Query 019873
Match_columns 334
No_of_seqs 156 out of 846
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 05:13:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019873.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019873hhsearch_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 4E-28 8.8E-33 221.2 16.8 153 116-296 7-206 (213)
2 KOG0734 AAA+-type ATPase conta 99.9 1.5E-26 3.2E-31 235.6 10.5 158 119-305 539-735 (752)
3 PRK10733 hflB ATP-dependent me 99.9 1.4E-24 3E-29 226.1 16.9 160 117-305 388-596 (644)
4 CHL00176 ftsH cell division pr 99.9 1.3E-24 2.7E-29 226.7 15.9 160 117-305 419-626 (638)
5 TIGR01241 FtsH_fam ATP-depende 99.9 2.1E-24 4.7E-29 217.2 16.5 157 118-302 292-494 (495)
6 COG0465 HflB ATP-dependent Zn 99.9 1.3E-23 2.8E-28 217.1 14.4 160 116-304 385-590 (596)
7 KOG0731 AAA+-type ATPase conta 99.9 5.9E-22 1.3E-26 208.9 12.0 200 83-312 503-756 (774)
8 CHL00206 ycf2 Ycf2; Provisiona 98.6 7.5E-08 1.6E-12 110.6 7.5 109 117-251 1873-1994(2281)
9 cd06163 S2P-M50_PDZ_RseP-like 96.7 0.0011 2.5E-08 60.1 3.1 25 137-161 11-35 (182)
10 cd06164 S2P-M50_SpoIVFB_CBS Sp 95.8 0.014 3E-07 54.6 5.1 27 137-163 55-81 (227)
11 TIGR00054 RIP metalloprotease 95.8 0.0079 1.7E-07 60.7 3.6 25 137-161 16-40 (420)
12 PF13398 Peptidase_M50B: Pepti 95.5 0.015 3.3E-07 53.2 3.9 27 137-163 24-50 (200)
13 PRK10779 zinc metallopeptidase 95.0 0.014 3.1E-07 59.2 2.5 26 137-162 17-42 (449)
14 cd05709 S2P-M50 Site-2 proteas 95.0 0.023 4.9E-07 50.2 3.4 25 137-161 10-34 (180)
15 cd06162 S2P-M50_PDZ_SREBP Ster 94.5 0.059 1.3E-06 52.4 5.3 27 137-163 137-163 (277)
16 cd06161 S2P-M50_SpoIVFB SpoIVF 94.3 0.031 6.8E-07 51.3 2.7 27 137-163 40-66 (208)
17 PF02163 Peptidase_M50: Peptid 93.5 0.048 1E-06 48.3 2.3 26 137-162 9-34 (192)
18 cd06160 S2P-M50_like_2 Unchara 91.5 0.16 3.5E-06 46.3 2.9 27 137-163 43-69 (183)
19 cd06158 S2P-M50_like_1 Unchara 88.0 0.37 7.9E-06 43.6 2.5 26 138-163 12-41 (181)
20 cd06159 S2P-M50_PDZ_Arch Uncha 87.6 0.31 6.7E-06 47.0 1.8 25 137-161 120-144 (263)
21 PF14247 DUF4344: Domain of un 84.8 0.67 1.5E-05 43.8 2.5 23 137-160 94-116 (220)
22 PF00413 Peptidase_M10: Matrix 82.1 0.64 1.4E-05 39.2 1.1 17 131-147 101-117 (154)
23 cd04279 ZnMc_MMP_like_1 Zinc-d 77.9 1.5 3.1E-05 37.9 1.9 20 132-151 101-120 (156)
24 cd04268 ZnMc_MMP_like Zinc-dep 75.9 1.7 3.7E-05 37.2 1.8 17 132-148 91-107 (165)
25 PF04298 Zn_peptidase_2: Putat 73.4 1.8 3.8E-05 41.2 1.4 12 137-148 91-102 (222)
26 KOG2921 Intramembrane metallop 71.6 2.7 5.8E-05 43.5 2.3 25 137-161 133-157 (484)
27 COG0750 Predicted membrane-ass 70.8 2.8 6E-05 40.8 2.1 26 137-162 15-40 (375)
28 cd04278 ZnMc_MMP Zinc-dependen 69.3 2.2 4.7E-05 37.0 0.9 17 131-147 103-119 (157)
29 PF02031 Peptidase_M7: Strepto 69.2 3.4 7.4E-05 36.5 2.1 52 119-182 63-115 (132)
30 cd04786 HTH_MerR-like_sg7 Heli 67.3 23 0.00049 30.6 6.8 68 240-307 41-116 (131)
31 PF05572 Peptidase_M43: Pregna 65.1 3.3 7.2E-05 36.7 1.3 18 131-148 65-82 (154)
32 cd04277 ZnMc_serralysin_like Z 64.8 4.3 9.3E-05 36.0 1.9 17 132-148 110-126 (186)
33 PF06114 DUF955: Domain of unk 63.9 7.7 0.00017 30.4 3.1 23 130-152 37-59 (122)
34 cd08316 Death_FAS_TNFRSF6 Deat 63.2 30 0.00065 28.8 6.5 62 243-305 20-91 (97)
35 cd04327 ZnMc_MMP_like_3 Zinc-d 58.8 6.5 0.00014 35.6 2.0 29 134-165 91-120 (198)
36 smart00235 ZnMc Zinc-dependent 57.6 5.4 0.00012 33.5 1.2 14 137-150 88-101 (140)
37 cd04769 HTH_MerR2 Helix-Turn-H 56.1 60 0.0013 27.0 7.2 66 240-305 40-115 (116)
38 PF08858 IDEAL: IDEAL domain; 53.5 32 0.0007 23.8 4.3 33 21-53 5-37 (37)
39 cd00203 ZnMc Zinc-dependent me 51.6 8 0.00017 32.9 1.3 18 133-150 94-111 (167)
40 COG0501 HtpX Zn-dependent prot 51.2 12 0.00025 35.1 2.5 24 129-152 151-174 (302)
41 PF11350 DUF3152: Protein of u 50.5 8.2 0.00018 36.4 1.3 18 132-150 136-153 (203)
42 PF09278 MerR-DNA-bind: MerR, 50.0 70 0.0015 23.4 6.1 42 250-291 10-57 (65)
43 smart00005 DEATH DEATH domain, 49.8 81 0.0018 24.2 6.7 48 244-291 18-75 (88)
44 PF01435 Peptidase_M48: Peptid 48.3 16 0.00034 32.5 2.7 24 130-153 84-107 (226)
45 PF13485 Peptidase_MA_2: Pepti 47.6 21 0.00046 28.1 3.1 23 131-153 21-43 (128)
46 PF13582 Reprolysin_3: Metallo 46.7 9.9 0.00021 31.0 1.1 11 137-147 109-119 (124)
47 cd04783 HTH_MerR1 Helix-Turn-H 41.9 1.2E+02 0.0026 25.5 7.0 52 240-291 41-98 (126)
48 cd04768 HTH_BmrR-like Helix-Tu 41.2 87 0.0019 25.3 5.8 50 241-290 42-93 (96)
49 cd08306 Death_FADD Fas-associa 40.7 1.5E+02 0.0031 23.8 6.9 46 246-291 16-71 (86)
50 COG2856 Predicted Zn peptidase 39.0 23 0.00051 33.3 2.4 22 130-151 67-88 (213)
51 cd01106 HTH_TipAL-Mta Helix-Tu 38.2 1E+02 0.0022 25.0 5.8 45 240-284 41-87 (103)
52 cd04773 HTH_TioE_rpt2 Second H 38.0 1.7E+02 0.0036 24.1 7.1 53 240-292 41-100 (108)
53 cd04788 HTH_NolA-AlbR Helix-Tu 37.8 93 0.002 25.1 5.5 50 240-289 41-92 (96)
54 PRK03982 heat shock protein Ht 37.6 20 0.00044 34.4 1.8 23 129-151 119-141 (288)
55 PRK02391 heat shock protein Ht 37.0 19 0.00042 35.1 1.6 27 125-151 123-149 (296)
56 cd01109 HTH_YyaN Helix-Turn-He 36.8 1.8E+02 0.004 23.8 7.2 52 240-291 41-100 (113)
57 TIGR01950 SoxR redox-sensitive 35.0 1.7E+02 0.0038 25.5 7.1 61 240-300 41-111 (142)
58 cd04782 HTH_BltR Helix-Turn-He 34.9 1.4E+02 0.003 24.1 6.1 50 241-290 42-94 (97)
59 COG2738 Predicted Zn-dependent 34.8 21 0.00044 34.0 1.3 13 137-149 94-106 (226)
60 cd08777 Death_RIP1 Death Domai 34.5 2.3E+02 0.005 22.8 7.2 34 246-279 16-54 (86)
61 cd08313 Death_TNFR1 Death doma 34.3 1.1E+02 0.0024 24.6 5.3 49 242-290 10-68 (80)
62 PRK03072 heat shock protein Ht 34.3 23 0.00049 34.3 1.6 25 128-152 120-144 (288)
63 PRK05457 heat shock protein Ht 34.2 31 0.00067 33.5 2.5 20 129-148 128-147 (284)
64 cd04776 HTH_GnyR Helix-Turn-He 33.7 2.8E+02 0.0061 23.3 8.0 50 240-289 39-99 (118)
65 cd04777 HTH_MerR-like_sg1 Heli 33.2 1.9E+02 0.0041 23.5 6.7 52 240-291 39-102 (107)
66 PRK03001 M48 family peptidase; 33.1 25 0.00054 33.7 1.7 23 129-151 118-140 (283)
67 cd08318 Death_NMPP84 Death dom 32.9 1.1E+02 0.0023 24.6 5.0 46 246-291 21-75 (86)
68 cd01110 HTH_SoxR Helix-Turn-He 32.9 1.6E+02 0.0034 25.5 6.5 61 240-300 41-111 (139)
69 cd08315 Death_TRAILR_DR4_DR5 D 32.2 1.6E+02 0.0035 24.2 6.0 48 244-291 20-76 (96)
70 PF12388 Peptidase_M57: Dual-a 31.7 30 0.00065 32.8 1.9 23 131-153 129-151 (211)
71 COG0339 Dcp Zn-dependent oligo 31.5 38 0.00083 37.2 2.8 32 137-169 469-503 (683)
72 PF13688 Reprolysin_5: Metallo 31.3 32 0.0007 30.3 2.0 23 131-153 138-160 (196)
73 TIGR02044 CueR Cu(I)-responsiv 31.2 1.9E+02 0.004 24.4 6.5 51 241-291 42-100 (127)
74 cd04784 HTH_CadR-PbrR Helix-Tu 31.1 2.2E+02 0.0047 23.9 6.9 51 240-290 41-99 (127)
75 PF13583 Reprolysin_4: Metallo 31.1 25 0.00055 32.3 1.3 17 137-153 139-155 (206)
76 cd06258 Peptidase_M3_like The 31.1 28 0.0006 34.0 1.6 18 137-154 156-173 (365)
77 PF12994 DUF3878: Domain of un 30.8 9.3 0.0002 37.9 -1.7 17 133-149 92-108 (299)
78 PRK04897 heat shock protein Ht 30.8 38 0.00082 33.0 2.5 22 129-150 131-152 (298)
79 TIGR02289 M3_not_pepF oligoend 30.2 41 0.0009 35.2 2.8 17 137-153 339-355 (549)
80 cd01108 HTH_CueR Helix-Turn-He 29.9 3E+02 0.0064 23.2 7.5 51 240-290 41-99 (127)
81 cd04770 HTH_HMRTR Helix-Turn-H 29.4 2.5E+02 0.0053 23.3 6.9 51 241-291 42-100 (123)
82 PF10728 DUF2520: Domain of un 28.7 1.9E+02 0.0042 25.0 6.2 62 236-297 6-67 (132)
83 cd08804 Death_ank2 Death domai 28.7 1.4E+02 0.003 23.9 5.0 46 246-291 18-73 (84)
84 cd04276 ZnMc_MMP_like_2 Zinc-d 28.5 40 0.00087 31.3 2.1 15 133-147 114-128 (197)
85 PRK01345 heat shock protein Ht 28.2 44 0.00096 32.9 2.5 23 130-152 119-141 (317)
86 cd08311 Death_p75NR Death doma 28.1 1.3E+02 0.0028 24.0 4.7 54 246-309 18-71 (77)
87 PRK01265 heat shock protein Ht 27.0 37 0.00081 33.9 1.7 23 128-150 133-155 (324)
88 PF01400 Astacin: Astacin (Pep 26.7 40 0.00088 30.5 1.8 34 136-170 80-116 (191)
89 cd01107 HTH_BmrR Helix-Turn-He 26.5 1.8E+02 0.004 23.8 5.5 44 241-284 43-89 (108)
90 cd04280 ZnMc_astacin_like Zinc 26.3 34 0.00075 30.7 1.2 35 136-170 75-111 (180)
91 cd04787 HTH_HMRTR_unk Helix-Tu 25.2 2.5E+02 0.0054 23.9 6.3 51 240-290 41-99 (133)
92 cd04275 ZnMc_pappalysin_like Z 24.8 9.9 0.00021 35.9 -2.6 20 132-151 134-153 (225)
93 PF13574 Reprolysin_2: Metallo 24.8 44 0.00095 29.8 1.6 20 135-154 111-130 (173)
94 TIGR02047 CadR-PbrR Cd(II)/Pb( 24.5 3.4E+02 0.0074 23.0 7.0 59 240-298 41-108 (127)
95 PF07998 Peptidase_M54: Peptid 24.3 49 0.0011 30.9 1.9 11 137-147 147-157 (194)
96 PRK02870 heat shock protein Ht 24.1 48 0.001 33.2 1.9 18 129-146 167-184 (336)
97 cd04267 ZnMc_ADAM_like Zinc-de 24.1 34 0.00074 30.2 0.8 21 133-153 131-151 (192)
98 TIGR02051 MerR Hg(II)-responsi 24.0 2.6E+02 0.0056 23.5 6.1 52 240-291 40-97 (124)
99 cd04779 HTH_MerR-like_sg4 Heli 23.6 3.5E+02 0.0076 23.5 7.0 22 240-261 40-63 (134)
100 cd04790 HTH_Cfa-like_unk Helix 23.3 2.8E+02 0.0061 24.9 6.5 22 241-262 43-66 (172)
101 cd01282 HTH_MerR-like_sg3 Heli 23.1 2.7E+02 0.0059 23.0 6.0 52 240-291 40-102 (112)
102 PF09471 Peptidase_M64: IgA Pe 23.1 40 0.00086 32.7 1.1 17 133-149 214-230 (264)
103 cd06459 M3B_Oligoendopeptidase 22.8 59 0.0013 32.0 2.2 17 137-153 224-240 (427)
104 PRK13267 archaemetzincin-like 22.7 56 0.0012 29.9 1.9 11 137-147 127-137 (179)
105 cd04283 ZnMc_hatching_enzyme Z 22.7 47 0.001 30.5 1.4 34 137-170 79-114 (182)
106 cd04785 HTH_CadR-PbrR-like Hel 22.4 3.9E+02 0.0083 22.5 6.8 50 241-290 42-99 (126)
107 PF01432 Peptidase_M3: Peptida 22.0 75 0.0016 32.1 2.9 18 137-154 244-261 (458)
108 cd04281 ZnMc_BMP1_TLD Zinc-dep 22.0 48 0.0011 30.8 1.4 17 137-153 89-105 (200)
109 cd04775 HTH_Cfa-like Helix-Tur 21.7 2.2E+02 0.0049 23.1 5.1 50 240-291 41-92 (102)
110 PRK01209 cobD cobalamin biosyn 21.6 1.9E+02 0.0041 28.4 5.5 67 25-110 96-162 (312)
111 PF03186 CobD_Cbib: CobD/Cbib 21.5 2E+02 0.0044 28.0 5.6 68 25-111 93-160 (295)
112 PRK15002 redox-sensitivie tran 21.2 4.4E+02 0.0095 23.5 7.2 60 240-299 51-120 (154)
113 PRK09514 zntR zinc-responsive 21.0 4E+02 0.0087 23.0 6.8 52 240-291 42-102 (140)
114 cd08789 CARD_IPS-1_RIG-I Caspa 20.9 87 0.0019 25.2 2.5 34 31-65 35-69 (84)
115 cd06461 M2_ACE Peptidase famil 20.8 65 0.0014 33.8 2.2 31 276-306 423-455 (477)
116 cd08317 Death_ank Death domain 20.6 2.7E+02 0.0058 21.9 5.2 46 246-291 18-73 (84)
117 PF14044 NETI: NETI protein 20.3 58 0.0013 25.1 1.2 28 290-318 5-32 (57)
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=4e-28 Score=221.24 Aligned_cols=153 Identities=26% Similarity=0.329 Sum_probs=120.2
Q ss_pred chhhHHhhcccC--CCCChhHHHHHHHHhHHHHHHHHHhC--CCCCceecCchhhhcccccccceeEEecchhhHHHHHH
Q 019873 116 DTVESIVEDGSY--VSLKEEDHFMCVQHEAGHFLTGYLLG--VLPKGYEIPSVEALKQDDFTVGRVQFVGFDFLKEVADA 191 (334)
Q Consensus 116 D~~~~llld~~~--r~ls~eer~RIA~HEAGHaLVAyLLg--iPV~gyTI~p~eal~~G~~g~gGv~f~~~e~~~e~~e~ 191 (334)
+++++++++... +.+++++|+|+|+||||||+|+|+++ .||.++||.| +|. ..|.+.|.+.+
T Consensus 7 ~a~drv~~G~~~~~~~~~~~~~~~~A~HEAGhAvva~~l~~~~~v~~vsi~p-----rg~-~~G~~~~~~~~-------- 72 (213)
T PF01434_consen 7 EAIDRVLMGPEKKSRKLSEEEKRRIAYHEAGHAVVAYLLPPADPVSKVSIVP-----RGS-ALGFTQFTPDE-------- 72 (213)
T ss_dssp HHHHHHHCCSCCTTS---HHHHHHHHHHHHHHHHHHHHSSS---EEEEESST-----TCC-CCHCCEECHHT--------
T ss_pred HHHHHHhcCcCcCCCCCCHHHHHHHHHHHHHHHHHHHHhcccccEEEEEEec-----CCC-cceeEEeccch--------
Confidence 366888888543 66899999999999999999999998 5999999999 332 33445554322
Q ss_pred hhhcccCCCCCCCCcccccCHHHHHHHHHHHhhHHHHHHHHhC--C-ccchhhHHHHHHHHHHH----hCCCcc------
Q 019873 192 RKQKKDTGQVGSWGNRGEISVKTLNNFSCVILGGLVAEHLVFG--H-SEGHYSDINKLDKVFQW----LGYNKS------ 258 (334)
Q Consensus 192 r~~~~d~~~~~~~~~~~~~t~~~L~r~~~VlLAGrAAE~LvfG--~-atGg~~Dl~qat~l~r~----lGms~~------ 258 (334)
+++..|+.++.+.++|+|||||||+++|| + ++|+++|++++|++++. |||+.+
T Consensus 73 --------------~~~~~t~~~l~~~i~v~LaGraAEe~~~g~~~~stGa~~DL~~At~iA~~mv~~~Gm~~~~g~~~~ 138 (213)
T PF01434_consen 73 --------------DRYIRTRSYLEDRICVLLAGRAAEELFFGEDNVSTGASSDLQQATEIARKMVASYGMGDSLGLLSY 138 (213)
T ss_dssp --------------T-SS-BHHHHHHHHHHHHHHHHHHHHHHSCCS-BGGGHHHHHHHHHHHHHHHHTST-TTTTTSS-S
T ss_pred --------------hcccccHHHHHhhHHHHHHHHHHHHhhcCcceecccchhHHHHHHHHHHHHHHHhCCCCCCceeee
Confidence 34568999999999999999999999999 4 57999999999999885 688751
Q ss_pred --------------------------hhHHHH----HHHHHHHHHHHHHcHHHHHHHHHHHHhhCcHH
Q 019873 259 --------------------------EADSQV----KWAALNTVLISHHHIQVRSRLAEAMALGRSIG 296 (334)
Q Consensus 259 --------------------------~id~ev----r~A~~~A~~LL~~hr~aleaLAeaL~e~esl~ 296 (334)
.++.++ ..||.+|++||++|++.+++||++|+++++|.
