Query 016454
Match_columns 389
No_of_seqs 142 out of 817
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 07:00:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016454.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016454hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0734 AAA+-type ATPase conta 100.0 5.3E-30 1.1E-34 264.9 12.2 157 206-375 536-724 (752)
2 PF01434 Peptidase_M41: Peptid 100.0 4.5E-29 9.8E-34 232.8 17.4 157 206-375 7-206 (213)
3 CHL00176 ftsH cell division pr 99.9 1.6E-26 3.4E-31 246.4 17.8 164 206-383 418-625 (638)
4 PRK10733 hflB ATP-dependent me 99.9 2.8E-26 6.1E-31 244.4 18.0 165 206-383 387-595 (644)
5 COG0465 HflB ATP-dependent Zn 99.9 1.9E-26 4E-31 243.0 13.9 157 206-375 385-580 (596)
6 TIGR01241 FtsH_fam ATP-depende 99.9 2.4E-24 5.2E-29 222.3 17.4 157 206-375 290-486 (495)
7 KOG0731 AAA+-type ATPase conta 99.9 1.2E-22 2.7E-27 218.2 12.2 163 206-383 548-748 (774)
8 CHL00206 ycf2 Ycf2; Provisiona 98.8 7.3E-09 1.6E-13 120.8 7.4 108 206-326 1872-1992(2281)
9 cd06163 S2P-M50_PDZ_RseP-like 97.0 0.0011 2.4E-08 61.6 5.3 24 231-254 11-34 (182)
10 cd06164 S2P-M50_SpoIVFB_CBS Sp 96.5 0.0024 5.2E-08 61.1 4.1 60 231-311 55-114 (227)
11 cd06161 S2P-M50_SpoIVFB SpoIVF 96.4 0.0027 5.8E-08 59.7 3.4 60 231-311 40-99 (208)
12 PRK10779 zinc metallopeptidase 96.2 0.0046 1E-07 64.2 4.1 26 231-256 17-42 (449)
13 cd05709 S2P-M50 Site-2 proteas 96.2 0.0032 7E-08 56.9 2.6 75 231-311 10-91 (180)
14 PF13398 Peptidase_M50B: Pepti 96.1 0.0059 1.3E-07 57.2 3.9 27 231-257 24-50 (200)
15 TIGR00054 RIP metalloprotease 95.9 0.0067 1.5E-07 62.7 3.9 22 231-252 16-37 (420)
16 PF02163 Peptidase_M50: Peptid 95.7 0.0092 2E-07 54.2 3.5 24 232-255 10-33 (192)
17 cd06162 S2P-M50_PDZ_SREBP Ster 94.9 0.025 5.4E-07 56.2 3.9 67 231-311 137-203 (277)
18 cd06160 S2P-M50_like_2 Unchara 94.2 0.038 8.2E-07 51.5 3.1 27 231-257 43-69 (183)
19 cd06159 S2P-M50_PDZ_Arch Uncha 92.3 0.056 1.2E-06 53.2 1.1 66 231-310 120-185 (263)
20 cd06158 S2P-M50_like_1 Unchara 89.4 0.26 5.7E-06 45.6 2.5 75 232-310 12-96 (181)
21 PF14247 DUF4344: Domain of un 83.2 0.84 1.8E-05 44.0 2.4 19 231-250 94-112 (220)
22 PF00413 Peptidase_M10: Matrix 80.5 0.81 1.8E-05 39.6 1.2 16 226-241 102-117 (154)
23 cd04279 ZnMc_MMP_like_1 Zinc-d 77.3 1.4 3.1E-05 38.9 1.8 17 226-242 101-117 (156)
