Query 034182
Match_columns 102
No_of_seqs 140 out of 429
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 10:41:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034182.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034182hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3456 NADH:ubiquinone oxidor 100.0 3.1E-37 6.8E-42 219.3 6.1 99 2-102 1-120 (120)
2 PF10276 zf-CHCC: Zinc-finger 99.8 3.7E-20 8E-25 110.8 3.7 39 58-97 1-40 (40)
3 COG4391 Uncharacterized protei 99.7 5.1E-18 1.1E-22 110.0 4.7 47 52-99 15-61 (62)
4 PLN02294 cytochrome c oxidase 98.3 7.1E-07 1.5E-11 67.9 4.9 41 58-99 114-154 (174)
5 cd00924 Cyt_c_Oxidase_Vb Cytoc 98.2 3.1E-06 6.8E-11 58.8 4.5 41 58-101 54-94 (97)
6 PF01215 COX5B: Cytochrome c o 98.1 2.8E-06 6E-11 62.3 3.8 40 58-99 86-125 (136)
7 PTZ00043 cytochrome c oxidase 97.9 1.4E-05 3E-10 63.9 4.3 43 58-101 154-196 (268)
8 KOG3352 Cytochrome c oxidase, 97.6 5.2E-05 1.1E-09 56.8 3.6 40 58-100 108-147 (153)
9 PF09538 FYDLN_acid: Protein o 96.6 0.00083 1.8E-08 47.4 1.1 21 78-99 19-39 (108)
10 TIGR02300 FYDLN_acid conserved 94.7 0.013 2.9E-07 42.9 1.0 20 78-98 19-38 (129)
11 PRK00398 rpoP DNA-directed RNA 93.4 0.063 1.4E-06 31.8 2.0 21 80-100 14-35 (46)
12 COG4530 Uncharacterized protei 90.1 0.12 2.6E-06 37.7 0.7 21 77-98 18-38 (129)
13 PF13465 zf-H2C2_2: Zinc-finge 89.8 0.22 4.8E-06 26.3 1.4 15 84-98 12-26 (26)
14 PF00096 zf-C2H2: Zinc finger, 89.1 0.16 3.5E-06 25.3 0.6 12 88-99 2-13 (23)
15 PF13913 zf-C2HC_2: zinc-finge 87.8 0.21 4.6E-06 26.5 0.5 12 87-98 3-14 (25)
16 smart00659 RPOLCX RNA polymera 87.3 0.44 9.6E-06 28.6 1.7 19 80-98 13-31 (44)
17 COG1996 RPC10 DNA-directed RNA 85.8 0.52 1.1E-05 29.4 1.5 16 83-98 21-36 (49)
18 PF13878 zf-C2H2_3: zinc-finge 84.8 0.71 1.5E-05 27.1 1.7 21 78-98 3-25 (41)
19 PF13894 zf-C2H2_4: C2H2-type 84.7 0.48 1E-05 22.9 0.8 11 88-98 2-12 (24)
20 PF02892 zf-BED: BED zinc fing 84.0 0.72 1.6E-05 26.4 1.5 17 83-99 13-29 (45)
21 PF08792 A2L_zn_ribbon: A2L zi 80.7 1.7 3.6E-05 24.7 2.2 24 72-97 9-32 (33)
22 TIGR02098 MJ0042_CXXC MJ0042 f 79.7 1.2 2.7E-05 24.9 1.4 12 86-97 25-36 (38)
23 PF03604 DNA_RNApol_7kD: DNA d 79.5 1.3 2.8E-05 25.1 1.4 18 81-98 12-29 (32)
24 PF05605 zf-Di19: Drought indu 78.4 0.86 1.9E-05 27.5 0.5 11 87-97 3-13 (54)
25 smart00614 ZnF_BED BED zinc fi 75.5 2.2 4.8E-05 25.4 1.7 15 85-99 17-31 (50)
26 PHA02768 hypothetical protein; 74.6 0.83 1.8E-05 29.0 -0.3 13 88-100 7-19 (55)
27 PF13240 zinc_ribbon_2: zinc-r 73.9 1.3 2.9E-05 23.1 0.4 13 84-96 11-23 (23)
28 cd00498 Hsp33 Heat shock prote 71.9 1.8 3.8E-05 34.2 0.9 13 86-98 262-274 (275)
29 PF02748 PyrI_C: Aspartate car 70.7 2.9 6.3E-05 25.9 1.5 23 77-99 25-48 (52)
30 COG1579 Zn-ribbon protein, pos 69.7 1.8 4E-05 34.4 0.5 16 84-99 219-234 (239)
31 PF08271 TF_Zn_Ribbon: TFIIB z 69.6 6 0.00013 22.9 2.6 22 74-96 8-29 (43)
32 TIGR03365 Bsubt_queE 7-cyano-7 69.6 4 8.7E-05 31.3 2.4 33 63-97 12-44 (238)
33 PF01430 HSP33: Hsp33 protein; 69.5 1.9 4.2E-05 33.9 0.6 14 86-99 266-279 (280)
34 PF14369 zf-RING_3: zinc-finge 69.4 3.5 7.5E-05 23.5 1.5 14 85-98 20-33 (35)
35 smart00154 ZnF_AN1 AN1-like Zi 68.4 3.3 7.2E-05 24.0 1.3 17 86-102 12-28 (39)
36 PRK00114 hslO Hsp33-like chape 68.3 2.3 5E-05 34.0 0.8 14 86-99 268-281 (293)
37 COG1281 Disulfide bond chapero 66.4 2.9 6.2E-05 34.2 1.0 15 86-100 266-280 (286)
38 PF06957 COPI_C: Coatomer (COP 66.1 3.1 6.7E-05 35.6 1.2 16 84-99 378-393 (422)
39 PF13408 Zn_ribbon_recom: Reco 65.6 3.3 7.2E-05 24.3 1.0 14 85-98 4-17 (58)
40 TIGR02605 CxxC_CxxC_SSSS putat 65.3 5 0.00011 23.6 1.7 18 77-94 17-34 (52)
41 PF13719 zinc_ribbon_5: zinc-r 64.3 3.6 7.8E-05 23.4 0.9 13 87-99 3-15 (37)
42 PF13248 zf-ribbon_3: zinc-rib 64.2 2.7 5.8E-05 22.2 0.3 12 84-95 14-25 (26)
43 PF08685 GON: GON domain; Int 63.7 9.9 0.00021 29.7 3.5 33 61-96 30-76 (201)
44 PF14353 CpXC: CpXC protein 63.5 4 8.6E-05 28.2 1.2 14 86-99 38-51 (128)
45 PF15616 TerY-C: TerY-C metal 62.3 5.7 0.00012 29.1 1.9 18 78-95 97-114 (131)
46 PF12660 zf-TFIIIC: Putative z 62.0 2.8 6.1E-05 28.7 0.2 39 59-98 29-67 (99)
47 PF02591 DUF164: Putative zinc 62.0 4.6 9.9E-05 24.5 1.1 39 53-95 16-55 (56)
48 PF09237 GAGA: GAGA factor; I 61.2 5.1 0.00011 25.5 1.2 20 80-99 18-37 (54)
49 PF14446 Prok-RING_1: Prokaryo 61.1 5.6 0.00012 25.2 1.4 16 83-98 18-33 (54)
50 smart00647 IBR In Between Ring 60.7 8.5 0.00019 22.7 2.2 36 58-98 15-52 (64)
51 KOG2462 C2H2-type Zn-finger pr 59.3 4.4 9.6E-05 33.2 0.9 18 81-98 156-173 (279)
52 KOG3623 Homeobox transcription 59.1 2.7 5.9E-05 39.1 -0.3 23 79-101 271-296 (1007)
53 PF01485 IBR: IBR domain; Int 59.1 4.8 0.0001 23.8 0.8 34 58-97 15-51 (64)
54 KOG1088 Uncharacterized conser 58.9 4.9 0.00011 29.4 1.0 15 84-98 96-110 (124)
55 PF09723 Zn-ribbon_8: Zinc rib 58.8 8.6 0.00019 22.3 1.9 18 77-94 17-34 (42)
56 PF06676 DUF1178: Protein of u 58.2 2.3 5E-05 31.6 -0.8 37 61-97 5-43 (148)
57 smart00355 ZnF_C2H2 zinc finge 57.8 4.1 9E-05 19.4 0.3 12 88-99 2-13 (26)
58 PF01428 zf-AN1: AN1-like Zinc 56.3 6 0.00013 23.0 0.9 15 86-100 13-27 (43)
59 PF05129 Elf1: Transcription e 55.2 9.2 0.0002 25.5 1.8 37 59-99 20-59 (81)
60 COG1645 Uncharacterized Zn-fin 55.0 6.4 0.00014 28.9 1.1 16 83-98 41-56 (131)
61 PF14447 Prok-RING_4: Prokaryo 53.2 7.4 0.00016 24.8 1.0 28 72-99 25-52 (55)
62 smart00834 CxxC_CXXC_SSSS Puta 52.9 12 0.00026 20.7 1.8 13 84-96 24-36 (41)
63 PF12171 zf-C2H2_jaz: Zinc-fin 52.8 7.3 0.00016 20.2 0.8 12 88-99 3-14 (27)
64 TIGR00240 ATCase_reg aspartate 51.2 13 0.00028 27.9 2.2 41 59-99 101-145 (150)
65 PRK00893 aspartate carbamoyltr 51.0 13 0.00027 28.0 2.1 41 59-99 103-147 (152)
66 PF04475 DUF555: Protein of un 50.9 9.4 0.0002 27.1 1.3 20 77-97 39-58 (102)
67 COG0602 NrdG Organic radical a 50.5 13 0.00029 28.3 2.2 31 65-97 14-44 (212)
68 PF13717 zinc_ribbon_4: zinc-r 49.8 8.9 0.00019 21.8 0.9 13 87-99 3-15 (36)
69 PF06226 DUF1007: Protein of u 48.7 9.7 0.00021 28.9 1.2 13 70-82 15-27 (212)
70 smart00507 HNHc HNH nucleases. 48.5 6.3 0.00014 21.7 0.1 11 87-97 11-21 (52)
71 PF03966 Trm112p: Trm112p-like 48.5 9.8 0.00021 23.9 1.0 15 84-98 51-65 (68)
72 PHA00616 hypothetical protein 48.3 4.9 0.00011 24.4 -0.4 12 88-99 3-14 (44)
73 PRK00432 30S ribosomal protein 48.1 12 0.00026 22.8 1.4 13 85-97 36-48 (50)
74 PRK03922 hypothetical protein; 48.0 11 0.00025 27.1 1.4 21 76-97 40-60 (113)
75 PF14690 zf-ISL3: zinc-finger 47.4 8.3 0.00018 22.0 0.5 11 86-96 2-12 (47)
76 PRK01402 hslO Hsp33-like chape 46.7 9.1 0.0002 31.5 0.9 14 86-99 308-321 (328)
77 PF12756 zf-C2H2_2: C2H2 type 46.2 12 0.00026 23.4 1.2 14 85-98 49-62 (100)
78 PF10571 UPF0547: Uncharacteri 44.7 10 0.00022 20.4 0.6 13 85-97 13-25 (26)
79 PF01783 Ribosomal_L32p: Ribos 44.6 17 0.00037 22.4 1.7 7 87-93 40-46 (56)
80 PF04423 Rad50_zn_hook: Rad50 44.1 7.8 0.00017 23.3 0.1 14 86-99 20-33 (54)
81 COG5189 SFP1 Putative transcri 43.3 11 0.00024 32.1 0.9 17 82-98 394-410 (423)
82 TIGR01031 rpmF_bact ribosomal 43.2 16 0.00034 22.7 1.4 7 87-93 40-46 (55)
83 TIGR02159 PA_CoA_Oxy4 phenylac 43.2 11 0.00023 27.7 0.7 13 86-98 105-117 (146)
84 PF10013 DUF2256: Uncharacteri 42.1 11 0.00024 22.9 0.5 12 86-97 8-19 (42)
85 PRK03824 hypA hydrogenase nick 41.9 12 0.00025 26.9 0.7 21 75-95 96-116 (135)
86 COG1655 Uncharacterized protei 41.9 9.9 0.00022 30.9 0.4 17 84-100 17-33 (267)
87 smart00531 TFIIE Transcription 41.8 18 0.00039 25.9 1.6 45 54-100 92-137 (147)
88 PF13912 zf-C2H2_6: C2H2-type 41.4 13 0.00028 18.8 0.7 12 87-98 2-13 (27)
89 COG2093 DNA-directed RNA polym 41.1 15 0.00033 24.1 1.1 12 84-95 16-27 (64)
90 COG1781 PyrI Aspartate carbamo 41.0 20 0.00043 27.1 1.8 57 43-99 80-148 (153)
91 cd00729 rubredoxin_SM Rubredox 41.0 17 0.00037 20.4 1.1 11 84-94 16-26 (34)
92 PF00653 BIR: Inhibitor of Apo 40.1 25 0.00054 21.9 1.9 17 81-97 31-47 (70)
93 cd00022 BIR Baculoviral inhibi 39.1 23 0.0005 21.6 1.6 15 84-98 32-46 (69)
94 COG1885 Uncharacterized protei 38.9 18 0.0004 26.1 1.3 23 74-97 38-60 (115)
95 PTZ00218 40S ribosomal protein 38.8 20 0.00044 22.7 1.4 23 70-96 4-26 (54)
96 COG4049 Uncharacterized protei 38.6 13 0.00028 24.3 0.4 15 84-98 15-29 (65)
97 PF12760 Zn_Tnp_IS1595: Transp 37.0 17 0.00036 21.3 0.7 10 86-95 18-27 (46)
98 PRK14892 putative transcriptio 37.0 31 0.00068 24.0 2.2 35 59-98 19-54 (99)
99 cd00085 HNHc HNH nucleases; HN 36.0 16 0.00034 20.4 0.5 10 87-96 12-21 (57)
100 TIGR00510 lipA lipoate synthas 35.4 30 0.00065 28.0 2.2 62 35-97 19-85 (302)
101 PRK11827 hypothetical protein; 34.4 35 0.00077 21.8 2.0 31 61-99 8-39 (60)
102 PF02489 Herpes_glycop_H: Herp 34.2 18 0.00039 31.7 0.8 34 61-97 537-572 (657)
103 COG1656 Uncharacterized conser 33.7 17 0.00037 27.7 0.5 23 75-99 121-143 (165)
104 cd00350 rubredoxin_like Rubred 33.6 28 0.0006 19.1 1.3 12 84-95 15-26 (33)
105 smart00238 BIR Baculoviral inh 33.5 34 0.00074 21.0 1.8 14 85-98 35-48 (71)
106 PHA03296 envelope glycoprotein 33.4 23 0.00049 32.8 1.3 23 74-97 682-704 (814)
107 PF11793 FANCL_C: FANCL C-term 32.9 23 0.0005 22.6 1.0 13 86-98 55-67 (70)
108 PF13824 zf-Mss51: Zinc-finger 32.9 13 0.00027 23.7 -0.3 15 84-98 12-26 (55)
109 PRK12495 hypothetical protein; 32.4 7.6 0.00016 31.0 -1.6 55 35-98 16-70 (226)
110 PRK13376 pyrB bifunctional asp 31.9 98 0.0021 27.3 4.9 37 62-99 479-520 (525)
111 TIGR01206 lysW lysine biosynth 31.4 38 0.00083 21.1 1.7 12 86-97 22-33 (54)
112 PHA00732 hypothetical protein 30.9 21 0.00046 23.6 0.5 13 88-100 29-41 (79)
113 PF14803 Nudix_N_2: Nudix N-te 30.7 48 0.001 18.8 1.9 27 71-97 5-33 (34)
114 COG1592 Rubrerythrin [Energy p 30.1 25 0.00054 26.6 0.9 17 78-95 142-158 (166)
115 smart00746 TRASH metallochaper 29.7 24 0.00052 17.1 0.5 9 89-97 1-9 (39)
116 PF05191 ADK_lid: Adenylate ki 29.7 25 0.00055 20.1 0.7 12 87-98 2-13 (36)
117 KOG1280 Uncharacterized conser 29.4 24 0.00052 30.1 0.7 18 78-95 71-88 (381)
118 PHA00733 hypothetical protein 29.0 32 0.00069 24.4 1.2 16 82-97 69-84 (128)
119 PF09180 ProRS-C_1: Prolyl-tRN 28.0 31 0.00067 21.9 0.9 12 84-95 46-57 (68)
120 COG4888 Uncharacterized Zn rib 27.0 39 0.00084 24.1 1.3 37 58-99 19-59 (104)
121 PF13821 DUF4187: Domain of un 26.4 24 0.00051 22.0 0.2 15 85-99 26-40 (55)
122 KOG0292 Vesicle coat complex C 26.3 32 0.00069 33.0 1.0 21 78-98 1155-1176(1202)
123 PF10058 DUF2296: Predicted in 25.9 31 0.00068 21.3 0.7 9 86-94 44-52 (54)
124 PF14569 zf-UDP: Zinc-binding 25.9 23 0.0005 24.2 0.1 16 83-98 48-63 (80)
125 TIGR03829 YokU_near_AblA uncha 25.5 60 0.0013 22.4 2.0 36 63-99 4-48 (89)
126 PF13451 zf-trcl: Probable zin 25.1 37 0.0008 21.0 0.8 15 84-98 2-16 (49)
127 smart00451 ZnF_U1 U1-like zinc 24.8 41 0.0009 17.7 0.9 13 86-98 3-15 (35)
128 PRK00420 hypothetical protein; 24.7 68 0.0015 22.8 2.2 16 83-98 37-52 (112)
