Query 021521
Match_columns 311
No_of_seqs 154 out of 700
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 03:39:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021521.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021521hhsearch_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 1.3E-28 2.9E-33 222.7 15.9 153 117-297 8-207 (213)
2 PRK10733 hflB ATP-dependent me 99.9 5.1E-25 1.1E-29 227.6 17.5 144 126-297 399-586 (644)
3 CHL00176 ftsH cell division pr 99.9 5.5E-25 1.2E-29 227.5 16.7 148 129-304 432-625 (638)
4 TIGR01241 FtsH_fam ATP-depende 99.9 1.1E-24 2.4E-29 217.7 16.9 146 125-298 301-488 (495)
5 KOG0734 AAA+-type ATPase conta 99.9 2E-25 4.4E-30 225.3 10.9 158 119-306 539-732 (752)
6 COG0465 HflB ATP-dependent Zn 99.9 7.7E-24 1.7E-28 216.9 14.7 152 117-296 386-580 (596)
7 KOG0731 AAA+-type ATPase conta 99.9 4.3E-22 9.4E-27 208.1 14.2 192 83-304 503-748 (774)
8 CHL00206 ycf2 Ycf2; Provisiona 98.6 5.5E-08 1.2E-12 110.6 7.3 109 117-251 1873-1994(2281)
9 cd06163 S2P-M50_PDZ_RseP-like 96.9 0.0014 3.1E-08 59.0 5.1 25 137-161 11-35 (182)
10 PRK10779 zinc metallopeptidase 96.5 0.002 4.4E-08 64.8 3.6 26 137-162 17-42 (449)
11 TIGR00054 RIP metalloprotease 96.0 0.006 1.3E-07 61.0 3.7 25 137-161 16-40 (420)
12 cd06161 S2P-M50_SpoIVFB SpoIVF 95.7 0.0087 1.9E-07 54.5 3.3 27 137-163 40-66 (208)
13 cd06164 S2P-M50_SpoIVFB_CBS Sp 95.6 0.014 3E-07 54.2 4.3 27 137-163 55-81 (227)
14 PF13398 Peptidase_M50B: Pepti 95.5 0.014 3.1E-07 52.9 3.9 27 137-163 24-50 (200)
15 cd06162 S2P-M50_PDZ_SREBP Ster 94.3 0.07 1.5E-06 51.4 5.2 27 137-163 137-163 (277)
16 PF02163 Peptidase_M50: Peptid 93.9 0.038 8.2E-07 48.5 2.2 25 137-161 9-33 (192)
17 cd05709 S2P-M50 Site-2 proteas 93.8 0.045 9.8E-07 47.8 2.7 25 137-161 10-34 (180)
18 cd06160 S2P-M50_like_2 Unchara 91.7 0.15 3.2E-06 46.1 3.0 27 137-163 43-69 (183)
19 cd06158 S2P-M50_like_1 Unchara 88.6 0.33 7.1E-06 43.5 2.5 26 138-163 12-41 (181)
20 cd06159 S2P-M50_PDZ_Arch Uncha 88.6 0.25 5.4E-06 47.1 1.8 25 137-161 120-144 (263)
21 PF14247 DUF4344: Domain of un 85.5 0.6 1.3E-05 43.6 2.5 23 137-160 94-116 (220)
22 PF00413 Peptidase_M10: Matrix 83.8 0.5 1.1E-05 39.6 1.1 17 131-147 101-117 (154)
23 cd04279 ZnMc_MMP_like_1 Zinc-d 80.0 1.2 2.5E-05 38.2 2.0 17 132-148 101-117 (156)
24 cd04268 ZnMc_MMP_like Zinc-dep 76.9 1.5 3.3E-05 37.1 1.8 16 132-147 91-106 (165)
25 KOG2921 Intramembrane metallop 74.5 2.1 4.5E-05 43.8 2.3 25 138-162 134-158 (484)
26 cd04786 HTH_MerR-like_sg7 Heli 72.7 18 0.00038 30.9 7.2 68 240-307 41-116 (131)
27 cd04278 ZnMc_MMP Zinc-dependen 71.9 1.8 3.9E-05 37.1 1.0 17 131-147 103-119 (157)
28 COG0750 Predicted membrane-ass 70.1 2.9 6.3E-05 40.3 2.1 26 137-162 15-40 (375)
29 cd04277 ZnMc_serralysin_like Z 69.2 3.1 6.8E-05 36.5 2.0 16 132-147 110-125 (186)
30 PF02031 Peptidase_M7: Strepto 68.9 3.5 7.6E-05 36.0 2.1 27 119-147 63-89 (132)
31 PF06114 DUF955: Domain of unk 67.1 6.3 0.00014 30.6 3.1 23 130-152 37-59 (122)
32 PF04298 Zn_peptidase_2: Putat 67.0 2.9 6.4E-05 39.3 1.4 13 137-149 91-103 (222)
33 cd04769 HTH_MerR2 Helix-Turn-H 65.4 35 0.00077 28.1 7.4 66 240-305 40-115 (116)
34 PF05572 Peptidase_M43: Pregna 63.5 3.7 8.1E-05 36.0 1.3 18 131-148 65-82 (154)
35 cd04327 ZnMc_MMP_like_3 Zinc-d 61.6 5.4 0.00012 35.8 2.0 25 134-158 91-116 (198)
36 cd08316 Death_FAS_TNFRSF6 Deat 61.3 42 0.00091 27.6 7.0 64 243-307 20-93 (97)
37 smart00235 ZnMc Zinc-dependent 58.9 5 0.00011 33.4 1.2 11 137-147 88-98 (140)
38 PF08858 IDEAL: IDEAL domain; 54.8 30 0.00066 23.6 4.3 33 21-53 5-37 (37)
39 cd08306 Death_FADD Fas-associa 52.9 73 0.0016 25.2 6.9 48 246-293 16-73 (86)
40 cd00203 ZnMc Zinc-dependent me 50.1 8.7 0.00019 32.4 1.3 16 133-148 94-109 (167)
41 PF09278 MerR-DNA-bind: MerR, 50.1 73 0.0016 23.0 6.1 42 250-291 10-57 (65)
42 smart00005 DEATH DEATH domain, 48.0 57 0.0012 24.8 5.5 48 244-291 18-75 (88)
43 PF13485 Peptidase_MA_2: Pepti 45.1 25 0.00054 27.4 3.1 23 131-153 21-43 (128)
44 PF11350 DUF3152: Protein of u 44.9 11 0.00025 35.1 1.3 18 132-150 136-153 (203)
45 cd04768 HTH_BmrR-like Helix-Tu 44.5 76 0.0017 25.3 5.9 50 241-290 42-93 (96)
46 PF13582 Reprolysin_3: Metallo 44.4 11 0.00025 30.4 1.1 11 137-147 109-119 (124)
47 COG0501 HtpX Zn-dependent prot 43.3 19 0.0004 33.4 2.5 24 129-152 151-174 (302)
48 cd04788 HTH_NolA-AlbR Helix-Tu 39.4 90 0.002 24.9 5.6 50 240-289 41-92 (96)
49 COG0339 Dcp Zn-dependent oligo 39.2 24 0.00053 38.3 2.8 30 137-167 469-501 (683)
50 cd01109 HTH_YyaN Helix-Turn-He 38.8 1.9E+02 0.0042 23.5 7.6 51 241-291 42-100 (113)
51 PF01435 Peptidase_M48: Peptid 38.7 25 0.00055 30.9 2.5 24 130-153 84-107 (226)
52 cd04773 HTH_TioE_rpt2 Second H 37.9 1.8E+02 0.0039 23.7 7.2 52 241-292 42-100 (108)
53 cd04783 HTH_MerR1 Helix-Turn-H 37.5 1.7E+02 0.0037 24.3 7.2 51 241-291 42-98 (126)
54 cd08777 Death_RIP1 Death Domai 36.3 1.4E+02 0.0031 23.7 6.2 47 246-292 16-74 (86)
55 TIGR01950 SoxR redox-sensitive 36.2 1.9E+02 0.004 25.1 7.4 60 240-299 41-110 (142)
56 cd04777 HTH_MerR-like_sg1 Heli 36.1 1.7E+02 0.0037 23.5 6.8 51 241-291 40-102 (107)
57 cd06258 Peptidase_M3_like The 35.3 21 0.00047 34.4 1.6 18 137-154 156-173 (365)
58 PF12994 DUF3878: Domain of un 35.3 7 0.00015 38.3 -1.7 29 116-149 80-108 (299)
59 cd01110 HTH_SoxR Helix-Turn-He 35.2 1.6E+02 0.0035 25.2 6.8 59 241-299 42-110 (139)
60 TIGR02044 CueR Cu(I)-responsiv 34.6 1.7E+02 0.0037 24.4 6.7 51 241-291 42-100 (127)
61 COG2856 Predicted Zn peptidase 34.3 32 0.00069 32.1 2.5 23 130-152 67-89 (213)
62 cd04782 HTH_BltR Helix-Turn-He 34.2 1.6E+02 0.0034 23.5 6.2 51 241-291 42-95 (97)
63 cd04784 HTH_CadR-PbrR Helix-Tu 34.1 1.9E+02 0.0041 24.0 7.0 51 240-290 41-99 (127)
64 PF12388 Peptidase_M57: Dual-a 33.2 28 0.0006 32.6 1.9 20 131-150 129-148 (211)
65 cd04776 HTH_GnyR Helix-Turn-He 33.1 2.8E+02 0.0062 23.0 8.6 63 240-302 39-113 (118)
66 cd01106 HTH_TipAL-Mta Helix-Tu 32.9 1.5E+02 0.0032 23.7 5.9 49 241-289 42-92 (103)
67 cd01108 HTH_CueR Helix-Turn-He 30.0 3.3E+02 0.0071 22.7 7.8 50 241-290 42-99 (127)
68 TIGR02289 M3_not_pepF oligoend 29.3 45 0.00098 34.6 2.9 17 137-153 339-355 (549)
69 PRK03982 heat shock protein Ht 29.0 28 0.00061 33.1 1.2 24 129-152 119-142 (288)
70 PF01400 Astacin: Astacin (Pep 28.8 35 0.00076 30.6 1.8 34 136-170 80-116 (191)
71 PF13583 Reprolysin_4: Metallo 28.8 29 0.00064 31.5 1.3 17 137-153 139-155 (206)
72 cd04280 ZnMc_astacin_like Zinc 28.7 29 0.00064 30.8 1.2 17 136-152 75-91 (180)
73 cd08315 Death_TRAILR_DR4_DR5 D 28.4 2.7E+02 0.0058 22.6 6.7 62 244-306 20-90 (96)
74 cd04779 HTH_MerR-like_sg4 Heli 28.3 3.1E+02 0.0067 23.6 7.4 21 241-261 41-63 (134)
75 PF13688 Reprolysin_5: Metallo 28.3 39 0.00085 29.5 1.9 24 130-153 137-160 (196)
76 cd08318 Death_NMPP84 Death dom 28.2 3E+02 0.0065 21.7 7.2 46 246-291 21-75 (86)
77 cd04770 HTH_HMRTR Helix-Turn-H 27.7 2.6E+02 0.0056 22.9 6.6 51 241-291 42-100 (123)
78 PF07998 Peptidase_M54: Peptid 27.2 40 0.00087 31.1 1.9 12 136-147 146-157 (194)
79 cd08311 Death_p75NR Death doma 27.0 1.4E+02 0.0029 23.5 4.6 33 246-279 18-50 (77)
80 cd04276 ZnMc_MMP_like_2 Zinc-d 26.9 45 0.00097 30.6 2.1 15 133-147 114-128 (197)
81 PRK02391 heat shock protein Ht 26.4 37 0.00081 32.8 1.6 27 126-152 124-150 (296)
82 TIGR02047 CadR-PbrR Cd(II)/Pb( 26.2 3.2E+02 0.007 22.8 7.1 52 240-291 41-100 (127)
83 cd04787 HTH_HMRTR_unk Helix-Tu 26.1 2.5E+02 0.0053 23.6 6.4 51 241-291 42-100 (133)
84 cd06459 M3B_Oligoendopeptidase 25.9 48 0.001 32.3 2.3 17 137-153 224-240 (427)
85 COG2738 Predicted Zn-dependent 25.7 37 0.0008 32.0 1.3 13 137-149 94-106 (226)
86 PRK15002 redox-sensitivie tran 25.4 3.8E+02 0.0082 23.6 7.6 60 240-299 51-120 (154)
87 cd08317 Death_ank Death domain 25.1 2.3E+02 0.0049 22.0 5.5 46 246-291 18-73 (84)
88 PRK05457 heat shock protein Ht 25.0 56 0.0012 31.4 2.5 20 129-148 128-147 (284)
89 PRK03001 M48 family peptidase; 25.0 36 0.00077 32.3 1.1 24 129-152 118-141 (283)
90 PF09471 Peptidase_M64: IgA Pe 24.7 36 0.00077 32.7 1.1 17 134-150 215-231 (264)
91 PF10728 DUF2520: Domain of un 24.7 2.4E+02 0.0053 24.1 6.1 62 236-297 6-67 (132)
92 cd04275 ZnMc_pappalysin_like Z 24.7 9.8 0.00021 35.5 -2.6 19 132-150 134-152 (225)
93 cd04283 ZnMc_hatching_enzyme Z 24.4 42 0.00091 30.4 1.4 17 137-153 79-95 (182)
94 cd08313 Death_TNFR1 Death doma 24.0 2.3E+02 0.0051 22.4 5.4 50 242-291 10-69 (80)
95 cd08804 Death_ank2 Death domai 23.9 2.2E+02 0.0047 22.5 5.3 46 246-291 18-73 (84)
96 TIGR02051 MerR Hg(II)-responsi 23.8 2.8E+02 0.006 23.1 6.2 51 241-291 41-97 (124)
97 cd06461 M2_ACE Peptidase famil 23.8 53 0.0011 34.1 2.2 20 276-295 423-442 (477)
98 cd08784 Death_DRs Death Domain 23.7 1.8E+02 0.0039 22.6 4.7 48 244-291 12-68 (79)
99 cd04281 ZnMc_BMP1_TLD Zinc-dep 23.5 44 0.00094 30.7 1.4 17 137-153 89-105 (200)
100 cd01282 HTH_MerR-like_sg3 Heli 23.5 2.8E+02 0.0061 22.6 6.1 52 240-291 40-102 (112)
101 PRK13267 archaemetzincin-like 23.1 55 0.0012 29.6 1.9 11 137-147 127-137 (179)
102 PF01432 Peptidase_M3: Peptida 22.8 70 0.0015 32.0 2.8 19 137-155 244-262 (458)
103 PRK03072 heat shock protein Ht 22.8 48 0.001 31.8 1.6 24 129-152 121-144 (288)
104 cd08779 Death_PIDD Death Domai 22.4 3.9E+02 0.0085 21.1 6.7 57 248-305 18-85 (86)
105 cd08789 CARD_IPS-1_RIG-I Caspa 22.0 80 0.0017 25.1 2.4 33 31-64 35-68 (84)
106 cd04785 HTH_CadR-PbrR-like Hel 21.7 4.3E+02 0.0093 22.0 6.9 49 241-289 42-98 (126)
107 PRK09514 zntR zinc-responsive 21.5 4.1E+02 0.0088 22.7 6.9 51 241-291 43-102 (140)
108 PRK04897 heat shock protein Ht 21.3 72 0.0016 30.7 2.5 22 130-151 132-153 (298)
109 cd01107 HTH_BmrR Helix-Turn-He 21.0 2.8E+02 0.0061 22.4 5.6 47 241-287 43-92 (108)
110 cd04790 HTH_Cfa-like_unk Helix 20.9 2.7E+02 0.0059 24.7 5.9 22 241-262 43-66 (172)
111 PRK01209 cobD cobalamin biosyn 20.9 1.6E+02 0.0034 28.6 4.7 33 25-57 96-128 (312)
112 COG1913 Predicted Zn-dependent 20.8 61 0.0013 29.8 1.7 16 132-147 118-136 (181)
113 cd08780 Death_TRADD Death Doma 20.7 2.9E+02 0.0064 22.8 5.5 46 246-291 16-77 (90)
114 cd04775 HTH_Cfa-like Helix-Tur 20.4 2.6E+02 0.0056 22.4 5.2 50 240-291 41-92 (102)
115 TIGR02043 ZntR Zn(II)-responsi 20.0 3.6E+02 0.0078 22.7 6.2 52 240-291 42-102 (131)
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=1.3e-28 Score=222.74 Aligned_cols=153 Identities=25% Similarity=0.321 Sum_probs=120.1
Q ss_pred hhhHHhhccc--cCCCChhHHHHHHHHHHhHHHHHHHhC--CCCCceecCchhhhccccccccceEEecchhhHHHHHhh
Q 021521 117 TVESIVEDGS--YVSLKEEDHFMCVQHEAGHFLTGYLLG--VLPKGYEIPSVEALKQDDFTVGRVQFVGFDFLKEVADAR 192 (311)
Q Consensus 117 ~~~~llld~~--~~~ls~eer~RIA~HEAGHaLVAyLLg--~PV~~yTI~~~ealr~G~~~~GG~~f~~~e~~~e~~~ar 192 (311)
++.+++++.. ++.+++++|+|+||||||||+|+|+++ .||.++||.| +|. ..|.+.|.+.+
T Consensus 8 a~drv~~G~~~~~~~~~~~~~~~~A~HEAGhAvva~~l~~~~~v~~vsi~p-----rg~-~~G~~~~~~~~--------- 72 (213)
T PF01434_consen 8 AIDRVLMGPEKKSRKLSEEEKRRIAYHEAGHAVVAYLLPPADPVSKVSIVP-----RGS-ALGFTQFTPDE--------- 72 (213)
T ss_dssp HHHHHHCCSCCTTS---HHHHHHHHHHHHHHHHHHHHSSS---EEEEESST-----TCC-CCHCCEECHHT---------
T ss_pred HHHHHhcCcCcCCCCCCHHHHHHHHHHHHHHHHHHHHhcccccEEEEEEec-----CCC-cceeEEeccch---------
Confidence 5567777743 366899999999999999999999998 5999999998 664 45666665422
Q ss_pred hhcccCCCCCCCCccccCCHHHHHHHHHHHhhHHHHHHHHhC--C-ccchhhHHHHHHHHHHH----hCCCch-------
Q 021521 193 KQKKDTGQVGSWGNRGEISVKTLNNFSCVILGGLVAEHLVFG--H-SEGHYSDINKLDKVFQW----LGYNKS------- 258 (311)
Q Consensus 193 ~~~~dd~~~~~~l~~~~~s~~~L~r~~~VlLAGrAAE~LvfG--~-atGg~~Dl~qat~lar~----lGms~~------- 258 (311)
+....|++++.+.++|+|||||||+++|| + ++|+++|++++|++++. |||+.+
T Consensus 73 -------------~~~~~t~~~l~~~i~v~LaGraAEe~~~g~~~~stGa~~DL~~At~iA~~mv~~~Gm~~~~g~~~~~ 139 (213)
T PF01434_consen 73 -------------DRYIRTRSYLEDRICVLLAGRAAEELFFGEDNVSTGASSDLQQATEIARKMVASYGMGDSLGLLSYS 139 (213)
T ss_dssp -------------T-SS-BHHHHHHHHHHHHHHHHHHHHHHSCCS-BGGGHHHHHHHHHHHHHHHHTST-TTTTTSS-SE
T ss_pred -------------hcccccHHHHHhhHHHHHHHHHHHHhhcCcceecccchhHHHHHHHHHHHHHHHhCCCCCCceeeee
Confidence 23457999999999999999999999999 5 68999999999999875 688641
Q ss_pred -------------------------hHHHH----HHHHHHHHHHHHHHcHHHHHHHHHHHHhhccHHH
Q 021521 259 -------------------------EADSQ----VKWAALNTVLISHHHIQVRSRLAEAMALGRSIGS 297 (311)
Q Consensus 259 -------------------------~~d~e----vr~A~~~A~~LL~~hr~~le~LAeaLle~esv~~ 297 (311)
.++++ ++.||.+|++||++|++.+++|+++|+++++|..
