Query 025765
Match_columns 248
No_of_seqs 223 out of 1185
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 09:15:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025765.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025765hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5034 TNG2 Chromatin remodel 100.0 2E-38 4.4E-43 276.3 17.2 227 8-241 6-270 (271)
2 KOG1973 Chromatin remodeling p 100.0 1.1E-33 2.3E-38 254.8 14.1 234 7-246 8-273 (274)
3 PF12998 ING: Inhibitor of gro 99.9 7.9E-23 1.7E-27 158.2 10.3 100 7-113 1-105 (105)
4 PF00628 PHD: PHD-finger; Int 98.9 4.9E-10 1.1E-14 75.8 0.5 44 194-240 1-50 (51)
5 smart00249 PHD PHD zinc finger 98.7 8.9E-09 1.9E-13 67.1 3.1 42 194-238 1-47 (47)
6 KOG1512 PHD Zn-finger protein 98.0 1.8E-06 3.9E-11 77.7 0.7 45 194-241 316-363 (381)
7 KOG0825 PHD Zn-finger protein 97.5 5.7E-05 1.2E-09 75.9 2.9 49 190-240 213-265 (1134)
8 KOG4299 PHD Zn-finger protein 97.5 3.2E-05 7E-10 75.9 1.1 47 192-241 253-305 (613)
9 KOG0954 PHD finger protein [Ge 97.5 4.4E-05 9.5E-10 76.2 1.7 50 187-239 266-319 (893)
10 KOG4323 Polycomb-like PHD Zn-f 97.4 5.1E-05 1.1E-09 72.8 1.1 47 194-243 173-226 (464)
11 KOG0383 Predicted helicase [Ge 97.3 9.9E-05 2.1E-09 74.3 1.7 50 192-246 47-99 (696)
12 KOG1244 Predicted transcriptio 97.3 8.4E-05 1.8E-09 66.7 1.1 51 191-244 280-334 (336)
13 KOG0956 PHD finger protein AF1 97.3 0.00012 2.5E-09 72.8 1.9 49 192-241 6-57 (900)
14 PF13831 PHD_2: PHD-finger; PD 97.2 5.4E-05 1.2E-09 48.0 -1.1 34 203-239 2-36 (36)
15 KOG1245 Chromatin remodeling c 96.8 0.00024 5.3E-09 76.6 -1.1 49 192-243 1108-1160(1404)
16 KOG0955 PHD finger protein BR1 96.7 0.001 2.3E-08 69.6 3.2 50 192-244 220-272 (1051)
17 KOG1632 Uncharacterized PHD Zn 96.4 0.0014 3E-08 61.3 1.3 48 192-242 60-114 (345)
18 COG5141 PHD zinc finger-contai 95.7 0.0041 8.8E-08 60.1 1.2 46 192-240 193-242 (669)
19 KOG0957 PHD finger protein [Ge 94.4 0.051 1.1E-06 52.9 4.4 52 185-239 112-177 (707)
20 KOG0957 PHD finger protein [Ge 93.2 2.9 6.3E-05 41.1 13.8 43 193-238 545-595 (707)
21 KOG1844 PHD Zn-finger proteins 92.8 0.056 1.2E-06 52.6 1.8 49 191-242 85-136 (508)
22 KOG2752 Uncharacterized conser 92.5 0.064 1.4E-06 49.3 1.7 31 191-224 127-165 (345)
23 KOG1632 Uncharacterized PHD Zn 91.6 0.027 5.8E-07 52.8 -2.0 48 190-240 237-294 (345)
24 PF13771 zf-HC5HC2H: PHD-like 89.7 0.17 3.7E-06 37.5 1.3 31 192-224 36-67 (90)
25 PF13832 zf-HC5HC2H_2: PHD-zin 88.8 0.18 4E-06 38.9 0.9 30 192-223 55-85 (110)
26 PF07227 DUF1423: Protein of u 86.9 0.49 1.1E-05 45.6 2.7 43 196-241 133-192 (446)
27 KOG4443 Putative transcription 78.6 1.2 2.6E-05 44.8 1.8 47 192-241 68-118 (694)
28 PF10497 zf-4CXXC_R1: Zinc-fin 78.0 1.4 3.1E-05 34.3 1.8 52 188-240 3-69 (105)
29 COG5034 TNG2 Chromatin remodel 72.1 66 0.0014 29.2 10.8 85 29-118 20-108 (271)
30 KOG1473 Nucleosome remodeling 71.6 2.5 5.4E-05 45.2 2.1 43 192-239 344-389 (1414)
31 PF11793 FANCL_C: FANCL C-term 61.6 6.9 0.00015 28.0 2.2 49 193-242 3-65 (70)
32 PF04100 Vps53_N: Vps53-like, 59.8 1.6E+02 0.0035 28.0 12.7 86 29-116 22-107 (383)
33 PF13341 RAG2_PHD: RAG2 PHD do 59.4 5.1 0.00011 29.1 1.1 32 204-237 29-67 (78)
34 COG3416 Uncharacterized protei 57.5 73 0.0016 28.1 8.1 71 43-116 7-77 (233)
35 PF13901 DUF4206: Domain of un 56.7 9 0.00019 33.1 2.5 43 192-244 152-201 (202)
36 KOG4460 Nuclear pore complex, 55.0 91 0.002 31.4 9.2 35 4-38 567-605 (741)
37 PF04012 PspA_IM30: PspA/IM30 53.5 1.4E+02 0.0031 25.5 15.4 28 1-28 2-34 (221)
38 COG1382 GimC Prefoldin, chaper 53.3 1.2E+02 0.0025 24.4 12.9 101 16-120 2-110 (119)
39 KOG4443 Putative transcription 53.3 3.9 8.5E-05 41.3 -0.4 48 192-242 18-72 (694)
40 PF11781 RRN7: RNA polymerase 53.3 10 0.00023 23.8 1.7 25 205-239 8-32 (36)
41 KOG1493 Anaphase-promoting com 52.2 5.4 0.00012 29.6 0.3 48 194-241 22-79 (84)
42 smart00744 RINGv The RING-vari 51.7 2.9 6.2E-05 28.0 -1.1 23 216-238 26-48 (49)
43 PF09755 DUF2046: Uncharacteri 51.3 2.1E+02 0.0045 26.7 10.6 35 76-110 110-151 (310)
44 PRK11546 zraP zinc resistance 49.7 1.5E+02 0.0032 24.5 9.8 33 16-48 42-77 (143)
45 KOG3579 Predicted E3 ubiquitin 49.4 18 0.0004 33.2 3.3 52 184-237 260-316 (352)
46 COG5415 Predicted integral mem 48.8 12 0.00026 33.0 1.9 32 206-242 193-224 (251)
47 KOG4796 RNA polymerase II elon 48.7 3E+02 0.0065 27.7 11.8 101 7-115 489-595 (604)
48 PF09755 DUF2046: Uncharacteri 47.4 2.4E+02 0.0052 26.3 13.2 41 76-116 153-193 (310)
49 PF09726 Macoilin: Transmembra 47.1 1.6E+02 0.0034 30.5 10.0 24 96-119 540-563 (697)
50 PF04668 Tsg: Twisted gastrula 46.4 7.4 0.00016 31.7 0.3 11 213-223 100-110 (132)
51 PRK10626 hypothetical protein; 46.0 78 0.0017 28.3 6.7 45 67-111 73-128 (239)
52 COG5194 APC11 Component of SCF 45.9 4.7 0.0001 30.1 -0.8 44 194-241 22-79 (88)
53 KOG4299 PHD Zn-finger protein 45.3 13 0.00029 37.3 1.9 44 192-240 47-94 (613)
54 PHA02562 46 endonuclease subun 45.3 3E+02 0.0065 26.8 13.8 50 67-116 215-270 (562)
55 PHA02862 5L protein; Provision 45.3 7.6 0.00017 32.2 0.2 46 193-241 3-51 (156)
56 PF14513 DAG_kinase_N: Diacylg 45.2 21 0.00045 29.3 2.7 26 2-28 51-76 (138)
57 PF07496 zf-CW: CW-type Zinc F 45.1 9.6 0.00021 25.5 0.6 28 205-237 3-34 (50)
58 KOG1829 Uncharacterized conser 44.4 5.7 0.00012 39.8 -0.8 32 205-244 531-562 (580)
59 PRK11637 AmiB activator; Provi 44.2 2.9E+02 0.0063 26.3 12.3 32 86-117 88-119 (428)
60 PF03194 LUC7: LUC7 N_terminus 43.3 1.7E+02 0.0036 26.3 8.5 46 66-115 124-170 (254)
61 KOG4552 Vitamin-D-receptor int 43.2 2.4E+02 0.0052 25.0 10.7 80 29-118 19-98 (272)
62 PF00038 Filament: Intermediat 42.3 2.6E+02 0.0055 25.1 11.5 99 19-117 164-271 (312)
63 PF08946 Osmo_CC: Osmosensory 41.8 33 0.00072 22.8 2.8 26 90-115 8-33 (46)
64 PHA02414 hypothetical protein 41.8 1.7E+02 0.0036 22.8 9.3 78 29-115 1-78 (111)
65 PF08702 Fib_alpha: Fibrinogen 40.7 2E+02 0.0044 23.5 12.7 40 76-115 93-132 (146)
66 PF13639 zf-RING_2: Ring finge 40.6 3.6 7.8E-05 26.3 -2.0 37 196-239 5-44 (44)
67 PF10367 Vps39_2: Vacuolar sor 38.9 24 0.00052 26.3 2.1 27 192-223 78-107 (109)
68 KOG1244 Predicted transcriptio 38.8 9.8 0.00021 34.8 -0.1 45 192-239 224-282 (336)
69 PRK13723 conjugal transfer pil 38.3 4E+02 0.0086 26.2 13.5 44 67-111 393-436 (451)
70 PHA02825 LAP/PHD finger-like p 37.7 15 0.00033 30.9 0.9 48 191-241 7-57 (162)
71 PF07649 C1_3: C1-like domain; 36.8 7.7 0.00017 22.9 -0.8 26 195-223 3-30 (30)
72 KOG1512 PHD Zn-finger protein 36.1 12 0.00026 34.4 0.0 33 204-239 278-315 (381)
73 PF12678 zf-rbx1: RING-H2 zinc 35.0 7.7 0.00017 27.9 -1.2 22 213-239 50-73 (73)
74 PF00641 zf-RanBP: Zn-finger i 34.8 25 0.00054 20.6 1.3 13 230-242 2-14 (30)
75 PF11101 DUF2884: Protein of u 34.7 2.6E+02 0.0055 24.6 8.2 53 67-119 51-110 (229)
76 KOG0994 Extracellular matrix g 34.2 5.8E+02 0.013 28.5 11.7 35 81-115 1571-1605(1758)
77 PF04286 DUF445: Protein of un 33.0 3.7E+02 0.008 24.2 10.6 20 90-109 269-288 (367)
78 KOG3053 Uncharacterized conser 32.9 21 0.00046 32.4 1.0 48 191-241 19-80 (293)
79 PF00130 C1_1: Phorbol esters/ 32.8 39 0.00085 22.1 2.2 34 191-227 10-47 (53)
80 PF04949 Transcrip_act: Transc 32.7 3E+02 0.0064 23.0 10.5 29 74-102 114-142 (159)
81 COG0497 RecN ATPase involved i 32.0 4E+02 0.0088 26.9 9.8 31 6-36 268-301 (557)
82 PRK08032 fliD flagellar cappin 31.6 3.6E+02 0.0079 26.2 9.4 51 2-53 387-441 (462)
83 PRK11519 tyrosine kinase; Prov 31.4 5.9E+02 0.013 26.1 14.8 32 29-63 271-302 (719)
84 PF02891 zf-MIZ: MIZ/SP-RING z 31.4 5.3 0.00012 26.8 -2.3 22 219-240 23-49 (50)
85 PF08535 KorB: KorB domain; I 31.1 2.2E+02 0.0047 21.0 6.3 48 6-53 17-66 (93)
86 cd00890 Prefoldin Prefoldin is 31.1 2.4E+02 0.0053 21.6 6.9 45 75-119 82-126 (129)
87 PF03791 KNOX2: KNOX2 domain ; 31.1 47 0.001 22.7 2.3 20 9-28 11-35 (52)
88 PRK09039 hypothetical protein; 30.9 4.5E+02 0.0097 24.6 14.0 27 16-42 63-91 (343)
89 COG1842 PspA Phage shock prote 30.6 3.8E+02 0.0082 23.6 15.7 32 85-116 104-135 (225)
90 KOG2041 WD40 repeat protein [G 30.1 51 0.0011 34.3 3.3 52 185-240 1109-1164(1189)
91 KOG2846 Predicted membrane pro 30.0 33 0.00072 32.0 1.8 38 205-247 220-257 (328)
92 cd04772 HTH_TioE_rpt1 First He 29.1 72 0.0016 24.1 3.3 23 94-116 76-98 (99)
93 PF08746 zf-RING-like: RING-li 29.1 11 0.00024 24.4 -1.0 32 206-238 12-43 (43)
94 KOG1671 Ubiquinol cytochrome c 28.8 28 0.00062 30.3 1.1 21 219-239 155-177 (210)
95 PF11690 DUF3287: Protein of u 28.5 2.4E+02 0.0051 22.3 6.1 43 73-115 43-86 (109)
96 cd04476 RPA1_DBD_C RPA1_DBD_C: 28.5 35 0.00077 28.0 1.6 26 216-241 31-60 (166)
97 cd02338 ZZ_PCMF_like Zinc fing 28.5 34 0.00075 22.7 1.3 31 206-240 1-32 (49)
98 smart00547 ZnF_RBZ Zinc finger 28.4 29 0.00063 19.5 0.8 11 231-241 1-11 (26)
99 PRK09841 cryptic autophosphory 28.1 6.8E+02 0.015 25.8 14.3 33 29-64 271-303 (726)
100 PF14169 YdjO: Cold-inducible 27.7 53 0.0011 23.1 2.1 34 207-246 20-53 (59)
101 PF00645 zf-PARP: Poly(ADP-rib 27.7 14 0.00031 26.8 -0.8 9 216-224 39-47 (82)
102 KOG0996 Structural maintenance 27.3 5.8E+02 0.013 28.3 10.4 47 72-118 885-931 (1293)
103 KOG2932 E3 ubiquitin ligase in 27.0 29 0.00063 32.4 0.9 38 193-240 91-131 (389)
104 KOG4628 Predicted E3 ubiquitin 26.7 63 0.0014 30.5 3.1 46 193-244 231-279 (348)
105 PRK10869 recombination and rep 26.3 5.1E+02 0.011 25.8 9.6 23 83-105 363-385 (553)
106 COG4575 ElaB Uncharacterized c 26.1 3.2E+02 0.007 21.4 8.7 62 35-100 11-73 (104)
107 PF08165 FerA: FerA (NUC095) d 26.0 93 0.002 22.1 3.2 36 4-40 15-53 (66)
108 TIGR02338 gimC_beta prefoldin, 25.7 3.1E+02 0.0067 21.0 11.5 45 75-119 62-106 (110)
109 COG5560 UBP12 Ubiquitin C-term 25.6 24 0.00052 36.0 0.1 17 230-246 693-709 (823)
110 KOG1473 Nucleosome remodeling 24.9 14 0.00029 39.9 -1.8 47 193-243 429-481 (1414)
111 PHA03158 hypothetical protein; 24.6 1.7E+02 0.0036 25.7 5.0 37 80-116 227-269 (273)
112 KOG1318 Helix loop helix trans 24.4 6.6E+02 0.014 24.4 10.4 79 29-117 228-320 (411)
113 PF05781 MRVI1: MRVI1 protein; 24.2 7.4E+02 0.016 24.9 10.7 27 92-118 290-316 (538)
114 PF07139 DUF1387: Protein of u 24.1 5.8E+02 0.013 23.7 11.7 51 66-116 201-258 (302)
115 PF08432 Vfa1: AAA-ATPase Vps4 24.1 47 0.001 28.2 1.6 28 192-224 13-41 (182)
116 KOG0129 Predicted RNA-binding 24.0 26 0.00057 34.6 0.0 14 232-245 482-495 (520)
117 PF10168 Nup88: Nuclear pore c 23.5 8.5E+02 0.018 25.3 11.0 24 5-28 545-569 (717)
118 PF10737 GerPC: Spore germinat 23.0 2E+02 0.0044 24.5 5.3 34 17-50 95-136 (176)
119 PRK06798 fliD flagellar cappin 23.0 5.7E+02 0.012 24.8 9.0 52 3-54 361-415 (440)
120 PF12861 zf-Apc11: Anaphase-pr 22.8 33 0.00071 25.9 0.4 28 213-242 52-81 (85)
121 KOG0955 PHD finger protein BR1 22.8 36 0.00078 36.7 0.8 34 193-227 330-367 (1051)
122 KOG2626 Histone H3 (Lys4) meth 22.4 1E+02 0.0023 30.7 3.8 47 192-241 20-76 (544)
123 KOG4637 Adaptor for phosphoino 22.2 7.2E+02 0.016 24.0 12.2 12 3-14 139-150 (464)
124 PRK09343 prefoldin subunit bet 22.1 3.9E+02 0.0085 21.0 11.4 99 17-119 4-110 (121)
125 PF02370 M: M protein repeat; 22.1 1.3E+02 0.0028 16.8 2.5 15 104-118 4-18 (21)
126 PF02996 Prefoldin: Prefoldin 21.6 3.6E+02 0.0079 20.4 6.3 44 76-119 73-116 (120)
127 TIGR00634 recN DNA repair prot 21.5 7.3E+02 0.016 24.6 9.7 11 18-28 285-295 (563)
128 KOG1011 Neurotransmitter relea 21.4 4.7E+02 0.01 27.4 8.1 91 21-114 860-954 (1283)
129 KOG1246 DNA-binding protein ju 21.0 77 0.0017 33.5 2.8 51 188-241 151-204 (904)
130 PF07195 FliD_C: Flagellar hoo 20.9 3.9E+02 0.0084 23.3 6.9 51 2-53 173-228 (239)
131 cd00584 Prefoldin_alpha Prefol 20.8 4.1E+02 0.0088 20.6 6.9 45 75-119 82-126 (129)
132 PRK10132 hypothetical protein; 20.7 4.1E+02 0.009 20.7 9.4 50 29-82 9-58 (108)
133 PF00412 LIM: LIM domain; Int 20.7 44 0.00095 22.0 0.6 39 196-239 3-54 (58)
134 PF04216 FdhE: Protein involve 20.5 40 0.00087 30.5 0.5 27 191-219 171-209 (290)
No 1
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=100.00 E-value=2e-38 Score=276.26 Aligned_cols=227 Identities=29% Similarity=0.434 Sum_probs=156.9
Q ss_pred HHHHhhh-ccCChHHHHHHHHH--hHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCChhhhhhHHHHHHHHHHHHHH
Q 025765 8 FLLTFMD-IFFPPLVRDAQMQC--FFVHTLAEIQRQNEQRCEQEIEDLMREIRAGNITPNTSLIRFSDDALDEQKHSIRI 84 (248)
Q Consensus 8 yle~fie-~~~lP~EL~r~~~~--elD~~~qel~~~~~~~~~~~l~~~~k~~~~gs~~~~~k~~~l~~~I~~~~~~~~~l 84 (248)
-|++|++ +.|+|++..+.|++ ++|.++.++++.+.+... |.+++. ++|++..++.+..|.+.|++.|-.+..+
T Consensus 6 ~Lnd~~d~l~n~P~et~~~~t~l~~iD~k~~d~~k~l~q~~s--i~k~~~--~~~~~t~~e~ed~l~k~i~Ell~~a~~~ 81 (271)
T COG5034 6 GLNDITDHLANVPSETDIRFTELSEIDAKVCDIIKNLRQMIS--ILKKII--DLDSQTYEEVEDGLLKEIRELLLKAIYI 81 (271)
T ss_pred HHHHHHHHHHhCChhhhhhhhhhhhhhHHHHHHHHHHHHHHH--HHHHHh--hcccCccccchhHHHHHHHHHHHHHHHH
Confidence 4899999 99999999999999 999999999999999888 555777 8999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----Hhhccccccc--cCCCCCCC--------CCCCCCCCCCCCCCC
Q 025765 85 ADEKVALAVQAYDLVDTHIQQLDQYLKNFDEE-----LRRERDSVAT--TASPAPSL--------DGSTKSGRSSEGGRG 149 (248)
Q Consensus 85 ~dEKv~lA~~~~~lvd~hir~LD~dl~~~e~e-----l~~~~~~~~~--~~~~~~~~--------~~~~~~~~~~~~~~~ 149 (248)
+.+|+.||+.+..++++|+++||..+++...+ ++........ .++..++. ++++..|+.. ...
