Query 020000
Match_columns 332
No_of_seqs 156 out of 824
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 06:13:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020000.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020000hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01434 Peptidase_M41: Peptid 100.0 5.1E-28 1.1E-32 220.7 17.1 153 116-294 7-206 (213)
2 PRK10733 hflB ATP-dependent me 99.9 2.3E-25 5E-30 231.9 16.5 159 119-303 390-596 (644)
3 CHL00176 ftsH cell division pr 99.9 2.5E-25 5.5E-30 231.9 16.6 161 117-303 419-626 (638)
4 KOG0734 AAA+-type ATPase conta 99.9 6.1E-26 1.3E-30 230.9 10.8 158 119-303 539-735 (752)
5 TIGR01241 FtsH_fam ATP-depende 99.9 2.5E-24 5.4E-29 216.9 16.2 148 127-300 303-494 (495)
6 COG0465 HflB ATP-dependent Zn 99.9 3.8E-24 8.2E-29 221.0 14.7 161 116-303 385-591 (596)
7 KOG0731 AAA+-type ATPase conta 99.9 2.7E-22 5.9E-27 211.3 12.2 199 83-309 503-755 (774)
8 CHL00206 ycf2 Ycf2; Provisiona 98.6 5.8E-08 1.3E-12 111.4 7.4 109 117-249 1873-1994(2281)
9 cd06163 S2P-M50_PDZ_RseP-like 96.3 0.0037 8E-08 56.8 3.8 26 137-162 11-36 (182)
10 PF13398 Peptidase_M50B: Pepti 96.0 0.0073 1.6E-07 55.3 4.1 27 137-163 24-50 (200)
11 cd06161 S2P-M50_SpoIVFB SpoIVF 95.8 0.0082 1.8E-07 55.1 3.7 27 137-163 40-66 (208)
12 cd06164 S2P-M50_SpoIVFB_CBS Sp 95.8 0.013 2.8E-07 54.8 4.9 27 137-163 55-81 (227)
13 PRK10779 zinc metallopeptidase 95.2 0.013 2.8E-07 59.6 2.6 26 137-162 17-42 (449)
14 cd05709 S2P-M50 Site-2 proteas 95.1 0.023 4.9E-07 50.2 3.6 25 137-161 10-34 (180)
15 cd06162 S2P-M50_PDZ_SREBP Ster 94.7 0.036 7.8E-07 53.9 4.2 27 137-163 137-163 (277)
16 PF02163 Peptidase_M50: Peptid 93.9 0.039 8.4E-07 48.9 2.5 26 137-162 9-34 (192)
17 TIGR00054 RIP metalloprotease 93.8 0.035 7.7E-07 56.1 2.3 26 137-162 16-41 (420)
18 cd06160 S2P-M50_like_2 Unchara 92.0 0.13 2.8E-06 46.9 3.0 27 137-163 43-69 (183)
19 cd06159 S2P-M50_PDZ_Arch Uncha 88.2 0.27 6E-06 47.3 1.8 25 137-161 120-144 (263)
20 cd06158 S2P-M50_like_1 Unchara 88.2 0.36 7.8E-06 43.7 2.5 26 138-163 12-41 (181)
21 PF00413 Peptidase_M10: Matrix 83.0 0.56 1.2E-05 39.6 1.1 17 131-147 101-117 (154)
22 PF14247 DUF4344: Domain of un 82.3 0.87 1.9E-05 43.0 2.1 21 137-158 94-114 (220)
23 cd04279 ZnMc_MMP_like_1 Zinc-d 78.8 1.3 2.8E-05 38.2 1.9 22 132-153 101-122 (156)
24 cd04268 ZnMc_MMP_like Zinc-dep 76.7 1.6 3.4E-05 37.4 1.8 19 131-149 90-108 (165)
25 PF04298 Zn_peptidase_2: Putat 73.0 1.8 4E-05 41.1 1.4 12 137-148 91-102 (222)
26 COG0750 Predicted membrane-ass 71.7 2.6 5.7E-05 40.9 2.2 26 137-162 15-40 (375)
27 cd04786 HTH_MerR-like_sg7 Heli 71.1 22 0.00047 30.7 7.5 68 238-305 41-116 (131)
28 cd04278 ZnMc_MMP Zinc-dependen 70.6 2 4.3E-05 37.2 1.0 17 131-147 103-119 (157)
29 KOG2921 Intramembrane metallop 70.2 3.1 6.7E-05 43.0 2.3 26 137-162 133-158 (484)
30 PF02031 Peptidase_M7: Strepto 68.7 3.6 7.7E-05 36.3 2.1 27 119-147 63-89 (132)
31 cd04277 ZnMc_serralysin_like Z 66.8 3.7 8.1E-05 36.4 1.9 18 132-149 110-127 (186)
32 PF06114 DUF955: Domain of unk 63.8 7.6 0.00016 30.4 3.0 25 128-152 35-59 (122)
33 PF05572 Peptidase_M43: Pregna 62.1 4.1 8.8E-05 36.1 1.3 21 131-151 65-85 (154)
34 cd08316 Death_FAS_TNFRSF6 Deat 61.7 42 0.0009 27.9 7.1 60 242-302 21-90 (97)
35 cd04327 ZnMc_MMP_like_3 Zinc-d 60.3 5.9 0.00013 35.9 2.0 26 133-158 90-116 (198)
36 smart00235 ZnMc Zinc-dependent 58.8 5 0.00011 33.7 1.2 14 137-150 88-101 (140)
37 cd04769 HTH_MerR2 Helix-Turn-H 58.1 68 0.0015 26.6 7.9 66 238-303 40-115 (116)
38 smart00005 DEATH DEATH domain, 53.8 81 0.0018 24.2 7.2 47 243-289 19-75 (88)
39 PF09278 MerR-DNA-bind: MerR, 53.3 77 0.0017 23.2 6.7 43 247-289 9-57 (65)
40 cd00203 ZnMc Zinc-dependent me 50.6 8.4 0.00018 32.8 1.3 19 133-151 94-112 (167)
41 COG0501 HtpX Zn-dependent prot 49.6 13 0.00028 34.8 2.5 24 129-152 151-174 (302)
42 PF08858 IDEAL: IDEAL domain; 48.7 43 0.00092 23.1 4.3 33 21-53 5-37 (37)
43 PF11350 DUF3152: Protein of u 46.8 10 0.00022 35.7 1.3 18 132-150 136-153 (203)
44 cd04783 HTH_MerR1 Helix-Turn-H 45.7 1.2E+02 0.0026 25.5 7.6 60 238-297 41-107 (126)
45 PF13485 Peptidase_MA_2: Pepti 45.7 24 0.00051 27.8 3.1 23 131-153 21-43 (128)
46 PF13582 Reprolysin_3: Metallo 45.2 11 0.00023 30.8 1.1 12 136-147 108-119 (124)
47 PF01435 Peptidase_M48: Peptid 45.1 18 0.00038 32.1 2.5 24 130-153 84-107 (226)
48 cd04768 HTH_BmrR-like Helix-Tu 45.1 91 0.002 25.1 6.5 51 238-288 41-93 (96)
49 cd04788 HTH_NolA-AlbR Helix-Tu 43.4 84 0.0018 25.3 6.0 50 238-287 41-92 (96)
50 cd04784 HTH_CadR-PbrR Helix-Tu 43.1 1.7E+02 0.0037 24.5 8.1 60 238-297 41-109 (127)
51 cd08306 Death_FADD Fas-associa 42.7 1.2E+02 0.0027 24.2 6.8 46 244-289 16-71 (86)
52 COG0339 Dcp Zn-dependent oligo 42.2 20 0.00043 39.3 2.8 32 137-169 469-503 (683)
53 TIGR01950 SoxR redox-sensitive 41.6 1.5E+02 0.0033 25.8 7.8 61 238-298 41-111 (142)
54 cd01109 HTH_YyaN Helix-Turn-He 40.4 2E+02 0.0042 23.7 7.9 52 238-289 41-100 (113)
55 cd04773 HTH_TioE_rpt2 Second H 39.3 1.9E+02 0.0042 23.7 7.7 53 238-290 41-100 (108)
56 cd01110 HTH_SoxR Helix-Turn-He 39.0 1.4E+02 0.0031 25.8 7.2 61 238-298 41-111 (139)
57 cd04782 HTH_BltR Helix-Turn-He 38.8 1.4E+02 0.0031 24.0 6.7 52 238-289 41-95 (97)
58 cd01106 HTH_TipAL-Mta Helix-Tu 36.8 1.4E+02 0.003 24.2 6.4 48 238-285 41-90 (103)
59 cd04770 HTH_HMRTR Helix-Turn-H 36.7 2.4E+02 0.0052 23.3 8.0 52 238-289 41-100 (123)
60 cd04777 HTH_MerR-like_sg1 Heli 36.7 1.9E+02 0.0042 23.4 7.3 52 238-289 39-102 (107)
61 TIGR02044 CueR Cu(I)-responsiv 36.2 1.7E+02 0.0037 24.6 7.1 60 238-297 41-109 (127)
62 cd06258 Peptidase_M3_like The 35.4 21 0.00046 34.7 1.6 18 137-154 156-173 (365)
63 TIGR02047 CadR-PbrR Cd(II)/Pb( 34.3 2E+02 0.0043 24.4 7.2 60 238-297 41-109 (127)
64 cd08311 Death_p75NR Death doma 34.3 1.1E+02 0.0024 24.2 5.3 54 244-307 18-71 (77)
65 COG2856 Predicted Zn peptidase 34.0 34 0.00073 32.3 2.6 24 128-151 65-88 (213)
66 cd01108 HTH_CueR Helix-Turn-He 33.5 2.9E+02 0.0064 23.2 8.1 52 238-289 41-100 (127)
67 PF12994 DUF3878: Domain of un 33.4 7.9 0.00017 38.4 -1.7 17 133-149 92-108 (299)
68 cd08313 Death_TNFR1 Death doma 33.1 1.2E+02 0.0027 24.3 5.4 48 241-288 11-68 (80)
69 cd01282 HTH_MerR-like_sg3 Heli 32.7 1.7E+02 0.0036 24.2 6.4 52 238-289 40-102 (112)
70 COG2738 Predicted Zn-dependent 32.6 24 0.00051 33.6 1.3 13 137-149 94-106 (226)
71 cd08318 Death_NMPP84 Death dom 32.5 1.6E+02 0.0035 23.5 6.0 46 244-289 21-75 (86)
72 PRK02391 heat shock protein Ht 31.8 26 0.00057 34.2 1.6 24 128-151 126-149 (296)
73 cd08777 Death_RIP1 Death Domai 31.4 2.8E+02 0.006 22.3 7.8 34 244-277 16-54 (86)
74 PRK03982 heat shock protein Ht 31.4 29 0.00064 33.3 1.8 23 129-151 119-141 (288)
75 PRK05457 heat shock protein Ht 31.4 37 0.00079 32.9 2.5 19 129-147 128-146 (284)
76 PF12388 Peptidase_M57: Dual-a 31.3 31 0.00067 32.7 1.9 23 131-153 129-151 (211)
77 cd08315 Death_TRAILR_DR4_DR5 D 31.2 2.3E+02 0.0051 23.2 6.9 48 242-289 20-76 (96)
78 PF10728 DUF2520: Domain of un 30.2 1.4E+02 0.0029 25.9 5.6 62 234-295 6-67 (132)
79 PRK03072 heat shock protein Ht 29.9 30 0.00065 33.5 1.6 25 128-152 120-144 (288)
80 PF13583 Reprolysin_4: Metallo 29.4 28 0.00061 32.0 1.3 17 137-153 139-155 (206)
81 cd04790 HTH_Cfa-like_unk Helix 28.5 2.3E+02 0.005 25.4 6.9 23 238-260 42-66 (172)
82 cd04276 ZnMc_MMP_like_2 Zinc-d 28.0 41 0.0009 31.1 2.1 15 133-147 114-128 (197)
83 PRK04897 heat shock protein Ht 28.0 45 0.00098 32.4 2.5 21 129-149 131-151 (298)
84 cd04787 HTH_HMRTR_unk Helix-Tu 28.0 2.5E+02 0.0055 23.8 6.8 52 238-289 41-100 (133)
85 cd04280 ZnMc_astacin_like Zinc 28.0 31 0.00067 31.0 1.2 35 136-170 75-111 (180)
86 cd01107 HTH_BmrR Helix-Turn-He 27.9 2.1E+02 0.0046 23.4 6.1 48 238-285 42-92 (108)
87 PF01400 Astacin: Astacin (Pep 27.9 37 0.00081 30.7 1.8 34 136-170 80-116 (191)
88 PRK03001 M48 family peptidase; 27.3 36 0.00079 32.6 1.7 23 129-151 118-140 (283)
89 PF13688 Reprolysin_5: Metallo 27.2 42 0.00091 29.6 2.0 24 130-153 137-160 (196)
90 TIGR02289 M3_not_pepF oligoend 27.0 50 0.0011 34.6 2.8 17 137-153 339-355 (549)
91 cd08804 Death_ank2 Death domai 26.6 1.9E+02 0.0042 23.0 5.5 46 244-289 18-73 (84)
92 TIGR02051 MerR Hg(II)-responsi 26.5 2.7E+02 0.0059 23.4 6.7 52 238-289 40-97 (124)
93 PF07998 Peptidase_M54: Peptid 26.2 43 0.00092 31.2 1.9 11 137-147 147-157 (194)
94 PRK15002 redox-sensitivie tran 25.9 4E+02 0.0087 23.7 7.9 77 221-297 20-120 (154)
95 cd08784 Death_DRs Death Domain 25.8 3.1E+02 0.0067 21.5 6.4 37 242-278 12-51 (79)
96 cd04776 HTH_GnyR Helix-Turn-He 25.8 4E+02 0.0086 22.3 8.5 51 238-288 39-100 (118)
97 PRK01345 heat shock protein Ht 25.0 55 0.0012 32.3 2.5 23 130-152 119-141 (317)
98 PF03186 CobD_Cbib: CobD/Cbib 24.8 1.6E+02 0.0035 28.7 5.6 68 25-111 93-160 (295)
99 cd06459 M3B_Oligoendopeptidase 24.6 53 0.0011 32.4 2.3 17 137-153 224-240 (427)
100 PF09471 Peptidase_M64: IgA Pe 24.3 37 0.00079 32.9 1.1 18 133-150 214-231 (264)
101 PRK01209 cobD cobalamin biosyn 24.0 1.5E+02 0.0033 29.1 5.3 67 25-110 96-162 (312)
102 cd04283 ZnMc_hatching_enzyme Z 23.9 43 0.00093 30.7 1.4 18 136-153 78-95 (182)
103 cd04785 HTH_CadR-PbrR-like Hel 23.9 4.3E+02 0.0093 22.2 7.4 52 238-289 41-100 (126)
104 cd04275 ZnMc_pappalysin_like Z 23.5 11 0.00023 35.6 -2.6 21 132-152 134-154 (225)
105 PRK09514 zntR zinc-responsive 23.5 4.1E+02 0.0089 22.9 7.4 53 238-290 42-103 (140)
106 cd08789 CARD_IPS-1_RIG-I Caspa 23.3 72 0.0016 25.6 2.5 35 30-65 34-69 (84)
107 cd04281 ZnMc_BMP1_TLD Zinc-dep 23.2 45 0.00097 31.0 1.4 33 137-170 89-124 (200)
108 PF13574 Reprolysin_2: Metallo 23.1 49 0.0011 29.4 1.6 20 135-154 111-130 (173)
109 cd04775 HTH_Cfa-like Helix-Tur 22.9 2.5E+02 0.0055 22.7 5.7 50 238-289 41-92 (102)
110 cd06461 M2_ACE Peptidase famil 22.7 57 0.0012 34.2 2.2 36 273-308 422-459 (477)
111 PRK13267 archaemetzincin-like 22.6 57 0.0012 29.8 1.9 11 137-147 127-137 (179)
112 PRK01265 heat shock protein Ht 22.4 52 0.0011 32.8 1.7 21 129-149 134-154 (324)
113 PF01432 Peptidase_M3: Peptida 22.3 72 0.0016 32.2 2.8 19 137-155 244-262 (458)
114 TIGR00380 cobD cobalamin biosy 21.9 1.9E+02 0.0041 28.6 5.5 67 25-110 100-166 (305)
115 TIGR02043 ZntR Zn(II)-responsi 21.8 3.7E+02 0.0079 22.9 6.7 52 238-289 42-102 (131)
116 cd04267 ZnMc_ADAM_like Zinc-de 20.7 44 0.00095 29.5 0.8 21 133-153 131-151 (192)
117 PRK02870 heat shock protein Ht 20.7 62 0.0014 32.4 1.9 18 129-146 167-184 (336)
118 COG5549 Predicted Zn-dependent 20.3 55 0.0012 31.5 1.4 20 130-149 182-201 (236)
119 PHA00101 internal virion prote 20.3 5.5E+02 0.012 24.2 7.8 79 234-316 26-114 (194)
120 PRK05427 putative manganese-de 20.1 2.5E+02 0.0054 27.3 5.9 51 215-265 136-186 (308)
121 cd08317 Death_ank Death domain 20.1 3.2E+02 0.007 21.4 5.6 46 244-289 18-73 (84)
No 1
>PF01434 Peptidase_M41: Peptidase family M41 This is family M41 in the peptidase classification. ; InterPro: IPR000642 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 []. This group of metallopeptidases belong to MEROPS peptidase family M41 (FtsH endopeptidase family, clan MA(E)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The peptidase M41 family belong to a larger family of zinc metalloproteases. This family includes the cell division protein FtsH, and the yeast mitochondrial respiratory chain complexes assembly protein, which is a putative ATP-dependent protease required for assembly of the mitochondrial respiratory chain and ATPase complexes. FtsH is an integral membrane protein, which seems to act as an ATP-dependent zinc metallopeptidase that binds one zinc ion.; GO: 0004222 metalloendopeptidase activity, 0005524 ATP binding, 0006508 proteolysis; PDB: 4EIW_C 2DHR_E 1IY1_A 1IY2_A 1IY0_A 1IXZ_A 2CE7_F 2CEA_F 3KDS_E 2QZ4_A ....
Probab=99.96 E-value=5.1e-28 Score=220.67 Aligned_cols=153 Identities=27% Similarity=0.325 Sum_probs=116.9
Q ss_pred hhhhHHhhccc--CCCCChhHHHHHHHHHHhHHHHHHHhC--CCCCceecCchhhhcccccccceeEEechhhhHHHHHh
Q 020000 116 DTVESIVEDGS--YVSLKEEDHFMCVQHEAGHFLTGYLLG--VLPKGYEIPSVEALKQDDFTVGRVQFVGFDFLKEVADA 191 (332)
Q Consensus 116 D~~~~llld~~--~r~ls~eer~RVA~HEAGHaLVAyLLg--~PV~kyTI~p~eal~~G~~g~gG~~f~~~e~~~~l~~~ 191 (332)
+++++++++.. ++.+++++|+++||||||||+|+|+++ .||.++||.| +|. ..|.+.|. |..+.
T Consensus 7 ~a~drv~~G~~~~~~~~~~~~~~~~A~HEAGhAvva~~l~~~~~v~~vsi~p-----rg~-~~G~~~~~-~~~~~----- 74 (213)
T PF01434_consen 7 EAIDRVLMGPEKKSRKLSEEEKRRIAYHEAGHAVVAYLLPPADPVSKVSIVP-----RGS-ALGFTQFT-PDEDR----- 74 (213)
T ss_dssp HHHHHHHCCSCCTTS---HHHHHHHHHHHHHHHHHHHHSSS---EEEEESST-----TCC-CCHCCEEC-HHTT------
T ss_pred HHHHHHhcCcCcCCCCCCHHHHHHHHHHHHHHHHHHHHhcccccEEEEEEec-----CCC-cceeEEec-cchhc-----
Confidence 36688888854 366899999999999999999999998 5999999999 442 23344443 32111
Q ss_pred hhhcccCCCcCCCCCccCHHHHHHHHHHHhhhHHHHHHHhC--C-ccchhhHHHHHHHHHHH----hCCChh--------
Q 020000 192 RKQKKDTGQVGSWGNRGEISTLNNFSCVILGGLVAEHLVFG--H-SEGHYSDINKLDKVFQW----LGYNKS-------- 256 (332)
Q Consensus 192 r~~~~d~~~~~s~~~~g~~s~L~r~i~VaLAGrAAE~LvfG--~-stGga~Dl~qat~iar~----lGmS~~-------- 256 (332)
...+.+++.+.++|+|||||||+++|| + ++|+++|+++||++++. |||+.+
T Consensus 75 --------------~~~t~~~l~~~i~v~LaGraAEe~~~g~~~~stGa~~DL~~At~iA~~mv~~~Gm~~~~g~~~~~~ 140 (213)
T PF01434_consen 75 --------------YIRTRSYLEDRICVLLAGRAAEELFFGEDNVSTGASSDLQQATEIARKMVASYGMGDSLGLLSYSP 140 (213)
T ss_dssp --------------SS-BHHHHHHHHHHHHHHHHHHHHHHSCCS-BGGGHHHHHHHHHHHHHHHHTST-TTTTTSS-SEE
T ss_pred --------------ccccHHHHHhhHHHHHHHHHHHHhhcCcceecccchhHHHHHHHHHHHHHHHhCCCCCCceeeeec
Confidence 013555889999999999999999999 5 57999999999999886 788751
Q ss_pred ------------------------HHHHHHH----HHHHHHHHHHHHhHHHHHHHHHHHHhhCcHH
Q 020000 257 ------------------------EADSQVK----WAALNTVLISHHHIQVRSRLAEAMALGRSIG 294 (332)
Q Consensus 257 ------------------------~id~evr----~A~~~A~~LL~~hr~ale~LAeaLle~esl~ 294 (332)
.++.+++ .||.+|++||++|++.+++|+++|+++++|.