24 cd04268 ZnMc_MMP_like Zinc-dep 73.6 2.1 4.6E-05 37.5 1.9 16 226-241 91-106 (165)
25 cd04278 ZnMc_MMP Zinc-dependen 69.1 2.2 4.8E-05 37.8 1.0 16 226-241 104-119 (157)
26 PF02031 Peptidase_M7: Strepto 67.2 3.7 8.1E-05 36.9 2.0 15 227-241 75-89 (132)
27 cd04277 ZnMc_serralysin_like Z 65.0 4.1 8.9E-05 37.0 1.9 17 226-242 110-126 (186)
28 PF04298 Zn_peptidase_2: Putat 61.5 4.2 9.1E-05 39.5 1.3 13 231-243 91-103 (222)
29 COG0750 Predicted membrane-ass 60.8 6.6 0.00014 39.2 2.6 26 231-256 15-40 (375)
30 KOG2921 Intramembrane metallop 59.8 7 0.00015 41.2 2.7 25 232-256 134-158 (484)
31 cd04327 ZnMc_MMP_like_3 Zinc-d 58.3 6.3 0.00014 36.6 1.9 17 228-244 91-107 (198)
32 smart00235 ZnMc Zinc-dependent 56.7 5.5 0.00012 34.3 1.1 11 231-241 88-98 (140)
33 PF05572 Peptidase_M43: Pregna 51.2 6.8 0.00015 35.5 0.8 16 226-241 66-81 (154)
34 PF13812 PPR_3: Pentatricopept 49.7 24 0.00053 22.3 3.1 28 104-131 7-34 (34)
35 cd00203 ZnMc Zinc-dependent me 46.4 10 0.00023 33.1 1.3 16 227-242 94-109 (167)
36 PF06114 DUF955: Domain of unk 44.6 22 0.00047 28.5 2.8 23 224-246 37-59 (122)
37 PF07035 Mic1: Colon cancer-as 41.4 97 0.0021 28.8 6.8 63 42-129 83-151 (167)
38 PF13582 Reprolysin_3: Metallo 35.0 19 0.00041 30.1 1.0 12 230-241 108-119 (124)
39 smart00762 Cog4 COG4 transport 33.7 32 0.00069 34.7 2.6 21 47-67 13-33 (324)
40 PF13485 Peptidase_MA_2: Pepti 33.3 43 0.00093 27.0 2.9 23 225-247 21-43 (128)
41 TIGR00756 PPR pentatricopeptid 29.7 89 0.0019 19.2 3.4 29 104-132 6-34 (35)
42 PF07998 Peptidase_M54: Peptid 27.9 30 0.00065 33.0 1.2 11 231-241 147-157 (194)
43 cd06258 Peptidase_M3_like The 27.7 33 0.00072 34.3 1.6 22 227-248 152-173 (365)
44 cd04280 ZnMc_astacin_like Zinc 26.8 32 0.0007 31.6 1.2 14 230-243 75-88 (180)
45 PF01400 Astacin: Astacin (Pep 26.6 41 0.00089 31.2 1.9 16 229-244 79-94 (191)
46 PF12388 Peptidase_M57: Dual-a 26.0 46 0.00099 32.2 2.1 20 224-243 128-147 (211)
47 PF12994 DUF3878: Domain of un 25.9 14 0.0003 37.5 -1.5 17 227-243 92-108 (299)
48 COG2738 Predicted Zn-dependent 24.1 40 0.00087 32.7 1.3 13 231-243 94-106 (226)
49 PF11350 DUF3152: Protein of u 24.0 38 0.00083 32.6 1.1 18 226-244 136-153 (203)
50 PF01535 PPR: PPR repeat; Int 23.7 1.1E+02 0.0024 18.6 3.0 26 104-129 6-31 (31)