T Consensus 82 ~~~~~~l~d~~~~l~~Rh~~~~d~~~a~~~h~~~~~~ie~~~~~~s~~~~~~~ss~a~~ss~~~~saassqgs~~--t~~ 159 (271)
T COG5034 82 QKEKSDLADRAEKLLRRHRKLLDDRIAKRPHEKVAARIENCHDAVSRLERNSYSSAARRSSGEHRSAASSQGSRH--TKL 159 (271)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhHHHhhhhhhhhhhhhhhhhhhhhhhccccchhhhccccccccccccccccC--chh
Confidence 99999999999999999999999999776655 2221111100 00000000 0000011100 000
Q ss_pred CCcc-h-----hhhhHHHH--------------HHHHhhhhccCCCCCCCCCCCCCCCCCCCCceeeeCCCCCCCceecC
Q 025765 150 GRKK-T-----RLATAAAA--------------AAAAVTEAAATPVANPTGMELDLPVDPNEPTYCVCNQVSYGEMVACD 209 (248)
Q Consensus 150 ~rk~-~-----~~~~~~~~--------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~C~~~~~g~mi~Cd 209 (248)
++++ . +.+...+. ....+.++.. ....+...-+..+...++.+||+|++++||+||+||
T Consensus 160 ~~R~n~~~~k~~~p~~~S~r~~~~t~~sp~v~~t~t~v~e~~~-~~s~~~~~vss~d~se~e~lYCfCqqvSyGqMVaCD 238 (271)
T COG5034 160 KKRKNIHNLKRRSPELSSKREVSFTLESPSVPDTATRVKEGNN-GGSTKSRGVSSEDNSEGEELYCFCQQVSYGQMVACD 238 (271)
T ss_pred HHHHhhcccccCCcchhhhccCCccCCCCCcccchhhhhcccC-CCCccccCcCccccccCceeEEEecccccccceecC
Confidence 0000 0 00000000 0000000000 001111112223444678999999999999999999
Q ss_pred CCCCCCcceecccCCCCcCCCCceeCCCCccc
Q 025765 210 NPNCKIEWFHFGCVGLKEQPKGKWYCPDCAAL 241 (248)
Q Consensus 210 ~~~C~~~WfH~~Cvgl~~~p~~~w~C~~C~~~ 241 (248)
|.||++||||+.||||..+|+|+|||+.|...
T Consensus 239 n~nCkrEWFH~~CVGLk~pPKG~WYC~eCk~~ 270 (271)
T COG5034 239 NANCKREWFHLECVGLKEPPKGKWYCPECKKA 270 (271)
T ss_pred CCCCchhheeccccccCCCCCCcEeCHHhHhc
Confidence 99999999999999999999999999999753
No 2
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=100.00 E-value=1.1e-33 Score=254.80 Aligned_cols=234 Identities=29% Similarity=0.543 Sum_probs=145.3
Q ss_pred HHHHHhhh-----ccCChHHHHHHHHH--hHHHH--HHHHHHHHH-HHHHHHHHHHHHHHhhCCCCCChhhhhhHHHHHH
Q 025765 7 VFLLTFMD-----IFFPPLVRDAQMQC--FFVHT--LAEIQRQNE-QRCEQEIEDLMREIRAGNITPNTSLIRFSDDALD 76 (248)
Q Consensus 7 ~yle~fie-----~~~lP~EL~r~~~~--elD~~--~qel~~~~~-~~~~~~l~~~~k~~~~gs~~~~~k~~~l~~~I~~ 76 (248)
.|++.|+. +.++|..++++|.. ++|.. ......+++ ..... +++ ...+....+....+...|+.
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~f~~l~~~~~~~~~~~~~~e~~~~~~~~----~~~--~~~~~~~~~~~~~~~~~~~~ 81 (274)
T KOG1973|consen 8 ILIEEVDDDIDMAVQNLPRNLQHNFDVIEDIDIFGRSENQKKELDLKVAVE----YMS--KGRSQLSKPQKDPLLEAIRS 81 (274)
T ss_pred hhhhhcccccccccccCCccchhHHHHHhhhhccchhHHHHhhhhhhhhhc----ccc--ccccccCccccchhHHHHHH
Confidence 45556665 56999999999999 88884 455555444 22222 222 33332223334445568889
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc-ccccccC-----CCCCC----CC--CCCCCCCCC
Q 025765 77 EQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELRRER-DSVATTA-----SPAPS----LD--GSTKSGRSS 144 (248)
Q Consensus 77 ~~~~~~~l~dEKv~lA~~~~~lvd~hir~LD~dl~~~e~el~~~~-~~~~~~~-----~~~~~----~~--~~~~~~~~~ 144 (248)
.+..+.++++||+++|.++++++.+||+++|..++.|+.++.... ......+ ..... .. .+......+
T Consensus 82 ~~~~~~~~~~ek~~~~~~~~e~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~ 161 (274)
T KOG1973|consen 82 ALRKCKELSDEKVQIAMQTVELIPKHIGRLETALKSFEVELELAKAESSSKRSSSLKSAKKKEREVFKEKKESKQGSSEK 161 (274)
T ss_pred HHhhhhhhhhHHHHHHHHHHHhhHhhhcchhHHHHhcccchhhhhhhcccccccchhccCccccccccchhhcCCCCCCC
Confidence 999999999999999999999999999999999999988766531 1110000 00000 00 000000000
Q ss_pred CCCCCCCcchhh--hhHH--HHHHHHh---hhh-ccCCCCC--CCCCCCCCCCCCCCCceeeeCCCCCCCceecCCCCCC
Q 025765 145 EGGRGGRKKTRL--ATAA--AAAAAAV---TEA-AATPVAN--PTGMELDLPVDPNEPTYCVCNQVSYGEMVACDNPNCK 214 (248)
Q Consensus 145 ~~~~~~rk~~~~--~~~~--~~~~~~~---~~~-~~~~~~~--~~~~~~~~~~~~~~~~~C~C~~~~~g~mi~Cd~~~C~ 214 (248)
.+...+.++... .... ......+ ... ......+ ......+...++++++||+|++++||+||+|||.+|+
T Consensus 162 ~s~~~~~~~~~~~~~~~~~~rekk~~v~~~~~~~t~~~~~s~~~~~~~~~~~~d~~e~~yC~Cnqvsyg~Mi~CDn~~C~ 241 (274)
T KOG1973|consen 162 PSSVDKAKKGSKVNRRPCGAREKKRKVVEAKKEKTPKNKSSRPAESMESEEAVDPDEPTYCICNQVSYGKMIGCDNPGCP 241 (274)
T ss_pred cccccccccccccccccchhhhhhhhhccccccccccCCCCCcccccccccccCCCCCEEEEecccccccccccCCCCCC
Confidence 000000000000 0000 0000000 000 0000111 2235667889999999999999999999999999999
Q ss_pred CcceecccCCCCcCCCCceeCCCCccccccCC
Q 025765 215 IEWFHFGCVGLKEQPKGKWYCPDCAALKNRRK 246 (248)
Q Consensus 215 ~~WfH~~Cvgl~~~p~~~w~C~~C~~~~~~~k 246 (248)
|+||||.||||+.+|+|+||||.|+..+.+.+
T Consensus 242 ~eWFH~~CVGL~~~PkgkWyC~~C~~~~~~~~ 273 (274)
T KOG1973|consen 242 IEWFHFTCVGLKTKPKGKWYCPRCKAENKKKG 273 (274)
T ss_pred cceEEEeccccccCCCCcccchhhhhhhhccC
Confidence 99999999999999999999999998876543
No 3
>PF12998 ING: Inhibitor of growth proteins N-terminal histone-binding; InterPro: IPR024610 Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterised C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail. This entry represents the N-terminal histone binding domain found in inhibitor proteins.; PDB: 4AFL_A.
Probab=99.89 E-value=7.9e-23 Score=158.24 Aligned_cols=100 Identities=31% Similarity=0.480 Sum_probs=87.6
Q ss_pred HHHHHhhh-ccCChHHHHHHHHH--hHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC--CCCChhhhhhHHHHHHHHHHH
Q 025765 7 VFLLTFMD-IFFPPLVRDAQMQC--FFVHTLAEIQRQNEQRCEQEIEDLMREIRAGN--ITPNTSLIRFSDDALDEQKHS 81 (248)
Q Consensus 7 ~yle~fie-~~~lP~EL~r~~~~--elD~~~qel~~~~~~~~~~~l~~~~k~~~~gs--~~~~~k~~~l~~~I~~~~~~~ 81 (248)
||||+||| +++||.||+|+|++ |||.+++++..++++....++. ..++ ++++ ....+.++|+..+.++
T Consensus 1 ~~le~f~d~~~~LP~el~r~l~~irelD~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~-~~~~~~~~I~~~~~~~ 73 (105)
T PF12998_consen 1 TYLEDFLDSLENLPAELQRNLTLIRELDAKSQDLLEELDQQIQKFIK------NHGSPSLSPE-KRRELLKEIQEEYERA 73 (105)
T ss_dssp HHHHHHHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT------CTTS--S-HH-HHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHChHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHh------hcccccCChH-HHHHHHHHHHHHHHHH
Confidence 79999999 99999999999999 9999999999999999888765 5554 5555 5566668999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 82 IRIADEKVALAVQAYDLVDTHIQQLDQYLKNF 113 (248)
Q Consensus 82 ~~l~dEKv~lA~~~~~lvd~hir~LD~dl~~~ 113 (248)
+.+++|||.||+++|++|++||+|||.++++|
T Consensus 74 ~~l~deKv~lA~~~~d~v~~hi~rLD~dl~~f 105 (105)
T PF12998_consen 74 LELSDEKVALAQQAYDLVDRHIRRLDQDLKKF 105 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHCT---
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 99999999999999999999999999999887
No 4
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=98.86 E-value=4.9e-10 Score=75.82 Aligned_cols=44 Identities=52% Similarity=1.476 Sum_probs=36.5
Q ss_pred ee-eeCCCC-CCCceecCCCCCCCcceecccCCCCcC----CCCceeCCCCcc
Q 025765 194 YC-VCNQVS-YGEMVACDNPNCKIEWFHFGCVGLKEQ----PKGKWYCPDCAA 240 (248)
Q Consensus 194 ~C-~C~~~~-~g~mi~Cd~~~C~~~WfH~~Cvgl~~~----p~~~w~C~~C~~ 240 (248)
|| +|++.. .++||.||. |. .|||..|+++... +.+.|+|+.|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~~--C~-~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDS--CN-RWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBST--TS-CEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCC--CC-hhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 68 999864 368999999 77 9999999998864 346899999974
No 5
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.98 E-value=1.8e-06 Score=77.65 Aligned_cols=45 Identities=33% Similarity=0.783 Sum_probs=38.2
Q ss_pred ee-eeCCCCC-CCceecCCCCCCCcceecccCCCCcCCCCceeCC-CCccc
Q 025765 194 YC-VCNQVSY-GEMVACDNPNCKIEWFHFGCVGLKEQPKGKWYCP-DCAAL 241 (248)
Q Consensus 194 ~C-~C~~~~~-g~mi~Cd~~~C~~~WfH~~Cvgl~~~p~~~w~C~-~C~~~ 241 (248)
.| +|++|-- .+|+.||-|| +.||..||||...|.|.|.|. .|...
T Consensus 316 lC~IC~~P~~E~E~~FCD~CD---RG~HT~CVGL~~lP~G~WICD~~C~~~ 363 (381)
T KOG1512|consen 316 LCRICLGPVIESEHLFCDVCD---RGPHTLCVGLQDLPRGEWICDMRCREA 363 (381)
T ss_pred hhhccCCcccchheecccccc---CCCCccccccccccCccchhhhHHHHh
Confidence 36 8999864 6899999955 889999999999999999998 57544
No 7
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.51 E-value=5.7e-05 Score=75.85 Aligned_cols=49 Identities=31% Similarity=0.922 Sum_probs=39.4
Q ss_pred CCCcee-eeCCCCCC-CceecCCCCCCCcceecccCC--CCcCCCCceeCCCCcc
Q 025765 190 NEPTYC-VCNQVSYG-EMVACDNPNCKIEWFHFGCVG--LKEQPKGKWYCPDCAA 240 (248)
Q Consensus 190 ~~~~~C-~C~~~~~g-~mi~Cd~~~C~~~WfH~~Cvg--l~~~p~~~w~C~~C~~ 240 (248)
.+..-| +|..++.. -||.||. |....||..|+. |.+.|.+.|||+.|..
T Consensus 213 ~E~~~C~IC~~~DpEdVLLLCDs--CN~~~YH~YCLDPdl~eiP~~eWYC~NC~d 265 (1134)
T KOG0825|consen 213 QEEVKCDICTVHDPEDVLLLCDS--CNKVYYHVYCLDPDLSESPVNEWYCTNCSL 265 (1134)
T ss_pred cccccceeeccCChHHhheeecc--cccceeeccccCcccccccccceecCcchh
Confidence 346668 99988754 5999999 554559999996 5668999999999964
No 8
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.50 E-value=3.2e-05 Score=75.92 Aligned_cols=47 Identities=32% Similarity=1.073 Sum_probs=37.2
Q ss_pred Ccee-eeCCCC-CCCceecCCCCCCCcceecccCC----CCcCCCCceeCCCCccc
Q 025765 192 PTYC-VCNQVS-YGEMVACDNPNCKIEWFHFGCVG----LKEQPKGKWYCPDCAAL 241 (248)
Q Consensus 192 ~~~C-~C~~~~-~g~mi~Cd~~~C~~~WfH~~Cvg----l~~~p~~~w~C~~C~~~ 241 (248)
..|| .|++.. +-..|+||. |+ .-||+.|+. ....|.|.|||+.|...
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD~--Cp-~sFH~~CLePPl~~eniP~g~W~C~ec~~k 305 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCDG--CP-RSFHQTCLEPPLEPENIPPGSWFCPECKIK 305 (613)
T ss_pred HHHHHHhCCccccccceeecC--Cc-hHHHHhhcCCCCCcccCCCCccccCCCeee
Confidence 4599 999883 345599999 88 789999995 23368999999999754
No 9
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=97.48 E-value=4.4e-05 Score=76.19 Aligned_cols=50 Identities=40% Similarity=0.953 Sum_probs=42.1
Q ss_pred CCCCCCcee-eeCCCCC---CCceecCCCCCCCcceecccCCCCcCCCCceeCCCCc
Q 025765 187 VDPNEPTYC-VCNQVSY---GEMVACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCA 239 (248)
Q Consensus 187 ~~~~~~~~C-~C~~~~~---g~mi~Cd~~~C~~~WfH~~Cvgl~~~p~~~w~C~~C~ 239 (248)
+.-+|.+.| ||+.++. .+||.||+ |. --.|..|.||...|.|.|.|..|.
T Consensus 266 ie~dedviCDvCrspD~e~~neMVfCd~--Cn-~cVHqaCyGIle~p~gpWlCr~Ca 319 (893)
T KOG0954|consen 266 IEYDEDVICDVCRSPDSEEANEMVFCDK--CN-ICVHQACYGILEVPEGPWLCRTCA 319 (893)
T ss_pred eeccccceeceecCCCccccceeEEecc--ch-hHHHHhhhceeecCCCCeeehhcc
Confidence 334478999 9999964 47999999 55 668999999999999999998874
No 10
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=97.40 E-value=5.1e-05 Score=72.81 Aligned_cols=47 Identities=30% Similarity=0.927 Sum_probs=33.0
Q ss_pred eeeeCCCC-CCCceecCCCCCCCcceecccCC--CCc----CCCCceeCCCCccccc
Q 025765 194 YCVCNQVS-YGEMVACDNPNCKIEWFHFGCVG--LKE----QPKGKWYCPDCAALKN 243 (248)
Q Consensus 194 ~C~C~~~~-~g~mi~Cd~~~C~~~WfH~~Cvg--l~~----~p~~~w~C~~C~~~~~ 243 (248)
||.|..+. +..||+|+. |. .|||..|.- ++. .+...|||..|...++
T Consensus 173 vC~~g~~~~~NrmlqC~~--C~-~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~ 226 (464)
T KOG4323|consen 173 VCYCGGPGAGNRMLQCDK--CR-QWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPK 226 (464)
T ss_pred eeecCCcCccceeeeecc--cc-cHHHHHhccCCCCHhhccCccceEeehhhccchh
Confidence 34444442 237999999 66 999999984 222 2467899999986654
No 11
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.30 E-value=9.9e-05 Score=74.27 Aligned_cols=50 Identities=42% Similarity=0.983 Sum_probs=40.1
Q ss_pred Ccee-eeCCCCCCCceecCCCCCCCcceecccCC--CCcCCCCceeCCCCccccccCC
Q 025765 192 PTYC-VCNQVSYGEMVACDNPNCKIEWFHFGCVG--LKEQPKGKWYCPDCAALKNRRK 246 (248)
Q Consensus 192 ~~~C-~C~~~~~g~mi~Cd~~~C~~~WfH~~Cvg--l~~~p~~~w~C~~C~~~~~~~k 246 (248)
..+| +|... |+.|+||. |+ .|||..|.+ ++..|.+.|.|+.|..+..++|
T Consensus 47 ~e~c~ic~~~--g~~l~c~t--C~-~s~h~~cl~~pl~~~p~~~~~c~Rc~~p~~~~k 99 (696)
T KOG0383|consen 47 QEACRICADG--GELLWCDT--CP-ASFHASCLGPPLTPQPNGEFICPRCFCPKNAGK 99 (696)
T ss_pred hhhhhhhcCC--CcEEEecc--cc-HHHHHHccCCCCCcCCccceeeeeeccCCCccc
Confidence 4455 99888 99999999 99 999999997 4556667799999966655444
No 12
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=97.29 E-value=8.4e-05 Score=66.67 Aligned_cols=51 Identities=27% Similarity=0.774 Sum_probs=41.3
Q ss_pred CCcee-eeCCCCC-CCceecCCCCCCCcceecccCC--CCcCCCCceeCCCCcccccc
Q 025765 191 EPTYC-VCNQVSY-GEMVACDNPNCKIEWFHFGCVG--LKEQPKGKWYCPDCAALKNR 244 (248)
Q Consensus 191 ~~~~C-~C~~~~~-g~mi~Cd~~~C~~~WfH~~Cvg--l~~~p~~~w~C~~C~~~~~~ 244 (248)
|-.|| +|+-..+ .+++.||.|| +.||..|+. +..+|.|.|-|..|....++
T Consensus 280 eck~csicgtsenddqllfcddcd---rgyhmyclsppm~eppegswsc~KOG~~~~e 334 (336)
T KOG1244|consen 280 ECKYCSICGTSENDDQLLFCDDCD---RGYHMYCLSPPMVEPPEGSWSCHLCLEELKE 334 (336)
T ss_pred ecceeccccCcCCCceeEeecccC---CceeeEecCCCcCCCCCCchhHHHHHHHHhh
Confidence 45578 8987765 5689999955 889999995 67789999999999876654
No 13
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=97.27 E-value=0.00012 Score=72.79 Aligned_cols=49 Identities=33% Similarity=0.913 Sum_probs=41.6
Q ss_pred CceeeeCCC-CC--CCceecCCCCCCCcceecccCCCCcCCCCceeCCCCccc
Q 025765 192 PTYCVCNQV-SY--GEMVACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCAAL 241 (248)
Q Consensus 192 ~~~C~C~~~-~~--g~mi~Cd~~~C~~~WfH~~Cvgl~~~p~~~w~C~~C~~~ 241 (248)
..+|||-.- .+ ..+|.||+-+|. -..|..|.||...|.|.|||..|...
T Consensus 6 GGCCVCSDErGWaeNPLVYCDG~nCs-VAVHQaCYGIvqVPtGpWfCrKCesq 57 (900)
T KOG0956|consen 6 GGCCVCSDERGWAENPLVYCDGHNCS-VAVHQACYGIVQVPTGPWFCRKCESQ 57 (900)
T ss_pred cceeeecCcCCCccCceeeecCCCce-eeeehhcceeEecCCCchhhhhhhhh
Confidence 468999654 23 358999999999 78999999999999999999999643
No 14
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=97.16 E-value=5.4e-05 Score=47.97 Aligned_cols=34 Identities=38% Similarity=1.031 Sum_probs=20.1
Q ss_pred CCceecCCCCCCCcceecccCCCCcCCCC-ceeCCCCc
Q 025765 203 GEMVACDNPNCKIEWFHFGCVGLKEQPKG-KWYCPDCA 239 (248)
Q Consensus 203 g~mi~Cd~~~C~~~WfH~~Cvgl~~~p~~-~w~C~~C~ 239 (248)
..||.|++ |. -++|.+|-|+...|.+ .|+|..|.
T Consensus 2 n~ll~C~~--C~-v~VH~~CYGv~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDN--CN-VAVHQSCYGVSEVPDGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SS--S---EEEHHHHT-SS--SS-----HHH-
T ss_pred CceEEeCC--CC-CcCChhhCCcccCCCCCcEECCcCC
Confidence 46899999 66 7899999999998876 89998874
No 15
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=96.76 E-value=0.00024 Score=76.56 Aligned_cols=49 Identities=35% Similarity=0.916 Sum_probs=41.1
Q ss_pred Ccee-eeCCCCCC-CceecCCCCCCCcceecccCC--CCcCCCCceeCCCCccccc
Q 025765 192 PTYC-VCNQVSYG-EMVACDNPNCKIEWFHFGCVG--LKEQPKGKWYCPDCAALKN 243 (248)
Q Consensus 192 ~~~C-~C~~~~~g-~mi~Cd~~~C~~~WfH~~Cvg--l~~~p~~~w~C~~C~~~~~ 243 (248)
...| +|+..... .|+.||. |. .|||+.|+. +...|.|.|+||.|+....