T Consensus 139 ~~~~~~~~~~~~~~~~~~~~s~~~~~~i~~ev~~lL~~a~~~a~~iL~~~r~~l~~la~~Lle~~~L~ 206 (213)
T PF01434_consen 139 SPNDDDEVFLGREWNSRRPMSEETRALIDREVRKLLEEAYARAKEILEENREALEALAEALLEKETLS 206 (213)
T ss_dssp EEEE-S-SSS-E---EEESS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHSEEE
T ss_pred eccccccccccccccccCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCeeC
Confidence 123333 36999999999999999999999999999995
No 2
>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=1.5e-26 Score=235.57 Aligned_cols=158 Identities=20% Similarity=0.189 Sum_probs=135.1
Q ss_pred hHHhhccc--CCCCChhHHHHHHHHhHHHHHHHHHhC--CCCCceecCchhhhccccccc-ceeEEecchhhHHHHHHhh
Q 019873 119 ESIVEDGS--YVSLKEEDHFMCVQHEAGHFLTGYLLG--VLPKGYEIPSVEALKQDDFTV-GRVQFVGFDFLKEVADARK 193 (334)
Q Consensus 119 ~~llld~~--~r~ls~eer~RIA~HEAGHaLVAyLLg--iPV~gyTI~p~eal~~G~~g~-gGv~f~~~e~~~e~~e~r~ 193 (334)
++|+++.. +++++++-|+.+||||+||+|||+.+. .|++|.||.| +|+ .|..+..|+.
T Consensus 539 DrIlMG~ERks~~i~~eak~~TAyHE~GHAivA~yTk~A~PlhKaTImP--------RG~sLG~t~~LPe~--------- 601 (752)
T KOG0734|consen 539 DRILMGPERKSMVIDEEAKKITAYHEGGHAIVALYTKGAMPLHKATIMP--------RGPSLGHTSQLPEK--------- 601 (752)
T ss_pred hheeecccccccccChhhhhhhhhhccCceEEEeecCCCccccceeecc--------CCccccceeecCcc---------
Confidence 88999854 678899999999999999999999998 5999999999 665 3444544441
Q ss_pred hcccCCCCCCCCcccccCHHHHHHHHHHHhhHHHHHHHHhCC---ccchhhHHHHHHHHHHH----hCCCcc--------
Q 019873 194 QKKDTGQVGSWGNRGEISVKTLNNFSCVILGGLVAEHLVFGH---SEGHYSDINKLDKVFQW----LGYNKS-------- 258 (334)
Q Consensus 194 ~~~d~~~~~~~~~~~~~t~~~L~r~~~VlLAGrAAE~LvfG~---atGg~~Dl~qat~l~r~----lGms~~-------- 258 (334)
|++.+|+.++..++-|+||||+||+|+||. .+|+++|++|+|++++. ||||++
T Consensus 602 ------------D~~~~Tk~q~LA~lDV~MGGRvAEELIfG~D~iTsGAssDl~qAT~lA~~MVt~fGMSd~vG~v~~~~ 669 (752)
T KOG0734|consen 602 ------------DRYSITKAQLLARLDVCMGGRVAEELIFGTDKITSGASSDLDQATKLARRMVTKFGMSDKVGPVTLSA 669 (752)
T ss_pred ------------chhhHHHHHHHHHHHHhhcchHHHHHhccCCcccccccchHHHHHHHHHHHHHHcCccccccceeeec
Confidence 678999999999999999999999999997 36999999999999875 899862
Q ss_pred -------------hhHHHH----HHHHHHHHHHHHHcHHHHHHHHHHHHhhCcHH--HHHHHHhch
Q 019873 259 -------------EADSQV----KWAALNTVLISHHHIQVRSRLAEAMALGRSIG--SYTSKILTE 305 (334)
Q Consensus 259 -------------~id~ev----r~A~~~A~~LL~~hr~aleaLAeaL~e~esl~--eci~~Ie~~ 305 (334)
.+|+|| +.+|++|+.||+.|...+++||+||+++||++ |..++++..
T Consensus 670 ~~~~~s~~~~t~~lidaEi~~lL~~sYeRak~iL~~h~kEl~~LA~ALleYETL~A~eik~vl~g~ 735 (752)
T KOG0734|consen 670 EDNSSSLSPRTQELIDAEIKRLLRDSYERAKSILKTHKKELHALAEALLEYETLDAKEIKRVLKGK 735 (752)
T ss_pred cCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHhcc
Confidence 267776 46999999999999999999999999999996 555555544
No 3
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=99.92 E-value=1.4e-24 Score=226.10 Aligned_cols=160 Identities=18% Similarity=0.211 Sum_probs=129.1
Q ss_pred hhhHHhhcc--cCCCCChhHHHHHHHHhHHHHHHHHHhC--CCCCceecCchhhhccccccc-ceeEEecchhhHHHHHH
Q 019873 117 TVESIVEDG--SYVSLKEEDHFMCVQHEAGHFLTGYLLG--VLPKGYEIPSVEALKQDDFTV-GRVQFVGFDFLKEVADA 191 (334)
Q Consensus 117 ~~~~llld~--~~r~ls~eer~RIA~HEAGHaLVAyLLg--iPV~gyTI~p~eal~~G~~g~-gGv~f~~~e~~~e~~e~ 191 (334)
++.++..+. ....+++++|+++|||||||++|+++++ .||+++||.| +|. +|+++..|+
T Consensus 388 a~~~v~~g~~~~~~~~~~~~~~~~a~he~gha~~~~~~~~~~~~~~v~i~p--------rg~~~g~~~~~~~-------- 451 (644)
T PRK10733 388 AKDKIMMGAERRSMVMTEAQKESTAYHEAGHAIIGRLVPEHDPVHKVTIIP--------RGRALGVTFFLPE-------- 451 (644)
T ss_pred HHHHHhcccccccccccHHHHHHHHHHHHHHHHHHHHccCCCceeEEEEec--------cCCCcceeEECCC--------
Confidence 335555543 2345789999999999999999999998 6999999999 332 354443332
Q ss_pred hhhcccCCCCCCCCcccccCHHHHHHHHHHHhhHHHHHHHHhCC---ccchhhHHHHHHHHHHH----hCCCcc------
Q 019873 192 RKQKKDTGQVGSWGNRGEISVKTLNNFSCVILGGLVAEHLVFGH---SEGHYSDINKLDKVFQW----LGYNKS------ 258 (334)
Q Consensus 192 r~~~~d~~~~~~~~~~~~~t~~~L~r~~~VlLAGrAAE~LvfG~---atGg~~Dl~qat~l~r~----lGms~~------ 258 (334)
+ ++...|+++|.+.++|+|||||||+++||. ++|+++|+++||++++. ||||++
T Consensus 452 -----~--------~~~~~~~~~l~~~i~~~lgGraAE~~~~g~~~~ttGa~~Dl~~AT~lA~~mv~~~Gms~~lg~~~~ 518 (644)
T PRK10733 452 -----G--------DAISASRQKLESQISTLYGGRLAEEIIYGPEHVSTGASNDIKVATNLARNMVTQWGFSEKLGPLLY 518 (644)
T ss_pred -----c--------ccccccHHHHHHHHHHHHhhHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhCCCccccchhh
Confidence 1 455689999999999999999999999984 57999999999999874 798851
Q ss_pred -------------------------hhHHHH----HHHHHHHHHHHHHcHHHHHHHHHHHHhhCcHH--HHHHHHhch
Q 019873 259 -------------------------EADSQV----KWAALNTVLISHHHIQVRSRLAEAMALGRSIG--SYTSKILTE 305 (334)
Q Consensus 259 -------------------------~id~ev----r~A~~~A~~LL~~hr~aleaLAeaL~e~esl~--eci~~Ie~~ 305 (334)
.+|+++ ..||.+|++||++|++.+++||++|+++|||+ +..++|...
T Consensus 519 ~~~~~~~~lg~~~~~~~~~s~~~~~~id~ev~~il~~~~~~a~~iL~~~~~~l~~la~~Lle~etl~~~ei~~i~~~~ 596 (644)
T PRK10733 519 AEEEGEVFLGRSVAKAKHMSDETARIIDQEVKALIERNYNRARQLLTDNMDILHAMKDALMKYETIDAPQIDDLMARR 596 (644)
T ss_pred cccccccccccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhceeCHHHHHHHHhcC
Confidence 145664 47999999999999999999999999999995 777777654
No 4
>CHL00176 ftsH cell division protein; Validated
Probab=99.92 E-value=1.3e-24 Score=226.70 Aligned_cols=160 Identities=16% Similarity=0.206 Sum_probs=129.8
Q ss_pred hhhHHhhcccC-CCCChhHHHHHHHHhHHHHHHHHHhC--CCCCceecCchhhhcccccc-cceeEEecchhhHHHHHHh
Q 019873 117 TVESIVEDGSY-VSLKEEDHFMCVQHEAGHFLTGYLLG--VLPKGYEIPSVEALKQDDFT-VGRVQFVGFDFLKEVADAR 192 (334)
Q Consensus 117 ~~~~llld~~~-r~ls~eer~RIA~HEAGHaLVAyLLg--iPV~gyTI~p~eal~~G~~g-~gGv~f~~~e~~~e~~e~r 192 (334)
++..++.+... ...++++|++|||||||||+|+++++ .||+++||.| +| .+|+++..|+
T Consensus 419 Ai~rv~~g~~~~~~~~~~~~~~vA~hEaGhA~v~~~l~~~~~v~kvtI~p--------rg~~~G~~~~~p~--------- 481 (638)
T CHL00176 419 AIDRVIAGLEGTPLEDSKNKRLIAYHEVGHAIVGTLLPNHDPVQKVTLIP--------RGQAKGLTWFTPE--------- 481 (638)
T ss_pred HHHHHHhhhccCccccHHHHHHHHHHhhhhHHHHhhccCCCceEEEEEee--------cCCCCCceEecCC---------
Confidence 44666665332 34578999999999999999999998 5999999999 33 2455544332
Q ss_pred hhcccCCCCCCCCcccccCHHHHHHHHHHHhhHHHHHHHHhCC---ccchhhHHHHHHHHHHH----hCCCc--------
Q 019873 193 KQKKDTGQVGSWGNRGEISVKTLNNFSCVILGGLVAEHLVFGH---SEGHYSDINKLDKVFQW----LGYNK-------- 257 (334)
Q Consensus 193 ~~~~d~~~~~~~~~~~~~t~~~L~r~~~VlLAGrAAE~LvfG~---atGg~~Dl~qat~l~r~----lGms~-------- 257 (334)
+ +++.+|+.++...++++|||||||+++||. ++|+++|++++|++++. |||+.
T Consensus 482 ----~--------~~~~~t~~~l~~~i~~~LgGraAE~~~fg~~~~~~Ga~~Dl~~AT~iA~~mv~~~Gm~~~g~~~~~~ 549 (638)
T CHL00176 482 ----E--------DQSLVSRSQILARIVGALGGRAAEEVVFGSTEVTTGASNDLQQVTNLARQMVTRFGMSSIGPISLES 549 (638)
T ss_pred ----c--------ccccccHHHHHHHHHHHhhhHHHHHHhcCCCCcCCCchhHHHHHHHHHHHHHHHhCCCcCCceeecC
Confidence 1 567899999999999999999999999994 57999999999999885 78862
Q ss_pred -----------------------chhHHHH----HHHHHHHHHHHHHcHHHHHHHHHHHHhhCcHH--HHHHHHhch
Q 019873 258 -----------------------SEADSQV----KWAALNTVLISHHHIQVRSRLAEAMALGRSIG--SYTSKILTE 305 (334)
Q Consensus 258 -----------------------~~id~ev----r~A~~~A~~LL~~hr~aleaLAeaL~e~esl~--eci~~Ie~~ 305 (334)
..+|.++ +.||.+|++||++|++.+++||++|+++|||+ |+.++++..
T Consensus 550 ~~~~~~~~~~~~~~~~~~s~~~~~~iD~ev~~~l~~~~~~a~~iL~~~~~~l~~la~~Lle~Etl~~~ei~~il~~~ 626 (638)
T CHL00176 550 NNSTDPFLGRFMQRNSEYSEEIADKIDMEVRSILHTCYQYAYQILKDNRVLIDLLVELLLQKETIDGDEFREIVNSY 626 (638)
T ss_pred CCCcccccccccccccCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCccCHHHHHHHHhhc
Confidence 0245554 47999999999999999999999999999995 777777654
No 5
>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
Probab=99.92 E-value=2.1e-24 Score=217.20 Aligned_cols=157 Identities=21% Similarity=0.236 Sum_probs=124.2
Q ss_pred hhHHhhcc--cCCCCChhHHHHHHHHhHHHHHHHHHhC--CCCCceecCchhhhcccccccceeEEecchhhHHHHHHhh
Q 019873 118 VESIVEDG--SYVSLKEEDHFMCVQHEAGHFLTGYLLG--VLPKGYEIPSVEALKQDDFTVGRVQFVGFDFLKEVADARK 193 (334)
Q Consensus 118 ~~~llld~--~~r~ls~eer~RIA~HEAGHaLVAyLLg--iPV~gyTI~p~eal~~G~~g~gGv~f~~~e~~~e~~e~r~ 193 (334)
+..+..+. ....+++++|+++|||||||+||+|+++ .|+.++||.|+ |. .+|+.+..+.