T Consensus 141 ~~~~~~~~~~~~~~~~~~s~~~~~~i~~ev~~lL~~a~~~a~~iL~~~r~~l~~la~~Lle~~~L~ 206 (213)
T PF01434_consen 141 NDDDEVFLGREWNSRRPMSEETRALIDREVRKLLEEAYARAKEILEENREALEALAEALLEKETLS 206 (213)
T ss_dssp EE-S-SSS-E---EEESS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHSEEE
T ss_pred cccccccccccccccCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCeeC
Confidence 1344443 6899999999999999999999999999984
No 2
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=99.93 E-value=2.3e-25 Score=231.93 Aligned_cols=159 Identities=18% Similarity=0.210 Sum_probs=127.0
Q ss_pred hHHhhcc--cCCCCChhHHHHHHHHHHhHHHHHHHhC--CCCCceecCchhhhcccccccceeEEechhhhHHHHHhhhh
Q 020000 119 ESIVEDG--SYVSLKEEDHFMCVQHEAGHFLTGYLLG--VLPKGYEIPSVEALKQDDFTVGRVQFVGFDFLKEVADARKQ 194 (332)
Q Consensus 119 ~~llld~--~~r~ls~eer~RVA~HEAGHaLVAyLLg--~PV~kyTI~p~eal~~G~~g~gG~~f~~~e~~~~l~~~r~~ 194 (332)
.++..+. .+..+++++|+++||||||||+|+++++ .||+++||.| +| ..+|+++..|+.+..
T Consensus 390 ~~v~~g~~~~~~~~~~~~~~~~a~he~gha~~~~~~~~~~~~~~v~i~p-----rg--~~~g~~~~~~~~~~~------- 455 (644)
T PRK10733 390 DKIMMGAERRSMVMTEAQKESTAYHEAGHAIIGRLVPEHDPVHKVTIIP-----RG--RALGVTFFLPEGDAI------- 455 (644)
T ss_pred HHHhcccccccccccHHHHHHHHHHHHHHHHHHHHccCCCceeEEEEec-----cC--CCcceeEECCCcccc-------
Confidence 4444542 2345789999999999999999999998 6999999999 33 134666655542211
Q ss_pred cccCCCcCCCCCccCHHHHHHHHHHHhhhHHHHHHHhCC---ccchhhHHHHHHHHHHH----hCCChh-----------
Q 020000 195 KKDTGQVGSWGNRGEISTLNNFSCVILGGLVAEHLVFGH---SEGHYSDINKLDKVFQW----LGYNKS----------- 256 (332)
Q Consensus 195 ~~d~~~~~s~~~~g~~s~L~r~i~VaLAGrAAE~LvfG~---stGga~Dl~qat~iar~----lGmS~~----------- 256 (332)
..+.++|.+.++|+|||||||+++||. ++|++||+++||+|++. ||||++
T Consensus 456 ------------~~~~~~l~~~i~~~lgGraAE~~~~g~~~~ttGa~~Dl~~AT~lA~~mv~~~Gms~~lg~~~~~~~~~ 523 (644)
T PRK10733 456 ------------SASRQKLESQISTLYGGRLAEEIIYGPEHVSTGASNDIKVATNLARNMVTQWGFSEKLGPLLYAEEEG 523 (644)
T ss_pred ------------cccHHHHHHHHHHHHhhHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhCCCccccchhhccccc
Confidence 134458999999999999999999994 57999999999999875 899851
Q ss_pred --------------------HHHHHHH----HHHHHHHHHHHHhHHHHHHHHHHHHhhCcHH--HHHHHHhcc
Q 020000 257 --------------------EADSQVK----WAALNTVLISHHHIQVRSRLAEAMALGRSIG--SYTSKILTE 303 (332)
Q Consensus 257 --------------------~id~evr----~A~~~A~~LL~~hr~ale~LAeaLle~esl~--ec~~~Ie~~ 303 (332)
.+|++++ .||.+|++||++|++.+++||++|+++|||+ |..++|...
T Consensus 524 ~~~lg~~~~~~~~~s~~~~~~id~ev~~il~~~~~~a~~iL~~~~~~l~~la~~Lle~etl~~~ei~~i~~~~ 596 (644)
T PRK10733 524 EVFLGRSVAKAKHMSDETARIIDQEVKALIERNYNRARQLLTDNMDILHAMKDALMKYETIDAPQIDDLMARR 596 (644)
T ss_pred ccccccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhceeCHHHHHHHHhcC
Confidence 2466654 7999999999999999999999999999994 788888764
No 3
>CHL00176 ftsH cell division protein; Validated
Probab=99.93 E-value=2.5e-25 Score=231.91 Aligned_cols=161 Identities=16% Similarity=0.194 Sum_probs=127.7
Q ss_pred hhhHHhhccc-CCCCChhHHHHHHHHHHhHHHHHHHhC--CCCCceecCchhhhcccccccceeEEechhhhHHHHHhhh
Q 020000 117 TVESIVEDGS-YVSLKEEDHFMCVQHEAGHFLTGYLLG--VLPKGYEIPSVEALKQDDFTVGRVQFVGFDFLKEVADARK 193 (332)
Q Consensus 117 ~~~~llld~~-~r~ls~eer~RVA~HEAGHaLVAyLLg--~PV~kyTI~p~eal~~G~~g~gG~~f~~~e~~~~l~~~r~ 193 (332)
++..++.+.. ....++++|++|||||||||+|+++++ .||+++||.| +| ..+|+++..|+.++.+
T Consensus 419 Ai~rv~~g~~~~~~~~~~~~~~vA~hEaGhA~v~~~l~~~~~v~kvtI~p-----rg--~~~G~~~~~p~~~~~~----- 486 (638)
T CHL00176 419 AIDRVIAGLEGTPLEDSKNKRLIAYHEVGHAIVGTLLPNHDPVQKVTLIP-----RG--QAKGLTWFTPEEDQSL----- 486 (638)
T ss_pred HHHHHHhhhccCccccHHHHHHHHHHhhhhHHHHhhccCCCceEEEEEee-----cC--CCCCceEecCCccccc-----
Confidence 4456655533 234688999999999999999999998 6999999999 33 2346666555422221
Q ss_pred hcccCCCcCCCCCccCHHHHHHHHHHHhhhHHHHHHHhCC---ccchhhHHHHHHHHHHH----hCCCh-----------
Q 020000 194 QKKDTGQVGSWGNRGEISTLNNFSCVILGGLVAEHLVFGH---SEGHYSDINKLDKVFQW----LGYNK----------- 255 (332)
Q Consensus 194 ~~~d~~~~~s~~~~g~~s~L~r~i~VaLAGrAAE~LvfG~---stGga~Dl~qat~iar~----lGmS~----------- 255 (332)
.+.+++...++++|||||||+++||+ ++|++||+++||++++. |||+.
T Consensus 487 --------------~t~~~l~~~i~~~LgGraAE~~~fg~~~~~~Ga~~Dl~~AT~iA~~mv~~~Gm~~~g~~~~~~~~~ 552 (638)
T CHL00176 487 --------------VSRSQILARIVGALGGRAAEEVVFGSTEVTTGASNDLQQVTNLARQMVTRFGMSSIGPISLESNNS 552 (638)
T ss_pred --------------ccHHHHHHHHHHHhhhHHHHHHhcCCCCcCCCchhHHHHHHHHHHHHHHHhCCCcCCceeecCCCC
Confidence 34458888899999999999999995 57999999999999885 78861
Q ss_pred --------------------hHHHHHHH----HHHHHHHHHHHHhHHHHHHHHHHHHhhCcHH--HHHHHHhcc
Q 020000 256 --------------------SEADSQVK----WAALNTVLISHHHIQVRSRLAEAMALGRSIG--SYTSKILTE 303 (332)
Q Consensus 256 --------------------~~id~evr----~A~~~A~~LL~~hr~ale~LAeaLle~esl~--ec~~~Ie~~ 303 (332)
..+|.+++ .||.+|++||++|++++++||++|+++|||+ |+.++++..
T Consensus 553 ~~~~~~~~~~~~~~~s~~~~~~iD~ev~~~l~~~~~~a~~iL~~~~~~l~~la~~Lle~Etl~~~ei~~il~~~ 626 (638)
T CHL00176 553 TDPFLGRFMQRNSEYSEEIADKIDMEVRSILHTCYQYAYQILKDNRVLIDLLVELLLQKETIDGDEFREIVNSY 626 (638)
T ss_pred cccccccccccccCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCccCHHHHHHHHhhc
Confidence 12566654 7999999999999999999999999999994 888888764
No 4
>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=6.1e-26 Score=230.87 Aligned_cols=158 Identities=20% Similarity=0.156 Sum_probs=132.9
Q ss_pred hHHhhcc--cCCCCChhHHHHHHHHHHhHHHHHHHhC--CCCCceecCchhhhccccccc-ceeEEechhhhHHHHHhhh
Q 020000 119 ESIVEDG--SYVSLKEEDHFMCVQHEAGHFLTGYLLG--VLPKGYEIPSVEALKQDDFTV-GRVQFVGFDFLKEVADARK 193 (332)
Q Consensus 119 ~~llld~--~~r~ls~eer~RVA~HEAGHaLVAyLLg--~PV~kyTI~p~eal~~G~~g~-gG~~f~~~e~~~~l~~~r~ 193 (332)
++|+++. -++.++++-|+.+||||+||+|||+... .|++|.||.| +|+ .|.++..|+.++.
T Consensus 539 DrIlMG~ERks~~i~~eak~~TAyHE~GHAivA~yTk~A~PlhKaTImP--------RG~sLG~t~~LPe~D~~------ 604 (752)
T KOG0734|consen 539 DRILMGPERKSMVIDEEAKKITAYHEGGHAIVALYTKGAMPLHKATIMP--------RGPSLGHTSQLPEKDRY------ 604 (752)
T ss_pred hheeecccccccccChhhhhhhhhhccCceEEEeecCCCccccceeecc--------CCccccceeecCccchh------
Confidence 7888884 3778899999999999999999999998 5999999999 665 4788877775433
Q ss_pred hcccCCCcCCCCCccCHHHHHHHHHHHhhhHHHHHHHhCC---ccchhhHHHHHHHHHHH----hCCChh----------
Q 020000 194 QKKDTGQVGSWGNRGEISTLNNFSCVILGGLVAEHLVFGH---SEGHYSDINKLDKVFQW----LGYNKS---------- 256 (332)
Q Consensus 194 ~~~d~~~~~s~~~~g~~s~L~r~i~VaLAGrAAE~LvfG~---stGga~Dl~qat~iar~----lGmS~~---------- 256 (332)
+-+..++..++-|+||||+||+|+||. .+|+.+|++|||++++. ||||++
T Consensus 605 -------------~~Tk~q~LA~lDV~MGGRvAEELIfG~D~iTsGAssDl~qAT~lA~~MVt~fGMSd~vG~v~~~~~~ 671 (752)
T KOG0734|consen 605 -------------SITKAQLLARLDVCMGGRVAEELIFGTDKITSGASSDLDQATKLARRMVTKFGMSDKVGPVTLSAED 671 (752)
T ss_pred -------------hHHHHHHHHHHHHhhcchHHHHHhccCCcccccccchHHHHHHHHHHHHHHcCccccccceeeeccC
Confidence 123337777789999999999999997 36999999999998775 899862
Q ss_pred -----------HHHHHHH----HHHHHHHHHHHHhHHHHHHHHHHHHhhCcHH--HHHHHHhcc
Q 020000 257 -----------EADSQVK----WAALNTVLISHHHIQVRSRLAEAMALGRSIG--SYTSKILTE 303 (332)
Q Consensus 257 -----------~id~evr----~A~~~A~~LL~~hr~ale~LAeaLle~esl~--ec~~~Ie~~ 303 (332)
.||.|++ .+|++|+.||+.|...+++||++|+++||++ |..+++.+.
T Consensus 672 ~~~s~~~~t~~lidaEi~~lL~~sYeRak~iL~~h~kEl~~LA~ALleYETL~A~eik~vl~g~ 735 (752)
T KOG0734|consen 672 NSSSLSPRTQELIDAEIKRLLRDSYERAKSILKTHKKELHALAEALLEYETLDAKEIKRVLKGK 735 (752)
T ss_pred CCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHhcc
Confidence 3777754 6999999999999999999999999999995 777777665
No 5
>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
Probab=99.92 E-value=2.5e-24 Score=216.90 Aligned_cols=148 Identities=24% Similarity=0.208 Sum_probs=118.3
Q ss_pred CCCCChhHHHHHHHHHHhHHHHHHHhC--CCCCceecCchhhhcccccccceeEEechhhhHHHHHhhhhcccCCCcCCC
Q 020000 127 YVSLKEEDHFMCVQHEAGHFLTGYLLG--VLPKGYEIPSVEALKQDDFTVGRVQFVGFDFLKEVADARKQKKDTGQVGSW 204 (332)
Q Consensus 127 ~r~ls~eer~RVA~HEAGHaLVAyLLg--~PV~kyTI~p~eal~~G~~g~gG~~f~~~e~~~~l~~~r~~~~d~~~~~s~ 204 (332)
...+++++|+++||||||||+|+|+++ .|+.++||.| +|. .+|+++..+..+.
T Consensus 303 ~~~~~~~~~~~~A~hEaGhAlv~~~l~~~~~v~~vsi~p-----rg~--~~G~~~~~~~~~~------------------ 357 (495)
T TIGR01241 303 SRVISEKEKKLVAYHEAGHALVGLLLKDADPVHKVTIIP-----RGQ--ALGYTQFLPEEDK------------------ 357 (495)
T ss_pred cccccHHHHHHHHHHHHhHHHHHHhcCCCCceEEEEEee-----cCC--ccceEEecCcccc------------------
Confidence 445789999999999999999999996 6999999999 232 3455443332111
Q ss_pred CCccCHHHHHHHHHHHhhhHHHHHHHhCCc-cchhhHHHHHHHHHHH----hCCChh-----------------------
Q 020000 205 GNRGEISTLNNFSCVILGGLVAEHLVFGHS-EGHYSDINKLDKVFQW----LGYNKS----------------------- 256 (332)
Q Consensus 205 ~~~g~~s~L~r~i~VaLAGrAAE~LvfG~s-tGga~Dl~qat~iar~----lGmS~~----------------------- 256 (332)
...+.++++++++|+|||||||+++||+. +|+.+|+++||++++. |||++.
T Consensus 358 -~~~t~~~l~~~i~v~LaGraAE~~~~G~~s~Ga~~Dl~~At~lA~~mv~~~Gm~~~~g~~~~~~~~~~~~l~~~~~~~~ 436 (495)
T TIGR01241 358 -YLYTKSQLLAQIAVLLGGRAAEEIIFGEVTTGASNDIKQATNIARAMVTEWGMSDKLGPVAYGSDGGDVFLGRGFAKAK 436 (495)
T ss_pred -ccCCHHHHHHHHHHHhhHHHHHHHHhcCCCCCchHHHHHHHHHHHHHHHHhCCCcccCceeeccCcccccccccccccc
Confidence 11345599999999999999999999985 6999999999999774 788751
Q ss_pred --------HHHHHH----HHHHHHHHHHHHHhHHHHHHHHHHHHhhCcHH--HHHHHH
Q 020000 257 --------EADSQV----KWAALNTVLISHHHIQVRSRLAEAMALGRSIG--SYTSKI 300 (332)
Q Consensus 257 --------~id~ev----r~A~~~A~~LL~~hr~ale~LAeaLle~esl~--ec~~~I 300 (332)
.+|.++ ++||.+|++||++|++++++||++|+++++|+ |..++|
T Consensus 437 ~~s~~~~~~id~~v~~lL~~a~~ra~~lL~~~~~~l~~la~~Ll~~e~L~~~ei~~il 494 (495)
T TIGR01241 437 EYSEETAREIDEEVKRIIEEAYKRAKQILTENRDELELLAKALLEKETITREEIKELL 494 (495)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCeeCHHHHHHHh
Confidence 234554 48999999999999999999999999999985 555554
No 6
>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]
Probab=99.91 E-value=3.8e-24 Score=221.03 Aligned_cols=161 Identities=22% Similarity=0.221 Sum_probs=132.6
Q ss_pred hhhhHHhhcc--cCCCCChhHHHHHHHHHHhHHHHHHHhCC--CCCceecCchhhhcccccc-cceeEEechhhhHHHHH
Q 020000 116 DTVESIVEDG--SYVSLKEEDHFMCVQHEAGHFLTGYLLGV--LPKGYEIPSVEALKQDDFT-VGRVQFVGFDFLKEVAD 190 (332)
Q Consensus 116 D~~~~llld~--~~r~ls~eer~RVA~HEAGHaLVAyLLg~--PV~kyTI~p~eal~~G~~g-~gG~~f~~~e~~~~l~~ 190 (332)
++.+.++.+. .++.+++++|+.+|||||||++|+++++. ||+|+||.| +| .+|+++..|+.++.+
T Consensus 385 ea~drv~~G~erks~vise~ek~~~AYhEaghalv~~~l~~~d~v~KvtIiP--------rG~alG~t~~~Pe~d~~l-- 454 (596)
T COG0465 385 EAIDRVIAGPERKSRVISEAEKKITAYHEAGHALVGLLLPDADPVHKVTIIP--------RGRALGYTLFLPEEDKYL-- 454 (596)
T ss_pred HHHHHHhcCcCcCCcccChhhhcchHHHHHHHHHHHHhCCCCcccceeeecc--------CchhhcchhcCCcccccc--
Confidence 4679999984 46778999999999999999999999994 999999999 44 457777766632221
Q ss_pred hhhhcccCCCcCCCCCccCHHHHHHHHHHHhhhHHHHHHHhC-C-ccchhhHHHHHHHHHHH----hCCCh---------
Q 020000 191 ARKQKKDTGQVGSWGNRGEISTLNNFSCVILGGLVAEHLVFG-H-SEGHYSDINKLDKVFQW----LGYNK--------- 255 (332)
Q Consensus 191 ~r~~~~d~~~~~s~~~~g~~s~L~r~i~VaLAGrAAE~LvfG-~-stGga~Dl~qat~iar~----lGmS~--------- 255 (332)
.+...+...++++|||||||+++|| + +||+.||++++|+++|. ||||+
T Consensus 455 -----------------~sk~~l~~~i~~~lgGRaAEel~~g~e~ttGa~~D~~~at~~ar~mVt~~Gms~~lG~v~~~~ 517 (596)
T COG0465 455 -----------------MSKEELLDRIDVLLGGRAAEELIFGYEITTGASNDLEKATDLARAMVTEYGMSAKLGPVAYEQ 517 (596)
T ss_pred -----------------ccHHHHHHHHHHHhCCcHhhhhhhcccccccchhhHHHHHHHHHHhhhhcCcchhhCceehhh
Confidence 2334777788999999999999999 7 47999999999999885 89984
Q ss_pred --------------------hHHHHHHH----HHHHHHHHHHHHhHHHHHHHHHHHHhhCcHH--HHHHHHhcc
Q 020000 256 --------------------SEADSQVK----WAALNTVLISHHHIQVRSRLAEAMALGRSIG--SYTSKILTE 303 (332)
Q Consensus 256 --------------------~~id~evr----~A~~~A~~LL~~hr~ale~LAeaLle~esl~--ec~~~Ie~~ 303 (332)
..||.+++ .+|.+++.||.+|++.++.++++|+++||++ +..++++..