T Consensus 1108 ~~~c~~cr~k~~~~~m~lc~~--c~-~~~h~~C~rp~~~~~~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1108 NALCKVCRRKKQDEKMLLCDE--CL-SGFHLFCLRPALSSVPPGDWMCPSCRKEHR 1160 (1404)
T ss_pred hhhhhhhhhcccchhhhhhHh--hh-hhHHHHhhhhhhccCCcCCccCCccchhhh
Confidence 5678 99887543 6999999 55 999999985 6678999999999998774
No 16
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=96.72 E-value=0.001 Score=69.64 Aligned_cols=50 Identities=30% Similarity=0.767 Sum_probs=40.4
Q ss_pred CceeeeCCCCC---CCceecCCCCCCCcceecccCCCCcCCCCceeCCCCcccccc
Q 025765 192 PTYCVCNQVSY---GEMVACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCAALKNR 244 (248)
Q Consensus 192 ~~~C~C~~~~~---g~mi~Cd~~~C~~~WfH~~Cvgl~~~p~~~w~C~~C~~~~~~ 244 (248)
..+|||....- ...|.||+ |. -..|..|+|+..+|.|.|+|-.|...+.+
T Consensus 220 ~~C~iC~~~~~~n~n~ivfCD~--Cn-l~VHq~Cygi~~ipeg~WlCr~Cl~s~~~ 272 (1051)
T KOG0955|consen 220 AVCCICLDGECQNSNVIVFCDG--CN-LAVHQECYGIPFIPEGQWLCRRCLQSPQR 272 (1051)
T ss_pred ccceeecccccCCCceEEEcCC--Cc-chhhhhccCCCCCCCCcEeehhhccCcCc
Confidence 34459988742 46899999 55 66999999999999999999999876544
No 17
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=96.37 E-value=0.0014 Score=61.35 Aligned_cols=48 Identities=31% Similarity=0.789 Sum_probs=39.6
Q ss_pred CceeeeCCCCCC--CceecCCCCCCCcceeccc--CCCCc---CCCCceeCCCCcccc
Q 025765 192 PTYCVCNQVSYG--EMVACDNPNCKIEWFHFGC--VGLKE---QPKGKWYCPDCAALK 242 (248)
Q Consensus 192 ~~~C~C~~~~~g--~mi~Cd~~~C~~~WfH~~C--vgl~~---~p~~~w~C~~C~~~~ 242 (248)
..||.|..+... .|+.||. |. .|||..| ||+.. .+...|+|..|....
T Consensus 60 ~~~~~~~~~~~p~~~~~~cd~--C~-~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~ 114 (345)
T KOG1632|consen 60 QRYCKCYKPCDPDDLMEQCDL--CE-DWYHGECWEVGTAEKEAPKEDPKVCDECKEAQ 114 (345)
T ss_pred hchhhcccccCchhhhhcccc--cc-ccccccccccCchhhcCCccccccccccchhh
Confidence 348999888765 8999999 88 9999999 99776 346789999997654
No 18
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=95.73 E-value=0.0041 Score=60.10 Aligned_cols=46 Identities=30% Similarity=0.827 Sum_probs=37.7
Q ss_pred Ccee-eeCCCCC---CCceecCCCCCCCcceecccCCCCcCCCCceeCCCCcc
Q 025765 192 PTYC-VCNQVSY---GEMVACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCAA 240 (248)
Q Consensus 192 ~~~C-~C~~~~~---g~mi~Cd~~~C~~~WfH~~Cvgl~~~p~~~w~C~~C~~ 240 (248)
...| +|..... ...|.||+ |. -..|.+|.|+...|.|+|+|..|.-
T Consensus 193 d~~C~~c~~t~~eN~naiVfCdg--C~-i~VHq~CYGI~f~peG~WlCrkCi~ 242 (669)
T COG5141 193 DDICTKCTSTHNENSNAIVFCDG--CE-ICVHQSCYGIQFLPEGFWLCRKCIY 242 (669)
T ss_pred hhhhHhccccccCCcceEEEecC--cc-hhhhhhcccceecCcchhhhhhhcc
Confidence 4467 8887754 35899999 55 4589999999999999999999953
No 19
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=94.40 E-value=0.051 Score=52.89 Aligned_cols=52 Identities=37% Similarity=0.945 Sum_probs=35.3
Q ss_pred CCCCCCCC-ceeeeCC-C--CCCCceecCCCCCCCcceecccCCCCc---CC-------CCceeCCCCc
Q 025765 185 LPVDPNEP-TYCVCNQ-V--SYGEMVACDNPNCKIEWFHFGCVGLKE---QP-------KGKWYCPDCA 239 (248)
Q Consensus 185 ~~~~~~~~-~~C~C~~-~--~~g~mi~Cd~~~C~~~WfH~~Cvgl~~---~p-------~~~w~C~~C~ 239 (248)
.+..|-.. ..|||-. . +.|+.|+||+ |.| -.|-.|.|+.. +| ...|||..|.
T Consensus 112 ~~Sapkk~~iCcVClg~rs~da~ei~qCd~--CGi-~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~ 177 (707)
T KOG0957|consen 112 TPSAPKKAVICCVCLGQRSVDAGEILQCDK--CGI-NVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACL 177 (707)
T ss_pred ccCccccceEEEEeecCccccccceeeccc--cCc-eecccccccccccccCCCCccCCCCchhhhhHh
Confidence 33444445 4459943 2 3489999999 664 48999999763 12 3679998885
No 20
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=93.17 E-value=2.9 Score=41.11 Aligned_cols=43 Identities=33% Similarity=1.002 Sum_probs=33.5
Q ss_pred cee-eeCCCCC-CCceecCCCCCCCcceecccCC--CCcCCCC----ceeCCCC
Q 025765 193 TYC-VCNQVSY-GEMVACDNPNCKIEWFHFGCVG--LKEQPKG----KWYCPDC 238 (248)
Q Consensus 193 ~~C-~C~~~~~-g~mi~Cd~~~C~~~WfH~~Cvg--l~~~p~~----~w~C~~C 238 (248)
.-| ||...-. --.++||- |. --||+.|+. |+..|+. -|.|..|
T Consensus 545 ysCgiCkks~dQHll~~CDt--C~-lhYHlGCL~PPLTR~Pkk~kn~gWqCsEC 595 (707)
T KOG0957|consen 545 YSCGICKKSTDQHLLTQCDT--CH-LHYHLGCLSPPLTRLPKKNKNFGWQCSEC 595 (707)
T ss_pred eeeeeeccchhhHHHhhcch--hh-ceeeccccCCccccCcccccCcceeeccc
Confidence 448 9987743 34789999 66 779999995 7887754 4999999
No 21
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=92.78 E-value=0.056 Score=52.55 Aligned_cols=49 Identities=31% Similarity=0.666 Sum_probs=39.7
Q ss_pred CCceeeeCCC-C-CCCceecCCCCCCCcceecccCCCCcCC-CCceeCCCCcccc
Q 025765 191 EPTYCVCNQV-S-YGEMVACDNPNCKIEWFHFGCVGLKEQP-KGKWYCPDCAALK 242 (248)
Q Consensus 191 ~~~~C~C~~~-~-~g~mi~Cd~~~C~~~WfH~~Cvgl~~~p-~~~w~C~~C~~~~ 242 (248)
....|.|+.. + .|.||+|+. |+ .|-|..|+|....- +..|.|..|....
T Consensus 85 ~~~~c~c~~~~~~~g~~i~c~~--c~-~Wqh~~C~g~~~~~~p~~y~c~~c~~~~ 136 (508)
T KOG1844|consen 85 EISRCDCGLEDDMEGLMIQCDW--CG-RWQHKICCGSFKSTKPDKYVCEICTPRN 136 (508)
T ss_pred cccccccccccCCCceeeCCcc--cC-cccCceeeeecCCCCchhceeeeecccc
Confidence 4667999866 3 578999999 88 99999999966543 5899999997653
No 22
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=92.54 E-value=0.064 Score=49.33 Aligned_cols=31 Identities=39% Similarity=1.073 Sum_probs=25.6
Q ss_pred CCceeeeCCCCC-------CCceecCCCCCCCccee-cccCC
Q 025765 191 EPTYCVCNQVSY-------GEMVACDNPNCKIEWFH-FGCVG 224 (248)
Q Consensus 191 ~~~~C~C~~~~~-------g~mi~Cd~~~C~~~WfH-~~Cvg 224 (248)
...||.|..++. |+|++|-. |+ .||| -.|+.
T Consensus 127 qG~~C~Cd~~Ypdp~~~~e~~m~QC~i--CE-DWFHce~c~~ 165 (345)
T KOG2752|consen 127 QGLFCKCDTPYPDPVRTEEGEMLQCVI--CE-DWFHCEGCMQ 165 (345)
T ss_pred cceeEEecCCCCCccccccceeeeEEe--cc-chhcccccCc
Confidence 478999998864 46999999 88 9999 67763
No 23
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=91.58 E-value=0.027 Score=52.83 Aligned_cols=48 Identities=31% Similarity=0.751 Sum_probs=36.5
Q ss_pred CCCcee-eeCCCCC--CCceecCCCCCCCcceecccCCCCcCCC---Cc----eeCCCCcc
Q 025765 190 NEPTYC-VCNQVSY--GEMVACDNPNCKIEWFHFGCVGLKEQPK---GK----WYCPDCAA 240 (248)
Q Consensus 190 ~~~~~C-~C~~~~~--g~mi~Cd~~~C~~~WfH~~Cvgl~~~p~---~~----w~C~~C~~ 240 (248)
.+..+| .|+..+- -.||+|+. |. .|||..||.+...++ .. |+|+.|..
T Consensus 237 ~~~~~~~~cg~~~~~~~~~~~~~~--~e-~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~ 294 (345)
T KOG1632|consen 237 YSKLICDPCGLSDANKKFEICCDL--CE-SWFHGDCVQIFEARKRLNEIRNEVYKCPHCTV 294 (345)
T ss_pred cccccccccCcchHHHHHHHHHHH--HH-HHhcccccccccchhhhhhhhccceecCceee
Confidence 345667 6666542 46899999 77 999999999988652 34 99999975
No 24
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=89.74 E-value=0.17 Score=37.53 Aligned_cols=31 Identities=29% Similarity=0.860 Sum_probs=26.5
Q ss_pred Ccee-eeCCCCCCCceecCCCCCCCcceecccCC
Q 025765 192 PTYC-VCNQVSYGEMVACDNPNCKIEWFHFGCVG 224 (248)
Q Consensus 192 ~~~C-~C~~~~~g~mi~Cd~~~C~~~WfH~~Cvg 224 (248)
...| +|+++ .|-.|.|...+|. .+||+.|.-
T Consensus 36 ~~~C~~C~~~-~Ga~i~C~~~~C~-~~fH~~CA~ 67 (90)
T PF13771_consen 36 KLKCSICKKK-GGACIGCSHPGCS-RSFHVPCAR 67 (90)
T ss_pred CCCCcCCCCC-CCeEEEEeCCCCC-cEEChHHHc
Confidence 4567 99987 5789999999999 999999973
No 25
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=88.75 E-value=0.18 Score=38.91 Aligned_cols=30 Identities=30% Similarity=0.846 Sum_probs=25.9
Q ss_pred Ccee-eeCCCCCCCceecCCCCCCCcceecccC
Q 025765 192 PTYC-VCNQVSYGEMVACDNPNCKIEWFHFGCV 223 (248)
Q Consensus 192 ~~~C-~C~~~~~g~mi~Cd~~~C~~~WfH~~Cv 223 (248)
...| +|++. .|..|.|...+|. .+||..|.
T Consensus 55 ~~~C~iC~~~-~G~~i~C~~~~C~-~~fH~~CA 85 (110)
T PF13832_consen 55 KLKCSICGKS-GGACIKCSHPGCS-TAFHPTCA 85 (110)
T ss_pred CCcCcCCCCC-CceeEEcCCCCCC-cCCCHHHH
Confidence 4456 99987 5889999999999 99999997
No 26
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=86.88 E-value=0.49 Score=45.62 Aligned_cols=43 Identities=23% Similarity=0.741 Sum_probs=30.5
Q ss_pred eeCCCCC--C--CceecCCCCCCCcceecccC--------CCCc-C----CCCceeCCCCccc
Q 025765 196 VCNQVSY--G--EMVACDNPNCKIEWFHFGCV--------GLKE-Q----PKGKWYCPDCAAL 241 (248)
Q Consensus 196 ~C~~~~~--g--~mi~Cd~~~C~~~WfH~~Cv--------gl~~-~----p~~~w~C~~C~~~ 241 (248)
+|++.++ + -.|.||. |. .|-|..|. |.+. - ..+.|||..|-..
T Consensus 133 iC~kfD~~~n~~~Wi~Cd~--Cg-H~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~ 192 (446)
T PF07227_consen 133 ICSKFDDNKNTCSWIGCDV--CG-HWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKT 192 (446)
T ss_pred ccCCcccCCCCeeEEeccC--CC-ceehhhhhcccccccCCccCCCCCccCceEEEccCCCCh
Confidence 8888654 2 3899999 77 99999996 2111 1 2458999999643
No 27
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=78.63 E-value=1.2 Score=44.84 Aligned_cols=47 Identities=21% Similarity=0.614 Sum_probs=34.0
Q ss_pred Ccee-eeCCCC-CCCceecCCCCCCCcceecccCC--CCcCCCCceeCCCCccc
Q 025765 192 PTYC-VCNQVS-YGEMVACDNPNCKIEWFHFGCVG--LKEQPKGKWYCPDCAAL 241 (248)
Q Consensus 192 ~~~C-~C~~~~-~g~mi~Cd~~~C~~~WfH~~Cvg--l~~~p~~~w~C~~C~~~ 241 (248)
-+.| .|+... .+-...|+.|| .-||..|.- ++.++.|.|+|+.|...
T Consensus 68 crvCe~c~~~gD~~kf~~Ck~cD---vsyh~yc~~P~~~~v~sg~~~ckk~~~c 118 (694)
T KOG4443|consen 68 CRVCEACGTTGDPKKFLLCKRCD---VSYHCYCQKPPNDKVPSGPWLCKKCTRC 118 (694)
T ss_pred ceeeeeccccCCccccccccccc---ccccccccCCccccccCcccccHHHHhh
Confidence 4567 777442 23466899965 669999984 67788999999988643
No 28
>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=78.00 E-value=1.4 Score=34.30 Aligned_cols=52 Identities=29% Similarity=0.702 Sum_probs=33.1
Q ss_pred CCCCCcee-eeCCCCCCCceec----CCCCC---CCcceecccC----CCCc---CCCCceeCCCCcc
Q 025765 188 DPNEPTYC-VCNQVSYGEMVAC----DNPNC---KIEWFHFGCV----GLKE---QPKGKWYCPDCAA 240 (248)
Q Consensus 188 ~~~~~~~C-~C~~~~~g~mi~C----d~~~C---~~~WfH~~Cv----gl~~---~p~~~w~C~~C~~ 240 (248)
|+.....| .|++...+..+.| .+..| . .=|=..|+ |... ...+.|.||.|+.
T Consensus 3 d~~~g~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~-~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 3 DSVNGKTCHQCRQKTLDFKTICTGHWKNSSCRGCR-GKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred cCCCCCCchhhcCCCCCCceEcCCCCCCCCCccCc-ceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 44556788 9998877666677 33335 5 44556776 2211 2467899999964
No 29
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=72.07 E-value=66 Score=29.16 Aligned_cols=85 Identities=13% Similarity=0.043 Sum_probs=62.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHh----hCCCCCChhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 29 FFVHTLAEIQRQNEQRCEQEIEDLMREIR----AGNITPNTSLIRFSDDALDEQKHSIRIADEKVALAVQAYDLVDTHIQ 104 (248)
Q Consensus 29 elD~~~qel~~~~~~~~~~~l~~~~k~~~----~gs~~~~~k~~~l~~~I~~~~~~~~~l~dEKv~lA~~~~~lvd~hir 104 (248)
|.+.++.+ +.+++.++-..+..+...+. .-.....+..+.. ..|.+.+.+.+..++.|...+.+|.+-++.-|+
T Consensus 20 et~~~~t~-l~~iD~k~~d~~k~l~q~~si~k~~~~~~~~t~~e~e-d~l~k~i~Ell~~a~~~~~~~~~l~d~~~~l~~ 97 (271)
T COG5034 20 ETDIRFTE-LSEIDAKVCDIIKNLRQMISILKKIIDLDSQTYEEVE-DGLLKEIRELLLKAIYIQKEKSDLADRAEKLLR 97 (271)
T ss_pred hhhhhhhh-hhhhhHHHHHHHHHHHHHHHHHHHHhhcccCccccch-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 89988888 56788888877766655211 1122223334455 689999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHh
Q 025765 105 QLDQYLKNFDEELR 118 (248)
Q Consensus 105 ~LD~dl~~~e~el~ 118 (248)
|++.- ++..+.
T Consensus 98 Rh~~~---~d~~~a 108 (271)
T COG5034 98 RHRKL---LDDRIA 108 (271)
T ss_pred HHHHh---hhhHHH
Confidence 99883 554433
No 30
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=71.65 E-value=2.5 Score=45.16 Aligned_cols=43 Identities=28% Similarity=0.857 Sum_probs=35.8
Q ss_pred Ccee-eeCCCCCCCceecCCCCCCCcceecccCCCC--cCCCCceeCCCCc
Q 025765 192 PTYC-VCNQVSYGEMVACDNPNCKIEWFHFGCVGLK--EQPKGKWYCPDCA 239 (248)
Q Consensus 192 ~~~C-~C~~~~~g~mi~Cd~~~C~~~WfH~~Cvgl~--~~p~~~w~C~~C~ 239 (248)
...| +|+.. |..+||.+ || .-+|..||-.. ..|...|-|.-|.
T Consensus 344 ddhcrf~~d~--~~~lc~Et--~p-rvvhlEcv~hP~~~~~s~~~e~evc~ 389 (1414)
T KOG1473|consen 344 DDHCRFCHDL--GDLLCCET--CP-RVVHLECVFHPRFAVPSAFWECEVCN 389 (1414)
T ss_pred cccccccCcc--cceeeccc--CC-ceEEeeecCCccccCCCccchhhhhh
Confidence 3468 99988 89999999 99 78999999644 4678899999886
No 31
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=61.55 E-value=6.9 Score=28.04 Aligned_cols=49 Identities=33% Similarity=0.675 Sum_probs=19.1
Q ss_pred cee-eeCCCC--CCC--ceecCCCCCCCcceecccCC-----CCcCC----CCceeCCCCcccc
Q 025765 193 TYC-VCNQVS--YGE--MVACDNPNCKIEWFHFGCVG-----LKEQP----KGKWYCPDCAALK 242 (248)
Q Consensus 193 ~~C-~C~~~~--~g~--mi~Cd~~~C~~~WfH~~Cvg-----l~~~p----~~~w~C~~C~~~~ 242 (248)
..| ||...- .++ -+.|+++.|. .=||..|+- +.... .-.+-||.|..+.
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~-~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i 65 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCG-KKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPI 65 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT-----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEE
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccC-CHHHHHHHHHHHHHcccCCeeecccccCCcCCCCee
Confidence 345 776552 332 5889988898 779999992 11111 2357799998653
No 32
>PF04100 Vps53_N: Vps53-like, N-terminal ; InterPro: IPR007234 Vps53 complexes with Vps52 and Vps54 to form a multi-subunit complex involved in regulating membrane trafficking events [].
Probab=59.77 E-value=1.6e+02 Score=27.96 Aligned_cols=86 Identities=15% Similarity=0.158 Sum_probs=53.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCChhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 29 FFVHTLAEIQRQNEQRCEQEIEDLMREIRAGNITPNTSLIRFSDDALDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQ 108 (248)
Q Consensus 29 elD~~~qel~~~~~~~~~~~l~~~~k~~~~gs~~~~~k~~~l~~~I~~~~~~~~~l~dEKv~lA~~~~~lvd~hir~LD~ 108 (248)
.+|.-...+...+.+...............|. ......+.....|.+.+.++.++ .+|-.=++++..-|.+-|++||.
T Consensus 22 ~ld~~i~~l~~~i~~ld~eI~~~v~~q~~~~~-~~~~~l~~a~~~i~~L~~~i~~i-k~kA~~sE~~V~~it~dIk~LD~ 99 (383)
T PF04100_consen 22 NLDELIAKLRKEIRELDEEIKELVREQSSSGQ-DAEEDLEEAQEAIQELFEKISEI-KSKAEESEQMVQEITRDIKQLDN 99 (383)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc-cccccHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 67777777777777666664443222101121 11222334445566666666655 35777788888999999999998
Q ss_pred HHHHHHHH
Q 025765 109 YLKNFDEE 116 (248)
Q Consensus 109 dl~~~e~e 116 (248)
--.+|...
T Consensus 100 AKrNLT~S 107 (383)
T PF04100_consen 100 AKRNLTQS 107 (383)
T ss_pred HHHHHHHH
Confidence 77776665
No 33
>PF13341 RAG2_PHD: RAG2 PHD domain; PDB: 2JWO_A 2V86_B 2V85_B 2V87_A 2V83_C 2V89_A 2V88_A.
Probab=59.37 E-value=5.1 Score=29.15 Aligned_cols=32 Identities=31% Similarity=0.785 Sum_probs=19.1
Q ss_pred CceecCCCCCCCcceecccCCCCcC-------CCCceeCCC
Q 025765 204 EMVACDNPNCKIEWFHFGCVGLKEQ-------PKGKWYCPD 237 (248)
Q Consensus 204 ~mi~Cd~~~C~~~WfH~~Cvgl~~~-------p~~~w~C~~ 237 (248)
-||.|.+. .-.|.|..|+.|++. ...+|||-.
