Query 019829
Match_columns 335
No_of_seqs 192 out of 915
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 04:52:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019829.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019829hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01434 Peptidase_M41: Peptid 100.0 1.6E-29 3.5E-34 231.9 18.0 154 146-319 7-205 (213)
2 CHL00176 ftsH cell division pr 100.0 2.5E-28 5.4E-33 255.6 18.2 188 106-328 392-625 (638)
3 PRK10733 hflB ATP-dependent me 100.0 6.1E-28 1.3E-32 252.9 18.4 190 105-328 360-595 (644)
4 KOG0734 AAA+-type ATPase conta 100.0 9E-29 1.9E-33 250.6 11.4 217 77-327 467-733 (752)
5 COG0465 HflB ATP-dependent Zn 100.0 6.7E-28 1.5E-32 249.1 16.7 191 104-328 357-590 (596)
6 TIGR01241 FtsH_fam ATP-depende 99.9 1.3E-26 2.8E-31 235.5 18.2 187 106-326 264-494 (495)
7 KOG0731 AAA+-type ATPase conta 99.9 2.8E-25 6.1E-30 233.9 13.3 188 106-329 522-749 (774)
8 CHL00206 ycf2 Ycf2; Provisiona 99.1 1E-10 2.3E-15 133.0 7.5 138 104-275 1844-1994(2281)
9 cd06163 S2P-M50_PDZ_RseP-like 97.2 0.00071 1.5E-08 61.5 5.7 24 177-200 12-35 (182)
10 cd06164 S2P-M50_SpoIVFB_CBS Sp 96.7 0.0024 5.3E-08 59.8 5.1 60 176-258 55-114 (227)
11 cd06161 S2P-M50_SpoIVFB SpoIVF 96.4 0.0034 7.3E-08 57.8 4.3 60 176-258 40-99 (208)
12 PRK10779 zinc metallopeptidase 96.4 0.0036 7.9E-08 63.8 4.4 26 176-201 17-42 (449)
13 TIGR00054 RIP metalloprotease 96.3 0.0037 8.1E-08 63.3 3.8 22 176-197 16-37 (420)
14 cd05709 S2P-M50 Site-2 proteas 95.9 0.0066 1.4E-07 53.9 3.0 76 177-258 11-91 (180)
15 PF02163 Peptidase_M50: Peptid 95.8 0.0083 1.8E-07 53.5 3.3 25 177-201 10-34 (192)
16 PF13398 Peptidase_M50B: Pepti 95.5 0.015 3.2E-07 53.4 4.1 27 176-202 24-50 (200)
17 cd06162 S2P-M50_PDZ_SREBP Ster 94.8 0.046 9.9E-07 53.1 5.4 67 176-258 137-203 (277)
18 cd06158 S2P-M50_like_1 Unchara 94.5 0.041 8.9E-07 49.8 4.0 77 177-257 12-96 (181)
19 cd06160 S2P-M50_like_2 Unchara 93.1 0.083 1.8E-06 48.1 3.2 64 176-256 43-106 (183)
20 cd06159 S2P-M50_PDZ_Arch Uncha 91.7 0.071 1.5E-06 51.3 1.0 66 177-258 121-186 (263)
21 PF14247 DUF4344: Domain of un 81.4 1.1 2.3E-05 42.3 2.4 22 176-198 94-115 (220)
22 PF00413 Peptidase_M10: Matrix 81.1 0.66 1.4E-05 39.4 0.8 17 170-186 101-117 (154)
23 cd04279 ZnMc_MMP_like_1 Zinc-d 78.4 1.4 2.9E-05 38.3 1.9 19 171-189 101-119 (156)
24 cd04268 ZnMc_MMP_like Zinc-dep 75.4 1.8 3.8E-05 37.3 1.8 17 171-187 91-107 (165)
25 PF02031 Peptidase_M7: Strepto 71.0 2.6 5.6E-05 36.9 1.8 59 154-225 59-117 (132)
26 KOG2921 Intramembrane metallop 70.0 3.4 7.4E-05 42.4 2.6 25 177-201 134-158 (484)
27 cd04278 ZnMc_MMP Zinc-dependen 69.7 2.1 4.5E-05 37.2 0.9 16 171-186 104-119 (157)
28 cd04786 HTH_MerR-like_sg7 Heli 68.8 27 0.00059 30.0 7.6 68 264-331 41-116 (131)
29 COG0750 Predicted membrane-ass 68.7 3.6 7.7E-05 40.3 2.4 26 176-201 15-40 (375)
30 PF04298 Zn_peptidase_2: Putat 68.2 2.7 5.8E-05 39.8 1.4 13 176-188 91-103 (222)
31 cd04277 ZnMc_serralysin_like Z 66.8 3.6 7.9E-05 36.6 1.9 17 171-187 110-126 (186)
32 cd04327 ZnMc_MMP_like_3 Zinc-d 63.9 6.7 0.00014 35.6 3.1 25 173-197 91-116 (198)
33 PF05572 Peptidase_M43: Pregna 63.3 3.7 8.1E-05 36.3 1.2 20 170-189 65-84 (154)
34 cd08316 Death_FAS_TNFRSF6 Deat 57.4 63 0.0014 26.7 7.4 62 268-330 21-92 (97)
35 smart00235 ZnMc Zinc-dependent 56.0 5.9 0.00013 33.4 1.2 14 176-189 88-101 (140)
36 COG0501 HtpX Zn-dependent prot 54.1 7.9 0.00017 36.5 1.8 42 150-191 130-174 (302)
37 cd04769 HTH_MerR2 Helix-Turn-H 52.7 85 0.0018 26.0 7.7 66 264-329 40-115 (116)
38 PF06114 DUF955: Domain of unk 49.1 20 0.00044 28.1 3.2 24 169-192 37-60 (122)
39 PF13485 Peptidase_MA_2: Pepti 48.7 19 0.00042 28.5 3.1 23 170-192 21-43 (128)
40 cd00203 ZnMc Zinc-dependent me 48.1 9.7 0.00021 32.6 1.3 19 172-190 94-112 (167)
41 smart00005 DEATH DEATH domain, 46.6 1.2E+02 0.0025 23.3 7.2 58 269-327 19-86 (88)
42 cd08306 Death_FADD Fas-associa 45.9 1.5E+02 0.0033 23.5 7.9 58 270-328 16-83 (86)
43 PF09278 MerR-DNA-bind: MerR, 43.3 1.2E+02 0.0027 22.0 6.5 42 274-315 10-57 (65)
44 PF13582 Reprolysin_3: Metallo 39.5 15 0.00032 30.1 1.1 13 175-187 108-120 (124)
45 PRK02391 heat shock protein Ht 38.6 22 0.00047 34.8 2.2 27 163-189 122-148 (296)
46 PRK03982 heat shock protein Ht 36.9 25 0.00054 33.9 2.3 30 161-190 112-141 (288)
47 PRK05457 heat shock protein Ht 36.6 26 0.00057 33.9 2.5 22 165-186 125-146 (284)
48 PF12388 Peptidase_M57: Dual-a 36.1 23 0.0005 33.3 1.9 19 170-188 129-147 (211)
49 PF00531 Death: Death domain; 35.5 1.9E+02 0.0041 21.6 7.1 57 270-328 15-81 (83)
50 cd04782 HTH_BltR Helix-Turn-He 35.0 1.7E+02 0.0037 23.5 6.6 51 265-315 42-95 (97)
51 cd04768 HTH_BmrR-like Helix-Tu 34.6 1.6E+02 0.0035 23.6 6.4 50 265-314 42-93 (96)
52 PF11350 DUF3152: Protein of u 32.8 23 0.0005 33.2 1.3 18 171-188 136-153 (203)
53 PF01435 Peptidase_M48: Peptid 32.5 36 0.00078 30.3 2.5 25 168-192 83-107 (226)
54 PF01890 CbiG_C: Cobalamin syn 31.9 4.9 0.00011 34.1 -3.0 86 33-118 11-99 (121)
55 cd06258 Peptidase_M3_like The 30.5 28 0.00061 34.0 1.6 17 176-192 156-172 (365)
56 PF07998 Peptidase_M54: Peptid 30.3 26 0.00057 32.5 1.2 11 176-186 147-157 (194)
57 cd01109 HTH_YyaN Helix-Turn-He 30.3 3E+02 0.0066 22.5 7.6 51 265-315 42-100 (113)
58 cd04788 HTH_NolA-AlbR Helix-Tu 30.1 1.8E+02 0.0039 23.3 6.0 50 264-313 41-92 (96)
59 COG1913 Predicted Zn-dependent 30.0 31 0.00067 31.8 1.6 16 171-186 118-136 (181)
60 cd04783 HTH_MerR1 Helix-Turn-H 29.7 2.6E+02 0.0057 23.4 7.2 51 265-315 42-98 (126)
61 cd08315 Death_TRAILR_DR4_DR5 D 29.0 1.9E+02 0.0041 23.6 5.9 62 268-330 20-90 (96)
62 COG2738 Predicted Zn-dependent 28.9 30 0.00064 32.7 1.3 13 176-188 94-106 (226)
63 cd04777 HTH_MerR-like_sg1 Heli 28.6 2.7E+02 0.0059 22.5 6.9 51 265-315 40-102 (107)
64 PRK04897 heat shock protein Ht 28.5 42 0.00091 32.7 2.4 25 165-189 128-152 (298)
65 cd04784 HTH_CadR-PbrR Helix-Tu 28.2 3.1E+02 0.0067 22.9 7.4 50 265-314 42-99 (127)
66 TIGR01950 SoxR redox-sensitive 28.1 3.1E+02 0.0066 23.9 7.5 60 264-323 41-110 (142)
67 PF12994 DUF3878: Domain of un 28.0 11 0.00024 37.1 -1.6 16 173-188 93-108 (299)
68 PF01400 Astacin: Astacin (Pep 28.0 37 0.00079 30.8 1.8 18 174-191 79-96 (191)
69 cd08318 Death_NMPP84 Death dom 27.7 1.3E+02 0.0029 23.9 4.7 45 270-315 21-75 (86)
70 PF10728 DUF2520: Domain of un 27.5 1.1E+02 0.0024 26.4 4.5 62 260-321 6-67 (132)
71 PF13583 Reprolysin_4: Metallo 27.1 32 0.0007 31.6 1.3 17 176-192 139-155 (206)
72 cd08311 Death_p75NR Death doma 26.9 1.7E+02 0.0037 23.1 5.1 34 270-304 18-51 (77)
73 cd04773 HTH_TioE_rpt2 Second H 26.6 3.6E+02 0.0078 22.1 7.5 51 265-315 42-99 (108)
74 cd04276 ZnMc_MMP_like_2 Zinc-d 26.1 47 0.001 30.7 2.1 15 172-186 114-128 (197)
75 cd04280 ZnMc_astacin_like Zinc 26.1 35 0.00075 30.7 1.2 17 175-191 75-91 (180)
76 PRK03001 M48 family peptidase; 26.0 42 0.00092 32.2 1.9 30 161-190 111-140 (283)
77 PRK03072 heat shock protein Ht 25.9 42 0.00091 32.5 1.8 26 165-190 118-143 (288)
78 cd01106 HTH_TipAL-Mta Helix-Tu 25.7 2.6E+02 0.0057 22.5 6.3 45 265-309 42-88 (103)
79 cd04275 ZnMc_pappalysin_like Z 25.7 9.7 0.00021 35.9 -2.5 20 171-190 134-153 (225)
80 PF08858 IDEAL: IDEAL domain; 25.6 1.4E+02 0.003 20.3 3.9 26 33-58 8-33 (37)
81 PF09471 Peptidase_M64: IgA Pe 25.4 34 0.00073 33.1 1.1 19 171-189 213-231 (264)
82 cd01110 HTH_SoxR Helix-Turn-He 25.3 3.1E+02 0.0067 23.7 7.0 23 265-287 42-66 (139)
83 TIGR02044 CueR Cu(I)-responsiv 24.9 3.2E+02 0.0068 22.9 6.8 50 265-314 42-99 (127)
84 PRK13267 archaemetzincin-like 24.7 48 0.0011 30.2 1.9 11 176-186 127-137 (179)
85 COG0339 Dcp Zn-dependent oligo 23.9 58 0.0013 35.7 2.6 36 170-207 464-502 (683)
86 cd04776 HTH_GnyR Helix-Turn-He 23.9 4.3E+02 0.0093 22.0 8.7 62 265-326 40-113 (118)
87 COG2856 Predicted Zn peptidase 23.8 61 0.0013 30.5 2.4 20 170-189 68-87 (213)
88 cd04283 ZnMc_hatching_enzyme Z 23.2 45 0.00097 30.5 1.4 17 175-191 78-94 (182)
89 COG2317 Zn-dependent carboxype 23.1 39 0.00084 35.6 1.0 10 178-187 263-272 (497)
90 PRK01265 heat shock protein Ht 23.0 53 0.0012 32.7 2.0 29 160-188 126-154 (324)
91 COG5549 Predicted Zn-dependent 22.9 45 0.00098 31.7 1.4 19 170-188 183-201 (236)
92 PF02074 Peptidase_M32: Carbox 22.2 46 0.001 35.1 1.4 15 178-194 263-277 (494)
93 cd04281 ZnMc_BMP1_TLD Zinc-dep 22.1 48 0.001 30.7 1.4 16 176-191 89-104 (200)
94 PF13688 Reprolysin_5: Metallo 21.8 61 0.0013 28.7 2.0 23 170-192 138-160 (196)
95 PRK01345 heat shock protein Ht 21.4 59 0.0013 32.1 1.9 28 164-191 114-141 (317)
96 TIGR02047 CadR-PbrR Cd(II)/Pb( 21.3 3.7E+02 0.0079 22.7 6.6 52 264-315 41-100 (127)
97 cd04770 HTH_HMRTR Helix-Turn-H 20.9 4.8E+02 0.01 21.5 7.3 50 266-315 43-100 (123)
98 cd04787 HTH_HMRTR_unk Helix-Tu 20.8 4E+02 0.0087 22.5 6.7 51 265-315 42-100 (133)
99 cd08313 Death_TNFR1 Death doma 20.5 3.2E+02 0.007 21.7 5.6 49 267-315 11-69 (80)
100 PRK02870 heat shock protein Ht 20.1 69 0.0015 32.1 2.1 25 161-185 160-184 (336)
101 cd06459 M3B_Oligoendopeptidase 20.1 74 0.0016 31.5 2.3 17 176-192 224-240 (427)
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=99.97 E-value=1.6e-29 Score=231.94 Aligned_cols=154 Identities=23% Similarity=0.303 Sum_probs=121.7
Q ss_pred HHHHHHhhcCCCCccccccccCCCCHhHHHHHHHHHHhHHHHHHHhC--CCCceeeecchhhhhhcCccccccceeeecc
Q 019829 146 WTVDSVSYNGGVGSLVLDTIGHTFSQKYHNRVIQHEAGHFLIAYLVG--ILPKGYTLTSFEALKKEGSLNVQAGTAFVDF 223 (335)
Q Consensus 146 ~aiD~V~lGg~~~~lvld~~~~~~s~~~r~RIA~HEAGHaLVAyllg--~PV~~~TI~preal~~~G~~~~~gG~~f~~~ 223 (335)
-++|+|++|.+... +.+++++|+|+||||||||+|+|+++ .||.++||+|+ | + .+|++...+
T Consensus 7 ~a~drv~~G~~~~~-------~~~~~~~~~~~A~HEAGhAvva~~l~~~~~v~~vsi~pr------g--~-~~G~~~~~~ 70 (213)
T PF01434_consen 7 EAIDRVLMGPEKKS-------RKLSEEEKRRIAYHEAGHAVVAYLLPPADPVSKVSIVPR------G--S-ALGFTQFTP 70 (213)
T ss_dssp HHHHHHHCCSCCTT-------S---HHHHHHHHHHHHHHHHHHHHSSS---EEEEESSTT------C--C-CCHCCEECH
T ss_pred HHHHHHhcCcCcCC-------CCCCHHHHHHHHHHHHHHHHHHHHhcccccEEEEEEecC------C--C-cceeEEecc
Confidence 48999999988532 23589999999999999999999998 58999999997 5 3 455554443
Q ss_pred hhhhhhccccCCHHHHHHHHHHHchhHHHHHHHhC--C-ccchhhHHHHHHHHHHh----cCCCH---------------
Q 019829 224 EFLEEVNSGKVSATTLNRFSCIALAGVATEYLLYG--Y-AEGGLADINKLDALLKG----LGFTQ--------------- 281 (335)
Q Consensus 224 ~~~~~~~~g~~t~~~L~r~i~VlLAGrAAE~lvyG--~-atGg~~Dl~qat~i~~~----lG~s~--------------- 281 (335)
.. +.+..|++++.+.++|+|||||||+++|| + ++|+++|++++++++.. +||+.