T Consensus 518 ~~~~flg~~~~~~~~Se~ta~~ID~evk~ii~~~y~~a~~il~~~~~~l~~~~~~Lle~Eti~~~~i~~i~~~~ 591 (596)
T COG0465 518 VEGVFLGRYQKAKNYSEETAQEIDREVKDIIDEAYERAKELLNENKDALETLAEMLLEKETIDAEEIKDILAGR 591 (596)
T ss_pred cccccccccccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhccCHHHHHHHHhcc
Confidence 13677765 6999999999999999999999999999984 555555544
No 7
>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.87 E-value=2.7e-22 Score=211.32 Aligned_cols=199 Identities=18% Similarity=0.157 Sum_probs=149.8
Q ss_pred hchhhhhhhhhhhhhhHHHHHhhh-----------hhccccccc-hhhhHHhhccc--CCCCChhHHHHHHHHHHhHHHH
Q 020000 83 DSKELLTLRALFDSVMESIERCNL-----------FDSLDEAPS-DTVESIVEDGS--YVSLKEEDHFMCVQHEAGHFLT 148 (332)
Q Consensus 83 ~~~t~~~ll~P~~~~s~~i~~~~~-----------~~~l~~~~~-D~~~~llld~~--~r~ls~eer~RVA~HEAGHaLV 148 (332)
+.++++.+-.-.-+.+++..++.. -..++...+ |+++.++.+.. ++.++.++++.+|||||||+++
T Consensus 503 e~~dl~~~a~~t~gf~gadl~n~~neaa~~a~r~~~~~i~~~~~~~a~~Rvi~G~~~~~~~~~~~~~~~~a~~eagha~~ 582 (774)
T KOG0731|consen 503 EDVDLSKLASLTPGFSGADLANLCNEAALLAARKGLREIGTKDLEYAIERVIAGMEKKSRVLSLEEKKTVAYHEAGHAVV 582 (774)
T ss_pred chhhHHHHHhcCCCCcHHHHHhhhhHHHHHHHHhccCccchhhHHHHHHHHhccccccchhcCHhhhhhhhhhhccchhh
Confidence 555566655555566666666653 111111111 36677777733 6778999999999999999999
Q ss_pred HHHhC--CCCCceecCchhhhcccccccceeEEechhhhHHHHHhhhhcccCCCcCCCCCccCHHHHHHHHHHHhhhHHH
Q 020000 149 GYLLG--VLPKGYEIPSVEALKQDDFTVGRVQFVGFDFLKEVADARKQKKDTGQVGSWGNRGEISTLNNFSCVILGGLVA 226 (332)
Q Consensus 149 AyLLg--~PV~kyTI~p~eal~~G~~g~gG~~f~~~e~~~~l~~~r~~~~d~~~~~s~~~~g~~s~L~r~i~VaLAGrAA 226 (332)
+|+++ .|+.++||+| |+ .. |+.+..|. |+ ++ .+..+|.+.+|++||||||
T Consensus 583 g~~l~~~dpl~kvsIiP------Gq-al-G~a~~~P~-------------~~-~l------~sk~ql~~rm~m~LGGRaA 634 (774)
T KOG0731|consen 583 GWLLEHADPLLKVSIIP------GQ-AL-GYAQYLPT-------------DD-YL------LSKEQLFDRMVMALGGRAA 634 (774)
T ss_pred hccccccCcceeEEecc------CC-cc-ceEEECCc-------------cc-cc------ccHHHHHHHHHHHhCcchh
Confidence 98888 5999999999 53 33 44444333 22 11 3445777778999999999
Q ss_pred HHHHhC-C-ccchhhHHHHHHHHHHH----hCCCh--------------------------hHHHHHHH----HHHHHHH
Q 020000 227 EHLVFG-H-SEGHYSDINKLDKVFQW----LGYNK--------------------------SEADSQVK----WAALNTV 270 (332)
Q Consensus 227 E~LvfG-~-stGga~Dl~qat~iar~----lGmS~--------------------------~~id~evr----~A~~~A~ 270 (332)
|+++|| + +||++||++|+|+|++. ||||+ ..||.+++ .||+.|.
T Consensus 635 Eev~fg~~iTtga~ddl~kvT~~A~~~V~~~Gms~kig~~~~~~~~~~~~~~~~p~s~~~~~~Id~ev~~lv~~ay~~~~ 714 (774)
T KOG0731|consen 635 EEVVFGSEITTGAQDDLEKVTKIARAMVASFGMSEKIGPISFQMLLPGDESFRKPYSEKTAQLIDTEVRRLVQKAYERTK 714 (774)
T ss_pred hheecCCccCchhhccHHHHHHHHHHHHHHcCcccccCceeccCcccccccccCccchhHHHHHHHHHHHHHhhHHHHHH
Confidence 999998 4 57999999999999886 78884 24677766 5999999
Q ss_pred HHHHHhHHHHHHHHHHHHhhCcH--HHHHHHHhcccchhhh
Q 020000 271 LISHHHIQVRSRLAEAMALGRSI--GSYTSKILTEQSLELL 309 (332)
Q Consensus 271 ~LL~~hr~ale~LAeaLle~esl--~ec~~~Ie~~~~~~~~ 309 (332)
.+|++|++.++.+++.|+++|++ ++++.++....+.+++
T Consensus 715 ~ll~~n~~~l~~ia~~LLeke~l~~ee~~~ll~~~~~~~~~ 755 (774)
T KOG0731|consen 715 ELLRTNRDKLDKIAEVLLEKEVLTGEEIIALLGERPPGMPE 755 (774)
T ss_pred HHHHHhHHHHHHHHHHHHHhhhccHHHHHHHhccCCCcccc
Confidence 99999999999999999999998 5999999888776543
No 8
>CHL00206 ycf2 Ycf2; Provisional
Probab=98.62 E-value=5.8e-08 Score=111.38 Aligned_cols=109 Identities=13% Similarity=-0.048 Sum_probs=71.0
Q ss_pred hhhHHhhcccCCCCChhHHHHHHHHHHhHHHHHHHhC--CCCCceecCc-hhhhcccccccceeEEechhhhHHHHHhhh
Q 020000 117 TVESIVEDGSYVSLKEEDHFMCVQHEAGHFLTGYLLG--VLPKGYEIPS-VEALKQDDFTVGRVQFVGFDFLKEVADARK 193 (332)
Q Consensus 117 ~~~~llld~~~r~ls~eer~RVA~HEAGHaLVAyLLg--~PV~kyTI~p-~eal~~G~~g~gG~~f~~~e~~~~l~~~r~ 193 (332)
++.+.+.|...+..+.+++ .||+||+|||+|+.++. .||+++||.+ -..++.| ...|.++..+..
T Consensus 1873 Al~Rq~~g~~~~~~~~~~~-~ia~yEiGhAvvq~~L~~~~pv~kISIy~~~~~~r~~--~~yl~~wyle~~--------- 1940 (2281)
T CHL00206 1873 ALHRQTWDLRSQVRSVQDH-GILFYQIGRAVAQNVLLSNCPIDPISIYMKKKSCKEG--DSYLYKWYFELG--------- 1940 (2281)
T ss_pred HHHHHHhhhhhcccCcchh-hhhhhHHhHHHHHHhccCCCCcceEEEecCCccccCc--ccceeEeecCCc---------
Confidence 5577777755555455555 47999999999999986 6999999953 1223333 222444443320
Q ss_pred hcccCCCcCCCCCccCHHHHHHHHHHHhhhHHHHHHHhCCcc---------c-hhhHHHHHHHHHH
Q 020000 194 QKKDTGQVGSWGNRGEISTLNNFSCVILGGLVAEHLVFGHSE---------G-HYSDINKLDKVFQ 249 (332)
Q Consensus 194 ~~~d~~~~~s~~~~g~~s~L~r~i~VaLAGrAAE~LvfG~st---------G-ga~Dl~qat~iar 249 (332)
...+..++..+++++|||+|||++.|.... | ..+|+.-+-.++.
T Consensus 1941 ------------~~mkk~tiL~~Il~cLAGraAedlwf~~~~~~~n~It~yg~vEnD~~La~glLe 1994 (2281)
T CHL00206 1941 ------------TSMKKLTILLYLLSCSAGSVAQDLWSLPGPDEKNGITSYGLVENDSDLVHGLLE 1994 (2281)
T ss_pred ------------ccCCHHHHHHHHHHHhhhhhhhhhccCcchhhhcCcccccchhhhhHHhHhHHH
Confidence 012333777889999999999999996421 2 2466666655554
No 9
>cd06163 S2P-M50_PDZ_RseP-like RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses. Also included in this group are such homologs as Bacillus subtilis YluC, Mycobacterium tuberculosis Rv2869c S2P, and Bordetella bronchiseptica HurP. Rv2869c S2P appears to have a role in the regulation of prokaryotic lipid biosynthesis and membrane composition and YluC of Bacillus has a role in transducing membrane stress. This group includes bacterial and eukaryotic S2P/M50s homologs with either one or two PDZ domains present. PDZ domains are believed to have a regulatory role. The RseP PDZ domain is required for the inhibitory reaction that prevents cleavage of its substrate, RseA.
Probab=96.32 E-value=0.0037 Score=56.82 Aligned_cols=26 Identities=38% Similarity=0.653 Sum_probs=22.9
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceecC
Q 020000 137 MCVQHEAGHFLTGYLLGVLPKGYEIP 162 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg~PV~kyTI~ 162 (332)
-|..||.||+++|...|.+|.+++|.
T Consensus 11 ~v~iHElGH~~~Ar~~Gv~v~~f~iG 36 (182)
T cd06163 11 LIFVHELGHFLVAKLFGVKVEEFSIG 36 (182)
T ss_pred HHHHHHHHHHHHHHHcCCeeeEeeee
Confidence 47899999999999999999986653
No 10
>PF13398 Peptidase_M50B: Peptidase M50B-like
Probab=96.01 E-value=0.0073 Score=55.27 Aligned_cols=27 Identities=33% Similarity=0.397 Sum_probs=25.8
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceecCc
Q 020000 137 MCVQHEAGHFLTGYLLGVLPKGYEIPS 163 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg~PV~kyTI~p 163 (332)
-+..||.||+++|.+.|..|+++++.|
T Consensus 24 ~t~~HE~gHal~a~l~G~~v~~i~l~~ 50 (200)
T PF13398_consen 24 VTFVHELGHALAALLTGGRVKGIVLFP 50 (200)
T ss_pred HHHHHHHHHHHHHHHhCCCcceEEEEe
Confidence 489999999999999999999999998
No 11
>cd06161 S2P-M50_SpoIVFB SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB.
Probab=95.85 E-value=0.0082 Score=55.10 Aligned_cols=27 Identities=22% Similarity=0.333 Sum_probs=25.7
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceecCc
Q 020000 137 MCVQHEAGHFLTGYLLGVLPKGYEIPS 163 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg~PV~kyTI~p 163 (332)
-+..||.||+++|..+|.+++++++.|
T Consensus 40 ~v~iHElgH~~~A~~~G~~v~~i~l~p 66 (208)
T cd06161 40 SVLLHELGHALVARRYGIRVRSITLLP 66 (208)
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEe
Confidence 578999999999999999999999998
No 12
>cd06164 S2P-M50_SpoIVFB_CBS SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. In this subgroup, SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. It has been proposed tha
Probab=95.82 E-value=0.013 Score=54.82 Aligned_cols=27 Identities=22% Similarity=0.277 Sum_probs=25.6
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceecCc
Q 020000 137 MCVQHEAGHFLTGYLLGVLPKGYEIPS 163 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg~PV~kyTI~p 163 (332)
-+..||.||+++|..+|.+|+++++.|
T Consensus 55 ~v~iHElgH~~~A~~~G~~v~~i~l~p 81 (227)
T cd06164 55 SVLLHELGHSLVARRYGIPVRSITLFL 81 (227)
T ss_pred HHHHHHHHHHHHHHHcCCeECeEEEEe
Confidence 578999999999999999999999998
No 13
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=95.15 E-value=0.013 Score=59.57 Aligned_cols=26 Identities=31% Similarity=0.454 Sum_probs=24.4
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceecC
Q 020000 137 MCVQHEAGHFLTGYLLGVLPKGYEIP 162 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg~PV~kyTI~ 162 (332)
.|..||.||||+|.+.|+.|.+++|.
T Consensus 17 li~vHElGHfl~Ar~~gv~V~~FsiG 42 (449)
T PRK10779 17 LITVHEFGHFWVARRCGVRVERFSIG 42 (449)
T ss_pred HHHHHHHHHHHHHHHcCCeeeEEEee
Confidence 68899999999999999999999986
No 14
>cd05709 S2P-M50 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. The domain core structure appears to contain at least three transmembrane helices with a catalytic zinc atom coordinated by three conserved residues contained within the consensus sequence HExxH, together with a conserved aspartate residue. The S2P/M50 family of RIP proteases is widely distributed; in eukaryotic cells, they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum (ER) stress responses. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of sterol regulatory element-bindin
Probab=95.06 E-value=0.023 Score=50.20 Aligned_cols=25 Identities=32% Similarity=0.345 Sum_probs=21.0
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceec
Q 020000 137 MCVQHEAGHFLTGYLLGVLPKGYEI 161 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg~PV~kyTI 161 (332)
-+..||.||+++|+..|+++.+.++
T Consensus 10 ~i~iHE~gH~~~A~~~G~~~~~~~~ 34 (180)
T cd05709 10 SVTVHELGHALVARRLGVKVARFSG 34 (180)
T ss_pred HHHHHHHHHHHHHHHcCCCchheee
Confidence 3789999999999999997765554
No 15
>cd06162 S2P-M50_PDZ_SREBP Sterol regulatory element-binding protein (SREBP) Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50A), regulates intramembrane proteolysis (RIP) of SREBP and is part of a signal transduction mechanism involved in sterol and lipid metabolism. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of SREBPs from membranes of the endoplasmic reticulum (ER). These domains translocate into the nucleus, where they activate genes of cholesterol and fatty acid biosynthesis. The first cleavage occurs at Site-1 within the ER lumen to generate an intermediate that is subsequently released from the membrane by cleavage at Site-2, which lies within the first transmembrane domain. It is the second proteolytic step that is carried out by the SREBP Site-2 protease (S2P) which is present in this CD family. This group appears to be limited to eumetazoan proteins and contains one PDZ domain.
Probab=94.69 E-value=0.036 Score=53.87 Aligned_cols=27 Identities=30% Similarity=0.238 Sum_probs=24.5
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceecCc
Q 020000 137 MCVQHEAGHFLTGYLLGVLPKGYEIPS 163 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg~PV~kyTI~p 163 (332)
-+..||.||+++|...|++|+.+.+.+
T Consensus 137 svvvHElgHal~A~~~gi~V~~iGl~l 163 (277)
T cd06162 137 SGVVHEMGHGVAAVREQVRVNGFGIFF 163 (277)
T ss_pred HHHHHHHHHHHHHHHcCCeeceEEEee
Confidence 478999999999999999999988765
No 16
>PF02163 Peptidase_M50: Peptidase family M50; InterPro: IPR008915 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 []. This entry contains metallopeptidases belonging to MEROPS peptidase family M50 (S2P protease family, clan MM). Members of the M50 metallopeptidase family include: mammalian sterol-regulatory element binding protein (SREBP) site 2 protease, Escherichia coli protease EcfE, stage IV sporulation protein FB and various hypothetical bacterial and eukaryotic homologues. A number of proteins are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity.; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3B4R_A 3ID4_A 3ID2_A 2ZPL_B 3ID1_A 2ZPM_A 3ID3_B 2HGA_A.
Probab=93.95 E-value=0.039 Score=48.93 Aligned_cols=26 Identities=35% Similarity=0.336 Sum_probs=18.5
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceecC
Q 020000 137 MCVQHEAGHFLTGYLLGVLPKGYEIP 162 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg~PV~kyTI~ 162 (332)
-+..||.||+++|+..|.++..+++.
T Consensus 9 ~i~~HE~gH~~~a~~~G~~~~~~~~~ 34 (192)
T PF02163_consen 9 SIVLHELGHALAARLYGDKVPRFEGG 34 (192)
T ss_dssp HHHHHHHHHHHHHHTTT--B--EEE-
T ss_pred cccccccccccccccccccccccccc
Confidence 36899999999999999988888544
No 17
>TIGR00054 RIP metalloprotease RseP. A model that detects fragments as well matches a number of members of the PEPTIDASE FAMILY S2C. The region of match appears not to overlap the active site domain.
Probab=93.83 E-value=0.035 Score=56.06 Aligned_cols=26 Identities=35% Similarity=0.613 Sum_probs=22.6
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceecC
Q 020000 137 MCVQHEAGHFLTGYLLGVLPKGYEIP 162 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg~PV~kyTI~ 162 (332)
.|..||.||+|+|...|..|.+++|.
T Consensus 16 ~v~~HE~gH~~~a~~~g~~v~~FsiG 41 (420)
T TIGR00054 16 LIFVHELGHFLAARLCGIKVERFSIG 41 (420)
T ss_pred HHHHHhHHHHHHHHHcCCEEEEEEEc
Confidence 58899999999999999988876553
No 18
>cd06160 S2P-M50_like_2 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with additional putative N- and C-terminal transmembrane spanning regions, relative to the core protein, and no PDZ domains.
Probab=92.01 E-value=0.13 Score=46.86 Aligned_cols=27 Identities=26% Similarity=0.230 Sum_probs=24.9
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceecCc
Q 020000 137 MCVQHEAGHFLTGYLLGVLPKGYEIPS 163 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg~PV~kyTI~p 163 (332)
-+..||.||+++|...|+++.+..+.|
T Consensus 43 ~l~iHElgH~~~A~~~G~~~~~~~l~P 69 (183)
T cd06160 43 ILGIHEMGHYLAARRHGVKASLPYFIP 69 (183)
T ss_pred HHHHHHHHHHHHHHHCCCCccceeeee
Confidence 578999999999999999999988887
No 19
>cd06159 S2P-M50_PDZ_Arch Uncharacterized Archaeal homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group appears to be limited to Archaeal S2P/M50s homologs with additional putative N-terminal transmembrane spanning regions, relative to the core protein, and either one or two PDZ domains present.
Probab=88.17 E-value=0.27 Score=47.28 Aligned_cols=25 Identities=24% Similarity=0.197 Sum_probs=22.0
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceec
Q 020000 137 MCVQHEAGHFLTGYLLGVLPKGYEI 161 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg~PV~kyTI 161 (332)
-+..||.||+++|...|++|+.+.+
T Consensus 120 sv~iHElgHa~~Ar~~G~~V~~iGl 144 (263)
T cd06159 120 GVVVHELSHGILARVEGIKVKSGGL 144 (263)
T ss_pred HHHHHHHHHHHHHHHcCCEECchhH
Confidence 4789999999999999999887654
No 20
>cd06158 S2P-M50_like_1 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with a minimal core protein and no PDZ domains.
Probab=88.16 E-value=0.36 Score=43.65 Aligned_cols=26 Identities=23% Similarity=0.273 Sum_probs=21.2
Q ss_pred HHHHHHhHHHHHHHhCCCCC----ceecCc
Q 020000 138 CVQHEAGHFLTGYLLGVLPK----GYEIPS 163 (332)
Q Consensus 138 VA~HEAGHaLVAyLLg~PV~----kyTI~p 163 (332)
+..||.||+++|+..|++.. ..|+.|
T Consensus 12 i~~HE~aHa~~A~~~Gd~t~~~~Grltlnp 41 (181)
T cd06158 12 ITLHEFAHAYVAYRLGDPTARRAGRLTLNP 41 (181)
T ss_pred HHHHHHHHHHHHHHcCCcHHHHcCceecCc
Confidence 67899999999999998655 356665
No 21
>PF00413 Peptidase_M10: Matrixin This Prosite motif covers only the active site.; InterPro: IPR001818 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 []. This group of metallopeptidases belong to the MEROPS peptidase family M10 (clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. Sequences having this domain are extracellular metalloproteases, such as collagenase and stromelysin, which degrade the extracellular matrix, are known as matrixins. They are zinc-dependent, calcium-activated proteases synthesised as inactive precursors (zymogens), which are proteolytically cleaved to yield the active enzyme [, ]. All matrixins and related proteins possess 2 domains: an N-terminal domain, and a zinc-binding active site domain. The N-terminal domain peptide, cleaved during the activation step, includes a conserved PRCGVPDV octapeptide, known as the cysteine switch, whose Cys residue chelates the active site zinc atom, rendering the enzyme inactive [, ]. The active enzyme degrades components of the extracellular matrix, playing a role in the initial steps of tissue remodelling during morphogenesis, wound healing, angiogenesis and tumour invasion [, ].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0031012 extracellular matrix; PDB: 1Q3A_C 3V96_B 1HV5_D 1CXV_A 1SRP_A 1FBL_A 1ZVX_A 1JH1_A 1I76_A 2OY4_A ....