129 PF08274 PhnA_Zn_Ribbon: PhnA 23.9 30 0.00065 19.3 0.2 14 87-100 3-16 (30)
130 PRK03681 hypA hydrogenase nick 23.5 1.1E+02 0.0023 21.3 3.0 30 58-95 67-96 (114)
131 PF07503 zf-HYPF: HypF finger; 23.2 46 0.00099 19.0 0.9 15 85-99 20-34 (35)
132 KOG3993 Transcription factor ( 22.9 25 0.00054 30.9 -0.3 15 84-98 354-368 (500)
133 cd00150 PlantTI Plant trypsin 22.9 48 0.001 18.4 0.9 10 75-84 2-11 (27)
134 TIGR03831 YgiT_finger YgiT-typ 22.7 63 0.0014 17.8 1.5 13 87-99 33-45 (46)
135 PRK00564 hypA hydrogenase nick 22.7 40 0.00087 23.5 0.8 12 85-96 87-98 (117)
136 PF07282 OrfB_Zn_ribbon: Putat 22.3 72 0.0016 19.5 1.8 25 71-97 33-57 (69)
137 PF03119 DNA_ligase_ZBD: NAD-d 22.1 41 0.00088 18.2 0.6 12 88-99 1-12 (28)
138 COG5034 TNG2 Chromatin remodel 21.8 53 0.0011 26.9 1.4 31 59-94 232-269 (271)
139 COG2835 Uncharacterized conser 21.8 96 0.0021 20.0 2.3 31 61-99 8-39 (60)
140 PF10080 DUF2318: Predicted me 21.4 48 0.001 23.1 1.0 20 78-99 46-65 (102)
141 TIGR02646 conserved hypothetic 21.2 45 0.00098 23.7 0.8 14 84-97 22-35 (144)
142 PF14921 APCDDC: Adenomatosis 21.1 43 0.00094 26.8 0.7 17 86-102 218-234 (240)
143 smart00286 PTI Plant trypsin i 20.4 46 0.001 18.8 0.5 20 74-93 3-29 (29)
144 cd04487 RecJ_OBF2_like RecJ_OB 20.4 1.1E+02 0.0024 19.5 2.4 30 56-91 2-32 (73)
145 PF01927 Mut7-C: Mut7-C RNAse 20.4 56 0.0012 23.3 1.1 38 59-98 92-136 (147)
146 cd03528 Rieske_RO_ferredoxin R 20.4 62 0.0013 20.6 1.2 16 84-99 55-70 (98)
No 1
>KOG3456 consensus NADH:ubiquinone oxidoreductase, NDUFS6/13 kDa subunit [Energy production and conversion]
Probab=100.00 E-value=3.1e-37 Score=219.32 Aligned_cols=99 Identities=56% Similarity=0.974 Sum_probs=87.2
Q ss_pred hhhHHHHHHHhcCCCCC-----cceeeeeecccc--cccceeee--------------ccCCCChhhhhccCCCEEecCe
Q 034182 2 ASSLLKILIKSSNLPST-----TRNLTAVANQIS--EHTAKWMQ--------------DVSKKSPMELINEVPPIKVEGR 60 (102)
Q Consensus 2 ~~~~l~~~~r~~~~~~~-----~r~~~~~~~~~~--~ht~~~~~--------------~~~~~~a~elI~e~p~i~V~~~ 60 (102)
||++|+++++...+|+. +|+|++++ +.. +||+|.+| +-|+++||+||.|+||++|++|
T Consensus 1 as~~l~~~lsr~~l~~rs~pl~~r~~~~r~-~~ekvThtGq~~D~~Dyr~~rf~~~kk~vn~n~~m~LI~e~Pp~e~d~R 79 (120)
T KOG3456|consen 1 ASNLLKALLSRQGLPSRSTPLTRRNFSVRT-QFEKVTHTGQVTDQSDYRGNRFVKWKKDVNENSAMELISEVPPIEVDGR 79 (120)
T ss_pred CchHHHHHHhcCCCcccccccccccceeec-ccceeeecCcccchHHHhHHHHHhhhhhcCccchhhhhhcCChhhccce
Confidence 78999999888877665 99999987 322 46665554 4489999999999999999999
Q ss_pred EEeecCCCCCCCCCCceEEEcCCCCceecCCCCcccccccCC
Q 034182 61 IVACEGDSNPALGHPIEFICLDLKEPAICKYCGLRYVQDHHH 102 (102)
Q Consensus 61 ~v~CdG~~~palGHPrVyI~Ld~~~~~~CpYCG~ry~~~~hh 102 (102)
+|+|||+++ |||||+||||||+++...|+|||+||+++|||
T Consensus 80 VV~CdGg~~-aLGHPkvyInLDk~~~~~CgYCGlrf~~dHhh 120 (120)
T KOG3456|consen 80 VVACDGGTP-ALGHPKVYINLDKPGPHICGYCGLRFVQDHHH 120 (120)
T ss_pred EEEecCCCC-CCCCCeEEEEcCCCCCcccccchhhhhhhhcC
Confidence 999999985 89999999999999999999999999999998
No 2
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=99.80 E-value=3.7e-20 Score=110.82 Aligned_cols=39 Identities=51% Similarity=1.140 Sum_probs=34.2
Q ss_pred cCeEEeecCCCCCCCCCCceEEEcCCC-CceecCCCCcccc
Q 034182 58 EGRIVACEGDSNPALGHPIEFICLDLK-EPAICKYCGLRYV 97 (102)
Q Consensus 58 ~~~~v~CdG~~~palGHPrVyI~Ld~~-~~~~CpYCG~ry~ 97 (102)
++++|+|||+++ ++|||||||+|+++ +++.|||||++|+
T Consensus 1 ~~~~v~CdG~~~-~lgHPrVyl~l~~~~~~~~CpYCg~~yv 40 (40)
T PF10276_consen 1 DGRRVSCDGGGG-ALGHPRVYLNLDDEPGPVVCPYCGTRYV 40 (40)
T ss_dssp -SSEEEEEESST-TSCCCCEEEE-TTTTCEEEETTTTEEEE
T ss_pred CCcEEEeCCCCC-CCCCCeEEEecCCCCCeEECCCCCCEEC
Confidence 478999999988 59999999999996 6799999999996
No 3
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.72 E-value=5.1e-18 Score=109.98 Aligned_cols=47 Identities=26% Similarity=0.573 Sum_probs=42.9
Q ss_pred CCCEEecCeEEeecCCCCCCCCCCceEEEcCCCCceecCCCCcccccc
Q 034182 52 VPPIKVEGRIVACEGDSNPALGHPIEFICLDLKEPAICKYCGLRYVQD 99 (102)
Q Consensus 52 ~p~i~V~~~~v~CdG~~~palGHPrVyI~Ld~~~~~~CpYCG~ry~~~ 99 (102)
...|.+++++++|+|.++| ++||||||+|.++++++|||||++|++.
T Consensus 15 ~~~I~~~~~~l~C~g~~~p-~~HPrV~L~mg~~gev~CPYC~t~y~l~ 61 (62)
T COG4391 15 HETIEIGDLPLMCPGPEPP-NDHPRVFLDMGDEGEVVCPYCSTRYRLN 61 (62)
T ss_pred ceEEEeCCeeEEcCCCCCC-CCCCEEEEEcCCCCcEecCccccEEEec
Confidence 3467789999999999985 9999999999999999999999999874
No 4
>PLN02294 cytochrome c oxidase subunit Vb
Probab=98.34 E-value=7.1e-07 Score=67.91 Aligned_cols=41 Identities=22% Similarity=0.481 Sum_probs=37.3
Q ss_pred cCeEEeecCCCCCCCCCCceEEEcCCCCceecCCCCcccccc
Q 034182 58 EGRIVACEGDSNPALGHPIEFICLDLKEPAICKYCGLRYVQD 99 (102)
Q Consensus 58 ~~~~v~CdG~~~palGHPrVyI~Ld~~~~~~CpYCG~ry~~~ 99 (102)
+.|+|.|.|+.+ ...|-.+|+.|.+..+.+||.||..|+++
T Consensus 114 d~RiVGCtg~~~-eDsh~v~Wf~L~kGkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 114 DKRIVGCPGGEG-EDEHDVVWFWLEKGKSFECPVCTQYFELE 154 (174)
T ss_pred CceEEeeCCCCC-CCCceeEEEEecCCCceeCCCCCCEEEEE
Confidence 699999999654 57999999999999999999999999986
No 5
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=98.16 E-value=3.1e-06 Score=58.80 Aligned_cols=41 Identities=24% Similarity=0.543 Sum_probs=37.5
Q ss_pred cCeEEeecCCCCCCCCCCceEEEcCCCCceecCCCCcccccccC
Q 034182 58 EGRIVACEGDSNPALGHPIEFICLDLKEPAICKYCGLRYVQDHH 101 (102)
Q Consensus 58 ~~~~v~CdG~~~palGHPrVyI~Ld~~~~~~CpYCG~ry~~~~h 101 (102)
+.|+|.|.|..+ .|-.+|+.|.+..+.+|+.||.-|+++++
T Consensus 54 ~~RiVGC~g~~~---~h~v~W~~l~~g~~~rC~eCG~~fkL~~v 94 (97)
T cd00924 54 DKRIVGCICEPD---SHDVIWMWLEKGKPKRCPECGHVFKLVDV 94 (97)
T ss_pred CCeEEeeeCCCC---CceEEEEEEeCCCceeCCCCCcEEEEEEC
Confidence 699999999843 89999999999999999999999999865
No 6
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=98.12 E-value=2.8e-06 Score=62.34 Aligned_cols=40 Identities=28% Similarity=0.633 Sum_probs=35.0
Q ss_pred cCeEEeecCCCCCCCCCCceEEEcCCCCceecCCCCcccccc
Q 034182 58 EGRIVACEGDSNPALGHPIEFICLDLKEPAICKYCGLRYVQD 99 (102)
Q Consensus 58 ~~~~v~CdG~~~palGHPrVyI~Ld~~~~~~CpYCG~ry~~~ 99 (102)
+.|+|.|.|..+ ..|-.+|+.|.+..+.+||.||.-|+++
T Consensus 86 ~~RiVGC~g~~~--~sH~v~W~~l~~g~~~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 86 DERIVGCTGEPD--DSHDVIWFWLHKGKPQRCPECGQVFKLK 125 (136)
T ss_dssp SCEEEEESSSTT---SSS-EEEEEETTSEEEETTTEEEEEEE
T ss_pred CceEEeeccCCC--CcceeEEEEEeCCCccCCCCCCeEEEEE
Confidence 799999999854 6999999999998899999999999985
No 7
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=97.90 E-value=1.4e-05 Score=63.86 Aligned_cols=43 Identities=16% Similarity=0.226 Sum_probs=38.1
Q ss_pred cCeEEeecCCCCCCCCCCceEEEcCCCCceecCCCCcccccccC
Q 034182 58 EGRIVACEGDSNPALGHPIEFICLDLKEPAICKYCGLRYVQDHH 101 (102)
Q Consensus 58 ~~~~v~CdG~~~palGHPrVyI~Ld~~~~~~CpYCG~ry~~~~h 101 (102)
+.|+|.|.|+.+ ...|-.+|+.+.+..+.+||.||..|+++++
T Consensus 154 deRyVGCTGg~~-EDeH~VvWFwLrEGkpqRCpECGqVFKLVr~ 196 (268)
T PTZ00043 154 TERVVGCTGGTG-EHEHVPLWFRCREGFLYRCGECDQIFMLVRV 196 (268)
T ss_pred CceEEeccCCCc-cCCceeEEEEecCCCCccCCCCCcEEEEEEE
Confidence 689999999755 4689999999998889999999999998763
No 8
>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]
Probab=97.64 E-value=5.2e-05 Score=56.81 Aligned_cols=40 Identities=28% Similarity=0.528 Sum_probs=35.1
Q ss_pred cCeEEeecCCCCCCCCCCceEEEcCCCCceecCCCCccccccc
Q 034182 58 EGRIVACEGDSNPALGHPIEFICLDLKEPAICKYCGLRYVQDH 100 (102)
Q Consensus 58 ~~~~v~CdG~~~palGHPrVyI~Ld~~~~~~CpYCG~ry~~~~ 100 (102)
+-|+|.| |.+ ...|+.+|+-|.|.+..+||.||.-|+++.
T Consensus 108 d~RiVGC-~c~--eD~~~V~Wmwl~Kge~~rc~eCG~~fkL~~ 147 (153)
T KOG3352|consen 108 DKRIVGC-GCE--EDSHAVVWMWLEKGETQRCPECGHYFKLVP 147 (153)
T ss_pred CceEEee-ccc--CCCcceEEEEEEcCCcccCCcccceEEeee
Confidence 6899999 443 479999999999999999999999999874
No 9
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=96.61 E-value=0.00083 Score=47.35 Aligned_cols=21 Identities=29% Similarity=0.819 Sum_probs=18.7
Q ss_pred EEEcCCCCceecCCCCcccccc
Q 034182 78 FICLDLKEPAICKYCGLRYVQD 99 (102)
Q Consensus 78 yI~Ld~~~~~~CpYCG~ry~~~ 99 (102)
|+.|++ .+++|||||+.|...
T Consensus 19 FYDLnk-~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 19 FYDLNK-DPIVCPKCGTEFPPE 39 (108)
T ss_pred hccCCC-CCccCCCCCCccCcc
Confidence 999998 899999999999653
No 10
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=94.73 E-value=0.013 Score=42.93 Aligned_cols=20 Identities=30% Similarity=0.597 Sum_probs=17.8
Q ss_pred EEEcCCCCceecCCCCccccc
Q 034182 78 FICLDLKEPAICKYCGLRYVQ 98 (102)
Q Consensus 78 yI~Ld~~~~~~CpYCG~ry~~ 98 (102)
|+.|++ .+++|||||..|..
T Consensus 19 FYDLnk-~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 19 FYDLNR-RPAVSPYTGEQFPP 38 (129)
T ss_pred ccccCC-CCccCCCcCCccCc
Confidence 999997 79999999999854
No 11
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=93.45 E-value=0.063 Score=31.75 Aligned_cols=21 Identities=33% Similarity=0.588 Sum_probs=15.1
Q ss_pred EcCCCC-ceecCCCCccccccc
Q 034182 80 CLDLKE-PAICKYCGLRYVQDH 100 (102)
Q Consensus 80 ~Ld~~~-~~~CpYCG~ry~~~~ 100 (102)
.++... ...|||||.++..++
T Consensus 14 ~~~~~~~~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 14 ELDEYGTGVRCPYCGYRILFKE 35 (46)
T ss_pred EECCCCCceECCCCCCeEEEcc
Confidence 344433 789999999987654
No 12
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.05 E-value=0.12 Score=37.68 Aligned_cols=21 Identities=29% Similarity=0.627 Sum_probs=17.2
Q ss_pred eEEEcCCCCceecCCCCccccc
Q 034182 77 EFICLDLKEPAICKYCGLRYVQ 98 (102)
Q Consensus 77 VyI~Ld~~~~~~CpYCG~ry~~ 98 (102)
-|++|++ .+++|||||..|-+
T Consensus 18 KFYDLNr-dPiVsPytG~s~P~ 38 (129)
T COG4530 18 KFYDLNR-DPIVSPYTGKSYPR 38 (129)
T ss_pred hhhccCC-CccccCcccccchH
Confidence 4888885 58999999999953
No 13
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=89.77 E-value=0.22 Score=26.33 Aligned_cols=15 Identities=33% Similarity=0.999 Sum_probs=12.6
Q ss_pred CCceecCCCCccccc
Q 034182 84 KEPAICKYCGLRYVQ 98 (102)
Q Consensus 84 ~~~~~CpYCG~ry~~ 98 (102)
+.+-.|++||..|..
T Consensus 12 ~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 12 EKPYKCPYCGKSFSN 26 (26)
T ss_dssp SSSEEESSSSEEESS
T ss_pred CCCCCCCCCcCeeCc
Confidence 567899999999963
No 14
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=89.14 E-value=0.16 Score=25.29 Aligned_cols=12 Identities=25% Similarity=0.797 Sum_probs=10.2
Q ss_pred ecCCCCcccccc
Q 034182 88 ICKYCGLRYVQD 99 (102)
Q Consensus 88 ~CpYCG~ry~~~ 99 (102)
.|++||..|...
T Consensus 2 ~C~~C~~~f~~~ 13 (23)
T PF00096_consen 2 KCPICGKSFSSK 13 (23)
T ss_dssp EETTTTEEESSH
T ss_pred CCCCCCCccCCH
Confidence 699999999753
No 15
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=87.79 E-value=0.21 Score=26.52 Aligned_cols=12 Identities=25% Similarity=0.805 Sum_probs=10.3
Q ss_pred eecCCCCccccc
Q 034182 87 AICKYCGLRYVQ 98 (102)
Q Consensus 87 ~~CpYCG~ry~~ 98 (102)
..||+||++|..