T Consensus 71 ~~----~~~~~t~~~l~~~i~v~LaGraAEe~~~g~~~~stGa~~DL~~At~iA~~mv~~~Gm~~~~g~~~~~~~~~~~~ 146 (213)
T PF01434_consen 71 DE----DRYIRTRSYLEDRICVLLAGRAAEELFFGEDNVSTGASSDLQQATEIARKMVASYGMGDSLGLLSYSPNDDDEV 146 (213)
T ss_dssp HT----T-SS-BHHHHHHHHHHHHHHHHHHHHHHSCCS-BGGGHHHHHHHHHHHHHHHHTST-TTTTTSS-SEEEE-S-S
T ss_pred ch----hcccccHHHHHhhHHHHHHHHHHHHhhcCcceecccchhHHHHHHHHHHHHHHHhCCCCCCceeeeeccccccc
Confidence 32 23458999999999999999999999999 5 56999999999999864 56532
Q ss_pred -----------------HHHHHHHH----HHHHHHHHHHHHcHHHHHHHHHHHHcccch
Q 019829 282 -----------------KKADSQVR----WSLLNTVLLLRRHKGARAKLAVAMTMGKSV 319 (335)
Q Consensus 282 -----------------~~id~evR----~A~~~A~~LL~~~r~aleaLaeaLl~~esl 319 (335)
..++.+++ .+|.+|+.+|++|++.+++|+++|+++++|
T Consensus 147 ~~~~~~~~~~~~s~~~~~~i~~ev~~lL~~a~~~a~~iL~~~r~~l~~la~~Lle~~~L 205 (213)
T PF01434_consen 147 FLGREWNSRRPMSEETRALIDREVRKLLEEAYARAKEILEENREALEALAEALLEKETL 205 (213)
T ss_dssp SS-E---EEESS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHSEE
T ss_pred cccccccccCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCee
Confidence 12344444 589999999999999999999999999998
No 2
>CHL00176 ftsH cell division protein; Validated
Probab=99.96 E-value=2.5e-28 Score=255.55 Aligned_cols=188 Identities=18% Similarity=0.211 Sum_probs=152.0
Q ss_pred hhhhHHHHHHHHHHhhhhhhhhcCCChhHHHHHHHHHHHHHHHHHHhhcCCCCccccccccCCCCHhHHHHHHHHHHhHH
Q 019829 106 LGSIERNLQLAAIVGGVSAWNVFGFNPQQILYLSLALLFLWTVDSVSYNGGVGSLVLDTIGHTFSQKYHNRVIQHEAGHF 185 (335)
Q Consensus 106 l~sv~n~~a~~a~~g~~~~~~~~~l~~~~~~~~~~~~l~~~aiD~V~lGg~~~~lvld~~~~~~s~~~r~RIA~HEAGHa 185 (335)
|..+.|++++.+.+.+...+..-++. .++|++++|.+..++ .++++|++|||||||||
T Consensus 392 L~~lvneAal~a~r~~~~~It~~dl~--------------~Ai~rv~~g~~~~~~--------~~~~~~~~vA~hEaGhA 449 (638)
T CHL00176 392 LANLLNEAAILTARRKKATITMKEID--------------TAIDRVIAGLEGTPL--------EDSKNKRLIAYHEVGHA 449 (638)
T ss_pred HHHHHHHHHHHHHHhCCCCcCHHHHH--------------HHHHHHHhhhccCcc--------ccHHHHHHHHHHhhhhH
Confidence 67777888887777665544433333 389999999775543 37899999999999999
Q ss_pred HHHHHhC--CCCceeeecchhhhhhcCccccccceeeecchhhhhhccccCCHHHHHHHHHHHchhHHHHHHHhCC---c
Q 019829 186 LIAYLVG--ILPKGYTLTSFEALKKEGSLNVQAGTAFVDFEFLEEVNSGKVSATTLNRFSCIALAGVATEYLLYGY---A 260 (335)
Q Consensus 186 LVAyllg--~PV~~~TI~preal~~~G~~~~~gG~~f~~~~~~~~~~~g~~t~~~L~r~i~VlLAGrAAE~lvyG~---a 260 (335)
+|+++++ .||+++||+|| | ..+|+++..|+. +.+.+|+.++..+++++|||||||+++||+ +
T Consensus 450 ~v~~~l~~~~~v~kvtI~pr------g---~~~G~~~~~p~~----~~~~~t~~~l~~~i~~~LgGraAE~~~fg~~~~~ 516 (638)
T CHL00176 450 IVGTLLPNHDPVQKVTLIPR------G---QAKGLTWFTPEE----DQSLVSRSQILARIVGALGGRAAEEVVFGSTEVT 516 (638)
T ss_pred HHHhhccCCCceEEEEEeec------C---CCCCceEecCCc----ccccccHHHHHHHHHHHhhhHHHHHHhcCCCCcC
Confidence 9999987 68999999998 5 356777665542 346789999999999999999999999994 4
Q ss_pred cchhhHHHHHHHHHHh----cCCC----------------------------H---HHHHHHHH----HHHHHHHHHHHH
Q 019829 261 EGGLADINKLDALLKG----LGFT----------------------------Q---KKADSQVR----WSLLNTVLLLRR 301 (335)
Q Consensus 261 tGg~~Dl~qat~i~~~----lG~s----------------------------~---~~id~evR----~A~~~A~~LL~~ 301 (335)
+|+++|++++|++++. +||+ + ..+|.+++ .||.+|+.+|++
T Consensus 517 ~Ga~~Dl~~AT~iA~~mv~~~Gm~~~g~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~iD~ev~~~l~~~~~~a~~iL~~ 596 (638)
T CHL00176 517 TGASNDLQQVTNLARQMVTRFGMSSIGPISLESNNSTDPFLGRFMQRNSEYSEEIADKIDMEVRSILHTCYQYAYQILKD 596 (638)
T ss_pred CCchhHHHHHHHHHHHHHHHhCCCcCCceeecCCCCcccccccccccccCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6999999999999864 5653 0 13566655 699999999999
Q ss_pred cHHHHHHHHHHHHcccch--HHHHHHHHh
Q 019829 302 HKGARAKLAVAMTMGKSV--GSCIDIIED 328 (335)
Q Consensus 302 ~r~aleaLaeaLl~~esl--~~ci~~Ie~ 328 (335)
|++.++++|++|+++||| +|+.++++.
T Consensus 597 ~~~~l~~la~~Lle~Etl~~~ei~~il~~ 625 (638)
T CHL00176 597 NRVLIDLLVELLLQKETIDGDEFREIVNS 625 (638)
T ss_pred hHHHHHHHHHHHHHhCccCHHHHHHHHhh
Confidence 999999999999999999 677788865
No 3
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=99.95 E-value=6.1e-28 Score=252.90 Aligned_cols=190 Identities=20% Similarity=0.231 Sum_probs=153.0
Q ss_pred hhhhhHHHHHHHHHHhhhhhhhhcCCChhHHHHHHHHHHHHHHHHHHhhcCCCCccccccccCCCCHhHHHHHHHHHHhH
Q 019829 105 TLGSIERNLQLAAIVGGVSAWNVFGFNPQQILYLSLALLFLWTVDSVSYNGGVGSLVLDTIGHTFSQKYHNRVIQHEAGH 184 (335)
Q Consensus 105 ~l~sv~n~~a~~a~~g~~~~~~~~~l~~~~~~~~~~~~l~~~aiD~V~lGg~~~~lvld~~~~~~s~~~r~RIA~HEAGH 184 (335)
-|..+.|++++.|.+.+-..+...++.. ++|++.+|..... ..+++++|+++|||||||
T Consensus 360 dl~~l~~eAa~~a~r~~~~~i~~~d~~~--------------a~~~v~~g~~~~~-------~~~~~~~~~~~a~he~gh 418 (644)
T PRK10733 360 DLANLVNEAALFAARGNKRVVSMVEFEK--------------AKDKIMMGAERRS-------MVMTEAQKESTAYHEAGH 418 (644)
T ss_pred HHHHHHHHHHHHHHHcCCCcccHHHHHH--------------HHHHHhccccccc-------ccccHHHHHHHHHHHHHH
Confidence 4667788999988888776555544444 8999999876432 235789999999999999
Q ss_pred HHHHHHhC--CCCceeeecchhhhhhcCccccccceeeecchhhhhhccccCCHHHHHHHHHHHchhHHHHHHHhCC---
Q 019829 185 FLIAYLVG--ILPKGYTLTSFEALKKEGSLNVQAGTAFVDFEFLEEVNSGKVSATTLNRFSCIALAGVATEYLLYGY--- 259 (335)
Q Consensus 185 aLVAyllg--~PV~~~TI~preal~~~G~~~~~gG~~f~~~~~~~~~~~g~~t~~~L~r~i~VlLAGrAAE~lvyG~--- 259 (335)
|+|+++++ .||+++||+|| | ..+|+++..|+. +....|+++|+++++|+|||||||+++||.
T Consensus 419 a~~~~~~~~~~~~~~v~i~pr------g---~~~g~~~~~~~~----~~~~~~~~~l~~~i~~~lgGraAE~~~~g~~~~ 485 (644)
T PRK10733 419 AIIGRLVPEHDPVHKVTIIPR------G---RALGVTFFLPEG----DAISASRQKLESQISTLYGGRLAEEIIYGPEHV 485 (644)
T ss_pred HHHHHHccCCCceeEEEEecc------C---CCcceeEECCCc----ccccccHHHHHHHHHHHHhhHHHHHHHhCCCCC
Confidence 99999997 68999999998 5 356776665542 234579999999999999999999999994
Q ss_pred ccchhhHHHHHHHHHHh----cCCCH-------------------------------HHHHHHHH----HHHHHHHHHHH
Q 019829 260 AEGGLADINKLDALLKG----LGFTQ-------------------------------KKADSQVR----WSLLNTVLLLR 300 (335)
Q Consensus 260 atGg~~Dl~qat~i~~~----lG~s~-------------------------------~~id~evR----~A~~~A~~LL~ 300 (335)
++|+++|++++|++++. +|||. ..+|++++ .||.+|+++|+
T Consensus 486 ttGa~~Dl~~AT~lA~~mv~~~Gms~~lg~~~~~~~~~~~~lg~~~~~~~~~s~~~~~~id~ev~~il~~~~~~a~~iL~ 565 (644)
T PRK10733 486 STGASNDIKVATNLARNMVTQWGFSEKLGPLLYAEEEGEVFLGRSVAKAKHMSDETARIIDQEVKALIERNYNRARQLLT 565 (644)
T ss_pred CCCcHHHHHHHHHHHHHHHHHhCCCccccchhhcccccccccccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46999999999998864 57642 13566665 69999999999
Q ss_pred HcHHHHHHHHHHHHcccch--HHHHHHHHh
Q 019829 301 RHKGARAKLAVAMTMGKSV--GSCIDIIED 328 (335)
Q Consensus 301 ~~r~aleaLaeaLl~~esl--~~ci~~Ie~ 328 (335)
+|++.+++||++|+++||| ++..+++..
T Consensus 566 ~~~~~l~~la~~Lle~etl~~~ei~~i~~~ 595 (644)
T PRK10733 566 DNMDILHAMKDALMKYETIDAPQIDDLMAR 595 (644)
T ss_pred HhHHHHHHHHHHHHHhceeCHHHHHHHHhc
Confidence 9999999999999999999 566677764
No 4
>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=9e-29 Score=250.59 Aligned_cols=217 Identities=18% Similarity=0.227 Sum_probs=173.3
Q ss_pred CCCccccC--hhHHh--hhccccccCCCCc----------cchhhhhHHHHHHHHHHhhhhhhhhcCCChhHHHHHHHHH
Q 019829 77 QIPQRLYT--LDELK--LNGIETRSLLSPV----------DETLGSIERNLQLAAIVGGVSAWNVFGFNPQQILYLSLAL 142 (335)
Q Consensus 77 ~vp~r~~~--~~elk--~~gi~~~~~lsp~----------~~~l~sv~n~~a~~a~~g~~~~~~~~~l~~~~~~~~~~~~ 142 (335)
.||.-++. .+=|+ +++|.-.+..-|+ ..-|+++-|.+|+-|-+.|.....+-||..
T Consensus 467 ~Vp~PDv~GR~eIL~~yl~ki~~~~~VD~~iiARGT~GFsGAdLaNlVNqAAlkAa~dga~~VtM~~LE~---------- 536 (752)
T KOG0734|consen 467 TVPLPDVRGRTEILKLYLSKIPLDEDVDPKIIARGTPGFSGADLANLVNQAALKAAVDGAEMVTMKHLEF---------- 536 (752)
T ss_pred ecCCCCcccHHHHHHHHHhcCCcccCCCHhHhccCCCCCchHHHHHHHHHHHHHHHhcCcccccHHHHhh----------
Confidence 45655554 23344 4666555433332 233778889999988888887777777774
Q ss_pred HHHHHHHHHhhcCCCCccccccccCCCCHhHHHHHHHHHHhHHHHHHHhC--CCCceeeecchhhhhhcCccccccceee
Q 019829 143 LFLWTVDSVSYNGGVGSLVLDTIGHTFSQKYHNRVIQHEAGHFLIAYLVG--ILPKGYTLTSFEALKKEGSLNVQAGTAF 220 (335)
Q Consensus 143 l~~~aiD~V~lGg~~~~lvld~~~~~~s~~~r~RIA~HEAGHaLVAyllg--~PV~~~TI~preal~~~G~~~~~gG~~f 220 (335)
+-|+|+||.++.+.+ ++++.|+..||||+|||+||+... .|++|.||.|| | -..|.++
T Consensus 537 ----akDrIlMG~ERks~~-------i~~eak~~TAyHE~GHAivA~yTk~A~PlhKaTImPR------G---~sLG~t~ 596 (752)
T KOG0734|consen 537 ----AKDRILMGPERKSMV-------IDEEAKKITAYHEGGHAIVALYTKGAMPLHKATIMPR------G---PSLGHTS 596 (752)
T ss_pred ----hhhheeecccccccc-------cChhhhhhhhhhccCceEEEeecCCCccccceeeccC------C---cccccee
Confidence 999999999977665 579999999999999999999986 69999999998 6 2456777
Q ss_pred ecchhhhhhccccCCHHHHHHHHHHHchhHHHHHHHhCC--c-cchhhHHHHHHHHHHh----cCCCH------------
Q 019829 221 VDFEFLEEVNSGKVSATTLNRFSCIALAGVATEYLLYGY--A-EGGLADINKLDALLKG----LGFTQ------------ 281 (335)
Q Consensus 221 ~~~~~~~~~~~g~~t~~~L~r~i~VlLAGrAAE~lvyG~--a-tGg~~Dl~qat~i~~~----lG~s~------------ 281 (335)
..|+. |++..|+.++..++-|+||||+||+|+||. + +|+++|++|+|++++. +|||.
T Consensus 597 ~LPe~----D~~~~Tk~q~LA~lDV~MGGRvAEELIfG~D~iTsGAssDl~qAT~lA~~MVt~fGMSd~vG~v~~~~~~~ 672 (752)
T KOG0734|consen 597 QLPEK----DRYSITKAQLLARLDVCMGGRVAEELIFGTDKITSGASSDLDQATKLARRMVTKFGMSDKVGPVTLSAEDN 672 (752)
T ss_pred ecCcc----chhhHHHHHHHHHHHHhhcchHHHHHhccCCcccccccchHHHHHHHHHHHHHHcCccccccceeeeccCC
Confidence 66653 568899999999999999999999999997 3 5999999999998764 68753
Q ss_pred ---------HHHHHHHH----HHHHHHHHHHHHcHHHHHHHHHHHHcccch--HHHHHHHH
Q 019829 282 ---------KKADSQVR----WSLLNTVLLLRRHKGARAKLAVAMTMGKSV--GSCIDIIE 327 (335)
Q Consensus 282 ---------~~id~evR----~A~~~A~~LL~~~r~aleaLaeaLl~~esl--~~ci~~Ie 327 (335)
..+|.|++ .+|+||+.||+.|...+++||+||++.||| +|..++++
T Consensus 673 ~~s~~~~t~~lidaEi~~lL~~sYeRak~iL~~h~kEl~~LA~ALleYETL~A~eik~vl~ 733 (752)
T KOG0734|consen 673 SSSLSPRTQELIDAEIKRLLRDSYERAKSILKTHKKELHALAEALLEYETLDAKEIKRVLK 733 (752)
T ss_pred CCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHh
Confidence 14777765 589999999999999999999999999999 55556664
No 5
>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=6.7e-28 Score=249.07 Aligned_cols=191 Identities=21% Similarity=0.211 Sum_probs=164.2
Q ss_pred chhhhhHHHHHHHHHHhhhhhhhhcCCChhHHHHHHHHHHHHHHHHHHhhcCCCCccccccccCCCCHhHHHHHHHHHHh
Q 019829 104 ETLGSIERNLQLAAIVGGVSAWNVFGFNPQQILYLSLALLFLWTVDSVSYNGGVGSLVLDTIGHTFSQKYHNRVIQHEAG 183 (335)
Q Consensus 104 ~~l~sv~n~~a~~a~~g~~~~~~~~~l~~~~~~~~~~~~l~~~aiD~V~lGg~~~~lvld~~~~~~s~~~r~RIA~HEAG 183 (335)
..|..+-|++|++|.+-+-..+.+.+++. ++|+|++|.+..+. ++++++|+-+||||||
T Consensus 357 AdL~nl~NEAal~aar~n~~~i~~~~i~e--------------a~drv~~G~erks~-------vise~ek~~~AYhEag 415 (596)
T COG0465 357 ADLANLLNEAALLAARRNKKEITMRDIEE--------------AIDRVIAGPERKSR-------VISEAEKKITAYHEAG 415 (596)
T ss_pred chHhhhHHHHHHHHHHhcCeeEeccchHH--------------HHHHHhcCcCcCCc-------ccChhhhcchHHHHHH
Confidence 45778889999999999999999999998 99999999996654 4699999999999999
Q ss_pred HHHHHHHhC--CCCceeeecchhhhhhcCccccccceeeecchhhhhhccccCCHHHHHHHHHHHchhHHHHHHHhC-Cc
Q 019829 184 HFLIAYLVG--ILPKGYTLTSFEALKKEGSLNVQAGTAFVDFEFLEEVNSGKVSATTLNRFSCIALAGVATEYLLYG-YA 260 (335)
Q Consensus 184 HaLVAyllg--~PV~~~TI~preal~~~G~~~~~gG~~f~~~~~~~~~~~g~~t~~~L~r~i~VlLAGrAAE~lvyG-~a 260 (335)
|++|+++++ +||+|+||+|| | ..+|+++..|+. |++.+|++++.++++++|||||||+++|| +.