Probab=83.02 E-value=0.56 Score=39.61 Aligned_cols=17 Identities=35% Similarity=0.399 Sum_probs=14.6
Q ss_pred ChhHHHHHHHHHHhHHH
Q 020000 131 KEEDHFMCVQHEAGHFL 147 (332)
Q Consensus 131 s~eer~RVA~HEAGHaL 147 (332)
+..+...|+.||.||+|
T Consensus 101 ~~~~~~~v~~HEiGHaL 117 (154)
T PF00413_consen 101 SGNDLQSVAIHEIGHAL 117 (154)
T ss_dssp SSEEHHHHHHHHHHHHT
T ss_pred hhhhhhhhhhhcccccc
Confidence 55678899999999985
No 22
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=82.27 E-value=0.87 Score=43.00 Aligned_cols=21 Identities=33% Similarity=0.428 Sum_probs=16.4
Q ss_pred HHHHHHHhHHHHHHHhCCCCCc
Q 020000 137 MCVQHEAGHFLTGYLLGVLPKG 158 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg~PV~k 158 (332)
-|.|||.||+|+..+ ++||.|
T Consensus 94 ~~l~HE~GHAlI~~~-~lPv~G 114 (220)
T PF14247_consen 94 FTLYHELGHALIDDL-DLPVLG 114 (220)
T ss_pred HHHHHHHHHHHHHHh-cCCccc
Confidence 578999999999865 456554
No 23
>cd04279 ZnMc_MMP_like_1 Zinc-dependent metalloprotease; MMP_like sub-family 1. A group of bacterial, archaeal, and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=78.79 E-value=1.3 Score=38.19 Aligned_cols=22 Identities=27% Similarity=0.243 Sum_probs=16.7
Q ss_pred hhHHHHHHHHHHhHHHHHHHhC
Q 020000 132 EEDHFMCVQHEAGHFLTGYLLG 153 (332)
Q Consensus 132 ~eer~RVA~HEAGHaLVAyLLg 153 (332)
..+.+.|+.||.||+|=-....
T Consensus 101 ~~~~~~~~~HEiGHaLGL~H~~ 122 (156)
T cd04279 101 AENLQAIALHELGHALGLWHHS 122 (156)
T ss_pred chHHHHHHHHHhhhhhcCCCCC
Confidence 4678899999999997544443
No 24
>cd04268 ZnMc_MMP_like Zinc-dependent metalloprotease, MMP_like subfamily. This group contains matrix metalloproteinases (MMPs), serralysins, and the astacin_like family of proteases.
Probab=76.71 E-value=1.6 Score=37.37 Aligned_cols=19 Identities=26% Similarity=0.181 Sum_probs=15.1
Q ss_pred ChhHHHHHHHHHHhHHHHH
Q 020000 131 KEEDHFMCVQHEAGHFLTG 149 (332)
Q Consensus 131 s~eer~RVA~HEAGHaLVA 149 (332)
+..+...++.||.||+|=-
T Consensus 90 ~~~~~~~~~~HEiGHaLGL 108 (165)
T cd04268 90 SGARLRNTAEHELGHALGL 108 (165)
T ss_pred HHHHHHHHHHHHHHHHhcc
Confidence 3467889999999999643
No 25
>PF04298 Zn_peptidase_2: Putative neutral zinc metallopeptidase; InterPro: IPR007395 Members of this family of bacterial proteins are described as hypothetical proteins or zinc-dependent proteases. The majority have a HExxH zinc-binding motif characteristic of neutral zinc metallopeptidases, however there is no evidence to support their function as metallopeptidases.
Probab=72.96 E-value=1.8 Score=41.07 Aligned_cols=12 Identities=33% Similarity=0.612 Sum_probs=10.5
Q ss_pred HHHHHHHhHHHH
Q 020000 137 MCVQHEAGHFLT 148 (332)
Q Consensus 137 RVA~HEAGHaLV 148 (332)
-||.||+|||+=
T Consensus 91 aVAAHEvGHAiQ 102 (222)
T PF04298_consen 91 AVAAHEVGHAIQ 102 (222)
T ss_pred HHHHHHHhHHHh
Confidence 589999999974
No 26
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=71.70 E-value=2.6 Score=40.95 Aligned_cols=26 Identities=31% Similarity=0.484 Sum_probs=23.6
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceecC
Q 020000 137 MCVQHEAGHFLTGYLLGVLPKGYEIP 162 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg~PV~kyTI~ 162 (332)
.|..||.||+|+++..+..|.++++.
T Consensus 15 lv~~he~gh~~~a~~~~~~v~~f~ig 40 (375)
T COG0750 15 LVFVHELGHFWVARRCGVKVERFSIG 40 (375)
T ss_pred HHHHHHHhhHHHHHhcCceeEEEEec
Confidence 68899999999999999888888875
No 27
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=71.13 E-value=22 Score=30.70 Aligned_cols=68 Identities=12% Similarity=0.113 Sum_probs=49.2
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHH-----HHHHHHHHHHHHhHHHHHHHHHHHHh-hCcHHHHHHHHhcccc
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVK-----WAALNTVLISHHHIQVRSRLAEAMAL-GRSIGSYTSKILTEQS 305 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr-----~A~~~A~~LL~~hr~ale~LAeaLle-~esl~ec~~~Ie~~~~ 305 (332)
.+|+..+..| ++.+|||-++|..-.. +...+...+|+++.+.++...+.|.+ +..|.+++..+++..+
T Consensus 41 ~~~v~~l~~I~~lr~~GfsL~eI~~ll~~~~~~~~~~~~~~~l~~k~~~i~~~i~~L~~~~~~L~~~i~~~~~~~~ 116 (131)
T cd04786 41 PETVWVLEIISSAQQAGFSLDEIRQLLPADASNWQHDELLAALERKVADIEALEARLAQNKAQLLVLIDLIESKPD 116 (131)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 4788877776 6679999877655432 23356678899999998888887777 5568888888876543
No 28
>cd04278 ZnMc_MMP Zinc-dependent metalloprotease, matrix metalloproteinase (MMP) sub-family. MMPs are responsible for a great deal of pericellular proteolysis of extracellular matrix and cell surface molecules, playing crucial roles in morphogenesis, cell fate specification, cell migration, tissue repair, tumorigenesis, gain or loss of tissue-specific functions, and apoptosis. In many instances, they are anchored to cell membranes via trans-membrane domains, and their activity is controlled via TIMPs (tissue inhibitors of metalloproteinases).
Probab=70.56 E-value=2 Score=37.18 Aligned_cols=17 Identities=41% Similarity=0.577 Sum_probs=14.3
Q ss_pred ChhHHHHHHHHHHhHHH
Q 020000 131 KEEDHFMCVQHEAGHFL 147 (332)
Q Consensus 131 s~eer~RVA~HEAGHaL 147 (332)
+..+...|+.||.||+|
T Consensus 103 ~~~~~~~~~~HEiGHaL 119 (157)
T cd04278 103 GGTDLFSVAAHEIGHAL 119 (157)
T ss_pred ccchHHHHHHHHhcccc
Confidence 34678899999999995
No 29
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=70.19 E-value=3.1 Score=42.97 Aligned_cols=26 Identities=38% Similarity=0.469 Sum_probs=22.3
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceecC
Q 020000 137 MCVQHEAGHFLTGYLLGVLPKGYEIP 162 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg~PV~kyTI~ 162 (332)
-+..||.||+|.|-.-|++|.++-|-
T Consensus 133 ~~vvHElGHalAA~segV~vngfgIf 158 (484)
T KOG2921|consen 133 TVVVHELGHALAAASEGVQVNGFGIF 158 (484)
T ss_pred HHHHHHhhHHHHHHhcCceeeeeEEE
Confidence 34689999999999999999987664
No 30
>PF02031 Peptidase_M7: Streptomyces extracellular neutral proteinase (M7) family; InterPro: IPR000013 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 []. This group of metallopeptidases belong to the MEROPS peptidase family M7 (snapalysin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. With a molecular weight of around 16kDa, Streptomyces extracellular neutral protease is one of the smallest known proteases []; it is capable of hydrolysing milk proteins []. The enzyme is synthesised as a proenzyme with a signal peptide, a propeptide and an active domain that contains the conserved HEXXH motif characteristic of metalloproteases. Although family M7 shows active site sequence similarity to other members, it differs in one major respect: the third zinc ligand appears to be an aspartate residue rather than the usual histidine.; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0005576 extracellular region; PDB: 1C7K_A 1KUH_A.
Probab=68.71 E-value=3.6 Score=36.33 Aligned_cols=27 Identities=26% Similarity=0.196 Sum_probs=16.6
Q ss_pred hHHhhcccCCCCChhHHHHHHHHHHhHHH
Q 020000 119 ESIVEDGSYVSLKEEDHFMCVQHEAGHFL 147 (332)
Q Consensus 119 ~~llld~~~r~ls~eer~RVA~HEAGHaL 147 (332)
+.|.+|.-. .-.=..-||+.||.||.|
T Consensus 63 G~I~l~~~~--~qgy~~~RIaaHE~GHiL 89 (132)
T PF02031_consen 63 GYIFLDYQQ--NQGYNSTRIAAHELGHIL 89 (132)
T ss_dssp EEEEEEHHH--HHHS-HHHHHHHHHHHHH
T ss_pred EEEEechHH--hhCCccceeeeehhcccc
Confidence 667776311 011234599999999975
No 31
>cd04277 ZnMc_serralysin_like Zinc-dependent metalloprotease, serralysin_like subfamily. Serralysins and related proteases are important virulence factors in pathogenic bacteria. They may be secreted into the medium via a mechanism found in gram-negative bacteria, that does not require n-terminal signal sequences which are cleaved after the transmembrane translocation. A calcium-binding domain c-terminal to the metalloprotease domain, which contains multiple tandem repeats of a nine-residue motif including the pattern GGxGxD, and which forms a parallel beta roll may be involved in the translocation mechanism and/or substrate binding. Serralysin family members may have a broad spectrum of substrates each, including host immunoglobulins, complement proteins, cell matrix and cytoskeletal proteins, as well as antimicrobial peptides.
Probab=66.77 E-value=3.7 Score=36.41 Aligned_cols=18 Identities=28% Similarity=0.327 Sum_probs=14.9
Q ss_pred hhHHHHHHHHHHhHHHHH
Q 020000 132 EEDHFMCVQHEAGHFLTG 149 (332)
Q Consensus 132 ~eer~RVA~HEAGHaLVA 149 (332)
..+...++.||.||+|==
T Consensus 110 g~~~~~t~~HEiGHaLGL 127 (186)
T cd04277 110 GSYGYQTIIHEIGHALGL 127 (186)
T ss_pred ChhhHHHHHHHHHHHhcC
Confidence 467889999999999743
No 32
>PF06114 DUF955: Domain of unknown function (DUF955); InterPro: IPR010359 This is a family of bacterial and viral proteins with undetermined function. A conserved H-E-X-X-H motif is suggestive of a catalytic active site and shows similarity to IPR001915 from INTERPRO.; PDB: 3DTE_A 3DTK_A 3DTI_A.
Probab=63.84 E-value=7.6 Score=30.42 Aligned_cols=25 Identities=28% Similarity=0.271 Sum_probs=19.3
Q ss_pred CCCChhHHHHHHHHHHhHHHHHHHh
Q 020000 128 VSLKEEDHFMCVQHEAGHFLTGYLL 152 (332)
Q Consensus 128 r~ls~eer~RVA~HEAGHaLVAyLL 152 (332)
...++..++=++.||.||.+...--
T Consensus 35 ~~~~~~~~~f~laHELgH~~~~~~~ 59 (122)
T PF06114_consen 35 SNLSPERQRFTLAHELGHILLHHGD 59 (122)
T ss_dssp SSS-HHHHHHHHHHHHHHHHHHH-H
T ss_pred CCCCHHHHHHHHHHHHHHHHhhhcc
Confidence 3358899999999999999987655
No 33
>PF05572 Peptidase_M43: Pregnancy-associated plasma protein-A; InterPro: IPR008754 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 []. This group of metallopeptidases belong to the MEROPS peptidase M43 (cytophagalysin family, clan MA(M)), subfamily M43. The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example of this family is the pregnancy-associated plasma protein A (PAPP-A), which cleaves insulin-like growth factor (IGF) binding protein-4 (IGFBP-4), causing a dramatic reduction in its affinity for IGF-I and -II. Through this mechanism, PAPP-A is a regulator of IGF bioactivity in several systems, including the Homo sapiens ovary and the cardiovascular system [, , , ].; PDB: 3LUN_A 3LUM_B 2J83_A 2CKI_A.
Probab=62.05 E-value=4.1 Score=36.10 Aligned_cols=21 Identities=29% Similarity=0.417 Sum_probs=14.2
Q ss_pred ChhHHHHHHHHHHhHHHHHHH
Q 020000 131 KEEDHFMCVQHEAGHFLTGYL 151 (332)
Q Consensus 131 s~eer~RVA~HEAGHaLVAyL 151 (332)
++....+++.||.||+|=-+.
T Consensus 65 ~~~~~g~TltHEvGH~LGL~H 85 (154)
T PF05572_consen 65 SQYNFGKTLTHEVGHWLGLYH 85 (154)
T ss_dssp TTS-SSHHHHHHHHHHTT---
T ss_pred Cccccccchhhhhhhhhcccc
Confidence 456667999999999984443
No 34
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=61.67 E-value=42 Score=27.91 Aligned_cols=60 Identities=15% Similarity=0.135 Sum_probs=39.9
Q ss_pred HHHHHHHHHhCCChhHHHHHH----HHHHHHHHHHHHHhHH------HHHHHHHHHHhhCcHHHHHHHHhc
Q 020000 242 NKLDKVFQWLGYNKSEADSQV----KWAALNTVLISHHHIQ------VRSRLAEAMALGRSIGSYTSKILT 302 (332)
Q Consensus 242 ~qat~iar~lGmS~~~id~ev----r~A~~~A~~LL~~hr~------ale~LAeaLle~esl~ec~~~Ie~ 302 (332)
.+..+++|.+|||+.+||.-. +...++..++|+.... ++..|.++|.. --+..|-..|+.
T Consensus 21 ~~wK~faR~lglse~~Id~I~~~~~~d~~Eq~~qmL~~W~~~~G~~a~~~~Li~aLr~-~~l~~~Ad~I~~ 90 (97)
T cd08316 21 KDVKKFVRKSGLSEPKIDEIKLDNPQDTAEQKVQLLRAWYQSHGKTGAYRTLIKTLRK-AKLCTKADKIQD 90 (97)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHcCCCChHHHHHHHHHHHHHHhCCCchHHHHHHHHHH-ccchhHHHHHHH
Confidence 466778999999998887653 3457888888876544 56777777665 333444444443
No 35
>cd04327 ZnMc_MMP_like_3 Zinc-dependent metalloprotease; MMP_like sub-family 3. A group of bacterial and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=60.26 E-value=5.9 Score=35.89 Aligned_cols=26 Identities=23% Similarity=0.059 Sum_probs=17.9
Q ss_pred hHHHHHHHHHHhHHHHHHHhCC-CCCc
Q 020000 133 EDHFMCVQHEAGHFLTGYLLGV-LPKG 158 (332)
Q Consensus 133 eer~RVA~HEAGHaLVAyLLg~-PV~k 158 (332)
-+...++.||.||+|=-+..-. |-+.
T Consensus 90 ~~~~~~i~HElgHaLG~~HEh~rpdrd 116 (198)
T cd04327 90 PEFSRVVLHEFGHALGFIHEHQSPAAN 116 (198)
T ss_pred hhHHHHHHHHHHHHhcCcccccCCCCC
Confidence 3456899999999986655543 4343
No 36
>smart00235 ZnMc Zinc-dependent metalloprotease. Neutral zinc metallopeptidases. This alignment represents a subset of known subfamilies. Highest similarity occurs in the HExxH zinc-binding site/ active site.
Probab=58.84 E-value=5 Score=33.75 Aligned_cols=14 Identities=43% Similarity=0.510 Sum_probs=11.2
Q ss_pred HHHHHHHhHHHHHH
Q 020000 137 MCVQHEAGHFLTGY 150 (332)
Q Consensus 137 RVA~HEAGHaLVAy 150 (332)
.|+.||.||+|=..
T Consensus 88 ~~~~HEigHaLGl~ 101 (140)
T smart00235 88 GVAAHELGHALGLY 101 (140)
T ss_pred ccHHHHHHHHhcCC
Confidence 39999999998433
No 37
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=58.10 E-value=68 Score=26.65 Aligned_cols=66 Identities=8% Similarity=0.013 Sum_probs=44.2
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHH-------HHHHHHHHHHHhHHHHHHHHHHHHh-hCcHHHHHHHHhcc
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKW-------AALNTVLISHHHIQVRSRLAEAMAL-GRSIGSYTSKILTE 303 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~-------A~~~A~~LL~~hr~ale~LAeaLle-~esl~ec~~~Ie~~ 303 (332)
.+|+..+..| ++.+|||-++|..-... .......+|.++...++.--+.|.+ ...++.++..++.+
T Consensus 40 ~~d~~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~~~~~~~~ 115 (116)
T cd04769 40 AQHVECLRFIKEARQLGFTLAELKAIFAGHEGRAVLPWPHLQQALEDKKQEIRAQITELQQLLARLDAFEASLKDA 115 (116)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHhccccCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 4788887776 67799998887654332 2345577788877777766666655 44467776666543
No 38
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=53.81 E-value=81 Score=24.22 Aligned_cols=47 Identities=19% Similarity=0.134 Sum_probs=31.5
Q ss_pred HHHHHHHHhCCChhHHHHHHHH----HHHHHHHHHHHhHH------HHHHHHHHHHh
Q 020000 243 KLDKVFQWLGYNKSEADSQVKW----AALNTVLISHHHIQ------VRSRLAEAMAL 289 (332)
Q Consensus 243 qat~iar~lGmS~~~id~evr~----A~~~A~~LL~~hr~------ale~LAeaLle 289 (332)
+-..+++.+||+..+++.-... ...++.++|+.-+. .++.|.++|.+
T Consensus 19 ~W~~la~~Lg~~~~~i~~i~~~~~~~~~~~~~~lL~~W~~~~g~~at~~~L~~aL~~ 75 (88)
T smart00005 19 DWRELARKLGLSEADIDQIRTEAPRDLAEQSVQLLRLWEQREGKNATLGTLLEALRK 75 (88)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHccchhhHHHHHHHHHHH
Confidence 4556788999998877654433 34788888886655 44555555544
No 39
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=53.26 E-value=77 Score=23.16 Aligned_cols=43 Identities=7% Similarity=0.085 Sum_probs=27.6
Q ss_pred HHHHhCCChhHHHHHH------HHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 020000 247 VFQWLGYNKSEADSQV------KWAALNTVLISHHHIQVRSRLAEAMAL 289 (332)
Q Consensus 247 iar~lGmS~~~id~ev------r~A~~~A~~LL~~hr~ale~LAeaLle 289 (332)
.++.+|||-++|..-. .........++.++.+.+++=-+.|..
T Consensus 9 ~~r~lGfsL~eI~~~l~l~~~~~~~~~~~~~~l~~~~~~i~~~i~~L~~ 57 (65)
T PF09278_consen 9 RLRELGFSLEEIRELLELYDQGDPPCADRRALLEEKLEEIEEQIAELQA 57 (65)
T ss_dssp HHHHTT--HHHHHHHHHHCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHcCCCHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3667999988876654 234566667888888777766555544
No 40
>cd00203 ZnMc Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease.
Probab=50.60 E-value=8.4 Score=32.81 Aligned_cols=19 Identities=32% Similarity=0.420 Sum_probs=14.6
Q ss_pred hHHHHHHHHHHhHHHHHHH
Q 020000 133 EDHFMCVQHEAGHFLTGYL 151 (332)
Q Consensus 133 eer~RVA~HEAGHaLVAyL 151 (332)
..-..++.||.||+|=.+.
T Consensus 94 ~~~~~~~~HElGH~LGl~H 112 (167)
T cd00203 94 KEGAQTIAHELGHALGFYH 112 (167)
T ss_pred ccchhhHHHHHHHHhCCCc
Confidence 3567999999999985443
No 41
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=49.65 E-value=13 Score=34.83 Aligned_cols=24 Identities=25% Similarity=0.360 Sum_probs=20.6
Q ss_pred CCChhHHHHHHHHHHhHHHHHHHh
Q 020000 129 SLKEEDHFMCVQHEAGHFLTGYLL 152 (332)
Q Consensus 129 ~ls~eer~RVA~HEAGHaLVAyLL 152 (332)
.++++|-+-|.-||.||..-.+.+
T Consensus 151 ~l~~dEl~aVlaHElgHi~~rd~~ 174 (302)
T COG0501 151 LLNDDELEAVLAHELGHIKNRHTL 174 (302)
T ss_pred hCCHHHHHHHHHHHHHHHhcccHH
Confidence 569999999999999998766554
No 42
>PF08858 IDEAL: IDEAL domain; InterPro: IPR014957 This entry represents the C-terminal domain of Bacteriophage SPP1, p90. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. his domain may also be referred to as the IDEAL domain, after the sequence of the most conserved region of the domain.; PDB: 3DO9_A.