51 PF10579 Rapsyn_N: Rapsyn N-te 23.1 77 0.0017 26.4 2.6 18 38-55 47-64 (80)
52 cd04283 ZnMc_hatching_enzyme Z 23.0 44 0.00096 31.3 1.4 16 230-245 78-93 (182)
53 PRK13379 protocatechuate 4,5-d 23.0 1.3E+02 0.0029 26.8 4.2 33 33-65 38-76 (119)
54 PF13583 Reprolysin_4: Metallo 22.4 44 0.00096 31.4 1.2 15 231-245 139-153 (206)
55 cd04281 ZnMc_BMP1_TLD Zinc-dep 21.9 47 0.001 31.5 1.3 15 231-245 89-103 (200)
56 COG0501 HtpX Zn-dependent prot 21.8 64 0.0014 31.0 2.2 25 222-246 150-174 (302)
57 cd04276 ZnMc_MMP_like_2 Zinc-d 21.6 59 0.0013 30.8 1.9 30 17-51 8-37 (197)
58 PRK13267 archaemetzincin-like 21.4 52 0.0011 30.8 1.4 11 231-241 127-137 (179)
59 cd03569 VHS_Hrs_Vps27p VHS dom 21.2 96 0.0021 27.7 3.1 27 101-129 111-137 (142)
60 COG5549 Predicted Zn-dependent 21.1 49 0.0011 32.4 1.2 19 224-242 182-200 (236)
61 cd04275 ZnMc_pappalysin_like Z 20.8 15 0.00033 35.4 -2.3 18 226-243 134-151 (225)
62 PF01435 Peptidase_M48: Peptid 20.8 71 0.0015 29.0 2.2 24 224-247 84-107 (226)
No 1
>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=5.3e-30 Score=264.90 Aligned_cols=157 Identities=20% Similarity=0.202 Sum_probs=134.8
Q ss_pred HHHHHHHhCcccccccCCCChhhhHHHHHHHHhHHHHHHHhC--CCcceEEecchhhhhcCccccccceecchhhhhhhh
Q 016454 206 ALVDAIFLGGVCLAQISSYWPPYKRRILVHEAGHLLIAYLMG--CPIRGVILDPIVAMQMGIQGQAGTQFWDEKMNNELA 283 (389)
Q Consensus 206 ~aiD~V~~Gg~~~~~l~~ls~~ekrRIAyHEAGHALVAyLLg--~PV~kvTIiP~~a~rrG~~gagGt~f~~p~~e~~l~ 283 (389)
.+-|||+||.+++.+ .++++.|+.+||||+|||+||+.+. .|++|+||.| ||. +.|.+.+.|++|++
T Consensus 536 ~akDrIlMG~ERks~--~i~~eak~~TAyHE~GHAivA~yTk~A~PlhKaTImP-----RG~--sLG~t~~LPe~D~~-- 604 (752)
T KOG0734|consen 536 FAKDRILMGPERKSM--VIDEEAKKITAYHEGGHAIVALYTKGAMPLHKATIMP-----RGP--SLGHTSQLPEKDRY-- 604 (752)
T ss_pred hhhhheeeccccccc--ccChhhhhhhhhhccCceEEEeecCCCccccceeecc-----CCc--cccceeecCccchh--
Confidence 579999999987544 4689999999999999999999997 5999999999 885 78999999988765
Q ss_pred ccCCCHHHHHHHHHHHchHHHHHHHHhCC---CcchHhHHHHHH----HHHHHhCCC----------------c---cHH
Q 016454 284 EGRLSGTAFDRYSMVLFAGIAAEALIYGE---AEGGENDENLFR----SICVLLQPP----------------L---SMA 337 (389)
Q Consensus 284 ~g~lT~~~L~~~i~VlLAGrAAEeLvfGe---atGgsnDL~~ar----~m~~~lG~~----------------~---s~~ 337 (389)
.+|+.++..++-|+||||+||+|+||. ++|+++|+++++ +|++.+|++ + ++.