T Consensus 416 halv~~~l~~~d~v~KvtIiPr------G---~alG~t~~~Pe~----d~~l~sk~~l~~~i~~~lgGRaAEel~~g~e~ 482 (596)
T COG0465 416 HALVGLLLPDADPVHKVTIIPR------G---RALGYTLFLPEE----DKYLMSKEELLDRIDVLLGGRAAEELIFGYEI 482 (596)
T ss_pred HHHHHHhCCCCcccceeeeccC------c---hhhcchhcCCcc----ccccccHHHHHHHHHHHhCCcHhhhhhhcccc
Confidence 999999997 59999999998 5 467888777653 57899999999999999999999999999 75
Q ss_pred -cchhhHHHHHHHHHHh----cCCCH-----------------------------HHHHHHHH----HHHHHHHHHHHHc
Q 019829 261 -EGGLADINKLDALLKG----LGFTQ-----------------------------KKADSQVR----WSLLNTVLLLRRH 302 (335)
Q Consensus 261 -tGg~~Dl~qat~i~~~----lG~s~-----------------------------~~id~evR----~A~~~A~~LL~~~ 302 (335)
+|++||++++|.+++. +|||. ..||.+++ .+|.+++.+|.+|
T Consensus 483 ttGa~~D~~~at~~ar~mVt~~Gms~~lG~v~~~~~~~~flg~~~~~~~~Se~ta~~ID~evk~ii~~~y~~a~~il~~~ 562 (596)
T COG0465 483 TTGASNDLEKATDLARAMVTEYGMSAKLGPVAYEQVEGVFLGRYQKAKNYSEETAQEIDREVKDIIDEAYERAKELLNEN 562 (596)
T ss_pred cccchhhHHHHHHHHHHhhhhcCcchhhCceehhhcccccccccccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 6999999999998764 56652 24677766 5999999999999
Q ss_pred HHHHHHHHHHHHcccch--HHHHHHHHh
Q 019829 303 KGARAKLAVAMTMGKSV--GSCIDIIED 328 (335)
Q Consensus 303 r~aleaLaeaLl~~esl--~~ci~~Ie~ 328 (335)
++.++.++++|+++||+ ++..++++.
T Consensus 563 ~~~l~~~~~~Lle~Eti~~~~i~~i~~~ 590 (596)
T COG0465 563 KDALETLAEMLLEKETIDAEEIKDILAG 590 (596)
T ss_pred HHHHHHHHHHHHHhhccCHHHHHHHHhc
Confidence 99999999999999998 333344443
No 6
>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=99.94 E-value=1.3e-26 Score=235.49 Aligned_cols=187 Identities=19% Similarity=0.211 Sum_probs=141.3
Q ss_pred hhhhHHHHHHHHHHhhhhhhhhcCCChhHHHHHHHHHHHHHHHHHHhhcCCCCccccccccCCCCHhHHHHHHHHHHhHH
Q 019829 106 LGSIERNLQLAAIVGGVSAWNVFGFNPQQILYLSLALLFLWTVDSVSYNGGVGSLVLDTIGHTFSQKYHNRVIQHEAGHF 185 (335)
Q Consensus 106 l~sv~n~~a~~a~~g~~~~~~~~~l~~~~~~~~~~~~l~~~aiD~V~lGg~~~~lvld~~~~~~s~~~r~RIA~HEAGHa 185 (335)
|..+.|++++.+.+.+-..+..-+ +..+++++.+|..... ..+++++++|+||||||||
T Consensus 264 l~~l~~eA~~~a~~~~~~~i~~~~--------------l~~a~~~~~~~~~~~~-------~~~~~~~~~~~A~hEaGhA 322 (495)
T TIGR01241 264 LANLLNEAALLAARKNKTEITMND--------------IEEAIDRVIAGPEKKS-------RVISEKEKKLVAYHEAGHA 322 (495)
T ss_pred HHHHHHHHHHHHHHcCCCCCCHHH--------------HHHHHHHHhccccccc-------ccccHHHHHHHHHHHHhHH
Confidence 445556666655554433222222 2347899999876332 2358999999999999999
Q ss_pred HHHHHhC--CCCceeeecchhhhhhcCccccccceeeecchhhhhhccccCCHHHHHHHHHHHchhHHHHHHHhCCc-cc
Q 019829 186 LIAYLVG--ILPKGYTLTSFEALKKEGSLNVQAGTAFVDFEFLEEVNSGKVSATTLNRFSCIALAGVATEYLLYGYA-EG 262 (335)
Q Consensus 186 LVAyllg--~PV~~~TI~preal~~~G~~~~~gG~~f~~~~~~~~~~~g~~t~~~L~r~i~VlLAGrAAE~lvyG~a-tG 262 (335)
||+|+++ .||.++||.|| | + .+|+++..+.. +.+..|+++++++++|+|||||||+++||++ +|
T Consensus 323 lv~~~l~~~~~v~~vsi~pr------g--~-~~G~~~~~~~~----~~~~~t~~~l~~~i~v~LaGraAE~~~~G~~s~G 389 (495)
T TIGR01241 323 LVGLLLKDADPVHKVTIIPR------G--Q-ALGYTQFLPEE----DKYLYTKSQLLAQIAVLLGGRAAEEIIFGEVTTG 389 (495)
T ss_pred HHHHhcCCCCceEEEEEeec------C--C-ccceEEecCcc----ccccCCHHHHHHHHHHHhhHHHHHHHHhcCCCCC
Confidence 9999995 68999999998 5 2 55655543321 3467899999999999999999999999996 59
Q ss_pred hhhHHHHHHHHHHh----cCCCH-------------------------------HHHHHHH----HHHHHHHHHHHHHcH
Q 019829 263 GLADINKLDALLKG----LGFTQ-------------------------------KKADSQV----RWSLLNTVLLLRRHK 303 (335)
Q Consensus 263 g~~Dl~qat~i~~~----lG~s~-------------------------------~~id~ev----R~A~~~A~~LL~~~r 303 (335)
+++|++++++++.. +||+. ..++.++ ++++.+|+++|++|+
T Consensus 390 a~~Dl~~At~lA~~mv~~~Gm~~~~g~~~~~~~~~~~~l~~~~~~~~~~s~~~~~~id~~v~~lL~~a~~ra~~lL~~~~ 469 (495)
T TIGR01241 390 ASNDIKQATNIARAMVTEWGMSDKLGPVAYGSDGGDVFLGRGFAKAKEYSEETAREIDEEVKRIIEEAYKRAKQILTENR 469 (495)
T ss_pred chHHHHHHHHHHHHHHHHhCCCcccCceeeccCccccccccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 99999999999753 56542 1234444 489999999999999
Q ss_pred HHHHHHHHHHHcccch--HHHHHHH
Q 019829 304 GARAKLAVAMTMGKSV--GSCIDII 326 (335)
Q Consensus 304 ~aleaLaeaLl~~esl--~~ci~~I 326 (335)
++++++|++|+++++| +|..++|
T Consensus 470 ~~l~~la~~Ll~~e~L~~~ei~~il 494 (495)
T TIGR01241 470 DELELLAKALLEKETITREEIKELL 494 (495)
T ss_pred HHHHHHHHHHHHcCeeCHHHHHHHh
Confidence 9999999999999998 4444444
No 7
>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.92 E-value=2.8e-25 Score=233.87 Aligned_cols=188 Identities=21% Similarity=0.252 Sum_probs=159.9
Q ss_pred hhhhHHHHHHHHHHhhhhhhhhcCCChhHHHHHHHHHHHHHHHHHHhhcCCCCccccccccCCCCHhHHHHHHHHHHhHH
Q 019829 106 LGSIERNLQLAAIVGGVSAWNVFGFNPQQILYLSLALLFLWTVDSVSYNGGVGSLVLDTIGHTFSQKYHNRVIQHEAGHF 185 (335)
Q Consensus 106 l~sv~n~~a~~a~~g~~~~~~~~~l~~~~~~~~~~~~l~~~aiD~V~lGg~~~~lvld~~~~~~s~~~r~RIA~HEAGHa 185 (335)
|-.|.|++|+.|++-+..++...+|.. ++|+++.|-...+ +.+++++++.+|||||||+
T Consensus 522 l~n~~neaa~~a~r~~~~~i~~~~~~~--------------a~~Rvi~G~~~~~-------~~~~~~~~~~~a~~eagha 580 (774)
T KOG0731|consen 522 LANLCNEAALLAARKGLREIGTKDLEY--------------AIERVIAGMEKKS-------RVLSLEEKKTVAYHEAGHA 580 (774)
T ss_pred HHhhhhHHHHHHHHhccCccchhhHHH--------------HHHHHhccccccc-------hhcCHhhhhhhhhhhccch
Confidence 678999999999999999888777776 8999999865333 3358999999999999999
Q ss_pred HHHHHhC--CCCceeeecchhhhhhcCccccccceeeecchhhhhhccccCCHHHHHHHHHHHchhHHHHHHHhC-C-cc
Q 019829 186 LIAYLVG--ILPKGYTLTSFEALKKEGSLNVQAGTAFVDFEFLEEVNSGKVSATTLNRFSCIALAGVATEYLLYG-Y-AE 261 (335)
Q Consensus 186 LVAyllg--~PV~~~TI~preal~~~G~~~~~gG~~f~~~~~~~~~~~g~~t~~~L~r~i~VlLAGrAAE~lvyG-~-at 261 (335)
++++++. +|+.++||+| | + ..|+++..|.. .+++|+++|..++|++|||||||+++|| + ++
T Consensus 581 ~~g~~l~~~dpl~kvsIiP-------G--q-alG~a~~~P~~-----~~l~sk~ql~~rm~m~LGGRaAEev~fg~~iTt 645 (774)
T KOG0731|consen 581 VVGWLLEHADPLLKVSIIP-------G--Q-ALGYAQYLPTD-----DYLLSKEQLFDRMVMALGGRAAEEVVFGSEITT 645 (774)
T ss_pred hhhccccccCcceeEEecc-------C--C-ccceEEECCcc-----cccccHHHHHHHHHHHhCcchhhheecCCccCc
Confidence 9998887 5999999999 5 2 45666666652 3899999999999999999999999998 4 46
Q ss_pred chhhHHHHHHHHHHh----cCCCH--------------------------HHHHHHHHH----HHHHHHHHHHHcHHHHH
Q 019829 262 GGLADINKLDALLKG----LGFTQ--------------------------KKADSQVRW----SLLNTVLLLRRHKGARA 307 (335)
Q Consensus 262 Gg~~Dl~qat~i~~~----lG~s~--------------------------~~id~evR~----A~~~A~~LL~~~r~ale 307 (335)
|+.+|++++|++++. +||++ +.||.++|+ ||++|.++|++|++.++
T Consensus 646 ga~ddl~kvT~~A~~~V~~~Gms~kig~~~~~~~~~~~~~~~~p~s~~~~~~Id~ev~~lv~~ay~~~~~ll~~n~~~l~ 725 (774)
T KOG0731|consen 646 GAQDDLEKVTKIARAMVASFGMSEKIGPISFQMLLPGDESFRKPYSEKTAQLIDTEVRRLVQKAYERTKELLRTNRDKLD 725 (774)
T ss_pred hhhccHHHHHHHHHHHHHHcCcccccCceeccCcccccccccCccchhHHHHHHHHHHHHHhhHHHHHHHHHHHhHHHHH
Confidence 999999999999865 56541 357777774 89999999999999999
Q ss_pred HHHHHHHcccch--HHHHHHHHhh
Q 019829 308 KLAVAMTMGKSV--GSCIDIIEDN 329 (335)
Q Consensus 308 aLaeaLl~~esl--~~ci~~Ie~~ 329 (335)
.+++.|+++|++ ++++.++..-
T Consensus 726 ~ia~~LLeke~l~~ee~~~ll~~~ 749 (774)
T KOG0731|consen 726 KIAEVLLEKEVLTGEEIIALLGER 749 (774)
T ss_pred HHHHHHHHhhhccHHHHHHHhccC
Confidence 999999999998 8888887653
No 8
>CHL00206 ycf2 Ycf2; Provisional
Probab=99.10 E-value=1e-10 Score=133.01 Aligned_cols=138 Identities=12% Similarity=0.015 Sum_probs=100.2
Q ss_pred chhhhhHHHHHHHHHHhhhhhhhhcCCChhHHHHHHHHHHHHHHHHHHhhcCCCCccccccccCCCCHhHHHHHHHHHHh
Q 019829 104 ETLGSIERNLQLAAIVGGVSAWNVFGFNPQQILYLSLALLFLWTVDSVSYNGGVGSLVLDTIGHTFSQKYHNRVIQHEAG 183 (335)
Q Consensus 104 ~~l~sv~n~~a~~a~~g~~~~~~~~~l~~~~~~~~~~~~l~~~aiD~V~lGg~~~~lvld~~~~~~s~~~r~RIA~HEAG 183 (335)
.-|..+.|+|++.|++-+-+.+..-.+.. |+|++++|-+.. ..+.+++ +|++||+|
T Consensus 1844 ADLanLvNEAaliAirq~ks~Id~~~I~~--------------Al~Rq~~g~~~~---------~~~~~~~-~ia~yEiG 1899 (2281)
T CHL00206 1844 RDLVALTNEALSISITQKKSIIDTNTIRS--------------ALHRQTWDLRSQ---------VRSVQDH-GILFYQIG 1899 (2281)
T ss_pred HHHHHHHHHHHHHHHHcCCCccCHHHHHH--------------HHHHHHhhhhhc---------ccCcchh-hhhhhHHh
Confidence 34788889999999999888776555554 899999996532 1134444 48999999
Q ss_pred HHHHHHHhC--CCCceeeecch-hhhhhcCccccccceeeecchhhhhhccccCCHHHHHHHHHHHchhHHHHHHHhCCc
Q 019829 184 HFLIAYLVG--ILPKGYTLTSF-EALKKEGSLNVQAGTAFVDFEFLEEVNSGKVSATTLNRFSCIALAGVATEYLLYGYA 260 (335)
Q Consensus 184 HaLVAyllg--~PV~~~TI~pr-eal~~~G~~~~~gG~~f~~~~~~~~~~~g~~t~~~L~r~i~VlLAGrAAE~lvyG~a 260 (335)
||+|+.++. +||.++||.|. +.++. | ...|+++..+. +..+++.++..+++++|||+|||++.|+..
T Consensus 1900 hAvvq~~L~~~~pv~kISIy~~~~~~r~-~---~~yl~~wyle~------~~~mkk~tiL~~Il~cLAGraAedlwf~~~ 1969 (2281)
T CHL00206 1900 RAVAQNVLLSNCPIDPISIYMKKKSCKE-G---DSYLYKWYFEL------GTSMKKLTILLYLLSCSAGSVAQDLWSLPG 1969 (2281)
T ss_pred HHHHHHhccCCCCcceEEEecCCccccC-c---ccceeEeecCC------cccCCHHHHHHHHHHHhhhhhhhhhccCcc
Confidence 999999985 79999999642 22222 2 23366665542 257899999999999999999999999632
Q ss_pred -------c--c-hhhHHHHHHHHHH
Q 019829 261 -------E--G-GLADINKLDALLK 275 (335)
Q Consensus 261 -------t--G-g~~Dl~qat~i~~ 275 (335)
+ | ..+|+.-+-.++.
T Consensus 1970 ~~~~n~It~yg~vEnD~~La~glLe 1994 (2281)
T CHL00206 1970 PDEKNGITSYGLVENDSDLVHGLLE 1994 (2281)
T ss_pred hhhhcCcccccchhhhhHHhHhHHH
Confidence 1 2 2567777766654
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=97.16 E-value=0.00071 Score=61.52 Aligned_cols=24 Identities=38% Similarity=0.801 Sum_probs=21.4
Q ss_pred HHHHHHhHHHHHHHhCCCCceeee
Q 019829 177 VIQHEAGHFLIAYLVGILPKGYTL 200 (335)
Q Consensus 177 IA~HEAGHaLVAyllg~PV~~~TI 200 (335)
|..||.||+++|...|.+|.+++|
T Consensus 12 v~iHElGH~~~Ar~~Gv~v~~f~i 35 (182)
T cd06163 12 IFVHELGHFLVAKLFGVKVEEFSI 35 (182)
T ss_pred HHHHHHHHHHHHHHcCCeeeEeee
Confidence 789999999999999999888543
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=96.68 E-value=0.0024 Score=59.77 Aligned_cols=60 Identities=35% Similarity=0.381 Sum_probs=45.3
Q ss_pred HHHHHHHhHHHHHHHhCCCCceeeecchhhhhhcCccccccceeeecchhhhhhccccCCHHHHHHHHHHHchhHHHHHH
Q 019829 176 RVIQHEAGHFLIAYLVGILPKGYTLTSFEALKKEGSLNVQAGTAFVDFEFLEEVNSGKVSATTLNRFSCIALAGVATEYL 255 (335)
Q Consensus 176 RIA~HEAGHaLVAyllg~PV~~~TI~preal~~~G~~~~~gG~~f~~~~~~~~~~~g~~t~~~L~r~i~VlLAGrAAE~l 255 (335)
-+..||.||+++|..+|.||+++++.|. | |++..++.+ .++ .+.+.|++||-++.-+
T Consensus 55 ~v~iHElgH~~~A~~~G~~v~~i~l~p~------G------g~~~~~~~~--------~~~---~~~~~IalAGPl~Nll 111 (227)
T cd06164 55 SVLLHELGHSLVARRYGIPVRSITLFLF------G------GVARLEREP--------ETP---GQEFVIAIAGPLVSLV 111 (227)
T ss_pred HHHHHHHHHHHHHHHcCCeECeEEEEee------e------EEEEecCCC--------CCH---HHHhhhhhhHHHHHHH
Confidence 4779999999999999999999999986 4 444433221 132 4567899999999877
Q ss_pred HhC
Q 019829 256 LYG 258 (335)
Q Consensus 256 vyG 258 (335)
...