Probab=48.70 E-value=43 Score=23.14 Aligned_cols=33 Identities=21% Similarity=0.232 Sum_probs=25.9
Q ss_pred hhHHHHHHHHHHHHHHHHccCchHHHHHHHHHh
Q 020000 21 AEYAKRRRQALKRVDRELSRGNFKVALSLVKQL 53 (332)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~g~~~~a~~~~~~l 53 (332)
+....++.+.++++|..|-+||.+.=..|.++|
T Consensus 5 ~~~~~~~~~L~~~ID~ALd~~D~e~F~~Ls~eL 37 (37)
T PF08858_consen 5 SLREFRKEQLLELIDEALDNRDKEWFYELSEEL 37 (37)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhC
Confidence 345678899999999999999988877776654
No 43
>PF11350 DUF3152: Protein of unknown function (DUF3152); InterPro: IPR022603 This entry represents Actinobacteria proteins of unknown function. Some are annotated as membrane proteins, however this cannot be confirmed.
Probab=46.85 E-value=10 Score=35.74 Aligned_cols=18 Identities=33% Similarity=0.508 Sum_probs=16.0
Q ss_pred hhHHHHHHHHHHhHHHHHH
Q 020000 132 EEDHFMCVQHEAGHFLTGY 150 (332)
Q Consensus 132 ~eer~RVA~HEAGHaLVAy 150 (332)
..||+-++-||.||+| +|
T Consensus 136 ~~YRqYvINHEVGH~L-Gh 153 (203)
T PF11350_consen 136 ASYRQYVINHEVGHAL-GH 153 (203)
T ss_pred HHHHHHhhhhhhhhhc-cc
Confidence 5899999999999999 44
No 44
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=45.69 E-value=1.2e+02 Score=25.45 Aligned_cols=60 Identities=10% Similarity=0.123 Sum_probs=36.1
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHHH----HHHHHHHHHHhHHHHHHHHHHHHh-hCcHHHHH
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKWA----ALNTVLISHHHIQVRSRLAEAMAL-GRSIGSYT 297 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~A----~~~A~~LL~~hr~ale~LAeaLle-~esl~ec~ 297 (332)
.+|+.++..| ++.+|||-++|.+-+... ......+|.++.+.++.=.+.|.+ ...|.+.+
T Consensus 41 ~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~l~~~~ 107 (126)
T cd04783 41 EETVTRLRFIKRAQELGFTLDEIAELLELDDGTDCSEARELAEQKLAEVDEKIADLQRMRASLQELV 107 (126)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4777776665 677999988776544321 345677777776666655554444 23344443
No 45
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=45.68 E-value=24 Score=27.81 Aligned_cols=23 Identities=26% Similarity=0.267 Sum_probs=19.2
Q ss_pred ChhHHHHHHHHHHhHHHHHHHhC
Q 020000 131 KEEDHFMCVQHEAGHFLTGYLLG 153 (332)
Q Consensus 131 s~eer~RVA~HEAGHaLVAyLLg 153 (332)
++..-.+++.||..|.+.....+
T Consensus 21 ~~~~~~~~l~HE~~H~~~~~~~~ 43 (128)
T PF13485_consen 21 DEDWLDRVLAHELAHQWFGNYFG 43 (128)
T ss_pred CHHHHHHHHHHHHHHHHHHHHcC
Confidence 45555799999999999998875
No 46
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=45.18 E-value=11 Score=30.80 Aligned_cols=12 Identities=42% Similarity=0.523 Sum_probs=10.5
Q ss_pred HHHHHHHHhHHH
Q 020000 136 FMCVQHEAGHFL 147 (332)
Q Consensus 136 ~RVA~HEAGHaL 147 (332)
..+..||.||.|
T Consensus 108 ~~~~~HEiGH~l 119 (124)
T PF13582_consen 108 VDTFAHEIGHNL 119 (124)
T ss_dssp TTHHHHHHHHHT
T ss_pred ceEeeehhhHhc
Confidence 389999999986
No 47
>PF01435 Peptidase_M48: Peptidase family M48 This is family M48 in the peptidase classification. ; InterPro: IPR001915 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 []. This group of metallopeptidases belong to MEROPS peptidase family M48 (Ste24 endopeptidase family, clan M-); members of both subfamily are represented. The members of this set of proteins are mostly described as probable protease htpX homologue (3.4.24 from EC) or CAAX prenyl protease 1, which proteolytically removes the C-terminal three residues of farnesylated proteins. They are integral membrane proteins associated with the endoplasmic reticulum and Golgi, binding one zinc ion per subunit. In Saccharomyces cerevisiae (Baker's yeast) Ste24p is required for the first NH2-terminal proteolytic processing event within the a-factor precursor, which takes place after COOH-terminal CAAX modification is complete. The Ste24p contains multiple predicted membrane spans, a zinc metalloprotease motif (HEXXH), and a COOH-terminal ER retrieval signal (KKXX). The HEXXH protease motif is critical for Ste24p activity, since Ste24p fails to function when conserved residues within this motif are mutated. The Ste24p homologues occur in a diverse group of organisms, including Escherichia coli, Schizosaccharomyces pombe (Fission yeast), Haemophilus influenzae, and Homo sapiens (Human), which indicates that the gene is highly conserved throughout evolution. Ste24p and the proteins related to it define a subfamily of proteins that are likely to function as intracellular, membrane-associated zinc metalloproteases []. HtpX is a zinc-dependent endoprotease member of the membrane-localized proteolytic system in E. coli, which participates in the proteolytic quality control of membrane proteins in conjunction with FtsH, a membrane-bound and ATP-dependent protease. Biochemical characterisation revealed that HtpX undergoes self-degradation upon cell disruption or membrane solubilization. It can also degraded casein and cleaves solubilized membrane proteins, for example, SecY []. Expression of HtpX in the plasma membrane is under the control of CpxR, with the metalloproteinase active site of HtpX located on the cytosolic side of the membrane. This suggests a potential role for HtpX in the response to mis-folded proteins [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis, 0016020 membrane; PDB: 3CQB_A 3C37_B.
Probab=45.10 E-value=18 Score=32.15 Aligned_cols=24 Identities=29% Similarity=0.444 Sum_probs=20.1
Q ss_pred CChhHHHHHHHHHHhHHHHHHHhC
Q 020000 130 LKEEDHFMCVQHEAGHFLTGYLLG 153 (332)
Q Consensus 130 ls~eer~RVA~HEAGHaLVAyLLg 153 (332)
++++|..-|..||.||..-.+..-
T Consensus 84 ~~~~el~aVlaHElgH~~~~h~~~ 107 (226)
T PF01435_consen 84 LSEDELAAVLAHELGHIKHRHILK 107 (226)
T ss_dssp SSHHHHHHHHHHHHHHHHTTHCCC
T ss_pred ccHHHHHHHHHHHHHHHHcCCcch
Confidence 488999999999999998666543
No 48
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=45.08 E-value=91 Score=25.11 Aligned_cols=51 Identities=12% Similarity=0.192 Sum_probs=34.9
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKWAALNTVLISHHHIQVRSRLAEAMA 288 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~A~~~A~~LL~~hr~ale~LAeaLl 288 (332)
.+|+..+..| ++.+|||-++|.+-....-.+...+|.++...++.=.+.|.
T Consensus 41 ~~~l~~l~~I~~lr~~G~~l~~I~~~l~~~~~~~~~~l~~~~~~l~~~i~~l~ 93 (96)
T cd04768 41 YAQLYQLQFILFLRELGFSLAEIKELLDTEMEELTAMLLEKKQAIQQKIDRLQ 93 (96)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHHHHH
Confidence 4677777765 67799998887655443333677778888777776665554
No 49
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=43.43 E-value=84 Score=25.29 Aligned_cols=50 Identities=14% Similarity=0.277 Sum_probs=32.6
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKWAALNTVLISHHHIQVRSRLAEAM 287 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~A~~~A~~LL~~hr~ale~LAeaL 287 (332)
.+|+..+..| ++.+||+-++|..-+........++|.++.+.++.=-+.|
T Consensus 41 ~~~l~~l~~I~~lr~~G~~l~eI~~~l~~~~~~~~~~l~~~~~~l~~~i~~l 92 (96)
T cd04788 41 RADIRRLHQIIALRRLGFSLREIGRALDGPDFDPLELLRRQLARLEEQLELA 92 (96)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHHH
Confidence 4788887776 6679999888765544322355667777776666544444
No 50
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=43.08 E-value=1.7e+02 Score=24.53 Aligned_cols=60 Identities=7% Similarity=0.093 Sum_probs=37.9
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHH------HHHHHHHHHHHhHHHHHHHHHHHHh-hCcHHHHH
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKW------AALNTVLISHHHIQVRSRLAEAMAL-GRSIGSYT 297 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~------A~~~A~~LL~~hr~ale~LAeaLle-~esl~ec~ 297 (332)
.+|+..+..| ++.+|||-++|..=+.. .......+|.++...+++--+.|.. ...|....
T Consensus 41 ~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~ 109 (127)
T cd04784 41 EEHLERLLFIRRCRSLDMSLDEIRTLLQLQDDPEASCAEVNALIDEHLAHVRARIAELQALEKQLQALR 109 (127)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4788877766 67799998887654432 2345677787777777755555443 33344433
No 51
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=42.73 E-value=1.2e+02 Score=24.18 Aligned_cols=46 Identities=13% Similarity=0.026 Sum_probs=30.8
Q ss_pred HHHHHHHhCCChhHHHHHHH----HHHHHHHHHHHHhHH------HHHHHHHHHHh
Q 020000 244 LDKVFQWLGYNKSEADSQVK----WAALNTVLISHHHIQ------VRSRLAEAMAL 289 (332)
Q Consensus 244 at~iar~lGmS~~~id~evr----~A~~~A~~LL~~hr~------ale~LAeaLle 289 (332)
-.+++|.+|+|+.+|+.=.. ...+++.++|+.-+. .++.|.++|.+
T Consensus 16 Wk~laR~LGlse~~Id~i~~~~~~~~~eq~~~mL~~W~~~~g~~At~~~L~~aL~~ 71 (86)
T cd08306 16 WRKLARKLGLSETKIESIEEAHPRNLREQVRQSLREWKKIKKKEAKVADLIKALRD 71 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHhHCcchHHHHHHHHHHH
Confidence 44578889999988875322 345778888874443 45566666665
No 52
>COG0339 Dcp Zn-dependent oligopeptidases [Amino acid transport and metabolism]
Probab=42.22 E-value=20 Score=39.26 Aligned_cols=32 Identities=25% Similarity=0.184 Sum_probs=23.8
Q ss_pred HHHHHHHhHHHHHHHhCC---CCCceecCchhhhcc
Q 020000 137 MCVQHEAGHFLTGYLLGV---LPKGYEIPSVEALKQ 169 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg~---PV~kyTI~p~eal~~ 169 (332)
.+.+||-||+|=..|..+ .|.|.. .|||++--
T Consensus 469 ~TLFHEfGHgLH~mlt~v~~~~vsGt~-v~wDfVEl 503 (683)
T COG0339 469 TTLFHEFGHGLHHLLTRVKYPGVSGTN-VPWDFVEL 503 (683)
T ss_pred HHHHHHhhhHHHHHhhcCCccccCCCC-CCcchhhc
Confidence 789999999998877764 556666 66665544
No 53
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=41.63 E-value=1.5e+02 Score=25.83 Aligned_cols=61 Identities=7% Similarity=0.037 Sum_probs=38.0
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHH-------HHHHHHHHHHHhHHHHHHHHHHHHh-hCcHHHHHH
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKW-------AALNTVLISHHHIQVRSRLAEAMAL-GRSIGSYTS 298 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~-------A~~~A~~LL~~hr~ale~LAeaLle-~esl~ec~~ 298 (332)
.+|+.++..| ++.+|||-++|..-+.. .......++.++...++.-.+.|.+ ...|..++.
T Consensus 41 ~~di~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~ki~~L~~~~~~L~~~~~ 111 (142)
T TIGR01950 41 RDVLRRVAVIKAAQRVGIPLATIGEALAVLPEGRTPTADDWARLSSQWREELDERIDQLNALRDQLDGCIG 111 (142)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4788888776 66799998877655431 1344556777776666655444444 444555553
No 54
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=40.40 E-value=2e+02 Score=23.66 Aligned_cols=52 Identities=8% Similarity=0.081 Sum_probs=33.2
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHH------HHHHHHHHHHHhHHHHHHHHHHHHh
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKW------AALNTVLISHHHIQVRSRLAEAMAL 289 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~------A~~~A~~LL~~hr~ale~LAeaLle 289 (332)
.+|+..+..| ++.+|||-++|..-... ...+...+|.++...++.-.+.|..
T Consensus 41 ~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (113)
T cd01109 41 EEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPERLELLEEHREELEEQIAELQE 100 (113)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHccCCccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4777777765 66799998877654321 1244567777777776665555544
No 55
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=39.32 E-value=1.9e+02 Score=23.75 Aligned_cols=53 Identities=13% Similarity=0.061 Sum_probs=34.8
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHH-----HHHHHHHHHHHhHHHHHHHHHHHHhh
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKW-----AALNTVLISHHHIQVRSRLAEAMALG 290 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~-----A~~~A~~LL~~hr~ale~LAeaLle~ 290 (332)
.+|+..+..| ++.+||+-++|..-+.. .......+|+++...++.=..+|..+
T Consensus 41 ~~dl~~l~~I~~lr~~G~~l~~I~~~l~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~ 100 (108)
T cd04773 41 PSDVRDARLIHLLRRGGYLLEQIATVVEQLRHAGGTEALAAALEQRRVALTQRGRAMLDA 100 (108)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4788887776 66789998776554331 12456677777777776666666543
No 56
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=39.00 E-value=1.4e+02 Score=25.79 Aligned_cols=61 Identities=8% Similarity=0.035 Sum_probs=36.7
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHH-------HHHHHHHHHHHhHHHHHHHHHHHHh-hCcHHHHHH
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKW-------AALNTVLISHHHIQVRSRLAEAMAL-GRSIGSYTS 298 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~-------A~~~A~~LL~~hr~ale~LAeaLle-~esl~ec~~ 298 (332)
.+|++++..| ++..|||-++|.+-+.. .......++.++.+.++.-.+.|.+ ...|.+++.
T Consensus 41 ~~dl~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~i~ 111 (139)
T cd01110 41 RDVLRRIAFIKVAQRLGLSLAEIAEALATLPEDRTPTKADWERLSRAWRDRLDERIAELQQLRDQLDGCIG 111 (139)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4788888776 56799998877654432 1233345666665555555555544 444566554
No 57
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=38.78 E-value=1.4e+02 Score=24.00 Aligned_cols=52 Identities=12% Similarity=0.127 Sum_probs=34.9
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHH-HHHHHHHHHHHHhHHHHHHHHHHHHh
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVK-WAALNTVLISHHHIQVRSRLAEAMAL 289 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr-~A~~~A~~LL~~hr~ale~LAeaLle 289 (332)
.+|+..+..| ++.+|||-+++..-.. ....+...+|.++.+.+++=.+.|.+
T Consensus 41 ~~~~~~l~~I~~lr~~G~~l~eI~~~l~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 95 (97)
T cd04782 41 LEQFEQLDIILLLKELGISLKEIKDYLDNRNPDELIELLKKQEKEIKEEIEELQK 95 (97)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3677666665 6779999887765433 23456677888888777776666543
No 58
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=36.81 E-value=1.4e+02 Score=24.17 Aligned_cols=48 Identities=15% Similarity=0.226 Sum_probs=29.0
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKWAALNTVLISHHHIQVRSRLAE 285 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~A~~~A~~LL~~hr~ale~LAe 285 (332)
.+|+..+..+ ++..|||-+++..-.+.......++|.+++..++.=-+
T Consensus 41 ~~di~~l~~i~~lr~~g~~l~~i~~~~~~~~~~~~~~l~~~~~~l~~~i~ 90 (103)
T cd01106 41 EEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALREQKELLEEKKE 90 (103)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHH
Confidence 4777777665 56689998776654432225556666666655554333
No 59
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=36.73 E-value=2.4e+02 Score=23.31 Aligned_cols=52 Identities=12% Similarity=0.142 Sum_probs=33.5
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHHH------HHHHHHHHHHhHHHHHHHHHHHHh
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKWA------ALNTVLISHHHIQVRSRLAEAMAL 289 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~A------~~~A~~LL~~hr~ale~LAeaLle 289 (332)
.+|+..+..| ++.+|||-++|..-.... ......+|+++...++.=.+.|..
T Consensus 41 ~~~i~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (123)
T cd04770 41 EADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPCAEVRALLEEKLAEVEAKIAELQA 100 (123)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3677776665 677999988776544321 245567777777777665555544
No 60
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=36.66 E-value=1.9e+02 Score=23.44 Aligned_cols=52 Identities=10% Similarity=0.049 Sum_probs=35.0
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHH----------HHHHHHHHHHHhHHHHHHHHHHHHh
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKW----------AALNTVLISHHHIQVRSRLAEAMAL 289 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~----------A~~~A~~LL~~hr~ale~LAeaLle 289 (332)
.+|+..+..| ++.+|||-++|..=+.. .......+|+++...++.-.+.|.+
T Consensus 39 ~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 102 (107)
T cd04777 39 EKCQDDLEFILELKGLGFSLIEIQKIFSYKRLTKSRTHEDQDYYKSFLKNKKDELEKEIEDLKK 102 (107)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHhcccccccchhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3777777776 66799998877653321 1234578888888887776666554
No 61
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=36.23 E-value=1.7e+02 Score=24.62 Aligned_cols=60 Identities=7% Similarity=0.145 Sum_probs=35.4
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHH------HHHHHHHHHHHhHHHHHHHHHHHHh-hCcHHHHH
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKW------AALNTVLISHHHIQVRSRLAEAMAL-GRSIGSYT 297 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~------A~~~A~~LL~~hr~ale~LAeaLle-~esl~ec~ 297 (332)
.+|+.++..| ++.+|||-++|.+=... .......+|.++...+++-.+.|.+ ...|.+++
T Consensus 41 ~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~ 109 (127)
T TIGR02044 41 QQHLDELRLISRARQVGFSLEECKELLNLWNDPNRTSADVKARTLEKVAEIERKISELQSMRDQLEALA 109 (127)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4788877776 66799998877654331 1234456666666666555544444 33344443
No 62
>cd06258 Peptidase_M3_like The peptidase M3-like family, also called neurolysin-like family, is part of the "zincins" metallopeptidases, and includes M3, M2 and M32 families of metallopeptidases. The M3 family is subdivided into two subfamilies: the widespread M3A, which comprises a number of high-molecular mass endo- and exopeptidases from bacteria, archaea, protozoa, fungi, plants and animals, and the small M3B, whose members are enzymes primarily from bacteria. Well-known mammalian/eukaryotic M3A endopeptidases are the thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (alias endopeptidase 3.4.24.16), and the mitochondrial intermediate peptidase. The first two are intracellular oligopeptidases, which act only on relatively short substrates of less than 20 amino acid residues, while the latter cleaves N-terminal octapeptides from proteins during their import into the mitochondria. The M3A subfamily also contains several bacterial endopeptidases, collectively called olig
Probab=35.41 E-value=21 Score=34.74 Aligned_cols=18 Identities=28% Similarity=0.274 Sum_probs=15.4
Q ss_pred HHHHHHHhHHHHHHHhCC
Q 020000 137 MCVQHEAGHFLTGYLLGV 154 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg~ 154 (332)
.+..||.||++=..+...
T Consensus 156 ~tl~HE~GHa~h~~l~~~ 173 (365)
T cd06258 156 NTLFHEFGHAVHFLLIQQ 173 (365)
T ss_pred HHHHHHHhHHHHHHHhcC
Confidence 779999999998877764
No 63
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=34.30 E-value=2e+02 Score=24.37 Aligned_cols=60 Identities=8% Similarity=0.097 Sum_probs=38.9
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHH------HHHHHHHHHHHhHHHHHHHHHHHHh-hCcHHHHH
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKW------AALNTVLISHHHIQVRSRLAEAMAL-GRSIGSYT 297 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~------A~~~A~~LL~~hr~ale~LAeaLle-~esl~ec~ 297 (332)
.+|+..+..| ++.+|||-++|.+-+.. ...+...+|.++.+.+++=.+.|.+ ...|.++.