T Consensus 292 ~~~~~~~~~~~~~~~~~~~~~~~A~hEaGhAlv~~~l~~~~~v~~vsi~pr-----g~--~~G~~~~~~~---------- 354 (495)
T TIGR01241 292 IDRVIAGPEKKSRVISEKEKKLVAYHEAGHALVGLLLKDADPVHKVTIIPR-----GQ--ALGYTQFLPE---------- 354 (495)
T ss_pred HHHHhcccccccccccHHHHHHHHHHHHhHHHHHHhcCCCCceEEEEEeec-----CC--ccceEEecCc----------
Confidence 34444432 2345789999999999999999999996 69999999982 21 2344433221
Q ss_pred hcccCCCCCCCCcccccCHHHHHHHHHHHhhHHHHHHHHhCCc-cchhhHHHHHHHHHHH----hCCCcc----------
Q 019873 194 QKKDTGQVGSWGNRGEISVKTLNNFSCVILGGLVAEHLVFGHS-EGHYSDINKLDKVFQW----LGYNKS---------- 258 (334)
Q Consensus 194 ~~~d~~~~~~~~~~~~~t~~~L~r~~~VlLAGrAAE~LvfG~a-tGg~~Dl~qat~l~r~----lGms~~---------- 258 (334)
+ +.+..|+++++++++|+|||+|||+++||+. +|+++|+++||++++. |||+..
T Consensus 355 ---~--------~~~~~t~~~l~~~i~v~LaGraAE~~~~G~~s~Ga~~Dl~~At~lA~~mv~~~Gm~~~~g~~~~~~~~ 423 (495)
T TIGR01241 355 ---E--------DKYLYTKSQLLAQIAVLLGGRAAEEIIFGEVTTGASNDIKQATNIARAMVTEWGMSDKLGPVAYGSDG 423 (495)
T ss_pred ---c--------ccccCCHHHHHHHHHHHhhHHHHHHHHhcCCCCCchHHHHHHHHHHHHHHHHhCCCcccCceeeccCc
Confidence 0 3568899999999999999999999999985 6999999999999774 788751
Q ss_pred ---------------------hhHHHH----HHHHHHHHHHHHHcHHHHHHHHHHHHhhCcHH--HHHHHH
Q 019873 259 ---------------------EADSQV----KWAALNTVLISHHHIQVRSRLAEAMALGRSIG--SYTSKI 302 (334)
Q Consensus 259 ---------------------~id~ev----r~A~~~A~~LL~~hr~aleaLAeaL~e~esl~--eci~~I 302 (334)
.++.++ ++|+.+|++||++|++++++||++|+++++|+ |..++|
T Consensus 424 ~~~~l~~~~~~~~~~s~~~~~~id~~v~~lL~~a~~ra~~lL~~~~~~l~~la~~Ll~~e~L~~~ei~~il 494 (495)
T TIGR01241 424 GDVFLGRGFAKAKEYSEETAREIDEEVKRIIEEAYKRAKQILTENRDELELLAKALLEKETITREEIKELL 494 (495)
T ss_pred cccccccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCeeCHHHHHHHh
Confidence 134443 58999999999999999999999999999996 555554
No 6
>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]
Probab=99.90 E-value=1.3e-23 Score=217.13 Aligned_cols=160 Identities=22% Similarity=0.254 Sum_probs=135.2
Q ss_pred chhhHHhhccc--CCCCChhHHHHHHHHhHHHHHHHHHhCC--CCCceecCchhhhcccccc-cceeEEecchhhHHHHH
Q 019873 116 DTVESIVEDGS--YVSLKEEDHFMCVQHEAGHFLTGYLLGV--LPKGYEIPSVEALKQDDFT-VGRVQFVGFDFLKEVAD 190 (334)
Q Consensus 116 D~~~~llld~~--~r~ls~eer~RIA~HEAGHaLVAyLLgi--PV~gyTI~p~eal~~G~~g-~gGv~f~~~e~~~e~~e 190 (334)
++.+.++.+.. ++++++++|+.+|||||||++|+++++. ||+++||.| +| .+|+++..|+
T Consensus 385 ea~drv~~G~erks~vise~ek~~~AYhEaghalv~~~l~~~d~v~KvtIiP--------rG~alG~t~~~Pe------- 449 (596)
T COG0465 385 EAIDRVIAGPERKSRVISEAEKKITAYHEAGHALVGLLLPDADPVHKVTIIP--------RGRALGYTLFLPE------- 449 (596)
T ss_pred HHHHHHhcCcCcCCcccChhhhcchHHHHHHHHHHHHhCCCCcccceeeecc--------CchhhcchhcCCc-------
Confidence 47799999954 5678999999999999999999999995 999999999 44 3566665544
Q ss_pred HhhhcccCCCCCCCCcccccCHHHHHHHHHHHhhHHHHHHHHhC-C-ccchhhHHHHHHHHHHH----hCCCc-------
Q 019873 191 ARKQKKDTGQVGSWGNRGEISVKTLNNFSCVILGGLVAEHLVFG-H-SEGHYSDINKLDKVFQW----LGYNK------- 257 (334)
Q Consensus 191 ~r~~~~d~~~~~~~~~~~~~t~~~L~r~~~VlLAGrAAE~LvfG-~-atGg~~Dl~qat~l~r~----lGms~------- 257 (334)
+ |++.+|++++...++++|||||||+++|| + ++|+++|++++|+++|. ||||.
T Consensus 450 ------~--------d~~l~sk~~l~~~i~~~lgGRaAEel~~g~e~ttGa~~D~~~at~~ar~mVt~~Gms~~lG~v~~ 515 (596)
T COG0465 450 ------E--------DKYLMSKEELLDRIDVLLGGRAAEELIFGYEITTGASNDLEKATDLARAMVTEYGMSAKLGPVAY 515 (596)
T ss_pred ------c--------ccccccHHHHHHHHHHHhCCcHhhhhhhcccccccchhhHHHHHHHHHHhhhhcCcchhhCceeh
Confidence 1 58999999999999999999999999999 7 57999999999999885 78884
Q ss_pred ----------------------chhHHHHH----HHHHHHHHHHHHcHHHHHHHHHHHHhhCcHH--HHHHHHhc
Q 019873 258 ----------------------SEADSQVK----WAALNTVLISHHHIQVRSRLAEAMALGRSIG--SYTSKILT 304 (334)
Q Consensus 258 ----------------------~~id~evr----~A~~~A~~LL~~hr~aleaLAeaL~e~esl~--eci~~Ie~ 304 (334)
..||.+++ .||.+++.||.+|++.++.++++|+++||+. +..++++.
T Consensus 516 ~~~~~~flg~~~~~~~~Se~ta~~ID~evk~ii~~~y~~a~~il~~~~~~l~~~~~~Lle~Eti~~~~i~~i~~~ 590 (596)
T COG0465 516 EQVEGVFLGRYQKAKNYSEETAQEIDREVKDIIDEAYERAKELLNENKDALETLAEMLLEKETIDAEEIKDILAG 590 (596)
T ss_pred hhcccccccccccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhccCHHHHHHHHhc
Confidence 12566654 6999999999999999999999999999985 44444443
No 7
>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.87 E-value=5.9e-22 Score=208.90 Aligned_cols=200 Identities=18% Similarity=0.162 Sum_probs=153.6
Q ss_pred hchhhhhhhhhhhhhhHHHHHhhh-----------hhccccccc-chhhHHhhccc--CCCCChhHHHHHHHHhHHHHHH
Q 019873 83 DSKELLTLRALFDSVMESIERCNL-----------FDSLDEAPS-DTVESIVEDGS--YVSLKEEDHFMCVQHEAGHFLT 148 (334)
Q Consensus 83 ~~it~~~ll~P~~~~s~~i~~~~~-----------~~~l~~~t~-D~~~~llld~~--~r~ls~eer~RIA~HEAGHaLV 148 (334)
+.++++.+-.-.-+.+++..++.+ -..++...+ |+++.++.+.. ++.+++++++.+|||||||+++
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 455555555555556666666543 111111111 36677777643 5778999999999999999999
Q ss_pred HHHhC--CCCCceecCchhhhcccccccceeEEecchhhHHHHHHhhhcccCCCCCCCCcccccCHHHHHHHHHHHhhHH
Q 019873 149 GYLLG--VLPKGYEIPSVEALKQDDFTVGRVQFVGFDFLKEVADARKQKKDTGQVGSWGNRGEISVKTLNNFSCVILGGL 226 (334)
Q Consensus 149 AyLLg--iPV~gyTI~p~eal~~G~~g~gGv~f~~~e~~~e~~e~r~~~~d~~~~~~~~~~~~~t~~~L~r~~~VlLAGr 226 (334)
+++++ .|+-++||+| |+ .. |+.+..|. +.+.+|+++|...+|++||||
T Consensus 583 g~~l~~~dpl~kvsIiP------Gq-al-G~a~~~P~----------------------~~~l~sk~ql~~rm~m~LGGR 632 (774)
T KOG0731|consen 583 GWLLEHADPLLKVSIIP------GQ-AL-GYAQYLPT----------------------DDYLLSKEQLFDRMVMALGGR 632 (774)
T ss_pred hccccccCcceeEEecc------CC-cc-ceEEECCc----------------------ccccccHHHHHHHHHHHhCcc
Confidence 98888 4999999999 53 33 44444333 348999999999999999999
Q ss_pred HHHHHHhC-C-ccchhhHHHHHHHHHHH----hCCCcc--------------------------hhHHHHH----HHHHH
Q 019873 227 VAEHLVFG-H-SEGHYSDINKLDKVFQW----LGYNKS--------------------------EADSQVK----WAALN 270 (334)
Q Consensus 227 AAE~LvfG-~-atGg~~Dl~qat~l~r~----lGms~~--------------------------~id~evr----~A~~~ 270 (334)
|||+++|| + ++|++||++++|++++. +|||+. .||.+++ .||+.
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 57999999999999885 788731 3677765 49999
Q ss_pred HHHHHHHcHHHHHHHHHHHHhhCcH--HHHHHHHhchhhhhhhh
Q 019873 271 TVLISHHHIQVRSRLAEAMALGRSI--GSYTSKILTEQSLELLR 312 (334)
Q Consensus 271 A~~LL~~hr~aleaLAeaL~e~esl--~eci~~Ie~~~~~~~l~ 312 (334)
|..+|++|++.++.+|+.|+++++| +++++++...-+.+++.
T Consensus 713 ~~~ll~~n~~~l~~ia~~LLeke~l~~ee~~~ll~~~~~~~~~~ 756 (774)
T KOG0731|consen 713 TKELLRTNRDKLDKIAEVLLEKEVLTGEEIIALLGERPPGMPEK 756 (774)
T ss_pred HHHHHHHhHHHHHHHHHHHHHhhhccHHHHHHHhccCCCccccc
Confidence 9999999999999999999999988 49999998877765433
No 8
>CHL00206 ycf2 Ycf2; Provisional
Probab=98.59 E-value=7.5e-08 Score=110.55 Aligned_cols=109 Identities=13% Similarity=-0.022 Sum_probs=75.3
Q ss_pred hhhHHhhcccCCCCChhHHHHHHHHhHHHHHHHHHhC--CCCCceecCc-hhhhcccccccceeEEecchhhHHHHHHhh
Q 019873 117 TVESIVEDGSYVSLKEEDHFMCVQHEAGHFLTGYLLG--VLPKGYEIPS-VEALKQDDFTVGRVQFVGFDFLKEVADARK 193 (334)
Q Consensus 117 ~~~~llld~~~r~ls~eer~RIA~HEAGHaLVAyLLg--iPV~gyTI~p-~eal~~G~~g~gGv~f~~~e~~~e~~e~r~ 193 (334)
++.+.+.|...+..+.+++ +||+||+|||+|+.++. .||.++||.+ -..++.| ...|+++..+.
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 5577777755555455555 48999999999999986 6999999843 2333333 22244443321
Q ss_pred hcccCCCCCCCCcccccCHHHHHHHHHHHhhHHHHHHHHhCCc-------c--ch-hhHHHHHHHHHH
Q 019873 194 QKKDTGQVGSWGNRGEISVKTLNNFSCVILGGLVAEHLVFGHS-------E--GH-YSDINKLDKVFQ 251 (334)
Q Consensus 194 ~~~d~~~~~~~~~~~~~t~~~L~r~~~VlLAGrAAE~LvfG~a-------t--Gg-~~Dl~qat~l~r 251 (334)
...+++.++..+++++|||+|||.+.|... + |- .+|+.-+-.++.
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 257899999999999999999999999532 1 21 356666666655
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=96.72 E-value=0.0011 Score=60.14 Aligned_cols=25 Identities=40% Similarity=0.700 Sum_probs=22.6
Q ss_pred HHHHHhHHHHHHHHHhCCCCCceec
Q 019873 137 MCVQHEAGHFLTGYLLGVLPKGYEI 161 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLgiPV~gyTI 161 (334)
-|..||.||+++|...|++|.++++
T Consensus 11 ~v~iHElGH~~~Ar~~Gv~v~~f~i 35 (182)
T cd06163 11 LIFVHELGHFLVAKLFGVKVEEFSI 35 (182)
T ss_pred HHHHHHHHHHHHHHHcCCeeeEeee
Confidence 4789999999999999999998765
No 10
>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=95.80 E-value=0.014 Score=54.61 Aligned_cols=27 Identities=22% Similarity=0.277 Sum_probs=25.5
Q ss_pred HHHHHhHHHHHHHHHhCCCCCceecCc
Q 019873 137 MCVQHEAGHFLTGYLLGVLPKGYEIPS 163 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLgiPV~gyTI~p 163 (334)
-+..||.||+++|..+|.+++++++.|
T Consensus 55 ~v~iHElgH~~~A~~~G~~v~~i~l~p 81 (227)
T cd06164 55 SVLLHELGHSLVARRYGIPVRSITLFL 81 (227)
T ss_pred HHHHHHHHHHHHHHHcCCeECeEEEEe
Confidence 588999999999999999999999987
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=95.79 E-value=0.0079 Score=60.69 Aligned_cols=25 Identities=36% Similarity=0.659 Sum_probs=22.3
Q ss_pred HHHHHhHHHHHHHHHhCCCCCceec
Q 019873 137 MCVQHEAGHFLTGYLLGVLPKGYEI 161 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLgiPV~gyTI 161 (334)
.|..||.||||+|...|+.|..++|
T Consensus 16 ~v~~HE~gH~~~a~~~g~~v~~Fsi 40 (420)
T TIGR00054 16 LIFVHELGHFLAARLCGIKVERFSI 40 (420)
T ss_pred HHHHHhHHHHHHHHHcCCEEEEEEE
Confidence 5899999999999999998887666
No 12
>PF13398 Peptidase_M50B: Peptidase M50B-like
Probab=95.47 E-value=0.015 Score=53.16 Aligned_cols=27 Identities=33% Similarity=0.397 Sum_probs=25.5
Q ss_pred HHHHHhHHHHHHHHHhCCCCCceecCc
Q 019873 137 MCVQHEAGHFLTGYLLGVLPKGYEIPS 163 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLgiPV~gyTI~p 163 (334)
-+..||.||+++|.++|.-++++++.|
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 489999999999999999999999987
No 13
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=95.00 E-value=0.014 Score=59.19 Aligned_cols=26 Identities=31% Similarity=0.454 Sum_probs=24.1
Q ss_pred HHHHHhHHHHHHHHHhCCCCCceecC
Q 019873 137 MCVQHEAGHFLTGYLLGVLPKGYEIP 162 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLgiPV~gyTI~ 162 (334)
.|..||.||||+|.+.|+.|..++|.