T Consensus 140 ~~~~~~~~~~~~~~~~~~~s~~~~~~i~~ev~~lL~~a~~~a~~iL~~~r~~l~~la~~Lle~~~L~~ 207 (213)
T PF01434_consen 140 PNDDDEVFLGREWNSRRPMSEETRALIDREVRKLLEEAYARAKEILEENREALEALAEALLEKETLSG 207 (213)
T ss_dssp EEE-S-SSS-E---EEESS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHSEEEH
T ss_pred ccccccccccccccccCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCeeCH
Confidence 12233 4579999999999999999999999999998854
No 2
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=99.93 E-value=5.1e-25 Score=227.56 Aligned_cols=144 Identities=18% Similarity=0.241 Sum_probs=119.1
Q ss_pred ccCCCChhHHHHHHHHHHhHHHHHHHhC--CCCCceecCchhhhccccccccceEEecchhhHHHHHhhhhcccCCCCCC
Q 021521 126 SYVSLKEEDHFMCVQHEAGHFLTGYLLG--VLPKGYEIPSVEALKQDDFTVGRVQFVGFDFLKEVADARKQKKDTGQVGS 203 (311)
Q Consensus 126 ~~~~ls~eer~RIA~HEAGHaLVAyLLg--~PV~~yTI~~~ealr~G~~~~GG~~f~~~e~~~e~~~ar~~~~dd~~~~~ 203 (311)
.+..+++++|+++|||||||++|+++++ .||+++||.| +|. . +|+.+..|+ +
T Consensus 399 ~~~~~~~~~~~~~a~he~gha~~~~~~~~~~~~~~v~i~p-----rg~-~-~g~~~~~~~---~---------------- 452 (644)
T PRK10733 399 RSMVMTEAQKESTAYHEAGHAIIGRLVPEHDPVHKVTIIP-----RGR-A-LGVTFFLPE---G---------------- 452 (644)
T ss_pred ccccccHHHHHHHHHHHHHHHHHHHHccCCCceeEEEEec-----cCC-C-cceeEECCC---c----------------
Confidence 4456789999999999999999999998 6999999998 663 3 344444332 1
Q ss_pred CCccccCCHHHHHHHHHHHhhHHHHHHHHhCC---ccchhhHHHHHHHHHHH----hCCCch------------------
Q 021521 204 WGNRGEISVKTLNNFSCVILGGLVAEHLVFGH---SEGHYSDINKLDKVFQW----LGYNKS------------------ 258 (311)
Q Consensus 204 ~l~~~~~s~~~L~r~~~VlLAGrAAE~LvfG~---atGg~~Dl~qat~lar~----lGms~~------------------ 258 (311)
+....|+++|.+.++|+|||||||+++||. ++|++||++++|++++. ||||.+
T Consensus 453 --~~~~~~~~~l~~~i~~~lgGraAE~~~~g~~~~ttGa~~Dl~~AT~lA~~mv~~~Gms~~lg~~~~~~~~~~~~lg~~ 530 (644)
T PRK10733 453 --DAISASRQKLESQISTLYGGRLAEEIIYGPEHVSTGASNDIKVATNLARNMVTQWGFSEKLGPLLYAEEEGEVFLGRS 530 (644)
T ss_pred --ccccccHHHHHHHHHHHHhhHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhCCCccccchhhcccccccccccc
Confidence 234579999999999999999999999984 57999999999998864 798741
Q ss_pred -------------hHHHH----HHHHHHHHHHHHHHcHHHHHHHHHHHHhhccHHH
Q 021521 259 -------------EADSQ----VKWAALNTVLISHHHIQVRSRLAEAMALGRSIGS 297 (311)
Q Consensus 259 -------------~~d~e----vr~A~~~A~~LL~~hr~~le~LAeaLle~esv~~ 297 (311)
.+|++ ++.||.+|++||++|++.+++||++|+++|||..
T Consensus 531 ~~~~~~~s~~~~~~id~ev~~il~~~~~~a~~iL~~~~~~l~~la~~Lle~etl~~ 586 (644)
T PRK10733 531 VAKAKHMSDETARIIDQEVKALIERNYNRARQLLTDNMDILHAMKDALMKYETIDA 586 (644)
T ss_pred cccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhceeCH
Confidence 13444 4589999999999999999999999999999854
No 3
>CHL00176 ftsH cell division protein; Validated
Probab=99.93 E-value=5.5e-25 Score=227.51 Aligned_cols=148 Identities=18% Similarity=0.239 Sum_probs=121.6
Q ss_pred CCChhHHHHHHHHHHhHHHHHHHhC--CCCCceecCchhhhccccccccceEEecchhhHHHHHhhhhcccCCCCCCCCc
Q 021521 129 SLKEEDHFMCVQHEAGHFLTGYLLG--VLPKGYEIPSVEALKQDDFTVGRVQFVGFDFLKEVADARKQKKDTGQVGSWGN 206 (311)
Q Consensus 129 ~ls~eer~RIA~HEAGHaLVAyLLg--~PV~~yTI~~~ealr~G~~~~GG~~f~~~e~~~e~~~ar~~~~dd~~~~~~l~ 206 (311)
..++++|++|||||||||+|+++++ .||+++||.| +|. ..|.+.+. |+ + +
T Consensus 432 ~~~~~~~~~vA~hEaGhA~v~~~l~~~~~v~kvtI~p-----rg~-~~G~~~~~-p~---~------------------~ 483 (638)
T CHL00176 432 LEDSKNKRLIAYHEVGHAIVGTLLPNHDPVQKVTLIP-----RGQ-AKGLTWFT-PE---E------------------D 483 (638)
T ss_pred cccHHHHHHHHHHhhhhHHHHhhccCCCceEEEEEee-----cCC-CCCceEec-CC---c------------------c
Confidence 4588999999999999999999998 6999999998 663 33444443 32 1 3
Q ss_pred cccCCHHHHHHHHHHHhhHHHHHHHHhCC---ccchhhHHHHHHHHHHH----hCCCc----------------------
Q 021521 207 RGEISVKTLNNFSCVILGGLVAEHLVFGH---SEGHYSDINKLDKVFQW----LGYNK---------------------- 257 (311)
Q Consensus 207 ~~~~s~~~L~r~~~VlLAGrAAE~LvfG~---atGg~~Dl~qat~lar~----lGms~---------------------- 257 (311)
+..+|+.+|...++++|||||||+++||+ ++|+++|++++|++++. |||+.
T Consensus 484 ~~~~t~~~l~~~i~~~LgGraAE~~~fg~~~~~~Ga~~Dl~~AT~iA~~mv~~~Gm~~~g~~~~~~~~~~~~~~~~~~~~ 563 (638)
T CHL00176 484 QSLVSRSQILARIVGALGGRAAEEVVFGSTEVTTGASNDLQQVTNLARQMVTRFGMSSIGPISLESNNSTDPFLGRFMQR 563 (638)
T ss_pred cccccHHHHHHHHHHHhhhHHHHHHhcCCCCcCCCchhHHHHHHHHHHHHHHHhCCCcCCceeecCCCCccccccccccc
Confidence 46789999999999999999999999994 57999999999998865 78851
Q ss_pred ---------hhHHHH----HHHHHHHHHHHHHHcHHHHHHHHHHHHhhccH--HHHHHHHHH
Q 021521 258 ---------SEADSQ----VKWAALNTVLISHHHIQVRSRLAEAMALGRSI--GSCIHSIEN 304 (311)
Q Consensus 258 ---------~~~d~e----vr~A~~~A~~LL~~hr~~le~LAeaLle~esv--~~C~~~Ie~ 304 (311)
..+|.+ ++.||.+|++||++|++.+++||++|+++||| +|+.++++.
T Consensus 564 ~~~~s~~~~~~iD~ev~~~l~~~~~~a~~iL~~~~~~l~~la~~Lle~Etl~~~ei~~il~~ 625 (638)
T CHL00176 564 NSEYSEEIADKIDMEVRSILHTCYQYAYQILKDNRVLIDLLVELLLQKETIDGDEFREIVNS 625 (638)
T ss_pred ccCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCccCHHHHHHHHhh
Confidence 123444 56899999999999999999999999999988 456666654
No 4
>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=1.1e-24 Score=217.66 Aligned_cols=146 Identities=23% Similarity=0.230 Sum_probs=119.5
Q ss_pred cccCCCChhHHHHHHHHHHhHHHHHHHhC--CCCCceecCchhhhccccccccceEEecchhhHHHHHhhhhcccCCCCC
Q 021521 125 GSYVSLKEEDHFMCVQHEAGHFLTGYLLG--VLPKGYEIPSVEALKQDDFTVGRVQFVGFDFLKEVADARKQKKDTGQVG 202 (311)
Q Consensus 125 ~~~~~ls~eer~RIA~HEAGHaLVAyLLg--~PV~~yTI~~~ealr~G~~~~GG~~f~~~e~~~e~~~ar~~~~dd~~~~ 202 (311)
.....+++++|+++|||||||+||+|+++ .|+.++||.| +|. . +|+.+..+. +
T Consensus 301 ~~~~~~~~~~~~~~A~hEaGhAlv~~~l~~~~~v~~vsi~p-----rg~-~-~G~~~~~~~---~--------------- 355 (495)
T TIGR01241 301 KKSRVISEKEKKLVAYHEAGHALVGLLLKDADPVHKVTIIP-----RGQ-A-LGYTQFLPE---E--------------- 355 (495)
T ss_pred cccccccHHHHHHHHHHHHhHHHHHHhcCCCCceEEEEEee-----cCC-c-cceEEecCc---c---------------
Confidence 34556789999999999999999999996 6999999988 453 2 344433222 0
Q ss_pred CCCccccCCHHHHHHHHHHHhhHHHHHHHHhCCc-cchhhHHHHHHHHHHH----hCCCch-------------------
Q 021521 203 SWGNRGEISVKTLNNFSCVILGGLVAEHLVFGHS-EGHYSDINKLDKVFQW----LGYNKS------------------- 258 (311)
Q Consensus 203 ~~l~~~~~s~~~L~r~~~VlLAGrAAE~LvfG~a-tGg~~Dl~qat~lar~----lGms~~------------------- 258 (311)
+.+..|+++++++++|+|||||||+++||+. +|+++|+++||++++. |||+..
T Consensus 356 ---~~~~~t~~~l~~~i~v~LaGraAE~~~~G~~s~Ga~~Dl~~At~lA~~mv~~~Gm~~~~g~~~~~~~~~~~~l~~~~ 432 (495)
T TIGR01241 356 ---DKYLYTKSQLLAQIAVLLGGRAAEEIIFGEVTTGASNDIKQATNIARAMVTEWGMSDKLGPVAYGSDGGDVFLGRGF 432 (495)
T ss_pred ---ccccCCHHHHHHHHHHHhhHHHHHHHHhcCCCCCchHHHHHHHHHHHHHHHHhCCCcccCceeeccCcccccccccc
Confidence 2467799999999999999999999999985 6999999999999864 788641
Q ss_pred ------------hHHHH----HHHHHHHHHHHHHHcHHHHHHHHHHHHhhccHHHH
Q 021521 259 ------------EADSQ----VKWAALNTVLISHHHIQVRSRLAEAMALGRSIGSC 298 (311)
Q Consensus 259 ------------~~d~e----vr~A~~~A~~LL~~hr~~le~LAeaLle~esv~~C 298 (311)
.+|++ +++||.+|++||++|++.+++||++|+++++|+.-
T Consensus 433 ~~~~~~s~~~~~~id~~v~~lL~~a~~ra~~lL~~~~~~l~~la~~Ll~~e~L~~~ 488 (495)
T TIGR01241 433 AKAKEYSEETAREIDEEVKRIIEEAYKRAKQILTENRDELELLAKALLEKETITRE 488 (495)
T ss_pred ccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCeeCHH
Confidence 12333 56999999999999999999999999999998653
No 5
>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.92 E-value=2e-25 Score=225.27 Aligned_cols=158 Identities=22% Similarity=0.271 Sum_probs=131.0
Q ss_pred hHHhhc--cccCCCChhHHHHHHHHHHhHHHHHHHhC--CCCCceecCchhhhccccccccceEEecchhhHHHHHhhhh
Q 021521 119 ESIVED--GSYVSLKEEDHFMCVQHEAGHFLTGYLLG--VLPKGYEIPSVEALKQDDFTVGRVQFVGFDFLKEVADARKQ 194 (311)
Q Consensus 119 ~~llld--~~~~~ls~eer~RIA~HEAGHaLVAyLLg--~PV~~yTI~~~ealr~G~~~~GG~~f~~~e~~~e~~~ar~~ 194 (311)
..|+++ ..+++++++-|+.+||||+||++||+.+. .|++|.||.| ||. ..|.|... |+.