T Consensus 3 ~~C~~CgR~F~~ 14 (25)
T PF13913_consen 3 VPCPICGRKFNP 14 (25)
T ss_pred CcCCCCCCEECH
Confidence 579999999964
No 16
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=87.32 E-value=0.44 Score=28.60 Aligned_cols=19 Identities=26% Similarity=0.592 Sum_probs=14.0
Q ss_pred EcCCCCceecCCCCccccc
Q 034182 80 CLDLKEPAICKYCGLRYVQ 98 (102)
Q Consensus 80 ~Ld~~~~~~CpYCG~ry~~ 98 (102)
+++....+.|||||-+-..
T Consensus 13 ~~~~~~~irC~~CG~rIly 31 (44)
T smart00659 13 EIKSKDVVRCRECGYRILY 31 (44)
T ss_pred ecCCCCceECCCCCceEEE
Confidence 4555678999999987543
No 17
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=85.79 E-value=0.52 Score=29.37 Aligned_cols=16 Identities=31% Similarity=0.665 Sum_probs=12.0
Q ss_pred CCCceecCCCCccccc
Q 034182 83 LKEPAICKYCGLRYVQ 98 (102)
Q Consensus 83 ~~~~~~CpYCG~ry~~ 98 (102)
......|||||-+-..
T Consensus 21 ~~~~irCp~Cg~rIl~ 36 (49)
T COG1996 21 ETRGIRCPYCGSRILV 36 (49)
T ss_pred ccCceeCCCCCcEEEE
Confidence 3458899999987543
No 18
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=84.81 E-value=0.71 Score=27.14 Aligned_cols=21 Identities=29% Similarity=0.653 Sum_probs=16.9
Q ss_pred EEEcCCCC--ceecCCCCccccc
Q 034182 78 FICLDLKE--PAICKYCGLRYVQ 98 (102)
Q Consensus 78 yI~Ld~~~--~~~CpYCG~ry~~ 98 (102)
.|+++... ..+|+-||..|..
T Consensus 3 ~Ld~gq~~~~~~~C~~CgM~Y~~ 25 (41)
T PF13878_consen 3 ILDLGQKSFGATTCPTCGMLYSP 25 (41)
T ss_pred EEeCCCCccCCcCCCCCCCEECC
Confidence 57777654 7899999999974
No 19
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=84.75 E-value=0.48 Score=22.86 Aligned_cols=11 Identities=27% Similarity=0.830 Sum_probs=7.8
Q ss_pred ecCCCCccccc
Q 034182 88 ICKYCGLRYVQ 98 (102)
Q Consensus 88 ~CpYCG~ry~~ 98 (102)
.|++||..|..
T Consensus 2 ~C~~C~~~~~~ 12 (24)
T PF13894_consen 2 QCPICGKSFRS 12 (24)
T ss_dssp E-SSTS-EESS
T ss_pred CCcCCCCcCCc
Confidence 69999999975
No 20
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=84.02 E-value=0.72 Score=26.44 Aligned_cols=17 Identities=41% Similarity=0.647 Sum_probs=10.6
Q ss_pred CCCceecCCCCcccccc
Q 034182 83 LKEPAICKYCGLRYVQD 99 (102)
Q Consensus 83 ~~~~~~CpYCG~ry~~~ 99 (102)
.+..+.|.||+..|...
T Consensus 13 ~~~~a~C~~C~~~~~~~ 29 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYS 29 (45)
T ss_dssp CSS-EEETTTTEE----
T ss_pred CcCeEEeCCCCeEEeeC
Confidence 46789999999998753
No 21
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=80.72 E-value=1.7 Score=24.70 Aligned_cols=24 Identities=17% Similarity=0.382 Sum_probs=18.4
Q ss_pred CCCCceEEEcCCCCceecCCCCcccc
Q 034182 72 LGHPIEFICLDLKEPAICKYCGLRYV 97 (102)
Q Consensus 72 lGHPrVyI~Ld~~~~~~CpYCG~ry~ 97 (102)
-+|+.||. .+++.-.|+-||..|.
T Consensus 9 C~~~~i~~--~~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 9 CGGNGIVN--KEDDYEVCIFCGSSFP 32 (33)
T ss_pred CCCCeEEE--ecCCeEEcccCCcEee
Confidence 36777776 4456899999999885
No 22
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=79.73 E-value=1.2 Score=24.86 Aligned_cols=12 Identities=25% Similarity=0.628 Sum_probs=10.6
Q ss_pred ceecCCCCcccc
Q 034182 86 PAICKYCGLRYV 97 (102)
Q Consensus 86 ~~~CpYCG~ry~ 97 (102)
.+.||+||..|.
T Consensus 25 ~v~C~~C~~~~~ 36 (38)
T TIGR02098 25 KVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCEEE
Confidence 689999999885
No 23
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=79.46 E-value=1.3 Score=25.13 Aligned_cols=18 Identities=33% Similarity=0.680 Sum_probs=12.7
Q ss_pred cCCCCceecCCCCccccc
Q 034182 81 LDLKEPAICKYCGLRYVQ 98 (102)
Q Consensus 81 Ld~~~~~~CpYCG~ry~~ 98 (102)
|....++.|+|||-|-..
T Consensus 12 ~~~~~~irC~~CG~RIly 29 (32)
T PF03604_consen 12 LKPGDPIRCPECGHRILY 29 (32)
T ss_dssp BSTSSTSSBSSSS-SEEB
T ss_pred cCCCCcEECCcCCCeEEE
Confidence 555568899999987544
No 24
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=78.39 E-value=0.86 Score=27.55 Aligned_cols=11 Identities=36% Similarity=1.056 Sum_probs=8.6
Q ss_pred eecCCCCcccc
Q 034182 87 AICKYCGLRYV 97 (102)
Q Consensus 87 ~~CpYCG~ry~ 97 (102)
-.|||||.-|-
T Consensus 3 f~CP~C~~~~~ 13 (54)
T PF05605_consen 3 FTCPYCGKGFS 13 (54)
T ss_pred cCCCCCCCccC
Confidence 47999999654
No 25
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=75.52 E-value=2.2 Score=25.39 Aligned_cols=15 Identities=40% Similarity=0.961 Sum_probs=12.3
Q ss_pred CceecCCCCcccccc
Q 034182 85 EPAICKYCGLRYVQD 99 (102)
Q Consensus 85 ~~~~CpYCG~ry~~~ 99 (102)
..+.|.||+..|...
T Consensus 17 ~~a~C~~C~~~l~~~ 31 (50)
T smart00614 17 QRAKCKYCGKKLSRS 31 (50)
T ss_pred eEEEecCCCCEeeeC
Confidence 369999999999654
No 26
>PHA02768 hypothetical protein; Provisional
Probab=74.60 E-value=0.83 Score=29.00 Aligned_cols=13 Identities=31% Similarity=0.848 Sum_probs=10.9
Q ss_pred ecCCCCccccccc
Q 034182 88 ICKYCGLRYVQDH 100 (102)
Q Consensus 88 ~CpYCG~ry~~~~ 100 (102)
.|++||.+|....
T Consensus 7 ~C~~CGK~Fs~~~ 19 (55)
T PHA02768 7 ECPICGEIYIKRK 19 (55)
T ss_pred CcchhCCeeccHH
Confidence 7999999998643
No 27
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=73.86 E-value=1.3 Score=23.14 Aligned_cols=13 Identities=23% Similarity=0.756 Sum_probs=9.6
Q ss_pred CCceecCCCCccc
Q 034182 84 KEPAICKYCGLRY 96 (102)
Q Consensus 84 ~~~~~CpYCG~ry 96 (102)
++...|++||..+
T Consensus 11 ~~~~fC~~CG~~l 23 (23)
T PF13240_consen 11 DDAKFCPNCGTPL 23 (23)
T ss_pred CcCcchhhhCCcC
Confidence 4567799999764
No 28
>cd00498 Hsp33 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat shock), the Cys are reversibly oxidized to disulfide bonds, which causes the chaperone activity to be turned on. Hsp33 is homodimeric in its functional form.
Probab=71.87 E-value=1.8 Score=34.24 Aligned_cols=13 Identities=31% Similarity=0.974 Sum_probs=11.8
Q ss_pred ceecCCCCccccc
Q 034182 86 PAICKYCGLRYVQ 98 (102)
Q Consensus 86 ~~~CpYCG~ry~~ 98 (102)
+++|.|||++|..
T Consensus 262 ev~C~FC~~~Y~f 274 (275)
T cd00498 262 EVTCEFCGEKYHF 274 (275)
T ss_pred EEEEeCCCCEEec
Confidence 7899999999975
No 29
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=70.67 E-value=2.9 Score=25.90 Aligned_cols=23 Identities=26% Similarity=0.527 Sum_probs=14.4
Q ss_pred eEEEcCC-CCceecCCCCcccccc
Q 034182 77 EFICLDL-KEPAICKYCGLRYVQD 99 (102)
Q Consensus 77 VyI~Ld~-~~~~~CpYCG~ry~~~ 99 (102)
.|.-+++ +..-+|-||++.|..+
T Consensus 25 ~F~v~~~~~~~~rC~YCe~~~~~~ 48 (52)
T PF02748_consen 25 RFYVIDKEPIKLRCHYCERIITED 48 (52)
T ss_dssp EEEEEETTTCEEEETTT--EEEHH
T ss_pred eEEEEeCCCCEEEeeCCCCEeccc
Confidence 3433655 4588999999998654
No 30
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=69.72 E-value=1.8 Score=34.39 Aligned_cols=16 Identities=38% Similarity=0.764 Sum_probs=12.2
Q ss_pred CCceecCCCCcccccc
Q 034182 84 KEPAICKYCGLRYVQD 99 (102)
Q Consensus 84 ~~~~~CpYCG~ry~~~ 99 (102)
+..+.|||||+--+.+
T Consensus 219 d~iv~CP~CgRILy~~ 234 (239)
T COG1579 219 DEIVFCPYCGRILYYD 234 (239)
T ss_pred CCCccCCccchHHHhh
Confidence 4589999999865543
No 31
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=69.62 E-value=6 Score=22.87 Aligned_cols=22 Identities=18% Similarity=0.321 Sum_probs=13.3
Q ss_pred CCceEEEcCCCCceecCCCCccc
Q 034182 74 HPIEFICLDLKEPAICKYCGLRY 96 (102)
Q Consensus 74 HPrVyI~Ld~~~~~~CpYCG~ry 96 (102)
...+..+ ...+..+|+.||..-
T Consensus 8 ~~~~~~D-~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 8 SKEIVFD-PERGELVCPNCGLVL 29 (43)
T ss_dssp SSEEEEE-TTTTEEEETTT-BBE
T ss_pred CCceEEc-CCCCeEECCCCCCEe
Confidence 3333334 345788999999764
No 32
>TIGR03365 Bsubt_queE 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE. This uncharacterized enzyme, designated QueE, participates in the biosynthesis, from GTP, of 7-cyano-7-deazaguanosine, also called preQ0 because in many species it is a precursor of queuosine. In most Archaea, it is instead the precursor of a different tRNA modified base, archaeosine.
Probab=69.59 E-value=4 Score=31.29 Aligned_cols=33 Identities=15% Similarity=0.386 Sum_probs=25.6
Q ss_pred eecCCCCCCCCCCceEEEcCCCCceecCCCCcccc
Q 034182 63 ACEGDSNPALGHPIEFICLDLKEPAICKYCGLRYV 97 (102)
Q Consensus 63 ~CdG~~~palGHPrVyI~Ld~~~~~~CpYCG~ry~ 97 (102)
|-.|-| +..|-|-|||.+.. =.-.|+||.+.|.
T Consensus 12 SiQGEG-~~~G~~~~FvR~~g-CNlrC~~Cdt~~~ 44 (238)
T TIGR03365 12 TIQGEG-MVIGQKTMFVRTGG-CDYRCSWCDSLFT 44 (238)
T ss_pred ccccCc-cccCCeEEEEEeCC-cCCcCcCCCCccc
Confidence 445544 57899999999983 2689999998773
No 33
>PF01430 HSP33: Hsp33 protein; InterPro: IPR000397 Hsp33 is a molecular chaperone, distinguished from all other known chaperones by its mode of functional regulation. Its activity is redox regulated. Hsp33 is a cytoplasmically localized protein with highly reactive cysteines that respond quickly to changes in the redox environment. Oxidizing conditions like H2O2 cause disulphide bonds to form in Hsp33, a process that leads to the activation of its chaperone function [].; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0005737 cytoplasm; PDB: 1VZY_B 1VQ0_A 1I7F_A 3M7M_X 1XJH_A 1HW7_A.
Probab=69.46 E-value=1.9 Score=33.93 Aligned_cols=14 Identities=29% Similarity=0.921 Sum_probs=9.3
Q ss_pred ceecCCCCcccccc
Q 034182 86 PAICKYCGLRYVQD 99 (102)
Q Consensus 86 ~~~CpYCG~ry~~~ 99 (102)
+++|.|||++|...
T Consensus 266 ev~C~fC~~~Y~f~ 279 (280)
T PF01430_consen 266 EVTCEFCGKKYRFT 279 (280)
T ss_dssp EEE-TTT--EEEEE
T ss_pred EEEeeCCCCEEEeC
Confidence 78999999999864
No 34
>PF14369 zf-RING_3: zinc-finger
Probab=69.45 E-value=3.5 Score=23.55 Aligned_cols=14 Identities=21% Similarity=0.543 Sum_probs=10.9
Q ss_pred CceecCCCCccccc
Q 034182 85 EPAICKYCGLRYVQ 98 (102)
Q Consensus 85 ~~~~CpYCG~ry~~ 98 (102)
....||+|+..|+-
T Consensus 20 ~~~~CP~C~~gFvE 33 (35)
T PF14369_consen 20 SDVACPRCHGGFVE 33 (35)
T ss_pred CCcCCcCCCCcEeE
Confidence 34469999999974
No 35
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=68.40 E-value=3.3 Score=24.04 Aligned_cols=17 Identities=24% Similarity=0.596 Sum_probs=14.3
Q ss_pred ceecCCCCcccccccCC
Q 034182 86 PAICKYCGLRYVQDHHH 102 (102)
Q Consensus 86 ~~~CpYCG~ry~~~~hh 102 (102)
+..|.||+..|=.+|++
T Consensus 12 ~f~C~~C~~~FC~~HR~ 28 (39)
T smart00154 12 GFKCRHCGNLFCGEHRL 28 (39)
T ss_pred CeECCccCCccccccCC
Confidence 57899999999888763
No 36
>PRK00114 hslO Hsp33-like chaperonin; Reviewed
Probab=68.30 E-value=2.3 Score=33.96 Aligned_cols=14 Identities=36% Similarity=1.177 Sum_probs=12.4
Q ss_pred ceecCCCCcccccc
Q 034182 86 PAICKYCGLRYVQD 99 (102)
Q Consensus 86 ~~~CpYCG~ry~~~ 99 (102)
+++|.|||++|...
T Consensus 268 ev~C~FC~~~Y~f~ 281 (293)
T PRK00114 268 EMVCQFCGNKYLFD 281 (293)
T ss_pred EEEEeCCCCEEEeC
Confidence 78999999999864
No 37
>COG1281 Disulfide bond chaperones of the HSP33 family [Posttranslational modification, protein turnover, chaperones]
Probab=66.40 E-value=2.9 Score=34.21 Aligned_cols=15 Identities=33% Similarity=1.074 Sum_probs=13.2
Q ss_pred ceecCCCCccccccc
Q 034182 86 PAICKYCGLRYVQDH 100 (102)
Q Consensus 86 ~~~CpYCG~ry~~~~ 100 (102)
++.|.|||++|.++.
T Consensus 266 ev~C~FC~~~Y~f~~ 280 (286)
T COG1281 266 EVTCEFCGTKYLFDE 280 (286)
T ss_pred EEEeeccCCEEecCH
Confidence 789999999998763
No 38
>PF06957 COPI_C: Coatomer (COPI) alpha subunit C-terminus; InterPro: IPR010714 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit [, ]. This domain is found along with the IPR006692 from INTERPRO domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat; PDB: 3MKR_B 3MV2_E 3MKQ_B 3MV3_A.
Probab=66.06 E-value=3.1 Score=35.56 Aligned_cols=16 Identities=31% Similarity=0.928 Sum_probs=9.5
Q ss_pred CCceecCCCCcccccc
Q 034182 84 KEPAICKYCGLRYVQD 99 (102)
Q Consensus 84 ~~~~~CpYCG~ry~~~ 99 (102)
...+.|||||.+|.-+
T Consensus 378 ~~~v~CP~cgA~y~~~ 393 (422)
T PF06957_consen 378 SPSVKCPYCGAKYHPE 393 (422)
T ss_dssp S-EEE-TTT--EEEGG
T ss_pred CCCeeCCCCCCccChh
Confidence 3478899999999754
No 39
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=65.59 E-value=3.3 Score=24.28 Aligned_cols=14 Identities=21% Similarity=0.513 Sum_probs=11.8
Q ss_pred CceecCCCCccccc
Q 034182 85 EPAICKYCGLRYVQ 98 (102)
Q Consensus 85 ~~~~CpYCG~ry~~ 98 (102)
+...|++||..+..