T Consensus 112 la~ 114 (227)
T cd06164 112 LAL 114 (227)
T ss_pred HHH
Confidence 654
No 11
>cd06161 S2P-M50_SpoIVFB SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB.
Probab=96.45 E-value=0.0034 Score=57.83 Aligned_cols=60 Identities=40% Similarity=0.486 Sum_probs=44.4
Q ss_pred HHHHHHHhHHHHHHHhCCCCceeeecchhhhhhcCccccccceeeecchhhhhhccccCCHHHHHHHHHHHchhHHHHHH
Q 019829 176 RVIQHEAGHFLIAYLVGILPKGYTLTSFEALKKEGSLNVQAGTAFVDFEFLEEVNSGKVSATTLNRFSCIALAGVATEYL 255 (335)
Q Consensus 176 RIA~HEAGHaLVAyllg~PV~~~TI~preal~~~G~~~~~gG~~f~~~~~~~~~~~g~~t~~~L~r~i~VlLAGrAAE~l 255 (335)
-+..||-||+++|..+|.|++++++.|. | |....+.. .. + -.+.+.|++||-.+.-+
T Consensus 40 ~v~iHElgH~~~A~~~G~~v~~i~l~p~------G------g~~~~~~~-------~~-~---~~~~~lIalAGPl~n~~ 96 (208)
T cd06161 40 SVLLHELGHALVARRYGIRVRSITLLPF------G------GVAELEEE-------PE-T---PKEEFVIALAGPLVSLL 96 (208)
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEee------e------eeeeeccC-------CC-C---hhHheeeeeehHHHHHH
Confidence 4789999999999999999999999986 4 33322211 11 2 24567799999999977
Q ss_pred HhC
Q 019829 256 LYG 258 (335)
Q Consensus 256 vyG 258 (335)
+..
T Consensus 97 la~ 99 (208)
T cd06161 97 LAG 99 (208)
T ss_pred HHH
Confidence 754
No 12
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=96.37 E-value=0.0036 Score=63.82 Aligned_cols=26 Identities=27% Similarity=0.523 Sum_probs=23.4
Q ss_pred HHHHHHHhHHHHHHHhCCCCceeeec
Q 019829 176 RVIQHEAGHFLIAYLVGILPKGYTLT 201 (335)
Q Consensus 176 RIA~HEAGHaLVAyllg~PV~~~TI~ 201 (335)
-|.+||.||||+|.+.|+.|.+++|-
T Consensus 17 li~vHElGHfl~Ar~~gv~V~~FsiG 42 (449)
T PRK10779 17 LITVHEFGHFWVARRCGVRVERFSIG 42 (449)
T ss_pred HHHHHHHHHHHHHHHcCCeeeEEEee
Confidence 38899999999999999999888774
No 13
>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=96.26 E-value=0.0037 Score=63.30 Aligned_cols=22 Identities=45% Similarity=0.653 Sum_probs=19.9
Q ss_pred HHHHHHHhHHHHHHHhCCCCce
Q 019829 176 RVIQHEAGHFLIAYLVGILPKG 197 (335)
Q Consensus 176 RIA~HEAGHaLVAyllg~PV~~ 197 (335)
-|.+||.||+|+|.+.|..|.+
T Consensus 16 ~v~~HE~gH~~~a~~~g~~v~~ 37 (420)
T TIGR00054 16 LIFVHELGHFLAARLCGIKVER 37 (420)
T ss_pred HHHHHhHHHHHHHHHcCCEEEE
Confidence 3899999999999999988875
No 14
>cd05709 S2P-M50 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. The domain core structure appears to contain at least three transmembrane helices with a catalytic zinc atom coordinated by three conserved residues contained within the consensus sequence HExxH, together with a conserved aspartate residue. The S2P/M50 family of RIP proteases is widely distributed; in eukaryotic cells, they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum (ER) stress responses. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of sterol regulatory element-bindin
Probab=95.86 E-value=0.0066 Score=53.91 Aligned_cols=76 Identities=25% Similarity=0.112 Sum_probs=40.6
Q ss_pred HHHHHHhHHHHHHHhCCCCceeeecc----hhhhhhcCc-cccccceeeecchhhhhhccccCCHHHHHHHHHHHchhHH
Q 019829 177 VIQHEAGHFLIAYLVGILPKGYTLTS----FEALKKEGS-LNVQAGTAFVDFEFLEEVNSGKVSATTLNRFSCIALAGVA 251 (335)
Q Consensus 177 IA~HEAGHaLVAyllg~PV~~~TI~p----real~~~G~-~~~~gG~~f~~~~~~~~~~~g~~t~~~L~r~i~VlLAGrA 251 (335)
+..||.||+++|+..|+++.+.++.. ..-....|. .---||++...+.. . .. .+..-.+++.|.+||-.
T Consensus 11 i~iHE~gH~~~A~~~G~~~~~~~~~~~~~~~~~~~~~~~~~ip~gG~~~~~~~~--~---~~-~~~~~~~~~~i~laGPl 84 (180)
T cd05709 11 VTVHELGHALVARRLGVKVARFSGGFTLNPLKHGDPYGIILIPLGGYAKPVGEN--P---RA-FKKPRWQRLLVALAGPL 84 (180)
T ss_pred HHHHHHHHHHHHHHcCCCchheeeeEEECCcCCCCEehHHHHhccCeeccCCCC--h---hh-hccchhhhhhhhhhhHH
Confidence 78999999999999999765544321 100000000 00013433222111 0 00 01123566789999999
Q ss_pred HHHHHhC
Q 019829 252 TEYLLYG 258 (335)
Q Consensus 252 AE~lvyG 258 (335)
+.-+...
T Consensus 85 ~nllla~ 91 (180)
T cd05709 85 ANLLLAL 91 (180)
T ss_pred HHHHHHH
Confidence 9987664
No 15
>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=95.77 E-value=0.0083 Score=53.52 Aligned_cols=25 Identities=32% Similarity=0.359 Sum_probs=18.0
Q ss_pred HHHHHHhHHHHHHHhCCCCceeeec
Q 019829 177 VIQHEAGHFLIAYLVGILPKGYTLT 201 (335)
Q Consensus 177 IA~HEAGHaLVAyllg~PV~~~TI~ 201 (335)
+..||.||+++|+..|+++.++++.
T Consensus 10 i~~HE~gH~~~a~~~G~~~~~~~~~ 34 (192)
T PF02163_consen 10 IVLHELGHALAARLYGDKVPRFEGG 34 (192)
T ss_dssp HHHHHHHHHHHHHTTT--B--EEE-
T ss_pred ccccccccccccccccccccccccc
Confidence 6899999999999999988888543
No 16
>PF13398 Peptidase_M50B: Peptidase M50B-like
Probab=95.54 E-value=0.015 Score=53.43 Aligned_cols=27 Identities=41% Similarity=0.436 Sum_probs=25.3
Q ss_pred HHHHHHHhHHHHHHHhCCCCceeeecc
Q 019829 176 RVIQHEAGHFLIAYLVGILPKGYTLTS 202 (335)
Q Consensus 176 RIA~HEAGHaLVAyllg~PV~~~TI~p 202 (335)
-+..||.||++++.+.|-.|+++++.|
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 389999999999999998999999987
No 17
>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=94.85 E-value=0.046 Score=53.10 Aligned_cols=67 Identities=22% Similarity=0.212 Sum_probs=45.5
Q ss_pred HHHHHHHhHHHHHHHhCCCCceeeecchhhhhhcCccccccceeeecchhhhhhccccCCHHHHHHHHHHHchhHHHHHH
Q 019829 176 RVIQHEAGHFLIAYLVGILPKGYTLTSFEALKKEGSLNVQAGTAFVDFEFLEEVNSGKVSATTLNRFSCIALAGVATEYL 255 (335)
Q Consensus 176 RIA~HEAGHaLVAyllg~PV~~~TI~preal~~~G~~~~~gG~~f~~~~~~~~~~~g~~t~~~L~r~i~VlLAGrAAE~l 255 (335)
-+..||-||+++|...|++|+++.+.+. .-..|| |.++.+++ . ...++ .+++.|++||.++.-+
T Consensus 137 svvvHElgHal~A~~~gi~V~~iGl~l~--------~~~pGa--~ve~~~e~-~--~~~~~---~~~l~Ia~AGp~~Nlv 200 (277)
T cd06162 137 SGVVHEMGHGVAAVREQVRVNGFGIFFF--------IIYPGA--YVDLFTDH-L--NLISP---VQQLRIFCAGVWHNFV 200 (277)
T ss_pred HHHHHHHHHHHHHHHcCCeeceEEEeee--------eccCee--EEeecccc-c--ccCCh---hhhhheehhhHHHHHH
Confidence 3579999999999999999999988754 011133 55543321 1 22333 3477899999999887
Q ss_pred HhC
Q 019829 256 LYG 258 (335)
Q Consensus 256 vyG 258 (335)
.-.
T Consensus 201 La~ 203 (277)
T cd06162 201 LGL 203 (277)
T ss_pred HHH
Confidence 654
No 18
>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=94.53 E-value=0.041 Score=49.82 Aligned_cols=77 Identities=18% Similarity=0.213 Sum_probs=42.7
Q ss_pred HHHHHHhHHHHHHHhCCCCc----eeeecchhhhhhcCcccc----ccceeeecchhhhhhccccCCHHHHHHHHHHHch
Q 019829 177 VIQHEAGHFLIAYLVGILPK----GYTLTSFEALKKEGSLNV----QAGTAFVDFEFLEEVNSGKVSATTLNRFSCIALA 248 (335)
Q Consensus 177 IA~HEAGHaLVAyllg~PV~----~~TI~preal~~~G~~~~----~gG~~f~~~~~~~~~~~g~~t~~~L~r~i~VlLA 248 (335)
+..||.||+++|+..|++-. ..|+.|..-+---|+.-. ..|..+..|.+.+. ..+ ++.-.+...|.+|
T Consensus 12 i~~HE~aHa~~A~~~Gd~t~~~~Grltlnp~~hid~~g~l~~~~~~~~~~G~a~p~~~~~---~~~-~~~r~~~~~valA 87 (181)
T cd06158 12 ITLHEFAHAYVAYRLGDPTARRAGRLTLNPLAHIDPIGTIILPLLLPFLFGWAKPVPVNP---RNF-KNPRRGMLLVSLA 87 (181)
T ss_pred HHHHHHHHHHHHHHcCCcHHHHcCceecCcHHhcCcchHHHHHHHHHhCeEEecccccCh---Hhh-cccHhhHhhhhhh
Confidence 68999999999999998633 467666411111111100 00333444433111 111 2222456779999
Q ss_pred hHHHHHHHh
Q 019829 249 GVATEYLLY 257 (335)
Q Consensus 249 GrAAE~lvy 257 (335)
|-++.-+..
T Consensus 88 GP~~n~~la 96 (181)
T cd06158 88 GPLSNLLLA 96 (181)
T ss_pred hHHHHHHHH
Confidence 999987554
No 19
>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=93.07 E-value=0.083 Score=48.14 Aligned_cols=64 Identities=25% Similarity=0.187 Sum_probs=41.3
Q ss_pred HHHHHHHhHHHHHHHhCCCCceeeecchhhhhhcCccccccceeeecchhhhhhccccCCHHHHHHHHHHHchhHHHHHH
Q 019829 176 RVIQHEAGHFLIAYLVGILPKGYTLTSFEALKKEGSLNVQAGTAFVDFEFLEEVNSGKVSATTLNRFSCIALAGVATEYL 255 (335)
Q Consensus 176 RIA~HEAGHaLVAyllg~PV~~~TI~preal~~~G~~~~~gG~~f~~~~~~~~~~~g~~t~~~L~r~i~VlLAGrAAE~l 255 (335)
-+..||.||+++|...|+++.+..+.|- ..-| .-|+..-++ + ...++ .+.+.|.+||-++--+
T Consensus 43 ~l~iHElgH~~~A~~~G~~~~~~~l~P~---~~~G---~~G~~~~~~-~-------~~~~~---~~~~~IalAGPl~nl~ 105 (183)
T cd06160 43 ILGIHEMGHYLAARRHGVKASLPYFIPF---PFIG---TFGAFIRMR-S-------PIPNR---KALFDIALAGPLAGLL 105 (183)
T ss_pred HHHHHHHHHHHHHHHCCCCccceeeeeh---HhcC---cEEEEEEec-C-------CCCCh---hHhehhhhhHHHHHHH
Confidence 4789999999999999999999988882 0012 123321111 1 11232 4566788888888755
Q ss_pred H
Q 019829 256 L 256 (335)
Q Consensus 256 v 256 (335)
.
T Consensus 106 l 106 (183)
T cd06160 106 L 106 (183)
T ss_pred H
Confidence 4
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=91.73 E-value=0.071 Score=51.30 Aligned_cols=66 Identities=26% Similarity=0.186 Sum_probs=40.8
Q ss_pred HHHHHHhHHHHHHHhCCCCceeeecchhhhhhcCccccccceeeecchhhhhhccccCCHHHHHHHHHHHchhHHHHHHH
Q 019829 177 VIQHEAGHFLIAYLVGILPKGYTLTSFEALKKEGSLNVQAGTAFVDFEFLEEVNSGKVSATTLNRFSCIALAGVATEYLL 256 (335)
Q Consensus 177 IA~HEAGHaLVAyllg~PV~~~TI~preal~~~G~~~~~gG~~f~~~~~~~~~~~g~~t~~~L~r~i~VlLAGrAAE~lv 256 (335)
+..||.||+++|...|++|+.+.+.-. . ---|| |..++.. + ....+ -.++..|++||-.+.-+.
T Consensus 121 v~iHElgHa~~Ar~~G~~V~~iGl~l~------~--ip~Gg--~v~~~~~-~--~~~~~---~~~~~~Ia~AGP~~Nlvl 184 (263)
T cd06159 121 VVVHELSHGILARVEGIKVKSGGLLLL------I--IPPGA--FVEPDEE-E--LNKAD---RRIRLRIFAAGVTANFVV 184 (263)
T ss_pred HHHHHHHHHHHHHHcCCEECchhHHHH------h--hhcEE--EEEecch-h--hccCC---hhheeeeeeehHHHHHHH
Confidence 779999999999999999887654210 0 00223 4444321 1 11122 245678999999988665
Q ss_pred hC
Q 019829 257 YG 258 (335)
Q Consensus 257 yG 258 (335)
..
T Consensus 185 a~ 186 (263)
T cd06159 185 AL 186 (263)
T ss_pred HH
Confidence 43
No 21
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=81.41 E-value=1.1 Score=42.31 Aligned_cols=22 Identities=36% Similarity=0.410 Sum_probs=17.1
Q ss_pred HHHHHHHhHHHHHHHhCCCCcee
Q 019829 176 RVIQHEAGHFLIAYLVGILPKGY 198 (335)
Q Consensus 176 RIA~HEAGHaLVAyllg~PV~~~ 198 (335)
-|.+||.||+|+..+ ++||.|=
T Consensus 94 ~~l~HE~GHAlI~~~-~lPv~Gr 115 (220)
T PF14247_consen 94 FTLYHELGHALIDDL-DLPVLGR 115 (220)
T ss_pred HHHHHHHHHHHHHHh-cCCcccc
Confidence 488999999999876 4466653
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=81.09 E-value=0.66 Score=39.41 Aligned_cols=17 Identities=41% Similarity=0.425 Sum_probs=14.1
Q ss_pred CHhHHHHHHHHHHhHHH
Q 019829 170 SQKYHNRVIQHEAGHFL 186 (335)
Q Consensus 170 s~~~r~RIA~HEAGHaL 186 (335)
+..+...|+.||.||+|
T Consensus 101 ~~~~~~~v~~HEiGHaL 117 (154)
T PF00413_consen 101 SGNDLQSVAIHEIGHAL 117 (154)
T ss_dssp SSEEHHHHHHHHHHHHT
T ss_pred hhhhhhhhhhhcccccc
Confidence 45677889999999985
No 23
>cd04279 ZnMc_MMP_like_1 Zinc-dependent metalloprotease; MMP_like sub-family 1. A group of bacterial, archaeal, and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=78.35 E-value=1.4 Score=38.25 Aligned_cols=19 Identities=26% Similarity=0.345 Sum_probs=15.1
Q ss_pred HhHHHHHHHHHHhHHHHHH
Q 019829 171 QKYHNRVIQHEAGHFLIAY 189 (335)
Q Consensus 171 ~~~r~RIA~HEAGHaLVAy 189 (335)
..+.+.|+.||-||+|--.
