 PCIKCNRQRDE---NLLVCSQSGCPISVHEN--------CLSCG-VKFDDVGNFYCPYCWYKCEL 94 (138)
Q Consensus 42 ~C~~C~~~G~e---~LL~Cd~~gCp~s~H~~--------Cl~~~-~~~dd~G~fyCP~C~yk~a~ 94 (138)
.|.+|+..... +++.|. +|-.=|... |.... -.++......|++|-+++-.
T Consensus 1 ~C~vC~~~~~~~hygv~~C~--aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl 63 (70)
T smart00399 1 LCCVCGDHASGFHFGVCSCR--ACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCL 63 (70)
T ss_pred CCeEeCCcCcccEeCCcEec--hhhhhhhhheeCCCCeecCCCcccccCCCccccCccCcChhHh
Confidence 37778766542 677788 776544433 22110 12234557889999887754
No 113
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=23.20 E-value=60 Score=23.05 Aligned_cols=53 Identities=17% Similarity=0.523 Sum_probs=34.3
Q ss_pred ccccccccCCCc---cEEecCCCCCcccccccc--------cCCC-CccCCCCCccccccchhhhhh
Q 037252 41 EPCIKCNRQRDE---NLLVCSQSGCPISVHENC--------LSCG-VKFDDVGNFYCPYCWYKCELM 95 (138)
Q Consensus 41 d~C~~C~~~G~e---~LL~Cd~~gCp~s~H~~C--------l~~~-~~~dd~G~fyCP~C~yk~a~~ 95 (138)
..|.+|+..... +++.|. +|-.=|...- .... -..+......|++|-+++-.+
T Consensus 7 ~~C~VCg~~~~g~hyGv~sC~--aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~ 71 (90)
T cd07168 7 KLCSICEDKATGLHYGIITCE--GCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIR 71 (90)
T ss_pred CCCcccCCcCcceEECceehh--hhhHhhhhhhcCCCCccCCCCCCccccccccccccccchhhhhh
Confidence 469999886553 789999 9987665433 2111 112344567899999887554
No 114
>cd06958 NR_DBD_COUP_TF DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. COUP-TFs homodimerize or heterodimerize with retinoid X receptor (RXR) and a few other nuclear receptors and bind to a variety of response elements that are composed of imperfect AGGTCA direct or inverted repeats with various spacings. COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone recept
Probab=23.02 E-value=53 Score=22.25 Aligned_cols=51 Identities=24% Similarity=0.569 Sum_probs=27.2
Q ss_pred ccccccCCCc---cEEecCCCCCccccccc--------ccCCC-CccCCCCCccccccchhhhhh
Q 037252 43 CIKCNRQRDE---NLLVCSQSGCPISVHEN--------CLSCG-VKFDDVGNFYCPYCWYKCELM 95 (138)
Q Consensus 43 C~~C~~~G~e---~LL~Cd~~gCp~s~H~~--------Cl~~~-~~~dd~G~fyCP~C~yk~a~~ 95 (138)
|.+|+..... +++.|. +|-.=|... |.... -..+..+.+.|++|-+++-.+
T Consensus 1 C~VCg~~~~g~hygv~sC~--aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~ 63 (73)
T cd06958 1 CVVCGDKSSGKHYGQFTCE--GCKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKKCLK 63 (73)
T ss_pred CCccCccCcceEEChhhhh--hhhhhhhhhhcCCCceeCCCCCcCccCCcccccCccchhhHhhH
Confidence 4556554432 566666 665444332 22110 112355678899999887553
No 115
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 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 short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=23.02 E-value=44 Score=20.99 Aligned_cols=15 Identities=47% Similarity=1.054 Sum_probs=9.9
Q ss_pred ccCCC-CCccccccch
Q 037252 76 KFDDV-GNFYCPYCWY 90 (138)
Q Consensus 76 ~~dd~-G~fyCP~C~y 90 (138)
.+++. +.-.||||-.