T Consensus 41 ~~~l~~l~~I~~lr~lG~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~ 109 (127)
T TIGR02047 41 VGHVERLAFIRNCRTLDMSLAEIRQLLRYQDKPEKSCSDVNALLDEHISHVRARIIKLQALIEQLVDLR 109 (127)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4788887776 66799998887654431 2345677888888877765555554 33344443
No 64
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptor
Probab=34.28 E-value=1.1e+02 Score=24.24 Aligned_cols=54 Identities=11% Similarity=0.101 Sum_probs=36.7
Q ss_pred HHHHHHHhCCChhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhhCcHHHHHHHHhcccchh
Q 020000 244 LDKVFQWLGYNKSEADSQVKWAALNTVLISHHHIQVRSRLAEAMALGRSIGSYTSKILTEQSLE 307 (332)
Q Consensus 244 at~iar~lGmS~~~id~evr~A~~~A~~LL~~hr~ale~LAeaLle~esl~ec~~~Ie~~~~~~ 307 (332)
-+.+++.+||++.+|+.=.+ -+.++.++|+.-.. .+++|++-.++++....-.|
T Consensus 18 W~~LA~~LG~~~~~I~~i~~-~~~p~~~lL~~W~~---------r~~ATv~~L~~aL~~i~R~D 71 (77)
T cd08311 18 WRSLAGELGYEDEAIDTFGR-EESPVRTLLADWSA---------QEGATLDALCTALRRIQRED 71 (77)
T ss_pred HHHHHHHcCCCHHHHHHHHc-ChhHHHHHHHHHHH---------CcCchHHHHHHHHHHcChHH
Confidence 56788899999988765432 25788888876654 14577777777666654433
No 65
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=34.00 E-value=34 Score=32.26 Aligned_cols=24 Identities=25% Similarity=0.180 Sum_probs=18.4
Q ss_pred CCCChhHHHHHHHHHHhHHHHHHH
Q 020000 128 VSLKEEDHFMCVQHEAGHFLTGYL 151 (332)
Q Consensus 128 r~ls~eer~RVA~HEAGHaLVAyL 151 (332)
...+++.++=+.-||-||+|..--
T Consensus 65 ~n~~~~r~rFtlAHELGH~llH~~ 88 (213)
T COG2856 65 ANNSLERKRFTLAHELGHALLHTD 88 (213)
T ss_pred CCCCHHHHHHHHHHHHhHHHhccc
Confidence 334777788889999999987543
No 66
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=33.46 E-value=2.9e+02 Score=23.24 Aligned_cols=52 Identities=19% Similarity=0.233 Sum_probs=33.4
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHH------HHHHHHHHHHHhHHHHHHHHHHHHh
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKW------AALNTVLISHHHIQVRSRLAEAMAL 289 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~------A~~~A~~LL~~hr~ale~LAeaLle 289 (332)
.+|+..+..| ++.+|||-++|.+-+.. .......+|+++...++.-.+.|..
T Consensus 41 ~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (127)
T cd01108 41 QRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRASADVKALALEHIAELERKIAELQA 100 (127)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4788887776 56799998877654331 1244566777777666655555543
No 67
>PF12994 DUF3878: Domain of unknown function, E. rectale Gene description (DUF3878); InterPro: IPR024538 This entry represents proteins of unknown function found primarily in Firmicutes. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture [].
Probab=33.44 E-value=7.9 Score=38.36 Aligned_cols=17 Identities=29% Similarity=0.462 Sum_probs=13.4
Q ss_pred hHHHHHHHHHHhHHHHH
Q 020000 133 EDHFMCVQHEAGHFLTG 149 (332)
Q Consensus 133 eer~RVA~HEAGHaLVA 149 (332)
.+..--=|||.|||||-
T Consensus 92 ~~~~lY~Y~~iGHFWVk 108 (299)
T PF12994_consen 92 EETHLYNYGEIGHFWVK 108 (299)
T ss_pred HHHHHhhccccceeeec
Confidence 45556679999999984
No 68
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=33.07 E-value=1.2e+02 Score=24.28 Aligned_cols=48 Identities=8% Similarity=0.082 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhCCChhHHHHHH---HHHHHHHHHHHHHh-------HHHHHHHHHHHH
Q 020000 241 INKLDKVFQWLGYNKSEADSQV---KWAALNTVLISHHH-------IQVRSRLAEAMA 288 (332)
Q Consensus 241 l~qat~iar~lGmS~~~id~ev---r~A~~~A~~LL~~h-------r~ale~LAeaLl 288 (332)
+.+..+++|.+|+|+.+||.-. +...++..++|+.- ...++.|.++|.
T Consensus 11 ~~~wk~~~R~LGlse~~Id~ie~~~~~~~Eq~yqmL~~W~~~~g~~~At~~~L~~aLr 68 (80)
T cd08313 11 PRRWKEFVRRLGLSDNEIERVELDHRRCRDAQYQMLKVWKERGPRPYATLQHLLSVLR 68 (80)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCCcchHHHHHHHHH
Confidence 4567788999999998877532 24556666777643 334555555543
No 69
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=32.67 E-value=1.7e+02 Score=24.22 Aligned_cols=52 Identities=6% Similarity=0.116 Sum_probs=32.7
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHH---------HHHHHHHHHHHhHHHHHHHHHHHHh
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKW---------AALNTVLISHHHIQVRSRLAEAMAL 289 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~---------A~~~A~~LL~~hr~ale~LAeaLle 289 (332)
.+|+..+..| ++.+|||-++|.+-... ...+..++|+++...++.=.+.|..
T Consensus 40 ~~~~~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 102 (112)
T cd01282 40 EAAVDRVRQIRRLLAAGLTLEEIREFLPCLRGGEPTFRPCPDLLAVLRRELARIDRQIADLTR 102 (112)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhCCCccCCccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4778777776 66799998777654331 1234566777777666665555544
No 70
>COG2738 Predicted Zn-dependent protease [General function prediction only]
Probab=32.58 E-value=24 Score=33.58 Aligned_cols=13 Identities=31% Similarity=0.567 Sum_probs=10.9
Q ss_pred HHHHHHHhHHHHH
Q 020000 137 MCVQHEAGHFLTG 149 (332)
Q Consensus 137 RVA~HEAGHaLVA 149 (332)
-||-||.||++=-
T Consensus 94 aVAAHEVGHAiQd 106 (226)
T COG2738 94 AVAAHEVGHAIQD 106 (226)
T ss_pred HHHHHHhhHHHhh
Confidence 5899999999853
No 71
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=32.46 E-value=1.6e+02 Score=23.49 Aligned_cols=46 Identities=9% Similarity=-0.004 Sum_probs=29.0
Q ss_pred HHHHHHHhCCChhHHHHH---HHHHHHHHHHHHHHhHHH------HHHHHHHHHh
Q 020000 244 LDKVFQWLGYNKSEADSQ---VKWAALNTVLISHHHIQV------RSRLAEAMAL 289 (332)
Q Consensus 244 at~iar~lGmS~~~id~e---vr~A~~~A~~LL~~hr~a------le~LAeaLle 289 (332)
-.++++.+||++.+|+.= -+....++.++|+.-++. ++.|.++|.+
T Consensus 21 Wk~Lar~LGls~~dI~~i~~~~~~~~eq~~~mL~~W~~r~g~~AT~~~L~~aL~~ 75 (86)
T cd08318 21 WKTLAPHLEMKDKEIRAIESDSEDIKMQAKQLLVAWQDREGSQATPETLITALNA 75 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCccccHHHHHHHHHH
Confidence 445788899999887542 123477888888765543 4455555543
No 72
>PRK02391 heat shock protein HtpX; Provisional
Probab=31.84 E-value=26 Score=34.18 Aligned_cols=24 Identities=17% Similarity=0.191 Sum_probs=19.0
Q ss_pred CCCChhHHHHHHHHHHhHHHHHHH
Q 020000 128 VSLKEEDHFMCVQHEAGHFLTGYL 151 (332)
Q Consensus 128 r~ls~eer~RVA~HEAGHaLVAyL 151 (332)
+.++++|.+-|.-||.||.--.+.
T Consensus 126 ~~L~~~El~aVlaHElgHi~~~di 149 (296)
T PRK02391 126 RRLDPDELEAVLAHELSHVKNRDV 149 (296)
T ss_pred hhCCHHHHHHHHHHHHHHHHcCCH
Confidence 345899999999999999754443
No 73
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=31.44 E-value=2.8e+02 Score=22.32 Aligned_cols=34 Identities=15% Similarity=0.110 Sum_probs=22.9
Q ss_pred HHHHHHHhCCChhHHHHHHHH-----HHHHHHHHHHHhH
Q 020000 244 LDKVFQWLGYNKSEADSQVKW-----AALNTVLISHHHI 277 (332)
Q Consensus 244 at~iar~lGmS~~~id~evr~-----A~~~A~~LL~~hr 277 (332)
-.++++.+|||+.+|+.=... -.+++.++|..-+
T Consensus 16 Wk~lar~LG~s~~eI~~ie~~~~r~~~~eq~~~mL~~W~ 54 (86)
T cd08777 16 WKRCARKLGFTESEIEEIDHDYERDGLKEKVHQMLHKWK 54 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHHhcccCCHHHHHHHHHHHHH
Confidence 345688899999888764322 2567777777554
No 74
>PRK03982 heat shock protein HtpX; Provisional
Probab=31.43 E-value=29 Score=33.33 Aligned_cols=23 Identities=22% Similarity=0.189 Sum_probs=18.9
Q ss_pred CCChhHHHHHHHHHHhHHHHHHH
Q 020000 129 SLKEEDHFMCVQHEAGHFLTGYL 151 (332)
Q Consensus 129 ~ls~eer~RVA~HEAGHaLVAyL 151 (332)
.++++|-+-|.-||.||.--.+.
T Consensus 119 ~l~~~El~AVlAHElgHi~~~h~ 141 (288)
T PRK03982 119 LLNEDELEGVIAHELTHIKNRDT 141 (288)
T ss_pred hCCHHHHHHHHHHHHHHHHcCCH
Confidence 34889999999999999875554
No 75
>PRK05457 heat shock protein HtpX; Provisional
Probab=31.35 E-value=37 Score=32.94 Aligned_cols=19 Identities=16% Similarity=0.345 Sum_probs=16.7
Q ss_pred CCChhHHHHHHHHHHhHHH
Q 020000 129 SLKEEDHFMCVQHEAGHFL 147 (332)
Q Consensus 129 ~ls~eer~RVA~HEAGHaL 147 (332)
.++++|-+-|.-||.||.-
T Consensus 128 ~L~~~El~aVlAHElgHi~ 146 (284)
T PRK05457 128 NMSRDEVEAVLAHEISHIA 146 (284)
T ss_pred hCCHHHHHHHHHHHHHHHH
Confidence 4588999999999999974
No 76
>PF12388 Peptidase_M57: Dual-action HEIGH metallo-peptidase; InterPro: IPR024653 This entry represents the metallopeptidases M10, M27 and M57. The catalytic triad for proteases in this entry is HE-H-H, which in many members is in the sequence motif HEIGH [].
Probab=31.33 E-value=31 Score=32.67 Aligned_cols=23 Identities=17% Similarity=0.062 Sum_probs=17.9
Q ss_pred ChhHHHHHHHHHHhHHHHHHHhC
Q 020000 131 KEEDHFMCVQHEAGHFLTGYLLG 153 (332)
Q Consensus 131 s~eer~RVA~HEAGHaLVAyLLg 153 (332)
+....+.|+.||.||.+=-....
T Consensus 129 ~~~~~~hvi~HEiGH~IGfRHTD 151 (211)
T PF12388_consen 129 SVNVIEHVITHEIGHCIGFRHTD 151 (211)
T ss_pred chhHHHHHHHHHhhhhccccccC
Confidence 66778889999999987555443
No 77
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=31.25 E-value=2.3e+02 Score=23.21 Aligned_cols=48 Identities=13% Similarity=0.199 Sum_probs=32.1
Q ss_pred HHHHHHHHHhCCChhHHHHHH---HHHHHHHHHHHHHhH------HHHHHHHHHHHh
Q 020000 242 NKLDKVFQWLGYNKSEADSQV---KWAALNTVLISHHHI------QVRSRLAEAMAL 289 (332)
Q Consensus 242 ~qat~iar~lGmS~~~id~ev---r~A~~~A~~LL~~hr------~ale~LAeaLle 289 (332)
.+..+++|.+|+|+.+|+.-. +...++..++|+.-+ ..++.|.++|..
T Consensus 20 ~~Wk~laR~LGLse~~I~~i~~~~~~~~eq~~qmL~~W~~~~G~~At~~~L~~aL~~ 76 (96)
T cd08315 20 DSWNRLMRQLGLSENEIDVAKANERVTREQLYQMLLTWVNKTGRKASVNTLLDALEA 76 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHhhCCCcHHHHHHHHHHH
Confidence 456778999999998876432 222677777777543 356666666655
No 78
>PF10728 DUF2520: Domain of unknown function (DUF2520); InterPro: IPR018931 This presumed domain is found C-terminal to a Rossmann-like domain suggesting that these proteins are oxidoreductases. ; PDB: 3D1L_A 2I76_A 3DFU_A.
Probab=30.21 E-value=1.4e+02 Score=25.89 Aligned_cols=62 Identities=18% Similarity=0.138 Sum_probs=52.1
Q ss_pred ccchhhHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhhCcHHH
Q 020000 234 SEGHYSDINKLDKVFQWLGYNKSEADSQVKWAALNTVLISHHHIQVRSRLAEAMALGRSIGS 295 (332)
Q Consensus 234 stGga~Dl~qat~iar~lGmS~~~id~evr~A~~~A~~LL~~hr~ale~LAeaLle~esl~e 295 (332)
.||...+++.+.+++..+|-..-.++.+.|..|--|--+-..+--.+-..+..|++..-++.
T Consensus 6 iEgd~~~~~~l~~l~~~lg~~~~~i~~~~r~~yHaAav~asNf~~~L~~~a~~ll~~~gi~~ 67 (132)
T PF10728_consen 6 IEGDEEALEVLQELAKELGGRPFEIDSEQRALYHAAAVFASNFLVALYALAAELLEQAGIDF 67 (132)
T ss_dssp EEESHHHHHHHHHHHHHTTSEEEE--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SH
T ss_pred EecCHHHHHHHHHHHHHhCCceEEeCHHhHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCCc
Confidence 46777888999999999999998999999999988888899999999999999998888765
No 79
>PRK03072 heat shock protein HtpX; Provisional
Probab=29.89 E-value=30 Score=33.53 Aligned_cols=25 Identities=24% Similarity=0.252 Sum_probs=19.4
Q ss_pred CCCChhHHHHHHHHHHhHHHHHHHh
Q 020000 128 VSLKEEDHFMCVQHEAGHFLTGYLL 152 (332)
Q Consensus 128 r~ls~eer~RVA~HEAGHaLVAyLL 152 (332)
+.++++|-+-|.-||.||.--.+.+
T Consensus 120 ~~l~~~El~aVlAHElgHi~~~d~~ 144 (288)
T PRK03072 120 QILNERELRGVLGHELSHVYNRDIL 144 (288)
T ss_pred HhCCHHHHHHHHHHHHHHHhcCCHH
Confidence 3458899999999999997644443
No 80
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=29.40 E-value=28 Score=31.95 Aligned_cols=17 Identities=29% Similarity=0.047 Sum_probs=13.7
Q ss_pred HHHHHHHhHHHHHHHhC
Q 020000 137 MCVQHEAGHFLTGYLLG 153 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg 153 (332)
.+..||.||.|=+..-+
T Consensus 139 ~~~aHEiGH~lGl~H~~ 155 (206)
T PF13583_consen 139 QTFAHEIGHNLGLRHDF 155 (206)
T ss_pred hHHHHHHHHHhcCCCCc
Confidence 66889999998776655
No 81
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=28.50 E-value=2.3e+02 Score=25.40 Aligned_cols=23 Identities=17% Similarity=0.434 Sum_probs=16.1
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHH
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADS 260 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~ 260 (332)
.+|+.++..| ++.+|||-++|..
T Consensus 42 ~~dl~rL~~I~~lr~~G~sL~eI~~ 66 (172)
T cd04790 42 ERDLERLEQICAYRSAGVSLEDIRS 66 (172)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 4678877665 5678999776544
No 82
>cd04276 ZnMc_MMP_like_2 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=28.03 E-value=41 Score=31.13 Aligned_cols=15 Identities=33% Similarity=0.432 Sum_probs=12.5
Q ss_pred hHHHHHHHHHHhHHH
Q 020000 133 EDHFMCVQHEAGHFL 147 (332)
Q Consensus 133 eer~RVA~HEAGHaL 147 (332)
+..+.++.||.||+|
T Consensus 114 ~~~~~~~~he~gh~l 128 (197)
T cd04276 114 ASLRYLLAHEVGHTL 128 (197)
T ss_pred HHHHHHHHHHHHHHh
Confidence 556678999999986
No 83
>PRK04897 heat shock protein HtpX; Provisional
Probab=27.98 E-value=45 Score=32.41 Aligned_cols=21 Identities=19% Similarity=0.189 Sum_probs=17.3
Q ss_pred CCChhHHHHHHHHHHhHHHHH
Q 020000 129 SLKEEDHFMCVQHEAGHFLTG 149 (332)
Q Consensus 129 ~ls~eer~RVA~HEAGHaLVA 149 (332)
.++++|.+-|.-||.||.--.
T Consensus 131 ~l~~~El~aVlAHElgHi~~~ 151 (298)
T PRK04897 131 IMNREELEGVIGHEISHIRNY 151 (298)
T ss_pred hCCHHHHHHHHHHHHHHHhcC
Confidence 358899999999999996533
No 84
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=27.97 E-value=2.5e+02 Score=23.82 Aligned_cols=52 Identities=12% Similarity=0.165 Sum_probs=33.0
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHHH------HHHHHHHHHHhHHHHHHHHHHHHh
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKWA------ALNTVLISHHHIQVRSRLAEAMAL 289 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~A------~~~A~~LL~~hr~ale~LAeaLle 289 (332)
.+|+..+..| ++.+|||-++|.+-+... .....++|+++...+++=...|.+
T Consensus 41 ~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (133)
T cd04787 41 EKDLSRLRFILSARQLGFSLKDIKEILSHADQGESPCPMVRRLIEQRLAETERRIKELLK 100 (133)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHhhhccCCCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4677777665 667999988876544321 134567777777766655555543
No 85
>cd04280 ZnMc_astacin_like Zinc-dependent metalloprotease, astacin_like subfamily or peptidase family M12A, a group of zinc-dependent proteolytic enzymes with a HExxH zinc-binding site/active site. Members of this family may have an amino terminal propeptide, which is cleaved to yield the active protease domain, which is consequently always found at the N-terminus in multi-domain architectures. This family includes: astacin, a digestive enzyme from Crayfish; meprin, a multiple domain membrane component that is constructed from a homologous alpha and beta chain, proteins involved in (bone) morphogenesis, tolloid from drosophila, and the sea urchin SPAN protein, which may also play a role in development.
Probab=27.96 E-value=31 Score=30.98 Aligned_cols=35 Identities=23% Similarity=0.207 Sum_probs=21.2
Q ss_pred HHHHHHHHhHHHHHHHhCCCCC--ceecCchhhhccc
Q 020000 136 FMCVQHEAGHFLTGYLLGVLPK--GYEIPSVEALKQD 170 (332)
Q Consensus 136 ~RVA~HEAGHaLVAyLLg~PV~--kyTI~p~eal~~G 170 (332)
..++.||.||+|=-+..-..+. .|-.+.|+.+..+
T Consensus 75 ~g~v~HE~~HalG~~HEh~R~DRD~yv~i~~~ni~~~ 111 (180)
T cd04280 75 LGTIVHELMHALGFYHEQSRPDRDDYVTINWENIQPG 111 (180)
T ss_pred CchhHHHHHHHhcCcchhcccccCCeEEEeecccChh
Confidence 5899999999976555443222 2434446555443
No 86
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=27.87 E-value=2.1e+02 Score=23.43 Aligned_cols=48 Identities=10% Similarity=0.142 Sum_probs=26.2
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHHHH-HHHHHHHHHhHHHHHHHHH
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKWAA-LNTVLISHHHIQVRSRLAE 285 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~A~-~~A~~LL~~hr~ale~LAe 285 (332)
.+|+..+..| ++.+|||-+++..=..... .....+|+.+.+.+++=.+
T Consensus 42 ~~~i~~l~~I~~lr~~G~sl~~i~~l~~~~~~~~~~~~l~~~~~~l~~~i~ 92 (108)
T cd01107 42 AEQLERLNRIKYLRDLGFPLEEIKEILDADNDDELRKLLREKLAELEAEIE 92 (108)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHH
Confidence 4667666655 5678998776643322111 4455555555555544333
No 87
>PF01400 Astacin: Astacin (Peptidase family M12A) This Prosite motif covers only the active site.; InterPro: IPR001506 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 []. This group of metallopeptidases belong to the MEROPS peptidase family M12, subfamily M12A (astacin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. The astacin () family of metalloendopeptidases encompasses a range of proteins found in hydra to humans, in mature and developmental systems []. Their functions include activation of growth factors, degradation of polypeptides, and processing of extracellular proteins []. The proteins are synthesised with N-terminal signal and pro-enzyme sequences, and many contain multiple domains C-terminal to the protease domain. They are either secreted from cells, or are associated with the plasma membrane. The astacin molecule adopts a kidney shape, with a deep active-site cleft between its N- and C-terminal domains []. The zinc ion, which lies at the bottom of the cleft, exhibits a unique penta-coordinated mode of binding, involving 3 histidine residues, a tyrosine and a water molecule (which is also bound to the carboxylate side chain of Glu93) []. The N-terminal domain comprises 2 alpha-helices and a 5-stranded beta-sheet. The overall topology of this domain is shared by the archetypal zinc-endopeptidase thermolysin. Astacin protease domains also share common features with serralysins, matrix metalloendopeptidases, and snake venom proteases; they cleave peptide bonds in polypeptides such as insulin B chain and bradykinin, and in proteins such as casein and gelatin; and they have arylamidase activity [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3LQB_A 3EDH_A 3EDG_A 3EDI_A 1IAE_A 1IAB_A 1IAA_A 1AST_A 1IAC_A 1QJJ_A ....