T Consensus 539 DrIlMG~ERks~~i~~eak~~TAyHE~GHAivA~yTk~A~PlhKaTImP-----RG~-sLG~t~~L-Pe~---------- 601 (752)
T KOG0734|consen 539 DRILMGPERKSMVIDEEAKKITAYHEGGHAIVALYTKGAMPLHKATIMP-----RGP-SLGHTSQL-PEK---------- 601 (752)
T ss_pred hheeecccccccccChhhhhhhhhhccCceEEEeecCCCccccceeecc-----CCc-cccceeec-Ccc----------
Confidence 455554 56788899999999999999999999998 5999999998 774 44555544 441
Q ss_pred cccCCCCCCCCccccCCHHHHHHHHHHHhhHHHHHHHHhCC---ccchhhHHHHHHHHHHH----hCCCch---------
Q 021521 195 KKDTGQVGSWGNRGEISVKTLNNFSCVILGGLVAEHLVFGH---SEGHYSDINKLDKVFQW----LGYNKS--------- 258 (311)
Q Consensus 195 ~~dd~~~~~~l~~~~~s~~~L~r~~~VlLAGrAAE~LvfG~---atGg~~Dl~qat~lar~----lGms~~--------- 258 (311)
++..+|+.++..++.|+||||+||+|+||. .+|+++|++|+|++++. ||||.+
T Consensus 602 -----------D~~~~Tk~q~LA~lDV~MGGRvAEELIfG~D~iTsGAssDl~qAT~lA~~MVt~fGMSd~vG~v~~~~~ 670 (752)
T KOG0734|consen 602 -----------DRYSITKAQLLARLDVCMGGRVAEELIFGTDKITSGASSDLDQATKLARRMVTKFGMSDKVGPVTLSAE 670 (752)
T ss_pred -----------chhhHHHHHHHHHHHHhhcchHHHHHhccCCcccccccchHHHHHHHHHHHHHHcCccccccceeeecc
Confidence 567889999999999999999999999996 36999999999998765 899752
Q ss_pred ------------hHHHH----HHHHHHHHHHHHHHcHHHHHHHHHHHHhhccHHHHHHHHHHhh
Q 021521 259 ------------EADSQ----VKWAALNTVLISHHHIQVRSRLAEAMALGRSIGSCIHSIENAL 306 (311)
Q Consensus 259 ------------~~d~e----vr~A~~~A~~LL~~hr~~le~LAeaLle~esv~~C~~~Ie~~~ 306 (311)
.+|.+ ++.+|++|+.||+.|...+++||++|+++||++--. |+..+
T Consensus 671 ~~~~s~~~~t~~lidaEi~~lL~~sYeRak~iL~~h~kEl~~LA~ALleYETL~A~e--ik~vl 732 (752)
T KOG0734|consen 671 DNSSSLSPRTQELIDAEIKRLLRDSYERAKSILKTHKKELHALAEALLEYETLDAKE--IKRVL 732 (752)
T ss_pred CCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHH--HHHHH
Confidence 25666 467999999999999999999999999999996544 44444
No 6
>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]
Probab=99.91 E-value=7.7e-24 Score=216.91 Aligned_cols=152 Identities=23% Similarity=0.274 Sum_probs=130.3
Q ss_pred hhhHHhhc--cccCCCChhHHHHHHHHHHhHHHHHHHhCC--CCCceecCchhhhccccccccceEEecchhhHHHHHhh
Q 021521 117 TVESIVED--GSYVSLKEEDHFMCVQHEAGHFLTGYLLGV--LPKGYEIPSVEALKQDDFTVGRVQFVGFDFLKEVADAR 192 (311)
Q Consensus 117 ~~~~llld--~~~~~ls~eer~RIA~HEAGHaLVAyLLg~--PV~~yTI~~~ealr~G~~~~GG~~f~~~e~~~e~~~ar 192 (311)
+...++.. ..++++++++|+.+|||||||++|+++++. ||+|+||.| +|+ .+|+++..|+ +
T Consensus 386 a~drv~~G~erks~vise~ek~~~AYhEaghalv~~~l~~~d~v~KvtIiP-----rG~--alG~t~~~Pe---~----- 450 (596)
T COG0465 386 AIDRVIAGPERKSRVISEAEKKITAYHEAGHALVGLLLPDADPVHKVTIIP-----RGR--ALGYTLFLPE---E----- 450 (596)
T ss_pred HHHHHhcCcCcCCcccChhhhcchHHHHHHHHHHHHhCCCCcccceeeecc-----Cch--hhcchhcCCc---c-----
Confidence 55777766 677789999999999999999999999994 999999999 662 3566666554 1
Q ss_pred hhcccCCCCCCCCccccCCHHHHHHHHHHHhhHHHHHHHHhC-C-ccchhhHHHHHHHHHHH----hCCCc---------
Q 021521 193 KQKKDTGQVGSWGNRGEISVKTLNNFSCVILGGLVAEHLVFG-H-SEGHYSDINKLDKVFQW----LGYNK--------- 257 (311)
Q Consensus 193 ~~~~dd~~~~~~l~~~~~s~~~L~r~~~VlLAGrAAE~LvfG-~-atGg~~Dl~qat~lar~----lGms~--------- 257 (311)
+++.+|++.+...++++|||||||+++|| + ++|++||++++|++++. ||||.
T Consensus 451 -------------d~~l~sk~~l~~~i~~~lgGRaAEel~~g~e~ttGa~~D~~~at~~ar~mVt~~Gms~~lG~v~~~~ 517 (596)
T COG0465 451 -------------DKYLMSKEELLDRIDVLLGGRAAEELIFGYEITTGASNDLEKATDLARAMVTEYGMSAKLGPVAYEQ 517 (596)
T ss_pred -------------ccccccHHHHHHHHHHHhCCcHhhhhhhcccccccchhhHHHHHHHHHHhhhhcCcchhhCceehhh
Confidence 46889999999999999999999999999 7 58999999999998864 78874
Q ss_pred --------------------hhHHHHH----HHHHHHHHHHHHHcHHHHHHHHHHHHhhccHH
Q 021521 258 --------------------SEADSQV----KWAALNTVLISHHHIQVRSRLAEAMALGRSIG 296 (311)
Q Consensus 258 --------------------~~~d~ev----r~A~~~A~~LL~~hr~~le~LAeaLle~esv~ 296 (311)
+.+|+++ ..+|.+++.||.+|++.++.+++.|+++||+.
T Consensus 518 ~~~~flg~~~~~~~~Se~ta~~ID~evk~ii~~~y~~a~~il~~~~~~l~~~~~~Lle~Eti~ 580 (596)
T COG0465 518 VEGVFLGRYQKAKNYSEETAQEIDREVKDIIDEAYERAKELLNENKDALETLAEMLLEKETID 580 (596)
T ss_pred cccccccccccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhccC
Confidence 1255554 57999999999999999999999999999986
No 7
>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.87 E-value=4.3e-22 Score=208.05 Aligned_cols=192 Identities=20% Similarity=0.231 Sum_probs=147.1
Q ss_pred cchhhhhhhhhhhhhhHHHHHHhhh-----------hccccccc-chhhHHhhc--cccCCCChhHHHHHHHHHHhHHHH
Q 021521 83 DSKELLTLRALFDSVMESIERCNLF-----------DSLDEAPS-DTVESIVED--GSYVSLKEEDHFMCVQHEAGHFLT 148 (311)
Q Consensus 83 ~~~t~~~ll~p~~~~s~~i~~~~~~-----------~~l~~~~~-D~~~~llld--~~~~~ls~eer~RIA~HEAGHaLV 148 (311)
+.++++.+-.-.-+.+++..++++- ..++...+ |+++.++.. ..++.+++++++.+|||||||++|
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 5666777666666777777777651 11111111 244544443 456778999999999999999999
Q ss_pred HHHhC--CCCCceecCchhhhccccccccceEEecchhhHHHHHhhhhcccCCCCCCCCccccCCHHHHHHHHHHHhhHH
Q 021521 149 GYLLG--VLPKGYEIPSVEALKQDDFTVGRVQFVGFDFLKEVADARKQKKDTGQVGSWGNRGEISVKTLNNFSCVILGGL 226 (311)
Q Consensus 149 AyLLg--~PV~~yTI~~~ealr~G~~~~GG~~f~~~e~~~e~~~ar~~~~dd~~~~~~l~~~~~s~~~L~r~~~VlLAGr 226 (311)
+|+++ .|+.++||+| |+ +.|.++|. |. +.+.+|+++|...+||+||||
T Consensus 583 g~~l~~~dpl~kvsIiP------Gq-alG~a~~~-P~----------------------~~~l~sk~ql~~rm~m~LGGR 632 (774)
T KOG0731|consen 583 GWLLEHADPLLKVSIIP------GQ-ALGYAQYL-PT----------------------DDYLLSKEQLFDRMVMALGGR 632 (774)
T ss_pred hccccccCcceeEEecc------CC-ccceEEEC-Cc----------------------ccccccHHHHHHHHHHHhCcc
Confidence 98888 5999999998 54 44444444 32 237889999999999999999
Q ss_pred HHHHHHhC-C-ccchhhHHHHHHHHHHH----hCCCc--------------------------hhHHHHH----HHHHHH
Q 021521 227 VAEHLVFG-H-SEGHYSDINKLDKVFQW----LGYNK--------------------------SEADSQV----KWAALN 270 (311)
Q Consensus 227 AAE~LvfG-~-atGg~~Dl~qat~lar~----lGms~--------------------------~~~d~ev----r~A~~~ 270 (311)
|||+++|| + ++|++||++|+|++++. +||++ +.+|.++ ..||..
T Consensus 633 aAEev~fg~~iTtga~ddl~kvT~~A~~~V~~~Gms~kig~~~~~~~~~~~~~~~~p~s~~~~~~Id~ev~~lv~~ay~~ 712 (774)
T KOG0731|consen 633 AAEEVVFGSEITTGAQDDLEKVTKIARAMVASFGMSEKIGPISFQMLLPGDESFRKPYSEKTAQLIDTEVRRLVQKAYER 712 (774)
T ss_pred hhhheecCCccCchhhccHHHHHHHHHHHHHHcCcccccCceeccCcccccccccCccchhHHHHHHHHHHHHHhhHHHH
Confidence 99999998 4 58999999999999875 78873 2355554 469999
Q ss_pred HHHHHHHcHHHHHHHHHHHHhhccH--HHHHHHHHH
Q 021521 271 TVLISHHHIQVRSRLAEAMALGRSI--GSCIHSIEN 304 (311)
Q Consensus 271 A~~LL~~hr~~le~LAeaLle~esv--~~C~~~Ie~ 304 (311)
|..+|++|++.++.+++.|+++|++ ++++.++..
T Consensus 713 ~~~ll~~n~~~l~~ia~~LLeke~l~~ee~~~ll~~ 748 (774)
T KOG0731|consen 713 TKELLRTNRDKLDKIAEVLLEKEVLTGEEIIALLGE 748 (774)
T ss_pred HHHHHHHhHHHHHHHHHHHHHhhhccHHHHHHHhcc
Confidence 9999999999999999999999965 778777654
No 8
>CHL00206 ycf2 Ycf2; Provisional
Probab=98.62 E-value=5.5e-08 Score=110.62 Aligned_cols=109 Identities=13% Similarity=-0.018 Sum_probs=74.7
Q ss_pred hhhHHhhccccCCCChhHHHHHHHHHHhHHHHHHHhC--CCCCceecC-chhhhccccccccceEEecchhhHHHHHhhh
Q 021521 117 TVESIVEDGSYVSLKEEDHFMCVQHEAGHFLTGYLLG--VLPKGYEIP-SVEALKQDDFTVGRVQFVGFDFLKEVADARK 193 (311)
Q Consensus 117 ~~~~llld~~~~~ls~eer~RIA~HEAGHaLVAyLLg--~PV~~yTI~-~~ealr~G~~~~GG~~f~~~e~~~e~~~ar~ 193 (311)
++...+.+...++.+.+++ +||+||+|||+|+.++. .||+++||. +-..++.| ...|+++..+.
T Consensus 1873 Al~Rq~~g~~~~~~~~~~~-~ia~yEiGhAvvq~~L~~~~pv~kISIy~~~~~~r~~--~~yl~~wyle~---------- 1939 (2281)
T CHL00206 1873 ALHRQTWDLRSQVRSVQDH-GILFYQIGRAVAQNVLLSNCPIDPISIYMKKKSCKEG--DSYLYKWYFEL---------- 1939 (2281)
T ss_pred HHHHHHhhhhhcccCcchh-hhhhhHHhHHHHHHhccCCCCcceEEEecCCccccCc--ccceeEeecCC----------
Confidence 4466666655665555555 48999999999999986 699999984 22333333 22355555332
Q ss_pred hcccCCCCCCCCccccCCHHHHHHHHHHHhhHHHHHHHHhCCcc---------c-hhhHHHHHHHHHH
Q 021521 194 QKKDTGQVGSWGNRGEISVKTLNNFSCVILGGLVAEHLVFGHSE---------G-HYSDINKLDKVFQ 251 (311)
Q Consensus 194 ~~~dd~~~~~~l~~~~~s~~~L~r~~~VlLAGrAAE~LvfG~at---------G-g~~Dl~qat~lar 251 (311)
...+++.++..+++++|||+|||.+.|.... | ..+|+.-+-.++.
T Consensus 1940 -------------~~~mkk~tiL~~Il~cLAGraAedlwf~~~~~~~n~It~yg~vEnD~~La~glLe 1994 (2281)
T CHL00206 1940 -------------GTSMKKLTILLYLLSCSAGSVAQDLWSLPGPDEKNGITSYGLVENDSDLVHGLLE 1994 (2281)
T ss_pred -------------cccCCHHHHHHHHHHHhhhhhhhhhccCcchhhhcCcccccchhhhhHHhHhHHH
Confidence 2467899999999999999999999996421 1 1356666655554
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=96.90 E-value=0.0014 Score=58.96 Aligned_cols=25 Identities=40% Similarity=0.700 Sum_probs=22.8
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceec
Q 021521 137 MCVQHEAGHFLTGYLLGVLPKGYEI 161 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg~PV~~yTI 161 (311)
-|..||.||+++|...|++|.+++|
T Consensus 11 ~v~iHElGH~~~Ar~~Gv~v~~f~i 35 (182)
T cd06163 11 LIFVHELGHFLVAKLFGVKVEEFSI 35 (182)
T ss_pred HHHHHHHHHHHHHHHcCCeeeEeee
Confidence 3789999999999999999998776
No 10
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=96.53 E-value=0.002 Score=64.76 Aligned_cols=26 Identities=31% Similarity=0.454 Sum_probs=24.2
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceecC
Q 021521 137 MCVQHEAGHFLTGYLLGVLPKGYEIP 162 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg~PV~~yTI~ 162 (311)
.|..||.||||+|.+.|+.|.+++|.