T Consensus 22 ~l~~~~~~~~CpYCg~ 37 (40)
T PF10276_consen 22 NLDDEPGPVVCPYCGT 37 (40)
T ss_dssp E-TTTTCEEEETTTTE
T ss_pred ecCCCCCeEECCCCCC
Confidence 44553 5589999964
No 116
>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers. DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding
Probab=22.49 E-value=47 Score=23.32 Aligned_cols=52 Identities=19% Similarity=0.380 Sum_probs=31.2
Q ss_pred cccccccCCCc---cEEecCCCCCcccccc--------cccCCC-CccCCCCCccccccchhhhhh
Q 037252 42 PCIKCNRQRDE---NLLVCSQSGCPISVHE--------NCLSCG-VKFDDVGNFYCPYCWYKCELM 95 (138)
Q Consensus 42 ~C~~C~~~G~e---~LL~Cd~~gCp~s~H~--------~Cl~~~-~~~dd~G~fyCP~C~yk~a~~ 95 (138)
+|.+|+..... +++.|. +|-.-|.. .|.... -..+..+...|++|-+++-.+
T Consensus 1 ~C~VCg~~~~g~hygv~sC~--aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~ 64 (87)
T cd07162 1 ICRVCGDRATGYHFNAMTCE--GCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLS 64 (87)
T ss_pred CCcccCCcCcceEECcceeh--hhHHHHHhhhccCceeEcCCCCceecCCcccccCccchhhHHhH
Confidence 47777765442 677788 77655533 232211 112355678899999988654
No 117
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=22.32 E-value=94 Score=21.04 Aligned_cols=23 Identities=30% Similarity=0.819 Sum_probs=17.3
Q ss_pred cccccCCCCccCCCCCccc-cccch
Q 037252 67 HENCLSCGVKFDDVGNFYC-PYCWY 90 (138)
Q Consensus 67 H~~Cl~~~~~~dd~G~fyC-P~C~y 90 (138)
|..|+.++.+.++. .-|| +.|.-
T Consensus 3 HkHC~~CG~~Ip~~-~~fCS~~C~~ 26 (59)
T PF09889_consen 3 HKHCPVCGKPIPPD-ESFCSPKCRE 26 (59)
T ss_pred CCcCCcCCCcCCcc-hhhhCHHHHH
Confidence 89999998776655 5566 78873
No 118
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=22.21 E-value=1.1e+02 Score=27.77 Aligned_cols=77 Identities=21% Similarity=0.456 Sum_probs=49.1
Q ss_pred cccccccccCCC--ccEEecCCCCCcccccccccCCCCccCCCCCccccccchhhhhhHHHHH-----------HHHHHH
Q 037252 40 EEPCIKCNRQRD--ENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKCELMRTKEL-----------RKKAKE 106 (138)
Q Consensus 40 ~d~C~~C~~~G~--e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~a~~~~~e~-----------kk~a~~ 106 (138)
..+|.+|+..=. -+++.|. |.-|+.+- ..++ +-.||.|.-+.+.-+--.+ =+...+
T Consensus 90 VHfCd~Cd~PI~IYGRmIPCk--------HvFCl~CA-r~~~--dK~Cp~C~d~VqrIeq~~~g~iFmC~~~~GC~RTyL 158 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIYGRMIPCK--------HVFCLECA-RSDS--DKICPLCDDRVQRIEQIMMGGIFMCAAPHGCLRTYL 158 (389)
T ss_pred eEeecccCCcceeeecccccc--------hhhhhhhh-hcCc--cccCcCcccHHHHHHHhcccceEEeecchhHHHHHh
Confidence 468999987532 1388898 77777763 2233 8899999876655432211 244567
Q ss_pred HHHHHHhhhccccc---cCccccc
Q 037252 107 TKKQLACFIDSKSF---SGDKKKE 127 (138)
Q Consensus 107 AkK~L~~Fl~~~~~---~~~~~~~ 127 (138)
.+..|.+-|..+.. .-+.++|
T Consensus 159 sqrDlqAHInhrH~~~~~p~~~~e 182 (389)
T KOG2932|consen 159 SQRDLQAHINHRHGSLLQPDAEKE 182 (389)
T ss_pred hHHHHHHHhhhhhccccCCchhhh
Confidence 78888888886653 4444443
No 119
>PRK14973 DNA topoisomerase I; Provisional
Probab=22.17 E-value=67 Score=31.88 Aligned_cols=54 Identities=24% Similarity=0.533 Sum_probs=32.1
Q ss_pred cccccccc--------CCCccEEecCC-CCCcccc--c-----------ccccCCC---CccCCCCC---cc-ccccchh
Q 037252 41 EPCIKCNR--------QRDENLLVCSQ-SGCPISV--H-----------ENCLSCG---VKFDDVGN---FY-CPYCWYK 91 (138)
Q Consensus 41 d~C~~C~~--------~G~e~LL~Cd~-~gCp~s~--H-----------~~Cl~~~---~~~dd~G~---fy-CP~C~yk 91 (138)
-.|.+|+. .|. .+-|++ .+|-..+ + ..|-.+. +.+...|+ |+ ||.|.|.