T Consensus 4 g~l~C~~CG~~m~~ 17 (58)
T PF13408_consen 4 GLLRCGHCGSKMTR 17 (58)
T ss_pred CcEEcccCCcEeEE
Confidence 56899999998865
No 40
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=65.33 E-value=5 Score=23.64 Aligned_cols=18 Identities=22% Similarity=0.300 Sum_probs=12.6
Q ss_pred eEEEcCCCCceecCCCCc
Q 034182 77 EFICLDLKEPAICKYCGL 94 (102)
Q Consensus 77 VyI~Ld~~~~~~CpYCG~ 94 (102)
++..++.+....||.||.
T Consensus 17 ~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 17 VLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEecCCCCCCCCCCCCC
Confidence 344455456788999997
No 41
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=64.35 E-value=3.6 Score=23.45 Aligned_cols=13 Identities=23% Similarity=0.588 Sum_probs=9.7
Q ss_pred eecCCCCcccccc
Q 034182 87 AICKYCGLRYVQD 99 (102)
Q Consensus 87 ~~CpYCG~ry~~~ 99 (102)
.+||-|+++|...
T Consensus 3 i~CP~C~~~f~v~ 15 (37)
T PF13719_consen 3 ITCPNCQTRFRVP 15 (37)
T ss_pred EECCCCCceEEcC
Confidence 5788888888754
No 42
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=64.15 E-value=2.7 Score=22.24 Aligned_cols=12 Identities=25% Similarity=0.891 Sum_probs=9.0
Q ss_pred CCceecCCCCcc
Q 034182 84 KEPAICKYCGLR 95 (102)
Q Consensus 84 ~~~~~CpYCG~r 95 (102)
++...||+||.+
T Consensus 14 ~~~~fC~~CG~~ 25 (26)
T PF13248_consen 14 PDAKFCPNCGAK 25 (26)
T ss_pred cccccChhhCCC
Confidence 456789999875
No 43
>PF08685 GON: GON domain; InterPro: IPR012314 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. The ADAMTSs (a disintegrin and metalloproteinase domain with thrombospondin type-1 modules) are a family of zinc dependent metalloproteinases that play important roles in a variety of normal and pathological conditions. These enzymes show a complex domain organisation including signal sequence, propeptide, metalloproteinase domain (see PDOC50215 from PROSITEDOC), disintegrin-like domain (see PDOC00351 from PROSITEDOC), central TS-1 motif (see PDOC50092 from PROSITEDOC), cysteine-rich region, and a variable number of TS-like repeats at the C-terminal region. The GON domain is an approximately 200-residue module, whose presence is the hallmark of a subfamily of structurally and evolutionarily related ADAMTSs, called GON- ADAMTSs. The GON domain is characterised by the presence of several conserved cysteine residues and is likely to be globular [], []. Some proteins known to contain a GON domain are listed below: Mammalian ADAMTS-9 Mammalian ADAMTS-20 Caenorhabditis elegans gon-1, a protease required for gonadal morphogenesis Proteins containing the GON domain belong to MEROPS peptidase subfamily M12B (adamalysin, clan MA).; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding
Probab=63.72 E-value=9.9 Score=29.71 Aligned_cols=33 Identities=33% Similarity=0.655 Sum_probs=24.9
Q ss_pred EEeecCCCCCCCCCCceEEEcCC---C-----------CceecCCCCccc
Q 034182 61 IVACEGDSNPALGHPIEFICLDL---K-----------EPAICKYCGLRY 96 (102)
Q Consensus 61 ~v~CdG~~~palGHPrVyI~Ld~---~-----------~~~~CpYCG~ry 96 (102)
.|.|-|. +.+.|++||+|.+ + .+-.|||=|.+.
T Consensus 30 ~IYCh~M---~s~~PkEYltL~~G~~eNyae~y~~Rl~~~~~Cp~ng~~~ 76 (201)
T PF08685_consen 30 KIYCHGM---ASSTPKEYLTLPSGPQENYAEVYGKRLQNPSECPYNGSRR 76 (201)
T ss_pred EEEcCCC---CCCCCceeEEcCCCCccchheecchhccCCCcCCCCCCCC
Confidence 5799887 4699999999993 1 245699877664
No 44
>PF14353 CpXC: CpXC protein
Probab=63.53 E-value=4 Score=28.23 Aligned_cols=14 Identities=21% Similarity=0.705 Sum_probs=11.8
Q ss_pred ceecCCCCcccccc
Q 034182 86 PAICKYCGLRYVQD 99 (102)
Q Consensus 86 ~~~CpYCG~ry~~~ 99 (102)
..+||.||..|...
T Consensus 38 ~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 38 SFTCPSCGHKFRLE 51 (128)
T ss_pred EEECCCCCCceecC
Confidence 57899999998754
No 45
>PF15616 TerY-C: TerY-C metal binding domain
Probab=62.31 E-value=5.7 Score=29.05 Aligned_cols=18 Identities=28% Similarity=0.879 Sum_probs=15.1
Q ss_pred EEEcCCCCceecCCCCcc
Q 034182 78 FICLDLKEPAICKYCGLR 95 (102)
Q Consensus 78 yI~Ld~~~~~~CpYCG~r 95 (102)
.+.++.++.++||+||..
T Consensus 97 l~Ci~g~~~~~CPwCg~~ 114 (131)
T PF15616_consen 97 LFCIDGEGEVTCPWCGNE 114 (131)
T ss_pred EEEeCCCCCEECCCCCCe
Confidence 467788889999999975
No 46
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=62.04 E-value=2.8 Score=28.69 Aligned_cols=39 Identities=18% Similarity=0.341 Sum_probs=20.0
Q ss_pred CeEEeecCCCCCCCCCCceEEEcCCCCceecCCCCccccc
Q 034182 59 GRIVACEGDSNPALGHPIEFICLDLKEPAICKYCGLRYVQ 98 (102)
Q Consensus 59 ~~~v~CdG~~~palGHPrVyI~Ld~~~~~~CpYCG~ry~~ 98 (102)
...+.|..|.- |.---.-|+.|...+..+|+.||.+|..
T Consensus 29 ~~~~~C~~GH~-w~RC~lT~l~i~~~~~r~C~~C~~~~l~ 67 (99)
T PF12660_consen 29 LDEAQCENGHV-WPRCALTFLPIQTPGVRVCPVCGRRALD 67 (99)
T ss_dssp SSEEE-TTS-E-EEB-SSS-SBS-SS-EEE-TTT--EEE-
T ss_pred cCEeECCCCCE-EeeeeeeeeeeccCCeeEcCCCCCEEec
Confidence 44566876654 5555566788888888888888888754
No 47
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=62.00 E-value=4.6 Score=24.53 Aligned_cols=39 Identities=28% Similarity=0.411 Sum_probs=26.6
Q ss_pred CCEEecCeEEeecCCCCCCCCCCceEEEcCCC-CceecCCCCcc
Q 034182 53 PPIKVEGRIVACEGDSNPALGHPIEFICLDLK-EPAICKYCGLR 95 (102)
Q Consensus 53 p~i~V~~~~v~CdG~~~palGHPrVyI~Ld~~-~~~~CpYCG~r 95 (102)
++..|++. .|.|=.. ---|.+|..|.+. +...||+||+-
T Consensus 16 ~va~v~~~--~C~gC~~--~l~~~~~~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 16 AVARVEGG--TCSGCHM--ELPPQELNEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred EEEEeeCC--ccCCCCE--EcCHHHHHHHHcCCCeEECcCCCcc
Confidence 34455554 7877754 3456777777665 68999999963
No 48
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=61.20 E-value=5.1 Score=25.54 Aligned_cols=20 Identities=30% Similarity=0.531 Sum_probs=10.6
Q ss_pred EcCCCCceecCCCCcccccc
Q 034182 80 CLDLKEPAICKYCGLRYVQD 99 (102)
Q Consensus 80 ~Ld~~~~~~CpYCG~ry~~~ 99 (102)
.+..+.+++||.||..+.+.
T Consensus 18 ~~~S~~PatCP~C~a~~~~s 37 (54)
T PF09237_consen 18 KSQSEQPATCPICGAVIRQS 37 (54)
T ss_dssp CCTTS--EE-TTT--EESSH
T ss_pred hhccCCCCCCCcchhhccch
Confidence 34456799999999988653
No 49
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=61.08 E-value=5.6 Score=25.20 Aligned_cols=16 Identities=25% Similarity=0.644 Sum_probs=12.8
Q ss_pred CCCceecCCCCccccc
Q 034182 83 LKEPAICKYCGLRYVQ 98 (102)
Q Consensus 83 ~~~~~~CpYCG~ry~~ 98 (102)
++..++||-||+.|-.
T Consensus 18 ~dDiVvCp~CgapyHR 33 (54)
T PF14446_consen 18 GDDIVVCPECGAPYHR 33 (54)
T ss_pred CCCEEECCCCCCcccH
Confidence 4568999999998853
No 50
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=60.65 E-value=8.5 Score=22.72 Aligned_cols=36 Identities=14% Similarity=0.330 Sum_probs=21.6
Q ss_pred cCeEEeecCCCCCCCCCCceEEEcC--CCCceecCCCCccccc
Q 034182 58 EGRIVACEGDSNPALGHPIEFICLD--LKEPAICKYCGLRYVQ 98 (102)
Q Consensus 58 ~~~~v~CdG~~~palGHPrVyI~Ld--~~~~~~CpYCG~ry~~ 98 (102)
+.....|++.+= ..+.+..+ ....+.|+.||..|=.
T Consensus 15 ~~~~~~CP~~~C-----~~~~~~~~~~~~~~v~C~~C~~~fC~ 52 (64)
T smart00647 15 NPDLKWCPAPDC-----SAAIIVTEEEGCNRVTCPKCGFSFCF 52 (64)
T ss_pred CCCccCCCCCCC-----cceEEecCCCCCCeeECCCCCCeECC
Confidence 345678986532 11222221 4558999999999854
No 51
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=59.26 E-value=4.4 Score=33.17 Aligned_cols=18 Identities=56% Similarity=1.019 Sum_probs=12.0
Q ss_pred cCCCCceecCCCCccccc
Q 034182 81 LDLKEPAICKYCGLRYVQ 98 (102)
Q Consensus 81 Ld~~~~~~CpYCG~ry~~ 98 (102)
|+....-.|+|||+.|+.
T Consensus 156 ~~s~ka~~C~~C~K~YvS 173 (279)
T KOG2462|consen 156 LDSKKAFSCKYCGKVYVS 173 (279)
T ss_pred ccccccccCCCCCceeee
Confidence 333445678888888873
No 52
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=59.14 E-value=2.7 Score=39.07 Aligned_cols=23 Identities=30% Similarity=0.569 Sum_probs=17.2
Q ss_pred EEcCCCC---ceecCCCCcccccccC
Q 034182 79 ICLDLKE---PAICKYCGLRYVQDHH 101 (102)
Q Consensus 79 I~Ld~~~---~~~CpYCG~ry~~~~h 101 (102)
+.|+..+ .-.|+.||+.|+++||
T Consensus 271 ~sltqsa~lRKFKCtECgKAFKfKHH 296 (1007)
T KOG3623|consen 271 ISLTQSALLRKFKCTECGKAFKFKHH 296 (1007)
T ss_pred ccccchhhhccccccccchhhhhHHH
Confidence 4455432 4679999999999987
No 53
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=59.07 E-value=4.8 Score=23.78 Aligned_cols=34 Identities=21% Similarity=0.370 Sum_probs=15.8
Q ss_pred cCeEEeecCCCCCCCCCCceEEEcCC-CCc--eecCCCCcccc
Q 034182 58 EGRIVACEGDSNPALGHPIEFICLDL-KEP--AICKYCGLRYV 97 (102)
Q Consensus 58 ~~~~v~CdG~~~palGHPrVyI~Ld~-~~~--~~CpYCG~ry~ 97 (102)
+.....|+.++= + . +|..++ ... +.|++||..|=
T Consensus 15 ~~~~~~Cp~~~C---~--~-~~~~~~~~~~~~~~C~~C~~~fC 51 (64)
T PF01485_consen 15 DPNIRWCPNPDC---E--Y-IIEKDDGCNSPIVTCPSCGTEFC 51 (64)
T ss_dssp ---CC--TTSST---------ECS-SSTTS--CCTTSCCSEEC
T ss_pred CCCccCCCCCCC---c--c-cEEecCCCCCCeeECCCCCCcCc
Confidence 334458988631 1 1 233332 333 89999999884
No 54
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=58.85 E-value=4.9 Score=29.45 Aligned_cols=15 Identities=13% Similarity=0.297 Sum_probs=13.3
Q ss_pred CCceecCCCCccccc
Q 034182 84 KEPAICKYCGLRYVQ 98 (102)
Q Consensus 84 ~~~~~CpYCG~ry~~ 98 (102)
+|.-.||.||+.|.-
T Consensus 96 EG~l~CpetG~vfpI 110 (124)
T KOG1088|consen 96 EGELVCPETGRVFPI 110 (124)
T ss_pred cceEecCCCCcEeec
Confidence 689999999999963
No 55
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=58.76 E-value=8.6 Score=22.34 Aligned_cols=18 Identities=22% Similarity=0.580 Sum_probs=14.1
Q ss_pred eEEEcCCCCceecCCCCc
Q 034182 77 EFICLDLKEPAICKYCGL 94 (102)
Q Consensus 77 VyI~Ld~~~~~~CpYCG~ 94 (102)
++..+.++....||-||.
T Consensus 17 ~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 17 VLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEEEcCCCCCCcCCCCCC
Confidence 455666667899999998
No 56
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=58.16 E-value=2.3 Score=31.64 Aligned_cols=37 Identities=19% Similarity=0.272 Sum_probs=26.8
Q ss_pred EEeecCCCCC--CCCCCceEEEcCCCCceecCCCCcccc
Q 034182 61 IVACEGDSNP--ALGHPIEFICLDLKEPAICKYCGLRYV 97 (102)
Q Consensus 61 ~v~CdG~~~p--alGHPrVyI~Ld~~~~~~CpYCG~ry~ 97 (102)
-+.|+.+... |+.----|=.....|-..||+||..=+
T Consensus 5 ~L~C~~gH~FEgWF~ss~~fd~Q~~~glv~CP~Cgs~~V 43 (148)
T PF06676_consen 5 DLRCENGHEFEGWFRSSAAFDRQQARGLVSCPVCGSTEV 43 (148)
T ss_pred EEecCCCCccceecCCHHHHHHHHHcCCccCCCCCCCeE
Confidence 3678766442 777666676666778999999998644
No 57
>smart00355 ZnF_C2H2 zinc finger.
Probab=57.79 E-value=4.1 Score=19.37 Aligned_cols=12 Identities=25% Similarity=0.664 Sum_probs=9.7
Q ss_pred ecCCCCcccccc
Q 034182 88 ICKYCGLRYVQD 99 (102)
Q Consensus 88 ~CpYCG~ry~~~ 99 (102)
.|++|+..|...
T Consensus 2 ~C~~C~~~f~~~ 13 (26)
T smart00355 2 RCPECGKVFKSK 13 (26)
T ss_pred CCCCCcchhCCH
Confidence 599999998653
No 58
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=56.35 E-value=6 Score=23.01 Aligned_cols=15 Identities=40% Similarity=0.921 Sum_probs=10.2
Q ss_pred ceecCCCCccccccc
Q 034182 86 PAICKYCGLRYVQDH 100 (102)
Q Consensus 86 ~~~CpYCG~ry~~~~ 100 (102)
+..|++|+..|=.+|
T Consensus 13 ~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 13 PFKCKHCGKSFCLKH 27 (43)
T ss_dssp HEE-TTTS-EE-TTT
T ss_pred CeECCCCCcccCccc
Confidence 688999999997765
No 59
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=55.22 E-value=9.2 Score=25.46 Aligned_cols=37 Identities=16% Similarity=0.310 Sum_probs=19.9
Q ss_pred CeEEeecCCCCCCCCCCceEEEcCCC---CceecCCCCcccccc
Q 034182 59 GRIVACEGDSNPALGHPIEFICLDLK---EPAICKYCGLRYVQD 99 (102)
Q Consensus 59 ~~~v~CdG~~~palGHPrVyI~Ld~~---~~~~CpYCG~ry~~~ 99 (102)
...+.|+==+ -.--|-+.||+. +.+.|..||..|...
T Consensus 20 ~~~F~CPfC~----~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 20 PKVFDCPFCN----HEKSVSVKIDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp SS----TTT------SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred CceEcCCcCC----CCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence 5677786432 123478888874 378899999999753
No 60
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=54.98 E-value=6.4 Score=28.94 Aligned_cols=16 Identities=31% Similarity=0.625 Sum_probs=14.0
Q ss_pred CCCceecCCCCccccc
Q 034182 83 LKEPAICKYCGLRYVQ 98 (102)
Q Consensus 83 ~~~~~~CpYCG~ry~~ 98 (102)
++|.+.||-||.+++.
T Consensus 41 KdG~v~CPvC~~~~~~ 56 (131)
T COG1645 41 KDGEVFCPVCGYREVV 56 (131)
T ss_pred eCCeEECCCCCceEEE
Confidence 8899999999977764
No 61
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=53.15 E-value=7.4 Score=24.78 Aligned_cols=28 Identities=29% Similarity=0.498 Sum_probs=20.0
Q ss_pred CCCCceEEEcCCCCceecCCCCcccccc
Q 034182 72 LGHPIEFICLDLKEPAICKYCGLRYVQD 99 (102)
Q Consensus 72 lGHPrVyI~Ld~~~~~~CpYCG~ry~~~ 99 (102)
-||=.=.-..+.+...-||.||++|...