T Consensus 17 li~vHElGHfl~Ar~~gv~V~~FsiG 42 (449)
T PRK10779 17 LITVHEFGHFWVARRCGVRVERFSIG 42 (449)
T ss_pred HHHHHHHHHHHHHHHcCCeeeEEEee
Confidence 58899999999999999999999884
No 14
>cd05709 S2P-M50 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. The domain core structure appears to contain at least three transmembrane helices with a catalytic zinc atom coordinated by three conserved residues contained within the consensus sequence HExxH, together with a conserved aspartate residue. The S2P/M50 family of RIP proteases is widely distributed; in eukaryotic cells, they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum (ER) stress responses. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of sterol regulatory element-bindin
Probab=94.98 E-value=0.023 Score=50.20 Aligned_cols=25 Identities=32% Similarity=0.345 Sum_probs=20.8
Q ss_pred HHHHHhHHHHHHHHHhCCCCCceec
Q 019873 137 MCVQHEAGHFLTGYLLGVLPKGYEI 161 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLgiPV~gyTI 161 (334)
-+..||.||+++|+..|+++...++
T Consensus 10 ~i~iHE~gH~~~A~~~G~~~~~~~~ 34 (180)
T cd05709 10 SVTVHELGHALVARRLGVKVARFSG 34 (180)
T ss_pred HHHHHHHHHHHHHHHcCCCchheee
Confidence 3789999999999999997765544
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=94.52 E-value=0.059 Score=52.43 Aligned_cols=27 Identities=30% Similarity=0.238 Sum_probs=24.3
Q ss_pred HHHHHhHHHHHHHHHhCCCCCceecCc
Q 019873 137 MCVQHEAGHFLTGYLLGVLPKGYEIPS 163 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLgiPV~gyTI~p 163 (334)
-+..||.||+++|...|++|+++.+.+
T Consensus 137 svvvHElgHal~A~~~gi~V~~iGl~l 163 (277)
T cd06162 137 SGVVHEMGHGVAAVREQVRVNGFGIFF 163 (277)
T ss_pred HHHHHHHHHHHHHHHcCCeeceEEEee
Confidence 478999999999999999999988764
No 16
>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=94.32 E-value=0.031 Score=51.30 Aligned_cols=27 Identities=22% Similarity=0.333 Sum_probs=25.6
Q ss_pred HHHHHhHHHHHHHHHhCCCCCceecCc
Q 019873 137 MCVQHEAGHFLTGYLLGVLPKGYEIPS 163 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLgiPV~gyTI~p 163 (334)
-+..||.||+++|..+|.+++++++.|
T Consensus 40 ~v~iHElgH~~~A~~~G~~v~~i~l~p 66 (208)
T cd06161 40 SVLLHELGHALVARRYGIRVRSITLLP 66 (208)
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEe
Confidence 589999999999999999999999987
No 17
>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=93.52 E-value=0.048 Score=48.30 Aligned_cols=26 Identities=35% Similarity=0.336 Sum_probs=18.5
Q ss_pred HHHHHhHHHHHHHHHhCCCCCceecC
Q 019873 137 MCVQHEAGHFLTGYLLGVLPKGYEIP 162 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLgiPV~gyTI~ 162 (334)
-+..||.||+++|+..|.++..+++.
T Consensus 9 ~i~~HE~gH~~~a~~~G~~~~~~~~~ 34 (192)
T PF02163_consen 9 SIVLHELGHALAARLYGDKVPRFEGG 34 (192)
T ss_dssp HHHHHHHHHHHHHHTTT--B--EEE-
T ss_pred cccccccccccccccccccccccccc
Confidence 37899999999999999988888543
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=91.45 E-value=0.16 Score=46.32 Aligned_cols=27 Identities=26% Similarity=0.230 Sum_probs=24.7
Q ss_pred HHHHHhHHHHHHHHHhCCCCCceecCc
Q 019873 137 MCVQHEAGHFLTGYLLGVLPKGYEIPS 163 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLgiPV~gyTI~p 163 (334)
-+..||.||+++|...|++++...+.|
T Consensus 43 ~l~iHElgH~~~A~~~G~~~~~~~l~P 69 (183)
T cd06160 43 ILGIHEMGHYLAARRHGVKASLPYFIP 69 (183)
T ss_pred HHHHHHHHHHHHHHHCCCCccceeeee
Confidence 578999999999999999999888877
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=88.03 E-value=0.37 Score=43.64 Aligned_cols=26 Identities=23% Similarity=0.273 Sum_probs=21.1
Q ss_pred HHHHhHHHHHHHHHhCCCCCc----eecCc
Q 019873 138 CVQHEAGHFLTGYLLGVLPKG----YEIPS 163 (334)
Q Consensus 138 IA~HEAGHaLVAyLLgiPV~g----yTI~p 163 (334)
+..||.||+++|+..|++..+ .|+.|
T Consensus 12 i~~HE~aHa~~A~~~Gd~t~~~~Grltlnp 41 (181)
T cd06158 12 ITLHEFAHAYVAYRLGDPTARRAGRLTLNP 41 (181)
T ss_pred HHHHHHHHHHHHHHcCCcHHHHcCceecCc
Confidence 688999999999999986553 55555
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=87.62 E-value=0.31 Score=46.97 Aligned_cols=25 Identities=24% Similarity=0.197 Sum_probs=22.0
Q ss_pred HHHHHhHHHHHHHHHhCCCCCceec
Q 019873 137 MCVQHEAGHFLTGYLLGVLPKGYEI 161 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLgiPV~gyTI 161 (334)
-+..||.||+++|...|++|+.+.+
T Consensus 120 sv~iHElgHa~~Ar~~G~~V~~iGl 144 (263)
T cd06159 120 GVVVHELSHGILARVEGIKVKSGGL 144 (263)
T ss_pred HHHHHHHHHHHHHHHcCCEECchhH
Confidence 4889999999999999999887654
No 21
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=84.85 E-value=0.67 Score=43.78 Aligned_cols=23 Identities=35% Similarity=0.417 Sum_probs=17.7
Q ss_pred HHHHHhHHHHHHHHHhCCCCCcee
Q 019873 137 MCVQHEAGHFLTGYLLGVLPKGYE 160 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLgiPV~gyT 160 (334)
-|.+||.||+|+..+ ++||.|-.
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 57766543
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=82.07 E-value=0.64 Score=39.24 Aligned_cols=17 Identities=35% Similarity=0.399 Sum_probs=14.4
Q ss_pred ChhHHHHHHHHhHHHHH
Q 019873 131 KEEDHFMCVQHEAGHFL 147 (334)
Q Consensus 131 s~eer~RIA~HEAGHaL 147 (334)
+..+...|+.||.||+|
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=77.86 E-value=1.5 Score=37.93 Aligned_cols=20 Identities=30% Similarity=0.292 Sum_probs=15.6
Q ss_pred hhHHHHHHHHhHHHHHHHHH
Q 019873 132 EEDHFMCVQHEAGHFLTGYL 151 (334)
Q Consensus 132 ~eer~RIA~HEAGHaLVAyL 151 (334)
..+.+.|+.||.||+|=-..
T Consensus 101 ~~~~~~~~~HEiGHaLGL~H 120 (156)
T cd04279 101 AENLQAIALHELGHALGLWH 120 (156)
T ss_pred chHHHHHHHHHhhhhhcCCC
Confidence 46788999999999874333
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=75.91 E-value=1.7 Score=37.15 Aligned_cols=17 Identities=29% Similarity=0.286 Sum_probs=14.3
Q ss_pred hhHHHHHHHHhHHHHHH
Q 019873 132 EEDHFMCVQHEAGHFLT 148 (334)
Q Consensus 132 ~eer~RIA~HEAGHaLV 148 (334)
..+...++.||.||+|=
T Consensus 91 ~~~~~~~~~HEiGHaLG 107 (165)
T cd04268 91 GARLRNTAEHELGHALG 107 (165)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 45788999999999963
No 25
>PF04298 Zn_peptidase_2: Putative neutral zinc metallopeptidase; InterPro: IPR007395 Members of this family of bacterial proteins are described as hypothetical proteins or zinc-dependent proteases. The majority have a HExxH zinc-binding motif characteristic of neutral zinc metallopeptidases, however there is no evidence to support their function as metallopeptidases.
Probab=73.36 E-value=1.8 Score=41.25 Aligned_cols=12 Identities=33% Similarity=0.612 Sum_probs=10.5
Q ss_pred HHHHHhHHHHHH
Q 019873 137 MCVQHEAGHFLT 148 (334)
Q Consensus 137 RIA~HEAGHaLV 148 (334)
-||.||+||++=
T Consensus 91 aVAAHEvGHAiQ 102 (222)
T PF04298_consen 91 AVAAHEVGHAIQ 102 (222)
T ss_pred HHHHHHHhHHHh
Confidence 589999999974
No 26
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=71.57 E-value=2.7 Score=43.47 Aligned_cols=25 Identities=40% Similarity=0.538 Sum_probs=22.1
Q ss_pred HHHHHhHHHHHHHHHhCCCCCceec
Q 019873 137 MCVQHEAGHFLTGYLLGVLPKGYEI 161 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLgiPV~gyTI 161 (334)
-+..||.||+|+|..-|+|+.++-|
T Consensus 133 ~~vvHElGHalAA~segV~vngfgI 157 (484)
T KOG2921|consen 133 TVVVHELGHALAAASEGVQVNGFGI 157 (484)
T ss_pred HHHHHHhhHHHHHHhcCceeeeeEE
Confidence 3578999999999999999998766
No 27
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=70.76 E-value=2.8 Score=40.79 Aligned_cols=26 Identities=31% Similarity=0.484 Sum_probs=23.4
Q ss_pred HHHHHhHHHHHHHHHhCCCCCceecC
Q 019873 137 MCVQHEAGHFLTGYLLGVLPKGYEIP 162 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLgiPV~gyTI~ 162 (334)
.|..||.||+|+++..+..|+.+++.
T Consensus 15 lv~~he~gh~~~a~~~~~~v~~f~ig 40 (375)
T COG0750 15 LVFVHELGHFWVARRCGVKVERFSIG 40 (375)
T ss_pred HHHHHHHhhHHHHHhcCceeEEEEec
Confidence 58999999999999999888888874
No 28
>cd04278 ZnMc_MMP Zinc-dependent metalloprotease, matrix metalloproteinase (MMP) sub-family. MMPs are responsible for a great deal of pericellular proteolysis of extracellular matrix and cell surface molecules, playing crucial roles in morphogenesis, cell fate specification, cell migration, tissue repair, tumorigenesis, gain or loss of tissue-specific functions, and apoptosis. In many instances, they are anchored to cell membranes via trans-membrane domains, and their activity is controlled via TIMPs (tissue inhibitors of metalloproteinases).
Probab=69.35 E-value=2.2 Score=36.96 Aligned_cols=17 Identities=41% Similarity=0.577 Sum_probs=14.2
Q ss_pred ChhHHHHHHHHhHHHHH
Q 019873 131 KEEDHFMCVQHEAGHFL 147 (334)
Q Consensus 131 s~eer~RIA~HEAGHaL 147 (334)
+..+...|+.||.||+|
T Consensus 103 ~~~~~~~~~~HEiGHaL 119 (157)
T cd04278 103 GGTDLFSVAAHEIGHAL 119 (157)
T ss_pred ccchHHHHHHHHhcccc
Confidence 34678899999999984
No 29
>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=69.20 E-value=3.4 Score=36.51 Aligned_cols=52 Identities=19% Similarity=0.174 Sum_probs=23.3
Q ss_pred hHHhhcccCCCCCh-hHHHHHHHHhHHHHHHHHHhCCCCCceecCchhhhcccccccceeEEecc
Q 019873 119 ESIVEDGSYVSLKE-EDHFMCVQHEAGHFLTGYLLGVLPKGYEIPSVEALKQDDFTVGRVQFVGF 182 (334)
Q Consensus 119 ~~llld~~~r~ls~-eer~RIA~HEAGHaLVAyLLgiPV~gyTI~p~eal~~G~~g~gGv~f~~~ 182 (334)
+.|++|.-. .+ =+.-||+.||.||.| |+| ..|+= |=-.|..| +..|+.+..+
T Consensus 63 G~I~l~~~~---~qgy~~~RIaaHE~GHiL-----GLP-D~y~G-pCS~LMSG--~~aG~sCtN~ 115 (132)
T PF02031_consen 63 GYIFLDYQQ---NQGYNSTRIAAHELGHIL-----GLP-DHYPG-PCSELMSG--GSAGTSCTNA 115 (132)
T ss_dssp EEEEEEHHH---HHHS-HHHHHHHHHHHHH-----T-----TTS--TT-GGGT--TTT-TT----
T ss_pred EEEEechHH---hhCCccceeeeehhcccc-----CCC-CCCCC-ccHHhhcC--CCCCCCCCCC
Confidence 677777321 12 234589999999964 654 22221 32334444 4456777544
No 30
>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=67.26 E-value=23 Score=30.58 Aligned_cols=68 Identities=12% Similarity=0.113 Sum_probs=47.2
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHH-----HHHHHHHHHHHHcHHHHHHHHHHHHh-hCcHHHHHHHHhchhh
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVK-----WAALNTVLISHHHIQVRSRLAEAMAL-GRSIGSYTSKILTEQS 307 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr-----~A~~~A~~LL~~hr~aleaLAeaL~e-~esl~eci~~Ie~~~~ 307 (334)
.+|+..+.-| ++.+|||-++|..-+. +.......+|+++...++...+.|.+ +..|.+++..+++..+
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 4677777766 5678998877655432 12346677888888888877777776 5577888888776543
No 31
>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=65.09 E-value=3.3 Score=36.69 Aligned_cols=18 Identities=28% Similarity=0.458 Sum_probs=14.0
Q ss_pred ChhHHHHHHHHhHHHHHH
Q 019873 131 KEEDHFMCVQHEAGHFLT 148 (334)
Q Consensus 131 s~eer~RIA~HEAGHaLV 148 (334)
++....+++.||.||+|=
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 456667999999999973
No 32
>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=64.83 E-value=4.3 Score=36.03 Aligned_cols=17 Identities=29% Similarity=0.432 Sum_probs=14.3
Q ss_pred hhHHHHHHHHhHHHHHH
Q 019873 132 EEDHFMCVQHEAGHFLT 148 (334)
Q Consensus 132 ~eer~RIA~HEAGHaLV 148 (334)
..+...++.||.||+|=
T Consensus 110 g~~~~~t~~HEiGHaLG 126 (186)
T cd04277 110 GSYGYQTIIHEIGHALG 126 (186)
T ss_pred ChhhHHHHHHHHHHHhc
Confidence 46778999999999974
No 33
>PF06114 DUF955: Domain of unknown function (DUF955); InterPro: IPR010359 This is a family of bacterial and viral proteins with undetermined function. A conserved H-E-X-X-H motif is suggestive of a catalytic active site and shows similarity to IPR001915 from INTERPRO.; PDB: 3DTE_A 3DTK_A 3DTI_A.
Probab=63.93 E-value=7.7 Score=30.37 Aligned_cols=23 Identities=30% Similarity=0.296 Sum_probs=18.4
Q ss_pred CChhHHHHHHHHhHHHHHHHHHh
Q 019873 130 LKEEDHFMCVQHEAGHFLTGYLL 152 (334)
Q Consensus 130 ls~eer~RIA~HEAGHaLVAyLL 152 (334)
.++..++=++.||.||.+...--
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 58888889999999999987655
No 34
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=63.18 E-value=30 Score=28.81 Aligned_cols=62 Identities=13% Similarity=0.112 Sum_probs=40.4
Q ss_pred HHHHHHHHHHhCCCcchhHHHH----HHHHHHHHHHHHHc------HHHHHHHHHHHHhhCcHHHHHHHHhch
Q 019873 243 INKLDKVFQWLGYNKSEADSQV----KWAALNTVLISHHH------IQVRSRLAEAMALGRSIGSYTSKILTE 305 (334)
Q Consensus 243 l~qat~l~r~lGms~~~id~ev----r~A~~~A~~LL~~h------r~aleaLAeaL~e~esl~eci~~Ie~~ 305 (334)
+.+..+++|.+|+|+.+|+.-. +...++..++|+.. ..++..|.++|.. --+..|-+.|+..
T Consensus 20 ~~~wK~faR~lglse~~Id~I~~~~~~d~~Eq~~qmL~~W~~~~G~~a~~~~Li~aLr~-~~l~~~Ad~I~~~ 91 (97)
T cd08316 20 LKDVKKFVRKSGLSEPKIDEIKLDNPQDTAEQKVQLLRAWYQSHGKTGAYRTLIKTLRK-AKLCTKADKIQDI 91 (97)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHcCCCChHHHHHHHHHHHHHHhCCCchHHHHHHHHHH-ccchhHHHHHHHH
Confidence 3567788999999998887653 34567777777654 4457788877766 3334444444443
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=58.76 E-value=6.5 Score=35.63 Aligned_cols=29 Identities=21% Similarity=0.035 Sum_probs=19.5
Q ss_pred HHHHHHHHhHHHHHHHHHhCC-CCCceecCchh
Q 019873 134 DHFMCVQHEAGHFLTGYLLGV-LPKGYEIPSVE 165 (334)
Q Consensus 134 er~RIA~HEAGHaLVAyLLgi-PV~gyTI~p~e 165 (334)
+...++.||.||+|=-+..-. |-+. ++|+
T Consensus 91 ~~~~~i~HElgHaLG~~HEh~rpdrd---i~w~ 120 (198)
T cd04327 91 EFSRVVLHEFGHALGFIHEHQSPAAN---IPWD 120 (198)
T ss_pred hHHHHHHHHHHHHhcCcccccCCCCC---CCcC
Confidence 456799999999986655543 4444 3554
No 36
>smart00235 ZnMc Zinc-dependent metalloprotease. Neutral zinc metallopeptidases. This alignment represents a subset of known subfamilies. Highest similarity occurs in the HExxH zinc-binding site/ active site.