T Consensus 17 li~vHElGHfl~Ar~~gv~V~~FsiG 42 (449)
T PRK10779 17 LITVHEFGHFWVARRCGVRVERFSIG 42 (449)
T ss_pred HHHHHHHHHHHHHHHcCCeeeEEEee
Confidence 48899999999999999999999984
No 11
>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=95.98 E-value=0.006 Score=60.99 Aligned_cols=25 Identities=36% Similarity=0.659 Sum_probs=22.6
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceec
Q 021521 137 MCVQHEAGHFLTGYLLGVLPKGYEI 161 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg~PV~~yTI 161 (311)
-|..||.||||+|...|+.|.+++|
T Consensus 16 ~v~~HE~gH~~~a~~~g~~v~~Fsi 40 (420)
T TIGR00054 16 LIFVHELGHFLAARLCGIKVERFSI 40 (420)
T ss_pred HHHHHhHHHHHHHHHcCCEEEEEEE
Confidence 4899999999999999999887766
No 12
>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=95.74 E-value=0.0087 Score=54.46 Aligned_cols=27 Identities=22% Similarity=0.333 Sum_probs=25.4
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceecCc
Q 021521 137 MCVQHEAGHFLTGYLLGVLPKGYEIPS 163 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg~PV~~yTI~~ 163 (311)
-+..||.||+++|..+|.+++++++.|
T Consensus 40 ~v~iHElgH~~~A~~~G~~v~~i~l~p 66 (208)
T cd06161 40 SVLLHELGHALVARRYGIRVRSITLLP 66 (208)
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEe
Confidence 489999999999999999999999987
No 13
>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=95.64 E-value=0.014 Score=54.17 Aligned_cols=27 Identities=22% Similarity=0.277 Sum_probs=25.3
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceecCc
Q 021521 137 MCVQHEAGHFLTGYLLGVLPKGYEIPS 163 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg~PV~~yTI~~ 163 (311)
-+..||.||+++|..+|.+|+++++.|
T Consensus 55 ~v~iHElgH~~~A~~~G~~v~~i~l~p 81 (227)
T cd06164 55 SVLLHELGHSLVARRYGIPVRSITLFL 81 (227)
T ss_pred HHHHHHHHHHHHHHHcCCeECeEEEEe
Confidence 478999999999999999999999986
No 14
>PF13398 Peptidase_M50B: Peptidase M50B-like
Probab=95.52 E-value=0.014 Score=52.91 Aligned_cols=27 Identities=33% Similarity=0.397 Sum_probs=25.4
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceecCc
Q 021521 137 MCVQHEAGHFLTGYLLGVLPKGYEIPS 163 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg~PV~~yTI~~ 163 (311)
-+..||.||++++.++|..|+++++.|
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 489999999999999999999999986
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=94.30 E-value=0.07 Score=51.40 Aligned_cols=27 Identities=30% Similarity=0.238 Sum_probs=24.4
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceecCc
Q 021521 137 MCVQHEAGHFLTGYLLGVLPKGYEIPS 163 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg~PV~~yTI~~ 163 (311)
-+..||.||+++|...|++|+.+.+.+
T Consensus 137 svvvHElgHal~A~~~gi~V~~iGl~l 163 (277)
T cd06162 137 SGVVHEMGHGVAAVREQVRVNGFGIFF 163 (277)
T ss_pred HHHHHHHHHHHHHHHcCCeeceEEEee
Confidence 378999999999999999999988764
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=93.85 E-value=0.038 Score=48.55 Aligned_cols=25 Identities=36% Similarity=0.371 Sum_probs=18.5
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceec
Q 021521 137 MCVQHEAGHFLTGYLLGVLPKGYEI 161 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg~PV~~yTI 161 (311)
-+..||.||+++|+..|+++..+++
T Consensus 9 ~i~~HE~gH~~~a~~~G~~~~~~~~ 33 (192)
T PF02163_consen 9 SIVLHELGHALAARLYGDKVPRFEG 33 (192)
T ss_dssp HHHHHHHHHHHHHHTTT--B--EEE
T ss_pred ccccccccccccccccccccccccc
Confidence 3789999999999999998888854
No 17
>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=93.84 E-value=0.045 Score=47.85 Aligned_cols=25 Identities=32% Similarity=0.345 Sum_probs=21.3
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceec
Q 021521 137 MCVQHEAGHFLTGYLLGVLPKGYEI 161 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg~PV~~yTI 161 (311)
-+..||.||+++|...|+++.+..+
T Consensus 10 ~i~iHE~gH~~~A~~~G~~~~~~~~ 34 (180)
T cd05709 10 SVTVHELGHALVARRLGVKVARFSG 34 (180)
T ss_pred HHHHHHHHHHHHHHHcCCCchheee
Confidence 3789999999999999998765554
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=91.70 E-value=0.15 Score=46.09 Aligned_cols=27 Identities=26% Similarity=0.230 Sum_probs=24.4
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceecCc
Q 021521 137 MCVQHEAGHFLTGYLLGVLPKGYEIPS 163 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg~PV~~yTI~~ 163 (311)
-+..||.||+++|...|+++....+.|
T Consensus 43 ~l~iHElgH~~~A~~~G~~~~~~~l~P 69 (183)
T cd06160 43 ILGIHEMGHYLAARRHGVKASLPYFIP 69 (183)
T ss_pred HHHHHHHHHHHHHHHCCCCccceeeee
Confidence 578999999999999999998888776
No 19
>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=88.57 E-value=0.33 Score=43.53 Aligned_cols=26 Identities=23% Similarity=0.273 Sum_probs=21.4
Q ss_pred HHHHHHhHHHHHHHhCCCCC----ceecCc
Q 021521 138 CVQHEAGHFLTGYLLGVLPK----GYEIPS 163 (311)
Q Consensus 138 IA~HEAGHaLVAyLLg~PV~----~yTI~~ 163 (311)
+..||.||+++|+..|++.. ..|++|
T Consensus 12 i~~HE~aHa~~A~~~Gd~t~~~~Grltlnp 41 (181)
T cd06158 12 ITLHEFAHAYVAYRLGDPTARRAGRLTLNP 41 (181)
T ss_pred HHHHHHHHHHHHHHcCCcHHHHcCceecCc
Confidence 68999999999999998654 356666
No 20
>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=88.55 E-value=0.25 Score=47.11 Aligned_cols=25 Identities=24% Similarity=0.197 Sum_probs=22.1
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceec
Q 021521 137 MCVQHEAGHFLTGYLLGVLPKGYEI 161 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg~PV~~yTI 161 (311)
-+..||.||+++|...|++|+.+.+
T Consensus 120 sv~iHElgHa~~Ar~~G~~V~~iGl 144 (263)
T cd06159 120 GVVVHELSHGILARVEGIKVKSGGL 144 (263)
T ss_pred HHHHHHHHHHHHHHHcCCEECchhH
Confidence 3889999999999999999887654
No 21
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=85.54 E-value=0.6 Score=43.64 Aligned_cols=23 Identities=35% Similarity=0.417 Sum_probs=17.8
Q ss_pred HHHHHHHhHHHHHHHhCCCCCcee
Q 021521 137 MCVQHEAGHFLTGYLLGVLPKGYE 160 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg~PV~~yT 160 (311)
-|.+||.||+|+..+ ++||.|=.
T Consensus 94 ~~l~HE~GHAlI~~~-~lPv~GrE 116 (220)
T PF14247_consen 94 FTLYHELGHALIDDL-DLPVLGRE 116 (220)
T ss_pred HHHHHHHHHHHHHHh-cCCcccch
Confidence 489999999999864 57776543
No 22
>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=83.83 E-value=0.5 Score=39.58 Aligned_cols=17 Identities=35% Similarity=0.399 Sum_probs=14.4
Q ss_pred ChhHHHHHHHHHHhHHH
Q 021521 131 KEEDHFMCVQHEAGHFL 147 (311)
Q Consensus 131 s~eer~RIA~HEAGHaL 147 (311)
+..+...|+.||.||+|
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 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=79.95 E-value=1.2 Score=38.17 Aligned_cols=17 Identities=35% Similarity=0.386 Sum_probs=14.3
Q ss_pred hhHHHHHHHHHHhHHHH
Q 021521 132 EEDHFMCVQHEAGHFLT 148 (311)
Q Consensus 132 ~eer~RIA~HEAGHaLV 148 (311)
..+.+.|+.||.||+|=
T Consensus 101 ~~~~~~~~~HEiGHaLG 117 (156)
T cd04279 101 AENLQAIALHELGHALG 117 (156)
T ss_pred chHHHHHHHHHhhhhhc
Confidence 46788999999999874
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=76.90 E-value=1.5 Score=37.14 Aligned_cols=16 Identities=31% Similarity=0.327 Sum_probs=13.8
Q ss_pred hhHHHHHHHHHHhHHH
Q 021521 132 EEDHFMCVQHEAGHFL 147 (311)
Q Consensus 132 ~eer~RIA~HEAGHaL 147 (311)
..+...++.||.||+|
T Consensus 91 ~~~~~~~~~HEiGHaL 106 (165)
T cd04268 91 GARLRNTAEHELGHAL 106 (165)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 3578899999999996
No 25
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=74.54 E-value=2.1 Score=43.75 Aligned_cols=25 Identities=40% Similarity=0.496 Sum_probs=22.4
Q ss_pred HHHHHHhHHHHHHHhCCCCCceecC
Q 021521 138 CVQHEAGHFLTGYLLGVLPKGYEIP 162 (311)
Q Consensus 138 IA~HEAGHaLVAyLLg~PV~~yTI~ 162 (311)
+..||.||+|.|-.-|+||.++-|-
T Consensus 134 ~vvHElGHalAA~segV~vngfgIf 158 (484)
T KOG2921|consen 134 VVVHELGHALAAASEGVQVNGFGIF 158 (484)
T ss_pred HHHHHhhHHHHHHhcCceeeeeEEE
Confidence 5789999999999999999988773
No 26
>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=72.74 E-value=18 Score=30.91 Aligned_cols=68 Identities=15% Similarity=0.145 Sum_probs=47.2
Q ss_pred hhHHHHHHHH--HHHhCCCchhHHHHHH-----HHHHHHHHHHHHcHHHHHHHHHHHHhh-ccHHHHHHHHHHhhc
Q 021521 240 YSDINKLDKV--FQWLGYNKSEADSQVK-----WAALNTVLISHHHIQVRSRLAEAMALG-RSIGSCIHSIENALS 307 (311)
Q Consensus 240 ~~Dl~qat~l--ar~lGms~~~~d~evr-----~A~~~A~~LL~~hr~~le~LAeaLle~-esv~~C~~~Ie~~~~ 307 (311)
.+|+..+..| ++.+|||-+++..-+. +.......+|+++...++...+.|.+- ..|.+++..+++..+
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 3577776665 4678999877765443 233566778888888888877777774 678888877776543
No 27
>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=71.90 E-value=1.8 Score=37.10 Aligned_cols=17 Identities=41% Similarity=0.577 Sum_probs=14.1
Q ss_pred ChhHHHHHHHHHHhHHH
Q 021521 131 KEEDHFMCVQHEAGHFL 147 (311)
Q Consensus 131 s~eer~RIA~HEAGHaL 147 (311)
+..+...|+.||.||+|
T Consensus 103 ~~~~~~~~~~HEiGHaL 119 (157)
T cd04278 103 GGTDLFSVAAHEIGHAL 119 (157)
T ss_pred ccchHHHHHHHHhcccc
Confidence 34678899999999984
No 28
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=70.12 E-value=2.9 Score=40.28 Aligned_cols=26 Identities=31% Similarity=0.484 Sum_probs=23.2
Q ss_pred HHHHHHHhHHHHHHHhCCCCCceecC
Q 021521 137 MCVQHEAGHFLTGYLLGVLPKGYEIP 162 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg~PV~~yTI~ 162 (311)
.|..||-||+|+++..+..|..+.+.
T Consensus 15 lv~~he~gh~~~a~~~~~~v~~f~ig 40 (375)
T COG0750 15 LVFVHELGHFWVARRCGVKVERFSIG 40 (375)
T ss_pred HHHHHHHhhHHHHHhcCceeEEEEec
Confidence 58899999999999999888888774
No 29
>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=69.20 E-value=3.1 Score=36.53 Aligned_cols=16 Identities=31% Similarity=0.482 Sum_probs=13.8
Q ss_pred hhHHHHHHHHHHhHHH
Q 021521 132 EEDHFMCVQHEAGHFL 147 (311)
Q Consensus 132 ~eer~RIA~HEAGHaL 147 (311)
..+...++.||.||+|
T Consensus 110 g~~~~~t~~HEiGHaL 125 (186)
T cd04277 110 GSYGYQTIIHEIGHAL 125 (186)
T ss_pred ChhhHHHHHHHHHHHh
Confidence 4677899999999987
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=68.94 E-value=3.5 Score=35.98 Aligned_cols=27 Identities=26% Similarity=0.196 Sum_probs=17.1
Q ss_pred hHHhhccccCCCChhHHHHHHHHHHhHHH
Q 021521 119 ESIVEDGSYVSLKEEDHFMCVQHEAGHFL 147 (311)
Q Consensus 119 ~~llld~~~~~ls~eer~RIA~HEAGHaL 147 (311)
+.|.+|.-. .-.-+.-||+-||.||.|
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 667777321 122345599999999975
No 31
>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=67.11 E-value=6.3 Score=30.61 Aligned_cols=23 Identities=30% Similarity=0.296 Sum_probs=18.6
Q ss_pred CChhHHHHHHHHHHhHHHHHHHh
Q 021521 130 LKEEDHFMCVQHEAGHFLTGYLL 152 (311)
Q Consensus 130 ls~eer~RIA~HEAGHaLVAyLL 152 (311)
.++..++-++.||.||.+...--
T Consensus 37 ~~~~~~~f~laHELgH~~~~~~~ 59 (122)
T PF06114_consen 37 LSPERQRFTLAHELGHILLHHGD 59 (122)
T ss_dssp S-HHHHHHHHHHHHHHHHHHH-H
T ss_pred CCHHHHHHHHHHHHHHHHhhhcc
Confidence 48888999999999999987765
No 32
>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=67.04 E-value=2.9 Score=39.32 Aligned_cols=13 Identities=31% Similarity=0.529 Sum_probs=11.0
Q ss_pred HHHHHHHhHHHHH
Q 021521 137 MCVQHEAGHFLTG 149 (311)
Q Consensus 137 RIA~HEAGHaLVA 149 (311)
-||-||+||++=.
T Consensus 91 aVAAHEvGHAiQ~ 103 (222)
T PF04298_consen 91 AVAAHEVGHAIQH 103 (222)
T ss_pred HHHHHHHhHHHhc
Confidence 5899999999754
No 33
>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=65.45 E-value=35 Score=28.06 Aligned_cols=66 Identities=11% Similarity=0.011 Sum_probs=46.6
Q ss_pred hhHHHHHHHH--HHHhCCCchhHHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHhh-ccHHHHHHHHHHh
Q 021521 240 YSDINKLDKV--FQWLGYNKSEADSQVKW-------AALNTVLISHHHIQVRSRLAEAMALG-RSIGSCIHSIENA 305 (311)
Q Consensus 240 ~~Dl~qat~l--ar~lGms~~~~d~evr~-------A~~~A~~LL~~hr~~le~LAeaLle~-esv~~C~~~Ie~~ 305 (311)
.+|+..+..| ++.+|||-+++..-.+. .......+|.++...++.--+.|... ..+..++..++++
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 4677777775 47799999888765432 23456778888888877766666664 6778887777654
No 34
>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=63.46 E-value=3.7 Score=35.99 Aligned_cols=18 Identities=28% Similarity=0.458 Sum_probs=13.8
Q ss_pred ChhHHHHHHHHHHhHHHH
Q 021521 131 KEEDHFMCVQHEAGHFLT 148 (311)
Q Consensus 131 s~eer~RIA~HEAGHaLV 148 (311)
++....+++.||.||+|=
T Consensus 65 ~~~~~g~TltHEvGH~LG 82 (154)
T PF05572_consen 65 SQYNFGKTLTHEVGHWLG 82 (154)
T ss_dssp TTS-SSHHHHHHHHHHTT
T ss_pred Cccccccchhhhhhhhhc
Confidence 455667999999999973
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=61.55 E-value=5.4 Score=35.76 Aligned_cols=25 Identities=24% Similarity=0.068 Sum_probs=17.0
Q ss_pred HHHHHHHHHHhHHHHHHHhCC-CCCc
Q 021521 134 DHFMCVQHEAGHFLTGYLLGV-LPKG 158 (311)
Q Consensus 134 er~RIA~HEAGHaLVAyLLg~-PV~~ 158 (311)
+...++.||.||+|=-+-... |-+.
T Consensus 91 ~~~~~i~HElgHaLG~~HEh~rpdrd 116 (198)
T cd04327 91 EFSRVVLHEFGHALGFIHEHQSPAAN 116 (198)
T ss_pred hHHHHHHHHHHHHhcCcccccCCCCC
Confidence 456799999999985544432 4444
No 36
>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=61.27 E-value=42 Score=27.60 Aligned_cols=64 Identities=11% Similarity=0.135 Sum_probs=43.6
Q ss_pred HHHHHHHHHHhCCCchhHHHHH----HHHHHHHHHHHHHcH------HHHHHHHHHHHhhccHHHHHHHHHHhhc
Q 021521 243 INKLDKVFQWLGYNKSEADSQV----KWAALNTVLISHHHI------QVRSRLAEAMALGRSIGSCIHSIENALS 307 (311)
Q Consensus 243 l~qat~lar~lGms~~~~d~ev----r~A~~~A~~LL~~hr------~~le~LAeaLle~esv~~C~~~Ie~~~~ 307 (311)
+.+..+++|.+|+|+.+||+-. +-..++..++|+..+ .++..|.++|.. --+..|-..|++.+.
T Consensus 20 ~~~wK~faR~lglse~~Id~I~~~~~~d~~Eq~~qmL~~W~~~~G~~a~~~~Li~aLr~-~~l~~~Ad~I~~~l~ 93 (97)
T cd08316 20 LKDVKKFVRKSGLSEPKIDEIKLDNPQDTAEQKVQLLRAWYQSHGKTGAYRTLIKTLRK-AKLCTKADKIQDIIE 93 (97)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHcCCCChHHHHHHHHHHHHHHhCCCchHHHHHHHHHH-ccchhHHHHHHHHHH
Confidence 3567788999999998887542 345677777777544 457788877765 445556666666553
No 37
>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=58.90 E-value=5 Score=33.43 Aligned_cols=11 Identities=45% Similarity=0.579 Sum_probs=10.0
Q ss_pred HHHHHHHhHHH
Q 021521 137 MCVQHEAGHFL 147 (311)
Q Consensus 137 RIA~HEAGHaL 147 (311)
.|+.||.||+|
T Consensus 88 ~~~~HEigHaL 98 (140)
T smart00235 88 GVAAHELGHAL 98 (140)
T ss_pred ccHHHHHHHHh
Confidence 39999999997
No 38
>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=54.84 E-value=30 Score=23.61 Aligned_cols=33 Identities=21% Similarity=0.232 Sum_probs=26.4
Q ss_pred hhHHHHHHHHHHHHHHHHcCCchHHHHHHHHHh
Q 021521 21 AEYAKRRRQALKRVDRELSRGNFKVALSLVKQL 53 (311)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~ 53 (311)
+....++.+.++++|..|.+||.+.=..|.++|
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 445678899999999999999999888777654
No 39
>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=52.90 E-value=73 Score=25.22 Aligned_cols=48 Identities=13% Similarity=0.026 Sum_probs=33.0
Q ss_pred HHHHHHHhCCCchhHHHHH----HHHHHHHHHHHHH------cHHHHHHHHHHHHhhc
Q 021521 246 LDKVFQWLGYNKSEADSQV----KWAALNTVLISHH------HIQVRSRLAEAMALGR 293 (311)
Q Consensus 246 at~lar~lGms~~~~d~ev----r~A~~~A~~LL~~------hr~~le~LAeaLle~e 293 (311)
-.++++.+|||+.+|+.-. +-...++.++|+. ...+++.|.++|.+-.