T Consensus 101 ~~~~~~~~~HEiGHaLGL~ 119 (156)
T cd04279 101 AENLQAIALHELGHALGLW 119 (156)
T ss_pred chHHHHHHHHHhhhhhcCC
Confidence 4577899999999987433
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=75.41 E-value=1.8 Score=37.29 Aligned_cols=17 Identities=29% Similarity=0.288 Sum_probs=14.2
Q ss_pred HhHHHHHHHHHHhHHHH
Q 019829 171 QKYHNRVIQHEAGHFLI 187 (335)
Q Consensus 171 ~~~r~RIA~HEAGHaLV 187 (335)
..+...++.||.||+|-
T Consensus 91 ~~~~~~~~~HEiGHaLG 107 (165)
T cd04268 91 GARLRNTAEHELGHALG 107 (165)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 35788999999999964
No 25
>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=71.00 E-value=2.6 Score=36.86 Aligned_cols=59 Identities=29% Similarity=0.362 Sum_probs=24.7
Q ss_pred cCCCCccccccccCCCCHhHHHHHHHHHHhHHHHHHHhCCCCceeeecchhhhhhcCccccccceeeecchh
Q 019829 154 NGGVGSLVLDTIGHTFSQKYHNRVIQHEAGHFLIAYLVGILPKGYTLTSFEALKKEGSLNVQAGTAFVDFEF 225 (335)
Q Consensus 154 Gg~~~~lvld~~~~~~s~~~r~RIA~HEAGHaLVAyllg~PV~~~TI~preal~~~G~~~~~gG~~f~~~~~ 225 (335)
|.+.+.+.+|.-. .-.-..-||+.||.||.| |+|=+ |+ .|=-.|+. | +.+|+....+.|
T Consensus 59 g~G~G~I~l~~~~--~qgy~~~RIaaHE~GHiL-----GLPD~-y~-GpCS~LMS-G---~~aG~sCtN~~P 117 (132)
T PF02031_consen 59 GLGSGYIFLDYQQ--NQGYNSTRIAAHELGHIL-----GLPDH-YP-GPCSELMS-G---GSAGTSCTNAYP 117 (132)
T ss_dssp SSS-EEEEEEHHH--HHHS-HHHHHHHHHHHHH-----T-----TT-S-TT-GGG-T---TTT-TT----S-
T ss_pred CCCcEEEEechHH--hhCCccceeeeehhcccc-----CCCCC-CC-CccHHhhc-C---CCCCCCCCCCCC
Confidence 3444566666422 112345599999999975 54411 11 02222333 4 366777776654
No 26
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=70.04 E-value=3.4 Score=42.41 Aligned_cols=25 Identities=36% Similarity=0.553 Sum_probs=21.5
Q ss_pred HHHHHHhHHHHHHHhCCCCceeeec
Q 019829 177 VIQHEAGHFLIAYLVGILPKGYTLT 201 (335)
Q Consensus 177 IA~HEAGHaLVAyllg~PV~~~TI~ 201 (335)
+.+||-||||+|..-|.||.++-|-
T Consensus 134 ~vvHElGHalAA~segV~vngfgIf 158 (484)
T KOG2921|consen 134 VVVHELGHALAAASEGVQVNGFGIF 158 (484)
T ss_pred HHHHHhhHHHHHHhcCceeeeeEEE
Confidence 4589999999999999998887654
No 27
>cd04278 ZnMc_MMP Zinc-dependent metalloprotease, matrix metalloproteinase (MMP) sub-family. MMPs are responsible for a great deal of pericellular proteolysis of extracellular matrix and cell surface molecules, playing crucial roles in morphogenesis, cell fate specification, cell migration, tissue repair, tumorigenesis, gain or loss of tissue-specific functions, and apoptosis. In many instances, they are anchored to cell membranes via trans-membrane domains, and their activity is controlled via TIMPs (tissue inhibitors of metalloproteinases).
Probab=69.66 E-value=2.1 Score=37.16 Aligned_cols=16 Identities=38% Similarity=0.347 Sum_probs=13.6
Q ss_pred HhHHHHHHHHHHhHHH
Q 019829 171 QKYHNRVIQHEAGHFL 186 (335)
Q Consensus 171 ~~~r~RIA~HEAGHaL 186 (335)
..+...|+.||-||+|
T Consensus 104 ~~~~~~~~~HEiGHaL 119 (157)
T cd04278 104 GTDLFSVAAHEIGHAL 119 (157)
T ss_pred cchHHHHHHHHhcccc
Confidence 4567889999999995
No 28
>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=68.80 E-value=27 Score=30.01 Aligned_cols=68 Identities=18% Similarity=0.258 Sum_probs=44.1
Q ss_pred hhHHHHHHHH--HHhcCCCHHHHHHHHH-----HHHHHHHHHHHHcHHHHHHHHHHHHcc-cchHHHHHHHHhhhc
Q 019829 264 LADINKLDAL--LKGLGFTQKKADSQVR-----WSLLNTVLLLRRHKGARAKLAVAMTMG-KSVGSCIDIIEDNID 331 (335)
Q Consensus 264 ~~Dl~qat~i--~~~lG~s~~~id~evR-----~A~~~A~~LL~~~r~aleaLaeaLl~~-esl~~ci~~Ie~~~~ 331 (335)
.+|+..+..| ++.+|||-++|..-+. +.......+|+++...+++..+.|.+- +.|.+++..+++..+
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 3556665554 4668888776654332 123455677888888887777777764 667888777776554
No 29
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=68.74 E-value=3.6 Score=40.30 Aligned_cols=26 Identities=31% Similarity=0.562 Sum_probs=22.2
Q ss_pred HHHHHHHhHHHHHHHhCCCCceeeec
Q 019829 176 RVIQHEAGHFLIAYLVGILPKGYTLT 201 (335)
Q Consensus 176 RIA~HEAGHaLVAyllg~PV~~~TI~ 201 (335)
-|..||.||+|+++..+..|.++++.
T Consensus 15 lv~~he~gh~~~a~~~~~~v~~f~ig 40 (375)
T COG0750 15 LVFVHELGHFWVARRCGVKVERFSIG 40 (375)
T ss_pred HHHHHHHhhHHHHHhcCceeEEEEec
Confidence 58899999999999999877777663
No 30
>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=68.25 E-value=2.7 Score=39.83 Aligned_cols=13 Identities=38% Similarity=0.562 Sum_probs=10.8
Q ss_pred HHHHHHHhHHHHH
Q 019829 176 RVIQHEAGHFLIA 188 (335)
Q Consensus 176 RIA~HEAGHaLVA 188 (335)
-||-||+|||+=-
T Consensus 91 aVAAHEvGHAiQ~ 103 (222)
T PF04298_consen 91 AVAAHEVGHAIQH 103 (222)
T ss_pred HHHHHHHhHHHhc
Confidence 4899999999753
No 31
>cd04277 ZnMc_serralysin_like Zinc-dependent metalloprotease, serralysin_like subfamily. Serralysins and related proteases are important virulence factors in pathogenic bacteria. They may be secreted into the medium via a mechanism found in gram-negative bacteria, that does not require n-terminal signal sequences which are cleaved after the transmembrane translocation. A calcium-binding domain c-terminal to the metalloprotease domain, which contains multiple tandem repeats of a nine-residue motif including the pattern GGxGxD, and which forms a parallel beta roll may be involved in the translocation mechanism and/or substrate binding. Serralysin family members may have a broad spectrum of substrates each, including host immunoglobulins, complement proteins, cell matrix and cytoskeletal proteins, as well as antimicrobial peptides.
Probab=66.79 E-value=3.6 Score=36.61 Aligned_cols=17 Identities=41% Similarity=0.516 Sum_probs=14.3
Q ss_pred HhHHHHHHHHHHhHHHH
Q 019829 171 QKYHNRVIQHEAGHFLI 187 (335)
Q Consensus 171 ~~~r~RIA~HEAGHaLV 187 (335)
..+...++.||.||+|-
T Consensus 110 g~~~~~t~~HEiGHaLG 126 (186)
T cd04277 110 GSYGYQTIIHEIGHALG 126 (186)
T ss_pred ChhhHHHHHHHHHHHhc
Confidence 46678899999999974
No 32
>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=63.87 E-value=6.7 Score=35.61 Aligned_cols=25 Identities=28% Similarity=0.173 Sum_probs=17.4
Q ss_pred HHHHHHHHHHhHHHHHHHhC-CCCce
Q 019829 173 YHNRVIQHEAGHFLIAYLVG-ILPKG 197 (335)
Q Consensus 173 ~r~RIA~HEAGHaLVAyllg-~PV~~ 197 (335)
+...++.||-||+|--+--- -|-+.
T Consensus 91 ~~~~~i~HElgHaLG~~HEh~rpdrd 116 (198)
T cd04327 91 EFSRVVLHEFGHALGFIHEHQSPAAN 116 (198)
T ss_pred hHHHHHHHHHHHHhcCcccccCCCCC
Confidence 45679999999998765543 24444
No 33
>PF05572 Peptidase_M43: Pregnancy-associated plasma protein-A; InterPro: IPR008754 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase M43 (cytophagalysin family, clan MA(M)), subfamily M43. The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example of this family is the pregnancy-associated plasma protein A (PAPP-A), which cleaves insulin-like growth factor (IGF) binding protein-4 (IGFBP-4), causing a dramatic reduction in its affinity for IGF-I and -II. Through this mechanism, PAPP-A is a regulator of IGF bioactivity in several systems, including the Homo sapiens ovary and the cardiovascular system [, , , ].; PDB: 3LUN_A 3LUM_B 2J83_A 2CKI_A.
Probab=63.27 E-value=3.7 Score=36.31 Aligned_cols=20 Identities=40% Similarity=0.654 Sum_probs=13.9
Q ss_pred CHhHHHHHHHHHHhHHHHHH
Q 019829 170 SQKYHNRVIQHEAGHFLIAY 189 (335)
Q Consensus 170 s~~~r~RIA~HEAGHaLVAy 189 (335)
++....+++.||.||+|-=+
T Consensus 65 ~~~~~g~TltHEvGH~LGL~ 84 (154)
T PF05572_consen 65 SQYNFGKTLTHEVGHWLGLY 84 (154)
T ss_dssp TTS-SSHHHHHHHHHHTT--
T ss_pred Cccccccchhhhhhhhhccc
Confidence 45566799999999997433
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=57.40 E-value=63 Score=26.70 Aligned_cols=62 Identities=21% Similarity=0.222 Sum_probs=41.7
Q ss_pred HHHHHHHHhcCCCHHHHHHHH----HHHHHHHHHHHHHcHH------HHHHHHHHHHcccchHHHHHHHHhhh
Q 019829 268 NKLDALLKGLGFTQKKADSQV----RWSLLNTVLLLRRHKG------ARAKLAVAMTMGKSVGSCIDIIEDNI 330 (335)
Q Consensus 268 ~qat~i~~~lG~s~~~id~ev----R~A~~~A~~LL~~~r~------aleaLaeaLl~~esl~~ci~~Ie~~~ 330 (335)
.+..++++.+|+|+.+|+.-. +-..++.+++|+..+. ++..|+++|.. --+..|-+.|++.+
T Consensus 21 ~~wK~faR~lglse~~Id~I~~~~~~d~~Eq~~qmL~~W~~~~G~~a~~~~Li~aLr~-~~l~~~Ad~I~~~l 92 (97)
T cd08316 21 KDVKKFVRKSGLSEPKIDEIKLDNPQDTAEQKVQLLRAWYQSHGKTGAYRTLIKTLRK-AKLCTKADKIQDII 92 (97)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHcCCCChHHHHHHHHHHHHHHhCCCchHHHHHHHHHH-ccchhHHHHHHHHH
Confidence 456778899999998887532 2357888888876544 56778877765 44455555555544
No 35
>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=55.98 E-value=5.9 Score=33.42 Aligned_cols=14 Identities=50% Similarity=0.624 Sum_probs=11.2
Q ss_pred HHHHHHHhHHHHHH
Q 019829 176 RVIQHEAGHFLIAY 189 (335)
Q Consensus 176 RIA~HEAGHaLVAy 189 (335)
.++.||-||+|--.
T Consensus 88 ~~~~HEigHaLGl~ 101 (140)
T smart00235 88 GVAAHELGHALGLY 101 (140)
T ss_pred ccHHHHHHHHhcCC
Confidence 49999999998433
No 36
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=54.06 E-value=7.9 Score=36.49 Aligned_cols=42 Identities=19% Similarity=0.253 Sum_probs=28.7
Q ss_pred HHhhcCC---CCccccccccCCCCHhHHHHHHHHHHhHHHHHHHh
Q 019829 150 SVSYNGG---VGSLVLDTIGHTFSQKYHNRVIQHEAGHFLIAYLV 191 (335)
Q Consensus 150 ~V~lGg~---~~~lvld~~~~~~s~~~r~RIA~HEAGHaLVAyll 191 (335)
.+.+|+. +.-.+-+.+-+.++++|-+=|.-||.||..-.+.+
T Consensus 130 AFa~g~~~~~~~V~vt~gLl~~l~~dEl~aVlaHElgHi~~rd~~ 174 (302)
T COG0501 130 AFALGGGPKNGRVVVTTGLLDLLNDDELEAVLAHELGHIKNRHTL 174 (302)
T ss_pred ceecCCCCCCeeEEecHHHHhhCCHHHHHHHHHHHHHHHhcccHH
Confidence 3455553 33334455555678999999999999998766554
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=52.73 E-value=85 Score=26.02 Aligned_cols=66 Identities=12% Similarity=0.078 Sum_probs=44.1
Q ss_pred hhHHHHHHHH--HHhcCCCHHHHHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHcc-cchHHHHHHHHhh
Q 019829 264 LADINKLDAL--LKGLGFTQKKADSQVRW-------SLLNTVLLLRRHKGARAKLAVAMTMG-KSVGSCIDIIEDN 329 (335)
Q Consensus 264 ~~Dl~qat~i--~~~lG~s~~~id~evR~-------A~~~A~~LL~~~r~aleaLaeaLl~~-esl~~ci~~Ie~~ 329 (335)
.+|+..+..| ++.+|||.++|..-... .......+|+++...+++=-+.|.+. ..+..++..++++
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 4577776665 57799998877754442 12355677888888777777666664 5577777766654
No 38
>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=49.08 E-value=20 Score=28.14 Aligned_cols=24 Identities=25% Similarity=0.307 Sum_probs=18.4
Q ss_pred CCHhHHHHHHHHHHhHHHHHHHhC
Q 019829 169 FSQKYHNRVIQHEAGHFLIAYLVG 192 (335)
Q Consensus 169 ~s~~~r~RIA~HEAGHaLVAyllg 192 (335)
.++..++=++.||.||.+...--.
T Consensus 37 ~~~~~~~f~laHELgH~~~~~~~~ 60 (122)
T PF06114_consen 37 LSPERQRFTLAHELGHILLHHGDE 60 (122)
T ss_dssp S-HHHHHHHHHHHHHHHHHHH-HH
T ss_pred CCHHHHHHHHHHHHHHHHhhhccc
Confidence 478888888999999999877654
No 39
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=48.70 E-value=19 Score=28.50 Aligned_cols=23 Identities=26% Similarity=0.525 Sum_probs=19.7
Q ss_pred CHhHHHHHHHHHHhHHHHHHHhC
Q 019829 170 SQKYHNRVIQHEAGHFLIAYLVG 192 (335)
Q Consensus 170 s~~~r~RIA~HEAGHaLVAyllg 192 (335)
+++...+++.||-+|.+.....+
T Consensus 21 ~~~~~~~~l~HE~~H~~~~~~~~ 43 (128)
T PF13485_consen 21 DEDWLDRVLAHELAHQWFGNYFG 43 (128)
T ss_pred CHHHHHHHHHHHHHHHHHHHHcC
Confidence 46666799999999999999876
No 40
>cd00203 ZnMc Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease.
Probab=48.10 E-value=9.7 Score=32.59 Aligned_cols=19 Identities=42% Similarity=0.455 Sum_probs=14.7
Q ss_pred hHHHHHHHHHHhHHHHHHH
Q 019829 172 KYHNRVIQHEAGHFLIAYL 190 (335)
Q Consensus 172 ~~r~RIA~HEAGHaLVAyl 190 (335)
.+-..++.||.||+|--+-
T Consensus 94 ~~~~~~~~HElGH~LGl~H 112 (167)
T cd00203 94 KEGAQTIAHELGHALGFYH 112 (167)
T ss_pred ccchhhHHHHHHHHhCCCc
Confidence 3567899999999986443
No 41
>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=46.60 E-value=1.2e+02 Score=23.30 Aligned_cols=58 Identities=17% Similarity=0.192 Sum_probs=36.8
Q ss_pred HHHHHHHhcCCCHHHHHHHHHH----HHHHHHHHHHHcHH------HHHHHHHHHHcccchHHHHHHHH
Q 019829 269 KLDALLKGLGFTQKKADSQVRW----SLLNTVLLLRRHKG------ARAKLAVAMTMGKSVGSCIDIIE 327 (335)
Q Consensus 269 qat~i~~~lG~s~~~id~evR~----A~~~A~~LL~~~r~------aleaLaeaLl~~esl~~ci~~Ie 327 (335)
.-..+++.+||+...++.-... ...+++.+|+.-+. .++.|.++|.+-. ..++.+.|+
T Consensus 19 ~W~~la~~Lg~~~~~i~~i~~~~~~~~~~~~~~lL~~W~~~~g~~at~~~L~~aL~~~~-~~d~a~~i~ 86 (88)
T smart00005 19 DWRELARKLGLSEADIDQIRTEAPRDLAEQSVQLLRLWEQREGKNATLGTLLEALRKMG-RDDAVELLR 86 (88)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHccchhhHHHHHHHHHHHcC-hHHHHHHHh
Confidence 3556788899998877752222 34789999877655 6677777776632 334444443
No 42
>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=45.86 E-value=1.5e+02 Score=23.53 Aligned_cols=58 Identities=22% Similarity=0.197 Sum_probs=36.2
Q ss_pred HHHHHHhcCCCHHHHHHHH-H---HHHHHHHHHHHHcH------HHHHHHHHHHHcccchHHHHHHHHh
Q 019829 270 LDALLKGLGFTQKKADSQV-R---WSLLNTVLLLRRHK------GARAKLAVAMTMGKSVGSCIDIIED 328 (335)
Q Consensus 270 at~i~~~lG~s~~~id~ev-R---~A~~~A~~LL~~~r------~aleaLaeaLl~~esl~~ci~~Ie~ 328 (335)
-.++++.||||+..|+.-. + -..++++++|+.-+ ..++.|.++|.+-.- ...-..|++
T Consensus 16 Wk~laR~LGlse~~Id~i~~~~~~~~~eq~~~mL~~W~~~~g~~At~~~L~~aL~~~~l-~~~ad~i~~ 83 (86)
T cd08306 16 WRKLARKLGLSETKIESIEEAHPRNLREQVRQSLREWKKIKKKEAKVADLIKALRDCQL-NLVADLVEE 83 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHhHCcchHHHHHHHHHHHcCc-HHHHHHHHH
Confidence 4456788999998887521 1 24578888886443 456678888876432 333344444
No 43
>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=43.33 E-value=1.2e+02 Score=21.97 Aligned_cols=42 Identities=14% Similarity=0.177 Sum_probs=27.2
Q ss_pred HHhcCCCHHHHHHHHH------HHHHHHHHHHHHcHHHHHHHHHHHHc
Q 019829 274 LKGLGFTQKKADSQVR------WSLLNTVLLLRRHKGARAKLAVAMTM 315 (335)
Q Consensus 274 ~~~lG~s~~~id~evR------~A~~~A~~LL~~~r~aleaLaeaLl~ 315 (335)
++.+|||-++|..-+. ........+++++.+.+++=-+.|.+
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 5679999988776542 34556667888888877776666554
No 44
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=39.53 E-value=15 Score=30.08 Aligned_cols=13 Identities=38% Similarity=0.414 Sum_probs=10.8
Q ss_pred HHHHHHHHhHHHH
Q 019829 175 NRVIQHEAGHFLI 187 (335)
Q Consensus 175 ~RIA~HEAGHaLV 187 (335)
..+..||.||.|=
T Consensus 108 ~~~~~HEiGH~lG 120 (124)
T PF13582_consen 108 VDTFAHEIGHNLG 120 (124)
T ss_dssp TTHHHHHHHHHTT
T ss_pred ceEeeehhhHhcC
Confidence 3799999999863
No 45
>PRK02391 heat shock protein HtpX; Provisional
Probab=38.56 E-value=22 Score=34.76 Aligned_cols=27 Identities=15% Similarity=0.122 Sum_probs=21.7
Q ss_pred ccccCCCCHhHHHHHHHHHHhHHHHHH
Q 019829 163 DTIGHTFSQKYHNRVIQHEAGHFLIAY 189 (335)
Q Consensus 163 d~~~~~~s~~~r~RIA~HEAGHaLVAy 189 (335)
|.+-+.++++|.+=|.-||.||.--.+
T Consensus 122 ~gLl~~L~~~El~aVlaHElgHi~~~d 148 (296)
T PRK02391 122 TGLMRRLDPDELEAVLAHELSHVKNRD 148 (296)
T ss_pred HHHHhhCCHHHHHHHHHHHHHHHHcCC
Confidence 556666789999999999999975444
No 46
>PRK03982 heat shock protein HtpX; Provisional
Probab=36.86 E-value=25 Score=33.87 Aligned_cols=30 Identities=23% Similarity=0.174 Sum_probs=23.5
Q ss_pred ccccccCCCCHhHHHHHHHHHHhHHHHHHH
Q 019829 161 VLDTIGHTFSQKYHNRVIQHEAGHFLIAYL 190 (335)
Q Consensus 161 vld~~~~~~s~~~r~RIA~HEAGHaLVAyl 190 (335)
+-|.+-+.++++|.+=|.-||.||.--.+.