Probab=27.86 E-value=37 Score=30.73 Aligned_cols=34 Identities=21% Similarity=0.185 Sum_probs=19.3
Q ss_pred HHHHHHHHhHHHHHHHhCCCCC---ceecCchhhhccc
Q 020000 136 FMCVQHEAGHFLTGYLLGVLPK---GYEIPSVEALKQD 170 (332)
Q Consensus 136 ~RVA~HEAGHaLVAyLLg~PV~---kyTI~p~eal~~G 170 (332)
..++.||.||+|=-+..-..+. -|+|. |+.+..+
T Consensus 80 ~~~i~HEl~HaLG~~HEh~RpDRd~yi~i~-~~~i~~~ 116 (191)
T PF01400_consen 80 VGTILHELGHALGFWHEHQRPDRDNYITIN-WDNIQPG 116 (191)
T ss_dssp HHHHHHHHHHHHTB--GGGSTTGGGTEEE--GGGB-TT
T ss_pred ccchHHHHHHHHhhhhhhhccccccEEEEe-hhcchhh
Confidence 4699999999985555442222 25554 6666555
No 88
>PRK03001 M48 family peptidase; Provisional
Probab=27.30 E-value=36 Score=32.62 Aligned_cols=23 Identities=22% Similarity=0.203 Sum_probs=18.6
Q ss_pred CCChhHHHHHHHHHHhHHHHHHH
Q 020000 129 SLKEEDHFMCVQHEAGHFLTGYL 151 (332)
Q Consensus 129 ~ls~eer~RVA~HEAGHaLVAyL 151 (332)
.++++|-+-|.-||.||.--.+.
T Consensus 118 ~l~~~El~aVlAHElgHi~~~h~ 140 (283)
T PRK03001 118 VLSEREIRGVMAHELAHVKHRDI 140 (283)
T ss_pred hCCHHHHHHHHHHHHHHHhCCCh
Confidence 34889999999999999865443
No 89
>PF13688 Reprolysin_5: Metallo-peptidase family M12; PDB: 2FV5_B 3EWJ_A 3KME_A 3L0T_B 1BKC_E 3G42_D 2I47_D 2FV9_B 3LEA_A 1ZXC_B ....
Probab=27.16 E-value=42 Score=29.61 Aligned_cols=24 Identities=25% Similarity=0.196 Sum_probs=15.0
Q ss_pred CChhHHHHHHHHHHhHHHHHHHhC
Q 020000 130 LKEEDHFMCVQHEAGHFLTGYLLG 153 (332)
Q Consensus 130 ls~eer~RVA~HEAGHaLVAyLLg 153 (332)
.+......+.-||.||-|=+..-+
T Consensus 137 ~~~~~~~~~~AHEiGH~lGa~HD~ 160 (196)
T PF13688_consen 137 PPTYNGAITFAHEIGHNLGAPHDG 160 (196)
T ss_dssp --HHHHHHHHHHHHHHHTT-----
T ss_pred CCCCceehhhHHhHHHhcCCCCCC
Confidence 356778899999999988766654
No 90
>TIGR02289 M3_not_pepF oligoendopeptidase, M3 family. This family consists of probable oligoendopeptidases in the M3 family, related to lactococcal PepF and group B streptococcal PepB (TIGR00181) but in a distinct clade with considerable sequence differences. The likely substrate is small peptides and not whole proteins, as with PepF, but members are not characterized and the activity profile may differ. Several bacteria have both a member of this family and a member of the PepF family.
Probab=27.04 E-value=50 Score=34.60 Aligned_cols=17 Identities=35% Similarity=0.421 Sum_probs=14.4
Q ss_pred HHHHHHHhHHHHHHHhC
Q 020000 137 MCVQHEAGHFLTGYLLG 153 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg 153 (332)
.+..||+||++=.|+..
T Consensus 339 ~TL~HElGHa~H~~~s~ 355 (549)
T TIGR02289 339 DVLTHEAGHAFHVYESR 355 (549)
T ss_pred HHHHHHhhHHHHHHHhc
Confidence 56889999999888775
No 91
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=26.56 E-value=1.9e+02 Score=23.01 Aligned_cols=46 Identities=4% Similarity=0.057 Sum_probs=30.1
Q ss_pred HHHHHHHhCCChhHHHHHH----HHHHHHHHHHHHHhHH------HHHHHHHHHHh
Q 020000 244 LDKVFQWLGYNKSEADSQV----KWAALNTVLISHHHIQ------VRSRLAEAMAL 289 (332)
Q Consensus 244 at~iar~lGmS~~~id~ev----r~A~~~A~~LL~~hr~------ale~LAeaLle 289 (332)
-.++++.+|||+.+|+.=. +....++.++|+.-++ ..+.|..+|..
T Consensus 18 Wk~LAr~Lg~se~dI~~i~~~~~~~~~eq~~~mL~~W~~r~g~~At~~~L~~aL~~ 73 (84)
T cd08804 18 WTELARELDFTEEQIHQIRIENPNSLQDQSHALLKYWLERDGKHATDTNLMKCLTK 73 (84)
T ss_pred HHHHHHHcCCCHHHHHHHHHHCcccHHHHHHHHHHHHHHccCCCchHHHHHHHHHH
Confidence 4567888999998887632 2346777788765443 34556666654
No 92
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=26.54 E-value=2.7e+02 Score=23.41 Aligned_cols=52 Identities=10% Similarity=0.105 Sum_probs=33.6
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHH----HHHHHHHHHHHhHHHHHHHHHHHHh
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKW----AALNTVLISHHHIQVRSRLAEAMAL 289 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~----A~~~A~~LL~~hr~ale~LAeaLle 289 (332)
.+|++.+..| ++.+|||-++|..-+.. .......+|+++...+++=.+.|..
T Consensus 40 ~~~l~~l~~I~~l~~~G~sl~eI~~~l~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 97 (124)
T TIGR02051 40 EETVKRLRFIKRAQELGFSLEEIGGLLGLVDGTHCREMYELASRKLKSVQAKMADLLR 97 (124)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4677776665 66799998877654432 2345677777777776655555544
No 93
>PF07998 Peptidase_M54: Peptidase family M54; InterPro: IPR012962 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 []. This entry represents zinc-dependent peptidases belonging to the MEROPS peptidase family M54, more commonly known as the archaemetzincins. The family has a wide taxonomic distribution, being found in archaea, bacteria and eukaryotes. Two human homologues have been characterised []. ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding; PDB: 3LMC_A 2XHQ_A 2X7M_A.
Probab=26.17 E-value=43 Score=31.24 Aligned_cols=11 Identities=36% Similarity=0.582 Sum_probs=9.3
Q ss_pred HHHHHHHhHHH
Q 020000 137 MCVQHEAGHFL 147 (332)
Q Consensus 137 RVA~HEAGHaL 147 (332)
..+.||.||.+
T Consensus 147 Kea~HElGH~~ 157 (194)
T PF07998_consen 147 KEAVHELGHLF 157 (194)
T ss_dssp HHHHHHHHHHT
T ss_pred HHHHHHHHHHc
Confidence 66999999965
No 94
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=25.93 E-value=4e+02 Score=23.69 Aligned_cols=77 Identities=13% Similarity=0.137 Sum_probs=45.8
Q ss_pred hhhHHHHHHHh----CC-----ccch-----hhHHHHHHHH--HHHhCCChhHHHHHHHH-------HHHHHHHHHHHhH
Q 020000 221 LGGLVAEHLVF----GH-----SEGH-----YSDINKLDKV--FQWLGYNKSEADSQVKW-------AALNTVLISHHHI 277 (332)
Q Consensus 221 LAGrAAE~Lvf----G~-----stGg-----a~Dl~qat~i--ar~lGmS~~~id~evr~-------A~~~A~~LL~~hr 277 (332)
+-|+-..+|-| |- ..|+ .+|+..+.-| ++.+|||-++|.+=+.. .......+|.++.
T Consensus 20 ~~gvs~~TlRyYE~~GLi~~~r~~~g~R~Y~~~~i~~L~~I~~lr~lG~sL~eIk~ll~~~~~~~~~~~~~~~~ll~~k~ 99 (154)
T PRK15002 20 RSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGVLPEGHTLSAKEWKQLSSQWR 99 (154)
T ss_pred HHCcCHHHHHHHHHCCCCCCccCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHHH
Confidence 34666777766 21 1233 4788888765 77899998877654321 2345567777776
Q ss_pred HHHHHHHHHHHh-hCcHHHHH
Q 020000 278 QVRSRLAEAMAL-GRSIGSYT 297 (332)
Q Consensus 278 ~ale~LAeaLle-~esl~ec~ 297 (332)
+.++.=.+.|.. ...|..++
T Consensus 100 ~~l~~~I~~L~~~~~~L~~~i 120 (154)
T PRK15002 100 EELDRRIHTLVALRDELDGCI 120 (154)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 666555555544 34455544
No 95
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=25.78 E-value=3.1e+02 Score=21.48 Aligned_cols=37 Identities=11% Similarity=0.070 Sum_probs=24.8
Q ss_pred HHHHHHHHHhCCChhHHHHHH---HHHHHHHHHHHHHhHH
Q 020000 242 NKLDKVFQWLGYNKSEADSQV---KWAALNTVLISHHHIQ 278 (332)
Q Consensus 242 ~qat~iar~lGmS~~~id~ev---r~A~~~A~~LL~~hr~ 278 (332)
.+-.+++|.+|||+.+|+.-. +...+++.++|..-+.
T Consensus 12 ~~Wk~laR~LGls~~~I~~ie~~~~~~~eq~~~mL~~W~~ 51 (79)
T cd08784 12 DQHKRFFRKLGLSDNEIKVAELDNPQHRDRVYELLRIWRN 51 (79)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHcCCchHHHHHHHHHHHHh
Confidence 345678999999998876532 1256777777765443
No 96
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=25.76 E-value=4e+02 Score=22.32 Aligned_cols=51 Identities=10% Similarity=0.055 Sum_probs=30.8
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHH---------HHHHHHHHHHHhHHHHHHHHHHHH
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKW---------AALNTVLISHHHIQVRSRLAEAMA 288 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~---------A~~~A~~LL~~hr~ale~LAeaLl 288 (332)
.+|+..+..| ++.+|||-++|..=+.. ...+...+|.++...++.--+.|.
T Consensus 39 ~~~l~~l~~I~~lr~~G~~L~~I~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~ 100 (118)
T cd04776 39 RRDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQLEKMLEKIEKRRAELEQQRRDID 100 (118)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHhhccCCchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4777777765 66789998766543321 233455667777766665444443
No 97
>PRK01345 heat shock protein HtpX; Provisional
Probab=24.95 E-value=55 Score=32.26 Aligned_cols=23 Identities=26% Similarity=0.231 Sum_probs=19.1
Q ss_pred CChhHHHHHHHHHHhHHHHHHHh
Q 020000 130 LKEEDHFMCVQHEAGHFLTGYLL 152 (332)
Q Consensus 130 ls~eer~RVA~HEAGHaLVAyLL 152 (332)
++++|.+-|.-||.||.--.+.+
T Consensus 119 L~~dEL~aVlAHElgHi~~~d~~ 141 (317)
T PRK01345 119 LSPEEVAGVMAHELAHVKNRDTL 141 (317)
T ss_pred CCHHHHHHHHHHHHHHHHcCCHH
Confidence 48899999999999998755544
No 98
>PF03186 CobD_Cbib: CobD/Cbib protein; InterPro: IPR004485 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents the CbiB protein, which is involved in cobalamin biosynthesis and porphyrin biosynthesis. It converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group. It is part of the cob operon [].; GO: 0009236 cobalamin biosynthetic process, 0016021 integral to membrane
Probab=24.85 E-value=1.6e+02 Score=28.69 Aligned_cols=68 Identities=18% Similarity=0.250 Sum_probs=48.0
Q ss_pred HHHHHHHHHHHHHHccCchHHHHHHHHHhccCCCCccccccccccccccccccchhhhhchhhhhhhhhhhhhhHHHHHh
Q 020000 25 KRRRQALKRVDRELSRGNFKVALSLVKQLQRKPAGGLRGFGAAKQVPKRLSSLDESELDSKELLTLRALFDSVMESIERC 104 (332)
Q Consensus 25 ~~~~~~~~~~~~~~~~g~~~~a~~~~~~l~~~~~~~l~~~gaa~~~p~r~~~l~el~l~~~t~~~ll~P~~~~s~~i~~~ 104 (332)
+.-.+..++|-+.|.+||...|-..+..+-+++ .-.|+|..+...+.+++ ..+++-.+-+.
T Consensus 93 r~l~~~~~~v~~aL~~gdl~~AR~~l~~lv~Rd----------------t~~L~~~~i~ra~iEs~---aen~~d~v~ap 153 (295)
T PF03186_consen 93 RSLREHAKAVYRALEAGDLEAARQALSPLVGRD----------------TDQLSEEGIARAAIESL---AENLSDGVFAP 153 (295)
T ss_pred hhHHHHHHHHHHHHhcCCHHHHHHHHHHhhCCC----------------cccCCHHHHHHHHHHHH---HHHhcchhHHH
Confidence 456778889999999999999999988886665 44566666666655555 55666666665
Q ss_pred hhhhccc
Q 020000 105 NLFDSLD 111 (332)
Q Consensus 105 ~~~~~l~ 111 (332)
+.|.+++
T Consensus 154 Lf~~~l~ 160 (295)
T PF03186_consen 154 LFWFALG 160 (295)
T ss_pred HHHHHHH
Confidence 5544443
No 99
>cd06459 M3B_Oligoendopeptidase_F Peptidase family M3B Oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and includes oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most bacterial PepFs are cytoplasmic endopeptidases; however, the PepF Bacillus amyloliquefaciens oligopeptidase is a secreted protein and may facilitate the process of sporulation. Specifically, the yjbG gene encoding the homolog of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when over expressed from a multicopy plasmid.
Probab=24.62 E-value=53 Score=32.36 Aligned_cols=17 Identities=35% Similarity=0.632 Sum_probs=15.2
Q ss_pred HHHHHHHhHHHHHHHhC
Q 020000 137 MCVQHEAGHFLTGYLLG 153 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg 153 (332)
.+..||.||++=.++..
T Consensus 224 ~tl~HE~GHa~h~~~~~ 240 (427)
T cd06459 224 FTLAHELGHAFHSYLSR 240 (427)
T ss_pred HHHHHHhhHHHHHHHHc
Confidence 67999999999988876
No 100
>PF09471 Peptidase_M64: IgA Peptidase M64; InterPro: IPR019026 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 []. This is a family of highly selective metallo-endopeptidases belonging to the MEROPS peptidase family M64 (IgA peptidase, clan MA). The primary structure of the Clostridium ramosum IgA peptidase shows no significant overall similarity to any other known metallo-endopeptidase []. ; PDB: 3P1V_A 4DF9_D.
Probab=24.31 E-value=37 Score=32.91 Aligned_cols=18 Identities=33% Similarity=0.410 Sum_probs=13.4
Q ss_pred hHHHHHHHHHHhHHHHHH
Q 020000 133 EDHFMCVQHEAGHFLTGY 150 (332)
Q Consensus 133 eer~RVA~HEAGHaLVAy 150 (332)
..=.-|+.||.||.+...
T Consensus 214 ~~~~~v~vHE~GHsf~~L 231 (264)
T PF09471_consen 214 PSFKQVVVHEFGHSFGGL 231 (264)
T ss_dssp TTHHHHHHHHHHHHTT--
T ss_pred ccccceeeeecccccccc
Confidence 356789999999987653
No 101
>PRK01209 cobD cobalamin biosynthesis protein; Provisional
Probab=24.04 E-value=1.5e+02 Score=29.09 Aligned_cols=67 Identities=16% Similarity=0.260 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHHHccCchHHHHHHHHHhccCCCCccccccccccccccccccchhhhhchhhhhhhhhhhhhhHHHHHh
Q 020000 25 KRRRQALKRVDRELSRGNFKVALSLVKQLQRKPAGGLRGFGAAKQVPKRLSSLDESELDSKELLTLRALFDSVMESIERC 104 (332)
Q Consensus 25 ~~~~~~~~~~~~~~~~g~~~~a~~~~~~l~~~~~~~l~~~gaa~~~p~r~~~l~el~l~~~t~~~ll~P~~~~s~~i~~~ 104 (332)
..-++..++|.+.|++||..+|-..++++.+++ ...|++-.+...+.+++ ..+++..+-+.
T Consensus 96 ~~l~~~~~~v~~al~~gd~~~AR~~l~~~v~Rd----------------t~~Ls~~~i~~a~iEs~---~en~~d~~~ap 156 (312)
T PRK01209 96 RSLADHARAVARALRAGDLEEARRAVSMIVGRD----------------TSQLDEEGIARAAIESV---AENTSDGVIAP 156 (312)
T ss_pred hhHHHHHHHHHHHHHcCCHHHHHHHHHHHhCCC----------------cccCCHHHHHHHHHHHH---HHhcccchHHH
Confidence 455677889999999999999999988885554 44455555555444444 44444455554
Q ss_pred hhhhcc
Q 020000 105 NLFDSL 110 (332)
Q Consensus 105 ~~~~~l 110 (332)
..|.++
T Consensus 157 lFwf~l 162 (312)
T PRK01209 157 LFYAAL 162 (312)
T ss_pred HHHHHH
Confidence 444333
No 102
>cd04283 ZnMc_hatching_enzyme Zinc-dependent metalloprotease, hatching enzyme-like subfamily. Hatching enzymes are secreted by teleost embryos to digest the egg envelope or chorion. In some teleosts, the hatching enzyme may be a system consisting of two evolutionary related metalloproteases, high choriolytic enzyme and low choriolytic enzyme (HCE and LCE), which may have different substrate specificities and cooperatively digest the chorion.
Probab=23.92 E-value=43 Score=30.68 Aligned_cols=18 Identities=33% Similarity=0.102 Sum_probs=14.4
Q ss_pred HHHHHHHHhHHHHHHHhC
Q 020000 136 FMCVQHEAGHFLTGYLLG 153 (332)
Q Consensus 136 ~RVA~HEAGHaLVAyLLg 153 (332)
.-++.||-||+|=.+..-
T Consensus 78 ~G~i~HEl~HaLG~~HEh 95 (182)
T cd04283 78 KGIIQHELLHALGFYHEQ 95 (182)
T ss_pred cchHHHHHHHHhCCcccc
Confidence 358999999998776654
No 103
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=23.86 E-value=4.3e+02 Score=22.21 Aligned_cols=52 Identities=12% Similarity=0.151 Sum_probs=32.0
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHH------HHHHHHHHHHHhHHHHHHHHHHHHh
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKW------AALNTVLISHHHIQVRSRLAEAMAL 289 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~------A~~~A~~LL~~hr~ale~LAeaLle 289 (332)
.+|++.+..| ++.+|||-++|.+-+.. .......+|.++.+.++.-.+.|.+
T Consensus 41 ~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (126)
T cd04785 41 AAHVERLRFIRRARDLGFSLEEIRALLALSDRPDRSCAEADAIARAHLADVRARIADLRR 100 (126)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHhhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4777777776 56789998776543321 1234566777766666655555544
No 104
>cd04275 ZnMc_pappalysin_like Zinc-dependent metalloprotease, pappalysin_like subfamily. The pregnancy-associated plasma protein A (PAPP-A or pappalysin-1) cleaves insulin-like growth factor-binding proteins 4 and 5, thereby promoting cell growth by releasing bound growth factor. This model includes pappalysins and related metalloprotease domains from all three kingdoms of life. The three-dimensional structure of an archaeal representative, ulilysin, has been solved.
Probab=23.52 E-value=11 Score=35.58 Aligned_cols=21 Identities=29% Similarity=0.279 Sum_probs=16.0
Q ss_pred hhHHHHHHHHHHhHHHHHHHh
Q 020000 132 EEDHFMCVQHEAGHFLTGYLL 152 (332)
Q Consensus 132 ~eer~RVA~HEAGHaLVAyLL 152 (332)
+-..-+++.||.||+|--+..