T Consensus 29 AMI~cs~~--~GHWvhaqCm~LsE~~L~~LSq~n~KYfC~d 67 (78)
T PF13341_consen 29 AMIFCSRG--GGHWVHAQCMDLSETMLIQLSQENTKYFCND 67 (78)
T ss_dssp -EEEE-ST--T-EEEETGGGT--HHHHHHHHHSSS-B--TT
T ss_pred eEEEEeCC--CceEeEeecccchHHHHHHHccCCceEEEhh
Confidence 49999875 238999999999883 356899964
No 34
>COG3416 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.52 E-value=73 Score=28.10 Aligned_cols=71 Identities=17% Similarity=0.186 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHHHHhhCCCCCChhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 43 QRCEQEIEDLMREIRAGNITPNTSLIRFSDDALDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEE 116 (248)
Q Consensus 43 ~~~~~~l~~~~k~~~~gs~~~~~k~~~l~~~I~~~~~~~~~l~dEKv~lA~~~~~lvd~hir~LD~dl~~~e~e 116 (248)
+..+.+++.+.+ .+.-.+++..+.+..+.-..+=.+-=|--+.|-|-.+++.-.+.||++|++.|+.++..
T Consensus 7 qlle~lf~rlk~---a~~~~rD~~Ae~lI~~~~~~qP~a~Y~laQ~vliqE~ALk~a~~~i~eLe~ri~~lq~~ 77 (233)
T COG3416 7 QLLENLFHRLKK---AEANERDPQAEALIAEAVAKQPDAAYYLAQRVLIQEQALKKASTQIKELEKRIAILQAG 77 (233)
T ss_pred HHHHHHHHHHhh---cccCCCChHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 344555553333 33335566555554333332323333444567777888888888888888888888873
No 35
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=56.66 E-value=9 Score=33.11 Aligned_cols=43 Identities=35% Similarity=0.816 Sum_probs=30.3
Q ss_pred Ccee-eeCCCC--C----CCceecCCCCCCCcceecccCCCCcCCCCceeCCCCcccccc
Q 025765 192 PTYC-VCNQVS--Y----GEMVACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCAALKNR 244 (248)
Q Consensus 192 ~~~C-~C~~~~--~----g~mi~Cd~~~C~~~WfH~~Cvgl~~~p~~~w~C~~C~~~~~~ 244 (248)
...| +|+..+ | ...+.|.. |. .-||-.|..- -.||.|.+-..+
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~~--C~-~v~H~~C~~~-------~~CpkC~R~~~r 201 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCPK--CK-SVFHKSCFRK-------KSCPKCARRQKR 201 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCCc--Cc-cccchhhcCC-------CCCCCcHhHhcc
Confidence 4567 887652 2 24678999 66 7799999962 229999876544
No 36
>KOG4460 consensus Nuclear pore complex, Nup88/rNup84 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=55.00 E-value=91 Score=31.44 Aligned_cols=35 Identities=11% Similarity=0.008 Sum_probs=26.0
Q ss_pred hHHHHHHHhhh-ccCChHHHHHHHHH---hHHHHHHHHH
Q 025765 4 RFQVFLLTFMD-IFFPPLVRDAQMQC---FFVHTLAEIQ 38 (248)
Q Consensus 4 ~~~~yle~fie-~~~lP~EL~r~~~~---elD~~~qel~ 38 (248)
-.++|=|+||+ -.-.-.||||+... -+|.+.|++.
T Consensus 567 a~~vfrEqYi~~~dlV~~e~qrH~~~l~~~k~~QlQ~l~ 605 (741)
T KOG4460|consen 567 ATQVFREQYILKQDLVKEEIQRHVKLLCDQKKKQLQDLS 605 (741)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35778889998 45667788888877 6777777654
No 37
>PF04012 PspA_IM30: PspA/IM30 family; InterPro: IPR007157 This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma54-containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator [].
Probab=53.50 E-value=1.4e+02 Score=25.49 Aligned_cols=28 Identities=14% Similarity=0.280 Sum_probs=18.9
Q ss_pred CchhHHHHHHHhhh-----ccCChHHHHHHHHH
Q 025765 1 MFKRFQVFLLTFMD-----IFFPPLVRDAQMQC 28 (248)
Q Consensus 1 ~~~~~~~yle~fie-----~~~lP~EL~r~~~~ 28 (248)
+|+||-+.+--++. ++.|=.-|.+.+.+
T Consensus 2 lf~Rl~~~~~a~~~~~ld~~EDP~~~l~q~ird 34 (221)
T PF04012_consen 2 LFKRLKTLVKANINELLDKAEDPEKMLEQAIRD 34 (221)
T ss_pred HHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHH
Confidence 58999888888887 56655445544444
No 38
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=53.33 E-value=1.2e+02 Score=24.35 Aligned_cols=101 Identities=11% Similarity=0.172 Sum_probs=63.7
Q ss_pred cCChHHHHHHHHH--hHHHHHHHHHHHHHHHHHHHHHHHHHHH-hhCCCCCChhhhhhHHH-----HHHHHHHHHHHHHH
Q 025765 16 FFPPLVRDAQMQC--FFVHTLAEIQRQNEQRCEQEIEDLMREI-RAGNITPNTSLIRFSDD-----ALDEQKHSIRIADE 87 (248)
Q Consensus 16 ~~lP~EL~r~~~~--elD~~~qel~~~~~~~~~~~l~~~~k~~-~~gs~~~~~k~~~l~~~-----I~~~~~~~~~l~dE 87 (248)
.++|.++++.+.. .|-..++.+..+.++.... |...-+++ .-..+.++. .+++. |......+..=-++
T Consensus 2 ~~lpp~~q~~l~q~QqLq~ql~~~~~qk~~le~q-L~E~~~al~Ele~l~eD~---~vYk~VG~llvk~~k~~~~~eL~e 77 (119)
T COG1382 2 EQLPPEVQAQLAQLQQLQQQLQKVILQKQQLEAQ-LKEIEKALEELEKLDEDA---PVYKKVGNLLVKVSKEEAVDELEE 77 (119)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcCCccc---HHHHHhhhHHhhhhHHHHHHHHHH
Confidence 5789999999888 7777777777766554443 44343332 112233332 22222 23445566666677
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 025765 88 KVALAVQAYDLVDTHIQQLDQYLKNFDEELRRE 120 (248)
Q Consensus 88 Kv~lA~~~~~lvd~hir~LD~dl~~~e~el~~~ 120 (248)
++..-.-=...+++..++|+..++.+...|...
T Consensus 78 r~E~Le~ri~tLekQe~~l~e~l~eLq~~i~~~ 110 (119)
T COG1382 78 RKETLELRIKTLEKQEEKLQERLEELQSEIQKA 110 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 777777777777888888888888888877654
No 39
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=53.31 E-value=3.9 Score=41.31 Aligned_cols=48 Identities=31% Similarity=0.798 Sum_probs=33.3
Q ss_pred Ccee-eeCCCC---CCCceecCCCCCCCcceecccCCCCcC---CCCceeCCCCcccc
Q 025765 192 PTYC-VCNQVS---YGEMVACDNPNCKIEWFHFGCVGLKEQ---PKGKWYCPDCAALK 242 (248)
Q Consensus 192 ~~~C-~C~~~~---~g~mi~Cd~~~C~~~WfH~~Cvgl~~~---p~~~w~C~~C~~~~ 242 (248)
...| +|.... .|-|+.|.+ |. .-||..||.+-.. -.+-|-||.|+.-.
T Consensus 18 ~~mc~l~~s~G~~~ag~m~ac~~--c~-~~yH~~cvt~~~~~~~l~~gWrC~~crvCe 72 (694)
T KOG4443|consen 18 CLMCPLCGSSGKGRAGRLLACSD--CG-QKYHPYCVTSWAQHAVLSGGWRCPSCRVCE 72 (694)
T ss_pred hhhhhhhccccccccCcchhhhh--hc-ccCCcchhhHHHhHHHhcCCcccCCceeee
Confidence 4556 776543 256999999 76 8899999984332 12349999997543
No 40
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=53.30 E-value=10 Score=23.75 Aligned_cols=25 Identities=32% Similarity=0.939 Sum_probs=17.1
Q ss_pred ceecCCCCCCCcceecccCCCCcCCCCceeCCCCc
Q 025765 205 MVACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCA 239 (248)
Q Consensus 205 mi~Cd~~~C~~~WfH~~Cvgl~~~p~~~w~C~~C~ 239 (248)
-+.|.. |.-.||. ...|.|||..|=
T Consensus 8 ~~~C~~--C~~~~~~--------~~dG~~yC~~cG 32 (36)
T PF11781_consen 8 NEPCPV--CGSRWFY--------SDDGFYYCDRCG 32 (36)
T ss_pred CCcCCC--CCCeEeE--------ccCCEEEhhhCc
Confidence 356777 6645654 457899998884
No 41
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=52.23 E-value=5.4 Score=29.57 Aligned_cols=48 Identities=27% Similarity=0.719 Sum_probs=31.6
Q ss_pred ee-eeCCCCCCCceecC--CCCCCCcc------eecccCC-CCcCCCCceeCCCCccc
Q 025765 194 YC-VCNQVSYGEMVACD--NPNCKIEW------FHFGCVG-LKEQPKGKWYCPDCAAL 241 (248)
Q Consensus 194 ~C-~C~~~~~g~mi~Cd--~~~C~~~W------fH~~Cvg-l~~~p~~~w~C~~C~~~ 241 (248)
.| +|+.+.+|---.|- ++|||+-| ||.-|+- --..|...-.||.|++.
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~ 79 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQT 79 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchhe
Confidence 68 99998777444443 23588755 8888873 22234445789999865
No 42
>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=51.75 E-value=2.9 Score=27.97 Aligned_cols=23 Identities=22% Similarity=0.481 Sum_probs=14.1
Q ss_pred cceecccCCCCcCCCCceeCCCC
Q 025765 216 EWFHFGCVGLKEQPKGKWYCPDC 238 (248)
Q Consensus 216 ~WfH~~Cvgl~~~p~~~w~C~~C 238 (248)
.|+|.+|+--=....+.-.|+.|
T Consensus 26 ~~vH~~Cl~~W~~~~~~~~C~iC 48 (49)
T smart00744 26 KYVHQECLERWINESGNKTCEIC 48 (49)
T ss_pred hHHHHHHHHHHHHHcCCCcCCCC
Confidence 79999999421111223478877
No 43
>PF09755 DUF2046: Uncharacterized conserved protein H4 (DUF2046); InterPro: IPR019152 This is the conserved N-terminal 350 residues of a family of proteins of unknown function possibly containing a coiled-coil domain.
Probab=51.31 E-value=2.1e+02 Score=26.68 Aligned_cols=35 Identities=23% Similarity=0.275 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHH
Q 025765 76 DEQKHSIRIADEKVALAVQAYD-------LVDTHIQQLDQYL 110 (248)
Q Consensus 76 ~~~~~~~~l~dEKv~lA~~~~~-------lvd~hir~LD~dl 110 (248)
....+..+|.+||+.|++++-. -+-+.|.+|..+.
T Consensus 110 ~L~rkl~qLr~EK~~lE~~Le~EqE~~V~kL~k~i~~Le~e~ 151 (310)
T PF09755_consen 110 DLSRKLNQLRQEKVELENQLEQEQEYLVNKLQKKIERLEKEK 151 (310)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 3456788999999999998864 2335555555443
No 44
>PRK11546 zraP zinc resistance protein; Provisional
Probab=49.73 E-value=1.5e+02 Score=24.50 Aligned_cols=33 Identities=12% Similarity=-0.068 Sum_probs=26.1
Q ss_pred cCChHHHHHHHHH---hHHHHHHHHHHHHHHHHHHH
Q 025765 16 FFPPLVRDAQMQC---FFVHTLAEIQRQNEQRCEQE 48 (248)
Q Consensus 16 ~~lP~EL~r~~~~---elD~~~qel~~~~~~~~~~~ 48 (248)
.+|+.|=|..++. ++..+..+++.++..+...+
T Consensus 42 ~~LT~EQQa~~q~I~~~f~~~t~~LRqqL~aKr~EL 77 (143)
T PRK11546 42 APLTTEQQAAWQKIHNDFYAQTSALRQQLVSKRYEY 77 (143)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3688888888887 88888888888887776663
No 45
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.43 E-value=18 Score=33.24 Aligned_cols=52 Identities=31% Similarity=0.721 Sum_probs=34.7
Q ss_pred CCCCCCCCCcee-eeCCC-CCCCceecCCCCCCCcceecccCC--CCcC-CCCceeCCC
Q 025765 184 DLPVDPNEPTYC-VCNQV-SYGEMVACDNPNCKIEWFHFGCVG--LKEQ-PKGKWYCPD 237 (248)
Q Consensus 184 ~~~~~~~~~~~C-~C~~~-~~g~mi~Cd~~~C~~~WfH~~Cvg--l~~~-p~~~w~C~~ 237 (248)
+...-++.++.| +|+.. .+-.+|+|-. -++.=|-|.|-. |+.. ..|..|||.
T Consensus 260 ~s~~A~~apLcCTLC~ERLEDTHFVQCPS--Vp~HKFCFPCSResIK~Qg~sgevYCPS 316 (352)
T KOG3579|consen 260 DSGAAPSAPLCCTLCHERLEDTHFVQCPS--VPSHKFCFPCSRESIKQQGASGEVYCPS 316 (352)
T ss_pred ccccCCCCceeehhhhhhhccCceeecCC--CcccceecccCHHHHHhhcCCCceeCCC
Confidence 445566778889 99866 4456899988 664445556653 3332 468999983
No 46
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=48.84 E-value=12 Score=32.99 Aligned_cols=32 Identities=31% Similarity=0.758 Sum_probs=25.7
Q ss_pred eecCCCCCCCcceecccCCCCcCCCCceeCCCCcccc
Q 025765 206 VACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCAALK 242 (248)
Q Consensus 206 i~Cd~~~C~~~WfH~~Cvgl~~~p~~~w~C~~C~~~~ 242 (248)
+-|-. |. +|..|+.+...|...|+||.|....
T Consensus 193 lIC~~--C~---hhngl~~~~ek~~~efiC~~Cn~~n 224 (251)
T COG5415 193 LICPQ--CH---HHNGLYRLAEKPIIEFICPHCNHKN 224 (251)
T ss_pred hcccc--cc---ccccccccccccchheecccchhhc
Confidence 45666 55 6899999999888899999997654
No 47
>KOG4796 consensus RNA polymerase II elongation factor [Transcription]
Probab=48.67 E-value=3e+02 Score=27.73 Aligned_cols=101 Identities=13% Similarity=0.203 Sum_probs=52.5
Q ss_pred HHHHHhhhccCChHHHHHHHHHhHHHH---HHHHHHHHHHHHHHHHH--HHHH-HHhhCCCCCChhhhhhHHHHHHHHHH
Q 025765 7 VFLLTFMDIFFPPLVRDAQMQCFFVHT---LAEIQRQNEQRCEQEIE--DLMR-EIRAGNITPNTSLIRFSDDALDEQKH 80 (248)
Q Consensus 7 ~yle~fie~~~lP~EL~r~~~~elD~~---~qel~~~~~~~~~~~l~--~~~k-~~~~gs~~~~~k~~~l~~~I~~~~~~ 80 (248)
-||-+|+.|.++ |-++.+..+|... |.+|..++..-...|++ ..++ .+..|+ +..+.+.++|..+|.+
T Consensus 489 dYllqY~aI~S~--eqr~~Yk~dF~~eY~EYreLharve~vs~rF~~Lea~L~srls~gS----~ey~~i~~qI~qEYek 562 (604)
T KOG4796|consen 489 DYLLQYGAISSL--EQRQRYKKDFEAEYDEYRELHARVETVSRRFRQLEAQLKSRLSPGS----PEYKQIEKQILQEYEK 562 (604)
T ss_pred chhhhccccccH--HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCC----CcHHHHHHHHHHHHHH
Confidence 377788887765 4455544422222 22333333332222211 1111 112332 4557788889999988
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 81 SIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDE 115 (248)
Q Consensus 81 ~~~l~dEKv~lA~~~~~lvd~hir~LD~dl~~~e~ 115 (248)
+. .|--.-=+.+=.+-+-..++.|-.-|..|+.
T Consensus 563 i~--~dp~y~eeK~RceYLhsKLaHIK~lI~efDk 595 (604)
T KOG4796|consen 563 IR--KDPNYMEEKQRCEYLHSKLAHIKTLIGEFDK 595 (604)
T ss_pred hh--cCccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77 3333333334456666666666666777775
No 48
>PF09755 DUF2046: Uncharacterized conserved protein H4 (DUF2046); InterPro: IPR019152 This is the conserved N-terminal 350 residues of a family of proteins of unknown function possibly containing a coiled-coil domain.
Probab=47.41 E-value=2.4e+02 Score=26.27 Aligned_cols=41 Identities=20% Similarity=0.238 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 76 DEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEE 116 (248)
Q Consensus 76 ~~~~~~~~l~dEKv~lA~~~~~lvd~hir~LD~dl~~~e~e 116 (248)
........|..|||.|-+++-.=-+--+.+|.+.+.+++.+
T Consensus 153 ~~q~~le~Lr~EKVdlEn~LE~EQE~lvN~L~Kqm~~l~~e 193 (310)
T PF09755_consen 153 AKQEELERLRREKVDLENTLEQEQEALVNRLWKQMDKLEAE 193 (310)
T ss_pred HhHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33455668999999998887544444444555555555554
No 49
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=47.05 E-value=1.6e+02 Score=30.48 Aligned_cols=24 Identities=25% Similarity=0.371 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhh
Q 025765 96 YDLVDTHIQQLDQYLKNFDEELRR 119 (248)
Q Consensus 96 ~~lvd~hir~LD~dl~~~e~el~~ 119 (248)
-+....+.+.||.++.+|..||..
T Consensus 540 ~e~~r~r~~~lE~E~~~lr~elk~ 563 (697)
T PF09726_consen 540 AESCRQRRRQLESELKKLRRELKQ 563 (697)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445667888999999999888764
No 50
>PF04668 Tsg: Twisted gastrulation (Tsg) protein conserved region; InterPro: IPR006761 Tsg was identified in Drosophila melanogaster as being required to specify the dorsal-most structures in the embryo, for example the amnioserosa. Biochemical experiments have revealed three key properties of Tsg: it can synergistically inhibit Dpp/BMP action in both D. melanogaster and vertebrates by forming a tripartite complete between itself, SOG/chordin and a BMP ligand; Tsg seems to enhance the Tld/BMP-1-mediated cleavage rate of SOG/chordin and may change the preference of site utilisation; Tsg can promote the dissociation of chordin cysteine-rich-containing fragments from the ligand to inhibit BMP signalling [, ].
Probab=46.45 E-value=7.4 Score=31.69 Aligned_cols=11 Identities=45% Similarity=1.232 Sum_probs=8.3
Q ss_pred CCCcceecccC
Q 025765 213 CKIEWFHFGCV 223 (248)
Q Consensus 213 C~~~WfH~~Cv 223 (248)
-.|+|||-.|-
T Consensus 100 ssYRWFHdgCC 110 (132)
T PF04668_consen 100 SSYRWFHDGCC 110 (132)
T ss_pred ccceeeccchh
Confidence 34799999763
No 51
>PRK10626 hypothetical protein; Provisional
Probab=45.95 E-value=78 Score=28.35 Aligned_cols=45 Identities=20% Similarity=0.128 Sum_probs=36.2
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHH
Q 025765 67 LIRFSDDALDEQKHSIRIADEKVALAVQAYDLVD-----------THIQQLDQYLK 111 (248)
Q Consensus 67 ~~~l~~~I~~~~~~~~~l~dEKv~lA~~~~~lvd-----------~hir~LD~dl~ 111 (248)
..+|++.|...+=++.+++.+.|.+|.++++.|- ..|..|+.+|+
T Consensus 73 ~~~Yq~~lr~~lP~i~~~a~~~l~~A~~alD~Vi~~~~G~~snvr~rl~~l~~~l~ 128 (239)
T PRK10626 73 AKDYQAALRQDLPWIDEGAKSRLEKARVALDKVIVQELGESSNVRNRLTKLDAQLK 128 (239)
T ss_pred HHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHHhccCccchHHHHHHHHHHHHH
Confidence 4568888999999999999999999999999863 35566666553
No 52
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=45.91 E-value=4.7 Score=30.11 Aligned_cols=44 Identities=30% Similarity=0.694 Sum_probs=26.9
Q ss_pred ee-eeCCCCCCCceecCC-----CCCCCcc------eecccCC--CCcCCCCceeCCCCccc
Q 025765 194 YC-VCNQVSYGEMVACDN-----PNCKIEW------FHFGCVG--LKEQPKGKWYCPDCAAL 241 (248)
Q Consensus 194 ~C-~C~~~~~g~mi~Cd~-----~~C~~~W------fH~~Cvg--l~~~p~~~w~C~~C~~~ 241 (248)
.| +|+-...|.-+.|-. .+|++.| ||+.|+. |.. +-.||.++++
T Consensus 22 ~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T----k~~CPld~q~ 79 (88)
T COG5194 22 VCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT----KGVCPLDRQT 79 (88)
T ss_pred hhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh----CCCCCCCCce
Confidence 46 777766665555543 2466555 9999984 333 3567776543
No 53
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=45.33 E-value=13 Score=37.30 Aligned_cols=44 Identities=30% Similarity=0.818 Sum_probs=32.5
Q ss_pred Ccee-eeCCCCCCCceecCCCCCCCcceecccCCCCcCCC---CceeCCCCcc
Q 025765 192 PTYC-VCNQVSYGEMVACDNPNCKIEWFHFGCVGLKEQPK---GKWYCPDCAA 240 (248)
Q Consensus 192 ~~~C-~C~~~~~g~mi~Cd~~~C~~~WfH~~Cvgl~~~p~---~~w~C~~C~~ 240 (248)
.+.| +|.+. |...+|+. |+ .-||..|-+...-|. ..|.|..|..