T Consensus 605 --~~Tk~q~LA~lDV~MGGRvAEELIfG~D~iTsGAssDl~qAT~lA~~MVt~fGMSd~vG~v~~~~~~~~~s~~~~t~~ 682 (752)
T KOG0734|consen 605 --SITKAQLLARLDVCMGGRVAEELIFGTDKITSGASSDLDQATKLARRMVTKFGMSDKVGPVTLSAEDNSSSLSPRTQE 682 (752)
T ss_pred --hHHHHHHHHHHHHhhcchHHHHHhccCCcccccccchHHHHHHHHHHHHHHcCccccccceeeeccCCCCCCCchhHH
Confidence 579999999999999999999999996 479999999985 666666631 1 222
Q ss_pred HHH----HHHHHHHHHHHHHHHHcHHHHHHHHHHHHhcCcHH
Q 016454 338 QMS----NQARWAVLQSYNLLKWHKHAHLEAVKALESGSSLS 375 (389)
Q Consensus 338 ~id----~~vr~A~~rA~~LLrehr~aLe~LAeaLle~ETL~ 375 (389)
.|| +.++.+|+||+.||+.|.+.+++||++|+++|||+
T Consensus 683 lidaEi~~lL~~sYeRak~iL~~h~kEl~~LA~ALleYETL~ 724 (752)
T KOG0734|consen 683 LIDAEIKRLLRDSYERAKSILKTHKKELHALAEALLEYETLD 724 (752)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 345 44567999999999999999999999999999994
No 2
>PF01434 Peptidase_M41: Peptidase family M41 This is family M41 in the peptidase classification. ; InterPro: IPR000642 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M41 (FtsH endopeptidase family, clan MA(E)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The peptidase M41 family belong to a larger family of zinc metalloproteases. This family includes the cell division protein FtsH, and the yeast mitochondrial respiratory chain complexes assembly protein, which is a putative ATP-dependent protease required for assembly of the mitochondrial respiratory chain and ATPase complexes. FtsH is an integral membrane protein, which seems to act as an ATP-dependent zinc metallopeptidase that binds one zinc ion.; GO: 0004222 metalloendopeptidase activity, 0005524 ATP binding, 0006508 proteolysis; PDB: 4EIW_C 2DHR_E 1IY1_A 1IY2_A 1IY0_A 1IXZ_A 2CE7_F 2CEA_F 3KDS_E 2QZ4_A ....
Probab=99.96 E-value=4.5e-29 Score=232.85 Aligned_cols=157 Identities=25% Similarity=0.314 Sum_probs=121.4
Q ss_pred HHHHHHHhCcccccccCCCChhhhHHHHHHHHhHHHHHHHhC--CCcceEEecchhhhhcCccccccceecchhhhhhhh
Q 016454 206 ALVDAIFLGGVCLAQISSYWPPYKRRILVHEAGHLLIAYLMG--CPIRGVILDPIVAMQMGIQGQAGTQFWDEKMNNELA 283 (389)
Q Consensus 206 ~aiD~V~~Gg~~~~~l~~ls~~ekrRIAyHEAGHALVAyLLg--~PV~kvTIiP~~a~rrG~~gagGt~f~~p~~e~~l~ 283 (389)
-++|+|++|..... ..+++++|+|+||||||||+|+++++ .||.++||+| +|. .+|++...|..++.
T Consensus 7 ~a~drv~~G~~~~~--~~~~~~~~~~~A~HEAGhAvva~~l~~~~~v~~vsi~p-----rg~--~~G~~~~~~~~~~~-- 75 (213)
T PF01434_consen 7 EAIDRVLMGPEKKS--RKLSEEEKRRIAYHEAGHAVVAYLLPPADPVSKVSIVP-----RGS--ALGFTQFTPDEDRY-- 75 (213)
T ss_dssp HHHHHHHCCSCCTT--S---HHHHHHHHHHHHHHHHHHHHSSS---EEEEESST-----TCC--CCHCCEECHHTT-S--
T ss_pred HHHHHHhcCcCcCC--CCCCHHHHHHHHHHHHHHHHHHHHhcccccEEEEEEec-----CCC--cceeEEeccchhcc--
Confidence 37999999987422 35689999999999999999999998 6999999999 774 55666666654432
Q ss_pred ccCCCHHHHHHHHHHHchHHHHHHHHhC--C-CcchHhHHHHHHHH----HHHhCC-------C----------------
Q 016454 284 EGRLSGTAFDRYSMVLFAGIAAEALIYG--E-AEGGENDENLFRSI----CVLLQP-------P---------------- 333 (389)
Q Consensus 284 ~g~lT~~~L~~~i~VlLAGrAAEeLvfG--e-atGgsnDL~~ar~m----~~~lG~-------~---------------- 333 (389)
..|++++.+.++|+|||||||+++|| + ++|+++|+++|+.+ +..+|+ .