Probab=57.58 E-value=5.4 Score=33.55 Aligned_cols=14 Identities=43% Similarity=0.510 Sum_probs=11.2
Q ss_pred HHHHHhHHHHHHHH
Q 019873 137 MCVQHEAGHFLTGY 150 (334)
Q Consensus 137 RIA~HEAGHaLVAy 150 (334)
.|+.||-||+|=..
T Consensus 88 ~~~~HEigHaLGl~ 101 (140)
T smart00235 88 GVAAHELGHALGLY 101 (140)
T ss_pred ccHHHHHHHHhcCC
Confidence 39999999998433
No 37
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=56.11 E-value=60 Score=26.99 Aligned_cols=66 Identities=8% Similarity=0.013 Sum_probs=43.0
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHh-hCcHHHHHHHHhch
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKW-------AALNTVLISHHHIQVRSRLAEAMAL-GRSIGSYTSKILTE 305 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~-------A~~~A~~LL~~hr~aleaLAeaL~e-~esl~eci~~Ie~~ 305 (334)
.+|+..+..| ++.+|||.++|..-... .......+|.++...++.--+.|.+ ...+..++..++.+
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 4688887776 66799998877654432 2345567777777777666555555 44666666666544
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=53.45 E-value=32 Score=23.81 Aligned_cols=33 Identities=21% Similarity=0.232 Sum_probs=25.9
Q ss_pred hhHHHHHHHHHHHHHHHHccCchHHHHHHHHHh
Q 019873 21 AEYAKRRRQALKRVDRELSRGNFKVALSLVKQL 53 (334)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~g~~~~a~~~~~~l 53 (334)
+....++.+.++++|..|-+||.+.=..|.++|
T Consensus 5 ~~~~~~~~~L~~~ID~ALd~~D~e~F~~Ls~eL 37 (37)
T PF08858_consen 5 SLREFRKEQLLELIDEALDNRDKEWFYELSEEL 37 (37)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhC
Confidence 345678899999999999999988877776654
No 39
>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=51.58 E-value=8 Score=32.92 Aligned_cols=18 Identities=33% Similarity=0.479 Sum_probs=14.0
Q ss_pred hHHHHHHHHhHHHHHHHH
Q 019873 133 EDHFMCVQHEAGHFLTGY 150 (334)
Q Consensus 133 eer~RIA~HEAGHaLVAy 150 (334)
..-..++.||.||+|=.+
T Consensus 94 ~~~~~~~~HElGH~LGl~ 111 (167)
T cd00203 94 KEGAQTIAHELGHALGFY 111 (167)
T ss_pred ccchhhHHHHHHHHhCCC
Confidence 356789999999997543
No 40
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=51.25 E-value=12 Score=35.08 Aligned_cols=24 Identities=25% Similarity=0.360 Sum_probs=20.6
Q ss_pred CCChhHHHHHHHHhHHHHHHHHHh
Q 019873 129 SLKEEDHFMCVQHEAGHFLTGYLL 152 (334)
Q Consensus 129 ~ls~eer~RIA~HEAGHaLVAyLL 152 (334)
.++++|-+-|+.||.||..-.+.+
T Consensus 151 ~l~~dEl~aVlaHElgHi~~rd~~ 174 (302)
T COG0501 151 LLNDDELEAVLAHELGHIKNRHTL 174 (302)
T ss_pred hCCHHHHHHHHHHHHHHHhcccHH
Confidence 569999999999999998766655
No 41
>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=50.54 E-value=8.2 Score=36.41 Aligned_cols=18 Identities=33% Similarity=0.508 Sum_probs=16.0
Q ss_pred hhHHHHHHHHhHHHHHHHH
Q 019873 132 EEDHFMCVQHEAGHFLTGY 150 (334)
Q Consensus 132 ~eer~RIA~HEAGHaLVAy 150 (334)
..||+-++-||.||+| +|
T Consensus 136 ~~YRqYvINHEVGH~L-Gh 153 (203)
T PF11350_consen 136 ASYRQYVINHEVGHAL-GH 153 (203)
T ss_pred HHHHHHhhhhhhhhhc-cc
Confidence 5899999999999999 44
No 42
>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=50.01 E-value=70 Score=23.38 Aligned_cols=42 Identities=7% Similarity=0.102 Sum_probs=26.9
Q ss_pred HHHhCCCcchhHHHH------HHHHHHHHHHHHHcHHHHHHHHHHHHh
Q 019873 250 FQWLGYNKSEADSQV------KWAALNTVLISHHHIQVRSRLAEAMAL 291 (334)
Q Consensus 250 ~r~lGms~~~id~ev------r~A~~~A~~LL~~hr~aleaLAeaL~e 291 (334)
++.+|||-++|..-. .........+++++.+.+++--+.|.+
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 667999988876655 235556667888888777766555543
No 43
>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=49.79 E-value=81 Score=24.24 Aligned_cols=48 Identities=19% Similarity=0.111 Sum_probs=31.6
Q ss_pred HHHHHHHHHhCCCcchhHHHHHH----HHHHHHHHHHHcHH------HHHHHHHHHHh
Q 019873 244 NKLDKVFQWLGYNKSEADSQVKW----AALNTVLISHHHIQ------VRSRLAEAMAL 291 (334)
Q Consensus 244 ~qat~l~r~lGms~~~id~evr~----A~~~A~~LL~~hr~------aleaLAeaL~e 291 (334)
..-..+++.+||+..+++.-... ...++..+|+.-+. .+..|.++|.+
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 34556788899998777654433 34788888886655 44555555544
No 44
>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=48.32 E-value=16 Score=32.47 Aligned_cols=24 Identities=29% Similarity=0.444 Sum_probs=20.3
Q ss_pred CChhHHHHHHHHhHHHHHHHHHhC
Q 019873 130 LKEEDHFMCVQHEAGHFLTGYLLG 153 (334)
Q Consensus 130 ls~eer~RIA~HEAGHaLVAyLLg 153 (334)
+++++..-|+.||.||..-.+..-
T Consensus 84 ~~~~el~aVlaHElgH~~~~h~~~ 107 (226)
T PF01435_consen 84 LSEDELAAVLAHELGHIKHRHILK 107 (226)
T ss_dssp SSHHHHHHHHHHHHHHHHTTHCCC
T ss_pred ccHHHHHHHHHHHHHHHHcCCcch
Confidence 488999999999999998666554
No 45
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=47.64 E-value=21 Score=28.09 Aligned_cols=23 Identities=26% Similarity=0.267 Sum_probs=19.2
Q ss_pred ChhHHHHHHHHhHHHHHHHHHhC
Q 019873 131 KEEDHFMCVQHEAGHFLTGYLLG 153 (334)
Q Consensus 131 s~eer~RIA~HEAGHaLVAyLLg 153 (334)
++..-.+++.||.+|.+.....+
T Consensus 21 ~~~~~~~~l~HE~~H~~~~~~~~ 43 (128)
T PF13485_consen 21 DEDWLDRVLAHELAHQWFGNYFG 43 (128)
T ss_pred CHHHHHHHHHHHHHHHHHHHHcC
Confidence 44555699999999999999876
No 46
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=46.71 E-value=9.9 Score=31.03 Aligned_cols=11 Identities=45% Similarity=0.567 Sum_probs=10.0
Q ss_pred HHHHHhHHHHH
Q 019873 137 MCVQHEAGHFL 147 (334)
Q Consensus 137 RIA~HEAGHaL 147 (334)
.+..||.||.|
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
>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=41.87 E-value=1.2e+02 Score=25.52 Aligned_cols=52 Identities=10% Similarity=0.125 Sum_probs=31.0
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHHH----HHHHHHHHHHcHHHHHHHHHHHHh
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKWA----ALNTVLISHHHIQVRSRLAEAMAL 291 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~A----~~~A~~LL~~hr~aleaLAeaL~e 291 (334)
.+|+..+..| ++.+|||.++|..-+... ......+|+.+...++.=.+.|.+
T Consensus 41 ~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 98 (126)
T cd04783 41 EETVTRLRFIKRAQELGFTLDEIAELLELDDGTDCSEARELAEQKLAEVDEKIADLQR 98 (126)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566666555 667999987776544321 244567777776666554444433
No 48
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=41.21 E-value=87 Score=25.26 Aligned_cols=50 Identities=10% Similarity=0.144 Sum_probs=32.0
Q ss_pred hHHHHHHHH--HHHhCCCcchhHHHHHHHHHHHHHHHHHcHHHHHHHHHHHH
Q 019873 241 SDINKLDKV--FQWLGYNKSEADSQVKWAALNTVLISHHHIQVRSRLAEAMA 290 (334)
Q Consensus 241 ~Dl~qat~l--~r~lGms~~~id~evr~A~~~A~~LL~~hr~aleaLAeaL~ 290 (334)
+|+..+..| ++.+||+.++|..-....-.....+|++++..++.-.+.|.
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 566666655 66789998777655443223667777777777666555543
No 49
>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=40.74 E-value=1.5e+02 Score=23.80 Aligned_cols=46 Identities=13% Similarity=0.014 Sum_probs=30.6
Q ss_pred HHHHHHHhCCCcchhHHHHH----HHHHHHHHHHHHcH------HHHHHHHHHHHh
Q 019873 246 LDKVFQWLGYNKSEADSQVK----WAALNTVLISHHHI------QVRSRLAEAMAL 291 (334)
Q Consensus 246 at~l~r~lGms~~~id~evr----~A~~~A~~LL~~hr------~aleaLAeaL~e 291 (334)
-.+++|.+|+|+.+|+.-.. ....++.++|+.-+ ..++.|.++|.+
T Consensus 16 Wk~laR~LGlse~~Id~i~~~~~~~~~eq~~~mL~~W~~~~g~~At~~~L~~aL~~ 71 (86)
T cd08306 16 WRKLARKLGLSETKIESIEEAHPRNLREQVRQSLREWKKIKKKEAKVADLIKALRD 71 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHhHCcchHHHHHHHHHHH
Confidence 45578889999988775432 24567777776443 355667777665
No 50
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=38.98 E-value=23 Score=33.35 Aligned_cols=22 Identities=27% Similarity=0.181 Sum_probs=17.2
Q ss_pred CChhHHHHHHHHhHHHHHHHHH
Q 019873 130 LKEEDHFMCVQHEAGHFLTGYL 151 (334)
Q Consensus 130 ls~eer~RIA~HEAGHaLVAyL 151 (334)
.+++.++=++.||-||+|..--
T Consensus 67 ~~~~r~rFtlAHELGH~llH~~ 88 (213)
T COG2856 67 NSLERKRFTLAHELGHALLHTD 88 (213)
T ss_pred CCHHHHHHHHHHHHhHHHhccc
Confidence 3667777789999999987543
No 51
>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=38.19 E-value=1e+02 Score=24.97 Aligned_cols=45 Identities=13% Similarity=0.233 Sum_probs=26.1
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHHHHHHHHHHHHHcHHHHHH
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKWAALNTVLISHHHIQVRSR 284 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~A~~~A~~LL~~hr~alea 284 (334)
.+|+..+..+ ++..||+.+++..-.+.......++|.+++..++.
T Consensus 41 ~~di~~l~~i~~lr~~g~~l~~i~~~~~~~~~~~~~~l~~~~~~l~~ 87 (103)
T cd01106 41 EEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALREQKELLEE 87 (103)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHcCcHHHHHHHHHHHHHHHH
Confidence 3566666665 45688887776554432224555566665555544
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=37.95 E-value=1.7e+02 Score=24.14 Aligned_cols=53 Identities=13% Similarity=0.061 Sum_probs=32.0
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHH-----HHHHHHHHHHHcHHHHHHHHHHHHhh
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKW-----AALNTVLISHHHIQVRSRLAEAMALG 292 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~-----A~~~A~~LL~~hr~aleaLAeaL~e~ 292 (334)
.+|+..+..+ ++.+||+.++|..-+.. .......+|+++...++.-...|..+
T Consensus 41 ~~dl~~l~~I~~lr~~G~~l~~I~~~l~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~ 100 (108)
T cd04773 41 PSDVRDARLIHLLRRGGYLLEQIATVVEQLRHAGGTEALAAALEQRRVALTQRGRAMLDA 100 (108)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3577776666 55678887766544331 12445677777777776666555543
No 53
>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=37.77 E-value=93 Score=25.07 Aligned_cols=50 Identities=14% Similarity=0.277 Sum_probs=30.3
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHHHHHHHHHHHHHcHHHHHHHHHHH
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKWAALNTVLISHHHIQVRSRLAEAM 289 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~A~~~A~~LL~~hr~aleaLAeaL 289 (334)
.+|+..+..| ++.+||+.+++..-+.........+|+++.+.+++=-+.|
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 4677777766 5678999877765543322245566666666665544333
No 54
>PRK03982 heat shock protein HtpX; Provisional
Probab=37.59 E-value=20 Score=34.43 Aligned_cols=23 Identities=22% Similarity=0.189 Sum_probs=18.9
Q ss_pred CCChhHHHHHHHHhHHHHHHHHH
Q 019873 129 SLKEEDHFMCVQHEAGHFLTGYL 151 (334)
Q Consensus 129 ~ls~eer~RIA~HEAGHaLVAyL 151 (334)
.++++|-.-|..||.||.--.+.
T Consensus 119 ~l~~~El~AVlAHElgHi~~~h~ 141 (288)
T PRK03982 119 LLNEDELEGVIAHELTHIKNRDT 141 (288)
T ss_pred hCCHHHHHHHHHHHHHHHHcCCH
Confidence 34889999999999999875554
No 55
>PRK02391 heat shock protein HtpX; Provisional
Probab=36.97 E-value=19 Score=35.12 Aligned_cols=27 Identities=19% Similarity=0.223 Sum_probs=20.3
Q ss_pred ccCCCCChhHHHHHHHHhHHHHHHHHH
Q 019873 125 GSYVSLKEEDHFMCVQHEAGHFLTGYL 151 (334)
Q Consensus 125 ~~~r~ls~eer~RIA~HEAGHaLVAyL 151 (334)
++-..++++|.+-|..||.||.--.+.
T Consensus 123 gLl~~L~~~El~aVlaHElgHi~~~di 149 (296)
T PRK02391 123 GLMRRLDPDELEAVLAHELSHVKNRDV 149 (296)
T ss_pred HHHhhCCHHHHHHHHHHHHHHHHcCCH
Confidence 333445899999999999999755443
No 56
>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=36.81 E-value=1.8e+02 Score=23.84 Aligned_cols=52 Identities=8% Similarity=0.081 Sum_probs=30.5
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHHh
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKW------AALNTVLISHHHIQVRSRLAEAMAL 291 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~------A~~~A~~LL~~hr~aleaLAeaL~e 291 (334)
.+|+..+..| ++.+|||.++|..-... .......+|+++...++.-.+.|..
T Consensus 41 ~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (113)
T cd01109 41 EEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPERLELLEEHREELEEQIAELQE 100 (113)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHccCCccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3577777665 55688888776554321 1234456676666666655554443
No 57
>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=35.00 E-value=1.7e+02 Score=25.52 Aligned_cols=61 Identities=7% Similarity=0.037 Sum_probs=34.5
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHh-hCcHHHHHH
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKW-------AALNTVLISHHHIQVRSRLAEAMAL-GRSIGSYTS 300 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~-------A~~~A~~LL~~hr~aleaLAeaL~e-~esl~eci~ 300 (334)
.+|+.++.-| ++.+|||.++|..-+.. .......++.++...+++-.+.|.+ ...|..++.
T Consensus 41 ~~di~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~ki~~L~~~~~~L~~~~~ 111 (142)
T TIGR01950 41 RDVLRRVAVIKAAQRVGIPLATIGEALAVLPEGRTPTADDWARLSSQWREELDERIDQLNALRDQLDGCIG 111 (142)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3577777666 56688888776654431 1234456666666665544444433 444554443
No 58
>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=34.93 E-value=1.4e+02 Score=24.12 Aligned_cols=50 Identities=12% Similarity=0.146 Sum_probs=32.2
Q ss_pred hHHHHHHHH--HHHhCCCcchhHHHHH-HHHHHHHHHHHHcHHHHHHHHHHHH
Q 019873 241 SDINKLDKV--FQWLGYNKSEADSQVK-WAALNTVLISHHHIQVRSRLAEAMA 290 (334)
Q Consensus 241 ~Dl~qat~l--~r~lGms~~~id~evr-~A~~~A~~LL~~hr~aleaLAeaL~ 290 (334)
+|+..+..| ++.+|||.+++..-+. ....+...+|.++.+.+++=.+.|.