T Consensus 47 ~ts~~~~~~~--gn~~~~~~--~~-~s~h~~~~~~~~sp~~~~~~~~~~~~~~ 94 (613)
T KOG4299|consen 47 ATSCGICKSG--GNLLCCDH--CP-ASFHLECDKPPLSPDLKGSEINCSRCPK 94 (613)
T ss_pred hhhcchhhhc--CCcccccc--Cc-cccchhccCcccCcccccccccccCCCc
Confidence 5567 77776 77889999 88 889999998655454 4566666654
No 54
>PHA02562 46 endonuclease subunit; Provisional
Probab=45.33 E-value=3e+02 Score=26.79 Aligned_cols=50 Identities=12% Similarity=0.134 Sum_probs=30.8
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHH
Q 025765 67 LIRFSDDALDEQKHSIRIADEKVALAVQAYDL------VDTHIQQLDQYLKNFDEE 116 (248)
Q Consensus 67 ~~~l~~~I~~~~~~~~~l~dEKv~lA~~~~~l------vd~hir~LD~dl~~~e~e 116 (248)
.+.+.+++......+..+..+.-.|-..+.++ ++..+..|...+..++.+
T Consensus 215 i~~l~~e~~~l~~~~~~l~~~l~~l~~~i~~l~~~i~~~~~~L~~l~~~~~~~~~~ 270 (562)
T PHA02562 215 IARKQNKYDELVEEAKTIKAEIEELTDELLNLVMDIEDPSAALNKLNTAAAKIKSK 270 (562)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHH
Confidence 45566666666777777777777777777777 444445555554444444
No 55
>PHA02862 5L protein; Provisional
Probab=45.30 E-value=7.6 Score=32.20 Aligned_cols=46 Identities=26% Similarity=0.438 Sum_probs=28.4
Q ss_pred cee-eeCCCCCCCceecCCCCCC--CcceecccCCCCcCCCCceeCCCCccc
Q 025765 193 TYC-VCNQVSYGEMVACDNPNCK--IEWFHFGCVGLKEQPKGKWYCPDCAAL 241 (248)
Q Consensus 193 ~~C-~C~~~~~g~mi~Cd~~~C~--~~WfH~~Cvgl~~~p~~~w~C~~C~~~ 241 (248)
..| +|.+... +.+. -|.|. +.|.|.+|+..=-.+.++-+|+.|..+
T Consensus 3 diCWIC~~~~~-e~~~--PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkte 51 (156)
T PHA02862 3 DICWICNDVCD-ERNN--FCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTK 51 (156)
T ss_pred CEEEEecCcCC-CCcc--cccccCcchhHHHHHHHHHHhcCCCcCccCCCCe
Confidence 467 8877743 2221 12232 399999998632244567899999765
No 56
>PF14513 DAG_kinase_N: Diacylglycerol kinase N-terminus; PDB: 1TUZ_A.
Probab=45.17 E-value=21 Score=29.29 Aligned_cols=26 Identities=15% Similarity=0.372 Sum_probs=20.4
Q ss_pred chhHHHHHHHhhhccCChHHHHHHHHH
Q 025765 2 FKRFQVFLLTFMDIFFPPLVRDAQMQC 28 (248)
Q Consensus 2 ~~~~~~yle~fie~~~lP~EL~r~~~~ 28 (248)
|.-|+.||..|+|++ +|.+|=++|-.
T Consensus 51 ~egF~~Fm~~yLe~d-~P~~lc~hLF~ 76 (138)
T PF14513_consen 51 YEGFKLFMKTYLEVD-LPEDLCQHLFL 76 (138)
T ss_dssp HHHHHHHHHHHTT-S---HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCC-CCHHHHHHHHH
Confidence 567899999999999 99999988887
No 57
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=45.11 E-value=9.6 Score=25.48 Aligned_cols=28 Identities=32% Similarity=0.926 Sum_probs=14.1
Q ss_pred ceecCCCCCCCcceecccCCCCc----CCCCceeCCC
Q 025765 205 MVACDNPNCKIEWFHFGCVGLKE----QPKGKWYCPD 237 (248)
Q Consensus 205 mi~Cd~~~C~~~WfH~~Cvgl~~----~p~~~w~C~~ 237 (248)
-|+||. |. .|=.+. .++.. .|. .|||..
T Consensus 3 WVQCd~--C~-KWR~lp-~~~~~~~~~~~d-~W~C~~ 34 (50)
T PF07496_consen 3 WVQCDS--CL-KWRRLP-EEVDPIREELPD-PWYCSM 34 (50)
T ss_dssp EEE-TT--T---EEEE--CCHHCTSCCSST-T--GGG
T ss_pred EEECCC--CC-ceeeCC-hhhCcccccCCC-eEEcCC
Confidence 489998 77 997766 33322 233 899986
No 58
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=44.40 E-value=5.7 Score=39.85 Aligned_cols=32 Identities=31% Similarity=0.723 Sum_probs=24.0
Q ss_pred ceecCCCCCCCcceecccCCCCcCCCCceeCCCCcccccc
Q 025765 205 MVACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCAALKNR 244 (248)
Q Consensus 205 mi~Cd~~~C~~~WfH~~Cvgl~~~p~~~w~C~~C~~~~~~ 244 (248)
..-|+. |. .|||-.|+.....- ||.|.+-.+|
T Consensus 531 ~~rC~~--C~-avfH~~C~~r~s~~-----CPrC~R~q~r 562 (580)
T KOG1829|consen 531 TRRCST--CL-AVFHKKCLRRKSPC-----CPRCERRQKR 562 (580)
T ss_pred ceeHHH--HH-HHHHHHHHhccCCC-----CCchHHHHHH
Confidence 467888 77 99999999655432 9999865543
No 59
>PRK11637 AmiB activator; Provisional
Probab=44.23 E-value=2.9e+02 Score=26.31 Aligned_cols=32 Identities=9% Similarity=0.306 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 86 DEKVALAVQAYDLVDTHIQQLDQYLKNFDEEL 117 (248)
Q Consensus 86 dEKv~lA~~~~~lvd~hir~LD~dl~~~e~el 117 (248)
.+++.-.+.-+..++..|..|+.+|..++.+|
T Consensus 88 ~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l 119 (428)
T PRK11637 88 SRKLRETQNTLNQLNKQIDELNASIAKLEQQQ 119 (428)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455555555555555555555555555543
No 60
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=43.30 E-value=1.7e+02 Score=26.28 Aligned_cols=46 Identities=13% Similarity=0.202 Sum_probs=35.1
Q ss_pred hhhhhHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 66 SLIRFSDDALDEQKHSIRIADE-KVALAVQAYDLVDTHIQQLDQYLKNFDE 115 (248)
Q Consensus 66 k~~~l~~~I~~~~~~~~~l~dE-Kv~lA~~~~~lvd~hir~LD~dl~~~e~ 115 (248)
....|...|...+.++..|+.+ +|.-|+.++..|+. |-...+.++.
T Consensus 124 ~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~----Lk~ek~~le~ 170 (254)
T PF03194_consen 124 KIDELDEKIGELLKEAEELGEEGDVDEAQKLMEEVEK----LKEEKEELEK 170 (254)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH----HHHHHHHHHh
Confidence 3456778899999999999998 99999999888875 4444444444
No 61
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=43.22 E-value=2.4e+02 Score=25.02 Aligned_cols=80 Identities=19% Similarity=0.336 Sum_probs=42.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCChhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 29 FFVHTLAEIQRQNEQRCEQEIEDLMREIRAGNITPNTSLIRFSDDALDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQ 108 (248)
Q Consensus 29 elD~~~qel~~~~~~~~~~~l~~~~k~~~~gs~~~~~k~~~l~~~I~~~~~~~~~l~dEKv~lA~~~~~lvd~hir~LD~ 108 (248)
+|...+.+++..+..+..+.+- ++|... ..-.|-..=...|.+.++++-|--.+ .++...++.|+.+=|.
T Consensus 19 DlE~i~kelie~l~~~~~qk~l------~~gE~v---~il~Ll~~kd~ef~~llkla~eq~k~-e~~m~~Lea~VEkrD~ 88 (272)
T KOG4552|consen 19 DLEHIVKELIETLINRDKQKML------KNGETV---NILKLLDSKDDEFKTLLKLAPEQQKR-EQLMRTLEAHVEKRDE 88 (272)
T ss_pred HHHHHHHHHHHHHHhhhHHHHH------hcchHH---HHHHHHHhccHHHHHHHHHhHhHHHH-HHHHHHHHHHHHHhHH
Confidence 6777777766665554444322 444311 11111111124456666666554333 4556667777777777
Q ss_pred HHHHHHHHHh
Q 025765 109 YLKNFDEELR 118 (248)
Q Consensus 109 dl~~~e~el~ 118 (248)
+|.+|+..|.
T Consensus 89 ~IQqLqk~LK 98 (272)
T KOG4552|consen 89 VIQQLQKNLK 98 (272)
T ss_pred HHHHHHHHHH
Confidence 7777777654
No 62
>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope. They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....
Probab=42.30 E-value=2.6e+02 Score=25.13 Aligned_cols=99 Identities=12% Similarity=0.142 Sum_probs=52.9
Q ss_pred hHHHHHHHHH---hHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC-CCCCCh--hhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 025765 19 PLVRDAQMQC---FFVHTLAEIQRQNEQRCEQEIEDLMREIRAG-NITPNT--SLIRFSDDALDEQKHSIRIADEKVALA 92 (248)
Q Consensus 19 P~EL~r~~~~---elD~~~qel~~~~~~~~~~~l~~~~k~~~~g-s~~~~~--k~~~l~~~I~~~~~~~~~l~dEKv~lA 92 (248)
..+|...+.+ ++|..+...+.+++..+...+..+....... ...... -...+...|......+..+...+-.|-
T Consensus 164 ~~dL~~~L~eiR~~ye~~~~~~~~e~e~~y~~k~~~l~~~~~~~~~~~~~~~~E~~~~r~~~~~l~~el~~l~~~~~~Le 243 (312)
T PF00038_consen 164 SSDLSAALREIRAQYEEIAQKNREELEEWYQSKLEELRQQSEKSSEELESAKEELKELRRQIQSLQAELESLRAKNASLE 243 (312)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cccchhhhhhHHHHHHHHHhhhhhhhhhhcccccccccccccccccccchhHhHHHHHHhhhhHhhhhhhccccchhhhh
Confidence 4456666655 6666666666666666666555443321110 000001 122455566777778888888898998
Q ss_pred HHHHHHHHH---HHHHHHHHHHHHHHHH
Q 025765 93 VQAYDLVDT---HIQQLDQYLKNFDEEL 117 (248)
Q Consensus 93 ~~~~~lvd~---hir~LD~dl~~~e~el 117 (248)
.++.++-.. ....++..|..++.+|
T Consensus 244 ~~l~~le~~~~~~~~~~~~~i~~le~el 271 (312)
T PF00038_consen 244 RQLRELEQRLDEEREEYQAEIAELEEEL 271 (312)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHHhhhccchhH
Confidence 888877433 2333334444444443
No 63
>PF08946 Osmo_CC: Osmosensory transporter coiled coil; InterPro: IPR015041 The osmosensory transporter coiled coil is a C-terminal domain found in various bacterial osmoprotective transporters, such as ProP, Proline/betaine transporter, Proline permease 2 and the citrate proton symporters. It adopts an antiparallel coiled-coil structure, and is essential for osmosensory and osmoprotectant transporter function []. ; PDB: 1R48_B.
Probab=41.81 E-value=33 Score=22.78 Aligned_cols=26 Identities=19% Similarity=0.516 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 90 ALAVQAYDLVDTHIQQLDQYLKNFDE 115 (248)
Q Consensus 90 ~lA~~~~~lvd~hir~LD~dl~~~e~ 115 (248)
.|-+..|+-|+..|..+|..|+.|++
T Consensus 8 elLqe~~d~IEqkiedid~qIaeLe~ 33 (46)
T PF08946_consen 8 ELLQEHYDNIEQKIEDIDEQIAELEA 33 (46)
T ss_dssp -------THHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhHHHhHHHHHHHHHHHHH
Confidence 45667899999999999999988876
No 64
>PHA02414 hypothetical protein
Probab=41.78 E-value=1.7e+02 Score=22.78 Aligned_cols=78 Identities=15% Similarity=0.204 Sum_probs=44.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCChhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 29 FFVHTLAEIQRQNEQRCEQEIEDLMREIRAGNITPNTSLIRFSDDALDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQ 108 (248)
Q Consensus 29 elD~~~qel~~~~~~~~~~~l~~~~k~~~~gs~~~~~k~~~l~~~I~~~~~~~~~l~dEKv~lA~~~~~lvd~hir~LD~ 108 (248)
++|...+.+..+++...+. ++.|.+..-....+|...+. ++..+..--|.-+++-..-+.-|-=+|.+||.
T Consensus 1 ~~D~~in~Lv~~v~~ledK--------iQ~Gelt~kgdn~eL~~av~-ELRdivvslDKd~Av~sEKqshi~yQi~~Lee 71 (111)
T PHA02414 1 EMDKEINNLVSQVETLEDK--------IQEGELTDKGDNKELEVAVA-ELRDIVVSLDKDVAVNSEKQSHIYYQIERLEE 71 (111)
T ss_pred CcchHHHHHHHHHHHHHHH--------HhcCccccCCchHHHHHHHH-HHHHHHHHhhhHhhhhHHHhhHHHHHHHHHHH
Confidence 4677788877777665554 26677665443344432222 22222222334444444445566667788998
Q ss_pred HHHHHHH
Q 025765 109 YLKNFDE 115 (248)
Q Consensus 109 dl~~~e~ 115 (248)
.+..|..
T Consensus 72 ~i~aL~~ 78 (111)
T PHA02414 72 KISALAE 78 (111)
T ss_pred HHHHHHh
Confidence 8888775
No 65
>PF08702 Fib_alpha: Fibrinogen alpha/beta chain family; InterPro: IPR012290 Fibrinogen plays key roles in both blood clotting and platelet aggregation. During blood clot formation, the conversion of soluble fibrinogen to insoluble fibrin is triggered by thrombin, resulting in the polymerisation of fibrin, which forms a soft clot; this is then converted to a hard clot by factor XIIIA, which cross-links fibrin molecules. Platelet aggregation involves the binding of the platelet protein receptor integrin alpha(IIb)-beta(3) to the C-terminal D domain of fibrinogen []. In addition to platelet aggregation, platelet-fibrinogen interaction mediates both adhesion and fibrin clot retraction. Fibrinogen occurs as a dimer, where each monomer is composed of three non-identical chains, alpha, beta and gamma, linked together by several disulphide bonds []. The N-terminals of all six chains come together to form the centre of the molecule (E domain), from which the monomers extend in opposite directions as coiled coils, followed by C-terminal globular domains (D domains). Therefore, the domain composition is: D-coil-E-coil-D. At each end, the C-terminal of the alpha chain extends beyond the D domain as a protuberance that is important for cross-linking the molecule. During clot formation, the N-terminal fragments of the alpha and beta chains (within the E domain) in fibrinogen are cleaved by thrombin, releasing fibrinopeptides A and B, respectively, and producing fibrin. This cleavage results in the exposure of four binding sites on the E domain, each of which can bind to a D domain from different fibrin molecules. The binding of fibrin molecules produces a polymer consisting of a lattice network of fibrins that form a long, branching, flexible fibre [, ]. Fibrin fibres interact with platelets to increase the size of the clot, as well as with several different proteins and cells, thereby promoting the inflammatory response and concentrating the cells required for wound repair at the site of damage. This entry represents the coiled-coil domain and part of the N-terminal E domain found in all three fibrinogen polypeptides, namely the alpha, beta and gamma chains. More information about these proteins can be found at Protein of the Month: Fibrinogen [].; GO: 0005102 receptor binding, 0030674 protein binding, bridging, 0007165 signal transduction, 0030168 platelet activation, 0051258 protein polymerization, 0005577 fibrinogen complex; PDB: 1LWU_D 1N73_D 1M1J_B 1JY2_R 1JY3_R 1RF0_A 2H43_D 1RE4_D 2XNY_D 2HPC_D ....
Probab=40.67 E-value=2e+02 Score=23.53 Aligned_cols=40 Identities=13% Similarity=0.080 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 76 DEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDE 115 (248)
Q Consensus 76 ~~~~~~~~l~dEKv~lA~~~~~lvd~hir~LD~dl~~~e~ 115 (248)
-.+....--...-+..-+.++.-....|.+|+.++..+++
T Consensus 93 ~~~e~~i~~~~~~I~~Lq~~~~~~~~ki~~Le~~i~~~~~ 132 (146)
T PF08702_consen 93 YILETKIINQPSNIRVLQNILRSNRQKIQRLEQDIDQQER 132 (146)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555666677778888888888899999999888776
No 66
>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=40.63 E-value=3.6 Score=26.27 Aligned_cols=37 Identities=35% Similarity=0.652 Sum_probs=21.0
Q ss_pred eeCCCC-CCCceecCCCCCCCcceecccCC--CCcCCCCceeCCCCc
Q 025765 196 VCNQVS-YGEMVACDNPNCKIEWFHFGCVG--LKEQPKGKWYCPDCA 239 (248)
Q Consensus 196 ~C~~~~-~g~mi~Cd~~~C~~~WfH~~Cvg--l~~~p~~~w~C~~C~ 239 (248)
||...- .++.+.--. |. -.||..|+. +.. ...||.|+
T Consensus 5 IC~~~~~~~~~~~~l~--C~-H~fh~~Ci~~~~~~----~~~CP~CR 44 (44)
T PF13639_consen 5 ICLEEFEDGEKVVKLP--CG-HVFHRSCIKEWLKR----NNSCPVCR 44 (44)
T ss_dssp TTTCBHHTTSCEEEET--TS-EEEEHHHHHHHHHH----SSB-TTTH
T ss_pred CCChhhcCCCeEEEcc--CC-CeeCHHHHHHHHHh----CCcCCccC
Confidence 676653 244333333 55 889999984 222 23888885
No 67
>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=38.90 E-value=24 Score=26.30 Aligned_cols=27 Identities=26% Similarity=0.527 Sum_probs=17.5
Q ss_pred Ccee-eeCCCCCCC--ceecCCCCCCCcceecccC
Q 025765 192 PTYC-VCNQVSYGE--MVACDNPNCKIEWFHFGCV 223 (248)
Q Consensus 192 ~~~C-~C~~~~~g~--mi~Cd~~~C~~~WfH~~Cv 223 (248)
...| +|+++-+.. .+..++ .-||+.|.
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~-----~v~H~~C~ 107 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCG-----HVVHYSCI 107 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCC-----eEEecccc
Confidence 4558 999985433 233333 56999997
No 68
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=38.84 E-value=9.8 Score=34.77 Aligned_cols=45 Identities=29% Similarity=0.753 Sum_probs=32.7
Q ss_pred Ccee-eeCCCC--C------CCceecCCCCCCCcceecccCCCCcC-----CCCceeCCCCc
Q 025765 192 PTYC-VCNQVS--Y------GEMVACDNPNCKIEWFHFGCVGLKEQ-----PKGKWYCPDCA 239 (248)
Q Consensus 192 ~~~C-~C~~~~--~------g~mi~Cd~~~C~~~WfH~~Cvgl~~~-----p~~~w~C~~C~ 239 (248)
..|| +|-..+ + .++|.|.. |. +--|.+|+-.+.. ..=.|.|..|.
T Consensus 224 n~YCDFclgdsr~nkkt~~peelvscsd--cg-rsghpsclqft~nm~~avk~yrwqcieck 282 (336)
T KOG1244|consen 224 NPYCDFCLGDSRENKKTGMPEELVSCSD--CG-RSGHPSCLQFTANMIAAVKTYRWQCIECK 282 (336)
T ss_pred CcccceeccccccccccCCchhhcchhh--cC-CCCCcchhhhhHHHHHHHHhheeeeeecc
Confidence 4689 996554 1 35899998 66 7789999976663 23469888885
No 69
>PRK13723 conjugal transfer pilus assembly protein TraH; Provisional
Probab=38.28 E-value=4e+02 Score=26.17 Aligned_cols=44 Identities=16% Similarity=0.240 Sum_probs=29.4
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 67 LIRFSDDALDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLK 111 (248)
Q Consensus 67 ~~~l~~~I~~~~~~~~~l~dEKv~lA~~~~~lvd~hir~LD~dl~ 111 (248)
..++.+.|.+.-..+.++..+ +..-+.+..+|++|++.+++.+.