T Consensus 76 --~~t~~~l~~~i~v~LaGraAEe~~~g~~~~stGa~~DL~~At~iA~~mv~~~Gm~~~~g~~~~~~~~~~~~~~~~~~~ 153 (213)
T PF01434_consen 76 --IRTRSYLEDRICVLLAGRAAEELFFGEDNVSTGASSDLQQATEIARKMVASYGMGDSLGLLSYSPNDDDEVFLGREWN 153 (213)
T ss_dssp --S-BHHHHHHHHHHHHHHHHHHHHHHSCCS-BGGGHHHHHHHHHHHHHHHHTST-TTTTTSS-SEEEE-S-SSS-E---
T ss_pred --cccHHHHHhhHHHHHHHHHHHHhhcCcceecccchhHHHHHHHHHHHHHHHhCCCCCCceeeeecccccccccccccc
Confidence 36999999999999999999999999 4 57889999998755 333332 0
Q ss_pred ----cc---HHHHH----HHHHHHHHHHHHHHHHcHHHHHHHHHHHHhcCcHH
Q 016454 334 ----LS---MAQMS----NQARWAVLQSYNLLKWHKHAHLEAVKALESGSSLS 375 (389)
Q Consensus 334 ----~s---~~~id----~~vr~A~~rA~~LLrehr~aLe~LAeaLle~ETL~ 375 (389)
++ ...++ ..++.+|.+|++||++|++.+++||++|+++++|+
T Consensus 154 ~~~~~s~~~~~~i~~ev~~lL~~a~~~a~~iL~~~r~~l~~la~~Lle~~~L~ 206 (213)
T PF01434_consen 154 SRRPMSEETRALIDREVRKLLEEAYARAKEILEENREALEALAEALLEKETLS 206 (213)
T ss_dssp EEESS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHSEEE
T ss_pred ccCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCeeC
Confidence 11 12344 44567999999999999999999999999999983
No 3
>CHL00176 ftsH cell division protein; Validated
Probab=99.94 E-value=1.6e-26 Score=246.35 Aligned_cols=164 Identities=19% Similarity=0.234 Sum_probs=133.7
Q ss_pred HHHHHHHhCcccccccCCCChhhhHHHHHHHHhHHHHHHHhC--CCcceEEecchhhhhcCccccccceecchhhhhhhh
Q 016454 206 ALVDAIFLGGVCLAQISSYWPPYKRRILVHEAGHLLIAYLMG--CPIRGVILDPIVAMQMGIQGQAGTQFWDEKMNNELA 283 (389)
Q Consensus 206 ~aiD~V~~Gg~~~~~l~~ls~~ekrRIAyHEAGHALVAyLLg--~PV~kvTIiP~~a~rrG~~gagGt~f~~p~~e~~l~ 283 (389)
.++|++++|.... ...++++|++|||||||||+|+++++ +||+++||+| ||. ++|+++..|+.+++
T Consensus 418 ~Ai~rv~~g~~~~---~~~~~~~~~~vA~hEaGhA~v~~~l~~~~~v~kvtI~p-----rg~--~~G~~~~~p~~~~~-- 485 (638)
T CHL00176 418 TAIDRVIAGLEGT---PLEDSKNKRLIAYHEVGHAIVGTLLPNHDPVQKVTLIP-----RGQ--AKGLTWFTPEEDQS-- 485 (638)
T ss_pred HHHHHHHhhhccC---ccccHHHHHHHHHHhhhhHHHHhhccCCCceEEEEEee-----cCC--CCCceEecCCcccc--
Confidence 4689999997632 23578999999999999999999997 7999999999 773 67888888876554
Q ss_pred ccCCCHHHHHHHHHHHchHHHHHHHHhCC---CcchHhHHHHHHH----HHHHhCCC-----------------------
Q 016454 284 EGRLSGTAFDRYSMVLFAGIAAEALIYGE---AEGGENDENLFRS----ICVLLQPP----------------------- 333 (389)
Q Consensus 284 ~g~lT~~~L~~~i~VlLAGrAAEeLvfGe---atGgsnDL~~ar~----m~~~lG~~----------------------- 333 (389)
.+|+.++.+.++++|||||||+++||+ ++|++||+++|+. |+..+|+.