T Consensus 589 ~~CP~CG~~l~ik~~k~gk--FigCS~Yp~Ck~t~~L~~~~~g~~~~~~~~Cp~CG~p~~~~~r~Gr~g~fl~CP~C~~~ 666 (936)
T PRK14973 589 GPCPVCGKDLRIKHIGSSQ--FIGCSGYPDCTFNIGLPGTTWGWAIRTDEVCPIHHLNHVRLIRKGARPWDIGCPLCSHI 666 (936)
T ss_pred ccCCcccccceeecccCce--eEECCCCCCCCccccCCccccccCCCCCCCCCCCCCCceEEeecCCCcccccCccccch
Confidence 47999964 233 688985 3465431 1 2365444 33334444 55 9999998
Q ss_pred hhhhH
Q 037252 92 CELMR 96 (138)
Q Consensus 92 ~a~~~ 96 (138)
+...+
T Consensus 667 ~~~~~ 671 (936)
T PRK14973 667 ESNTE 671 (936)
T ss_pred hhccc
Confidence 87655
No 120
>cd06965 NR_DBD_Ppar DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive gene
Probab=21.96 E-value=52 Score=23.02 Aligned_cols=50 Identities=22% Similarity=0.521 Sum_probs=29.7
Q ss_pred ccccccCCCc---cEEecCCCCCcccccc---------cccCCCCccCCCCCccccccchhhhhh
Q 037252 43 CIKCNRQRDE---NLLVCSQSGCPISVHE---------NCLSCGVKFDDVGNFYCPYCWYKCELM 95 (138)
Q Consensus 43 C~~C~~~G~e---~LL~Cd~~gCp~s~H~---------~Cl~~~~~~dd~G~fyCP~C~yk~a~~ 95 (138)
|.+|+..... +++.|. +|-.=|.. .|... -..+....+.|++|-+++-.+
T Consensus 2 C~VCg~~~~g~hyGv~sC~--aCk~FFRR~v~~~~~~~~C~~~-C~i~~~~r~~Cr~CRl~KCl~ 63 (84)
T cd06965 2 CRVCGDKASGFHYGVHACE--GCKGFFRRTIRLKLVYKPCDLS-CKIHKKSRNKCQYCRFQKCLN 63 (84)
T ss_pred CcccCccCcceEEChhhhh--hhhhheeeeeecCCCccccccC-CCcCccccccccchhhhhhhh
Confidence 6777765442 667777 77654432 23321 223456678899999887543
No 121
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=21.64 E-value=39 Score=32.30 Aligned_cols=51 Identities=27% Similarity=0.535 Sum_probs=37.1
Q ss_pred cccccccccccCCCccEEecCCCCCcccccccccCCCCccCC-----CCCccc----cccc
Q 037252 38 LEEEPCIKCNRQRDENLLVCSQSGCPISVHENCLSCGVKFDD-----VGNFYC----PYCW 89 (138)
Q Consensus 38 ~~~d~C~~C~~~G~e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd-----~G~fyC----P~C~ 89 (138)
...-.|..|++-|- .-+.|+..-|-.+||..|.-..--|+- .|-.|| |+|-
T Consensus 301 rwkl~C~iCk~~~G-tcIqCs~~nC~~aYHVtCArrag~f~~~~~s~n~~s~~id~e~~c~ 360 (669)
T COG5141 301 RWKLGCLICKEFGG-TCIQCSYFNCTRAYHVTCARRAGYFDLNIYSHNGISYCIDHEPLCR 360 (669)
T ss_pred hHhheeeEEcccCc-ceeeecccchhhhhhhhhhhhcchhhhhhhcccccceeecchhhhc
Confidence 34568999998764 599999999999999999875433332 454555 5664
No 122
>cd03025 DsbA_FrnE_like DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins.