T Consensus 25 CgH~I~~~~f~~~rYngCPfC~~~~~~~ 52 (55)
T PF14447_consen 25 CGHLICDNCFPGERYNGCPFCGTPFEFD 52 (55)
T ss_pred ccceeeccccChhhccCCCCCCCcccCC
Confidence 4664444455566788999999999754
No 62
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=52.87 E-value=12 Score=20.66 Aligned_cols=13 Identities=31% Similarity=0.514 Sum_probs=10.4
Q ss_pred CCceecCCCCccc
Q 034182 84 KEPAICKYCGLRY 96 (102)
Q Consensus 84 ~~~~~CpYCG~ry 96 (102)
+....||.||...
T Consensus 24 ~~~~~CP~Cg~~~ 36 (41)
T smart00834 24 DPLATCPECGGDV 36 (41)
T ss_pred CCCCCCCCCCCcc
Confidence 5578999999854
No 63
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=52.79 E-value=7.3 Score=20.18 Aligned_cols=12 Identities=17% Similarity=0.661 Sum_probs=10.0
Q ss_pred ecCCCCcccccc
Q 034182 88 ICKYCGLRYVQD 99 (102)
Q Consensus 88 ~CpYCG~ry~~~ 99 (102)
.|.+|++.|..+
T Consensus 3 ~C~~C~k~f~~~ 14 (27)
T PF12171_consen 3 YCDACDKYFSSE 14 (27)
T ss_dssp BBTTTTBBBSSH
T ss_pred CcccCCCCcCCH
Confidence 599999999753
No 64
>TIGR00240 ATCase_reg aspartate carbamoyltransferase, regulatory subunit. The presence of this regulatory subunit allows feedback inhibition by CTP on aspartate carbamoyltransferase, the first step in the synthesis of CTP from aspartate. In many species, this regulatory subunit is not present. In Thermotoga maritima, the catalytic and regulatory subunits are encoded by a fused gene and the regulatory region has enough sequence differences to score below the trusted cutoff.
Probab=51.17 E-value=13 Score=27.92 Aligned_cols=41 Identities=15% Similarity=0.275 Sum_probs=25.9
Q ss_pred CeEEeecCCCC--CCCCCCceEEEcCCCC--ceecCCCCcccccc
Q 034182 59 GRIVACEGDSN--PALGHPIEFICLDLKE--PAICKYCGLRYVQD 99 (102)
Q Consensus 59 ~~~v~CdG~~~--palGHPrVyI~Ld~~~--~~~CpYCG~ry~~~ 99 (102)
..++.|+.+.= ..-.=+..|.-++++. .-+|-||++.|..+
T Consensus 101 ~gi~kC~Np~CIT~~E~v~~~F~v~~~~~~~~lrC~YCe~~~~~~ 145 (150)
T TIGR00240 101 EGVLKCPNPNCISNAEPVSSKFYVRSEEPDIALRCYYCEKEIEHN 145 (150)
T ss_pred eeeEECCCCCCccCCCCCCcEEEEecCCCceEEEEECCCCEEecc
Confidence 44688987731 0112245566566653 68999999998643
No 65
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=51.02 E-value=13 Score=27.96 Aligned_cols=41 Identities=20% Similarity=0.394 Sum_probs=25.6
Q ss_pred CeEEeecCCCCC---CCCCCceEEEcCCC-CceecCCCCcccccc
Q 034182 59 GRIVACEGDSNP---ALGHPIEFICLDLK-EPAICKYCGLRYVQD 99 (102)
Q Consensus 59 ~~~v~CdG~~~p---alGHPrVyI~Ld~~-~~~~CpYCG~ry~~~ 99 (102)
..++.|+.+.== --.=+..|.-++++ ..-+|-||++.|..+
T Consensus 103 ~gi~kC~Np~CITn~~E~v~~~F~v~~~~~~~~rC~YCe~~~~~~ 147 (152)
T PRK00893 103 EGVLKCPNPNCITNTNEPVESRFYVVDKEPIKLRCKYCEKEFSED 147 (152)
T ss_pred cceEECCCCCCcCCCCcCcCcEEEEEeCCCCEEEeeCCCCEechh
Confidence 346889877420 01223345556654 478999999998754
No 66
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=50.92 E-value=9.4 Score=27.14 Aligned_cols=20 Identities=20% Similarity=0.607 Sum_probs=15.5
Q ss_pred eEEEcCCCCceecCCCCcccc
Q 034182 77 EFICLDLKEPAICKYCGLRYV 97 (102)
Q Consensus 77 VyI~Ld~~~~~~CpYCG~ry~ 97 (102)
-|.+++ -|...||+||.-|.
T Consensus 39 ~~VeIe-vG~~~cP~Cge~~~ 58 (102)
T PF04475_consen 39 DYVEIE-VGDTICPKCGEELD 58 (102)
T ss_pred CeEEEe-cCcccCCCCCCccC
Confidence 377777 57889999998764
No 67
>COG0602 NrdG Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]
Probab=50.45 E-value=13 Score=28.34 Aligned_cols=31 Identities=23% Similarity=0.536 Sum_probs=23.8
Q ss_pred cCCCCCCCCCCceEEEcCCCCceecCCCCcccc
Q 034182 65 EGDSNPALGHPIEFICLDLKEPAICKYCGLRYV 97 (102)
Q Consensus 65 dG~~~palGHPrVyI~Ld~~~~~~CpYCG~ry~ 97 (102)
.|.| ...|=|-||+.+.. =.-.|+||.+.+.
T Consensus 14 QGEG-~~~Gr~~vFVR~~G-C~l~C~~Cdt~~t 44 (212)
T COG0602 14 QGEG-KNIGRPSVFVRFAG-CNLRCPGCDTKYT 44 (212)
T ss_pred ecCc-ccccceeEEEEcCC-CCCCCCCCCChhh
Confidence 3444 46799999999873 2789999998765
No 68
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=49.83 E-value=8.9 Score=21.79 Aligned_cols=13 Identities=31% Similarity=0.738 Sum_probs=9.1
Q ss_pred eecCCCCcccccc
Q 034182 87 AICKYCGLRYVQD 99 (102)
Q Consensus 87 ~~CpYCG~ry~~~ 99 (102)
.+||-|+++|...
T Consensus 3 i~Cp~C~~~y~i~ 15 (36)
T PF13717_consen 3 ITCPNCQAKYEID 15 (36)
T ss_pred EECCCCCCEEeCC
Confidence 5677777777654
No 69
>PF06226 DUF1007: Protein of unknown function (DUF1007); InterPro: IPR010412 This is a family of conserved bacterial proteins with unknown function.
Probab=48.70 E-value=9.7 Score=28.91 Aligned_cols=13 Identities=46% Similarity=0.726 Sum_probs=11.4
Q ss_pred CCCCCCceEEEcC
Q 034182 70 PALGHPIEFICLD 82 (102)
Q Consensus 70 palGHPrVyI~Ld 82 (102)
++..||.|||++.
T Consensus 15 ~a~AHPHvfId~~ 27 (212)
T PF06226_consen 15 PAFAHPHVFIDAR 27 (212)
T ss_pred ccccCCcEEEEEE
Confidence 4789999999876
No 70
>smart00507 HNHc HNH nucleases.
Probab=48.55 E-value=6.3 Score=21.65 Aligned_cols=11 Identities=36% Similarity=1.041 Sum_probs=9.3
Q ss_pred eecCCCCcccc
Q 034182 87 AICKYCGLRYV 97 (102)
Q Consensus 87 ~~CpYCG~ry~ 97 (102)
..|.|||..+.
T Consensus 11 ~~C~~C~~~~~ 21 (52)
T smart00507 11 GVCAYCGKPAS 21 (52)
T ss_pred CCCcCCcCCCC
Confidence 58999999874
No 71
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=48.48 E-value=9.8 Score=23.92 Aligned_cols=15 Identities=33% Similarity=0.696 Sum_probs=12.8
Q ss_pred CCceecCCCCccccc
Q 034182 84 KEPAICKYCGLRYVQ 98 (102)
Q Consensus 84 ~~~~~CpYCG~ry~~ 98 (102)
+|.-+||-||+.|--
T Consensus 51 eg~L~Cp~c~r~YPI 65 (68)
T PF03966_consen 51 EGELICPECGREYPI 65 (68)
T ss_dssp TTEEEETTTTEEEEE
T ss_pred CCEEEcCCCCCEEeC
Confidence 578899999999953
No 72
>PHA00616 hypothetical protein
Probab=48.28 E-value=4.9 Score=24.42 Aligned_cols=12 Identities=25% Similarity=0.614 Sum_probs=10.3
Q ss_pred ecCCCCcccccc
Q 034182 88 ICKYCGLRYVQD 99 (102)
Q Consensus 88 ~CpYCG~ry~~~ 99 (102)
.|+-||..|.+.
T Consensus 3 qC~~CG~~F~~~ 14 (44)
T PHA00616 3 QCLRCGGIFRKK 14 (44)
T ss_pred ccchhhHHHhhH
Confidence 699999999863
No 73
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=48.08 E-value=12 Score=22.85 Aligned_cols=13 Identities=23% Similarity=0.503 Sum_probs=7.4
Q ss_pred CceecCCCCcccc
Q 034182 85 EPAICKYCGLRYV 97 (102)
Q Consensus 85 ~~~~CpYCG~ry~ 97 (102)
+.-.|+-||..|-
T Consensus 36 ~r~~C~~Cgyt~~ 48 (50)
T PRK00432 36 DRWHCGKCGYTEF 48 (50)
T ss_pred CcEECCCcCCEEe
Confidence 4556666665553
No 74
>PRK03922 hypothetical protein; Provisional
Probab=47.95 E-value=11 Score=27.15 Aligned_cols=21 Identities=19% Similarity=0.642 Sum_probs=16.4
Q ss_pred ceEEEcCCCCceecCCCCcccc
Q 034182 76 IEFICLDLKEPAICKYCGLRYV 97 (102)
Q Consensus 76 rVyI~Ld~~~~~~CpYCG~ry~ 97 (102)
.-|..++ -|...||+||.-|.
T Consensus 40 l~yVeie-vG~~~cP~cge~~~ 60 (113)
T PRK03922 40 LDYVEVE-VGLTICPKCGEPFD 60 (113)
T ss_pred CCeEEEe-cCcccCCCCCCcCC
Confidence 4477777 47889999998764
No 75
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=47.43 E-value=8.3 Score=22.02 Aligned_cols=11 Identities=36% Similarity=0.830 Sum_probs=8.4
Q ss_pred ceecCCCCccc
Q 034182 86 PAICKYCGLRY 96 (102)
Q Consensus 86 ~~~CpYCG~ry 96 (102)
+..||+||..=
T Consensus 2 ~~~Cp~Cg~~~ 12 (47)
T PF14690_consen 2 PPRCPHCGSPS 12 (47)
T ss_pred CccCCCcCCCc
Confidence 46899999653
No 76
>PRK01402 hslO Hsp33-like chaperonin; Reviewed
Probab=46.73 E-value=9.1 Score=31.45 Aligned_cols=14 Identities=29% Similarity=0.793 Sum_probs=12.5
Q ss_pred ceecCCCCcccccc
Q 034182 86 PAICKYCGLRYVQD 99 (102)
Q Consensus 86 ~~~CpYCG~ry~~~ 99 (102)
+++|.|||++|...
T Consensus 308 ev~CeFC~~~Y~f~ 321 (328)
T PRK01402 308 SVTCEFCSRVYRFD 321 (328)
T ss_pred EEEeeCCCCEEEeC
Confidence 78999999999864
No 77
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=46.18 E-value=12 Score=23.37 Aligned_cols=14 Identities=29% Similarity=0.736 Sum_probs=10.6
Q ss_pred CceecCCCCccccc
Q 034182 85 EPAICKYCGLRYVQ 98 (102)
Q Consensus 85 ~~~~CpYCG~ry~~ 98 (102)
..-.|+||+..|..
T Consensus 49 ~~~~C~~C~~~f~s 62 (100)
T PF12756_consen 49 ESFRCPYCNKTFRS 62 (100)
T ss_dssp SSEEBSSSS-EESS
T ss_pred CCCCCCccCCCCcC
Confidence 36899999999963
No 78
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=44.71 E-value=10 Score=20.40 Aligned_cols=13 Identities=23% Similarity=0.789 Sum_probs=10.3
Q ss_pred CceecCCCCcccc
Q 034182 85 EPAICKYCGLRYV 97 (102)
Q Consensus 85 ~~~~CpYCG~ry~ 97 (102)
....||.||-.|.
T Consensus 13 ~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 13 SAKFCPHCGYDFE 25 (26)
T ss_pred hcCcCCCCCCCCc
Confidence 4568999998885
No 79
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=44.62 E-value=17 Score=22.40 Aligned_cols=7 Identities=43% Similarity=1.407 Sum_probs=4.4
Q ss_pred eecCCCC
Q 034182 87 AICKYCG 93 (102)
Q Consensus 87 ~~CpYCG 93 (102)
..|+.||
T Consensus 40 ~vc~~cG 46 (56)
T PF01783_consen 40 RVCPSCG 46 (56)
T ss_dssp SBCTTTB
T ss_pred EeeCCCC
Confidence 5666666
No 80
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=44.10 E-value=7.8 Score=23.33 Aligned_cols=14 Identities=21% Similarity=0.624 Sum_probs=7.2
Q ss_pred ceecCCCCcccccc
Q 034182 86 PAICKYCGLRYVQD 99 (102)
Q Consensus 86 ~~~CpYCG~ry~~~ 99 (102)
...||-||+-|--+
T Consensus 20 ~~~CPlC~r~l~~e 33 (54)
T PF04423_consen 20 KGCCPLCGRPLDEE 33 (54)
T ss_dssp SEE-TTT--EE-HH
T ss_pred CCcCCCCCCCCCHH
Confidence 34999999988543
No 81
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=43.25 E-value=11 Score=32.13 Aligned_cols=17 Identities=29% Similarity=0.684 Sum_probs=14.2
Q ss_pred CCCCceecCCCCccccc
Q 034182 82 DLKEPAICKYCGLRYVQ 98 (102)
Q Consensus 82 d~~~~~~CpYCG~ry~~ 98 (102)
-++++-+|+.||+||+.
T Consensus 394 ~~~KPYrCevC~KRYKN 410 (423)
T COG5189 394 AKDKPYRCEVCDKRYKN 410 (423)
T ss_pred ccCCceeccccchhhcc
Confidence 35678999999999984
No 82
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=43.17 E-value=16 Score=22.75 Aligned_cols=7 Identities=43% Similarity=1.407 Sum_probs=4.3
Q ss_pred eecCCCC
Q 034182 87 AICKYCG 93 (102)
Q Consensus 87 ~~CpYCG 93 (102)
.+|+.||
T Consensus 40 ~vc~~cG 46 (55)
T TIGR01031 40 RVCPSCG 46 (55)
T ss_pred eECCccC
Confidence 4566666
No 83
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=43.15 E-value=11 Score=27.69 Aligned_cols=13 Identities=23% Similarity=0.521 Sum_probs=10.9
Q ss_pred ceecCCCCccccc
Q 034182 86 PAICKYCGLRYVQ 98 (102)
Q Consensus 86 ~~~CpYCG~ry~~ 98 (102)
.+.|||||.....
T Consensus 105 ~~~cp~c~s~~t~ 117 (146)
T TIGR02159 105 SVQCPRCGSADTT 117 (146)
T ss_pred CCcCCCCCCCCcE
Confidence 5899999998754
No 84
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=42.12 E-value=11 Score=22.86 Aligned_cols=12 Identities=33% Similarity=0.941 Sum_probs=10.2
Q ss_pred ceecCCCCcccc
Q 034182 86 PAICKYCGLRYV 97 (102)
Q Consensus 86 ~~~CpYCG~ry~ 97 (102)
.-.|+.||+.|.
T Consensus 8 ~K~C~~C~rpf~ 19 (42)
T PF10013_consen 8 SKICPVCGRPFT 19 (42)
T ss_pred CCcCcccCCcch
Confidence 468999999985
No 85
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=41.95 E-value=12 Score=26.88 Aligned_cols=21 Identities=33% Similarity=0.504 Sum_probs=13.8
Q ss_pred CceEEEcCCCCceecCCCCcc
Q 034182 75 PIEFICLDLKEPAICKYCGLR 95 (102)
Q Consensus 75 PrVyI~Ld~~~~~~CpYCG~r 95 (102)
|.-|++--......||+||..
T Consensus 96 ~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 96 AIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred cccccccccccCcCCcCCCCC
Confidence 445555444455779999975
No 86
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.86 E-value=9.9 Score=30.93 Aligned_cols=17 Identities=18% Similarity=0.630 Sum_probs=13.9
Q ss_pred CCceecCCCCccccccc
Q 034182 84 KEPAICKYCGLRYVQDH 100 (102)
Q Consensus 84 ~~~~~CpYCG~ry~~~~ 100 (102)
+....||-|++.|+.+.