T Consensus 16 Wk~laR~LGlse~~Id~i~~~~~~~~~eq~~~mL~~W~~~~g~~At~~~L~~aL~~~~ 73 (86)
T cd08306 16 WRKLARKLGLSETKIESIEEAHPRNLREQVRQSLREWKKIKKKEAKVADLIKALRDCQ 73 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHhHCcchHHHHHHHHHHHcC
Confidence 4557888999998887532 2345777777763 3456778888887743
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=50.15 E-value=8.7 Score=32.39 Aligned_cols=16 Identities=31% Similarity=0.484 Sum_probs=13.1
Q ss_pred hHHHHHHHHHHhHHHH
Q 021521 133 EDHFMCVQHEAGHFLT 148 (311)
Q Consensus 133 eer~RIA~HEAGHaLV 148 (311)
..-..++.||.||+|=
T Consensus 94 ~~~~~~~~HElGH~LG 109 (167)
T cd00203 94 KEGAQTIAHELGHALG 109 (167)
T ss_pred ccchhhHHHHHHHHhC
Confidence 3567899999999974
No 41
>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=50.12 E-value=73 Score=23.02 Aligned_cols=42 Identities=7% Similarity=0.102 Sum_probs=28.8
Q ss_pred HHHhCCCchhHHHHH------HHHHHHHHHHHHHcHHHHHHHHHHHHh
Q 021521 250 FQWLGYNKSEADSQV------KWAALNTVLISHHHIQVRSRLAEAMAL 291 (311)
Q Consensus 250 ar~lGms~~~~d~ev------r~A~~~A~~LL~~hr~~le~LAeaLle 291 (311)
++.+|||-+++..-+ .........++.++.+.+++--+.|..
T Consensus 10 ~r~lGfsL~eI~~~l~l~~~~~~~~~~~~~~l~~~~~~i~~~i~~L~~ 57 (65)
T PF09278_consen 10 LRELGFSLEEIRELLELYDQGDPPCADRRALLEEKLEEIEEQIAELQA 57 (65)
T ss_dssp HHHTT--HHHHHHHHHHCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHcCCCHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 577999998887765 345666778888888887776666554
No 42
>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=48.05 E-value=57 Score=24.83 Aligned_cols=48 Identities=19% Similarity=0.111 Sum_probs=33.4
Q ss_pred HHHHHHHHHhCCCchhHHHHHHH----HHHHHHHHHHHcHH------HHHHHHHHHHh
Q 021521 244 NKLDKVFQWLGYNKSEADSQVKW----AALNTVLISHHHIQ------VRSRLAEAMAL 291 (311)
Q Consensus 244 ~qat~lar~lGms~~~~d~evr~----A~~~A~~LL~~hr~------~le~LAeaLle 291 (311)
.+-..+++.+||+..+++.-... ...++..+|+.-+. .++.|.++|.+
T Consensus 18 ~~W~~la~~Lg~~~~~i~~i~~~~~~~~~~~~~~lL~~W~~~~g~~at~~~L~~aL~~ 75 (88)
T smart00005 18 LDWRELARKLGLSEADIDQIRTEAPRDLAEQSVQLLRLWEQREGKNATLGTLLEALRK 75 (88)
T ss_pred hHHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHccchhhHHHHHHHHHHH
Confidence 34556788999998877654332 44788888876544 66777777766
No 43
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=45.07 E-value=25 Score=27.44 Aligned_cols=23 Identities=26% Similarity=0.267 Sum_probs=19.0
Q ss_pred ChhHHHHHHHHHHhHHHHHHHhC
Q 021521 131 KEEDHFMCVQHEAGHFLTGYLLG 153 (311)
Q Consensus 131 s~eer~RIA~HEAGHaLVAyLLg 153 (311)
++..-.+++.||-.|.+.....+
T Consensus 21 ~~~~~~~~l~HE~~H~~~~~~~~ 43 (128)
T PF13485_consen 21 DEDWLDRVLAHELAHQWFGNYFG 43 (128)
T ss_pred CHHHHHHHHHHHHHHHHHHHHcC
Confidence 44555699999999999998875
No 44
>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=44.87 E-value=11 Score=35.05 Aligned_cols=18 Identities=33% Similarity=0.508 Sum_probs=16.0
Q ss_pred hhHHHHHHHHHHhHHHHHH
Q 021521 132 EEDHFMCVQHEAGHFLTGY 150 (311)
Q Consensus 132 ~eer~RIA~HEAGHaLVAy 150 (311)
..||+-++-||.||+| +|
T Consensus 136 ~~YRqYvINHEVGH~L-Gh 153 (203)
T PF11350_consen 136 ASYRQYVINHEVGHAL-GH 153 (203)
T ss_pred HHHHHHhhhhhhhhhc-cc
Confidence 3899999999999999 55
No 45
>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=44.53 E-value=76 Score=25.28 Aligned_cols=50 Identities=10% Similarity=0.144 Sum_probs=34.0
Q ss_pred hHHHHHHHH--HHHhCCCchhHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHH
Q 021521 241 SDINKLDKV--FQWLGYNKSEADSQVKWAALNTVLISHHHIQVRSRLAEAMA 290 (311)
Q Consensus 241 ~Dl~qat~l--ar~lGms~~~~d~evr~A~~~A~~LL~~hr~~le~LAeaLl 290 (311)
+|+..+..+ ++.+|||-+++..-+...-.....+|.+++..++.=.+.|.
T Consensus 42 ~~l~~l~~I~~lr~~G~~l~~I~~~l~~~~~~~~~~l~~~~~~l~~~i~~l~ 93 (96)
T cd04768 42 AQLYQLQFILFLRELGFSLAEIKELLDTEMEELTAMLLEKKQAIQQKIDRLQ 93 (96)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHHHHH
Confidence 466666554 57799998888766554334677788888877776665554
No 46
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=44.40 E-value=11 Score=30.38 Aligned_cols=11 Identities=45% Similarity=0.567 Sum_probs=10.0
Q ss_pred HHHHHHHhHHH
Q 021521 137 MCVQHEAGHFL 147 (311)
Q Consensus 137 RIA~HEAGHaL 147 (311)
.+..||.||.|
T Consensus 109 ~~~~HEiGH~l 119 (124)
T PF13582_consen 109 DTFAHEIGHNL 119 (124)
T ss_dssp THHHHHHHHHT
T ss_pred eEeeehhhHhc
Confidence 79999999976
No 47
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=43.28 E-value=19 Score=33.44 Aligned_cols=24 Identities=25% Similarity=0.360 Sum_probs=20.8
Q ss_pred CCChhHHHHHHHHHHhHHHHHHHh
Q 021521 129 SLKEEDHFMCVQHEAGHFLTGYLL 152 (311)
Q Consensus 129 ~ls~eer~RIA~HEAGHaLVAyLL 152 (311)
.++++|-+-|.-||.||..-.+.+
T Consensus 151 ~l~~dEl~aVlaHElgHi~~rd~~ 174 (302)
T COG0501 151 LLNDDELEAVLAHELGHIKNRHTL 174 (302)
T ss_pred hCCHHHHHHHHHHHHHHHhcccHH
Confidence 568999999999999999876665
No 48
>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=39.42 E-value=90 Score=24.86 Aligned_cols=50 Identities=14% Similarity=0.277 Sum_probs=31.6
Q ss_pred hhHHHHHHHH--HHHhCCCchhHHHHHHHHHHHHHHHHHHcHHHHHHHHHHH
Q 021521 240 YSDINKLDKV--FQWLGYNKSEADSQVKWAALNTVLISHHHIQVRSRLAEAM 289 (311)
Q Consensus 240 ~~Dl~qat~l--ar~lGms~~~~d~evr~A~~~A~~LL~~hr~~le~LAeaL 289 (311)
.+|+..+..+ ++.+|||-+++..-+.........+|.++.+.++.=-+.|
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 3577776665 5679999888876654332355667777766666544443
No 49
>COG0339 Dcp Zn-dependent oligopeptidases [Amino acid transport and metabolism]
Probab=39.17 E-value=24 Score=38.26 Aligned_cols=30 Identities=27% Similarity=0.201 Sum_probs=22.3
Q ss_pred HHHHHHHhHHHHHHHhCC---CCCceecCchhhh
Q 021521 137 MCVQHEAGHFLTGYLLGV---LPKGYEIPSVEAL 167 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg~---PV~~yTI~~~eal 167 (311)
.+.+||-||+|=+.|..+ -|.|.. .||+++
T Consensus 469 ~TLFHEfGHgLH~mlt~v~~~~vsGt~-v~wDfV 501 (683)
T COG0339 469 TTLFHEFGHGLHHLLTRVKYPGVSGTN-VPWDFV 501 (683)
T ss_pred HHHHHHhhhHHHHHhhcCCccccCCCC-CCcchh
Confidence 689999999998877765 455555 566654
No 50
>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=38.81 E-value=1.9e+02 Score=23.45 Aligned_cols=51 Identities=8% Similarity=0.100 Sum_probs=32.1
Q ss_pred hHHHHHHHH--HHHhCCCchhHHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHHh
Q 021521 241 SDINKLDKV--FQWLGYNKSEADSQVKW------AALNTVLISHHHIQVRSRLAEAMAL 291 (311)
Q Consensus 241 ~Dl~qat~l--ar~lGms~~~~d~evr~------A~~~A~~LL~~hr~~le~LAeaLle 291 (311)
.|+..+..| ++.+|||-+++..-+.. .......+|.++...++.-.+.|..
T Consensus 42 ~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (113)
T cd01109 42 EDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPERLELLEEHREELEEQIAELQE 100 (113)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHccCCccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 577776655 46789998887654432 1234566777777776666555544
No 51
>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=38.72 E-value=25 Score=30.88 Aligned_cols=24 Identities=29% Similarity=0.444 Sum_probs=20.1
Q ss_pred CChhHHHHHHHHHHhHHHHHHHhC
Q 021521 130 LKEEDHFMCVQHEAGHFLTGYLLG 153 (311)
Q Consensus 130 ls~eer~RIA~HEAGHaLVAyLLg 153 (311)
+++++..-|+-||.||..-.+...
T Consensus 84 ~~~~el~aVlaHElgH~~~~h~~~ 107 (226)
T PF01435_consen 84 LSEDELAAVLAHELGHIKHRHILK 107 (226)
T ss_dssp SSHHHHHHHHHHHHHHHHTTHCCC
T ss_pred ccHHHHHHHHHHHHHHHHcCCcch
Confidence 488999999999999998666553
No 52
>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=37.93 E-value=1.8e+02 Score=23.69 Aligned_cols=52 Identities=13% Similarity=0.082 Sum_probs=34.0
Q ss_pred hHHHHHHHH--HHHhCCCchhHHHHHHH-----HHHHHHHHHHHcHHHHHHHHHHHHhh
Q 021521 241 SDINKLDKV--FQWLGYNKSEADSQVKW-----AALNTVLISHHHIQVRSRLAEAMALG 292 (311)
Q Consensus 241 ~Dl~qat~l--ar~lGms~~~~d~evr~-----A~~~A~~LL~~hr~~le~LAeaLle~ 292 (311)
+|+..+..+ ++.+|||.+++.+-+.. .......+|+++...++.=..+|..+
T Consensus 42 ~dl~~l~~I~~lr~~G~~l~~I~~~l~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~ 100 (108)
T cd04773 42 SDVRDARLIHLLRRGGYLLEQIATVVEQLRHAGGTEALAAALEQRRVALTQRGRAMLDA 100 (108)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 577776665 46689988777655432 12456677887777777666666554
No 53
>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=37.45 E-value=1.7e+02 Score=24.30 Aligned_cols=51 Identities=10% Similarity=0.145 Sum_probs=29.5
Q ss_pred hHHHHHHHH--HHHhCCCchhHHHHHHHH----HHHHHHHHHHcHHHHHHHHHHHHh
Q 021521 241 SDINKLDKV--FQWLGYNKSEADSQVKWA----ALNTVLISHHHIQVRSRLAEAMAL 291 (311)
Q Consensus 241 ~Dl~qat~l--ar~lGms~~~~d~evr~A----~~~A~~LL~~hr~~le~LAeaLle 291 (311)
+|+..+..| ++.+|||-+++..-+... ......+|.++...++.=.+.|..
T Consensus 42 ~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 98 (126)
T cd04783 42 ETVTRLRFIKRAQELGFTLDEIAELLELDDGTDCSEARELAEQKLAEVDEKIADLQR 98 (126)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466665554 577899987776654321 234566666666555544444433
No 54
>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=36.33 E-value=1.4e+02 Score=23.71 Aligned_cols=47 Identities=17% Similarity=0.136 Sum_probs=30.3
Q ss_pred HHHHHHHhCCCchhHHHHHHH-----HHHHHHHHHHHcH-------HHHHHHHHHHHhh
Q 021521 246 LDKVFQWLGYNKSEADSQVKW-----AALNTVLISHHHI-------QVRSRLAEAMALG 292 (311)
Q Consensus 246 at~lar~lGms~~~~d~evr~-----A~~~A~~LL~~hr-------~~le~LAeaLle~ 292 (311)
-.++++.+|||..+|+.-... -..++.++|..-+ ..+..|.++|..-
T Consensus 16 Wk~lar~LG~s~~eI~~ie~~~~r~~~~eq~~~mL~~W~~r~g~~~ATv~~L~~aL~~~ 74 (86)
T cd08777 16 WKRCARKLGFTESEIEEIDHDYERDGLKEKVHQMLHKWKMKEGSKGATVGKLAQALEGC 74 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHHhcccCCHHHHHHHHHHHHHHccCCCCcHHHHHHHHHHHc
Confidence 345778899999888764322 2567777776443 4556666666553
No 55
>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=36.17 E-value=1.9e+02 Score=25.05 Aligned_cols=60 Identities=10% Similarity=0.127 Sum_probs=34.4
Q ss_pred hhHHHHHHHH--HHHhCCCchhHHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHh-hccHHHHH
Q 021521 240 YSDINKLDKV--FQWLGYNKSEADSQVKW-------AALNTVLISHHHIQVRSRLAEAMAL-GRSIGSCI 299 (311)
Q Consensus 240 ~~Dl~qat~l--ar~lGms~~~~d~evr~-------A~~~A~~LL~~hr~~le~LAeaLle-~esv~~C~ 299 (311)
.+|+..+..| ++.+|||-+++..-+.. .......++.++...++.-.+.|.. ...|.+|+
T Consensus 41 ~~di~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~ki~~L~~~~~~L~~~~ 110 (142)
T TIGR01950 41 RDVLRRVAVIKAAQRVGIPLATIGEALAVLPEGRTPTADDWARLSSQWREELDERIDQLNALRDQLDGCI 110 (142)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3577777665 46789998877665432 1234455666666655544444443 34455444
No 56
>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=36.08 E-value=1.7e+02 Score=23.52 Aligned_cols=51 Identities=10% Similarity=0.066 Sum_probs=34.4
Q ss_pred hHHHHHHHH--HHHhCCCchhHHHHHHHH----------HHHHHHHHHHcHHHHHHHHHHHHh
Q 021521 241 SDINKLDKV--FQWLGYNKSEADSQVKWA----------ALNTVLISHHHIQVRSRLAEAMAL 291 (311)
Q Consensus 241 ~Dl~qat~l--ar~lGms~~~~d~evr~A----------~~~A~~LL~~hr~~le~LAeaLle 291 (311)
+|+..+..| ++.+|||-+++..-+... ......+|.++...++.-.+.|.+
T Consensus 40 ~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 102 (107)
T cd04777 40 KCQDDLEFILELKGLGFSLIEIQKIFSYKRLTKSRTHEDQDYYKSFLKNKKDELEKEIEDLKK 102 (107)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHhcccccccchhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 577777665 577999998877654321 233578888888887776665544
No 57
>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=35.33 E-value=21 Score=34.39 Aligned_cols=18 Identities=28% Similarity=0.274 Sum_probs=15.4
Q ss_pred HHHHHHHhHHHHHHHhCC
Q 021521 137 MCVQHEAGHFLTGYLLGV 154 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg~ 154 (311)
.+..||.||++=..+...