T Consensus 42 ~~~~~l~~I~~lr~~G~~l~eI~~~l~~~~~~~~~~~l~~~~~~l~~~i~~l~ 94 (97)
T cd04782 42 EQFEQLDIILLLKELGISLKEIKDYLDNRNPDELIELLKKQEKEIKEEIEELQ 94 (97)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566666555 6778999877765433 2334566777777777776655554
No 59
>COG2738 Predicted Zn-dependent protease [General function prediction only]
Probab=34.79 E-value=21 Score=34.04 Aligned_cols=13 Identities=31% Similarity=0.567 Sum_probs=10.9
Q ss_pred HHHHHhHHHHHHH
Q 019873 137 MCVQHEAGHFLTG 149 (334)
Q Consensus 137 RIA~HEAGHaLVA 149 (334)
-||.||.||++=-
T Consensus 94 aVAAHEVGHAiQd 106 (226)
T COG2738 94 AVAAHEVGHAIQD 106 (226)
T ss_pred HHHHHHhhHHHhh
Confidence 5899999999853
No 60
>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=34.53 E-value=2.3e+02 Score=22.79 Aligned_cols=34 Identities=15% Similarity=0.110 Sum_probs=22.7
Q ss_pred HHHHHHHhCCCcchhHHHHHH-----HHHHHHHHHHHcH
Q 019873 246 LDKVFQWLGYNKSEADSQVKW-----AALNTVLISHHHI 279 (334)
Q Consensus 246 at~l~r~lGms~~~id~evr~-----A~~~A~~LL~~hr 279 (334)
-.++++.+||++.+|+.-... ...++.++|..-+
T Consensus 16 Wk~lar~LG~s~~eI~~ie~~~~r~~~~eq~~~mL~~W~ 54 (86)
T cd08777 16 WKRCARKLGFTESEIEEIDHDYERDGLKEKVHQMLHKWK 54 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHHhcccCCHHHHHHHHHHHHH
Confidence 455678899999888764322 2566777776544
No 61
>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=34.30 E-value=1.1e+02 Score=24.61 Aligned_cols=49 Identities=8% Similarity=0.076 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHhCCCcchhHHHH---HHHHHHHHHHHHHc-------HHHHHHHHHHHH
Q 019873 242 DINKLDKVFQWLGYNKSEADSQV---KWAALNTVLISHHH-------IQVRSRLAEAMA 290 (334)
Q Consensus 242 Dl~qat~l~r~lGms~~~id~ev---r~A~~~A~~LL~~h-------r~aleaLAeaL~ 290 (334)
.+.+..+++|.+|+|+.+||.-. +...++..++|+.- ...++.|.++|.
T Consensus 10 ~~~~wk~~~R~LGlse~~Id~ie~~~~~~~Eq~yqmL~~W~~~~g~~~At~~~L~~aLr 68 (80)
T cd08313 10 PPRRWKEFVRRLGLSDNEIERVELDHRRCRDAQYQMLKVWKERGPRPYATLQHLLSVLR 68 (80)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCCcchHHHHHHHHH
Confidence 35677889999999998877532 23445566666532 335555555554
No 62
>PRK03072 heat shock protein HtpX; Provisional
Probab=34.27 E-value=23 Score=34.35 Aligned_cols=25 Identities=24% Similarity=0.252 Sum_probs=19.5
Q ss_pred CCCChhHHHHHHHHhHHHHHHHHHh
Q 019873 128 VSLKEEDHFMCVQHEAGHFLTGYLL 152 (334)
Q Consensus 128 r~ls~eer~RIA~HEAGHaLVAyLL 152 (334)
+.++++|-.-|..||.||.--.+.+
T Consensus 120 ~~l~~~El~aVlAHElgHi~~~d~~ 144 (288)
T PRK03072 120 QILNERELRGVLGHELSHVYNRDIL 144 (288)
T ss_pred HhCCHHHHHHHHHHHHHHHhcCCHH
Confidence 3458899999999999997654443
No 63
>PRK05457 heat shock protein HtpX; Provisional
Probab=34.20 E-value=31 Score=33.48 Aligned_cols=20 Identities=15% Similarity=0.336 Sum_probs=17.1
Q ss_pred CCChhHHHHHHHHhHHHHHH
Q 019873 129 SLKEEDHFMCVQHEAGHFLT 148 (334)
Q Consensus 129 ~ls~eer~RIA~HEAGHaLV 148 (334)
.++++|-+-|..||.||.--
T Consensus 128 ~L~~~El~aVlAHElgHi~~ 147 (284)
T PRK05457 128 NMSRDEVEAVLAHEISHIAN 147 (284)
T ss_pred hCCHHHHHHHHHHHHHHHHc
Confidence 45889999999999999743
No 64
>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=33.66 E-value=2.8e+02 Score=23.26 Aligned_cols=50 Identities=10% Similarity=0.058 Sum_probs=27.9
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHH---------HHHHHHHHHHHcHHHHHHHHHHH
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKW---------AALNTVLISHHHIQVRSRLAEAM 289 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~---------A~~~A~~LL~~hr~aleaLAeaL 289 (334)
.+|+..+..| ++.+|||-++|..-+.. .......+|.++...++.--+.|
T Consensus 39 ~~~l~~l~~I~~lr~~G~~L~~I~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l 99 (118)
T cd04776 39 RRDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQLEKMLEKIEKRRAELEQQRRDI 99 (118)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHhhccCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566666655 55688887665443321 12344566666666666444443
No 65
>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=33.19 E-value=1.9e+02 Score=23.51 Aligned_cols=52 Identities=10% Similarity=0.049 Sum_probs=33.6
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHH----------HHHHHHHHHHHcHHHHHHHHHHHHh
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKW----------AALNTVLISHHHIQVRSRLAEAMAL 291 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~----------A~~~A~~LL~~hr~aleaLAeaL~e 291 (334)
.+|+..+..| ++.+|||-++|..=+.. .......+|+++...+++-.+.|.+
T Consensus 39 ~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 102 (107)
T cd04777 39 EKCQDDLEFILELKGLGFSLIEIQKIFSYKRLTKSRTHEDQDYYKSFLKNKKDELEKEIEDLKK 102 (107)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHhcccccccchhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3677777766 66799998876654322 1233567888888777766655543
No 66
>PRK03001 M48 family peptidase; Provisional
Probab=33.12 E-value=25 Score=33.71 Aligned_cols=23 Identities=22% Similarity=0.203 Sum_probs=18.7
Q ss_pred CCChhHHHHHHHHhHHHHHHHHH
Q 019873 129 SLKEEDHFMCVQHEAGHFLTGYL 151 (334)
Q Consensus 129 ~ls~eer~RIA~HEAGHaLVAyL 151 (334)
.++++|-.-|..||.||.--.+.
T Consensus 118 ~l~~~El~aVlAHElgHi~~~h~ 140 (283)
T PRK03001 118 VLSEREIRGVMAHELAHVKHRDI 140 (283)
T ss_pred hCCHHHHHHHHHHHHHHHhCCCh
Confidence 34889999999999999865544
No 67
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=32.95 E-value=1.1e+02 Score=24.55 Aligned_cols=46 Identities=9% Similarity=-0.010 Sum_probs=28.7
Q ss_pred HHHHHHHhCCCcchhHHHH---HHHHHHHHHHHHHcHHH------HHHHHHHHHh
Q 019873 246 LDKVFQWLGYNKSEADSQV---KWAALNTVLISHHHIQV------RSRLAEAMAL 291 (334)
Q Consensus 246 at~l~r~lGms~~~id~ev---r~A~~~A~~LL~~hr~a------leaLAeaL~e 291 (334)
-.++++.+||++.+|+.=. +....++.++|+.-++. ++.|.++|.+
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 4557888999998875422 23567777777765543 4455555543
No 68
>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=32.89 E-value=1.6e+02 Score=25.54 Aligned_cols=61 Identities=8% Similarity=0.035 Sum_probs=31.1
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHh-hCcHHHHHH
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKW-------AALNTVLISHHHIQVRSRLAEAMAL-GRSIGSYTS 300 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~-------A~~~A~~LL~~hr~aleaLAeaL~e-~esl~eci~ 300 (334)
.+|+.++.-| ++.+|||.++|.+-+.. ....-..++..+...++.-.+.|.+ ...|.+++.
T Consensus 41 ~~dl~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~i~ 111 (139)
T cd01110 41 RDVLRRIAFIKVAQRLGLSLAEIAEALATLPEDRTPTKADWERLSRAWRDRLDERIAELQQLRDQLDGCIG 111 (139)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3566666665 45678887766554332 1122334555555544444444443 334555553
No 69
>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=32.20 E-value=1.6e+02 Score=24.22 Aligned_cols=48 Identities=13% Similarity=0.199 Sum_probs=31.8
Q ss_pred HHHHHHHHHhCCCcchhHHHH---HHHHHHHHHHHHHcH------HHHHHHHHHHHh
Q 019873 244 NKLDKVFQWLGYNKSEADSQV---KWAALNTVLISHHHI------QVRSRLAEAMAL 291 (334)
Q Consensus 244 ~qat~l~r~lGms~~~id~ev---r~A~~~A~~LL~~hr------~aleaLAeaL~e 291 (334)
.+..+++|.+|+|+.+|+.-. +.-..+..++|+.-+ ..+..|.++|..
T Consensus 20 ~~Wk~laR~LGLse~~I~~i~~~~~~~~eq~~qmL~~W~~~~G~~At~~~L~~aL~~ 76 (96)
T cd08315 20 DSWNRLMRQLGLSENEIDVAKANERVTREQLYQMLLTWVNKTGRKASVNTLLDALEA 76 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHhhCCCcHHHHHHHHHHH
Confidence 567778999999998876532 122566666766433 456777777765
No 70
>PF12388 Peptidase_M57: Dual-action HEIGH metallo-peptidase; InterPro: IPR024653 This entry represents the metallopeptidases M10, M27 and M57. The catalytic triad for proteases in this entry is HE-H-H, which in many members is in the sequence motif HEIGH [].
Probab=31.72 E-value=30 Score=32.80 Aligned_cols=23 Identities=17% Similarity=0.062 Sum_probs=17.8
Q ss_pred ChhHHHHHHHHhHHHHHHHHHhC
Q 019873 131 KEEDHFMCVQHEAGHFLTGYLLG 153 (334)
Q Consensus 131 s~eer~RIA~HEAGHaLVAyLLg 153 (334)
+....+.|+.||.||.+=-....
T Consensus 129 ~~~~~~hvi~HEiGH~IGfRHTD 151 (211)
T PF12388_consen 129 SVNVIEHVITHEIGHCIGFRHTD 151 (211)
T ss_pred chhHHHHHHHHHhhhhccccccC
Confidence 56778889999999987555443
No 71
>COG0339 Dcp Zn-dependent oligopeptidases [Amino acid transport and metabolism]
Probab=31.46 E-value=38 Score=37.24 Aligned_cols=32 Identities=25% Similarity=0.184 Sum_probs=22.4
Q ss_pred HHHHHhHHHHHHHHHhCC---CCCceecCchhhhcc
Q 019873 137 MCVQHEAGHFLTGYLLGV---LPKGYEIPSVEALKQ 169 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLgi---PV~gyTI~p~eal~~ 169 (334)
.+..||-||+|=.-|..+ -|.|.. .|||++.-
T Consensus 469 ~TLFHEfGHgLH~mlt~v~~~~vsGt~-v~wDfVEl 503 (683)
T COG0339 469 TTLFHEFGHGLHHLLTRVKYPGVSGTN-VPWDFVEL 503 (683)
T ss_pred HHHHHHhhhHHHHHhhcCCccccCCCC-CCcchhhc
Confidence 689999999998877764 445555 55555443
No 72
>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=31.28 E-value=32 Score=30.34 Aligned_cols=23 Identities=26% Similarity=0.238 Sum_probs=15.0
Q ss_pred ChhHHHHHHHHhHHHHHHHHHhC
Q 019873 131 KEEDHFMCVQHEAGHFLTGYLLG 153 (334)
Q Consensus 131 s~eer~RIA~HEAGHaLVAyLLg 153 (334)
+......+..||.||-|=+..-+
T Consensus 138 ~~~~~~~~~AHEiGH~lGa~HD~ 160 (196)
T PF13688_consen 138 PTYNGAITFAHEIGHNLGAPHDG 160 (196)
T ss_dssp -HHHHHHHHHHHHHHHTT-----
T ss_pred CCCceehhhHHhHHHhcCCCCCC
Confidence 56778899999999987666554
No 73
>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=31.17 E-value=1.9e+02 Score=24.44 Aligned_cols=51 Identities=8% Similarity=0.165 Sum_probs=27.6
Q ss_pred hHHHHHHHH--HHHhCCCcchhHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHHh
Q 019873 241 SDINKLDKV--FQWLGYNKSEADSQVKW------AALNTVLISHHHIQVRSRLAEAMAL 291 (334)
Q Consensus 241 ~Dl~qat~l--~r~lGms~~~id~evr~------A~~~A~~LL~~hr~aleaLAeaL~e 291 (334)
+|+..+.-| ++.+|||-++|.+-+.. .......+|..+...+++-.+.|.+
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 566666655 55688887766544321 1233445566665555544444433
No 74
>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=31.14 E-value=2.2e+02 Score=23.91 Aligned_cols=51 Identities=8% Similarity=0.086 Sum_probs=31.3
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHH
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKW------AALNTVLISHHHIQVRSRLAEAMA 290 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~------A~~~A~~LL~~hr~aleaLAeaL~ 290 (334)
.+|+..+..| ++.+|||.++|..-+.. .......+|..+...+++--+.|.
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 4677766665 66789988777654432 124556777777666665444443
No 75
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=31.08 E-value=25 Score=32.28 Aligned_cols=17 Identities=29% Similarity=0.047 Sum_probs=13.7
Q ss_pred HHHHHhHHHHHHHHHhC
Q 019873 137 MCVQHEAGHFLTGYLLG 153 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLg 153 (334)
.+..||.||.|=+..-+
T Consensus 139 ~~~aHEiGH~lGl~H~~ 155 (206)
T PF13583_consen 139 QTFAHEIGHNLGLRHDF 155 (206)
T ss_pred hHHHHHHHHHhcCCCCc
Confidence 67899999998766655
No 76
>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=31.07 E-value=28 Score=33.96 Aligned_cols=18 Identities=28% Similarity=0.274 Sum_probs=15.3
Q ss_pred HHHHHhHHHHHHHHHhCC
Q 019873 137 MCVQHEAGHFLTGYLLGV 154 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLgi 154 (334)
.+..||.||++=..+...
T Consensus 156 ~tl~HE~GHa~h~~l~~~ 173 (365)
T cd06258 156 NTLFHEFGHAVHFLLIQQ 173 (365)
T ss_pred HHHHHHHhHHHHHHHhcC
Confidence 689999999998877763
No 77
>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=30.82 E-value=9.3 Score=37.94 Aligned_cols=17 Identities=29% Similarity=0.462 Sum_probs=13.3
Q ss_pred hHHHHHHHHhHHHHHHH
Q 019873 133 EDHFMCVQHEAGHFLTG 149 (334)
Q Consensus 133 eer~RIA~HEAGHaLVA 149 (334)
.+..--=|||.|||||-
T Consensus 92 ~~~~lY~Y~~iGHFWVk 108 (299)
T PF12994_consen 92 EETHLYNYGEIGHFWVK 108 (299)
T ss_pred HHHHHhhccccceeeec
Confidence 45556679999999984
No 78
>PRK04897 heat shock protein HtpX; Provisional
Probab=30.82 E-value=38 Score=32.96 Aligned_cols=22 Identities=18% Similarity=0.138 Sum_probs=17.8
Q ss_pred CCChhHHHHHHHHhHHHHHHHH
Q 019873 129 SLKEEDHFMCVQHEAGHFLTGY 150 (334)
Q Consensus 129 ~ls~eer~RIA~HEAGHaLVAy 150 (334)
.++++|.+-|..||.||.--.+
T Consensus 131 ~l~~~El~aVlAHElgHi~~~d 152 (298)
T PRK04897 131 IMNREELEGVIGHEISHIRNYD 152 (298)
T ss_pred hCCHHHHHHHHHHHHHHHhcCC
Confidence 3488999999999999975433
No 79
>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=30.23 E-value=41 Score=35.21 Aligned_cols=17 Identities=35% Similarity=0.421 Sum_probs=14.4
Q ss_pred HHHHHhHHHHHHHHHhC
Q 019873 137 MCVQHEAGHFLTGYLLG 153 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLg 153 (334)
.+..||+||++=.|+..