T Consensus 17 kk~ieCPvC~tkFkkee 33 (267)
T COG1655 17 KKTIECPVCNTKFKKEE 33 (267)
T ss_pred hceeccCcccchhhhhh
Confidence 35689999999998754
No 87
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=41.80 E-value=18 Score=25.93 Aligned_cols=45 Identities=18% Similarity=0.252 Sum_probs=25.0
Q ss_pred CEEecCeEEeecCCCCCCCCCCceEEEc-CCCCceecCCCCccccccc
Q 034182 54 PIKVEGRIVACEGDSNPALGHPIEFICL-DLKEPAICKYCGLRYVQDH 100 (102)
Q Consensus 54 ~i~V~~~~v~CdG~~~palGHPrVyI~L-d~~~~~~CpYCG~ry~~~~ 100 (102)
..+.+....-|+.-+.-+. -...+.+ +.++.-.||+||......+
T Consensus 92 ~~e~~~~~Y~Cp~C~~~y~--~~ea~~~~d~~~~f~Cp~Cg~~l~~~d 137 (147)
T smart00531 92 EDETNNAYYKCPNCQSKYT--FLEANQLLDMDGTFTCPRCGEELEEDD 137 (147)
T ss_pred hcccCCcEEECcCCCCEee--HHHHHHhcCCCCcEECCCCCCEEEEcC
Confidence 3445566778975542111 0111222 3345689999999876543
No 88
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=41.40 E-value=13 Score=18.80 Aligned_cols=12 Identities=25% Similarity=0.678 Sum_probs=10.1
Q ss_pred eecCCCCccccc
Q 034182 87 AICKYCGLRYVQ 98 (102)
Q Consensus 87 ~~CpYCG~ry~~ 98 (102)
-.|..|+..|..
T Consensus 2 ~~C~~C~~~F~~ 13 (27)
T PF13912_consen 2 FECDECGKTFSS 13 (27)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCccCCccCC
Confidence 479999999974
No 89
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=41.11 E-value=15 Score=24.09 Aligned_cols=12 Identities=33% Similarity=0.933 Sum_probs=9.6
Q ss_pred CCceecCCCCcc
Q 034182 84 KEPAICKYCGLR 95 (102)
Q Consensus 84 ~~~~~CpYCG~r 95 (102)
+....||+||..
T Consensus 16 ~d~e~CP~Cgs~ 27 (64)
T COG2093 16 EDTEICPVCGST 27 (64)
T ss_pred CCCccCCCCCCc
Confidence 456789999986
No 90
>COG1781 PyrI Aspartate carbamoyltransferase, regulatory subunit [Nucleotide transport and metabolism]
Probab=41.01 E-value=20 Score=27.09 Aligned_cols=57 Identities=18% Similarity=0.409 Sum_probs=31.6
Q ss_pred CChhhhhccCCCEE---e-----cCeEEeecCCCCCCCCC-C--ceEEEcC-CCCceecCCCCcccccc
Q 034182 43 KSPMELINEVPPIK---V-----EGRIVACEGDSNPALGH-P--IEFICLD-LKEPAICKYCGLRYVQD 99 (102)
Q Consensus 43 ~~a~elI~e~p~i~---V-----~~~~v~CdG~~~palGH-P--rVyI~Ld-~~~~~~CpYCG~ry~~~ 99 (102)
+..+..|....+++ + -..++.|+.+.=--+.. | --|.-++ ++..-.|.||++.|..+
T Consensus 80 ~ATvNiI~ny~VveK~~v~lP~~i~gvlkCpN~nCITn~e~pv~s~F~~~~~~~~~lrC~YCe~~~~~~ 148 (153)
T COG1781 80 NATVNIIRNYEVVEKFKVKLPEEIEGVLRCPNPNCITNAEEPVESKFYVVSKEPLALRCKYCEKTFSED 148 (153)
T ss_pred CCEEEEeeceEEEEeeccCCChhhccEEEcCCCCcccCCCccCCccEEEEecCCcEEEEEecCcEechh
Confidence 33455555554443 1 14578998874211111 1 1344444 44568999999998644
No 91
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=40.96 E-value=17 Score=20.41 Aligned_cols=11 Identities=36% Similarity=1.023 Sum_probs=8.6
Q ss_pred CCceecCCCCc
Q 034182 84 KEPAICKYCGL 94 (102)
Q Consensus 84 ~~~~~CpYCG~ 94 (102)
+-+..||.||.
T Consensus 16 ~~p~~CP~Cg~ 26 (34)
T cd00729 16 EAPEKCPICGA 26 (34)
T ss_pred cCCCcCcCCCC
Confidence 34679999997
No 92
>PF00653 BIR: Inhibitor of Apoptosis domain; InterPro: IPR001370 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The baculovirus inhibitor of apoptosis protein repeat (BIR) is a domain of tandem repeats separated by a variable length linker that seems to confer cell death-preventing activity [, ]. The BIR domains characterise the Inhibitor of Apoptosis (IAP) family of proteins (MEROPS proteinase inhibitor family I32, clan IV) that suppress apoptosis by interacting with and inhibiting the enzymatic activity of both initiator and effector caspases (MEROPS peptidase family C14, IPR002398 from INTERPRO). Several distinct mammalian IAPs including XIAP, c-IAP1, c-IAP2, and ML-IAP, have been identified, and they all exhibit antiapoptotic activity in cell culture. The functional unit in each IAP protein is the baculoviral IAP repeat (BIR), which contains approximately 80 amino acids folded around a zinc atom. Most mammalian IAPs have more than one BIR domain, with the different BIR domains performing distinct functions. For example, in XIAP, the third BIR domain (BIR3) potently inhibits the catalytic activity of caspase-9, whereas the linker sequences immediately preceding the second BIR domain (BIR2) selectively targets caspase-3 or -7. The first-recognised members of family MEROPS inhibitor family I32 were viral proteins that inhibited the apoptosis of infected cells: Cp-IAP from Cydia pomonella granulosis virus (CpGV) [] and Op-IAP from Orgyia pseudotsugata multicapsid polyhedrosis virus(OpMNPV) []. The discovery of homologous proteins in mammals followed soon after with the recognition that mutations in the gene for neuronal apoptosis inhibitory protein (NIAP) underlie spinal muscular atrophy []. The inhibitors in family I32 all possess one or more 80-residue domains known as BIR (baculovirus inhibitor repeat) domains and have accordingly been termed 'BIR-containing' or 'BIRC' proteins as well as IAP proteins. The mechanism of inhibition of caspases by the IAP proteins is complex, and reactive site residues cannot yet be identified with any confidence. Despite the conservation of the BIR or IAP (inhibitor of apoptosis) domains throughout the family it seems clear that other parts of the molecules also make essential contributions to inhibitory activity. Homologs of most components in the mammalian apoptotic pathway have been identified in fruit flies. The Drosophila Apaf-1, known as Dapaf-1, HAC-1 or Dark, shares significant sequence similarity with its mammalian counterpart, and is critically important for the activation of the Drosophila initiator caspase Dronc. Dronc, in turn, cleaves and activates the effector caspase DrICE. The Drosophila IAP, DIAP1, binds to and in-activates both DrICE and Dronc through its BIR1 and BIR2 domains. During apoptosis, the anti-death function of DIAP1 is countered by at least four pro-apoptotic proteins, Reaper, Hid, Grim, and sickle, through direct physical interactions. These four proteins represent the functional homologs of the mammalian protein Smac, and they all share a conserved IAP-binding motif at their N termini. The three proteins Reaper, Hid, and Grim are collectively referred to as the RHG proteins [, ]. Both XIAP and DIAP1 contain a RING domain at their C termini, and can act as an E3 ubiquitin ligase. Indeed, both XIAP and DIAP1 have been shown to promote self-ubiquitination and degradation as well as to negatively regulate the target caspases. Nonetheless, important differences exist between XIAP and DIAP1. The primary function of XIAP is thought to inhibit the catalytic activities of caspases; to what extent the ubiquitinating activity of XIAP contributes to its function remains unclear. For DIAP1, however, the ubiquitinating activity appears to be essential for its function. Recently a Drosophila p53 protein has been identified that mediates apoptosis via a novel pathway involving the activation of the Reaper gene and subsequent inhibition of the inhibitors of apoptosis (IAPs). CIAP1, a major mammalian homologue of Drosophila IAPs, is irreversibly inhibited (cleaved) during p53-dependent apoptosis and this cleavage is mediated by a serine protease. Serine protease inhibitors that block CIAP1 cleavage inhibit p53-dependent apoptosis. Furthermore, activation of the p53 protein increases the transcription of the HTRA2 gene, which encodes a serine protease that interacts with CIAP1 and potentiates apoptosis. Therefore mammalian p53 protein activates apoptosis through a novel pathway functionally similar to that in Drosophila, which involves HTRA2 and subsequent inhibition of CIAP1 by cleavage [].; GO: 0005622 intracellular; PDB: 3HL5_B 3UW5_A 3CM7_A 1G3F_A 1G73_C 3G76_G 3CM2_C 2VSL_A 2OPZ_B 3CLX_A ....
Probab=40.07 E-value=25 Score=21.90 Aligned_cols=17 Identities=29% Similarity=0.618 Sum_probs=12.9
Q ss_pred cCCCCceecCCCCcccc
Q 034182 81 LDLKEPAICKYCGLRYV 97 (102)
Q Consensus 81 Ld~~~~~~CpYCG~ry~ 97 (102)
.+.+..+.|-|||....
T Consensus 31 ~~~~d~v~C~~C~~~l~ 47 (70)
T PF00653_consen 31 TGTGDRVRCFYCGLELD 47 (70)
T ss_dssp ESSTTEEEETTTTEEEE
T ss_pred cCCCCEEEEeccCCEEe
Confidence 33356899999999874
No 93
>cd00022 BIR Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
Probab=39.13 E-value=23 Score=21.65 Aligned_cols=15 Identities=27% Similarity=0.753 Sum_probs=12.2
Q ss_pred CCceecCCCCccccc
Q 034182 84 KEPAICKYCGLRYVQ 98 (102)
Q Consensus 84 ~~~~~CpYCG~ry~~ 98 (102)
+..+.|.||+..+..
T Consensus 32 ~d~v~C~~C~~~~~~ 46 (69)
T cd00022 32 GDEVKCFFCGLELKN 46 (69)
T ss_pred CCEEEeCCCCCCccC
Confidence 457999999998863
No 94
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=38.87 E-value=18 Score=26.10 Aligned_cols=23 Identities=13% Similarity=0.544 Sum_probs=17.7
Q ss_pred CCceEEEcCCCCceecCCCCcccc
Q 034182 74 HPIEFICLDLKEPAICKYCGLRYV 97 (102)
Q Consensus 74 HPrVyI~Ld~~~~~~CpYCG~ry~ 97 (102)
+..-|..++ -|...||-||.-|.
T Consensus 38 ~~LdyV~ie-~G~t~CP~Cg~~~e 60 (115)
T COG1885 38 PDLDYVEIE-VGSTSCPKCGEPFE 60 (115)
T ss_pred CCCCeEEEe-cccccCCCCCCccc
Confidence 445588887 47889999998774
No 95
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=38.82 E-value=20 Score=22.72 Aligned_cols=23 Identities=26% Similarity=0.405 Sum_probs=18.1
Q ss_pred CCCCCCceEEEcCCCCceecCCCCccc
Q 034182 70 PALGHPIEFICLDLKEPAICKYCGLRY 96 (102)
Q Consensus 70 palGHPrVyI~Ld~~~~~~CpYCG~ry 96 (102)
-|..||+-| ..|...|.-||..-
T Consensus 4 ~~~shpr~y----GkGsr~C~vCg~~~ 26 (54)
T PTZ00218 4 LFNTHPRTY----GKGSRQCRVCSNRH 26 (54)
T ss_pred cccCCCCcC----CCCCCeeecCCCcc
Confidence 388999965 35788999999864
No 96
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=38.58 E-value=13 Score=24.33 Aligned_cols=15 Identities=27% Similarity=0.667 Sum_probs=11.8
Q ss_pred CCceecCCCCccccc
Q 034182 84 KEPAICKYCGLRYVQ 98 (102)
Q Consensus 84 ~~~~~CpYCG~ry~~ 98 (102)
+..-.||-||..|..
T Consensus 15 E~~lrCPRC~~~FR~ 29 (65)
T COG4049 15 EEFLRCPRCGMVFRR 29 (65)
T ss_pred ceeeeCCchhHHHHH
Confidence 335689999999964
No 97
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=36.99 E-value=17 Score=21.28 Aligned_cols=10 Identities=30% Similarity=0.790 Sum_probs=7.7
Q ss_pred ceecCCCCcc
Q 034182 86 PAICKYCGLR 95 (102)
Q Consensus 86 ~~~CpYCG~r 95 (102)
..+||+||..
T Consensus 18 g~~CP~Cg~~ 27 (46)
T PF12760_consen 18 GFVCPHCGST 27 (46)
T ss_pred CCCCCCCCCe
Confidence 3669999963
No 98
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=36.97 E-value=31 Score=23.96 Aligned_cols=35 Identities=20% Similarity=0.274 Sum_probs=26.4
Q ss_pred CeEEeecCCCCCCCCCCceEEEcCCCC-ceecCCCCccccc
Q 034182 59 GRIVACEGDSNPALGHPIEFICLDLKE-PAICKYCGLRYVQ 98 (102)
Q Consensus 59 ~~~v~CdG~~~palGHPrVyI~Ld~~~-~~~CpYCG~ry~~ 98 (102)
...+.|+-= |++.|=+++++.. ...|+-||..|..
T Consensus 19 pt~f~CP~C-----ge~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 19 PKIFECPRC-----GKVSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred CcEeECCCC-----CCeEeeeecCCCcceEECCCCCCccCE
Confidence 467888754 4578888888743 7899999998864
No 99
>cd00085 HNHc HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.
Probab=36.04 E-value=16 Score=20.38 Aligned_cols=10 Identities=40% Similarity=1.102 Sum_probs=8.1
Q ss_pred eecCCCCccc
Q 034182 87 AICKYCGLRY 96 (102)
Q Consensus 87 ~~CpYCG~ry 96 (102)
..|+|||..+
T Consensus 12 ~~C~~c~~~~ 21 (57)
T cd00085 12 GLCPYCGKPG 21 (57)
T ss_pred CcCccCCCcC
Confidence 5799999864
No 100
>TIGR00510 lipA lipoate synthase. The family shows strong sequence conservation.
Probab=35.42 E-value=30 Score=27.97 Aligned_cols=62 Identities=11% Similarity=0.158 Sum_probs=38.3
Q ss_pred eeeeccCCCCh----h-hhhccCCCEEecCeEEeecCCCCCCCCCCceEEEcCCCCceecCCCCcccc
Q 034182 35 KWMQDVSKKSP----M-ELINEVPPIKVEGRIVACEGDSNPALGHPIEFICLDLKEPAICKYCGLRYV 97 (102)
Q Consensus 35 ~~~~~~~~~~a----~-elI~e~p~i~V~~~~v~CdG~~~palGHPrVyI~Ld~~~~~~CpYCG~ry~ 97 (102)
.|+....+... + +++.+...-.| =....|+.-+.-|.++=+.||.|..-=...|.||+..+.
T Consensus 19 ~w~~~~~~~~~~~~~~~~~~~~~~l~tv-c~~a~cpn~~ec~~~~tatfm~i~~gC~~~C~FC~v~~~ 85 (302)
T TIGR00510 19 EWLKIKLPLGTVIAQIKNTMKNKGLHTV-CEEASCPNLTECWNHGTATFMILGDICTRRCPFCDVAHG 85 (302)
T ss_pred cceEecCCCCchHHHHHHHHHHCCCcee-ecCCCCCCcccccCCCEEEEEecCcCcCCCCCcCCccCC
Confidence 47776544221 1 24444322222 112456666545889999999999644899999997653
No 101
>PRK11827 hypothetical protein; Provisional
Probab=34.43 E-value=35 Score=21.83 Aligned_cols=31 Identities=29% Similarity=0.474 Sum_probs=20.7
Q ss_pred EEeecCCCCCCCCCCceEEEcCC-CCceecCCCCcccccc
Q 034182 61 IVACEGDSNPALGHPIEFICLDL-KEPAICKYCGLRYVQD 99 (102)
Q Consensus 61 ~v~CdG~~~palGHPrVyI~Ld~-~~~~~CpYCG~ry~~~ 99 (102)
++.|+.-.++ | .| ++ .+.-+|+-||+.|--.