T Consensus 156 ~tl~HE~GHa~h~~l~~~ 173 (365)
T cd06258 156 NTLFHEFGHAVHFLLIQQ 173 (365)
T ss_pred HHHHHHHhHHHHHHHhcC
Confidence 789999999998887763
No 58
>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=35.30 E-value=7 Score=38.33 Aligned_cols=29 Identities=21% Similarity=0.285 Sum_probs=18.3
Q ss_pred chhhHHhhccccCCCChhHHHHHHHHHHhHHHHH
Q 021521 116 DTVESIVEDGSYVSLKEEDHFMCVQHEAGHFLTG 149 (311)
Q Consensus 116 D~~~~llld~~~~~ls~eer~RIA~HEAGHaLVA 149 (311)
|++-|+..+.+. .+..--=|||.|||||-
T Consensus 80 e~V~Tl~F~~l~-----~~~~lY~Y~~iGHFWVk 108 (299)
T PF12994_consen 80 ENVFTLFFEDLE-----EETHLYNYGEIGHFWVK 108 (299)
T ss_pred CceEEEehHhHH-----HHHHHhhccccceeeec
Confidence 444445444332 44556679999999984
No 59
>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=35.23 E-value=1.6e+02 Score=25.21 Aligned_cols=59 Identities=12% Similarity=0.127 Sum_probs=30.8
Q ss_pred hHHHHHHHH--HHHhCCCchhHHHHHHHH-------HHHHHHHHHHcHHHHHHHHHHHHh-hccHHHHH
Q 021521 241 SDINKLDKV--FQWLGYNKSEADSQVKWA-------ALNTVLISHHHIQVRSRLAEAMAL-GRSIGSCI 299 (311)
Q Consensus 241 ~Dl~qat~l--ar~lGms~~~~d~evr~A-------~~~A~~LL~~hr~~le~LAeaLle-~esv~~C~ 299 (311)
+|+..+..| ++.+|||.+++.+-+... ......++.++...++.-.+.|.. ...|.+|+
T Consensus 42 ~dl~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~i 110 (139)
T cd01110 42 DVLRRIAFIKVAQRLGLSLAEIAEALATLPEDRTPTKADWERLSRAWRDRLDERIAELQQLRDQLDGCI 110 (139)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566666655 356788877766544321 122334555555544444444443 33445544
No 60
>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=34.62 E-value=1.7e+02 Score=24.40 Aligned_cols=51 Identities=8% Similarity=0.165 Sum_probs=27.1
Q ss_pred hHHHHHHHH--HHHhCCCchhHHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHHh
Q 021521 241 SDINKLDKV--FQWLGYNKSEADSQVKW------AALNTVLISHHHIQVRSRLAEAMAL 291 (311)
Q Consensus 241 ~Dl~qat~l--ar~lGms~~~~d~evr~------A~~~A~~LL~~hr~~le~LAeaLle 291 (311)
+|+..+..| ++.+|||-+++.+-+.. .......+|.++...+++-.+.|..
T Consensus 42 ~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (127)
T TIGR02044 42 QHLDELRLISRARQVGFSLEECKELLNLWNDPNRTSADVKARTLEKVAEIERKISELQS 100 (127)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566666554 46688887776654331 1233445555555555544444433
No 61
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=34.28 E-value=32 Score=32.09 Aligned_cols=23 Identities=30% Similarity=0.231 Sum_probs=17.7
Q ss_pred CChhHHHHHHHHHHhHHHHHHHh
Q 021521 130 LKEEDHFMCVQHEAGHFLTGYLL 152 (311)
Q Consensus 130 ls~eer~RIA~HEAGHaLVAyLL 152 (311)
.+++.++=++-||-||+|..--.
T Consensus 67 ~~~~r~rFtlAHELGH~llH~~~ 89 (213)
T COG2856 67 NSLERKRFTLAHELGHALLHTDL 89 (213)
T ss_pred CCHHHHHHHHHHHHhHHHhcccc
Confidence 36677777899999999976443
No 62
>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=34.17 E-value=1.6e+02 Score=23.49 Aligned_cols=51 Identities=12% Similarity=0.130 Sum_probs=33.9
Q ss_pred hHHHHHHHH--HHHhCCCchhHHHHHH-HHHHHHHHHHHHcHHHHHHHHHHHHh
Q 021521 241 SDINKLDKV--FQWLGYNKSEADSQVK-WAALNTVLISHHHIQVRSRLAEAMAL 291 (311)
Q Consensus 241 ~Dl~qat~l--ar~lGms~~~~d~evr-~A~~~A~~LL~~hr~~le~LAeaLle 291 (311)
+|+..+..+ ++.+|||-+++..-+. ....+...+|.++.+.+++=.+.|..
T Consensus 42 ~~~~~l~~I~~lr~~G~~l~eI~~~l~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 95 (97)
T cd04782 42 EQFEQLDIILLLKELGISLKEIKDYLDNRNPDELIELLKKQEKEIKEEIEELQK 95 (97)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 466665554 5779999888776543 23455677888888777766665543
No 63
>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=34.13 E-value=1.9e+02 Score=23.97 Aligned_cols=51 Identities=8% Similarity=0.086 Sum_probs=30.3
Q ss_pred hhHHHHHHHH--HHHhCCCchhHHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHH
Q 021521 240 YSDINKLDKV--FQWLGYNKSEADSQVKW------AALNTVLISHHHIQVRSRLAEAMA 290 (311)
Q Consensus 240 ~~Dl~qat~l--ar~lGms~~~~d~evr~------A~~~A~~LL~~hr~~le~LAeaLl 290 (311)
.+|+..+..| ++.+|||-+++..-+.. .......+|.++...+++--+.|.
T Consensus 41 ~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~ 99 (127)
T cd04784 41 EEHLERLLFIRRCRSLDMSLDEIRTLLQLQDDPEASCAEVNALIDEHLAHVRARIAELQ 99 (127)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3567666654 46788888777655432 124456666666666664444443
No 64
>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=33.15 E-value=28 Score=32.65 Aligned_cols=20 Identities=20% Similarity=0.122 Sum_probs=16.0
Q ss_pred ChhHHHHHHHHHHhHHHHHH
Q 021521 131 KEEDHFMCVQHEAGHFLTGY 150 (311)
Q Consensus 131 s~eer~RIA~HEAGHaLVAy 150 (311)
+....+.|+.||.||.+==.
T Consensus 129 ~~~~~~hvi~HEiGH~IGfR 148 (211)
T PF12388_consen 129 SVNVIEHVITHEIGHCIGFR 148 (211)
T ss_pred chhHHHHHHHHHhhhhcccc
Confidence 66778889999999987433
No 65
>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=33.12 E-value=2.8e+02 Score=22.97 Aligned_cols=63 Identities=8% Similarity=0.044 Sum_probs=35.3
Q ss_pred hhHHHHHHHH--HHHhCCCchhHHHHHHH---------HHHHHHHHHHHcHHHHHHHHHHHHhh-ccHHHHHHHH
Q 021521 240 YSDINKLDKV--FQWLGYNKSEADSQVKW---------AALNTVLISHHHIQVRSRLAEAMALG-RSIGSCIHSI 302 (311)
Q Consensus 240 ~~Dl~qat~l--ar~lGms~~~~d~evr~---------A~~~A~~LL~~hr~~le~LAeaLle~-esv~~C~~~I 302 (311)
.+|+..+..| ++.+|||-+++..-++. .......+|.++...++.--+.|.+. +.+.+.+.-.
T Consensus 39 ~~~l~~l~~I~~lr~~G~~L~~I~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~L~~~~~~~ 113 (118)
T cd04776 39 RRDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQLEKMLEKIEKRRAELEQQRRDIDAALAELDAAEERC 113 (118)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHhhccCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3567776654 56789987776554321 22345567777777666555544432 3444444333
No 66
>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=32.89 E-value=1.5e+02 Score=23.71 Aligned_cols=49 Identities=14% Similarity=0.255 Sum_probs=30.0
Q ss_pred hHHHHHHHH--HHHhCCCchhHHHHHHHHHHHHHHHHHHcHHHHHHHHHHH
Q 021521 241 SDINKLDKV--FQWLGYNKSEADSQVKWAALNTVLISHHHIQVRSRLAEAM 289 (311)
Q Consensus 241 ~Dl~qat~l--ar~lGms~~~~d~evr~A~~~A~~LL~~hr~~le~LAeaL 289 (311)
+|+..+..+ ++..|||.+++..-++........+|.+++..++.=-+.|
T Consensus 42 ~di~~l~~i~~lr~~g~~l~~i~~~~~~~~~~~~~~l~~~~~~l~~~i~~l 92 (103)
T cd01106 42 EDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALREQKELLEEKKERL 92 (103)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHH
Confidence 567766655 4668999888776544322556666666666655443333
No 67
>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=29.99 E-value=3.3e+02 Score=22.71 Aligned_cols=50 Identities=20% Similarity=0.261 Sum_probs=28.0
Q ss_pred hHHHHHHHH--HHHhCCCchhHHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHH
Q 021521 241 SDINKLDKV--FQWLGYNKSEADSQVKW------AALNTVLISHHHIQVRSRLAEAMA 290 (311)
Q Consensus 241 ~Dl~qat~l--ar~lGms~~~~d~evr~------A~~~A~~LL~~hr~~le~LAeaLl 290 (311)
+|+..+..| ++.+|||-+++.+-+.. .......+|+++...++.--+.|.
T Consensus 42 ~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~ 99 (127)
T cd01108 42 RDIEELRFIRRARDLGFSLEEIRELLALWRDPSRASADVKALALEHIAELERKIAELQ 99 (127)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566666655 46688887776654331 123345566666655554444443
No 68
>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=29.25 E-value=45 Score=34.60 Aligned_cols=17 Identities=35% Similarity=0.421 Sum_probs=14.6
Q ss_pred HHHHHHHhHHHHHHHhC
Q 021521 137 MCVQHEAGHFLTGYLLG 153 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg 153 (311)
.+..||+||++=.|+..
T Consensus 339 ~TL~HElGHa~H~~~s~ 355 (549)
T TIGR02289 339 DVLTHEAGHAFHVYESR 355 (549)
T ss_pred HHHHHHhhHHHHHHHhc
Confidence 56889999999888775
No 69
>PRK03982 heat shock protein HtpX; Provisional
Probab=28.98 E-value=28 Score=33.13 Aligned_cols=24 Identities=25% Similarity=0.236 Sum_probs=19.4
Q ss_pred CCChhHHHHHHHHHHhHHHHHHHh
Q 021521 129 SLKEEDHFMCVQHEAGHFLTGYLL 152 (311)
Q Consensus 129 ~ls~eer~RIA~HEAGHaLVAyLL 152 (311)
.++++|-.-|.-||.||.--.+.+
T Consensus 119 ~l~~~El~AVlAHElgHi~~~h~~ 142 (288)
T PRK03982 119 LLNEDELEGVIAHELTHIKNRDTL 142 (288)
T ss_pred hCCHHHHHHHHHHHHHHHHcCCHH
Confidence 357899999999999998755543
No 70
>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=28.84 E-value=35 Score=30.58 Aligned_cols=34 Identities=18% Similarity=0.142 Sum_probs=18.2
Q ss_pred HHHHHHHHhHHHHHHHhCC-CCC--ceecCchhhhccc
Q 021521 136 FMCVQHEAGHFLTGYLLGV-LPK--GYEIPSVEALKQD 170 (311)
Q Consensus 136 ~RIA~HEAGHaLVAyLLg~-PV~--~yTI~~~ealr~G 170 (311)
..++.||.||+|=-+-.-. |=+ -|+| .|+.+..+
T Consensus 80 ~~~i~HEl~HaLG~~HEh~RpDRd~yi~i-~~~~i~~~ 116 (191)
T PF01400_consen 80 VGTILHELGHALGFWHEHQRPDRDNYITI-NWDNIQPG 116 (191)
T ss_dssp HHHHHHHHHHHHTB--GGGSTTGGGTEEE--GGGB-TT
T ss_pred ccchHHHHHHHHhhhhhhhccccccEEEE-ehhcchhh
Confidence 4699999999975444332 222 2444 35555544
No 71
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=28.79 E-value=29 Score=31.52 Aligned_cols=17 Identities=29% Similarity=0.047 Sum_probs=13.0
Q ss_pred HHHHHHHhHHHHHHHhC
Q 021521 137 MCVQHEAGHFLTGYLLG 153 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg 153 (311)
.+.-||.||.|=+.--+
T Consensus 139 ~~~aHEiGH~lGl~H~~ 155 (206)
T PF13583_consen 139 QTFAHEIGHNLGLRHDF 155 (206)
T ss_pred hHHHHHHHHHhcCCCCc
Confidence 67889999988665544
No 72
>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=28.65 E-value=29 Score=30.79 Aligned_cols=17 Identities=29% Similarity=0.178 Sum_probs=13.1
Q ss_pred HHHHHHHHhHHHHHHHh
Q 021521 136 FMCVQHEAGHFLTGYLL 152 (311)
Q Consensus 136 ~RIA~HEAGHaLVAyLL 152 (311)
..++.||.||+|=-+-.
T Consensus 75 ~g~v~HE~~HalG~~HE 91 (180)
T cd04280 75 LGTIVHELMHALGFYHE 91 (180)
T ss_pred CchhHHHHHHHhcCcch
Confidence 57999999999654443
No 73
>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=28.40 E-value=2.7e+02 Score=22.59 Aligned_cols=62 Identities=15% Similarity=0.210 Sum_probs=39.0
Q ss_pred HHHHHHHHHhCCCchhHHHH-H--HHHHHHHHHHHHHcH------HHHHHHHHHHHhhccHHHHHHHHHHhh
Q 021521 244 NKLDKVFQWLGYNKSEADSQ-V--KWAALNTVLISHHHI------QVRSRLAEAMALGRSIGSCIHSIENAL 306 (311)
Q Consensus 244 ~qat~lar~lGms~~~~d~e-v--r~A~~~A~~LL~~hr------~~le~LAeaLle~esv~~C~~~Ie~~~ 306 (311)
.+..+++|.+|+|+.+|+.- . +.-..+..++|+.-+ .+++.|.++|..- -+..|-..|++.+
T Consensus 20 ~~Wk~laR~LGLse~~I~~i~~~~~~~~eq~~qmL~~W~~~~G~~At~~~L~~aL~~~-~~~~~Ae~I~~~l 90 (96)
T cd08315 20 DSWNRLMRQLGLSENEIDVAKANERVTREQLYQMLLTWVNKTGRKASVNTLLDALEAI-GLRLAKESIQDEL 90 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHc-ccccHHHHHHHHH
Confidence 56777899999999888753 1 112567777776433 5678888888763 2233444445544
No 74
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). 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=28.35 E-value=3.1e+02 Score=23.57 Aligned_cols=21 Identities=10% Similarity=0.145 Sum_probs=11.0
Q ss_pred hHHHHHHHHH--HHhCCCchhHH
Q 021521 241 SDINKLDKVF--QWLGYNKSEAD 261 (311)
Q Consensus 241 ~Dl~qat~la--r~lGms~~~~d 261 (311)
+|+.++..|. +.+|||-+++.
T Consensus 41 ~~l~~l~~I~~lr~~G~sL~eI~ 63 (134)
T cd04779 41 TALDRLQLIEHLKGQRLSLAEIK 63 (134)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHH
Confidence 4555555542 44666655443
No 75
>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=28.28 E-value=39 Score=29.53 Aligned_cols=24 Identities=25% Similarity=0.196 Sum_probs=14.9
Q ss_pred CChhHHHHHHHHHHhHHHHHHHhC
Q 021521 130 LKEEDHFMCVQHEAGHFLTGYLLG 153 (311)
Q Consensus 130 ls~eer~RIA~HEAGHaLVAyLLg 153 (311)
++......+.-||.||-|=+.--+
T Consensus 137 ~~~~~~~~~~AHEiGH~lGa~HD~ 160 (196)
T PF13688_consen 137 PPTYNGAITFAHEIGHNLGAPHDG 160 (196)
T ss_dssp --HHHHHHHHHHHHHHHTT-----
T ss_pred CCCCceehhhHHhHHHhcCCCCCC
Confidence 356788899999999987665543
No 76
>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=28.17 E-value=3e+02 Score=21.66 Aligned_cols=46 Identities=9% Similarity=0.003 Sum_probs=30.8
Q ss_pred HHHHHHHhCCCchhHHHH---HHHHHHHHHHHHHHcH------HHHHHHHHHHHh
Q 021521 246 LDKVFQWLGYNKSEADSQ---VKWAALNTVLISHHHI------QVRSRLAEAMAL 291 (311)
Q Consensus 246 at~lar~lGms~~~~d~e---vr~A~~~A~~LL~~hr------~~le~LAeaLle 291 (311)
-.++++.+|||..+|+.- -+-...++.++|+.-+ ..++.|.++|.+
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 455788899999887642 1234677777777544 346677777765
No 77
>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=27.68 E-value=2.6e+02 Score=22.90 Aligned_cols=51 Identities=12% Similarity=0.162 Sum_probs=30.9
Q ss_pred hHHHHHHHH--HHHhCCCchhHHHHHHHH------HHHHHHHHHHcHHHHHHHHHHHHh
Q 021521 241 SDINKLDKV--FQWLGYNKSEADSQVKWA------ALNTVLISHHHIQVRSRLAEAMAL 291 (311)
Q Consensus 241 ~Dl~qat~l--ar~lGms~~~~d~evr~A------~~~A~~LL~~hr~~le~LAeaLle 291 (311)
+|+..+..| ++.+|||-+++..-+... ......+|+++...++.=.+.|..