T Consensus 393 ~~~~~~~l~~a~~~~~~~~~~-~~~~~~~~~~i~~~~~~~eqq~~ 436 (451)
T PRK13723 393 MDHLRENLNQAQRQIAAFQSQ-VQVQQDALLVVDRQMSYMRQQLS 436 (451)
T ss_pred HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555555555555555443 44448888999999999998873
No 70
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=37.72 E-value=15 Score=30.87 Aligned_cols=48 Identities=19% Similarity=0.333 Sum_probs=29.2
Q ss_pred CCcee-eeCCCCCCCceecCCCCCC--CcceecccCCCCcCCCCceeCCCCccc
Q 025765 191 EPTYC-VCNQVSYGEMVACDNPNCK--IEWFHFGCVGLKEQPKGKWYCPDCAAL 241 (248)
Q Consensus 191 ~~~~C-~C~~~~~g~mi~Cd~~~C~--~~WfH~~Cvgl~~~p~~~w~C~~C~~~ 241 (248)
....| +|..... ..+ --|.|. ..|.|.+|+..=-...+...|+.|..+
T Consensus 7 ~~~~CRIC~~~~~-~~~--~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~ 57 (162)
T PHA02825 7 MDKCCWICKDEYD-VVT--NYCNCKNENKIVHKECLEEWINTSKNKSCKICNGP 57 (162)
T ss_pred CCCeeEecCCCCC-Ccc--CCcccCCCchHHHHHHHHHHHhcCCCCcccccCCe
Confidence 45678 9987743 222 123343 369999999532223466788888654
No 71
>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=36.80 E-value=7.7 Score=22.93 Aligned_cols=26 Identities=27% Similarity=0.661 Sum_probs=9.9
Q ss_pred e-eeCCCCCC-CceecCCCCCCCcceecccC
Q 025765 195 C-VCNQVSYG-EMVACDNPNCKIEWFHFGCV 223 (248)
Q Consensus 195 C-~C~~~~~g-~mi~Cd~~~C~~~WfH~~Cv 223 (248)
| +|+.+.++ .+-.|.. |. -.+|..|+
T Consensus 3 C~~C~~~~~~~~~Y~C~~--Cd-f~lH~~Ca 30 (30)
T PF07649_consen 3 CDACGKPIDGGWFYRCSE--CD-FDLHEECA 30 (30)
T ss_dssp -TTTS----S--EEE-TT--T------HHHH
T ss_pred CCcCCCcCCCCceEECcc--CC-CccChhcC
Confidence 5 78777666 5567888 55 67888774
No 72
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=36.13 E-value=12 Score=34.43 Aligned_cols=33 Identities=24% Similarity=0.635 Sum_probs=25.5
Q ss_pred CceecCCCCCCCcceecccCCCCcC-----CCCceeCCCCc
Q 025765 204 EMVACDNPNCKIEWFHFGCVGLKEQ-----PKGKWYCPDCA 239 (248)
Q Consensus 204 ~mi~Cd~~~C~~~WfH~~Cvgl~~~-----p~~~w~C~~C~ 239 (248)
-||+|.. |. --+|..||.++.. ..=.|.|..|.
T Consensus 278 S~I~C~~--C~-~~~HP~Ci~M~~elv~~~KTY~W~C~~C~ 315 (381)
T KOG1512|consen 278 SWIVCKP--CA-TRPHPYCVAMIPELVGQYKTYFWKCSSCE 315 (381)
T ss_pred cceeecc--cc-cCCCCcchhcCHHHHhHHhhcchhhcccH
Confidence 5999999 77 5699999987663 23469888875
No 73
>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=34.95 E-value=7.7 Score=27.93 Aligned_cols=22 Identities=45% Similarity=1.100 Sum_probs=14.5
Q ss_pred CCCcceecccCC--CCcCCCCceeCCCCc
Q 025765 213 CKIEWFHFGCVG--LKEQPKGKWYCPDCA 239 (248)
Q Consensus 213 C~~~WfH~~Cvg--l~~~p~~~w~C~~C~ 239 (248)
|. -.||+.|+. |... ..||.|+
T Consensus 50 C~-H~FH~~Ci~~Wl~~~----~~CP~CR 73 (73)
T PF12678_consen 50 CG-HIFHFHCISQWLKQN----NTCPLCR 73 (73)
T ss_dssp TS-EEEEHHHHHHHHTTS----SB-TTSS
T ss_pred cC-CCEEHHHHHHHHhcC----CcCCCCC
Confidence 55 679999995 3332 3898885
No 74
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=34.84 E-value=25 Score=20.63 Aligned_cols=13 Identities=38% Similarity=1.367 Sum_probs=9.1
Q ss_pred CCceeCCCCcccc
Q 025765 230 KGKWYCPDCAALK 242 (248)
Q Consensus 230 ~~~w~C~~C~~~~ 242 (248)
.|.|.|+.|....
T Consensus 2 ~g~W~C~~C~~~N 14 (30)
T PF00641_consen 2 EGDWKCPSCTFMN 14 (30)
T ss_dssp SSSEEETTTTEEE
T ss_pred CcCccCCCCcCCc
Confidence 4678888886544
No 75
>PF11101 DUF2884: Protein of unknown function (DUF2884); InterPro: IPR021307 Some members in this bacterial family of proteins are annotated as YggN which currently has no known function.
Probab=34.71 E-value=2.6e+02 Score=24.58 Aligned_cols=53 Identities=19% Similarity=0.344 Sum_probs=39.6
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHhh
Q 025765 67 LIRFSDDALDEQKHSIRIADEKVALAVQAYDLVD-------THIQQLDQYLKNFDEELRR 119 (248)
Q Consensus 67 ~~~l~~~I~~~~~~~~~l~dEKv~lA~~~~~lvd-------~hir~LD~dl~~~e~el~~ 119 (248)
...|+..|+..+=++..++.+.|.||..+++-|- ..-.+|..-+..|...+..
T Consensus 51 l~~Y~~~lr~~lP~~~~~a~d~l~la~~ald~V~~~~~g~~~~~~~l~~l~~~l~~~~~~ 110 (229)
T PF11101_consen 51 LQQYQQGLRQQLPWVVQLASDGLELARDALDEVATSLLGDSNARDRLKQLMDQLKQQVDR 110 (229)
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHH
Confidence 4567788899999999999999999999998874 3334455555555555443
No 76
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=34.16 E-value=5.8e+02 Score=28.50 Aligned_cols=35 Identities=26% Similarity=0.220 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 81 SIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDE 115 (248)
Q Consensus 81 ~~~l~dEKv~lA~~~~~lvd~hir~LD~dl~~~e~ 115 (248)
+++.+++--..|+.+..-++.-|+.....|.+.++
T Consensus 1571 aL~~Ad~Aq~~a~~ai~~a~~~~~~a~~~l~kv~~ 1605 (1758)
T KOG0994|consen 1571 ALEEADVAQGEAQDAIQGADRDIRLAQQLLAKVQE 1605 (1758)
T ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 33444444444444444444444444444444433
No 77
>PF04286 DUF445: Protein of unknown function (DUF445); InterPro: IPR007383 This entry contains proteins of unknown function. They are predicted to be transmembrane proteins with 2 or 3 TM domains.
Probab=33.03 E-value=3.7e+02 Score=24.24 Aligned_cols=20 Identities=15% Similarity=0.225 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 025765 90 ALAVQAYDLVDTHIQQLDQY 109 (248)
Q Consensus 90 ~lA~~~~~lvd~hir~LD~d 109 (248)
.+.+.+..+++.....|..+
T Consensus 269 ~i~~~i~~~l~~~~~~l~~~ 288 (367)
T PF04286_consen 269 FIEQIISELLEELIDKLKED 288 (367)
T ss_pred HHHHHHHHHHHHHHHHHhcC
Confidence 56666666666666665544
No 78
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=32.93 E-value=21 Score=32.37 Aligned_cols=48 Identities=23% Similarity=0.667 Sum_probs=31.1
Q ss_pred CCcee-eeCCCCC--C--Cc---eecCCCCCCCcceecccCC--CCc----CCCCceeCCCCccc
Q 025765 191 EPTYC-VCNQVSY--G--EM---VACDNPNCKIEWFHFGCVG--LKE----QPKGKWYCPDCAAL 241 (248)
Q Consensus 191 ~~~~C-~C~~~~~--g--~m---i~Cd~~~C~~~WfH~~Cvg--l~~----~p~~~w~C~~C~~~ 241 (248)
...+| +|-..+. + .. -.|-+.+ .|.|.+|+- +++ .+.-.-.||.|..+
T Consensus 19 ~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~---KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTE 80 (293)
T KOG3053|consen 19 LERCCWICFATDEDNRLAAWVHPCRCRGTT---KWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTE 80 (293)
T ss_pred cceeEEEEeccCcccchhhhcccccccCcc---HHHHHHHHHHHHhHHhcCCCCceeechhhcch
Confidence 36788 9976643 2 12 2355533 999999994 333 23457899999754
No 79
>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=32.75 E-value=39 Score=22.09 Aligned_cols=34 Identities=29% Similarity=0.675 Sum_probs=24.5
Q ss_pred CCcee-eeCCCCC---CCceecCCCCCCCcceecccCCCCc
Q 025765 191 EPTYC-VCNQVSY---GEMVACDNPNCKIEWFHFGCVGLKE 227 (248)
Q Consensus 191 ~~~~C-~C~~~~~---g~mi~Cd~~~C~~~WfH~~Cvgl~~ 227 (248)
.+.+| +|+..-. ...+.|.. |. --.|-.|+....
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~--C~-~~~H~~C~~~~~ 47 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSW--CG-LVCHKKCLSKVP 47 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETT--TT--EEETTGGCTSS
T ss_pred CCCCCcccCcccCCCCCCeEEECC--CC-ChHhhhhhhhcC
Confidence 47889 9998863 45688999 77 679999986544
No 80
>PF04949 Transcrip_act: Transcriptional activator; InterPro: IPR007033 Golgins are a family of coiled-coil proteins associated with the Golgi apparatus necessary for tethering events in membrane fusion and as structural supports for Golgi cisternae []. This entry represents proteins annotated as RAB6-interacting golgins.
Probab=32.71 E-value=3e+02 Score=23.04 Aligned_cols=29 Identities=17% Similarity=0.132 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 74 ALDEQKHSIRIADEKVALAVQAYDLVDTH 102 (248)
Q Consensus 74 I~~~~~~~~~l~dEKv~lA~~~~~lvd~h 102 (248)
....+...-+.++||++|+..+.+||..-
T Consensus 114 ykealea~nEknkeK~~Lv~~L~eLv~eS 142 (159)
T PF04949_consen 114 YKEALEAFNEKNKEKAQLVTRLMELVSES 142 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44566667789999999999999999863
No 81
>COG0497 RecN ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=32.05 E-value=4e+02 Score=26.87 Aligned_cols=31 Identities=16% Similarity=0.055 Sum_probs=17.0
Q ss_pred HHHHH-HhhhccCChHHHHHHHHH-hHH-HHHHH
Q 025765 6 QVFLL-TFMDIFFPPLVRDAQMQC-FFV-HTLAE 36 (248)
Q Consensus 6 ~~yle-~fie~~~lP~EL~r~~~~-elD-~~~qe 36 (248)
...|+ -|++++-.-.+|++.+.. |+| .++++
T Consensus 268 ~~~l~ea~~~l~ea~~el~~~~~~le~Dp~~L~~ 301 (557)
T COG0497 268 AELLEEALYELEEASEELRAYLDELEFDPNRLEE 301 (557)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence 34444 333356666677777766 666 34444
No 82
>PRK08032 fliD flagellar capping protein; Reviewed
Probab=31.64 E-value=3.6e+02 Score=26.16 Aligned_cols=51 Identities=2% Similarity=-0.009 Sum_probs=29.1
Q ss_pred chhHHHHHHHhhhcc-CChHHHHHHHHH---hHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 2 FKRFQVFLLTFMDIF-FPPLVRDAQMQC---FFVHTLAEIQRQNEQRCEQEIEDLM 53 (248)
Q Consensus 2 ~~~~~~yle~fie~~-~lP~EL~r~~~~---elD~~~qel~~~~~~~~~~~l~~~~ 53 (248)
+.|+..||+.|+... .+.. ....+.. .++.+...+.++++.+.+.+..+|.
T Consensus 387 ~~~l~~~l~~~~~~~G~l~~-~~~~l~~~i~~l~~~i~~~~~rl~~~e~rl~~qF~ 441 (462)
T PRK08032 387 TTQIATNLKSWLSTTGIIKT-ATDGVNKTLKKLTKQYNAVSDSIDATIARYKAQFT 441 (462)
T ss_pred HHHHHHHHHHHHcCCccchh-HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467888999998832 2221 2222333 5666666666666666665555443
No 83
>PRK11519 tyrosine kinase; Provisional
Probab=31.40 E-value=5.9e+02 Score=26.14 Aligned_cols=32 Identities=9% Similarity=0.287 Sum_probs=23.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCC
Q 025765 29 FFVHTLAEIQRQNEQRCEQEIEDLMREIRAGNITP 63 (248)
Q Consensus 29 elD~~~qel~~~~~~~~~~~l~~~~k~~~~gs~~~ 63 (248)
-|+.++.++..+++..... ++.|.. ++|.+..
T Consensus 271 fL~~ql~~l~~~L~~aE~~-l~~fr~--~~~~vd~ 302 (719)
T PRK11519 271 FLAQQLPEVRSRLDVAENK-LNAFRQ--DKDSVDL 302 (719)
T ss_pred HHHHHHHHHHHHHHHHHHH-HHHHHH--HcCCCCc
Confidence 7888888888888776665 566777 7776543
No 84
>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=31.35 E-value=5.3 Score=26.80 Aligned_cols=22 Identities=41% Similarity=0.996 Sum_probs=9.5
Q ss_pred ecccCCCCc-----CCCCceeCCCCcc
Q 025765 219 HFGCVGLKE-----QPKGKWYCPDCAA 240 (248)
Q Consensus 219 H~~Cvgl~~-----~p~~~w~C~~C~~ 240 (248)
|+.|..+.. ...+.|.||.|..
T Consensus 23 H~~CFDl~~fl~~~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 23 HLQCFDLESFLESNQRTPKWKCPICNK 49 (50)
T ss_dssp SS--EEHHHHHHHHHHS---B-TTT--
T ss_pred ccceECHHHHHHHhhccCCeECcCCcC
Confidence 888886543 2245699999974
No 85
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=31.12 E-value=2.2e+02 Score=21.00 Aligned_cols=48 Identities=10% Similarity=0.095 Sum_probs=27.3
Q ss_pred HHHHHHhhhccCChHHHHHHHHH--hHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 6 QVFLLTFMDIFFPPLVRDAQMQC--FFVHTLAEIQRQNEQRCEQEIEDLM 53 (248)
Q Consensus 6 ~~yle~fie~~~lP~EL~r~~~~--elD~~~qel~~~~~~~~~~~l~~~~ 53 (248)
.+|+.+|+-+..||.+|+..+.. =.|...-..+..+..........++
T Consensus 17 ~s~Vs~~l~Ll~lP~~i~~~v~~g~~~~~~a~~~L~~~~~~~~~~~~~~v 66 (93)
T PF08535_consen 17 RSWVSNHLALLDLPEEIKELVRSGRISDIRALYELRKLAEKNPEEVEALV 66 (93)
T ss_dssp HHHHHHHHGGGS--HHHHHHHHTTS---HHHHHHHHHHHHH-HHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHcCCCchHHHHHHHHHHHHhCHHHHHHHH
Confidence 57999999999999999999997 2234433223333333333344444
No 86
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=31.10 E-value=2.4e+02 Score=21.56 Aligned_cols=45 Identities=11% Similarity=0.320 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025765 75 LDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELRR 119 (248)
Q Consensus 75 ~~~~~~~~~l~dEKv~lA~~~~~lvd~hir~LD~dl~~~e~el~~ 119 (248)
...+..|..+-++|+...+...+-+++.+..+...+..+...+..
T Consensus 82 e~~~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~~l~~ 126 (129)
T cd00890 82 EKSLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQEELQQ 126 (129)
T ss_pred EecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456778899999999999999999999999999999999887664
No 87
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=31.07 E-value=47 Score=22.69 Aligned_cols=20 Identities=20% Similarity=0.076 Sum_probs=11.4
Q ss_pred HHHhhh-----ccCChHHHHHHHHH
Q 025765 9 LLTFMD-----IFFPPLVRDAQMQC 28 (248)
Q Consensus 9 le~fie-----~~~lP~EL~r~~~~ 28 (248)
|++||+ +...-.||++.|.+
T Consensus 11 LDqFMeaYc~~L~kykeeL~~p~~E 35 (52)
T PF03791_consen 11 LDQFMEAYCDMLVKYKEELQRPFQE 35 (52)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555 34555666666664
No 88
>PRK09039 hypothetical protein; Validated
Probab=30.92 E-value=4.5e+02 Score=24.56 Aligned_cols=27 Identities=7% Similarity=-0.102 Sum_probs=13.2
Q ss_pred cCChHHHHHHHHH--hHHHHHHHHHHHHH
Q 025765 16 FFPPLVRDAQMQC--FFVHTLAEIQRQNE 42 (248)
Q Consensus 16 ~~lP~EL~r~~~~--elD~~~qel~~~~~ 42 (248)
..||..|.-.... .++.++.++..++.
T Consensus 63 a~L~e~L~le~~~~~~l~~~l~~l~~~l~ 91 (343)
T PRK09039 63 AELADLLSLERQGNQDLQDSVANLRASLS 91 (343)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 3455333333333 66666666555533
No 89
>COG1842 PspA Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]
Probab=30.62 E-value=3.8e+02 Score=23.64 Aligned_cols=32 Identities=9% Similarity=0.249 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 85 ADEKVALAVQAYDLVDTHIQQLDQYLKNFDEE 116 (248)
Q Consensus 85 ~dEKv~lA~~~~~lvd~hir~LD~dl~~~e~e 116 (248)
=+.=+..+....+-|...+.+|+..|..|+..
T Consensus 104 ~~~~~~~~~~~~~~l~~~~~~Le~Ki~e~~~~ 135 (225)
T COG1842 104 LEAELQQAEEQVEKLKKQLAALEQKIAELRAK 135 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445566666777777788888888777765
No 90
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=30.14 E-value=51 Score=34.32 Aligned_cols=52 Identities=31% Similarity=0.687 Sum_probs=30.8
Q ss_pred CCCCCCCC-cee-eeCCCCCCCceecCCCCCCCcceecccCCCCc--CCCCceeCCCCcc
Q 025765 185 LPVDPNEP-TYC-VCNQVSYGEMVACDNPNCKIEWFHFGCVGLKE--QPKGKWYCPDCAA 240 (248)
Q Consensus 185 ~~~~~~~~-~~C-~C~~~~~g~mi~Cd~~~C~~~WfH~~Cvgl~~--~p~~~w~C~~C~~ 240 (248)
.|.||+.+ +-| +|+-+-..--.+|.- |. .=| ..|+.-.. ...-.|.||.|..
T Consensus 1109 ~p~d~~~~~vdc~~cg~~i~~~~~~c~e--c~-~kf-P~CiasG~pIt~~~fWlC~~CkH 1164 (1189)
T KOG2041|consen 1109 PPVDPNSAKVDCSVCGAKIDPYDLQCSE--CQ-TKF-PVCIASGRPITDNIFWLCPRCKH 1164 (1189)
T ss_pred CCCCCCccceeeeecCCcCCccCCCChh--hc-CcC-ceeeccCCccccceEEEcccccc
Confidence 34555544 458 998865444568887 55 223 67773211 1234899999963
No 91
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=30.00 E-value=33 Score=32.04 Aligned_cols=38 Identities=29% Similarity=0.620 Sum_probs=27.7
Q ss_pred ceecCCCCCCCcceecccCCCCcCCCCceeCCCCccccccCCC
Q 025765 205 MVACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCAALKNRRKG 247 (248)
Q Consensus 205 mi~Cd~~~C~~~WfH~~Cvgl~~~p~~~w~C~~C~~~~~~~k~ 247 (248)
-+=|.+ |. .|..|+....-+--.|||+.|......+|.
T Consensus 220 ALIC~~--C~---~HNGla~~ee~~yi~F~C~~Cn~LN~~~k~ 257 (328)
T KOG2846|consen 220 ALICSQ--CH---HHNGLARKEEYEYITFRCPHCNALNPAKKS 257 (328)
T ss_pred hhcchh--hc---cccCcCChhhcCceEEECccccccCCCcCC
Confidence 345777 66 688888776666678999999877665553
No 92
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=29.10 E-value=72 Score=24.09 Aligned_cols=23 Identities=35% Similarity=0.528 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 025765 94 QAYDLVDTHIQQLDQYLKNFDEE 116 (248)
Q Consensus 94 ~~~~lvd~hir~LD~dl~~~e~e 116 (248)
.+.++++.|+..|+..++.++.+
T Consensus 76 ~~~~ll~~~~~~l~~~i~~L~~~ 98 (99)
T cd04772 76 SALALVDAAHALLQRYRQQLDQE 98 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 77899999999999999998865
No 93
>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=29.09 E-value=11 Score=24.43 Aligned_cols=32 Identities=25% Similarity=0.696 Sum_probs=14.3
Q ss_pred eecCCCCCCCcceecccCCCCcCCCCceeCCCC
Q 025765 206 VACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDC 238 (248)
Q Consensus 206 i~Cd~~~C~~~WfH~~Cvgl~~~p~~~w~C~~C 238 (248)
+.|.+.+|.+. +|..|+.-.......--||.|
T Consensus 12 ~~C~~~~C~~r-~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 12 QRCSNRDCNVR-LHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp EE-SS--S--E-E-HHHHHHHTTT-SS-B-TTT
T ss_pred ccCCCCccCch-HHHHHHHHHHhcCCCCCCcCC
Confidence 67888889955 699998532222111278877
No 94
>KOG1671 consensus Ubiquinol cytochrome c reductase, subunit RIP1 [Energy production and conversion]
Probab=28.77 E-value=28 Score=30.33 Aligned_cols=21 Identities=38% Similarity=1.004 Sum_probs=15.7
Q ss_pred ecccCCCCcCC-CCceeCC-CCc
Q 025765 219 HFGCVGLKEQP-KGKWYCP-DCA 239 (248)
Q Consensus 219 H~~Cvgl~~~p-~~~w~C~-~C~ 239 (248)
|+.||.+-... -|.|||| +|.