T Consensus 339 ~TL~HElGHa~H~~~s~ 355 (549)
T TIGR02289 339 DVLTHEAGHAFHVYESR 355 (549)
T ss_pred HHHHHHhhHHHHHHHhc
Confidence 46899999999888775
No 80
>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=29.95 E-value=3e+02 Score=23.23 Aligned_cols=51 Identities=20% Similarity=0.245 Sum_probs=29.3
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHH
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKW------AALNTVLISHHHIQVRSRLAEAMA 290 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~------A~~~A~~LL~~hr~aleaLAeaL~ 290 (334)
.+|+..+..| ++.+|||-++|..-+.. .......+|+.+...++.-.+.|.
T Consensus 41 ~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~ 99 (127)
T cd01108 41 QRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRASADVKALALEHIAELERKIAELQ 99 (127)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566666666 55688887776544331 123445667766666655444443
No 81
>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=29.41 E-value=2.5e+02 Score=23.29 Aligned_cols=51 Identities=12% Similarity=0.162 Sum_probs=30.5
Q ss_pred hHHHHHHHH--HHHhCCCcchhHHHHHHH------HHHHHHHHHHcHHHHHHHHHHHHh
Q 019873 241 SDINKLDKV--FQWLGYNKSEADSQVKWA------ALNTVLISHHHIQVRSRLAEAMAL 291 (334)
Q Consensus 241 ~Dl~qat~l--~r~lGms~~~id~evr~A------~~~A~~LL~~hr~aleaLAeaL~e 291 (334)
+|+..+..| ++.+|||.+++..-.... ......+|+++...++.=.+.|..
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 556655555 667899887766554322 234567777777666654444433
No 82
>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=28.75 E-value=1.9e+02 Score=25.00 Aligned_cols=62 Identities=18% Similarity=0.138 Sum_probs=51.3
Q ss_pred ccchhhHHHHHHHHHHHhCCCcchhHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHhhCcHHH
Q 019873 236 SEGHYSDINKLDKVFQWLGYNKSEADSQVKWAALNTVLISHHHIQVRSRLAEAMALGRSIGS 297 (334)
Q Consensus 236 atGg~~Dl~qat~l~r~lGms~~~id~evr~A~~~A~~LL~~hr~aleaLAeaL~e~esl~e 297 (334)
.+|...+++.+.+++..+|-..-.++.+.|..|--|--+-..+-..+-.++..|.+..-++.
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 36777889999999999999988899999988888888888888899999999998887765
No 83
>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=28.74 E-value=1.4e+02 Score=23.90 Aligned_cols=46 Identities=4% Similarity=0.057 Sum_probs=29.8
Q ss_pred HHHHHHHhCCCcchhHHHH----HHHHHHHHHHHHHcHH------HHHHHHHHHHh
Q 019873 246 LDKVFQWLGYNKSEADSQV----KWAALNTVLISHHHIQ------VRSRLAEAMAL 291 (334)
Q Consensus 246 at~l~r~lGms~~~id~ev----r~A~~~A~~LL~~hr~------aleaLAeaL~e 291 (334)
-.++++.+|||+.+|+.-. +....++.++|+.-+. ....|..+|..
T Consensus 18 Wk~LAr~Lg~se~dI~~i~~~~~~~~~eq~~~mL~~W~~r~g~~At~~~L~~aL~~ 73 (84)
T cd08804 18 WTELARELDFTEEQIHQIRIENPNSLQDQSHALLKYWLERDGKHATDTNLMKCLTK 73 (84)
T ss_pred HHHHHHHcCCCHHHHHHHHHHCcccHHHHHHHHHHHHHHccCCCchHHHHHHHHHH
Confidence 4567888999998887632 2356677777764433 34556666654
No 84
>cd04276 ZnMc_MMP_like_2 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=28.51 E-value=40 Score=31.26 Aligned_cols=15 Identities=33% Similarity=0.432 Sum_probs=12.4
Q ss_pred hHHHHHHHHhHHHHH
Q 019873 133 EDHFMCVQHEAGHFL 147 (334)
Q Consensus 133 eer~RIA~HEAGHaL 147 (334)
+..+-++.||.||+|
T Consensus 114 ~~~~~~~~he~gh~l 128 (197)
T cd04276 114 ASLRYLLAHEVGHTL 128 (197)
T ss_pred HHHHHHHHHHHHHHh
Confidence 556679999999986
No 85
>PRK01345 heat shock protein HtpX; Provisional
Probab=28.17 E-value=44 Score=32.94 Aligned_cols=23 Identities=26% Similarity=0.231 Sum_probs=19.2
Q ss_pred CChhHHHHHHHHhHHHHHHHHHh
Q 019873 130 LKEEDHFMCVQHEAGHFLTGYLL 152 (334)
Q Consensus 130 ls~eer~RIA~HEAGHaLVAyLL 152 (334)
++++|.+-|..||.||.--.+.+
T Consensus 119 L~~dEL~aVlAHElgHi~~~d~~ 141 (317)
T PRK01345 119 LSPEEVAGVMAHELAHVKNRDTL 141 (317)
T ss_pred CCHHHHHHHHHHHHHHHHcCCHH
Confidence 48899999999999998765544
No 86
>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=28.12 E-value=1.3e+02 Score=23.96 Aligned_cols=54 Identities=11% Similarity=0.101 Sum_probs=35.9
Q ss_pred HHHHHHHhCCCcchhHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHhhCcHHHHHHHHhchhhhh
Q 019873 246 LDKVFQWLGYNKSEADSQVKWAALNTVLISHHHIQVRSRLAEAMALGRSIGSYTSKILTEQSLE 309 (334)
Q Consensus 246 at~l~r~lGms~~~id~evr~A~~~A~~LL~~hr~aleaLAeaL~e~esl~eci~~Ie~~~~~~ 309 (334)
-+.+++.+||++.+|+.-.+ -+.++.++|+.-.. .++.|++-.++++....-.+
T Consensus 18 W~~LA~~LG~~~~~I~~i~~-~~~p~~~lL~~W~~---------r~~ATv~~L~~aL~~i~R~D 71 (77)
T cd08311 18 WRSLAGELGYEDEAIDTFGR-EESPVRTLLADWSA---------QEGATLDALCTALRRIQRED 71 (77)
T ss_pred HHHHHHHcCCCHHHHHHHHc-ChhHHHHHHHHHHH---------CcCchHHHHHHHHHHcChHH
Confidence 66778899999988765433 24777777776554 14577776666666554433
No 87
>PRK01265 heat shock protein HtpX; Provisional
Probab=27.00 E-value=37 Score=33.86 Aligned_cols=23 Identities=22% Similarity=0.245 Sum_probs=18.1
Q ss_pred CCCChhHHHHHHHHhHHHHHHHH
Q 019873 128 VSLKEEDHFMCVQHEAGHFLTGY 150 (334)
Q Consensus 128 r~ls~eer~RIA~HEAGHaLVAy 150 (334)
..++++|.+-|.-||-||.--.+
T Consensus 133 ~~l~~~El~aVlAHElgHik~~d 155 (324)
T PRK01265 133 KILNRDEIKAVAGHELGHLKHRD 155 (324)
T ss_pred hhCCHHHHHHHHHHHHHHHHccc
Confidence 33588999999999999964333
No 88
>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=26.69 E-value=40 Score=30.53 Aligned_cols=34 Identities=18% Similarity=0.185 Sum_probs=18.8
Q ss_pred HHHHHHhHHHHHHHHHhCC-CCC-c-eecCchhhhccc
Q 019873 136 FMCVQHEAGHFLTGYLLGV-LPK-G-YEIPSVEALKQD 170 (334)
Q Consensus 136 ~RIA~HEAGHaLVAyLLgi-PV~-g-yTI~p~eal~~G 170 (334)
..++.||.||+|=-+..-. |=+ . ++| -|+.+..+
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 4699999999985554432 222 2 444 46666554
No 89
>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=26.49 E-value=1.8e+02 Score=23.83 Aligned_cols=44 Identities=9% Similarity=0.171 Sum_probs=21.4
Q ss_pred hHHHHHHHH--HHHhCCCcchhHHHHHHHH-HHHHHHHHHcHHHHHH
Q 019873 241 SDINKLDKV--FQWLGYNKSEADSQVKWAA-LNTVLISHHHIQVRSR 284 (334)
Q Consensus 241 ~Dl~qat~l--~r~lGms~~~id~evr~A~-~~A~~LL~~hr~alea 284 (334)
+|+..+..+ ++.+|||.+++..-..... .....+|+.+.+.+++
T Consensus 43 ~~i~~l~~I~~lr~~G~sl~~i~~l~~~~~~~~~~~~l~~~~~~l~~ 89 (108)
T cd01107 43 EQLERLNRIKYLRDLGFPLEEIKEILDADNDDELRKLLREKLAELEA 89 (108)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Confidence 455555544 4567777665543222111 3444555555444444
No 90
>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=26.27 E-value=34 Score=30.69 Aligned_cols=35 Identities=23% Similarity=0.207 Sum_probs=21.6
Q ss_pred HHHHHHhHHHHHHHHHhCCCCC--ceecCchhhhccc
Q 019873 136 FMCVQHEAGHFLTGYLLGVLPK--GYEIPSVEALKQD 170 (334)
Q Consensus 136 ~RIA~HEAGHaLVAyLLgiPV~--gyTI~p~eal~~G 170 (334)
..++.||-||+|=-+..-.-+. .|-.+.|+.+..+
T Consensus 75 ~g~v~HE~~HalG~~HEh~R~DRD~yv~i~~~ni~~~ 111 (180)
T cd04280 75 LGTIVHELMHALGFYHEQSRPDRDDYVTINWENIQPG 111 (180)
T ss_pred CchhHHHHHHHhcCcchhcccccCCeEEEeecccChh
Confidence 5799999999976655543222 2444556555543
No 91
>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=25.23 E-value=2.5e+02 Score=23.92 Aligned_cols=51 Identities=12% Similarity=0.182 Sum_probs=30.3
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHHH------HHHHHHHHHHcHHHHHHHHHHHH
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKWA------ALNTVLISHHHIQVRSRLAEAMA 290 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~A------~~~A~~LL~~hr~aleaLAeaL~ 290 (334)
.+|+..+.-| ++.+|||-++|..-+... ......+|+++...+++=.+.|.
T Consensus 41 ~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~ 99 (133)
T cd04787 41 EKDLSRLRFILSARQLGFSLKDIKEILSHADQGESPCPMVRRLIEQRLAETERRIKELL 99 (133)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHhhhccCCCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566666555 667999988766544321 12445677777666665544443
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=24.80 E-value=9.9 Score=35.86 Aligned_cols=20 Identities=30% Similarity=0.315 Sum_probs=15.5
Q ss_pred hhHHHHHHHHhHHHHHHHHH
Q 019873 132 EEDHFMCVQHEAGHFLTGYL 151 (334)
Q Consensus 132 ~eer~RIA~HEAGHaLVAyL 151 (334)
+-..-+++.||.||+|--+.
T Consensus 134 ~~n~g~t~~HEvGH~lGL~H 153 (225)
T cd04275 134 PYNLGDTATHEVGHWLGLYH 153 (225)
T ss_pred cccccceeEEeccceeeeee
Confidence 45667899999999985444
No 93
>PF13574 Reprolysin_2: Metallo-peptidase family M12B Reprolysin-like; PDB: 1KAP_P 1JIW_P 1AKL_A 1OM7_A 1OM8_A 1O0T_A 1OM6_A 1H71_P 1O0Q_A 1OMJ_A ....
Probab=24.78 E-value=44 Score=29.78 Aligned_cols=20 Identities=25% Similarity=0.014 Sum_probs=14.1
Q ss_pred HHHHHHHhHHHHHHHHHhCC
Q 019873 135 HFMCVQHEAGHFLTGYLLGV 154 (334)
Q Consensus 135 r~RIA~HEAGHaLVAyLLgi 154 (334)
-..++.||.||.|=+..-+.
T Consensus 111 ~~~~~aHElGH~lGa~Hd~~ 130 (173)
T PF13574_consen 111 GIDTFAHELGHQLGAPHDFD 130 (173)
T ss_dssp HHHHHHHHHHHHHT---SSS
T ss_pred eeeeehhhhHhhcCCCCCCC
Confidence 45789999999998888764
No 94
>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=24.46 E-value=3.4e+02 Score=22.95 Aligned_cols=59 Identities=8% Similarity=0.099 Sum_probs=35.9
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHHh-hCcHHHH
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKW------AALNTVLISHHHIQVRSRLAEAMAL-GRSIGSY 298 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~------A~~~A~~LL~~hr~aleaLAeaL~e-~esl~ec 298 (334)
.+|+..+.-| ++.+|||.++|..-+.. .......+|+.+...+++=.+.|.+ ...|.+.
T Consensus 41 ~~~l~~l~~I~~lr~lG~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~ 108 (127)
T TIGR02047 41 VGHVERLAFIRNCRTLDMSLAEIRQLLRYQDKPEKSCSDVNALLDEHISHVRARIIKLQALIEQLVDL 108 (127)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4677777766 56789998877654431 2245567777777777755555544 3334443
No 95
>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=24.30 E-value=49 Score=30.92 Aligned_cols=11 Identities=36% Similarity=0.582 Sum_probs=9.2
Q ss_pred HHHHHhHHHHH
Q 019873 137 MCVQHEAGHFL 147 (334)
Q Consensus 137 RIA~HEAGHaL 147 (334)
..+.||.||.+
T Consensus 147 Kea~HElGH~~ 157 (194)
T PF07998_consen 147 KEAVHELGHLF 157 (194)
T ss_dssp HHHHHHHHHHT
T ss_pred HHHHHHHHHHc
Confidence 56999999965
No 96
>PRK02870 heat shock protein HtpX; Provisional
Probab=24.15 E-value=48 Score=33.21 Aligned_cols=18 Identities=22% Similarity=0.416 Sum_probs=16.2
Q ss_pred CCChhHHHHHHHHhHHHH
Q 019873 129 SLKEEDHFMCVQHEAGHF 146 (334)
Q Consensus 129 ~ls~eer~RIA~HEAGHa 146 (334)
.++++|-.-|..||.||.
T Consensus 167 ~L~~dEL~aVlAHELgHi 184 (336)
T PRK02870 167 KLDRDELQAVMAHELSHI 184 (336)
T ss_pred hCCHHHHHHHHHHHHHHH
Confidence 458899999999999997
No 97
>cd04267 ZnMc_ADAM_like Zinc-dependent metalloprotease, ADAM_like or reprolysin_like subgroup. The adamalysin_like or ADAM family of metalloproteases contains proteolytic domains from snake venoms, proteases from the mammalian reproductive tract, and the tumor necrosis factor alpha convertase, TACE. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
Probab=24.13 E-value=34 Score=30.22 Aligned_cols=21 Identities=29% Similarity=0.218 Sum_probs=15.5
Q ss_pred hHHHHHHHHhHHHHHHHHHhC
Q 019873 133 EDHFMCVQHEAGHFLTGYLLG 153 (334)
Q Consensus 133 eer~RIA~HEAGHaLVAyLLg 153 (334)
-.-..++.||.||.|=+..-+
T Consensus 131 ~~~~~~~aHElGH~lG~~HD~ 151 (192)
T cd04267 131 LLTALTMAHELGHNLGAEHDG 151 (192)
T ss_pred eeehhhhhhhHHhhcCCcCCC
Confidence 445679999999987655544
No 98
>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=23.99 E-value=2.6e+02 Score=23.55 Aligned_cols=52 Identities=10% Similarity=0.105 Sum_probs=31.5
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHH----HHHHHHHHHHHcHHHHHHHHHHHHh
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKW----AALNTVLISHHHIQVRSRLAEAMAL 291 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~----A~~~A~~LL~~hr~aleaLAeaL~e 291 (334)
.+|+..+.-| ++.+|||.++|..-+.. .......+|+++...+++=.+.|..
T Consensus 40 ~~~l~~l~~I~~l~~~G~sl~eI~~~l~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 97 (124)
T TIGR02051 40 EETVKRLRFIKRAQELGFSLEEIGGLLGLVDGTHCREMYELASRKLKSVQAKMADLLR 97 (124)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566666555 66789998877655432 2345567777777666655444433
No 99
>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=23.60 E-value=3.5e+02 Score=23.52 Aligned_cols=22 Identities=9% Similarity=0.187 Sum_probs=12.4
Q ss_pred hhHHHHHHHH--HHHhCCCcchhH
Q 019873 240 YSDINKLDKV--FQWLGYNKSEAD 261 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id 261 (334)
.+|+.++..| ++.+|||-++|.