T Consensus 42 ~~i~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (123)
T cd04770 42 ADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPCAEVRALLEEKLAEVEAKIAELQA 100 (123)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555554 577899988776654432 234567777777666655544443
No 78
>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=27.17 E-value=40 Score=31.09 Aligned_cols=12 Identities=33% Similarity=0.512 Sum_probs=9.7
Q ss_pred HHHHHHHHhHHH
Q 021521 136 FMCVQHEAGHFL 147 (311)
Q Consensus 136 ~RIA~HEAGHaL 147 (311)
.+.+.||.||.+
T Consensus 146 ~Kea~HElGH~~ 157 (194)
T PF07998_consen 146 CKEAVHELGHLF 157 (194)
T ss_dssp HHHHHHHHHHHT
T ss_pred HHHHHHHHHHHc
Confidence 367999999965
No 79
>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=26.96 E-value=1.4e+02 Score=23.52 Aligned_cols=33 Identities=12% Similarity=0.029 Sum_probs=23.4
Q ss_pred HHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHcH
Q 021521 246 LDKVFQWLGYNKSEADSQVKWAALNTVLISHHHI 279 (311)
Q Consensus 246 at~lar~lGms~~~~d~evr~A~~~A~~LL~~hr 279 (311)
-+.+++.+||+..+|+.-. .-+.++.++|+.-.
T Consensus 18 W~~LA~~LG~~~~~I~~i~-~~~~p~~~lL~~W~ 50 (77)
T cd08311 18 WRSLAGELGYEDEAIDTFG-REESPVRTLLADWS 50 (77)
T ss_pred HHHHHHHcCCCHHHHHHHH-cChhHHHHHHHHHH
Confidence 6778899999998887543 22467777777544
No 80
>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=26.91 E-value=45 Score=30.59 Aligned_cols=15 Identities=33% Similarity=0.432 Sum_probs=12.3
Q ss_pred hHHHHHHHHHHhHHH
Q 021521 133 EDHFMCVQHEAGHFL 147 (311)
Q Consensus 133 eer~RIA~HEAGHaL 147 (311)
+..+.++.||.||+|
T Consensus 114 ~~~~~~~~he~gh~l 128 (197)
T cd04276 114 ASLRYLLAHEVGHTL 128 (197)
T ss_pred HHHHHHHHHHHHHHh
Confidence 556678999999985
No 81
>PRK02391 heat shock protein HtpX; Provisional
Probab=26.40 E-value=37 Score=32.81 Aligned_cols=27 Identities=15% Similarity=0.127 Sum_probs=20.3
Q ss_pred ccCCCChhHHHHHHHHHHhHHHHHHHh
Q 021521 126 SYVSLKEEDHFMCVQHEAGHFLTGYLL 152 (311)
Q Consensus 126 ~~~~ls~eer~RIA~HEAGHaLVAyLL 152 (311)
+-..++++|.+-|.-||.||.--.+.+
T Consensus 124 Ll~~L~~~El~aVlaHElgHi~~~di~ 150 (296)
T PRK02391 124 LMRRLDPDELEAVLAHELSHVKNRDVA 150 (296)
T ss_pred HHhhCCHHHHHHHHHHHHHHHHcCCHH
Confidence 333458899999999999997655443
No 82
>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=26.17 E-value=3.2e+02 Score=22.83 Aligned_cols=52 Identities=10% Similarity=0.137 Sum_probs=32.6
Q ss_pred hhHHHHHHHH--HHHhCCCchhHHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHHh
Q 021521 240 YSDINKLDKV--FQWLGYNKSEADSQVKW------AALNTVLISHHHIQVRSRLAEAMAL 291 (311)
Q Consensus 240 ~~Dl~qat~l--ar~lGms~~~~d~evr~------A~~~A~~LL~~hr~~le~LAeaLle 291 (311)
.+|+..+..| ++.+|||-++|.+-+.. .......+|.++...+++=-+.|.+
T Consensus 41 ~~~l~~l~~I~~lr~lG~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (127)
T TIGR02047 41 VGHVERLAFIRNCRTLDMSLAEIRQLLRYQDKPEKSCSDVNALLDEHISHVRARIIKLQA 100 (127)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3577776665 46789998887765431 2245567777777776655555544
No 83
>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=26.08 E-value=2.5e+02 Score=23.65 Aligned_cols=51 Identities=12% Similarity=0.186 Sum_probs=30.5
Q ss_pred hHHHHHHHH--HHHhCCCchhHHHHHHHH------HHHHHHHHHHcHHHHHHHHHHHHh
Q 021521 241 SDINKLDKV--FQWLGYNKSEADSQVKWA------ALNTVLISHHHIQVRSRLAEAMAL 291 (311)
Q Consensus 241 ~Dl~qat~l--ar~lGms~~~~d~evr~A------~~~A~~LL~~hr~~le~LAeaLle 291 (311)
+|+..+..| ++.+|||-+++..-+... ......+|+++...+++=.+.|..
T Consensus 42 ~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (133)
T cd04787 42 KDLSRLRFILSARQLGFSLKDIKEILSHADQGESPCPMVRRLIEQRLAETERRIKELLK 100 (133)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhhhccCCCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555554 577999988876654321 124456777776666655555443
No 84
>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=25.93 E-value=48 Score=32.31 Aligned_cols=17 Identities=35% Similarity=0.632 Sum_probs=15.2
Q ss_pred HHHHHHHhHHHHHHHhC
Q 021521 137 MCVQHEAGHFLTGYLLG 153 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg 153 (311)
.+..||.||++=.++..
T Consensus 224 ~tl~HE~GHa~h~~~~~ 240 (427)
T cd06459 224 FTLAHELGHAFHSYLSR 240 (427)
T ss_pred HHHHHHhhHHHHHHHHc
Confidence 67999999999988875
No 85
>COG2738 Predicted Zn-dependent protease [General function prediction only]
Probab=25.69 E-value=37 Score=31.99 Aligned_cols=13 Identities=31% Similarity=0.567 Sum_probs=10.9
Q ss_pred HHHHHHHhHHHHH
Q 021521 137 MCVQHEAGHFLTG 149 (311)
Q Consensus 137 RIA~HEAGHaLVA 149 (311)
-||-||-||++=-
T Consensus 94 aVAAHEVGHAiQd 106 (226)
T COG2738 94 AVAAHEVGHAIQD 106 (226)
T ss_pred HHHHHHhhHHHhh
Confidence 4899999999854
No 86
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=25.45 E-value=3.8e+02 Score=23.62 Aligned_cols=60 Identities=12% Similarity=0.108 Sum_probs=35.4
Q ss_pred hhHHHHHHHH--HHHhCCCchhHHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHh-hccHHHHH
Q 021521 240 YSDINKLDKV--FQWLGYNKSEADSQVKW-------AALNTVLISHHHIQVRSRLAEAMAL-GRSIGSCI 299 (311)
Q Consensus 240 ~~Dl~qat~l--ar~lGms~~~~d~evr~-------A~~~A~~LL~~hr~~le~LAeaLle-~esv~~C~ 299 (311)
.+|+..+.-| ++.+|||-+++.+-+.. .......+|.++...++.=.+.|.. ...|..|+
T Consensus 51 ~~~i~~L~~I~~lr~lG~sL~eIk~ll~~~~~~~~~~~~~~~~ll~~k~~~l~~~I~~L~~~~~~L~~~i 120 (154)
T PRK15002 51 RDVLRYVAIIKIAQRIGIPLATIGEAFGVLPEGHTLSAKEWKQLSSQWREELDRRIHTLVALRDELDGCI 120 (154)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3677777654 57799998887765431 2344566666665555554444444 23444444
No 87
>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=25.06 E-value=2.3e+02 Score=22.03 Aligned_cols=46 Identities=13% Similarity=0.111 Sum_probs=30.5
Q ss_pred HHHHHHHhCCCchhHHHHH----HHHHHHHHHHHHHcH------HHHHHHHHHHHh
Q 021521 246 LDKVFQWLGYNKSEADSQV----KWAALNTVLISHHHI------QVRSRLAEAMAL 291 (311)
Q Consensus 246 at~lar~lGms~~~~d~ev----r~A~~~A~~LL~~hr------~~le~LAeaLle 291 (311)
-.++++.+|||..+++.-. +-...++.++|+.-+ .+.+.|.++|..
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 4557788999988777532 235677888876433 456677777765
No 88
>PRK05457 heat shock protein HtpX; Provisional
Probab=25.04 E-value=56 Score=31.39 Aligned_cols=20 Identities=15% Similarity=0.336 Sum_probs=17.0
Q ss_pred CCChhHHHHHHHHHHhHHHH
Q 021521 129 SLKEEDHFMCVQHEAGHFLT 148 (311)
Q Consensus 129 ~ls~eer~RIA~HEAGHaLV 148 (311)
.++++|-+-|.-||.||.--
T Consensus 128 ~L~~~El~aVlAHElgHi~~ 147 (284)
T PRK05457 128 NMSRDEVEAVLAHEISHIAN 147 (284)
T ss_pred hCCHHHHHHHHHHHHHHHHc
Confidence 45889999999999999743
No 89
>PRK03001 M48 family peptidase; Provisional
Probab=24.98 E-value=36 Score=32.35 Aligned_cols=24 Identities=25% Similarity=0.250 Sum_probs=19.1
Q ss_pred CCChhHHHHHHHHHHhHHHHHHHh
Q 021521 129 SLKEEDHFMCVQHEAGHFLTGYLL 152 (311)
Q Consensus 129 ~ls~eer~RIA~HEAGHaLVAyLL 152 (311)
.++++|-+-|.-||.||.--.+.+
T Consensus 118 ~l~~~El~aVlAHElgHi~~~h~~ 141 (283)
T PRK03001 118 VLSEREIRGVMAHELAHVKHRDIL 141 (283)
T ss_pred hCCHHHHHHHHHHHHHHHhCCChH
Confidence 357899999999999998655543
No 90
>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=24.72 E-value=36 Score=32.66 Aligned_cols=17 Identities=35% Similarity=0.444 Sum_probs=12.7
Q ss_pred HHHHHHHHHHhHHHHHH
Q 021521 134 DHFMCVQHEAGHFLTGY 150 (311)
Q Consensus 134 er~RIA~HEAGHaLVAy 150 (311)
.-.-|++||.||.+...
T Consensus 215 ~~~~v~vHE~GHsf~~L 231 (264)
T PF09471_consen 215 SFKQVVVHEFGHSFGGL 231 (264)
T ss_dssp THHHHHHHHHHHHTT--
T ss_pred cccceeeeecccccccc
Confidence 55679999999987653
No 91
>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=24.69 E-value=2.4e+02 Score=24.06 Aligned_cols=62 Identities=18% Similarity=0.138 Sum_probs=47.2
Q ss_pred ccchhhHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHhhccHHH
Q 021521 236 SEGHYSDINKLDKVFQWLGYNKSEADSQVKWAALNTVLISHHHIQVRSRLAEAMALGRSIGS 297 (311)
Q Consensus 236 atGg~~Dl~qat~lar~lGms~~~~d~evr~A~~~A~~LL~~hr~~le~LAeaLle~esv~~ 297 (311)
.+|...+++.+..+++.+|-..-.++.+.|..|--|--+-.++--.+-.++..|++..-++.
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 36767788999999999998887788777877777777777777788888888877766555
No 92
>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=24.68 E-value=9.8 Score=35.49 Aligned_cols=19 Identities=32% Similarity=0.364 Sum_probs=14.6
Q ss_pred hhHHHHHHHHHHhHHHHHH
Q 021521 132 EEDHFMCVQHEAGHFLTGY 150 (311)
Q Consensus 132 ~eer~RIA~HEAGHaLVAy 150 (311)
+-..-+++.||.||+|--|
T Consensus 134 ~~n~g~t~~HEvGH~lGL~ 152 (225)
T cd04275 134 PYNLGDTATHEVGHWLGLY 152 (225)
T ss_pred cccccceeEEeccceeeee
Confidence 3456689999999998433
No 93
>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=24.38 E-value=42 Score=30.45 Aligned_cols=17 Identities=35% Similarity=0.172 Sum_probs=13.5
Q ss_pred HHHHHHHhHHHHHHHhC
Q 021521 137 MCVQHEAGHFLTGYLLG 153 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg 153 (311)
-++.||-||+|=-+-.-
T Consensus 79 G~i~HEl~HaLG~~HEh 95 (182)
T cd04283 79 GIIQHELLHALGFYHEQ 95 (182)
T ss_pred chHHHHHHHHhCCcccc
Confidence 58999999998665543
No 94
>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=24.00 E-value=2.3e+02 Score=22.45 Aligned_cols=50 Identities=8% Similarity=0.046 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHhCCCchhHHHHH---HHHHHHHHHHHHH-------cHHHHHHHHHHHHh
Q 021521 242 DINKLDKVFQWLGYNKSEADSQV---KWAALNTVLISHH-------HIQVRSRLAEAMAL 291 (311)
Q Consensus 242 Dl~qat~lar~lGms~~~~d~ev---r~A~~~A~~LL~~-------hr~~le~LAeaLle 291 (311)
.+.+..+++|.+|+|+.+||.-. +...++..++|+. +...++.|.++|..
T Consensus 10 ~~~~wk~~~R~LGlse~~Id~ie~~~~~~~Eq~yqmL~~W~~~~g~~~At~~~L~~aLr~ 69 (80)
T cd08313 10 PPRRWKEFVRRLGLSDNEIERVELDHRRCRDAQYQMLKVWKERGPRPYATLQHLLSVLRD 69 (80)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCCcchHHHHHHHHHH
Confidence 45677889999999998887531 2344566666653 24466777776654
No 95
>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=23.86 E-value=2.2e+02 Score=22.47 Aligned_cols=46 Identities=4% Similarity=0.045 Sum_probs=30.7
Q ss_pred HHHHHHHhCCCchhHHHH----HHHHHHHHHHHHHHcH------HHHHHHHHHHHh
Q 021521 246 LDKVFQWLGYNKSEADSQ----VKWAALNTVLISHHHI------QVRSRLAEAMAL 291 (311)
Q Consensus 246 at~lar~lGms~~~~d~e----vr~A~~~A~~LL~~hr------~~le~LAeaLle 291 (311)
-.++++.+|||+.+|++- -+-...++..+|+.-+ ...+.|..+|.+
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 456788899999888863 2335677777776433 445667777754
No 96
>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=23.84 E-value=2.8e+02 Score=23.09 Aligned_cols=51 Identities=10% Similarity=0.125 Sum_probs=30.1
Q ss_pred hHHHHHHHH--HHHhCCCchhHHHHHHH----HHHHHHHHHHHcHHHHHHHHHHHHh
Q 021521 241 SDINKLDKV--FQWLGYNKSEADSQVKW----AALNTVLISHHHIQVRSRLAEAMAL 291 (311)
Q Consensus 241 ~Dl~qat~l--ar~lGms~~~~d~evr~----A~~~A~~LL~~hr~~le~LAeaLle 291 (311)
+|+..+..| ++.+|||-+++..-+.. .......+|.++...+++=.+.|..
T Consensus 41 ~~l~~l~~I~~l~~~G~sl~eI~~~l~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 97 (124)
T TIGR02051 41 ETVKRLRFIKRAQELGFSLEEIGGLLGLVDGTHCREMYELASRKLKSVQAKMADLLR 97 (124)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466665544 56789998877665432 2244566676666666554444433
No 97
>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=23.82 E-value=53 Score=34.09 Aligned_cols=20 Identities=20% Similarity=0.248 Sum_probs=15.6
Q ss_pred HHcHHHHHHHHHHHHhhccH
Q 021521 276 HHHIQVRSRLAEAMALGRSI 295 (311)
Q Consensus 276 ~~hr~~le~LAeaLle~esv 295 (311)
...+++.+.+.+.|.-+.|.