T Consensus 486 --~~t~~~l~~~i~~~LgGraAE~~~fg~~~~~~Ga~~Dl~~AT~iA~~mv~~~Gm~~~g~~~~~~~~~~~~~~~~~~~~ 563 (638)
T CHL00176 486 --LVSRSQILARIVGALGGRAAEEVVFGSTEVTTGASNDLQQVTNLARQMVTRFGMSSIGPISLESNNSTDPFLGRFMQR 563 (638)
T ss_pred --cccHHHHHHHHHHHhhhHHHHHHhcCCCCcCCCchhHHHHHHHHHHHHHHHhCCCcCCceeecCCCCccccccccccc
Confidence 479999999999999999999999995 5799999999864 44444431
Q ss_pred ---cc---HHHHHHH----HHHHHHHHHHHHHHcHHHHHHHHHHHHhcCcH--HHHHHHHHH
Q 016454 334 ---LS---MAQMSNQ----ARWAVLQSYNLLKWHKHAHLEAVKALESGSSL--SVVIRRIEE 383 (389)
Q Consensus 334 ---~s---~~~id~~----vr~A~~rA~~LLrehr~aLe~LAeaLle~ETL--~~Ci~~IE~ 383 (389)
++ ..++|.+ ++.||.+|++||++|++.+++||++|+++||| +++.++++.
T Consensus 564 ~~~~s~~~~~~iD~ev~~~l~~~~~~a~~iL~~~~~~l~~la~~Lle~Etl~~~ei~~il~~ 625 (638)
T CHL00176 564 NSEYSEEIADKIDMEVRSILHTCYQYAYQILKDNRVLIDLLVELLLQKETIDGDEFREIVNS 625 (638)
T ss_pred ccCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCccCHHHHHHHHhh
Confidence 12 2335544 56799999999999999999999999999999 556677765
No 4
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=99.94 E-value=2.8e-26 Score=244.39 Aligned_cols=165 Identities=20% Similarity=0.230 Sum_probs=132.2
Q ss_pred HHHHHHHhCcccccccCCCChhhhHHHHHHHHhHHHHHHHhC--CCcceEEecchhhhhcCccccccceecchhhhhhhh
Q 016454 206 ALVDAIFLGGVCLAQISSYWPPYKRRILVHEAGHLLIAYLMG--CPIRGVILDPIVAMQMGIQGQAGTQFWDEKMNNELA 283 (389)
Q Consensus 206 ~aiD~V~~Gg~~~~~l~~ls~~ekrRIAyHEAGHALVAyLLg--~PV~kvTIiP~~a~rrG~~gagGt~f~~p~~e~~l~ 283 (389)
-++|+|.+|... +...+++++|+++||||+|||+|+++++ +||+++||+| ||. ++|+++..|+.++.
T Consensus 387 ~a~~~v~~g~~~--~~~~~~~~~~~~~a~he~gha~~~~~~~~~~~~~~v~i~p-----rg~--~~g~~~~~~~~~~~-- 455 (644)
T PRK10733 387 KAKDKIMMGAER--RSMVMTEAQKESTAYHEAGHAIIGRLVPEHDPVHKVTIIP-----RGR--ALGVTFFLPEGDAI-- 455 (644)
T ss_pred HHHHHHhccccc--ccccccHHHHHHHHHHHHHHHHHHHHccCCCceeEEEEec-----cCC--CcceeEECCCcccc--
Confidence 468999998753 2224678999999999999999999997 7999999999 773 67888888865543
Q ss_pred ccCCCHHHHHHHHHHHchHHHHHHHHhCC---CcchHhHHHHHHH----HHHHhCCC-----------------------
Q 016454 284 EGRLSGTAFDRYSMVLFAGIAAEALIYGE---AEGGENDENLFRS----ICVLLQPP----------------------- 333 (389)
Q Consensus 284 ~g~lT~~~L~~~i~VlLAGrAAEeLvfGe---atGgsnDL~~ar~----m~~~lG~~----------------------- 333 (389)
..|+++++++++|+|||||||+++||. ++|++||+++|+. |+.++|+.