Probab=21.55 E-value=59 Score=24.04 Aligned_cols=13 Identities=23% Similarity=0.544 Sum_probs=10.2
Q ss_pred Cccccccchhhhh
Q 037252 82 NFYCPYCWYKCEL 94 (138)
Q Consensus 82 ~fyCP~C~yk~a~ 94 (138)
|+.||+||.....
T Consensus 8 D~~cp~c~~~~~~ 20 (193)
T cd03025 8 DPLCGWCYGFEPL 20 (193)
T ss_pred CCCCchhhCchHH
Confidence 6889999976653
No 123
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=21.43 E-value=37 Score=31.97 Aligned_cols=41 Identities=22% Similarity=0.639 Sum_probs=27.0
Q ss_pred Cccccccccccc---CCCccEEecCCCCCcccccccccCCCCccCCCCCccccccchhhhhh
Q 037252 37 FLEEEPCIKCNR---QRDENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKCELM 95 (138)
Q Consensus 37 ~~~~d~C~~C~~---~G~e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~a~~ 95 (138)
.+|+-.|..|+. +|+ --++- .-+.+|+- .||++||.+.-..
T Consensus 452 v~eDq~CdeC~g~~c~~q--~aPfF------C~n~~C~Q----------YYCe~CWa~~HS~ 495 (520)
T KOG0129|consen 452 VMEDQLCDECGGRRCGGQ--FAPFF------CRNATCFQ----------YYCESCWAKIHSG 495 (520)
T ss_pred eccccchhhhcCeeccCc--cCCcc------cCCccHHh----------hhchHHHHHhhcC
Confidence 347889999988 666 32221 22556654 8999999765443
No 124
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=21.17 E-value=33 Score=21.88 Aligned_cols=19 Identities=42% Similarity=0.934 Sum_probs=14.5
Q ss_pred cccccccccCC---CccEEecC
Q 037252 40 EEPCIKCNRQR---DENLLVCS 58 (138)
Q Consensus 40 ~d~C~~C~~~G---~e~LL~Cd 58 (138)
.++|++|.+-= .++.|.||
T Consensus 6 ~~yC~~Cdk~~~~~~~~~lYCS 27 (43)
T PF12855_consen 6 NDYCIVCDKQIDPPDDGSLYCS 27 (43)
T ss_pred hhHHHHhhccccCCCCCccccC
Confidence 47999999866 45677887
No 125
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=20.53 E-value=46 Score=27.65 Aligned_cols=15 Identities=33% Similarity=0.795 Sum_probs=11.9
Q ss_pred ccCCCCCccccccch
Q 037252 76 KFDDVGNFYCPYCWY 90 (138)
Q Consensus 76 ~~dd~G~fyCP~C~y 90 (138)
.+-..+.||||.|+-
T Consensus 259 ~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 259 KQGGRSTFFCPRCQK 273 (274)
T ss_pred EECCCCcEECcCCCC
Confidence 344789999999974
No 126
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=20.33 E-value=25 Score=23.56 Aligned_cols=44 Identities=27% Similarity=0.514 Sum_probs=21.4
Q ss_pred cccccccCCCccEEecCCCCCcccccccccCCCCccCCCCCccccccchhhhh
Q 037252 42 PCIKCNRQRDENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKCEL 94 (138)
Q Consensus 42 ~C~~C~~~G~e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~a~ 94 (138)
.|--|.-... +|+.|+ =|-=|+.. ++.-=+-.-+||.|++.-+.