T Consensus 112 vt~gLl~~l~~~El~AVlAHElgHi~~~h~ 141 (288)
T PRK03982 112 VTEGILNLLNEDELEGVIAHELTHIKNRDT 141 (288)
T ss_pred eehHHHhhCCHHHHHHHHHHHHHHHHcCCH
Confidence 455555667899999999999999875554
No 47
>PRK05457 heat shock protein HtpX; Provisional
Probab=36.57 E-value=26 Score=33.91 Aligned_cols=22 Identities=23% Similarity=0.342 Sum_probs=18.4
Q ss_pred ccCCCCHhHHHHHHHHHHhHHH
Q 019829 165 IGHTFSQKYHNRVIQHEAGHFL 186 (335)
Q Consensus 165 ~~~~~s~~~r~RIA~HEAGHaL 186 (335)
+-+.++++|.+=|.-||.||.-
T Consensus 125 Ll~~L~~~El~aVlAHElgHi~ 146 (284)
T PRK05457 125 LLQNMSRDEVEAVLAHEISHIA 146 (284)
T ss_pred HhhhCCHHHHHHHHHHHHHHHH
Confidence 4455689999999999999973
No 48
>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=36.07 E-value=23 Score=33.33 Aligned_cols=19 Identities=37% Similarity=0.417 Sum_probs=15.8
Q ss_pred CHhHHHHHHHHHHhHHHHH
Q 019829 170 SQKYHNRVIQHEAGHFLIA 188 (335)
Q Consensus 170 s~~~r~RIA~HEAGHaLVA 188 (335)
+....+.|+.||-||.+-=
T Consensus 129 ~~~~~~hvi~HEiGH~IGf 147 (211)
T PF12388_consen 129 SVNVIEHVITHEIGHCIGF 147 (211)
T ss_pred chhHHHHHHHHHhhhhccc
Confidence 5677889999999998743
No 49
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=35.54 E-value=1.9e+02 Score=21.62 Aligned_cols=57 Identities=18% Similarity=0.184 Sum_probs=35.6
Q ss_pred HHHHHHhcCCCHHHHHHHHHH----HHHHHHHHHHHcHHH------HHHHHHHHHcccchHHHHHHHHh
Q 019829 270 LDALLKGLGFTQKKADSQVRW----SLLNTVLLLRRHKGA------RAKLAVAMTMGKSVGSCIDIIED 328 (335)
Q Consensus 270 at~i~~~lG~s~~~id~evR~----A~~~A~~LL~~~r~a------leaLaeaLl~~esl~~ci~~Ie~ 328 (335)
-..++..+||+...++. ++. ...++..+|..-+.. ++.|.++|.+-+ ..++++.|++
T Consensus 15 Wk~La~~Lg~~~~~i~~-i~~~~~~~~~~~~~~L~~W~~~~~~~at~~~L~~aL~~~~-~~d~~~~i~~ 81 (83)
T PF00531_consen 15 WKRLARKLGLSESEIEN-IEEENPDLREQTYEMLQRWRQREGPNATVDQLIQALRDIG-RNDLAEKIEQ 81 (83)
T ss_dssp HHHHHHHTTS-HHHHHH-HHHHSTSHHHHHHHHHHHHHHHHGSTSSHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred HHHHHHHhCcCHHHHHH-HHHhCCChHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHCC-cHHHHHHHHh
Confidence 34556778999887774 332 347888888665544 777888876533 3555555554
No 50
>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=35.01 E-value=1.7e+02 Score=23.49 Aligned_cols=51 Identities=18% Similarity=0.258 Sum_probs=32.6
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHH-HHHHHHHHHHHHcHHHHHHHHHHHHc
Q 019829 265 ADINKLDAL--LKGLGFTQKKADSQVR-WSLLNTVLLLRRHKGARAKLAVAMTM 315 (335)
Q Consensus 265 ~Dl~qat~i--~~~lG~s~~~id~evR-~A~~~A~~LL~~~r~aleaLaeaLl~ 315 (335)
+|+..+..+ ++.+|||-+++..-+. ....+...+|+++...+++=.+.|.+
T Consensus 42 ~~~~~l~~I~~lr~~G~~l~eI~~~l~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 95 (97)
T cd04782 42 EQFEQLDIILLLKELGISLKEIKDYLDNRNPDELIELLKKQEKEIKEEIEELQK 95 (97)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455555444 5778999877765433 23445677888888877776666653
No 51
>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=34.63 E-value=1.6e+02 Score=23.56 Aligned_cols=50 Identities=18% Similarity=0.243 Sum_probs=31.6
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHH
Q 019829 265 ADINKLDAL--LKGLGFTQKKADSQVRWSLLNTVLLLRRHKGARAKLAVAMT 314 (335)
Q Consensus 265 ~Dl~qat~i--~~~lG~s~~~id~evR~A~~~A~~LL~~~r~aleaLaeaLl 314 (335)
+|+..+..+ ++.+|||-++|..-..........+|++++..+++=.+.|.
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 455555544 56789988777654443223667777777777776666554
No 52
>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=32.82 E-value=23 Score=33.23 Aligned_cols=18 Identities=44% Similarity=0.630 Sum_probs=16.1
Q ss_pred HhHHHHHHHHHHhHHHHH
Q 019829 171 QKYHNRVIQHEAGHFLIA 188 (335)
Q Consensus 171 ~~~r~RIA~HEAGHaLVA 188 (335)
..||+=++-||-||+|--
T Consensus 136 ~~YRqYvINHEVGH~LGh 153 (203)
T PF11350_consen 136 ASYRQYVINHEVGHALGH 153 (203)
T ss_pred HHHHHHhhhhhhhhhccc
Confidence 689999999999999943
No 53
>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=32.46 E-value=36 Score=30.33 Aligned_cols=25 Identities=24% Similarity=0.359 Sum_probs=20.5
Q ss_pred CCCHhHHHHHHHHHHhHHHHHHHhC
Q 019829 168 TFSQKYHNRVIQHEAGHFLIAYLVG 192 (335)
Q Consensus 168 ~~s~~~r~RIA~HEAGHaLVAyllg 192 (335)
.++++|..=|.-||.||..-.+..-
T Consensus 83 ~~~~~el~aVlaHElgH~~~~h~~~ 107 (226)
T PF01435_consen 83 SLSEDELAAVLAHELGHIKHRHILK 107 (226)
T ss_dssp HSSHHHHHHHHHHHHHHHHTTHCCC
T ss_pred cccHHHHHHHHHHHHHHHHcCCcch
Confidence 3579999999999999998666544
No 54
>PF01890 CbiG_C: Cobalamin synthesis G C-terminus; InterPro: IPR002750 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. CbiG proteins are specific for anaerobic cobalamin biosynthesis. CbiG, which shows homology with CobE of the aerobic pathway, participates in the conversion of cobalt-precorrin 5 into cobalt-precorrin 6 []. CbiG is responsible for the opening of the delta-lactone ring and extrusion of the C2-unit []. The aerobic pathway uses molecular oxygen to trigger the events at C-20 leading to contraction and expulsion of the C2-unit as acetic acid from a metal-free intermediate, whereas the anaerobic route involves the internal delivery of oxygen from a carboxylic acid terminus to C-20 followed by extrusion of the C2-unit as acetaldehyde, using cobalt complexes as substrates []. This entry represents the core domain of CibG.; GO: 0009236 cobalamin biosynthetic process; PDB: 3BY5_A 2W6K_A 2W6L_A 3EEQ_B.
Probab=31.93 E-value=4.9 Score=34.15 Aligned_cols=86 Identities=19% Similarity=0.283 Sum_probs=46.6
Q ss_pred hhhHHHHHHHHHHHHccCch-HHHHHHHHhhcCCC--CcccccccccCCCccccChhHHhhhccccccCCCCccchhhhh
Q 019829 33 EVSKRRVLKQVDEELSKGDE-RAALALVKDLQGKP--GGLRCFGAARQIPQRLYTLDELKLNGIETRSLLSPVDETLGSI 109 (335)
Q Consensus 33 ~~~~~~~~~~~d~~~~~~~~-~~al~~~~~l~~~~--g~l~~~g~~~~vp~r~~~~~elk~~gi~~~~~lsp~~~~l~sv 109 (335)
+.....+.+.++..+.+.+. ...++.+-+...|. -+|..+.....+|-+.|+++||+....-+.+..+-+..+..||
T Consensus 11 ~~~~~~i~~ai~~~l~~~~~~~~~i~~iasi~~K~~E~~l~~~A~~l~~~~~~~~~eeL~~~~~~~~S~~v~~~~Gv~sV 90 (121)
T PF01890_consen 11 GAPAEEIEEAIEQALAEAGLSPRSIAAIASIDIKADEPGLLELAEELGIPLRFFSAEELNAVEVPTPSEFVKKTTGVGSV 90 (121)
T ss_dssp S--HHHHHHHHHHHHHHCT--GGGEEEEEESSSSS--HHHHHHHHHCTSEEEEE-HHHHHCHHCSCT-CHHHCCCSSS-H
T ss_pred CCCHHHHHHHHHHHHHHcCCChhhccEEEeccccCCCHHHHHHHHHhCCCeEEECHHHHhcCCCCCCCHHHHHHcCCchH
Confidence 45667777777777776553 11222222222222 2455555556799999999999843222222223344578899
Q ss_pred HHHHHHHHH
Q 019829 110 ERNLQLAAI 118 (335)
Q Consensus 110 ~n~~a~~a~ 118 (335)
...+|+++.
T Consensus 91 aEaaAl~aa 99 (121)
T PF01890_consen 91 AEAAALLAA 99 (121)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHhc
Confidence 888777665
No 55
>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=30.51 E-value=28 Score=34.04 Aligned_cols=17 Identities=29% Similarity=0.423 Sum_probs=14.9
Q ss_pred HHHHHHHhHHHHHHHhC
Q 019829 176 RVIQHEAGHFLIAYLVG 192 (335)
Q Consensus 176 RIA~HEAGHaLVAyllg 192 (335)
.+..||.||++=..+..
T Consensus 156 ~tl~HE~GHa~h~~l~~ 172 (365)
T cd06258 156 NTLFHEFGHAVHFLLIQ 172 (365)
T ss_pred HHHHHHHhHHHHHHHhc
Confidence 58999999999888776
No 56
>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=30.32 E-value=26 Score=32.49 Aligned_cols=11 Identities=36% Similarity=0.712 Sum_probs=9.1
Q ss_pred HHHHHHHhHHH
Q 019829 176 RVIQHEAGHFL 186 (335)
Q Consensus 176 RIA~HEAGHaL 186 (335)
+.+.||.||.+
T Consensus 147 Kea~HElGH~~ 157 (194)
T PF07998_consen 147 KEAVHELGHLF 157 (194)
T ss_dssp HHHHHHHHHHT
T ss_pred HHHHHHHHHHc
Confidence 46899999975
No 57
>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=30.29 E-value=3e+02 Score=22.45 Aligned_cols=51 Identities=16% Similarity=0.285 Sum_probs=28.6
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHHc
Q 019829 265 ADINKLDAL--LKGLGFTQKKADSQVRW------SLLNTVLLLRRHKGARAKLAVAMTM 315 (335)
Q Consensus 265 ~Dl~qat~i--~~~lG~s~~~id~evR~------A~~~A~~LL~~~r~aleaLaeaLl~ 315 (335)
.|+.++..| ++.+|||.++|..-+.. .......+|+++...++.-.+.|..
T Consensus 42 ~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (113)
T cd01109 42 EDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPERLELLEEHREELEEQIAELQE 100 (113)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHccCCccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456665554 45678887766543321 1234456666666666655555544
No 58
>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=30.06 E-value=1.8e+02 Score=23.31 Aligned_cols=50 Identities=24% Similarity=0.341 Sum_probs=28.8
Q ss_pred hhHHHHHHHH--HHhcCCCHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHH
Q 019829 264 LADINKLDAL--LKGLGFTQKKADSQVRWSLLNTVLLLRRHKGARAKLAVAM 313 (335)
Q Consensus 264 ~~Dl~qat~i--~~~lG~s~~~id~evR~A~~~A~~LL~~~r~aleaLaeaL 313 (335)
.+|+..+..+ ++.+|||.+++..-+.........+|+++...+++=-+.|
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 3566666655 5678998877765443222244566666666665544433
No 59
>COG1913 Predicted Zn-dependent proteases [General function prediction only]
Probab=30.04 E-value=31 Score=31.83 Aligned_cols=16 Identities=44% Similarity=0.891 Sum_probs=12.3
Q ss_pred HhHHHHH---HHHHHhHHH
Q 019829 171 QKYHNRV---IQHEAGHFL 186 (335)
Q Consensus 171 ~~~r~RI---A~HEAGHaL 186 (335)
+=.++|+ +.||+||.+
T Consensus 118 ~lf~ERv~KEv~HElGH~~ 136 (181)
T COG1913 118 ELFKERVVKEVLHELGHLL 136 (181)
T ss_pred HHHHHHHHHHHHHHhhhhc
Confidence 4566777 799999965
No 60
>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=29.73 E-value=2.6e+02 Score=23.38 Aligned_cols=51 Identities=12% Similarity=0.155 Sum_probs=26.8
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHHH----HHHHHHHHHHcHHHHHHHHHHHHc
Q 019829 265 ADINKLDAL--LKGLGFTQKKADSQVRWS----LLNTVLLLRRHKGARAKLAVAMTM 315 (335)
Q Consensus 265 ~Dl~qat~i--~~~lG~s~~~id~evR~A----~~~A~~LL~~~r~aleaLaeaLl~ 315 (335)
+|+..+..| ++.+|||-++|..-+... ......+|+++...++.=.+.|..