T Consensus 155 hLGCVp~~~AGd~gg~~CPCHGS 177 (210)
T KOG1671|consen 155 HLGCVPIANAGDYGGYYCPCHGS 177 (210)
T ss_pred cccccccccccccCceecccccc
Confidence 89999876654 4789999 453
No 95
>PF11690 DUF3287: Protein of unknown function (DUF3287); InterPro: IPR021704 This eukaryotic family of proteins has no known function.
Probab=28.54 E-value=2.4e+02 Score=22.25 Aligned_cols=43 Identities=19% Similarity=0.220 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHH
Q 025765 73 DALDEQKHSIRIADEKVALAVQAYDL-VDTHIQQLDQYLKNFDE 115 (248)
Q Consensus 73 ~I~~~~~~~~~l~dEKv~lA~~~~~l-vd~hir~LD~dl~~~e~ 115 (248)
-|...-.+-+.+.+|+-.|...+.+| |++.++.|+.+-..-+.
T Consensus 43 F~~kV~~qH~~~~~e~r~L~kKi~~l~veRkmr~Les~p~~W~~ 86 (109)
T PF11690_consen 43 FIDKVVDQHQRYCDERRKLRKKIQDLRVERKMRALESHPFDWER 86 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCChHHHHH
Confidence 45555566678999999999999997 99999999988765543
No 96
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=28.51 E-value=35 Score=27.99 Aligned_cols=26 Identities=27% Similarity=0.811 Sum_probs=17.2
Q ss_pred cceecccCC----CCcCCCCceeCCCCccc
Q 025765 216 EWFHFGCVG----LKEQPKGKWYCPDCAAL 241 (248)
Q Consensus 216 ~WfH~~Cvg----l~~~p~~~w~C~~C~~~ 241 (248)
.||...|-. +...+.+.|+|+.|-..
T Consensus 31 ~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~ 60 (166)
T cd04476 31 NWWYPACPGCNKKVVEEGNGTYRCEKCNKS 60 (166)
T ss_pred CeEEccccccCcccEeCCCCcEECCCCCCc
Confidence 467777763 33333478999999764
No 97
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=28.46 E-value=34 Score=22.67 Aligned_cols=31 Identities=23% Similarity=0.426 Sum_probs=19.3
Q ss_pred eecCCCC-CCCcceecccCCCCcCCCCceeCCCCcc
Q 025765 206 VACDNPN-CKIEWFHFGCVGLKEQPKGKWYCPDCAA 240 (248)
Q Consensus 206 i~Cd~~~-C~~~WfH~~Cvgl~~~p~~~w~C~~C~~ 240 (248)
|.||+|. .+|.++.+.|+. -.+.-+|..|..
T Consensus 1 i~C~~C~~~~i~g~R~~C~~----C~d~dlC~~Cf~ 32 (49)
T cd02338 1 VSCDGCGKSNFTGRRYKCLI----CYDYDLCADCYD 32 (49)
T ss_pred CCCCCCcCCCcEEeeEEeCC----CCCCccchhHHh
Confidence 5677765 556677777772 234566777754
No 98
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=28.41 E-value=29 Score=19.45 Aligned_cols=11 Identities=55% Similarity=1.549 Sum_probs=7.5
Q ss_pred CceeCCCCccc
Q 025765 231 GKWYCPDCAAL 241 (248)
Q Consensus 231 ~~w~C~~C~~~ 241 (248)
|.|.|+.|.-.
T Consensus 1 g~W~C~~C~~~ 11 (26)
T smart00547 1 GDWECPACTFL 11 (26)
T ss_pred CcccCCCCCCc
Confidence 46888888543
No 99
>PRK09841 cryptic autophosphorylating protein tyrosine kinase Etk; Provisional
Probab=28.05 E-value=6.8e+02 Score=25.76 Aligned_cols=33 Identities=18% Similarity=0.336 Sum_probs=24.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCC
Q 025765 29 FFVHTLAEIQRQNEQRCEQEIEDLMREIRAGNITPN 64 (248)
Q Consensus 29 elD~~~qel~~~~~~~~~~~l~~~~k~~~~gs~~~~ 64 (248)
-|+.++.++..++.+.... +..|.+ ++|.+...
T Consensus 271 fL~~qL~~l~~~L~~aE~~-l~~fr~--~~~~~d~~ 303 (726)
T PRK09841 271 FLQRQLPEVRSELDQAEEK-LNVYRQ--QRDSVDLN 303 (726)
T ss_pred HHHHHHHHHHHHHHHHHHH-HHHHHH--HcCCCCCC
Confidence 7888888888888776655 666877 77765544
No 100
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=27.74 E-value=53 Score=23.06 Aligned_cols=34 Identities=18% Similarity=0.463 Sum_probs=22.1
Q ss_pred ecCCCCCCCcceecccCCCCcCCCCceeCCCCccccccCC
Q 025765 207 ACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCAALKNRRK 246 (248)
Q Consensus 207 ~Cd~~~C~~~WfH~~Cvgl~~~p~~~w~C~~C~~~~~~~k 246 (248)
.|-+.+|. .|-- -...-...-.||.|..++.++.
T Consensus 20 ~Ct~e~C~-gWmR-----~nFs~~~~p~CPlC~s~M~~~~ 53 (59)
T PF14169_consen 20 ECTSEDCN-GWMR-----DNFSFEEEPVCPLCKSPMVSGT 53 (59)
T ss_pred EeCCCCCC-cccc-----cccccCCCccCCCcCCccccce
Confidence 47777788 8842 2222244578999998876543
No 101
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=27.67 E-value=14 Score=26.75 Aligned_cols=9 Identities=33% Similarity=1.353 Sum_probs=8.1
Q ss_pred cceecccCC
Q 025765 216 EWFHFGCVG 224 (248)
Q Consensus 216 ~WfH~~Cvg 224 (248)
.|||+.|+.
T Consensus 39 ~W~H~~C~~ 47 (82)
T PF00645_consen 39 KWYHWDCFF 47 (82)
T ss_dssp EEEEHHHHH
T ss_pred ceECccccc
Confidence 899999984
No 102
>KOG0996 consensus Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]
Probab=27.25 E-value=5.8e+02 Score=28.26 Aligned_cols=47 Identities=13% Similarity=0.221 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025765 72 DDALDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELR 118 (248)
Q Consensus 72 ~~I~~~~~~~~~l~dEKv~lA~~~~~lvd~hir~LD~dl~~~e~el~ 118 (248)
.+|...+.++..+.++||+.-..=.+-|-..|..|.++|.++...+.
T Consensus 885 ~~i~~lq~~i~~i~~e~~q~qk~kv~~~~~~~~~l~~~i~k~~~~i~ 931 (1293)
T KOG0996|consen 885 ARIKELQNKIDEIGGEKVQAQKDKVEKINEQLDKLEADIAKLTVAIK 931 (1293)
T ss_pred HHHHHHHHHHHHhhchhhHHhHHHHHHHHHHHHHHHHHHHHhHHHHh
Confidence 45666677777788888887777777777777777777777666544
No 103
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=27.04 E-value=29 Score=32.38 Aligned_cols=38 Identities=29% Similarity=0.818 Sum_probs=24.1
Q ss_pred cee-eeCCC--CCCCceecCCCCCCCcceecccCCCCcCCCCceeCCCCcc
Q 025765 193 TYC-VCNQV--SYGEMVACDNPNCKIEWFHFGCVGLKEQPKGKWYCPDCAA 240 (248)
Q Consensus 193 ~~C-~C~~~--~~g~mi~Cd~~~C~~~WfH~~Cvgl~~~p~~~w~C~~C~~ 240 (248)
.+| -|..+ -||-||-|+- -|=+.|..+.. +-.|+.|..
T Consensus 91 HfCd~Cd~PI~IYGRmIPCkH------vFCl~CAr~~~----dK~Cp~C~d 131 (389)
T KOG2932|consen 91 HFCDRCDFPIAIYGRMIPCKH------VFCLECARSDS----DKICPLCDD 131 (389)
T ss_pred EeecccCCcceeeecccccch------hhhhhhhhcCc----cccCcCccc
Confidence 356 77776 3799998764 35566665544 346777753
No 104
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.66 E-value=63 Score=30.54 Aligned_cols=46 Identities=24% Similarity=0.577 Sum_probs=29.0
Q ss_pred ceeeeCCCC-CCCceecCCCCCCCcceecccCC--CCcCCCCceeCCCCcccccc
Q 025765 193 TYCVCNQVS-YGEMVACDNPNCKIEWFHFGCVG--LKEQPKGKWYCPDCAALKNR 244 (248)
Q Consensus 193 ~~C~C~~~~-~g~mi~Cd~~~C~~~WfH~~Cvg--l~~~p~~~w~C~~C~~~~~~ 244 (248)
++|+|-..+ .|+-+.==. |. .-||..||. |+.. .-+||-|+++-.+
T Consensus 231 ~CaIClEdY~~GdklRiLP--C~-H~FH~~CIDpWL~~~---r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 231 TCAICLEDYEKGDKLRILP--CS-HKFHVNCIDPWLTQT---RTFCPVCKRDIRT 279 (348)
T ss_pred eEEEeecccccCCeeeEec--CC-CchhhccchhhHhhc---CccCCCCCCcCCC
Confidence 445998764 366444334 44 449999995 3322 3579999886543
No 105
>PRK10869 recombination and repair protein; Provisional
Probab=26.33 E-value=5.1e+02 Score=25.81 Aligned_cols=23 Identities=9% Similarity=0.270 Sum_probs=9.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 025765 83 RIADEKVALAVQAYDLVDTHIQQ 105 (248)
Q Consensus 83 ~l~dEKv~lA~~~~~lvd~hir~ 105 (248)
.|+.....-|..+-..|..+++.
T Consensus 363 ~LS~~R~~aA~~l~~~v~~~L~~ 385 (553)
T PRK10869 363 KLHQSRQRYAKELAQLITESMHE 385 (553)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333333444444444433333
No 106
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=26.08 E-value=3.2e+02 Score=21.35 Aligned_cols=62 Identities=13% Similarity=0.255 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhCCCCCChhhhhhHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Q 025765 35 AEIQRQNEQRCEQEIEDLMREIRAGNITPNTSLIRFSDDALDEQKHSI-RIADEKVALAVQAYDLVD 100 (248)
Q Consensus 35 qel~~~~~~~~~~~l~~~~k~~~~gs~~~~~k~~~l~~~I~~~~~~~~-~l~dEKv~lA~~~~~lvd 100 (248)
++++.++....+. ++...+ +.|+.+.+. .+.++.+|++.+.++. .+++-+=.+++++...|+
T Consensus 11 ~~l~~el~~L~d~-lEevL~--ssg~~a~~e-~~~lR~r~~~~Lk~~r~rl~~~~d~v~~~sk~a~~ 73 (104)
T COG4575 11 DQLLAELQELLDT-LEEVLK--SSGSLAGDE-AEELRSKAESALKEARDRLGDTGDAVVQRSKAAAD 73 (104)
T ss_pred HHHHHHHHHHHHH-HHHHHH--hcccchhhH-HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence 4444444444444 333444 566655433 4556666767665554 344444444444444443
No 107
>PF08165 FerA: FerA (NUC095) domain; InterPro: IPR012560 The ferlin gene family are characterised by multiple tandem C2 domains and a C-terminal transmembrane domain. They are found in a wide range of species and their function remains unknown, however, mutations in its two most well-characterised members, dysferlin and otoferlin, have been implicated in human disease []. This is central domain A in proteins of the Ferlin family [].; GO: 0016021 integral to membrane
Probab=25.95 E-value=93 Score=22.08 Aligned_cols=36 Identities=8% Similarity=0.095 Sum_probs=25.8
Q ss_pred hHHHHHHHhhh--ccCChHHHHHHHHH-hHHHHHHHHHHH
Q 025765 4 RFQVFLLTFMD--IFFPPLVRDAQMQC-FFVHTLAEIQRQ 40 (248)
Q Consensus 4 ~~~~yle~fie--~~~lP~EL~r~~~~-elD~~~qel~~~ 40 (248)
.|.-.|++.|+ ...|| .++..-.- +||.....++..
T Consensus 15 ~~~~lLdqlIeD~~~pLP-~~~~~~~~t~LD~~l~~lR~~ 53 (66)
T PF08165_consen 15 LWLKLLDQLIEDCSKPLP-SLEGKPNATELDRQLRKLRSR 53 (66)
T ss_pred HHHHHHHHHHHHhcCCCC-CCCCCCCCCHHHHHHHHHHHH
Confidence 58889999999 46888 34433333 999988886655
No 108
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=25.66 E-value=3.1e+02 Score=20.99 Aligned_cols=45 Identities=16% Similarity=0.238 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025765 75 LDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELRR 119 (248)
Q Consensus 75 ~~~~~~~~~l~dEKv~lA~~~~~lvd~hir~LD~dl~~~e~el~~ 119 (248)
......+..--.+++........-+++.+..|...+..++..|..
T Consensus 62 ~~~~~e~~~~l~~r~e~ie~~i~~lek~~~~l~~~l~e~q~~l~~ 106 (110)
T TIGR02338 62 KTDKEEAIQELKEKKETLELRVKTLQRQEERLREQLKELQEKIQE 106 (110)
T ss_pred eecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555556666666666677777777777777777766553
No 109
>COG5560 UBP12 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=25.59 E-value=24 Score=36.03 Aligned_cols=17 Identities=35% Similarity=1.183 Sum_probs=12.6
Q ss_pred CCceeCCCCccccccCC
Q 025765 230 KGKWYCPDCAALKNRRK 246 (248)
Q Consensus 230 ~~~w~C~~C~~~~~~~k 246 (248)
.+.||||.|...+.-.|
T Consensus 693 ~DswyCpgCkefrqasK 709 (823)
T COG5560 693 SDSWYCPGCKEFRQASK 709 (823)
T ss_pred cccccCCchHhhhhhhh
Confidence 57899999987665433
No 110
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=24.94 E-value=14 Score=39.94 Aligned_cols=47 Identities=11% Similarity=0.196 Sum_probs=36.1
Q ss_pred cee-eeCCCCCCCceecCCCCCCCcceec-ccCCCCc----CCCCceeCCCCccccc
Q 025765 193 TYC-VCNQVSYGEMVACDNPNCKIEWFHF-GCVGLKE----QPKGKWYCPDCAALKN 243 (248)
Q Consensus 193 ~~C-~C~~~~~g~mi~Cd~~~C~~~WfH~-~Cvgl~~----~p~~~w~C~~C~~~~~ 243 (248)
..| +|.+. +..++|++- |+ ..||. .|++-+. .+++.|+|+.|.-..+
T Consensus 429 rrl~Ie~~d--et~l~yysT-~p-qly~ll~cLd~~~~e~~L~d~i~~~~ee~~rqM 481 (1414)
T KOG1473|consen 429 RRLRIEGMD--ETLLWYYST-CP-QLYHLLRCLDRTYVEMYLCDGIWERREEIIRQM 481 (1414)
T ss_pred eeeEEecCC--CcEEEEecC-cH-HHHHHHHHhchHHHHHhhccchhhhHHHHHHhc
Confidence 347 88755 778999974 88 89999 9999333 5789999999975543
No 111
>PHA03158 hypothetical protein; Provisional
Probab=24.59 E-value=1.7e+02 Score=25.69 Aligned_cols=37 Identities=22% Similarity=0.380 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHH
Q 025765 80 HSIRIADEKVALAVQAYDLVD------THIQQLDQYLKNFDEE 116 (248)
Q Consensus 80 ~~~~l~dEKv~lA~~~~~lvd------~hir~LD~dl~~~e~e 116 (248)
.+..-+.||..|.+|++..-. .|+++|+.+|+.++..
T Consensus 227 WCv~t~~EK~~~~kQllka~kkc~~~s~~~~~leeei~eleks 269 (273)
T PHA03158 227 WCIKTAKEKAAILKQLLKAAKKCCKNSEHEKELEEEIEELEKS 269 (273)
T ss_pred cEeecHHHhHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHh
Confidence 356778999999999988754 5777888887777763
No 112
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=24.38 E-value=6.6e+02 Score=24.38 Aligned_cols=79 Identities=13% Similarity=0.207 Sum_probs=46.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCh--------------hhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 29 FFVHTLAEIQRQNEQRCEQEIEDLMREIRAGNITPNT--------------SLIRFSDDALDEQKHSIRIADEKVALAVQ 94 (248)
Q Consensus 29 elD~~~qel~~~~~~~~~~~l~~~~k~~~~gs~~~~~--------------k~~~l~~~I~~~~~~~~~l~dEKv~lA~~ 94 (248)
+.|.+-.+..++++.+-..-|..+|+ +-|.+-+.- +...+...+++...++.+++..+-.|..
T Consensus 228 ~rdr~Krd~HNeVERRRR~nIN~~Ik--eLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~~E~~~rqk~le~- 304 (411)
T KOG1318|consen 228 ERDRRKRDNHNEVERRRRENINDRIK--ELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRARELENRQKKLES- 304 (411)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHHH--HHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHHHHHHhhhhHHHh-
Confidence 77777778888888888888888888 444333211 1233444555666666666655554443
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 025765 95 AYDLVDTHIQQLDQYLKNFDEEL 117 (248)
Q Consensus 95 ~~~lvd~hir~LD~dl~~~e~el 117 (248)
.+++|-..++.|+..+
T Consensus 305 -------~n~~L~~rieeLk~~~ 320 (411)
T KOG1318|consen 305 -------TNQELALRIEELKSEA 320 (411)
T ss_pred -------HHHHHHHHHHHHHHHH
Confidence 3344444455555543
No 113
>PF05781 MRVI1: MRVI1 protein; InterPro: IPR008677 This family consists of mammalian MRVI1 proteins which are related to the lymphoid-restricted membrane protein (JAW1) and the IP3 receptor associated cGMP kinase substrates A and B (IRAGA and IRAGB). The function of MRVI1 is unknown although mutations in the Mrvi1 gene induces myeloid leukaemia by altering the expression of a gene important for myeloid cell growth and/or differentiation so it has been speculated that Mrvi1 is a tumour suppressor gene []. IRAG is very similar in sequence to MRVI1 and is an essential NO/cGKI-dependent regulator of IP3-induced calcium release. Activation of cGKI decreases IP3-stimulated elevations in intracellular calcium, induces smooth muscle relaxation and contributes to the antiproliferative and pro-apoptotic effects of NO/cGMP []. Jaw1 is a member of a class of proteins with COOH-terminal hydrophobic membrane anchors and is structurally similar to proteins involved in vesicle targeting and fusion. This suggests that the function and/or the structure of the ER in lymphocytes may be modified by lymphoid-restricted resident ER proteins [].
Probab=24.16 E-value=7.4e+02 Score=24.91 Aligned_cols=27 Identities=19% Similarity=0.347 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025765 92 AVQAYDLVDTHIQQLDQYLKNFDEELR 118 (248)
Q Consensus 92 A~~~~~lvd~hir~LD~dl~~~e~el~ 118 (248)
...|.+++.+|+..|..-.++.-++|.
T Consensus 290 ~SkAvevM~qhvenLkr~~~kehaeL~ 316 (538)
T PF05781_consen 290 VSKAVEVMIQHVENLKRMYEKEHAELE 316 (538)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346778888888888777766666654
No 114
>PF07139 DUF1387: Protein of unknown function (DUF1387); InterPro: IPR009816 This family represents a conserved region approximately 300 residues long within a number of hypothetical proteins of unknown function that seem to be restricted to mammals.
Probab=24.13 E-value=5.8e+02 Score=23.68 Aligned_cols=51 Identities=16% Similarity=0.217 Sum_probs=27.6
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH
Q 025765 66 SLIRFSDDALDEQKHSIRIADEKVALAVQAYDL-------VDTHIQQLDQYLKNFDEE 116 (248)
Q Consensus 66 k~~~l~~~I~~~~~~~~~l~dEKv~lA~~~~~l-------vd~hir~LD~dl~~~e~e 116 (248)
++..|..+|..-..+|++|-+..-.=|..+.-| =+..+-.|=+||+.|-.+
T Consensus 201 REvaLl~EmdkVK~EAmeiL~aRqkkAeeLkrltd~A~~MsE~Ql~ELRadIK~fvs~ 258 (302)
T PF07139_consen 201 REVALLAEMDKVKAEAMEILDARQKKAEELKRLTDRASQMSEEQLAELRADIKHFVSE 258 (302)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhhh
Confidence 444555566565566665555554444444444 445555566666555543
No 115
>PF08432 Vfa1: AAA-ATPase Vps4-associated protein 1; InterPro: IPR013640 This is a family of fungal proteins of unknown function.