T Consensus 8 ILaCP~ckg~-L----~~---~~~~~~Lic~~~~laYPI~ 39 (60)
T PRK11827 8 IIACPVCNGK-L----WY---NQEKQELICKLDNLAFPLR 39 (60)
T ss_pred heECCCCCCc-C----eE---cCCCCeEECCccCeecccc
Confidence 5788876553 2 22 33 3578899999999543
No 102
>PF02489 Herpes_glycop_H: Herpesvirus glycoprotein H; InterPro: IPR003493 Herpesviruses are enveloped by a lipid bilayer that contains at least a dozen glycoproteins. The virion surface glycoproteins mediate recognition of susceptible cells and promote fusion of the viral envelope with the cell membrane, leading to virus entry. No single glycoprotein associated with the virion membrane has been identified as the fusogen []. Glycoprotein L (gL) forms a non-covalently linked heterodimer with glycoprotein H (gH). This heterodimer is essential for virus-cell and cell-cell fusion since the association of gH and gL is necessary for correct localisation of gH to the virion or cell surface. gH anchoring the heterodimer to the plasma membrane through its transmembrane domain. gL lacks a transmembrane domain and is secreted from cells when expressed in the absence of gH []. This entry represents Herpesvirus glycoprotein H (gH), which is a virion associated envelope glycoprotein []. Heterodimer formation between gH and gL has been demonstrated in both virions and infected cells []. Heterodimer formation between gL and gH is important for the proper folding of gH and its insertion into the membrane because the anti-gH conformation-dependent monoclonal antibodies (mAbs) 53S and LP11 bind gH only when gL is present [, ].; PDB: 3PHF_S 3M1C_A 2LQY_A 2XQY_A.
Probab=34.22 E-value=18 Score=31.70 Aligned_cols=34 Identities=15% Similarity=0.505 Sum_probs=14.2
Q ss_pred EEeecCCCCC--CCCCCceEEEcCCCCceecCCCCcccc
Q 034182 61 IVACEGDSNP--ALGHPIEFICLDLKEPAICKYCGLRYV 97 (102)
Q Consensus 61 ~v~CdG~~~p--alGHPrVyI~Ld~~~~~~CpYCG~ry~ 97 (102)
.-.|...... ..-=|++| |+. ....|+|||..|.
T Consensus 537 ~~~C~~~~~~~~~~~i~~~~-Nit--~~~~C~~Cgsv~l 572 (657)
T PF02489_consen 537 NSTCSSSTGIIETRRIPVVY-NIT--PSKDCPFCGSVFL 572 (657)
T ss_dssp TT-S-CCEE-SEEEE--EE---SS--S-SS-STTT-EEE
T ss_pred CCCCcCCCCCCCccccCCCc-CCC--CCCCCCCCCcEEE
Confidence 4467765321 12224455 555 3458999998875
No 103
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=33.73 E-value=17 Score=27.66 Aligned_cols=23 Identities=22% Similarity=0.342 Sum_probs=16.7
Q ss_pred CceEEEcCCCCceecCCCCcccccc
Q 034182 75 PIEFICLDLKEPAICKYCGLRYVQD 99 (102)
Q Consensus 75 PrVyI~Ld~~~~~~CpYCG~ry~~~ 99 (102)
|+||.+-+ ...+||-||+.|=.-
T Consensus 121 ~~~~~~~~--~f~~C~~CgkiYW~G 143 (165)
T COG1656 121 EKVYRNYE--EFYRCPKCGKIYWKG 143 (165)
T ss_pred hhhhhccc--ceeECCCCcccccCc
Confidence 45776655 468899999999543
No 104
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=33.58 E-value=28 Score=19.14 Aligned_cols=12 Identities=33% Similarity=0.946 Sum_probs=9.2
Q ss_pred CCceecCCCCcc
Q 034182 84 KEPAICKYCGLR 95 (102)
Q Consensus 84 ~~~~~CpYCG~r 95 (102)
+.+..||-||..
T Consensus 15 ~~~~~CP~Cg~~ 26 (33)
T cd00350 15 EAPWVCPVCGAP 26 (33)
T ss_pred cCCCcCcCCCCc
Confidence 357799999973
No 105
>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
Probab=33.49 E-value=34 Score=20.97 Aligned_cols=14 Identities=21% Similarity=0.605 Sum_probs=11.2
Q ss_pred CceecCCCCccccc
Q 034182 85 EPAICKYCGLRYVQ 98 (102)
Q Consensus 85 ~~~~CpYCG~ry~~ 98 (102)
..+.|.|||..+..
T Consensus 35 d~v~C~~C~~~l~~ 48 (71)
T smart00238 35 DEVKCFFCGGELDN 48 (71)
T ss_pred CEEEeCCCCCCcCC
Confidence 36999999998753
No 106
>PHA03296 envelope glycoprotein H; Provisional
Probab=33.41 E-value=23 Score=32.81 Aligned_cols=23 Identities=17% Similarity=0.268 Sum_probs=16.9
Q ss_pred CCceEEEcCCCCceecCCCCcccc
Q 034182 74 HPIEFICLDLKEPAICKYCGLRYV 97 (102)
Q Consensus 74 HPrVyI~Ld~~~~~~CpYCG~ry~ 97 (102)
=|.+++|+.. ....|+|||..|.
T Consensus 682 Ip~v~LN~t~-~~k~C~yCGSVfL 704 (814)
T PHA03296 682 IEDGHLNLHG-AAIACILCGHAIL 704 (814)
T ss_pred ccceeecCCC-CCCcCCcCCEEEE
Confidence 3566677764 4678999998875
No 107
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=32.91 E-value=23 Score=22.58 Aligned_cols=13 Identities=23% Similarity=0.442 Sum_probs=8.1
Q ss_pred ceecCCCCccccc
Q 034182 86 PAICKYCGLRYVQ 98 (102)
Q Consensus 86 ~~~CpYCG~ry~~ 98 (102)
.+.||||.....-
T Consensus 55 ~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 55 FGECPYCSSPISW 67 (70)
T ss_dssp EEE-TTT-SEEEG
T ss_pred ccCCcCCCCeeeE
Confidence 4789999987653
No 108
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=32.87 E-value=13 Score=23.65 Aligned_cols=15 Identities=20% Similarity=0.326 Sum_probs=11.3
Q ss_pred CCceecCCCCccccc
Q 034182 84 KEPAICKYCGLRYVQ 98 (102)
Q Consensus 84 ~~~~~CpYCG~ry~~ 98 (102)
...-.||+||..+.-
T Consensus 12 ~v~~~Cp~cGipthc 26 (55)
T PF13824_consen 12 HVNFECPDCGIPTHC 26 (55)
T ss_pred ccCCcCCCCCCcCcc
Confidence 346789999988753
No 109
>PRK12495 hypothetical protein; Provisional
Probab=32.37 E-value=7.6 Score=30.99 Aligned_cols=55 Identities=20% Similarity=0.355 Sum_probs=33.0
Q ss_pred eeeeccCCCChhhhhccCCCEEecCeEEeecCCCCCCCCCCceEEEcCCCCceecCCCCccccc
Q 034182 35 KWMQDVSKKSPMELINEVPPIKVEGRIVACEGDSNPALGHPIEFICLDLKEPAICKYCGLRYVQ 98 (102)
Q Consensus 35 ~~~~~~~~~~a~elI~e~p~i~V~~~~v~CdG~~~palGHPrVyI~Ld~~~~~~CpYCG~ry~~ 98 (102)
|+.+++.+..+++.|++.=.....-.-..|.-=|.| + | ..+|...|+.|+..+..
T Consensus 16 Kye~d~~~R~~~~~ma~lL~~gatmsa~hC~~CG~P-I-----p---a~pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 16 KYEQDEQKREATERMSELLLQGATMTNAHCDECGDP-I-----F---RHDGQEFCPTCQQPVTE 70 (226)
T ss_pred HHhhhHHHHHHHHHHHHHHHhhcccchhhcccccCc-c-----c---CCCCeeECCCCCCcccc
Confidence 444555566666666554333344555667555444 2 1 33789999999988753
No 110
>PRK13376 pyrB bifunctional aspartate carbamoyltransferase catalytic subunit/aspartate carbamoyltransferase regulatory subunit; Provisional
Probab=31.92 E-value=98 Score=27.29 Aligned_cols=37 Identities=24% Similarity=0.540 Sum_probs=24.1
Q ss_pred EeecCCCC---CCCC--CCceEEEcCCCCceecCCCCcccccc
Q 034182 62 VACEGDSN---PALG--HPIEFICLDLKEPAICKYCGLRYVQD 99 (102)
Q Consensus 62 v~CdG~~~---palG--HPrVyI~Ld~~~~~~CpYCG~ry~~~ 99 (102)
+.|+.+.= ...+ =+..|.-. ..+.-+|.||++.|..+
T Consensus 479 ~~C~Np~CIt~~~~~e~~~~~F~~~-~~~~~~C~YCe~~~~~~ 520 (525)
T PRK13376 479 LRCKNENCITNPAHGENVSASFVRN-EKGRFVCEYCETPHTFE 520 (525)
T ss_pred EEeCCCCCcCCCCCCCcCCceEEEc-cCCEEEeeCCCCEeccc
Confidence 89988742 1111 24456655 34589999999998654
No 111
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=31.37 E-value=38 Score=21.14 Aligned_cols=12 Identities=33% Similarity=0.736 Sum_probs=10.3
Q ss_pred ceecCCCCcccc
Q 034182 86 PAICKYCGLRYV 97 (102)
Q Consensus 86 ~~~CpYCG~ry~ 97 (102)
.+.||-||..|.
T Consensus 22 iV~Cp~CGaele 33 (54)
T TIGR01206 22 LVICDECGAELE 33 (54)
T ss_pred EEeCCCCCCEEE
Confidence 678999999885
No 112
>PHA00732 hypothetical protein
Probab=30.94 E-value=21 Score=23.55 Aligned_cols=13 Identities=23% Similarity=0.559 Sum_probs=10.7
Q ss_pred ecCCCCccccccc
Q 034182 88 ICKYCGLRYVQDH 100 (102)
Q Consensus 88 ~CpYCG~ry~~~~ 100 (102)
.|+.||..|....
T Consensus 29 ~C~~CgKsF~~l~ 41 (79)
T PHA00732 29 KCPVCNKSYRRLN 41 (79)
T ss_pred ccCCCCCEeCChh
Confidence 7999999997543
No 113
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=30.72 E-value=48 Score=18.83 Aligned_cols=27 Identities=26% Similarity=0.433 Sum_probs=14.2
Q ss_pred CCCCCceEEEcCCC--CceecCCCCcccc
Q 034182 71 ALGHPIEFICLDLK--EPAICKYCGLRYV 97 (102)
Q Consensus 71 alGHPrVyI~Ld~~--~~~~CpYCG~ry~ 97 (102)
.-|+|..+.-.+.+ ...+|+=||...+
T Consensus 5 ~CG~~l~~~ip~gd~r~R~vC~~Cg~IhY 33 (34)
T PF14803_consen 5 QCGGPLERRIPEGDDRERLVCPACGFIHY 33 (34)
T ss_dssp TT--B-EEE--TT-SS-EEEETTTTEEE-
T ss_pred cccChhhhhcCCCCCccceECCCCCCEEe
Confidence 35788888777444 4788999997653
No 114
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=30.10 E-value=25 Score=26.62 Aligned_cols=17 Identities=24% Similarity=0.757 Sum_probs=13.5
Q ss_pred EEEcCCCCceecCCCCcc
Q 034182 78 FICLDLKEPAICKYCGLR 95 (102)
Q Consensus 78 yI~Ld~~~~~~CpYCG~r 95 (102)
|+-.+ +.+..||-||..
T Consensus 142 y~~~g-e~P~~CPiCga~ 158 (166)
T COG1592 142 YTHEG-EAPEVCPICGAP 158 (166)
T ss_pred CcccC-CCCCcCCCCCCh
Confidence 56666 789999999954
No 115
>smart00746 TRASH metallochaperone-like domain.
Probab=29.69 E-value=24 Score=17.11 Aligned_cols=9 Identities=33% Similarity=1.132 Sum_probs=7.2
Q ss_pred cCCCCcccc
Q 034182 89 CKYCGLRYV 97 (102)
Q Consensus 89 CpYCG~ry~ 97 (102)
|++||....
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 889988765
No 116
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=29.66 E-value=25 Score=20.09 Aligned_cols=12 Identities=42% Similarity=0.822 Sum_probs=9.4
Q ss_pred eecCCCCccccc
Q 034182 87 AICKYCGLRYVQ 98 (102)
Q Consensus 87 ~~CpYCG~ry~~ 98 (102)
.+|+-||..|-.
T Consensus 2 r~C~~Cg~~Yh~ 13 (36)
T PF05191_consen 2 RICPKCGRIYHI 13 (36)
T ss_dssp EEETTTTEEEET
T ss_pred cCcCCCCCcccc
Confidence 468999998854
No 117
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=29.36 E-value=24 Score=30.14 Aligned_cols=18 Identities=28% Similarity=0.521 Sum_probs=12.4
Q ss_pred EEEcCCCCceecCCCCcc
Q 034182 78 FICLDLKEPAICKYCGLR 95 (102)
Q Consensus 78 yI~Ld~~~~~~CpYCG~r 95 (102)
||....+.--+|||||..
T Consensus 71 ~i~~y~~qSftCPyC~~~ 88 (381)
T KOG1280|consen 71 PISHYDPQSFTCPYCGIM 88 (381)
T ss_pred cccccccccccCCccccc
Confidence 344444556789999975
No 118
>PHA00733 hypothetical protein
Probab=29.04 E-value=32 Score=24.40 Aligned_cols=16 Identities=19% Similarity=0.632 Sum_probs=9.4
Q ss_pred CCCCceecCCCCcccc
Q 034182 82 DLKEPAICKYCGLRYV 97 (102)
Q Consensus 82 d~~~~~~CpYCG~ry~ 97 (102)
..+.+..|++||..|.
T Consensus 69 ~~~kPy~C~~Cgk~Fs 84 (128)
T PHA00733 69 KAVSPYVCPLCLMPFS 84 (128)
T ss_pred CCCCCccCCCCCCcCC
Confidence 3344566666666665
No 119
>PF09180 ProRS-C_1: Prolyl-tRNA synthetase, C-terminal; InterPro: IPR016061 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Prolyl tRNA synthetase (6.1.1.15 from EC) exists in two forms, which are loosely related. The first form is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota. Prolyl-tRNA synthetase belongs to class IIa. This domain is found at the C-terminal in archaeal and eukaryotic enzymes, as well as in certain bacterial ones.; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1NJ6_A 1NJ2_A 1NJ5_A 1NJ1_A 1H4T_C 1H4S_A 1HC7_C 1H4Q_B 3IAL_B.
Probab=28.03 E-value=31 Score=21.91 Aligned_cols=12 Identities=33% Similarity=0.645 Sum_probs=6.7
Q ss_pred CCceecCCCCcc
Q 034182 84 KEPAICKYCGLR 95 (102)
Q Consensus 84 ~~~~~CpYCG~r 95 (102)
.....|.+||..
T Consensus 46 ~~~~~Ci~cgk~ 57 (68)
T PF09180_consen 46 PEGGKCIVCGKP 57 (68)
T ss_dssp BTT-B-TTT-SB
T ss_pred CCCCeeecCCCh
Confidence 457899999964
No 120
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=27.01 E-value=39 Score=24.12 Aligned_cols=37 Identities=24% Similarity=0.476 Sum_probs=25.1
Q ss_pred cCeEEeecCCCCCCCCCCceEEEcCC----CCceecCCCCcccccc
Q 034182 58 EGRIVACEGDSNPALGHPIEFICLDL----KEPAICKYCGLRYVQD 99 (102)
Q Consensus 58 ~~~~v~CdG~~~palGHPrVyI~Ld~----~~~~~CpYCG~ry~~~ 99 (102)
=.+.+-|+- -||-.|=+.+-+ -+.+.|+-||++|.-+
T Consensus 19 L~k~FtCp~-----Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~e 59 (104)
T COG4888 19 LPKTFTCPR-----CGHEKVSSCTVKKTVNIGTAVCGNCGLSFECE 59 (104)
T ss_pred CCceEecCc-----cCCeeeeEEEEEecCceeEEEcccCcceEEEe
Confidence 466777864 467777644332 2478999999999743
No 121
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=26.37 E-value=24 Score=21.98 Aligned_cols=15 Identities=33% Similarity=0.928 Sum_probs=11.4
Q ss_pred CceecCCCCcccccc
Q 034182 85 EPAICKYCGLRYVQD 99 (102)
Q Consensus 85 ~~~~CpYCG~ry~~~ 99 (102)
.-.-|=|||.+|...
T Consensus 26 ~~~YC~~Cg~~Y~d~ 40 (55)
T PF13821_consen 26 EHNYCFWCGTKYDDE 40 (55)
T ss_pred hCceeeeeCCccCCH
Confidence 345699999999753
No 122
>KOG0292 consensus Vesicle coat complex COPI, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.26 E-value=32 Score=33.04 Aligned_cols=21 Identities=24% Similarity=0.659 Sum_probs=15.0
Q ss_pred EEEcCCCC-ceecCCCCccccc
Q 034182 78 FICLDLKE-PAICKYCGLRYVQ 98 (102)
Q Consensus 78 yI~Ld~~~-~~~CpYCG~ry~~ 98 (102)
|-+|=... ...|||||..|+.
T Consensus 1155 ~~Piy~g~p~~~cp~cga~y~~ 1176 (1202)
T KOG0292|consen 1155 YVPIYRGRPDVSCPYCGACFVP 1176 (1202)
T ss_pred ceeeecCCCCcCCCcccceecc
Confidence 45554433 5789999999974
No 123
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=25.92 E-value=31 Score=21.35 Aligned_cols=9 Identities=44% Similarity=1.139 Sum_probs=7.6
Q ss_pred ceecCCCCc
Q 034182 86 PAICKYCGL 94 (102)
Q Consensus 86 ~~~CpYCG~ 94 (102)
.-+|+|||.