T Consensus 40 ~~~l~~l~~I~~lr~~G~sL~eI~ 63 (134)
T cd04779 40 ETALDRLQLIEHLKGQRLSLAEIK 63 (134)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHH
Confidence 3566666655 345677765543
No 100
>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=23.30 E-value=2.8e+02 Score=24.89 Aligned_cols=22 Identities=18% Similarity=0.495 Sum_probs=13.0
Q ss_pred hHHHHHHHH--HHHhCCCcchhHH
Q 019873 241 SDINKLDKV--FQWLGYNKSEADS 262 (334)
Q Consensus 241 ~Dl~qat~l--~r~lGms~~~id~ 262 (334)
+|+.++..| ++.+|||.++|..
T Consensus 43 ~dl~rL~~I~~lr~~G~sL~eI~~ 66 (172)
T cd04790 43 RDLERLEQICAYRSAGVSLEDIRS 66 (172)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHH
Confidence 466666554 4557777655443
No 101
>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=23.11 E-value=2.7e+02 Score=23.00 Aligned_cols=52 Identities=6% Similarity=0.116 Sum_probs=29.5
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHH---------HHHHHHHHHHHcHHHHHHHHHHHHh
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKW---------AALNTVLISHHHIQVRSRLAEAMAL 291 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~---------A~~~A~~LL~~hr~aleaLAeaL~e 291 (334)
.+|+..+..| ++.+|||.++|..-+.. ...+..++|+++...++.=.+.|..
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 3567776666 55688887776544321 1223456666666666555544433
No 102
>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=23.11 E-value=40 Score=32.69 Aligned_cols=17 Identities=35% Similarity=0.434 Sum_probs=12.9
Q ss_pred hHHHHHHHHhHHHHHHH
Q 019873 133 EDHFMCVQHEAGHFLTG 149 (334)
Q Consensus 133 eer~RIA~HEAGHaLVA 149 (334)
..=.-|+.||.||.+..
T Consensus 214 ~~~~~v~vHE~GHsf~~ 230 (264)
T PF09471_consen 214 PSFKQVVVHEFGHSFGG 230 (264)
T ss_dssp TTHHHHHHHHHHHHTT-
T ss_pred ccccceeeeeccccccc
Confidence 35567999999998754
No 103
>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=22.85 E-value=59 Score=32.01 Aligned_cols=17 Identities=35% Similarity=0.632 Sum_probs=15.1
Q ss_pred HHHHHhHHHHHHHHHhC
Q 019873 137 MCVQHEAGHFLTGYLLG 153 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLg 153 (334)
.+..||.||++=.++..
T Consensus 224 ~tl~HE~GHa~h~~~~~ 240 (427)
T cd06459 224 FTLAHELGHAFHSYLSR 240 (427)
T ss_pred HHHHHHhhHHHHHHHHc
Confidence 67999999999988875
No 104
>PRK13267 archaemetzincin-like protein; Reviewed
Probab=22.74 E-value=56 Score=29.89 Aligned_cols=11 Identities=55% Similarity=0.661 Sum_probs=8.8
Q ss_pred HHHHHhHHHHH
Q 019873 137 MCVQHEAGHFL 147 (334)
Q Consensus 137 RIA~HEAGHaL 147 (334)
+.+.||.||.|
T Consensus 127 k~~~HElGH~l 137 (179)
T PRK13267 127 KEVTHELGHTL 137 (179)
T ss_pred HHHHHHHHHHc
Confidence 34899999974
No 105
>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=22.68 E-value=47 Score=30.47 Aligned_cols=34 Identities=26% Similarity=0.151 Sum_probs=20.6
Q ss_pred HHHHHhHHHHHHHHHhCC-CCC-ceecCchhhhccc
Q 019873 137 MCVQHEAGHFLTGYLLGV-LPK-GYEIPSVEALKQD 170 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLgi-PV~-gyTI~p~eal~~G 170 (334)
-++.||-||+|=.+..-- |=+ .|-.+-|+.+..+
T Consensus 79 G~i~HEl~HaLG~~HEhsRpDRD~yV~I~~~nI~~~ 114 (182)
T cd04283 79 GIIQHELLHALGFYHEQTRSDRDKYVRINWENIIPD 114 (182)
T ss_pred chHHHHHHHHhCCcccccccccCceEEEehhhcCch
Confidence 589999999987766542 111 3333345555444
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=22.36 E-value=3.9e+02 Score=22.52 Aligned_cols=50 Identities=12% Similarity=0.186 Sum_probs=26.0
Q ss_pred hHHHHHHHH--HHHhCCCcchhHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHH
Q 019873 241 SDINKLDKV--FQWLGYNKSEADSQVKW------AALNTVLISHHHIQVRSRLAEAMA 290 (334)
Q Consensus 241 ~Dl~qat~l--~r~lGms~~~id~evr~------A~~~A~~LL~~hr~aleaLAeaL~ 290 (334)
+|+..+..| ++.+|||.++|..-+.. .......+|+.+...++.-.+.|.
T Consensus 42 ~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~ 99 (126)
T cd04785 42 AHVERLRFIRRARDLGFSLEEIRALLALSDRPDRSCAEADAIARAHLADVRARIADLR 99 (126)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHhhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456655555 45677777665543321 123345566665555554444443
No 107
>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=22.04 E-value=75 Score=32.08 Aligned_cols=18 Identities=28% Similarity=0.337 Sum_probs=16.1
Q ss_pred HHHHHhHHHHHHHHHhCC
Q 019873 137 MCVQHEAGHFLTGYLLGV 154 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLgi 154 (334)
.+..||.||++=.++...
T Consensus 244 ~tLfHE~GHa~H~~ls~~ 261 (458)
T PF01432_consen 244 ETLFHEFGHAMHSLLSRT 261 (458)
T ss_dssp HHHHHHHHHHHHHHHCCC
T ss_pred HHHHHHHhHHHHHHHhcc
Confidence 689999999999998874
No 108
>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=22.00 E-value=48 Score=30.79 Aligned_cols=17 Identities=29% Similarity=0.255 Sum_probs=13.8
Q ss_pred HHHHHhHHHHHHHHHhC
Q 019873 137 MCVQHEAGHFLTGYLLG 153 (334)
Q Consensus 137 RIA~HEAGHaLVAyLLg 153 (334)
=++.||.||+|=-+..-
T Consensus 89 Gti~HEl~HaLGf~HEh 105 (200)
T cd04281 89 GIVVHELGHVIGFWHEH 105 (200)
T ss_pred chHHHHHHHHhcCcchh
Confidence 48999999998766655
No 109
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=21.66 E-value=2.2e+02 Score=23.11 Aligned_cols=50 Identities=18% Similarity=0.187 Sum_probs=29.4
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHh
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKWAALNTVLISHHHIQVRSRLAEAMAL 291 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~A~~~A~~LL~~hr~aleaLAeaL~e 291 (334)
.+|+..+..| ++..||+.+++..-+.. .....++.++.+.+++-.+.|.+
T Consensus 41 ~~dl~~l~~I~~l~~~G~~l~ei~~~~~~--~~~~~~l~~~~~~l~~~i~~l~~ 92 (102)
T cd04775 41 EADLSRLEKIVFLQAGGLPLEEIAGCLAQ--PHVQAILEERLQSLNREIQRLRQ 92 (102)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHcC--CcHHHHHHHHHHHHHHHHHHHHH
Confidence 4677777776 55689998776643321 11355666666665555555443
No 110
>PRK01209 cobD cobalamin biosynthesis protein; Provisional
Probab=21.61 E-value=1.9e+02 Score=28.40 Aligned_cols=67 Identities=16% Similarity=0.260 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHHHccCchHHHHHHHHHhccCCCCccccccccccccccccccchhhhhchhhhhhhhhhhhhhHHHHHh
Q 019873 25 KRRRQALKRVDRELSRGNFKVALSLVKQLQRKPAGGLRGFGAAKQVPKRLSSLDESELDSKELLTLRALFDSVMESIERC 104 (334)
Q Consensus 25 ~~~~~~~~~~~~~~~~g~~~~a~~~~~~l~~~~~g~l~~~gaa~~~p~r~~~l~el~l~~it~~~ll~P~~~~s~~i~~~ 104 (334)
..-++..++|.+.|.+||..+|-..++++.++. ...|++-.+...+.+++ ..+++..+-+.
T Consensus 96 ~~l~~~~~~v~~al~~gd~~~AR~~l~~~v~Rd----------------t~~Ls~~~i~~a~iEs~---~en~~d~~~ap 156 (312)
T PRK01209 96 RSLADHARAVARALRAGDLEEARRAVSMIVGRD----------------TSQLDEEGIARAAIESV---AENTSDGVIAP 156 (312)
T ss_pred hhHHHHHHHHHHHHHcCCHHHHHHHHHHHhCCC----------------cccCCHHHHHHHHHHHH---HHhcccchHHH
Confidence 445677889999999999999999988885553 44455555555444444 44555555555
Q ss_pred hhhhcc
Q 019873 105 NLFDSL 110 (334)
Q Consensus 105 ~~~~~l 110 (334)
..|.++
T Consensus 157 lFwf~l 162 (312)
T PRK01209 157 LFYAAL 162 (312)
T ss_pred HHHHHH
Confidence 544433
No 111
>PF03186 CobD_Cbib: CobD/Cbib protein; InterPro: IPR004485 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents the CbiB protein, which is involved in cobalamin biosynthesis and porphyrin biosynthesis. It converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group. It is part of the cob operon [].; GO: 0009236 cobalamin biosynthetic process, 0016021 integral to membrane
Probab=21.52 E-value=2e+02 Score=28.01 Aligned_cols=68 Identities=18% Similarity=0.250 Sum_probs=47.8
Q ss_pred HHHHHHHHHHHHHHccCchHHHHHHHHHhccCCCCccccccccccccccccccchhhhhchhhhhhhhhhhhhhHHHHHh
Q 019873 25 KRRRQALKRVDRELSRGNFKVALSLVKQLQRKPAGGLRGFGAAKQVPKRLSSLDESELDSKELLTLRALFDSVMESIERC 104 (334)
Q Consensus 25 ~~~~~~~~~~~~~~~~g~~~~a~~~~~~l~~~~~g~l~~~gaa~~~p~r~~~l~el~l~~it~~~ll~P~~~~s~~i~~~ 104 (334)
+.-.+..++|-+.|.+||...|-..+..+-++. .-.|+|..+...+.+++ ..+++-.+-+.
T Consensus 93 r~l~~~~~~v~~aL~~gdl~~AR~~l~~lv~Rd----------------t~~L~~~~i~ra~iEs~---aen~~d~v~ap 153 (295)
T PF03186_consen 93 RSLREHAKAVYRALEAGDLEAARQALSPLVGRD----------------TDQLSEEGIARAAIESL---AENLSDGVFAP 153 (295)
T ss_pred hhHHHHHHHHHHHHhcCCHHHHHHHHHHhhCCC----------------cccCCHHHHHHHHHHHH---HHHhcchhHHH
Confidence 455677889999999999999999988886665 44566666666555555 55666666665
Q ss_pred hhhhccc
Q 019873 105 NLFDSLD 111 (334)
Q Consensus 105 ~~~~~l~ 111 (334)
+.|.+++
T Consensus 154 Lf~~~l~ 160 (295)
T PF03186_consen 154 LFWFALG 160 (295)
T ss_pred HHHHHHH
Confidence 5544443
No 112
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=21.24 E-value=4.4e+02 Score=23.50 Aligned_cols=60 Identities=8% Similarity=0.016 Sum_probs=35.7
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHh-hCcHHHHH
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKW-------AALNTVLISHHHIQVRSRLAEAMAL-GRSIGSYT 299 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~-------A~~~A~~LL~~hr~aleaLAeaL~e-~esl~eci 299 (334)
.+|+..+.-| ++.+|||-+++..-+.. .......+|.++...++.=.+.|.. ...|..++
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 4677777765 67799998876654431 2344566777766555554444443 33445444
No 113
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=20.95 E-value=4e+02 Score=23.02 Aligned_cols=52 Identities=12% Similarity=0.122 Sum_probs=31.7
Q ss_pred hhHHHHHHHH--HHHhCCCcchhHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHh
Q 019873 240 YSDINKLDKV--FQWLGYNKSEADSQVKW-------AALNTVLISHHHIQVRSRLAEAMAL 291 (334)
Q Consensus 240 ~~Dl~qat~l--~r~lGms~~~id~evr~-------A~~~A~~LL~~hr~aleaLAeaL~e 291 (334)
.+|+.++..| ++.+|||.++|..-+.. .......+|.++.+.+++-.+.|.+
T Consensus 42 ~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 102 (140)
T PRK09514 42 EQDLQRLRFIRRAKQLGFTLEEIRELLSIRLDPEHHTCQEVKGIVDEKLAEVEAKIAELQH 102 (140)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHhcccCCcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3577776666 55688887766544321 2344566777777776666555544
No 114
>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=20.87 E-value=87 Score=25.21 Aligned_cols=34 Identities=29% Similarity=0.396 Sum_probs=26.2
Q ss_pred HHHHHHHHc-cCchHHHHHHHHHhccCCCCcccccc
Q 019873 31 LKRVDRELS-RGNFKVALSLVKQLQRKPAGGLRGFG 65 (334)
Q Consensus 31 ~~~~~~~~~-~g~~~~a~~~~~~l~~~~~g~l~~~g 65 (334)
-|+|..+-. +||..+|--|++.|..++ |..+.|=
T Consensus 35 ~e~I~a~~~~~G~~~aa~~Ll~~L~r~~-~Wf~~Fl 69 (84)
T cd08789 35 KERIQAAENNSGNIKAAWTLLDTLVRRD-NWLEPFL 69 (84)
T ss_pred HHHHHHHHhcCChHHHHHHHHHHHhccC-ChHHHHH
Confidence 455666554 699999999999999777 7777663
No 115
>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=20.78 E-value=65 Score=33.79 Aligned_cols=31 Identities=16% Similarity=0.165 Sum_probs=24.3
Q ss_pred HHcHHHHHHHHHHHHhhCcHH--HHHHHHhchh
Q 019873 276 HHHIQVRSRLAEAMALGRSIG--SYTSKILTEQ 306 (334)
Q Consensus 276 ~~hr~aleaLAeaL~e~esl~--eci~~Ie~~~ 306 (334)
...+++.+.+.+.|.-+.|.. +.++.+....
T Consensus 423 ~~s~~Ag~~l~~~l~lG~S~~w~e~le~~~g~~ 455 (477)
T cd06461 423 YGSKEAGKKLRAMLSLGSSKPWPEALEALTGER 455 (477)
T ss_pred cChHHHHHHHHHHHhCcCCCCHHHHHHHhcCCC
Confidence 458899999999999988764 8877766543
No 116
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=20.58 E-value=2.7e+02 Score=21.89 Aligned_cols=46 Identities=13% Similarity=0.116 Sum_probs=28.6
Q ss_pred HHHHHHHhCCCcchhHHHHH----HHHHHHHHHHHHcHH------HHHHHHHHHHh
Q 019873 246 LDKVFQWLGYNKSEADSQVK----WAALNTVLISHHHIQ------VRSRLAEAMAL 291 (334)
Q Consensus 246 at~l~r~lGms~~~id~evr----~A~~~A~~LL~~hr~------aleaLAeaL~e 291 (334)
-.++++.+||++.+|+.-.. ....++.++|+.-++ ..+.|.++|..
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 45567889999877765322 356788888775443 34455555543
No 117
>PF14044 NETI: NETI protein
Probab=20.32 E-value=58 Score=25.13 Aligned_cols=28 Identities=11% Similarity=0.125 Sum_probs=22.2
Q ss_pred HhhCcHHHHHHHHhchhhhhhhhcccCcc
Q 019873 290 ALGRSIGSYTSKILTEQSLELLRSRTNVT 318 (334)
Q Consensus 290 ~e~esl~eci~~Ie~~~~~~~l~~~~~~~ 318 (334)
.+.|||++|++-+...--. +.|.+++--
T Consensus 5 ~enETI~~CL~RM~~eGY~-PvrR~EkPi 32 (57)
T PF14044_consen 5 EENETISDCLARMKKEGYM-PVRRIEKPI 32 (57)
T ss_pred cCCCcHHHHHHHHHHcCCC-ceeeccccc
Confidence 4689999999999998777 777666543
Done!