T Consensus 423 ~~s~~Ag~~l~~~l~lG~S~ 442 (477)
T cd06461 423 YGSKEAGKKLRAMLSLGSSK 442 (477)
T ss_pred cChHHHHHHHHHHHhCcCCC
Confidence 45788999999888887643
No 98
>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=23.72 E-value=1.8e+02 Score=22.57 Aligned_cols=48 Identities=13% Similarity=0.074 Sum_probs=31.8
Q ss_pred HHHHHHHHHhCCCchhHHHHH---HHHHHHHHHHHHHcH------HHHHHHHHHHHh
Q 021521 244 NKLDKVFQWLGYNKSEADSQV---KWAALNTVLISHHHI------QVRSRLAEAMAL 291 (311)
Q Consensus 244 ~qat~lar~lGms~~~~d~ev---r~A~~~A~~LL~~hr------~~le~LAeaLle 291 (311)
.+-.+++|.+||+..+|+.-. +....++.++|+.-+ ..++.|.++|..
T Consensus 12 ~~Wk~laR~LGls~~~I~~ie~~~~~~~eq~~~mL~~W~~k~G~~At~~~L~~aL~~ 68 (79)
T cd08784 12 DQHKRFFRKLGLSDNEIKVAELDNPQHRDRVYELLRIWRNKEGRKATLNTLIKALKD 68 (79)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHcCCchHHHHHHHHHHHHhccCcCcHHHHHHHHHHH
Confidence 455678999999998877531 125677777776433 456666666655
No 99
>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=23.53 E-value=44 Score=30.75 Aligned_cols=17 Identities=29% Similarity=0.255 Sum_probs=13.1
Q ss_pred HHHHHHHhHHHHHHHhC
Q 021521 137 MCVQHEAGHFLTGYLLG 153 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg 153 (311)
=++.||.||+|=-+-.-
T Consensus 89 Gti~HEl~HaLGf~HEh 105 (200)
T cd04281 89 GIVVHELGHVIGFWHEH 105 (200)
T ss_pred chHHHHHHHHhcCcchh
Confidence 48999999998655543
No 100
>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=23.49 E-value=2.8e+02 Score=22.64 Aligned_cols=52 Identities=6% Similarity=0.116 Sum_probs=32.4
Q ss_pred hhHHHHHHHH--HHHhCCCchhHHHHHHH---------HHHHHHHHHHHcHHHHHHHHHHHHh
Q 021521 240 YSDINKLDKV--FQWLGYNKSEADSQVKW---------AALNTVLISHHHIQVRSRLAEAMAL 291 (311)
Q Consensus 240 ~~Dl~qat~l--ar~lGms~~~~d~evr~---------A~~~A~~LL~~hr~~le~LAeaLle 291 (311)
.+|+..+..| ++.+|||.+++.+-++. ...+...+|+++...++.=.+.|..
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 3577776665 46689998877654432 2234567777777766665555544
No 101
>PRK13267 archaemetzincin-like protein; Reviewed
Probab=23.12 E-value=55 Score=29.61 Aligned_cols=11 Identities=55% Similarity=0.661 Sum_probs=8.8
Q ss_pred HHHHHHHhHHH
Q 021521 137 MCVQHEAGHFL 147 (311)
Q Consensus 137 RIA~HEAGHaL 147 (311)
+.+.||.||.|
T Consensus 127 k~~~HElGH~l 137 (179)
T PRK13267 127 KEVTHELGHTL 137 (179)
T ss_pred HHHHHHHHHHc
Confidence 34899999973
No 102
>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=22.85 E-value=70 Score=32.02 Aligned_cols=19 Identities=26% Similarity=0.282 Sum_probs=16.4
Q ss_pred HHHHHHHhHHHHHHHhCCC
Q 021521 137 MCVQHEAGHFLTGYLLGVL 155 (311)
Q Consensus 137 RIA~HEAGHaLVAyLLg~P 155 (311)
.+..||.||++=.++...+
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 6899999999999988743
No 103
>PRK03072 heat shock protein HtpX; Provisional
Probab=22.79 E-value=48 Score=31.78 Aligned_cols=24 Identities=25% Similarity=0.284 Sum_probs=19.3
Q ss_pred CCChhHHHHHHHHHHhHHHHHHHh
Q 021521 129 SLKEEDHFMCVQHEAGHFLTGYLL 152 (311)
Q Consensus 129 ~ls~eer~RIA~HEAGHaLVAyLL 152 (311)
.++++|-+-|.-||.||.--.+.+
T Consensus 121 ~l~~~El~aVlAHElgHi~~~d~~ 144 (288)
T PRK03072 121 ILNERELRGVLGHELSHVYNRDIL 144 (288)
T ss_pred hCCHHHHHHHHHHHHHHHhcCCHH
Confidence 458899999999999997655544
No 104
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. 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
Probab=22.44 E-value=3.9e+02 Score=21.06 Aligned_cols=57 Identities=9% Similarity=-0.016 Sum_probs=36.0
Q ss_pred HHHHHhCCCchhHHHH----HHHHHHHHHHHHHH----c---HHHHHHHHHHHHhhccHHHHHHHHHHh
Q 021521 248 KVFQWLGYNKSEADSQ----VKWAALNTVLISHH----H---IQVRSRLAEAMALGRSIGSCIHSIENA 305 (311)
Q Consensus 248 ~lar~lGms~~~~d~e----vr~A~~~A~~LL~~----h---r~~le~LAeaLle~esv~~C~~~Ie~~ 305 (311)
.+++.+|+|..+++.= -+-...++..+|+. + ...++.|.++|.+ --..+|..-|++.
T Consensus 18 ~lar~LGlse~~Id~Ie~~~~~dl~eq~~~mL~~W~~~~~~~~atv~~L~~AL~~-~gr~dlae~l~~~ 85 (86)
T cd08779 18 AIGLHLGLSYRELQRIKYNNRDDLDEQIFDMLFSWAQRQAGDPDAVGKLVTALEE-SGRQDLADEVRAV 85 (86)
T ss_pred HHHHHcCCCHHHHHHHHHHCccCHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHH-cCHHHHHHHHHhh
Confidence 4567789999887642 12245666666632 1 3557788888876 4456676666654
No 105
>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=21.96 E-value=80 Score=25.09 Aligned_cols=33 Identities=30% Similarity=0.453 Sum_probs=25.7
Q ss_pred HHHHHHHHc-CCchHHHHHHHHHhccCCCCCcccc
Q 021521 31 LKRVDRELS-RGNFKVALSLVKQLQRKPAGGLRGF 64 (311)
Q Consensus 31 ~~~~~~~~~-~~~~~~a~~~~~~~~~~~~~~l~~~ 64 (311)
-|++..+-. +||.++|--|+..|..+| |-.+.|
T Consensus 35 ~e~I~a~~~~~G~~~aa~~Ll~~L~r~~-~Wf~~F 68 (84)
T cd08789 35 KERIQAAENNSGNIKAAWTLLDTLVRRD-NWLEPF 68 (84)
T ss_pred HHHHHHHHhcCChHHHHHHHHHHHhccC-ChHHHH
Confidence 455666554 799999999999999777 777666
No 106
>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=21.68 E-value=4.3e+02 Score=21.96 Aligned_cols=49 Identities=12% Similarity=0.194 Sum_probs=23.3
Q ss_pred hHHHHHHHH--HHHhCCCchhHHHHHHH------HHHHHHHHHHHcHHHHHHHHHHH
Q 021521 241 SDINKLDKV--FQWLGYNKSEADSQVKW------AALNTVLISHHHIQVRSRLAEAM 289 (311)
Q Consensus 241 ~Dl~qat~l--ar~lGms~~~~d~evr~------A~~~A~~LL~~hr~~le~LAeaL 289 (311)
+|+..+..| ++.+|||-+++.+-+.. .......+|.++...++.-.+.|
T Consensus 42 ~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L 98 (126)
T cd04785 42 AHVERLRFIRRARDLGFSLEEIRALLALSDRPDRSCAEADAIARAHLADVRARIADL 98 (126)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHhhhhcCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555544 35577776665543321 11233455555554444433333
No 107
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=21.51 E-value=4.1e+02 Score=22.70 Aligned_cols=51 Identities=12% Similarity=0.142 Sum_probs=27.6
Q ss_pred hHHHHHHHH--HHHhCCCchhHHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHh
Q 021521 241 SDINKLDKV--FQWLGYNKSEADSQVKW-------AALNTVLISHHHIQVRSRLAEAMAL 291 (311)
Q Consensus 241 ~Dl~qat~l--ar~lGms~~~~d~evr~-------A~~~A~~LL~~hr~~le~LAeaLle 291 (311)
+|+..+..| ++.+|||-+++..-+.. .......+|.++.+.+++-.+.|.+
T Consensus 43 ~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 102 (140)
T PRK09514 43 QDLQRLRFIRRAKQLGFTLEEIRELLSIRLDPEHHTCQEVKGIVDEKLAEVEAKIAELQH 102 (140)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHhcccCCcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466666654 45678877666544321 2334455666665555555444443
No 108
>PRK04897 heat shock protein HtpX; Provisional
Probab=21.32 E-value=72 Score=30.69 Aligned_cols=22 Identities=18% Similarity=0.208 Sum_probs=17.8
Q ss_pred CChhHHHHHHHHHHhHHHHHHH
Q 021521 130 LKEEDHFMCVQHEAGHFLTGYL 151 (311)
Q Consensus 130 ls~eer~RIA~HEAGHaLVAyL 151 (311)
++++|.+-|.-||.||.--.+.
T Consensus 132 l~~~El~aVlAHElgHi~~~d~ 153 (298)
T PRK04897 132 MNREELEGVIGHEISHIRNYDI 153 (298)
T ss_pred CCHHHHHHHHHHHHHHHhcCCH
Confidence 4789999999999999764443
No 109
>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=21.03 E-value=2.8e+02 Score=22.45 Aligned_cols=47 Identities=11% Similarity=0.160 Sum_probs=25.2
Q ss_pred hHHHHHHHH--HHHhCCCchhHHHHHHHHH-HHHHHHHHHcHHHHHHHHH
Q 021521 241 SDINKLDKV--FQWLGYNKSEADSQVKWAA-LNTVLISHHHIQVRSRLAE 287 (311)
Q Consensus 241 ~Dl~qat~l--ar~lGms~~~~d~evr~A~-~~A~~LL~~hr~~le~LAe 287 (311)
.|+..+..+ ++.+|||.+++..-.+... .....+|+++.+.+++=.+
T Consensus 43 ~~i~~l~~I~~lr~~G~sl~~i~~l~~~~~~~~~~~~l~~~~~~l~~~i~ 92 (108)
T cd01107 43 EQLERLNRIKYLRDLGFPLEEIKEILDADNDDELRKLLREKLAELEAEIE 92 (108)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHH
Confidence 455655544 4668888777654332111 3455555555555554333
No 110
>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=20.95 E-value=2.7e+02 Score=24.69 Aligned_cols=22 Identities=18% Similarity=0.495 Sum_probs=13.5
Q ss_pred hHHHHHHHH--HHHhCCCchhHHH
Q 021521 241 SDINKLDKV--FQWLGYNKSEADS 262 (311)
Q Consensus 241 ~Dl~qat~l--ar~lGms~~~~d~ 262 (311)
+|+.++..| ++.+|||-+++..
T Consensus 43 ~dl~rL~~I~~lr~~G~sL~eI~~ 66 (172)
T cd04790 43 RDLERLEQICAYRSAGVSLEDIRS 66 (172)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHH
Confidence 466666554 3567887766554
No 111
>PRK01209 cobD cobalamin biosynthesis protein; Provisional
Probab=20.90 E-value=1.6e+02 Score=28.64 Aligned_cols=33 Identities=18% Similarity=0.258 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHcCCchHHHHHHHHHhccCC
Q 021521 25 KRRRQALKRVDRELSRGNFKVALSLVKQLQRKP 57 (311)
Q Consensus 25 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~ 57 (311)
..-++..++|.+.|.+||..+|-..++++.|++
T Consensus 96 ~~l~~~~~~v~~al~~gd~~~AR~~l~~~v~Rd 128 (312)
T PRK01209 96 RSLADHARAVARALRAGDLEEARRAVSMIVGRD 128 (312)
T ss_pred hhHHHHHHHHHHHHHcCCHHHHHHHHHHHhCCC
Confidence 345677888999999999999999999987666
No 112
>COG1913 Predicted Zn-dependent proteases [General function prediction only]
Probab=20.81 E-value=61 Score=29.85 Aligned_cols=16 Identities=44% Similarity=0.420 Sum_probs=11.6
Q ss_pred hhHHHHH---HHHHHhHHH
Q 021521 132 EEDHFMC---VQHEAGHFL 147 (311)
Q Consensus 132 ~eer~RI---A~HEAGHaL 147 (311)
+-.++|+ +.||+||.+
T Consensus 118 ~lf~ERv~KEv~HElGH~~ 136 (181)
T COG1913 118 ELFKERVVKEVLHELGHLL 136 (181)
T ss_pred HHHHHHHHHHHHHHhhhhc
Confidence 4455666 799999964
No 113
>cd08780 Death_TRADD Death Domain of Tumor Necrosis Factor Receptor 1-Associated Death Domain protein. Death domain (DD) of TRADD (TNF Receptor 1-Associated Death Domain or TNFRSF1A-associated via death domain) protein. TRADD is a central signaling adaptor for TNF-receptor 1 (TNFR1), mediating activation of Nuclear Factor -kappaB (NF-kB) and c-Jun N-terminal kinase (JNK), as well as caspase-dependent apoptosis. It also carries important immunological roles including germinal center formation, DR3-mediated T-cell stimulation, and TNFalpha-mediated inflammatory responses. 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 s
Probab=20.72 E-value=2.9e+02 Score=22.80 Aligned_cols=46 Identities=17% Similarity=0.077 Sum_probs=30.7
Q ss_pred HHHHHHHhC-----CCchhHHHH----HHH-HHHHHHHHHHHcHH------HHHHHHHHHHh
Q 021521 246 LDKVFQWLG-----YNKSEADSQ----VKW-AALNTVLISHHHIQ------VRSRLAEAMAL 291 (311)
Q Consensus 246 at~lar~lG-----ms~~~~d~e----vr~-A~~~A~~LL~~hr~------~le~LAeaLle 291 (311)
-.+++|.+| ++...||+- -|. =+++++++|++-+. .++.|+.+|..
T Consensus 16 WK~laR~Lg~~cral~d~~ID~I~~~y~r~gL~EqvyQ~L~~W~~~eg~~Atv~~Lv~AL~~ 77 (90)
T cd08780 16 WKPVGRSLQKNCRALRDPAIDNLAYEYDREGLYEQAYQLLRRFIQSEGKKATLQRLVQALEE 77 (90)
T ss_pred HHHHHHHHcccccccchhHHHHHHhhcccccHHHHHHHHHHHHHHhccccchHHHHHHHHHH
Confidence 344677899 888777753 233 67788888876543 56666666654
No 114
>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=20.42 E-value=2.6e+02 Score=22.44 Aligned_cols=50 Identities=18% Similarity=0.204 Sum_probs=30.8
Q ss_pred hhHHHHHHHH--HHHhCCCchhHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHh
Q 021521 240 YSDINKLDKV--FQWLGYNKSEADSQVKWAALNTVLISHHHIQVRSRLAEAMAL 291 (311)
Q Consensus 240 ~~Dl~qat~l--ar~lGms~~~~d~evr~A~~~A~~LL~~hr~~le~LAeaLle 291 (311)
.+|+..+..+ ++..|||-+++..-+... ....+|.++.+.+++-.+.|.+
T Consensus 41 ~~dl~~l~~I~~l~~~G~~l~ei~~~~~~~--~~~~~l~~~~~~l~~~i~~l~~ 92 (102)
T cd04775 41 EADLSRLEKIVFLQAGGLPLEEIAGCLAQP--HVQAILEERLQSLNREIQRLRQ 92 (102)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHcCC--cHHHHHHHHHHHHHHHHHHHHH
Confidence 3577777765 467899988776543211 1456666666666665555544
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=20.00 E-value=3.6e+02 Score=22.67 Aligned_cols=52 Identities=12% Similarity=0.161 Sum_probs=31.1
Q ss_pred hhHHHHHHHH--HHHhCCCchhHHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHh
Q 021521 240 YSDINKLDKV--FQWLGYNKSEADSQVKW-------AALNTVLISHHHIQVRSRLAEAMAL 291 (311)
Q Consensus 240 ~~Dl~qat~l--ar~lGms~~~~d~evr~-------A~~~A~~LL~~hr~~le~LAeaLle 291 (311)
.+|+..+..| ++.+|||-+++..-+.. .......+|.++...+++-.+.|.+
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 3577777665 46688888776654331 2345566777766666655555443
Done!