T Consensus 4 nCKsCWf~~k-~Li~C~-------dHYLCl~C-Lt~ml~~s~~C~iC~~~LPt 47 (50)
T PF03854_consen 4 NCKSCWFANK-GLIKCS-------DHYLCLNC-LTLMLSRSDRCPICGKPLPT 47 (50)
T ss_dssp ---SS-S--S-SEEE-S-------S-EEEHHH-HHHT-SSSSEETTTTEE---
T ss_pred cChhhhhcCC-Ceeeec-------chhHHHHH-HHHHhccccCCCcccCcCcc
Confidence 4666776663 799998 47767665 23333334479999987553
No 127
>PF02977 CarbpepA_inh: Carboxypeptidase A inhibitor; InterPro: IPR004231 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. This family is represented by the well-characterised metallocarboxypeptidase A inhibitor (MCPI) from potatoes, which belongs to the MEROPS inhibitor family I37, clan IE. It inhibits metallopeptidases belonging to MEROPS peptidase family M14, carboxypeptidase A. In Russet Burbank potatoes, it is a mixture of approximately equal amounts of two polypeptide chains containing 38 or 39 amino acid residues. The chains differ in their amino terminal sequence only [] and are resistant to fragmentation by proteases []. The structure of the complex between bovine carboxypeptidase A and the 39-amino-acid carboxypeptidase A inhibitor from potatoes has been determined at 2.5-A resolution []. The potato inhibitor is synthesised as a precursor, having a 29 residue N-terminal signal peptide, a 27 residue pro-peptide, the 39 residue mature inhibitor region and a 7 residue C-terminal extension. The 7 residue C-terminal extension is involved in inhibitor inactivation and may be required for targeting to the vacuole where the mature active inhibitor accumulates []. The N-terminal region and the mature inhibitor are weakly related to other solananaceous proteins found in this entry, from potato, tomato and henbane, which have been incorrectly described as metallocarboxipeptidase inhibitors [].; GO: 0008191 metalloendopeptidase inhibitor activity; PDB: 4CPA_I 1H20_A 2HLG_A.
Probab=20.29 E-value=72 Score=21.00 Aligned_cols=15 Identities=33% Similarity=0.868 Sum_probs=10.4
Q ss_pred ccCCCCCccccccch
Q 037252 76 KFDDVGNFYCPYCWY 90 (138)
Q Consensus 76 ~~dd~G~fyCP~C~y 90 (138)
..|=.|-|+||.||.
T Consensus 15 ~sDC~g~tlC~~C~k 29 (46)
T PF02977_consen 15 NSDCSGITLCQWCWK 29 (46)
T ss_dssp SCCCTTSSSS-EE-C
T ss_pred CccccceeehHHHHh
Confidence 457788999999964
No 128
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=20.20 E-value=50 Score=25.79 Aligned_cols=20 Identities=30% Similarity=0.766 Sum_probs=15.9
Q ss_pred CccCCCCCccccccchhhhh
Q 037252 75 VKFDDVGNFYCPYCWYKCEL 94 (138)
Q Consensus 75 ~~~dd~G~fyCP~C~yk~a~ 94 (138)
|.|.--|+-|||.|-|+...