T Consensus 134 ~~n~g~t~~HEvGH~lGL~Ht 154 (225)
T cd04275 134 PYNLGDTATHEVGHWLGLYHT 154 (225)
T ss_pred cccccceeEEeccceeeeeee
Confidence 446668999999999865543
No 105
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=23.46 E-value=4.1e+02 Score=22.92 Aligned_cols=53 Identities=11% Similarity=0.104 Sum_probs=36.0
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHH-------HHHHHHHHHHHHhHHHHHHHHHHHHhh
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVK-------WAALNTVLISHHHIQVRSRLAEAMALG 290 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr-------~A~~~A~~LL~~hr~ale~LAeaLle~ 290 (332)
.+|+.++..| ++.+|||-++|..-+. +.......+|.++.+.+++-.+.|.+-
T Consensus 42 ~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~ 103 (140)
T PRK09514 42 EQDLQRLRFIRRAKQLGFTLEEIRELLSIRLDPEHHTCQEVKGIVDEKLAEVEAKIAELQHM 103 (140)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHhcccCCcCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4788887776 6679999887765432 124556778888877777766666553
No 106
>cd08789 CARD_IPS-1_RIG-I Caspase activation and recruitment domains (CARDs) found in IPS-1 and RIG-I-like RNA helicases. Caspase activation and recruitment domains (CARDs) found in IPS-1 (Interferon beta promoter stimulator protein 1) and Retinoic acid Inducible Gene I (RIG-I)-like DEAD box helicases. RIG-I-like helicases and IPS-1 play important roles in the induction of interferons in response to viral infection. They are crucial in triggering innate immunity and in developing adaptive immunity against viral pathogens. RIG-I-like helicases, including MDA5 and RIG-I, contain two N-terminal CARD domains and a C-terminal DEAD box RNA helicase domain. They are cytoplasmic RNA helicases that play an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. MDA5 and RIG-I associate with IPS-1 through a CARD-CAR
Probab=23.32 E-value=72 Score=25.63 Aligned_cols=35 Identities=29% Similarity=0.382 Sum_probs=26.8
Q ss_pred HHHHHHHHHc-cCchHHHHHHHHHhccCCCCcccccc
Q 020000 30 ALKRVDRELS-RGNFKVALSLVKQLQRKPAGGLRGFG 65 (332)
Q Consensus 30 ~~~~~~~~~~-~g~~~~a~~~~~~l~~~~~~~l~~~g 65 (332)
--|++..+-. +||..+|--|++.|..++ |..+.|=
T Consensus 34 d~e~I~a~~~~~G~~~aa~~Ll~~L~r~~-~Wf~~Fl 69 (84)
T cd08789 34 DKERIQAAENNSGNIKAAWTLLDTLVRRD-NWLEPFL 69 (84)
T ss_pred HHHHHHHHHhcCChHHHHHHHHHHHhccC-ChHHHHH
Confidence 3456666555 799999999999999777 7777663
No 107
>cd04281 ZnMc_BMP1_TLD Zinc-dependent metalloprotease; BMP1/TLD-like subfamily. BMP1 (Bone morphogenetic protein 1) and TLD (tolloid)-like metalloproteases play vital roles in extracellular matrix formation, by cleaving precursor proteins such as enzymes, structural proteins, and proteins involved in the mineralization of the extracellular matrix. The drosophila protein tolloid and its Xenopus homologue xolloid cleave and inactivate Sog and chordin, respectively, which are inhibitors of Dpp (the Drosophila decapentaplegic gene product) and its homologue BMP4, involved in dorso-ventral patterning.
Probab=23.15 E-value=45 Score=30.99 Aligned_cols=33 Identities=24% Similarity=0.235 Sum_probs=20.5
Q ss_pred HHHHHHHhHHHHHHHhCCCCC---ceecCchhhhccc
Q 020000 137 MCVQHEAGHFLTGYLLGVLPK---GYEIPSVEALKQD 170 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg~PV~---kyTI~p~eal~~G 170 (332)
=++.||.||+|=-+..-..+. -|+|. |+.++.|
T Consensus 89 Gti~HEl~HaLGf~HEhsRpDRD~yV~I~-~~nI~~~ 124 (200)
T cd04281 89 GIVVHELGHVIGFWHEHTRPDRDDHVTII-RENIQPG 124 (200)
T ss_pred chHHHHHHHHhcCcchhccccccceEEEe-ecccCcc
Confidence 489999999987666543222 24443 5555544
No 108
>PF13574 Reprolysin_2: Metallo-peptidase family M12B Reprolysin-like; PDB: 1KAP_P 1JIW_P 1AKL_A 1OM7_A 1OM8_A 1O0T_A 1OM6_A 1H71_P 1O0Q_A 1OMJ_A ....
Probab=23.06 E-value=49 Score=29.42 Aligned_cols=20 Identities=25% Similarity=0.014 Sum_probs=14.1
Q ss_pred HHHHHHHHHhHHHHHHHhCC
Q 020000 135 HFMCVQHEAGHFLTGYLLGV 154 (332)
Q Consensus 135 r~RVA~HEAGHaLVAyLLg~ 154 (332)
-..++-||.||.|=+..-+.
T Consensus 111 ~~~~~aHElGH~lGa~Hd~~ 130 (173)
T PF13574_consen 111 GIDTFAHELGHQLGAPHDFD 130 (173)
T ss_dssp HHHHHHHHHHHHHT---SSS
T ss_pred eeeeehhhhHhhcCCCCCCC
Confidence 45789999999998888764
No 109
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=22.95 E-value=2.5e+02 Score=22.75 Aligned_cols=50 Identities=18% Similarity=0.187 Sum_probs=31.3
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVKWAALNTVLISHHHIQVRSRLAEAMAL 289 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr~A~~~A~~LL~~hr~ale~LAeaLle 289 (332)
.+|+..+..| ++..|||-+++..-+.. .....++.++.+.+++-.+.|.+
T Consensus 41 ~~dl~~l~~I~~l~~~G~~l~ei~~~~~~--~~~~~~l~~~~~~l~~~i~~l~~ 92 (102)
T cd04775 41 EADLSRLEKIVFLQAGGLPLEEIAGCLAQ--PHVQAILEERLQSLNREIQRLRQ 92 (102)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHcC--CcHHHHHHHHHHHHHHHHHHHHH
Confidence 4788888776 56799998777643221 11456666666666665555544
No 110
>cd06461 M2_ACE Peptidase family M2 Angiotensin converting enzyme (ACE, EC 3.4.15.1) is a membrane-bound, zinc dependent dipeptidase that catalyzes the conversion of the decapeptide angiotensin I to the potent vasopressor ocatapeptide angiotensin II, by removing two C-terminal amino acids. There are two forms of the enzyme in humans, the ubiquitous somatic ACE and the sperm-specific germinal ACE, both encoded by the same gene through transcription from alternative promoters. Somatic ACE has two tandem active sites with distinct catalytic properties, whereas germinal ACE, the function of which is largely unknown, has just a single active site. Recently, an ACE homolog, ACE2, has been identified in humans that differs from ACE; it preferentially removes carboxy-terminal hydrophobic or basic amino acids and appears to be important in cardiac function. ACE homologs (also known as members of the M2 gluzincin family) have been found in a wide variety of species, including those that neither h
Probab=22.67 E-value=57 Score=34.18 Aligned_cols=36 Identities=14% Similarity=0.168 Sum_probs=27.9
Q ss_pred HHHhHHHHHHHHHHHHhhCcH--HHHHHHHhcccchhh
Q 020000 273 SHHHIQVRSRLAEAMALGRSI--GSYTSKILTEQSLEL 308 (332)
Q Consensus 273 L~~hr~ale~LAeaLle~esl--~ec~~~Ie~~~~~~~ 308 (332)
+.+.+++.+.+.+.|.-+.|. .|.++.+..+.+.+.
T Consensus 422 ~~~s~~Ag~~l~~~l~lG~S~~w~e~le~~~g~~~~s~ 459 (477)
T cd06461 422 IYGSKEAGKKLRAMLSLGSSKPWPEALEALTGEREMDA 459 (477)
T ss_pred ccChHHHHHHHHHHHhCcCCCCHHHHHHHhcCCCCCCh
Confidence 355889999999999998885 588888777655443
No 111
>PRK13267 archaemetzincin-like protein; Reviewed
Probab=22.62 E-value=57 Score=29.83 Aligned_cols=11 Identities=55% Similarity=0.661 Sum_probs=8.8
Q ss_pred HHHHHHHhHHH
Q 020000 137 MCVQHEAGHFL 147 (332)
Q Consensus 137 RVA~HEAGHaL 147 (332)
+.+.||.||.|
T Consensus 127 k~~~HElGH~l 137 (179)
T PRK13267 127 KEVTHELGHTL 137 (179)
T ss_pred HHHHHHHHHHc
Confidence 34999999974
No 112
>PRK01265 heat shock protein HtpX; Provisional
Probab=22.36 E-value=52 Score=32.84 Aligned_cols=21 Identities=24% Similarity=0.340 Sum_probs=17.4
Q ss_pred CCChhHHHHHHHHHHhHHHHH
Q 020000 129 SLKEEDHFMCVQHEAGHFLTG 149 (332)
Q Consensus 129 ~ls~eer~RVA~HEAGHaLVA 149 (332)
.++++|.+-|.-||-||.--.
T Consensus 134 ~l~~~El~aVlAHElgHik~~ 154 (324)
T PRK01265 134 ILNRDEIKAVAGHELGHLKHR 154 (324)
T ss_pred hCCHHHHHHHHHHHHHHHHcc
Confidence 358899999999999996433
No 113
>PF01432 Peptidase_M3: Peptidase family M3 This Prosite motif covers only the active site. This family belongs to family M3 of the peptidase classification.; InterPro: IPR001567 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 []. This group of metallopeptidases belong to MEROPS peptidase family M3 (clan MA(E)), subfamilies M3A and M3B. The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. The Thimet oligopeptidase family, is a large family of archaeal, bacterial and eukaryotic oligopeptidases that cleave medium sized peptides. The group contains: mitochondrial intermediate peptidase (3.4.24.59 from EC) Neurolysin, mitochondrial precursor, (3.4.24.16 from EC) Thimet oligopeptidase (3.4.24.15 from EC) Dipeptidyl carboxypeptidase (3.4.15.5 from EC) Oligopeptidase A (3.4.24.70 from EC) Oligoendopeptidase F ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2QR4_B 3CE2_A 1Y79_1 2H1J_A 2H1N_A 2O36_A 1S4B_P 2O3E_A 1I1I_P.
Probab=22.35 E-value=72 Score=32.23 Aligned_cols=19 Identities=26% Similarity=0.282 Sum_probs=16.5
Q ss_pred HHHHHHHhHHHHHHHhCCC
Q 020000 137 MCVQHEAGHFLTGYLLGVL 155 (332)
Q Consensus 137 RVA~HEAGHaLVAyLLg~P 155 (332)
.+..||.||++=.++...+
T Consensus 244 ~tLfHE~GHa~H~~ls~~~ 262 (458)
T PF01432_consen 244 ETLFHEFGHAMHSLLSRTK 262 (458)
T ss_dssp HHHHHHHHHHHHHHHCCCS
T ss_pred HHHHHHHhHHHHHHHhccc
Confidence 7899999999999988753
No 114
>TIGR00380 cobD cobalamin biosynthesis protein CobD. This protein is involved in cobalamin (vitamin B12) biosynthesis and porphyrin biosynthesis. It converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group. It is part of the cob operon.
Probab=21.88 E-value=1.9e+02 Score=28.64 Aligned_cols=67 Identities=16% Similarity=0.256 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHHHHccCchHHHHHHHHHhccCCCCccccccccccccccccccchhhhhchhhhhhhhhhhhhhHHHHHh
Q 020000 25 KRRRQALKRVDRELSRGNFKVALSLVKQLQRKPAGGLRGFGAAKQVPKRLSSLDESELDSKELLTLRALFDSVMESIERC 104 (332)
Q Consensus 25 ~~~~~~~~~~~~~~~~g~~~~a~~~~~~l~~~~~~~l~~~gaa~~~p~r~~~l~el~l~~~t~~~ll~P~~~~s~~i~~~ 104 (332)
+.-.+..+.|.+.|++||..+|-..++.+-+++ ...|++-.+...+.+++ ..+++-.+-+.
T Consensus 100 r~L~~~~~~V~~aL~~gdl~~AR~~l~~iv~Rd----------------t~~Ls~~~i~ra~iEs~---aen~~d~~~ap 160 (305)
T TIGR00380 100 KSLVQAAQSVIESLKAGDLETARKKLQMIVSRD----------------TNNLSEEQILSAAVESV---AENIVDGVTAP 160 (305)
T ss_pred hhHHHHHHHHHHHHHcCCHHHHHHHHHHHhCCC----------------cccCCHHHHHHHHHHHH---HHHhcchhHHH
Confidence 455666778999999999999999998887765 45566666666555555 45555555555
Q ss_pred hhhhcc
Q 020000 105 NLFDSL 110 (332)
Q Consensus 105 ~~~~~l 110 (332)
+.|.++
T Consensus 161 lF~~~l 166 (305)
T TIGR00380 161 LFYAIL 166 (305)
T ss_pred HHHHHH
Confidence 544333
No 115
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=21.84 E-value=3.7e+02 Score=22.88 Aligned_cols=52 Identities=12% Similarity=0.167 Sum_probs=35.3
Q ss_pred hhHHHHHHHH--HHHhCCChhHHHHHHH-------HHHHHHHHHHHHhHHHHHHHHHHHHh
Q 020000 238 YSDINKLDKV--FQWLGYNKSEADSQVK-------WAALNTVLISHHHIQVRSRLAEAMAL 289 (332)
Q Consensus 238 a~Dl~qat~i--ar~lGmS~~~id~evr-------~A~~~A~~LL~~hr~ale~LAeaLle 289 (332)
.+|+..+..| ++.+|||-++|..-.. +.......+|.++.+.+++-.+.|.+
T Consensus 42 ~~~l~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 102 (131)
T TIGR02043 42 DEDQKRLRFILKAKELGFTLDEIKELLSIKLDATEHSCAEVKAIVDAKLELVDEKINELTK 102 (131)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4788888876 6679999887654332 12345677888887777766665544
No 116
>cd04267 ZnMc_ADAM_like Zinc-dependent metalloprotease, ADAM_like or reprolysin_like subgroup. The adamalysin_like or ADAM family of metalloproteases contains proteolytic domains from snake venoms, proteases from the mammalian reproductive tract, and the tumor necrosis factor alpha convertase, TACE. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
Probab=20.75 E-value=44 Score=29.52 Aligned_cols=21 Identities=29% Similarity=0.218 Sum_probs=15.5
Q ss_pred hHHHHHHHHHHhHHHHHHHhC
Q 020000 133 EDHFMCVQHEAGHFLTGYLLG 153 (332)
Q Consensus 133 eer~RVA~HEAGHaLVAyLLg 153 (332)
-.--.++.||.||.|=+..-+
T Consensus 131 ~~~~~~~aHElGH~lG~~HD~ 151 (192)
T cd04267 131 LLTALTMAHELGHNLGAEHDG 151 (192)
T ss_pred eeehhhhhhhHHhhcCCcCCC
Confidence 455679999999987655544
No 117
>PRK02870 heat shock protein HtpX; Provisional
Probab=20.72 E-value=62 Score=32.41 Aligned_cols=18 Identities=22% Similarity=0.416 Sum_probs=16.3
Q ss_pred CCChhHHHHHHHHHHhHH
Q 020000 129 SLKEEDHFMCVQHEAGHF 146 (332)
Q Consensus 129 ~ls~eer~RVA~HEAGHa 146 (332)
.++++|.+-|.-||.||.
T Consensus 167 ~L~~dEL~aVlAHELgHi 184 (336)
T PRK02870 167 KLDRDELQAVMAHELSHI 184 (336)
T ss_pred hCCHHHHHHHHHHHHHHH
Confidence 458899999999999997
No 118
>COG5549 Predicted Zn-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=20.30 E-value=55 Score=31.45 Aligned_cols=20 Identities=30% Similarity=0.204 Sum_probs=16.4
Q ss_pred CChhHHHHHHHHHHhHHHHH
Q 020000 130 LKEEDHFMCVQHEAGHFLTG 149 (332)
Q Consensus 130 ls~eer~RVA~HEAGHaLVA 149 (332)
.+++...-+|.||-||+|=-
T Consensus 182 ~~~e~L~~tarhElGhaLgi 201 (236)
T COG5549 182 ELRENLNPTARHELGHALGI 201 (236)
T ss_pred cchhhhhHHHHHhhcchhee
Confidence 46788888999999999743
No 119
>PHA00101 internal virion protein B
Probab=20.27 E-value=5.5e+02 Score=24.18 Aligned_cols=79 Identities=13% Similarity=0.165 Sum_probs=51.5
Q ss_pred ccchhhHH--HHHHHHHHHhCCChhHHHHHHHHHHH--------HHHHHHHHhHHHHHHHHHHHHhhCcHHHHHHHHhcc
Q 020000 234 SEGHYSDI--NKLDKVFQWLGYNKSEADSQVKWAAL--------NTVLISHHHIQVRSRLAEAMALGRSIGSYTSKILTE 303 (332)
Q Consensus 234 stGga~Dl--~qat~iar~lGmS~~~id~evr~A~~--------~A~~LL~~hr~ale~LAeaLle~esl~ec~~~Ie~~ 303 (332)
+.|++.|- .|+.+++++..+......-+.|-..+ ...+-++..-...-++.+-|+|+.|.+...++.|+.
T Consensus 26 A~~Aq~da~RrQa~emvkqmN~qnANL~Lq~rd~~e~a~~Elt~~nm~~vr~~GtIRaAIgEs~LEGnSM~RI~rv~eg~ 105 (194)
T PHA00101 26 AEGAQIDAGRRQAMEMVKEMNIQNANLSLEARDKLEEASAELTEANMQKVRNMGTIRAAIGEGMLEGNSMDRIKRVTEGD 105 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHhChhcchhhhhhHHhHHHHHHHHHHHHHHHHHhcchHHHHHhccccccchHHHHHHHhhhH
Confidence 35887774 45777899887776544333333322 233445555666778999999999999888887776
Q ss_pred cchhhhhhccccc
Q 020000 304 QSLELLRSRTNVT 316 (332)
Q Consensus 304 ~~~~~~~~~~~~~ 316 (332)
-+|++.-+|
T Consensus 106 ----~ire~~~iT 114 (194)
T PHA00101 106 ----FIREANGIT 114 (194)
T ss_pred ----HHHHhhcch
Confidence 455554443
No 120
>PRK05427 putative manganese-dependent inorganic pyrophosphatase; Provisional
Probab=20.15 E-value=2.5e+02 Score=27.33 Aligned_cols=51 Identities=12% Similarity=0.203 Sum_probs=42.0
Q ss_pred HHHHHHhhhHHHHHHHhCCccchhhHHHHHHHHHHHhCCChhHHHHHHHHH
Q 020000 215 NFSCVILGGLVAEHLVFGHSEGHYSDINKLDKVFQWLGYNKSEADSQVKWA 265 (332)
Q Consensus 215 r~i~VaLAGrAAE~LvfG~stGga~Dl~qat~iar~lGmS~~~id~evr~A 265 (332)
+....+++|+...+..|-..+....|++-+..+++..|.+..++-.++-.+
T Consensus 136 ~iA~~L~~gIltDT~~F~~~~tt~~d~~~a~~L~~~~g~d~~~~~~~l~~~ 186 (308)
T PRK05427 136 EIAGLMLSAILSDTLLFKSPTTTEQDKAAAEELAEIAGVDIEAYGLEMLKA 186 (308)
T ss_pred HHHHHHHHHHHHHhcccCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 445789999999999999877889999999999988898877766665433
No 121
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=20.08 E-value=3.2e+02 Score=21.38 Aligned_cols=46 Identities=13% Similarity=0.116 Sum_probs=28.9
Q ss_pred HHHHHHHhCCChhHHHHHHH----HHHHHHHHHHHHhHH------HHHHHHHHHHh
Q 020000 244 LDKVFQWLGYNKSEADSQVK----WAALNTVLISHHHIQ------VRSRLAEAMAL 289 (332)
Q Consensus 244 at~iar~lGmS~~~id~evr----~A~~~A~~LL~~hr~------ale~LAeaLle 289 (332)
-.++++.+||++.+|+.=.. ....++.++|..-++ ..+.|.++|..
T Consensus 18 W~~LAr~Lg~~~~dI~~i~~~~~~~~~eq~~~mL~~W~~r~g~~at~~~L~~AL~~ 73 (84)
T cd08317 18 WPQLARELGVSETDIDLIKAENPNSLAQQAQAMLKLWLEREGKKATGNSLEKALKK 73 (84)
T ss_pred HHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHhcCCcchHHHHHHHHHH
Confidence 45568889999887765322 346888888875443 34455555543
Done!