Probab=24.09 E-value=47 Score=28.19 Aligned_cols=28 Identities=25% Similarity=0.585 Sum_probs=20.1
Q ss_pred Ccee-eeCCCCCCCceecCCCCCCCcceecccCC
Q 025765 192 PTYC-VCNQVSYGEMVACDNPNCKIEWFHFGCVG 224 (248)
Q Consensus 192 ~~~C-~C~~~~~g~mi~Cd~~~C~~~WfH~~Cvg 224 (248)
.--| ||..|+..-+|.=++. .||| .|-+
T Consensus 13 ~k~C~IC~KpsttVL~t~~~~----DfFY-~C~~ 41 (182)
T PF08432_consen 13 AKACFICYKPSTTVLITPDNK----DFFY-VCPS 41 (182)
T ss_pred CCceeEecCCCceEEecCCCC----CeEE-eCcc
Confidence 4568 9999987777754443 6886 7865
No 116
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=23.98 E-value=26 Score=34.56 Aligned_cols=14 Identities=29% Similarity=0.738 Sum_probs=10.6
Q ss_pred ceeCCCCccccccC
Q 025765 232 KWYCPDCAALKNRR 245 (248)
Q Consensus 232 ~w~C~~C~~~~~~~ 245 (248)
.|||+.|......+
T Consensus 482 QYYCe~CWa~~HS~ 495 (520)
T KOG0129|consen 482 QYYCESCWAKIHSG 495 (520)
T ss_pred hhhchHHHHHhhcC
Confidence 59999998766543
No 117
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=23.45 E-value=8.5e+02 Score=25.32 Aligned_cols=24 Identities=4% Similarity=0.019 Sum_probs=10.3
Q ss_pred HHHHHHHhhh-ccCChHHHHHHHHH
Q 025765 5 FQVFLLTFMD-IFFPPLVRDAQMQC 28 (248)
Q Consensus 5 ~~~yle~fie-~~~lP~EL~r~~~~ 28 (248)
.+++-|.||+ .+.-=.+|++.+..
T Consensus 545 ~~vlreeYi~~~~~ar~ei~~rv~~ 569 (717)
T PF10168_consen 545 TKVLREEYIEKQDLAREEIQRRVKL 569 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444455555 22223344444433
No 118
>PF10737 GerPC: Spore germination protein GerPC; InterPro: IPR019673 GerPC is required for the formation of functionally normal spores. The gerP locus encodes a number of proteins which are thought to be involved in the establishment of normal spore coat structure and/or permeability, which allows the access of germinants to their receptor [].
Probab=23.02 E-value=2e+02 Score=24.50 Aligned_cols=34 Identities=18% Similarity=0.113 Sum_probs=23.4
Q ss_pred CChHHHHHHHHH---hHHHHHH-----HHHHHHHHHHHHHHH
Q 025765 17 FPPLVRDAQMQC---FFVHTLA-----EIQRQNEQRCEQEIE 50 (248)
Q Consensus 17 ~lP~EL~r~~~~---elD~~~q-----el~~~~~~~~~~~l~ 50 (248)
.+|..|.+.-.. .||..+. +|++++.++...|++
T Consensus 95 e~p~~l~~~e~~~~~~ld~~y~~~IieDIrKQl~~RI~~Ylq 136 (176)
T PF10737_consen 95 EAPQRLEQLEQQYNVPLDDSYRSFIIEDIRKQLPQRIQFYLQ 136 (176)
T ss_pred HHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHhHHHHHHHHh
Confidence 457777766666 6666554 667778888877776
No 119
>PRK06798 fliD flagellar capping protein; Validated
Probab=23.00 E-value=5.7e+02 Score=24.79 Aligned_cols=52 Identities=12% Similarity=0.057 Sum_probs=30.0
Q ss_pred hhHHHHHHHhhh-ccCChHHHHHHHHH--hHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 3 KRFQVFLLTFMD-IFFPPLVRDAQMQC--FFVHTLAEIQRQNEQRCEQEIEDLMR 54 (248)
Q Consensus 3 ~~~~~yle~fie-~~~lP~EL~r~~~~--elD~~~qel~~~~~~~~~~~l~~~~k 54 (248)
.|+..||+.|+. -..+...+...-.. .++.+...+-++++.+.+.+..+|..
T Consensus 361 ~~l~~~l~~~~~~~G~i~~r~~~l~~~i~~l~~~~~~~e~rl~~~e~~l~~qf~a 415 (440)
T PRK06798 361 KEMEKSLDKIFGDEGIIGERSKSIDNRVSKLDLKITDIDTQNKQKQDNIVDKYQK 415 (440)
T ss_pred HHHHHHHHhhhCCCceeehhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578889999986 23444443333222 56666666666666655555554433
No 120
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=22.84 E-value=33 Score=25.87 Aligned_cols=28 Identities=36% Similarity=0.685 Sum_probs=18.8
Q ss_pred CCCcceecccCC--CCcCCCCceeCCCCcccc
Q 025765 213 CKIEWFHFGCVG--LKEQPKGKWYCPDCAALK 242 (248)
Q Consensus 213 C~~~WfH~~Cvg--l~~~p~~~w~C~~C~~~~ 242 (248)
|. .-||..|+- |... ..+=.||.|++.=
T Consensus 52 C~-H~FH~hCI~kWl~~~-~~~~~CPmCR~~w 81 (85)
T PF12861_consen 52 CS-HNFHMHCILKWLSTQ-SSKGQCPMCRQPW 81 (85)
T ss_pred Cc-cHHHHHHHHHHHccc-cCCCCCCCcCCee
Confidence 55 569999984 4432 2345999998753
No 121
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=22.80 E-value=36 Score=36.67 Aligned_cols=34 Identities=35% Similarity=0.847 Sum_probs=27.6
Q ss_pred cee-eeCCCCCCCceecCCCCCCCcceecccC---CCCc
Q 025765 193 TYC-VCNQVSYGEMVACDNPNCKIEWFHFGCV---GLKE 227 (248)
Q Consensus 193 ~~C-~C~~~~~g~mi~Cd~~~C~~~WfH~~Cv---gl~~ 227 (248)
..| +|.+...|--|+|..-+|. -|||..|. ||..
T Consensus 330 L~cy~cK~~~~gaciqcs~~~c~-~a~hvtca~~agl~m 367 (1051)
T KOG0955|consen 330 LTCYICKQKGLGACIQCSKANCY-TAFHVTCARRAGLYM 367 (1051)
T ss_pred ceeeeeccCCCCcceecchhhhh-hhhhhhhHhhcCceE
Confidence 446 9988877888999977899 99999996 5544
No 122
>KOG2626 consensus Histone H3 (Lys4) methyltransferase complex, subunit CPS60/ASH2/BRE2 [Chromatin structure and dynamics; Transcription]
Probab=22.37 E-value=1e+02 Score=30.66 Aligned_cols=47 Identities=23% Similarity=0.639 Sum_probs=33.0
Q ss_pred CceeeeCCCCCC--CceecCCCCCCCcceecccCCCCc-----CC---CCceeCCCCccc
Q 025765 192 PTYCVCNQVSYG--EMVACDNPNCKIEWFHFGCVGLKE-----QP---KGKWYCPDCAAL 241 (248)
Q Consensus 192 ~~~C~C~~~~~g--~mi~Cd~~~C~~~WfH~~Cvgl~~-----~p---~~~w~C~~C~~~ 241 (248)
.++|+|....+. .-++|.. |. .|||..|+-... .| .-.+.|-.|...
T Consensus 20 ~~~~y~e~~r~l~~~elqcs~--cl-k~~~~~~~~~~~~~~s~~pf~t~y~fvc~~c~~~ 76 (544)
T KOG2626|consen 20 ATVCYCEGERNLGIVELQCST--CL-KWFHLPTLEAFHLIKSSLPFMTSYEFVCKECTPS 76 (544)
T ss_pred ccccccccccccCceeeEeee--cc-cccccccccccccccccCCcccceeEEeccccCc
Confidence 678999877553 4689999 77 999986663222 22 236889888765
No 123
>KOG4637 consensus Adaptor for phosphoinositide 3-kinase [Signal transduction mechanisms]
Probab=22.18 E-value=7.2e+02 Score=24.04 Aligned_cols=12 Identities=8% Similarity=0.357 Sum_probs=7.1
Q ss_pred hhHHHHHHHhhh
Q 025765 3 KRFQVFLLTFMD 14 (248)
Q Consensus 3 ~~~~~yle~fie 14 (248)
+++..|-++|=+
T Consensus 139 ~~~~~~~q~lq~ 150 (464)
T KOG4637|consen 139 KKLREYHQQLQE 150 (464)
T ss_pred HHHHHHHHHHHH
Confidence 456666666655
No 124
>PRK09343 prefoldin subunit beta; Provisional
Probab=22.09 E-value=3.9e+02 Score=20.95 Aligned_cols=99 Identities=12% Similarity=0.122 Sum_probs=49.3
Q ss_pred CChHHHHHHHHH--hHHHHHHHHHHHHHHHHHHHHHHHHHHH-hhCCCCCChhhhhhHHH-----HHHHHHHHHHHHHHH
Q 025765 17 FPPLVRDAQMQC--FFVHTLAEIQRQNEQRCEQEIEDLMREI-RAGNITPNTSLIRFSDD-----ALDEQKHSIRIADEK 88 (248)
Q Consensus 17 ~lP~EL~r~~~~--elD~~~qel~~~~~~~~~~~l~~~~k~~-~~gs~~~~~k~~~l~~~-----I~~~~~~~~~l~dEK 88 (248)
+||.+|+..+.. .+=..++.+.....+..... ...-..+ .-..+.++. .+++- |......+..--.++
T Consensus 4 ~~~~~~q~~~~~~q~lq~~l~~~~~q~~~le~q~-~e~~~~~~EL~~L~~d~---~VYk~VG~vlv~qd~~e~~~~l~~r 79 (121)
T PRK09343 4 NIPPEVQAQLAQLQQLQQQLERLLQQKSQIDLEL-REINKALEELEKLPDDT---PIYKIVGNLLVKVDKTKVEKELKER 79 (121)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHcCCCcc---hhHHHhhHHHhhccHHHHHHHHHHH
Confidence 678788777766 55444544444443333321 1111110 112222222 22222 344555566666666
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025765 89 VALAVQAYDLVDTHIQQLDQYLKNFDEELRR 119 (248)
Q Consensus 89 v~lA~~~~~lvd~hir~LD~dl~~~e~el~~ 119 (248)
+.....-..-+++....|...+..++..|..
T Consensus 80 ~E~ie~~ik~lekq~~~l~~~l~e~q~~l~~ 110 (121)
T PRK09343 80 KELLELRSRTLEKQEKKLREKLKELQAKINE 110 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6666666666666666666666666665553
No 125
>PF02370 M: M protein repeat; InterPro: IPR003345 This short repeat is found in multiple copies in bacterial M proteins. The M proteins bind to IgA and are closely associated with virulence. The M protein has been postulated to be a major group A streptococcal (GAS) virulence factor because of its contribution to the bacterial resistance to opsonophagocytosis [].; PDB: 2KK9_A.
Probab=22.08 E-value=1.3e+02 Score=16.76 Aligned_cols=15 Identities=20% Similarity=0.357 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHh
Q 025765 104 QQLDQYLKNFDEELR 118 (248)
Q Consensus 104 r~LD~dl~~~e~el~ 118 (248)
+.|+.++.+|+++.+
T Consensus 4 k~lEa~~qkLe~e~q 18 (21)
T PF02370_consen 4 KQLEADHQKLEAEKQ 18 (21)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHh
Confidence 578888888888654
No 126
>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits. Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal alpha subunit, eukaryotic prefoldin subunits 3 and 5 and the UXT (ubiquitously expressed transcript) family. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 1FXK_C 2ZDI_C.
Probab=21.57 E-value=3.6e+02 Score=20.37 Aligned_cols=44 Identities=7% Similarity=0.275 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025765 76 DEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELRR 119 (248)
Q Consensus 76 ~~~~~~~~l~dEKv~lA~~~~~lvd~hir~LD~dl~~~e~el~~ 119 (248)
..+..|.++-+.|+...+...+-+...++.+...+..++..+..
T Consensus 73 ~s~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~~~~~l~~ 116 (120)
T PF02996_consen 73 MSLEEAIEFLKKRIKELEEQLEKLEKELAELQAQIEQLEQTLQQ 116 (120)
T ss_dssp EEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHH
T ss_pred ecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34667888888999888888888888888888888888776653
No 127
>TIGR00634 recN DNA repair protein RecN. All proteins in this family for which functions are known are ATP binding proteins involved in the initiation of recombination and recombinational repair.
Probab=21.47 E-value=7.3e+02 Score=24.58 Aligned_cols=11 Identities=0% Similarity=-0.188 Sum_probs=4.2
Q ss_pred ChHHHHHHHHH
Q 025765 18 PPLVRDAQMQC 28 (248)
Q Consensus 18 lP~EL~r~~~~ 28 (248)
+-.+|++.++.
T Consensus 285 ~~~~l~~~~~~ 295 (563)
T TIGR00634 285 ATRELQNYLDE 295 (563)
T ss_pred HHHHHHHHHHh
Confidence 33344443333
No 128
>KOG1011 consensus Neurotransmitter release regulator, UNC-13 [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=21.42 E-value=4.7e+02 Score=27.36 Aligned_cols=91 Identities=11% Similarity=0.090 Sum_probs=56.9
Q ss_pred HHHHHHHH----hHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCChhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 21 VRDAQMQC----FFVHTLAEIQRQNEQRCEQEIEDLMREIRAGNITPNTSLIRFSDDALDEQKHSIRIADEKVALAVQAY 96 (248)
Q Consensus 21 EL~r~~~~----elD~~~qel~~~~~~~~~~~l~~~~k~~~~gs~~~~~k~~~l~~~I~~~~~~~~~l~dEKv~lA~~~~ 96 (248)
.|...|.- |||....+++.+++.+.+..+..+..... .++.++-.+.- .++-..+..+..-+..|-+.|+.+-
T Consensus 860 qlekmfeamggkeld~ea~d~lk~lqvkln~vldels~~f~-tsfqphi~e~v--~qmg~il~qvkgt~~a~~sva~dad 936 (1283)
T KOG1011|consen 860 QLEKMFEAMGGKELDEEAGDVLKELQVKLNSVLDELSAVFV-TSFQPHIHECV--IQMGDILVQVKGTGLAKTSVAQDAD 936 (1283)
T ss_pred HHHHHHHHhcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHH-hhcCccHHHHH--HHHHHHHhhhcccccchhhcccchH
Confidence 34444544 99999999999999988888776554211 24444432222 2455666667777777777777765
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 025765 97 DLVDTHIQQLDQYLKNFD 114 (248)
Q Consensus 97 ~lvd~hir~LD~dl~~~e 114 (248)
..++--+.-||..|..|-
T Consensus 937 ~vl~plmdlldgnlt~fa 954 (1283)
T KOG1011|consen 937 AVLEPLMDLLDGNLTLFA 954 (1283)
T ss_pred HHHHHHHHHHhchHHHHH
Confidence 555555555555554443
No 129
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=20.95 E-value=77 Score=33.52 Aligned_cols=51 Identities=27% Similarity=0.804 Sum_probs=36.1
Q ss_pred CCCCCcee-eeCCCCCCCceecCCCCCCCcceecccCC--CCcCCCCceeCCCCccc
Q 025765 188 DPNEPTYC-VCNQVSYGEMVACDNPNCKIEWFHFGCVG--LKEQPKGKWYCPDCAAL 241 (248)
Q Consensus 188 ~~~~~~~C-~C~~~~~g~mi~Cd~~~C~~~WfH~~Cvg--l~~~p~~~w~C~~C~~~ 241 (248)
.+.....| .|.......++.|+. |. .=+|..|.. ++..+.+.|.|+.|...
T Consensus 151 ~~~~~~~~~~~~k~~~~~~~~~~~--~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 204 (904)
T KOG1246|consen 151 EFIDYPQCNTCSKGKEEKLLLCDS--CD-DSYHTYCLRPPLTRVPDGDWRCPKCIPT 204 (904)
T ss_pred ccccchhhhccccCCCccceeccc--cc-CcccccccCCCCCcCCcCcccCCccccc
Confidence 33334446 777664334558999 55 779999985 55678999999999765
No 130
>PF07195 FliD_C: Flagellar hook-associated protein 2 C-terminus; InterPro: IPR010809 The flagellar hook-associated protein 2 (HAP2 or FliD) forms the distal end of the flagella, and plays a role in mucin specific adhesion of the bacteria []. This alignment covers the C-terminal region of the flagellar hook-associated protein 2.; GO: 0007155 cell adhesion, 0009288 bacterial-type flagellum
Probab=20.90 E-value=3.9e+02 Score=23.27 Aligned_cols=51 Identities=10% Similarity=0.110 Sum_probs=30.4
Q ss_pred chhHHHHHHHhhhc--cCChHHHHHHHHH---hHHHHHHHHHHHHHHHHHHHHHHHH
Q 025765 2 FKRFQVFLLTFMDI--FFPPLVRDAQMQC---FFVHTLAEIQRQNEQRCEQEIEDLM 53 (248)
Q Consensus 2 ~~~~~~yle~fie~--~~lP~EL~r~~~~---elD~~~qel~~~~~~~~~~~l~~~~ 53 (248)
..++..||+.|+.. ..+. .....+.. .++.+...+.++++.+.+.+..+|.
T Consensus 173 ~~~l~~~l~~~~~~~~G~i~-~~~~~l~~~~~~~~~~i~~~~~rl~~~~~~l~~qf~ 228 (239)
T PF07195_consen 173 ATRLNDYLDSYTGSSTGSIT-SRIDSLNSQIKSLDKQIEDLEERLESKEERLRKQFS 228 (239)
T ss_pred HHHHHHHHHHHhCCCCcchh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677888888873 3444 33333333 6666666666666666666555443
No 131
>cd00584 Prefoldin_alpha Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=20.77 E-value=4.1e+02 Score=20.60 Aligned_cols=45 Identities=13% Similarity=0.330 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025765 75 LDEQKHSIRIADEKVALAVQAYDLVDTHIQQLDQYLKNFDEELRR 119 (248)
Q Consensus 75 ~~~~~~~~~l~dEKv~lA~~~~~lvd~hir~LD~dl~~~e~el~~ 119 (248)
+..+.+|.++-+.|+.......+-+.+-+.+|-.++..++..+..
T Consensus 82 E~~~~eA~~~l~~r~~~l~~~~~~l~~~l~~l~~~~~~~~~~l~~ 126 (129)
T cd00584 82 EKDLEEAIEFLDKKIEELTKQIEKLQKELAKLKDQINTLEAELQE 126 (129)
T ss_pred EecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356677889999999999999999999999999999888876653
No 132
>PRK10132 hypothetical protein; Provisional
Probab=20.70 E-value=4.1e+02 Score=20.67 Aligned_cols=50 Identities=14% Similarity=0.082 Sum_probs=26.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCChhhhhhHHHHHHHHHHHH
Q 025765 29 FFVHTLAEIQRQNEQRCEQEIEDLMREIRAGNITPNTSLIRFSDDALDEQKHSI 82 (248)
Q Consensus 29 elD~~~qel~~~~~~~~~~~l~~~~k~~~~gs~~~~~k~~~l~~~I~~~~~~~~ 82 (248)
++|...+.+..++...... ++.+.+ ..++... .....+..++...+..+.
T Consensus 9 ~~~~q~e~L~~Dl~~L~~~-le~ll~--~~~~~~~-~~~~~lR~r~~~~L~~ar 58 (108)
T PRK10132 9 DVDDGVQDIQNDVNQLADS-LESVLK--SWGSDAK-GEAEAARRKAQALLKETR 58 (108)
T ss_pred hhhhHHHHHHHHHHHHHHH-HHHHHH--HHhhhhH-HHHHHHHHHHHHHHHHHH
Confidence 5666666777776666665 443444 3332221 223555556666555554
No 133
>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=20.69 E-value=44 Score=21.97 Aligned_cols=39 Identities=33% Similarity=0.732 Sum_probs=21.3
Q ss_pred eeCCCCC-CCce-ecCCCCCCCcceecccCC-------CCcC----CCCceeCCCCc
Q 025765 196 VCNQVSY-GEMV-ACDNPNCKIEWFHFGCVG-------LKEQ----PKGKWYCPDCA 239 (248)
Q Consensus 196 ~C~~~~~-g~mi-~Cd~~~C~~~WfH~~Cvg-------l~~~----p~~~w~C~~C~ 239 (248)
.|+++-. ++++ .-.+ .-||..|.. |... ..|..||..|-
T Consensus 3 ~C~~~I~~~~~~~~~~~-----~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~ 54 (58)
T PF00412_consen 3 RCGKPIYGTEIVIKAMG-----KFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCY 54 (58)
T ss_dssp TTSSBESSSSEEEEETT-----EEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHH
T ss_pred CCCCCccCcEEEEEeCC-----cEEEccccccCCCCCccCCCeeEeECCEEECHHHH
Confidence 4666543 3333 3444 557888872 3222 25678887664
No 134
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=20.48 E-value=40 Score=30.52 Aligned_cols=27 Identities=33% Similarity=0.902 Sum_probs=13.2
Q ss_pred CCcee-eeCCCCC----------C-CceecCCCCCCCccee
Q 025765 191 EPTYC-VCNQVSY----------G-EMVACDNPNCKIEWFH 219 (248)
Q Consensus 191 ~~~~C-~C~~~~~----------g-~mi~Cd~~~C~~~WfH 219 (248)
...|| +|+.... | -+..|.- |..+|.+
T Consensus 171 ~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~--C~t~W~~ 209 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRGGEREGKRYLHCSL--CGTEWRF 209 (290)
T ss_dssp T-SS-TTT---EEEEEEE------EEEEEETT--T--EEE-
T ss_pred cCCcCCCCCCcCceEEEecCCCCccEEEEcCC--CCCeeee
Confidence 35799 9998621 3 3788999 7788954
Done!