T Consensus 42 ~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 98 (126)
T cd04783 42 ETVTRLRFIKRAQELGFTLDEIAELLELDDGTDCSEARELAEQKLAEVDEKIADLQR 98 (126)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444433 567888877666543321 234456666666555544444433
No 61
>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=29.05 E-value=1.9e+02 Score=23.65 Aligned_cols=62 Identities=16% Similarity=0.223 Sum_probs=38.6
Q ss_pred HHHHHHHHhcCCCHHHHHHH-H--HHHHHHHHHHHHHcH------HHHHHHHHHHHcccchHHHHHHHHhhh
Q 019829 268 NKLDALLKGLGFTQKKADSQ-V--RWSLLNTVLLLRRHK------GARAKLAVAMTMGKSVGSCIDIIEDNI 330 (335)
Q Consensus 268 ~qat~i~~~lG~s~~~id~e-v--R~A~~~A~~LL~~~r------~aleaLaeaLl~~esl~~ci~~Ie~~~ 330 (335)
.+..++++.+|+|+.+|+.- . +.-.++.+++|+.-+ ..++.|.++|..- -+..|-+-|++.+
T Consensus 20 ~~Wk~laR~LGLse~~I~~i~~~~~~~~eq~~qmL~~W~~~~G~~At~~~L~~aL~~~-~~~~~Ae~I~~~l 90 (96)
T cd08315 20 DSWNRLMRQLGLSENEIDVAKANERVTREQLYQMLLTWVNKTGRKASVNTLLDALEAI-GLRLAKESIQDEL 90 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHc-ccccHHHHHHHHH
Confidence 35667889999999888751 1 112677888886544 4677888887662 2333444445443
No 62
>COG2738 Predicted Zn-dependent protease [General function prediction only]
Probab=28.91 E-value=30 Score=32.65 Aligned_cols=13 Identities=38% Similarity=0.575 Sum_probs=10.9
Q ss_pred HHHHHHHhHHHHH
Q 019829 176 RVIQHEAGHFLIA 188 (335)
Q Consensus 176 RIA~HEAGHaLVA 188 (335)
-||-||.|||+=-
T Consensus 94 aVAAHEVGHAiQd 106 (226)
T COG2738 94 AVAAHEVGHAIQD 106 (226)
T ss_pred HHHHHHhhHHHhh
Confidence 4899999999854
No 63
>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=28.58 E-value=2.7e+02 Score=22.53 Aligned_cols=51 Identities=20% Similarity=0.225 Sum_probs=32.9
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHHH----------HHHHHHHHHHcHHHHHHHHHHHHc
Q 019829 265 ADINKLDAL--LKGLGFTQKKADSQVRWS----------LLNTVLLLRRHKGARAKLAVAMTM 315 (335)
Q Consensus 265 ~Dl~qat~i--~~~lG~s~~~id~evR~A----------~~~A~~LL~~~r~aleaLaeaLl~ 315 (335)
.|+..+..| ++.+|||-++|..-+... ......+|+++...+++-.+.|.+
T Consensus 40 ~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 102 (107)
T cd04777 40 KCQDDLEFILELKGLGFSLIEIQKIFSYKRLTKSRTHEDQDYYKSFLKNKKDELEKEIEDLKK 102 (107)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHhcccccccchhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566666655 567999988776543321 123567888888887776666544
No 64
>PRK04897 heat shock protein HtpX; Provisional
Probab=28.54 E-value=42 Score=32.66 Aligned_cols=25 Identities=20% Similarity=0.137 Sum_probs=19.4
Q ss_pred ccCCCCHhHHHHHHHHHHhHHHHHH
Q 019829 165 IGHTFSQKYHNRVIQHEAGHFLIAY 189 (335)
Q Consensus 165 ~~~~~s~~~r~RIA~HEAGHaLVAy 189 (335)
+-+.++++|.+=|.-||-||.--.+
T Consensus 128 Ll~~l~~~El~aVlAHElgHi~~~d 152 (298)
T PRK04897 128 LLAIMNREELEGVIGHEISHIRNYD 152 (298)
T ss_pred HHhhCCHHHHHHHHHHHHHHHhcCC
Confidence 4445689999999999999975333
No 65
>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=28.19 E-value=3.1e+02 Score=22.91 Aligned_cols=50 Identities=8% Similarity=0.135 Sum_probs=26.6
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHHH------HHHHHHHHHHcHHHHHHHHHHHH
Q 019829 265 ADINKLDAL--LKGLGFTQKKADSQVRWS------LLNTVLLLRRHKGARAKLAVAMT 314 (335)
Q Consensus 265 ~Dl~qat~i--~~~lG~s~~~id~evR~A------~~~A~~LL~~~r~aleaLaeaLl 314 (335)
+|+..+..| ++.+|||.++|..-+... ......+|+++...+++--+.|.
T Consensus 42 ~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~ 99 (127)
T cd04784 42 EHLERLLFIRRCRSLDMSLDEIRTLLQLQDDPEASCAEVNALIDEHLAHVRARIAELQ 99 (127)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555544 456777776665433321 23445666666666554444443
No 66
>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=28.14 E-value=3.1e+02 Score=23.87 Aligned_cols=60 Identities=7% Similarity=0.111 Sum_probs=31.4
Q ss_pred hhHHHHHHHH--HHhcCCCHHHHHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHc-ccchHHHH
Q 019829 264 LADINKLDAL--LKGLGFTQKKADSQVRW-------SLLNTVLLLRRHKGARAKLAVAMTM-GKSVGSCI 323 (335)
Q Consensus 264 ~~Dl~qat~i--~~~lG~s~~~id~evR~-------A~~~A~~LL~~~r~aleaLaeaLl~-~esl~~ci 323 (335)
.+|+.++..| ++.+|||.+++..-+.. .......++.++...+++-.+.|.+ +..|.+++
T Consensus 41 ~~di~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~ki~~L~~~~~~L~~~~ 110 (142)
T TIGR01950 41 RDVLRRVAVIKAAQRVGIPLATIGEALAVLPEGRTPTADDWARLSSQWREELDERIDQLNALRDQLDGCI 110 (142)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566666655 45678887766654331 1233445666665555544444443 34444443
No 67
>PF12994 DUF3878: Domain of unknown function, E. rectale Gene description (DUF3878); InterPro: IPR024538 This entry represents proteins of unknown function found primarily in Firmicutes. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture [].
Probab=28.05 E-value=11 Score=37.10 Aligned_cols=16 Identities=25% Similarity=0.281 Sum_probs=11.9
Q ss_pred HHHHHHHHHHhHHHHH
Q 019829 173 YHNRVIQHEAGHFLIA 188 (335)
Q Consensus 173 ~r~RIA~HEAGHaLVA 188 (335)
+..--=|||.|||||-
T Consensus 93 ~~~lY~Y~~iGHFWVk 108 (299)
T PF12994_consen 93 ETHLYNYGEIGHFWVK 108 (299)
T ss_pred HHHHhhccccceeeec
Confidence 3334469999999984
No 68
>PF01400 Astacin: Astacin (Peptidase family M12A) This Prosite motif covers only the active site.; InterPro: IPR001506 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M12, subfamily M12A (astacin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. The astacin () family of metalloendopeptidases encompasses a range of proteins found in hydra to humans, in mature and developmental systems []. Their functions include activation of growth factors, degradation of polypeptides, and processing of extracellular proteins []. The proteins are synthesised with N-terminal signal and pro-enzyme sequences, and many contain multiple domains C-terminal to the protease domain. They are either secreted from cells, or are associated with the plasma membrane. The astacin molecule adopts a kidney shape, with a deep active-site cleft between its N- and C-terminal domains []. The zinc ion, which lies at the bottom of the cleft, exhibits a unique penta-coordinated mode of binding, involving 3 histidine residues, a tyrosine and a water molecule (which is also bound to the carboxylate side chain of Glu93) []. The N-terminal domain comprises 2 alpha-helices and a 5-stranded beta-sheet. The overall topology of this domain is shared by the archetypal zinc-endopeptidase thermolysin. Astacin protease domains also share common features with serralysins, matrix metalloendopeptidases, and snake venom proteases; they cleave peptide bonds in polypeptides such as insulin B chain and bradykinin, and in proteins such as casein and gelatin; and they have arylamidase activity [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3LQB_A 3EDH_A 3EDG_A 3EDI_A 1IAE_A 1IAB_A 1IAA_A 1AST_A 1IAC_A 1QJJ_A ....
Probab=28.01 E-value=37 Score=30.79 Aligned_cols=18 Identities=33% Similarity=0.283 Sum_probs=12.8
Q ss_pred HHHHHHHHHhHHHHHHHh
Q 019829 174 HNRVIQHEAGHFLIAYLV 191 (335)
Q Consensus 174 r~RIA~HEAGHaLVAyll 191 (335)
...++.||-||||--+--
T Consensus 79 ~~~~i~HEl~HaLG~~HE 96 (191)
T PF01400_consen 79 SVGTILHELGHALGFWHE 96 (191)
T ss_dssp SHHHHHHHHHHHHTB--G
T ss_pred CccchHHHHHHHHhhhhh
Confidence 346999999999865553
No 69
>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=27.71 E-value=1.3e+02 Score=23.85 Aligned_cols=45 Identities=16% Similarity=0.156 Sum_probs=30.7
Q ss_pred HHHHHHhcCCCHHHHHHHHH----HHHHHHHHHHHHcHH------HHHHHHHHHHc
Q 019829 270 LDALLKGLGFTQKKADSQVR----WSLLNTVLLLRRHKG------ARAKLAVAMTM 315 (335)
Q Consensus 270 at~i~~~lG~s~~~id~evR----~A~~~A~~LL~~~r~------aleaLaeaLl~ 315 (335)
-.++++.|||+...|+. ++ -...+++++|+.-+. .++.|.++|.+
T Consensus 21 Wk~Lar~LGls~~dI~~-i~~~~~~~~eq~~~mL~~W~~r~g~~AT~~~L~~aL~~ 75 (86)
T cd08318 21 WKTLAPHLEMKDKEIRA-IESDSEDIKMQAKQLLVAWQDREGSQATPETLITALNA 75 (86)
T ss_pred HHHHHHHcCCCHHHHHH-HHhcCCCHHHHHHHHHHHHHHhcCccccHHHHHHHHHH
Confidence 44567789999987764 33 247788888876654 35567777665
No 70
>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=27.53 E-value=1.1e+02 Score=26.37 Aligned_cols=62 Identities=21% Similarity=0.139 Sum_probs=48.0
Q ss_pred ccchhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHcccchHH
Q 019829 260 AEGGLADINKLDALLKGLGFTQKKADSQVRWSLLNTVLLLRRHKGARAKLAVAMTMGKSVGS 321 (335)
Q Consensus 260 atGg~~Dl~qat~i~~~lG~s~~~id~evR~A~~~A~~LL~~~r~aleaLaeaLl~~esl~~ 321 (335)
.+|...+++.+.+++..+|-..-.++.+.|..|.-|.-+-.++--.+-..+..|+++.-+++
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 35767788889999999997777777788888888888888888888888888888777655
No 71
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=27.13 E-value=32 Score=31.56 Aligned_cols=17 Identities=29% Similarity=0.141 Sum_probs=13.6
Q ss_pred HHHHHHHhHHHHHHHhC
Q 019829 176 RVIQHEAGHFLIAYLVG 192 (335)
Q Consensus 176 RIA~HEAGHaLVAyllg 192 (335)
.+..||.||.|-+.--+
T Consensus 139 ~~~aHEiGH~lGl~H~~ 155 (206)
T PF13583_consen 139 QTFAHEIGHNLGLRHDF 155 (206)
T ss_pred hHHHHHHHHHhcCCCCc
Confidence 57899999998776654
No 72
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptor
Probab=26.87 E-value=1.7e+02 Score=23.06 Aligned_cols=34 Identities=18% Similarity=0.190 Sum_probs=25.0
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHcHH
Q 019829 270 LDALLKGLGFTQKKADSQVRWSLLNTVLLLRRHKG 304 (335)
Q Consensus 270 at~i~~~lG~s~~~id~evR~A~~~A~~LL~~~r~ 304 (335)
-..+++.|||+...|+. ++.-+.++..+|+.-..
T Consensus 18 W~~LA~~LG~~~~~I~~-i~~~~~p~~~lL~~W~~ 51 (77)
T cd08311 18 WRSLAGELGYEDEAIDT-FGREESPVRTLLADWSA 51 (77)
T ss_pred HHHHHHHcCCCHHHHHH-HHcChhHHHHHHHHHHH
Confidence 66778889999988875 44446788888866543
No 73
>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=26.63 E-value=3.6e+02 Score=22.07 Aligned_cols=51 Identities=16% Similarity=0.145 Sum_probs=26.5
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHH-----HHHHHHHHHHHcHHHHHHHHHHHHc
Q 019829 265 ADINKLDAL--LKGLGFTQKKADSQVRW-----SLLNTVLLLRRHKGARAKLAVAMTM 315 (335)
Q Consensus 265 ~Dl~qat~i--~~~lG~s~~~id~evR~-----A~~~A~~LL~~~r~aleaLaeaLl~ 315 (335)
.|+..+..+ ++.+|||.++|..-+.. .......+|+++...++.=..+|..
T Consensus 42 ~dl~~l~~I~~lr~~G~~l~~I~~~l~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~ 99 (108)
T cd04773 42 SDVRDARLIHLLRRGGYLLEQIATVVEQLRHAGGTEALAAALEQRRVALTQRGRAMLD 99 (108)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555444 35567776655543321 0234456666666666555555544
No 74
>cd04276 ZnMc_MMP_like_2 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=26.10 E-value=47 Score=30.71 Aligned_cols=15 Identities=33% Similarity=0.507 Sum_probs=12.2
Q ss_pred hHHHHHHHHHHhHHH
Q 019829 172 KYHNRVIQHEAGHFL 186 (335)
Q Consensus 172 ~~r~RIA~HEAGHaL 186 (335)
+..+-++.||.||+|
T Consensus 114 ~~~~~~~~he~gh~l 128 (197)
T cd04276 114 ASLRYLLAHEVGHTL 128 (197)
T ss_pred HHHHHHHHHHHHHHh
Confidence 556668999999986
No 75
>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=26.09 E-value=35 Score=30.66 Aligned_cols=17 Identities=35% Similarity=0.165 Sum_probs=13.5
Q ss_pred HHHHHHHHhHHHHHHHh
Q 019829 175 NRVIQHEAGHFLIAYLV 191 (335)
Q Consensus 175 ~RIA~HEAGHaLVAyll 191 (335)
..++.||-||||--+--
T Consensus 75 ~g~v~HE~~HalG~~HE 91 (180)
T cd04280 75 LGTIVHELMHALGFYHE 91 (180)
T ss_pred CchhHHHHHHHhcCcch
Confidence 57999999999765543
No 76
>PRK03001 M48 family peptidase; Provisional
Probab=26.04 E-value=42 Score=32.21 Aligned_cols=30 Identities=20% Similarity=0.187 Sum_probs=22.5
Q ss_pred ccccccCCCCHhHHHHHHHHHHhHHHHHHH
Q 019829 161 VLDTIGHTFSQKYHNRVIQHEAGHFLIAYL 190 (335)
Q Consensus 161 vld~~~~~~s~~~r~RIA~HEAGHaLVAyl 190 (335)
+-|.+-+.++++|.+=|.-||-||.--.+.
T Consensus 111 vt~gLl~~l~~~El~aVlAHElgHi~~~h~ 140 (283)
T PRK03001 111 ATTGILRVLSEREIRGVMAHELAHVKHRDI 140 (283)
T ss_pred ecHHHHhhCCHHHHHHHHHHHHHHHhCCCh
Confidence 344555556899999999999999865544
No 77
>PRK03072 heat shock protein HtpX; Provisional
Probab=25.85 E-value=42 Score=32.54 Aligned_cols=26 Identities=19% Similarity=0.244 Sum_probs=20.0
Q ss_pred ccCCCCHhHHHHHHHHHHhHHHHHHH
Q 019829 165 IGHTFSQKYHNRVIQHEAGHFLIAYL 190 (335)
Q Consensus 165 ~~~~~s~~~r~RIA~HEAGHaLVAyl 190 (335)
+-+.++++|.+=|.-||.||.-=.+.
T Consensus 118 Ll~~l~~~El~aVlAHElgHi~~~d~ 143 (288)
T PRK03072 118 ILQILNERELRGVLGHELSHVYNRDI 143 (288)
T ss_pred HHHhCCHHHHHHHHHHHHHHHhcCCH
Confidence 33456899999999999999764444
No 78
>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=25.68 E-value=2.6e+02 Score=22.46 Aligned_cols=45 Identities=24% Similarity=0.350 Sum_probs=23.3
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHHHHHHHHHHHHHcHHHHHHH
Q 019829 265 ADINKLDAL--LKGLGFTQKKADSQVRWSLLNTVLLLRRHKGARAKL 309 (335)
Q Consensus 265 ~Dl~qat~i--~~~lG~s~~~id~evR~A~~~A~~LL~~~r~aleaL 309 (335)
+|+..+..+ ++.+|||.+.+..-++........+|++++..+++=
T Consensus 42 ~di~~l~~i~~lr~~g~~l~~i~~~~~~~~~~~~~~l~~~~~~l~~~ 88 (103)
T cd01106 42 EDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALREQKELLEEK 88 (103)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHcCcHHHHHHHHHHHHHHHHH
Confidence 455555444 355788776665543322244555555555555443
No 79
>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=25.67 E-value=9.7 Score=35.86 Aligned_cols=20 Identities=30% Similarity=0.398 Sum_probs=15.2
Q ss_pred HhHHHHHHHHHHhHHHHHHH
Q 019829 171 QKYHNRVIQHEAGHFLIAYL 190 (335)
Q Consensus 171 ~~~r~RIA~HEAGHaLVAyl 190 (335)
+...-+++.||.||+|--+-
T Consensus 134 ~~n~g~t~~HEvGH~lGL~H 153 (225)
T cd04275 134 PYNLGDTATHEVGHWLGLYH 153 (225)
T ss_pred cccccceeEEeccceeeeee
Confidence 45566899999999985443
No 80
>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=25.58 E-value=1.4e+02 Score=20.33 Aligned_cols=26 Identities=31% Similarity=0.438 Sum_probs=19.7
Q ss_pred hhhHHHHHHHHHHHHccCchHHHHHH
Q 019829 33 EVSKRRVLKQVDEELSKGDERAALAL 58 (335)
Q Consensus 33 ~~~~~~~~~~~d~~~~~~~~~~al~~ 58 (335)
.-++...+++||..|-+||.+.=+.+
T Consensus 8 ~~~~~~L~~~ID~ALd~~D~e~F~~L 33 (37)
T PF08858_consen 8 EFRKEQLLELIDEALDNRDKEWFYEL 33 (37)
T ss_dssp HHHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence 45778899999999999998744443
No 81
>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=25.40 E-value=34 Score=33.10 Aligned_cols=19 Identities=26% Similarity=0.361 Sum_probs=13.7
Q ss_pred HhHHHHHHHHHHhHHHHHH
Q 019829 171 QKYHNRVIQHEAGHFLIAY 189 (335)
Q Consensus 171 ~~~r~RIA~HEAGHaLVAy 189 (335)
...-+-|++||.||.+..-
T Consensus 213 ~~~~~~v~vHE~GHsf~~L 231 (264)
T PF09471_consen 213 NPSFKQVVVHEFGHSFGGL 231 (264)
T ss_dssp STTHHHHHHHHHHHHTT--
T ss_pred cccccceeeeecccccccc
Confidence 3456679999999987653
No 82
>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=25.32 E-value=3.1e+02 Score=23.65 Aligned_cols=23 Identities=9% Similarity=0.250 Sum_probs=12.5
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHH
Q 019829 265 ADINKLDAL--LKGLGFTQKKADSQ 287 (335)
Q Consensus 265 ~Dl~qat~i--~~~lG~s~~~id~e 287 (335)
.|++++..| ++.+|||.++|.+-
T Consensus 42 ~dl~~l~~I~~lr~~G~sl~eI~~~ 66 (139)
T cd01110 42 DVLRRIAFIKVAQRLGLSLAEIAEA 66 (139)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 455555544 34567766655543
No 83
>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=24.91 E-value=3.2e+02 Score=22.95 Aligned_cols=50 Identities=6% Similarity=0.147 Sum_probs=23.0
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHH
Q 019829 265 ADINKLDAL--LKGLGFTQKKADSQVRW------SLLNTVLLLRRHKGARAKLAVAMT 314 (335)
Q Consensus 265 ~Dl~qat~i--~~~lG~s~~~id~evR~------A~~~A~~LL~~~r~aleaLaeaLl 314 (335)
+|+.++..+ ++.+|||-++|.+-+.. .......+|.++...+++-.+.|.