T Consensus 44 ~y~C~~Cg~ 52 (54)
T PF10058_consen 44 QYRCPYCGA 52 (54)
T ss_pred EEEcCCCCC
Confidence 568999995
No 124
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=25.86 E-value=23 Score=24.17 Aligned_cols=16 Identities=25% Similarity=0.644 Sum_probs=7.7
Q ss_pred CCCceecCCCCccccc
Q 034182 83 LKEPAICKYCGLRYVQ 98 (102)
Q Consensus 83 ~~~~~~CpYCG~ry~~ 98 (102)
+++...||-|+++|+.
T Consensus 48 keg~q~CpqCkt~ykr 63 (80)
T PF14569_consen 48 KEGNQVCPQCKTRYKR 63 (80)
T ss_dssp HTS-SB-TTT--B---
T ss_pred hcCcccccccCCCccc
Confidence 4788899999999974
No 125
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=25.46 E-value=60 Score=22.37 Aligned_cols=36 Identities=22% Similarity=0.451 Sum_probs=23.8
Q ss_pred eecCCCCCCCCCCceEEEcCC--------CC-ceecCCCCcccccc
Q 034182 63 ACEGDSNPALGHPIEFICLDL--------KE-PAICKYCGLRYVQD 99 (102)
Q Consensus 63 ~CdG~~~palGHPrVyI~Ld~--------~~-~~~CpYCG~ry~~~ 99 (102)
.|.|++. ..|-=.+|.++.+ +- ...|+-||-.|..+
T Consensus 4 ~C~~~~~-~~~~tTv~~el~~G~~~IvIknVPa~~C~~CGe~y~~d 48 (89)
T TIGR03829 4 WCEEEKA-IARTTTVYWELPDGTKAIEIKETPSISCSHCGMEYQDD 48 (89)
T ss_pred ccCCCce-ecceEEEEEEecCCceEEEEecCCcccccCCCcEeecH
Confidence 5766543 4566677777743 12 35799999999753
No 126
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=25.08 E-value=37 Score=21.00 Aligned_cols=15 Identities=33% Similarity=0.780 Sum_probs=12.3
Q ss_pred CCceecCCCCccccc
Q 034182 84 KEPAICKYCGLRYVQ 98 (102)
Q Consensus 84 ~~~~~CpYCG~ry~~ 98 (102)
+..-+|.-||..|+.
T Consensus 2 Dk~l~C~dCg~~Fvf 16 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVF 16 (49)
T ss_pred CeeEEcccCCCeEEE
Confidence 456789999999985
No 127
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=24.79 E-value=41 Score=17.66 Aligned_cols=13 Identities=23% Similarity=0.759 Sum_probs=10.6
Q ss_pred ceecCCCCccccc
Q 034182 86 PAICKYCGLRYVQ 98 (102)
Q Consensus 86 ~~~CpYCG~ry~~ 98 (102)
.-.|.+|+..|..
T Consensus 3 ~~~C~~C~~~~~~ 15 (35)
T smart00451 3 GFYCKLCNVTFTD 15 (35)
T ss_pred CeEccccCCccCC
Confidence 4579999999873
No 128
>PRK00420 hypothetical protein; Validated
Probab=24.69 E-value=68 Score=22.84 Aligned_cols=16 Identities=19% Similarity=0.432 Sum_probs=13.2
Q ss_pred CCCceecCCCCccccc
Q 034182 83 LKEPAICKYCGLRYVQ 98 (102)
Q Consensus 83 ~~~~~~CpYCG~ry~~ 98 (102)
++|...||-||..+.-
T Consensus 37 k~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 37 KDGEVVCPVHGKVYIV 52 (112)
T ss_pred CCCceECCCCCCeeee
Confidence 5789999999997753
No 129
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=23.86 E-value=30 Score=19.30 Aligned_cols=14 Identities=29% Similarity=0.826 Sum_probs=3.9
Q ss_pred eecCCCCccccccc
Q 034182 87 AICKYCGLRYVQDH 100 (102)
Q Consensus 87 ~~CpYCG~ry~~~~ 100 (102)
-.||.||..|.+.+
T Consensus 3 p~Cp~C~se~~y~D 16 (30)
T PF08274_consen 3 PKCPLCGSEYTYED 16 (30)
T ss_dssp ---TTT-----EE-
T ss_pred CCCCCCCCcceecc
Confidence 36999998887643
No 130
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=23.45 E-value=1.1e+02 Score=21.29 Aligned_cols=30 Identities=17% Similarity=0.266 Sum_probs=17.8
Q ss_pred cCeEEeecCCCCCCCCCCceEEEcCCCCceecCCCCcc
Q 034182 58 EGRIVACEGDSNPALGHPIEFICLDLKEPAICKYCGLR 95 (102)
Q Consensus 58 ~~~~v~CdG~~~palGHPrVyI~Ld~~~~~~CpYCG~r 95 (102)
-.-.+.|.-=+. +.++.......||.||..
T Consensus 67 ~p~~~~C~~Cg~--------~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 67 QEAECWCETCQQ--------YVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred eCcEEEcccCCC--------eeecCCccCCcCcCcCCC
Confidence 345667754332 455543334679999965
No 131
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=23.24 E-value=46 Score=19.03 Aligned_cols=15 Identities=33% Similarity=0.603 Sum_probs=9.4
Q ss_pred CceecCCCCcccccc
Q 034182 85 EPAICKYCGLRYVQD 99 (102)
Q Consensus 85 ~~~~CpYCG~ry~~~ 99 (102)
....|+.||=+|.+.
T Consensus 20 ~~isC~~CGPr~~i~ 34 (35)
T PF07503_consen 20 QFISCTNCGPRYSII 34 (35)
T ss_dssp TT--BTTCC-SCCCE
T ss_pred cCccCCCCCCCEEEe
Confidence 467899999998753
No 132
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=22.93 E-value=25 Score=30.91 Aligned_cols=15 Identities=20% Similarity=0.581 Sum_probs=12.6
Q ss_pred CCceecCCCCccccc
Q 034182 84 KEPAICKYCGLRYVQ 98 (102)
Q Consensus 84 ~~~~~CpYCG~ry~~ 98 (102)
++...|.|||+.|..
T Consensus 354 ~gi~~C~~C~KkFrR 368 (500)
T KOG3993|consen 354 SGIFSCHTCGKKFRR 368 (500)
T ss_pred CceeecHHhhhhhHH
Confidence 457889999999974
No 133
>cd00150 PlantTI Plant trypsin inhibitors such as squash trypsin inhibitor. Plant proteinase inhibitors play important roles in natural plant defense. Proteinase inhibitors from squash seeds form an uniform family of small proteins cross-linked with three disulfide bridges.
Probab=22.85 E-value=48 Score=18.38 Aligned_cols=10 Identities=10% Similarity=0.046 Sum_probs=7.4
Q ss_pred CceEEEcCCC
Q 034182 75 PIEFICLDLK 84 (102)
Q Consensus 75 PrVyI~Ld~~ 84 (102)
||+++.-..+
T Consensus 2 PrIlm~Ck~D 11 (27)
T cd00150 2 PRILMECKRD 11 (27)
T ss_pred cchheecccc
Confidence 7888877764
No 134
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=22.75 E-value=63 Score=17.83 Aligned_cols=13 Identities=31% Similarity=0.948 Sum_probs=10.2
Q ss_pred eecCCCCcccccc
Q 034182 87 AICKYCGLRYVQD 99 (102)
Q Consensus 87 ~~CpYCG~ry~~~ 99 (102)
..|+.||..|...
T Consensus 33 ~~C~~CGE~~~~~ 45 (46)
T TIGR03831 33 LVCPQCGEEYLDA 45 (46)
T ss_pred cccccCCCEeeCC
Confidence 4699999988653
No 135
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.67 E-value=40 Score=23.53 Aligned_cols=12 Identities=17% Similarity=0.642 Sum_probs=8.6
Q ss_pred CceecCCCCccc
Q 034182 85 EPAICKYCGLRY 96 (102)
Q Consensus 85 ~~~~CpYCG~ry 96 (102)
....||+||..-
T Consensus 87 ~~~~CP~Cgs~~ 98 (117)
T PRK00564 87 DYGVCEKCHSKN 98 (117)
T ss_pred cCCcCcCCCCCc
Confidence 345699999754
No 136
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=22.26 E-value=72 Score=19.48 Aligned_cols=25 Identities=20% Similarity=0.289 Sum_probs=14.9
Q ss_pred CCCCCceEEEcCCCCceecCCCCcccc
Q 034182 71 ALGHPIEFICLDLKEPAICKYCGLRYV 97 (102)
Q Consensus 71 alGHPrVyI~Ld~~~~~~CpYCG~ry~ 97 (102)
.-||...- -.......||-||..+-
T Consensus 33 ~CG~~~~~--~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 33 RCGHRNKK--RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred Cccccccc--ccccceEEcCCCCCEEC
Confidence 34665555 11234778888887753
No 137
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=22.12 E-value=41 Score=18.17 Aligned_cols=12 Identities=33% Similarity=0.985 Sum_probs=6.1
Q ss_pred ecCCCCcccccc
Q 034182 88 ICKYCGLRYVQD 99 (102)
Q Consensus 88 ~CpYCG~ry~~~ 99 (102)
.||.||..-+++
T Consensus 1 ~CP~C~s~l~~~ 12 (28)
T PF03119_consen 1 TCPVCGSKLVRE 12 (28)
T ss_dssp B-TTT--BEEE-
T ss_pred CcCCCCCEeEcC
Confidence 499999887643
No 138
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=21.82 E-value=53 Score=26.95 Aligned_cols=31 Identities=29% Similarity=0.566 Sum_probs=21.9
Q ss_pred CeEEeecCCCCCCCCCCceEEEcC-------CCCceecCCCCc
Q 034182 59 GRIVACEGDSNPALGHPIEFICLD-------LKEPAICKYCGL 94 (102)
Q Consensus 59 ~~~v~CdG~~~palGHPrVyI~Ld-------~~~~~~CpYCG~ 94 (102)
+..|+|||.+ -++.|+-++ .+|...||.|-.
T Consensus 232 GqMVaCDn~n-----CkrEWFH~~CVGLk~pPKG~WYC~eCk~ 269 (271)
T COG5034 232 GQMVACDNAN-----CKREWFHLECVGLKEPPKGKWYCPECKK 269 (271)
T ss_pred ccceecCCCC-----CchhheeccccccCCCCCCcEeCHHhHh
Confidence 7789999874 445555544 467899999953
No 139
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=21.82 E-value=96 Score=20.05 Aligned_cols=31 Identities=32% Similarity=0.618 Sum_probs=22.1
Q ss_pred EEeecCCCCCCCCCCceEEEcCCC-CceecCCCCcccccc
Q 034182 61 IVACEGDSNPALGHPIEFICLDLK-EPAICKYCGLRYVQD 99 (102)
Q Consensus 61 ~v~CdG~~~palGHPrVyI~Ld~~-~~~~CpYCG~ry~~~ 99 (102)
+++|+--.++ |.++++ +.-.|+-|++.|--.
T Consensus 8 iLaCP~~kg~--------L~~~~~~~~L~c~~~~~aYpI~ 39 (60)
T COG2835 8 ILACPVCKGP--------LVYDEEKQELICPRCKLAYPIR 39 (60)
T ss_pred eeeccCcCCc--------ceEeccCCEEEecccCceeecc
Confidence 6788776653 455554 478999999999643
No 140
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=21.45 E-value=48 Score=23.08 Aligned_cols=20 Identities=25% Similarity=0.738 Sum_probs=15.4
Q ss_pred EEEcCCCCceecCCCCcccccc
Q 034182 78 FICLDLKEPAICKYCGLRYVQD 99 (102)
Q Consensus 78 yI~Ld~~~~~~CpYCG~ry~~~ 99 (102)
|. .+.+..+|..||.+|.+.
T Consensus 46 Y~--q~g~~lvC~~C~~~~~~~ 65 (102)
T PF10080_consen 46 YY--QEGDQLVCKNCGVRFNLP 65 (102)
T ss_pred eE--EECCEEEEecCCCEEehh
Confidence 66 234689999999999754
No 141
>TIGR02646 conserved hypothetical protein TIGR02646. Members of this uncharacterized protein family are found exclusively in bacteria. Neighboring genes in various genomes are also uncharacterized or may annotated as similar to restriction system proteins.
Probab=21.20 E-value=45 Score=23.69 Aligned_cols=14 Identities=21% Similarity=0.631 Sum_probs=10.4
Q ss_pred CCceecCCCCcccc
Q 034182 84 KEPAICKYCGLRYV 97 (102)
Q Consensus 84 ~~~~~CpYCG~ry~ 97 (102)
.....|.||+..+.
T Consensus 22 ~~~~~C~YC~~~~~ 35 (144)
T TIGR02646 22 LQGGLCAYCEREIE 35 (144)
T ss_pred HhCCCcCccCCCcC
Confidence 34578999999554
No 142
>PF14921 APCDDC: Adenomatosis polyposis coli down-regulated 1
Probab=21.08 E-value=43 Score=26.78 Aligned_cols=17 Identities=41% Similarity=0.925 Sum_probs=15.3
Q ss_pred ceecCCCCcccccccCC
Q 034182 86 PAICKYCGLRYVQDHHH 102 (102)
Q Consensus 86 ~~~CpYCG~ry~~~~hh 102 (102)
...||-||..|..++||
T Consensus 218 ~~~C~~C~~i~rs~e~~ 234 (240)
T PF14921_consen 218 AHPCPACGIIYRSDEHH 234 (240)
T ss_pred CCCCCccceeeecccCC
Confidence 56799999999999887
No 143
>smart00286 PTI Plant trypsin inhibitors.
Probab=20.41 E-value=46 Score=18.75 Aligned_cols=20 Identities=35% Similarity=0.675 Sum_probs=12.6
Q ss_pred CCceEEEcCCCC--ce--ec---CCCC
Q 034182 74 HPIEFICLDLKE--PA--IC---KYCG 93 (102)
Q Consensus 74 HPrVyI~Ld~~~--~~--~C---pYCG 93 (102)
-||+++.-..+. .+ +| +|||
T Consensus 3 CPrIlm~Ck~DsDCl~~CiC~~~G~CG 29 (29)
T smart00286 3 CPRILMECKRDSDCMAECICLANGYCG 29 (29)
T ss_pred CchhhhccccccCcccCCEEccccccC
Confidence 588888777653 23 33 6776
No 144
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=20.41 E-value=1.1e+02 Score=19.49 Aligned_cols=30 Identities=17% Similarity=0.248 Sum_probs=17.7
Q ss_pred EecCeEEeecCCCCCCCCCCceEEEcCCCC-ceecCC
Q 034182 56 KVEGRIVACEGDSNPALGHPIEFICLDLKE-PAICKY 91 (102)
Q Consensus 56 ~V~~~~v~CdG~~~palGHPrVyI~Ld~~~-~~~CpY 91 (102)
.|.+.+..+.- .-|| +|+.|.+++ ...|-.
T Consensus 2 ~v~GeVs~~~~----~~GH--vyfsLkD~~a~i~cv~ 32 (73)
T cd04487 2 HIEGEVVQIKQ----TSGP--TIFTLRDETGTVWAAA 32 (73)
T ss_pred EEEEEEecccc----CCCC--EEEEEEcCCEEEEEEE
Confidence 34455555543 1477 999996554 566743
No 145
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=20.40 E-value=56 Score=23.29 Aligned_cols=38 Identities=29% Similarity=0.455 Sum_probs=23.2
Q ss_pred CeEEeecCCCCC-------CCCCCceEEEcCCCCceecCCCCccccc
Q 034182 59 GRIVACEGDSNP-------ALGHPIEFICLDLKEPAICKYCGLRYVQ 98 (102)
Q Consensus 59 ~~~v~CdG~~~p-------alGHPrVyI~Ld~~~~~~CpYCG~ry~~ 98 (102)
.|=..|.|.--+ ..-.|.||-..+ ....||=||+.|=.
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~--~f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYD--EFWRCPGCGKIYWE 136 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCC--eEEECCCCCCEecc
Confidence 455566664211 234556665554 37899999999943
No 146
>cd03528 Rieske_RO_ferredoxin Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The ferredoxin component contains either a plant-type or Rieske-type [2Fe-2S] cluster. The Rieske ferredoxin component in this family carries an electron from the RO reductase component to the terminal RO oxygenase component. BPDO degrades biphenyls and polychlorinated biphenyls. BPDO ferredoxin (BphF) has structural features consistent with a minimal and perhaps archetypical Rieske protein in that the in
Probab=20.39 E-value=62 Score=20.63 Aligned_cols=16 Identities=19% Similarity=0.202 Sum_probs=13.3
Q ss_pred CCceecCCCCcccccc
Q 034182 84 KEPAICKYCGLRYVQD 99 (102)
Q Consensus 84 ~~~~~CpYCG~ry~~~ 99 (102)
++..+|||-|.+|-++
T Consensus 55 ~~~i~Cp~Hg~~fd~~ 70 (98)
T cd03528 55 GGVIECPLHGGRFDLR 70 (98)
T ss_pred CCEEEeCCcCCEEECC
Confidence 4689999999999763
Done!