T Consensus 37 PLF~KdG~v~CPvC~~~~~~ 56 (131)
T COG1645 37 PLFRKDGEVFCPVCGYREVV 56 (131)
T ss_pred cceeeCCeEECCCCCceEEE
Confidence 56778899999999975543
No 129
>PHA02929 N1R/p28-like protein; Provisional
Probab=20.19 E-value=27 Score=29.36 Aligned_cols=48 Identities=19% Similarity=0.418 Sum_probs=30.7
Q ss_pred ccccccccccCCCcc------EEecCCCCCcccccccccCCCCccCCCCCccccccchhh
Q 037252 39 EEEPCIKCNRQRDEN------LLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKC 92 (138)
Q Consensus 39 ~~d~C~~C~~~G~e~------LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~ 92 (138)
.+..|.+|-..-.+. +..=. .|--.||..|+..-+. ..--||.|....
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~--~C~H~FC~~CI~~Wl~----~~~tCPlCR~~~ 226 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILS--NCNHVFCIECIDIWKK----EKNTCPVCRTPF 226 (238)
T ss_pred CCCCCccCCcccccCccccccceecC--CCCCcccHHHHHHHHh----cCCCCCCCCCEe
Confidence 467899998864311 11112 5779999999974322 244799997543
No 130
>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=20.12 E-value=53 Score=29.98 Aligned_cols=36 Identities=25% Similarity=0.805 Sum_probs=23.1
Q ss_pred cEEecCCCCCcccccccccCCCCccCCCCCccccccchhhhhh
Q 037252 53 NLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKCELM 95 (138)
Q Consensus 53 ~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~a~~ 95 (138)
.|++|. .|-.--...|+. .+---||||-|..-....
T Consensus 4 ~L~fC~--~C~~irc~~c~~-----~Ei~~~yCp~CL~~~p~~ 39 (483)
T PF05502_consen 4 ELYFCE--HCHKIRCPRCVS-----EEIDSYYCPNCLFEVPSS 39 (483)
T ss_pred cceecc--cccccCChhhcc-----cccceeECccccccCChh
Confidence 477777 776666666766 344467777776555443
No 131
>PF14047 DCR: Dppa2/4 conserved region
Probab=20.11 E-value=45 Score=23.41 Aligned_cols=28 Identities=18% Similarity=0.450 Sum_probs=18.7
Q ss_pred cccccccccCCCCccCCCCCccccccchhh
Q 037252 63 PISVHENCLSCGVKFDDVGNFYCPYCWYKC 92 (138)
Q Consensus 63 p~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~ 92 (138)
++-.=..|+-+|+.++ -|+.||.|+.+.
T Consensus 38 ~LfLlPac~fpppgle--DNmLCp~Cv~rN 65 (66)
T PF14047_consen 38 SLFLLPACIFPPPGLE--DNMLCPECVKRN 65 (66)
T ss_pred eeeecccccCCCCCcc--ccccCHhHhhcc
Confidence 3444456777666554 489999998653
No 132
>KOG3456 consensus NADH:ubiquinone oxidoreductase, NDUFS6/13 kDa subunit [Energy production and conversion]
Probab=20.06 E-value=81 Score=24.41 Aligned_cols=45 Identities=24% Similarity=0.513 Sum_probs=31.4
Q ss_pred cccccccccCCCccEEecCCCCCcccccccccCCCCccCCCCCccccccchhh
Q 037252 40 EEPCIKCNRQRDENLLVCSQSGCPISVHENCLSCGVKFDDVGNFYCPYCWYKC 92 (138)
Q Consensus 40 ~d~C~~C~~~G~e~LL~Cd~~gCp~s~H~~Cl~~~~~~dd~G~fyCP~C~yk~ 92 (138)
+--=+.| ++- ++.|||.+ |.-=|.+=.- .+|-.|.-.|-||-.+.
T Consensus 70 e~Pp~e~--d~R--VV~CdGg~-~aLGHPkvyI---nLDk~~~~~CgYCGlrf 114 (120)
T KOG3456|consen 70 EVPPIEV--DGR--VVACDGGT-PALGHPKVYI---NLDKPGPHICGYCGLRF 114 (120)
T ss_pred cCChhhc--cce--EEEecCCC-CCCCCCeEEE---EcCCCCCcccccchhhh
Confidence 3333455 555 99999988 7766765332 45778889999997654
Done!