T Consensus 42 ~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~ 99 (127)
T TIGR02044 42 QHLDELRLISRARQVGFSLEECKELLNLWNDPNRTSADVKARTLEKVAEIERKISELQ 99 (127)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555444 45567776655543321 122334445555554444443333
No 84
>PRK13267 archaemetzincin-like protein; Reviewed
Probab=24.74 E-value=48 Score=30.19 Aligned_cols=11 Identities=45% Similarity=0.809 Sum_probs=8.8
Q ss_pred HHHHHHHhHHH
Q 019829 176 RVIQHEAGHFL 186 (335)
Q Consensus 176 RIA~HEAGHaL 186 (335)
+.+.||.||.|
T Consensus 127 k~~~HElGH~l 137 (179)
T PRK13267 127 KEVTHELGHTL 137 (179)
T ss_pred HHHHHHHHHHc
Confidence 34899999974
No 85
>COG0339 Dcp Zn-dependent oligopeptidases [Amino acid transport and metabolism]
Probab=23.93 E-value=58 Score=35.71 Aligned_cols=36 Identities=22% Similarity=0.276 Sum_probs=26.6
Q ss_pred CHhHHHHHHHHHHhHHHHHHHhCC--C-Cceeeecchhhhh
Q 019829 170 SQKYHNRVIQHEAGHFLIAYLVGI--L-PKGYTLTSFEALK 207 (335)
Q Consensus 170 s~~~r~RIA~HEAGHaLVAyllg~--P-V~~~TI~preal~ 207 (335)
+-++- ++.+||-||+|=..+... | |.+.. +|||+..
T Consensus 464 s~dEV-~TLFHEfGHgLH~mlt~v~~~~vsGt~-v~wDfVE 502 (683)
T COG0339 464 SHDEV-TTLFHEFGHGLHHLLTRVKYPGVSGTN-VPWDFVE 502 (683)
T ss_pred eHHHH-HHHHHHhhhHHHHHhhcCCccccCCCC-CCcchhh
Confidence 34444 589999999998888764 3 77888 7887744
No 86
>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=23.89 E-value=4.3e+02 Score=22.04 Aligned_cols=62 Identities=11% Similarity=0.170 Sum_probs=31.2
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHH---------HHHHHHHHHHHcHHHHHHHHHHHHcc-cchHHHHHHH
Q 019829 265 ADINKLDAL--LKGLGFTQKKADSQVRW---------SLLNTVLLLRRHKGARAKLAVAMTMG-KSVGSCIDII 326 (335)
Q Consensus 265 ~Dl~qat~i--~~~lG~s~~~id~evR~---------A~~~A~~LL~~~r~aleaLaeaLl~~-esl~~ci~~I 326 (335)
.|+..+..+ ++.+|||-+.+..-+.. .......+|+++...++.--+.|.+. +.+.+.+.-.
T Consensus 40 ~~l~~l~~I~~lr~~G~~L~~I~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~L~~~~~~~ 113 (118)
T cd04776 40 RDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQLEKMLEKIEKRRAELEQQRRDIDAALAELDAAEERC 113 (118)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHhhccCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555544 45677776655543321 12234556666666666554444432 3344444333
No 87
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=23.83 E-value=61 Score=30.46 Aligned_cols=20 Identities=30% Similarity=0.386 Sum_probs=15.4
Q ss_pred CHhHHHHHHHHHHhHHHHHH
Q 019829 170 SQKYHNRVIQHEAGHFLIAY 189 (335)
Q Consensus 170 s~~~r~RIA~HEAGHaLVAy 189 (335)
+++.++=++-||-||+|..-
T Consensus 68 ~~~r~rFtlAHELGH~llH~ 87 (213)
T COG2856 68 SLERKRFTLAHELGHALLHT 87 (213)
T ss_pred CHHHHHHHHHHHHhHHHhcc
Confidence 56666667999999998653
No 88
>cd04283 ZnMc_hatching_enzyme Zinc-dependent metalloprotease, hatching enzyme-like subfamily. Hatching enzymes are secreted by teleost embryos to digest the egg envelope or chorion. In some teleosts, the hatching enzyme may be a system consisting of two evolutionary related metalloproteases, high choriolytic enzyme and low choriolytic enzyme (HCE and LCE), which may have different substrate specificities and cooperatively digest the chorion.
Probab=23.23 E-value=45 Score=30.48 Aligned_cols=17 Identities=41% Similarity=0.364 Sum_probs=13.9
Q ss_pred HHHHHHHHhHHHHHHHh
Q 019829 175 NRVIQHEAGHFLIAYLV 191 (335)
Q Consensus 175 ~RIA~HEAGHaLVAyll 191 (335)
.-++.||-||+|--+--
T Consensus 78 ~G~i~HEl~HaLG~~HE 94 (182)
T cd04283 78 KGIIQHELLHALGFYHE 94 (182)
T ss_pred cchHHHHHHHHhCCccc
Confidence 35999999999877664
No 89
>COG2317 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]
Probab=23.05 E-value=39 Score=35.59 Aligned_cols=10 Identities=50% Similarity=0.710 Sum_probs=8.8
Q ss_pred HHHHHhHHHH
Q 019829 178 IQHEAGHFLI 187 (335)
Q Consensus 178 A~HEAGHaLV 187 (335)
.+||+|||+=
T Consensus 263 ~iHE~GHAlY 272 (497)
T COG2317 263 TIHETGHALY 272 (497)
T ss_pred HHHhhhhHHH
Confidence 5899999984
No 90
>PRK01265 heat shock protein HtpX; Provisional
Probab=22.96 E-value=53 Score=32.71 Aligned_cols=29 Identities=17% Similarity=0.174 Sum_probs=22.4
Q ss_pred cccccccCCCCHhHHHHHHHHHHhHHHHH
Q 019829 160 LVLDTIGHTFSQKYHNRVIQHEAGHFLIA 188 (335)
Q Consensus 160 lvld~~~~~~s~~~r~RIA~HEAGHaLVA 188 (335)
.+.|.+-+.++++|.+=|.-||-||.--.
T Consensus 126 vvt~gLl~~l~~~El~aVlAHElgHik~~ 154 (324)
T PRK01265 126 AITLPLLKILNRDEIKAVAGHELGHLKHR 154 (324)
T ss_pred EEehHHHhhCCHHHHHHHHHHHHHHHHcc
Confidence 34556666678999999999999996433
No 91
>COG5549 Predicted Zn-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=22.90 E-value=45 Score=31.72 Aligned_cols=19 Identities=32% Similarity=0.323 Sum_probs=15.9
Q ss_pred CHhHHHHHHHHHHhHHHHH
Q 019829 170 SQKYHNRVIQHEAGHFLIA 188 (335)
Q Consensus 170 s~~~r~RIA~HEAGHaLVA 188 (335)
++++..-+|.||-||||-=
T Consensus 183 ~~e~L~~tarhElGhaLgi 201 (236)
T COG5549 183 LRENLNPTARHELGHALGI 201 (236)
T ss_pred chhhhhHHHHHhhcchhee
Confidence 5788888999999999743
No 92
>PF02074 Peptidase_M32: Carboxypeptidase Taq (M32) metallopeptidase; InterPro: IPR001333 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 M32 (carboxypeptidase Taq 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. Carboxypeptidase Taq is a zinc-containing thermostable metallopeptidase. It was originally discovered and purified from Thermus aquaticus; optimal enzymatic activity occurs at 80 celcius. Although very little is known about this enzyme, it is thought either to be associated with a membrane or to be particle bound.; GO: 0004181 metallocarboxypeptidase activity, 0006508 proteolysis; PDB: 1K9X_A 1KA4_A 1KA2_A 3DWC_A 1WGZ_A 3HQ2_A 3HOA_B.
Probab=22.23 E-value=46 Score=35.09 Aligned_cols=15 Identities=47% Similarity=0.724 Sum_probs=11.1
Q ss_pred HHHHHhHHHHHHHhCCC
Q 019829 178 IQHEAGHFLIAYLVGIL 194 (335)
Q Consensus 178 A~HEAGHaLVAyllg~P 194 (335)
.+||+||+| |-.|+|
T Consensus 263 ~iHE~GHal--YEq~~~ 277 (494)
T PF02074_consen 263 TIHETGHAL--YEQGLP 277 (494)
T ss_dssp HHHHHHHHH--HHHTS-
T ss_pred HHHHHHHHH--HHcCCC
Confidence 579999998 555655
No 93
>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=22.07 E-value=48 Score=30.72 Aligned_cols=16 Identities=25% Similarity=0.441 Sum_probs=13.1
Q ss_pred HHHHHHHhHHHHHHHh
Q 019829 176 RVIQHEAGHFLIAYLV 191 (335)
Q Consensus 176 RIA~HEAGHaLVAyll 191 (335)
-++.||-||+|--+--
T Consensus 89 Gti~HEl~HaLGf~HE 104 (200)
T cd04281 89 GIVVHELGHVIGFWHE 104 (200)
T ss_pred chHHHHHHHHhcCcch
Confidence 4899999999876654
No 94
>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=21.78 E-value=61 Score=28.66 Aligned_cols=23 Identities=30% Similarity=0.183 Sum_probs=15.1
Q ss_pred CHhHHHHHHHHHHhHHHHHHHhC
Q 019829 170 SQKYHNRVIQHEAGHFLIAYLVG 192 (335)
Q Consensus 170 s~~~r~RIA~HEAGHaLVAyllg 192 (335)
.+.....+.-||.||-|-+.--+
T Consensus 138 ~~~~~~~~~AHEiGH~lGa~HD~ 160 (196)
T PF13688_consen 138 PTYNGAITFAHEIGHNLGAPHDG 160 (196)
T ss_dssp -HHHHHHHHHHHHHHHTT-----
T ss_pred CCCceehhhHHhHHHhcCCCCCC
Confidence 46778889999999998777654
No 95
>PRK01345 heat shock protein HtpX; Provisional
Probab=21.36 E-value=59 Score=32.09 Aligned_cols=28 Identities=18% Similarity=0.126 Sum_probs=21.4
Q ss_pred cccCCCCHhHHHHHHHHHHhHHHHHHHh
Q 019829 164 TIGHTFSQKYHNRVIQHEAGHFLIAYLV 191 (335)
Q Consensus 164 ~~~~~~s~~~r~RIA~HEAGHaLVAyll 191 (335)
.+-+.++++|.+=|.-||.||.--.+.+
T Consensus 114 gLL~~L~~dEL~aVlAHElgHi~~~d~~ 141 (317)
T PRK01345 114 GLLQRLSPEEVAGVMAHELAHVKNRDTL 141 (317)
T ss_pred HHHhhCCHHHHHHHHHHHHHHHHcCCHH
Confidence 3334468999999999999998765543
No 96
>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=21.35 E-value=3.7e+02 Score=22.68 Aligned_cols=52 Identities=13% Similarity=0.232 Sum_probs=30.0
Q ss_pred hhHHHHHHHH--HHhcCCCHHHHHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHHc
Q 019829 264 LADINKLDAL--LKGLGFTQKKADSQVRW------SLLNTVLLLRRHKGARAKLAVAMTM 315 (335)
Q Consensus 264 ~~Dl~qat~i--~~~lG~s~~~id~evR~------A~~~A~~LL~~~r~aleaLaeaLl~ 315 (335)
.+|+.++..| ++.+|||.++|..-+.. .......+|+++...+++=.+.|.+
T Consensus 41 ~~~l~~l~~I~~lr~lG~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (127)
T TIGR02047 41 VGHVERLAFIRNCRTLDMSLAEIRQLLRYQDKPEKSCSDVNALLDEHISHVRARIIKLQA 100 (127)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566666554 46688887766654331 1234566677776666655555544
No 97
>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=20.92 E-value=4.8e+02 Score=21.47 Aligned_cols=50 Identities=14% Similarity=0.209 Sum_probs=26.6
Q ss_pred HHHHHHHH--HHhcCCCHHHHHHHHHHH------HHHHHHHHHHcHHHHHHHHHHHHc
Q 019829 266 DINKLDAL--LKGLGFTQKKADSQVRWS------LLNTVLLLRRHKGARAKLAVAMTM 315 (335)
Q Consensus 266 Dl~qat~i--~~~lG~s~~~id~evR~A------~~~A~~LL~~~r~aleaLaeaLl~ 315 (335)
|+..+..| ++.+|||.+++..-+... ......+|+++...+++=.+.|..
T Consensus 43 ~i~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (123)
T cd04770 43 DLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPCAEVRALLEEKLAEVEAKIAELQA 100 (123)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44443433 466788777665443321 234456666666666655444443
No 98
>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=20.82 E-value=4e+02 Score=22.53 Aligned_cols=51 Identities=14% Similarity=0.210 Sum_probs=27.9
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHHH------HHHHHHHHHHcHHHHHHHHHHHHc
Q 019829 265 ADINKLDAL--LKGLGFTQKKADSQVRWS------LLNTVLLLRRHKGARAKLAVAMTM 315 (335)
Q Consensus 265 ~Dl~qat~i--~~~lG~s~~~id~evR~A------~~~A~~LL~~~r~aleaLaeaLl~ 315 (335)
+|+..+..| ++.+|||-++|..-+... ......+|+++...+++=.+.|.+
T Consensus 42 ~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (133)
T cd04787 42 KDLSRLRFILSARQLGFSLKDIKEILSHADQGESPCPMVRRLIEQRLAETERRIKELLK 100 (133)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhhhccCCCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444433 567888877766544321 123456666666666655555543
No 99
>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=20.55 E-value=3.2e+02 Score=21.73 Aligned_cols=49 Identities=10% Similarity=0.140 Sum_probs=32.0
Q ss_pred HHHHHHHHHhcCCCHHHHHHH---HHHHHHHHHHHHHHc-------HHHHHHHHHHHHc
Q 019829 267 INKLDALLKGLGFTQKKADSQ---VRWSLLNTVLLLRRH-------KGARAKLAVAMTM 315 (335)
Q Consensus 267 l~qat~i~~~lG~s~~~id~e---vR~A~~~A~~LL~~~-------r~aleaLaeaLl~ 315 (335)
+.+..++++.+|+|+.+||.- -+...++.+++|+.- ...++.|.++|..
T Consensus 11 ~~~wk~~~R~LGlse~~Id~ie~~~~~~~Eq~yqmL~~W~~~~g~~~At~~~L~~aLr~ 69 (80)
T cd08313 11 PRRWKEFVRRLGLSDNEIERVELDHRRCRDAQYQMLKVWKERGPRPYATLQHLLSVLRD 69 (80)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCCcchHHHHHHHHHH
Confidence 456778899999999888752 113456777777543 3456666666643
No 100
>PRK02870 heat shock protein HtpX; Provisional
Probab=20.14 E-value=69 Score=32.06 Aligned_cols=25 Identities=16% Similarity=0.283 Sum_probs=20.5
Q ss_pred ccccccCCCCHhHHHHHHHHHHhHH
Q 019829 161 VLDTIGHTFSQKYHNRVIQHEAGHF 185 (335)
Q Consensus 161 vld~~~~~~s~~~r~RIA~HEAGHa 185 (335)
+-|.+-+.++++|.+=|.-||-||.
T Consensus 160 vt~GLL~~L~~dEL~aVlAHELgHi 184 (336)
T PRK02870 160 ITTGLLEKLDRDELQAVMAHELSHI 184 (336)
T ss_pred EehHHhhhCCHHHHHHHHHHHHHHH
Confidence 4455556678999999999999997
No 101
>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=20.10 E-value=74 Score=31.49 Aligned_cols=17 Identities=35% Similarity=0.565 Sum_probs=15.0
Q ss_pred HHHHHHHhHHHHHHHhC
Q 019829 176 RVIQHEAGHFLIAYLVG 192 (335)
Q Consensus 176 RIA~HEAGHaLVAyllg 192 (335)
.+..||.||++=.++..
T Consensus 224 ~tl~HE~GHa~h~~~~~ 240 (427)
T cd06459 224 FTLAHELGHAFHSYLSR 240 (427)
T ss_pred HHHHHHhhHHHHHHHHc
Confidence 57999999999988875
Done!