T Consensus 456 --~~~~~~l~~~i~~~lgGraAE~~~~g~~~~ttGa~~Dl~~AT~lA~~mv~~~Gms~~lg~~~~~~~~~~~~lg~~~~~ 533 (644)
T PRK10733 456 --SASRQKLESQISTLYGGRLAEEIIYGPEHVSTGASNDIKVATNLARNMVTQWGFSEKLGPLLYAEEEGEVFLGRSVAK 533 (644)
T ss_pred --cccHHHHHHHHHHHHhhHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhCCCccccchhhccccccccccccccc
Confidence 368999999999999999999999994 5799999999864 54445431
Q ss_pred ---cc---HHHHHH----HHHHHHHHHHHHHHHcHHHHHHHHHHHHhcCcHH--HHHHHHHH
Q 016454 334 ---LS---MAQMSN----QARWAVLQSYNLLKWHKHAHLEAVKALESGSSLS--VVIRRIEE 383 (389)
Q Consensus 334 ---~s---~~~id~----~vr~A~~rA~~LLrehr~aLe~LAeaLle~ETL~--~Ci~~IE~ 383 (389)
++ ...+|+ .++.+|.+|++||++|++.+++||++|+++|||+ ++.+++..
T Consensus 534 ~~~~s~~~~~~id~ev~~il~~~~~~a~~iL~~~~~~l~~la~~Lle~etl~~~ei~~i~~~ 595 (644)
T PRK10733 534 AKHMSDETARIIDQEVKALIERNYNRARQLLTDNMDILHAMKDALMKYETIDAPQIDDLMAR 595 (644)
T ss_pred ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhceeCHHHHHHHHhc
Confidence 12 223454 4567999999999999999999999999999983 44455553
No 5
>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=1.9e-26 Score=243.01 Aligned_cols=157 Identities=23% Similarity=0.263 Sum_probs=134.2
Q ss_pred HHHHHHHhCcccccccCCCChhhhHHHHHHHHhHHHHHHHhC--CCcceEEecchhhhhcCccccccceecchhhhhhhh
Q 016454 206 ALVDAIFLGGVCLAQISSYWPPYKRRILVHEAGHLLIAYLMG--CPIRGVILDPIVAMQMGIQGQAGTQFWDEKMNNELA 283 (389)
Q Consensus 206 ~aiD~V~~Gg~~~~~l~~ls~~ekrRIAyHEAGHALVAyLLg--~PV~kvTIiP~~a~rrG~~gagGt~f~~p~~e~~l~ 283 (389)
-++|+|++|.+...+ .+++++|+.+||||+||++|+++++ +||+|+||+| || .++|+++..|++|+
T Consensus 385 ea~drv~~G~erks~--vise~ek~~~AYhEaghalv~~~l~~~d~v~KvtIiP-----rG--~alG~t~~~Pe~d~--- 452 (596)
T COG0465 385 EAIDRVIAGPERKSR--VISEAEKKITAYHEAGHALVGLLLPDADPVHKVTIIP-----RG--RALGYTLFLPEEDK--- 452 (596)
T ss_pred HHHHHHhcCcCcCCc--ccChhhhcchHHHHHHHHHHHHhCCCCcccceeeecc-----Cc--hhhcchhcCCcccc---
Confidence 479999999986544 5889999999999999999999998 5999999999 88 47899999997654
Q ss_pred ccCCCHHHHHHHHHHHchHHHHHHHHhC-C-CcchHhHHHHHH----HHHHHhCCC------------------------
Q 016454 284 EGRLSGTAFDRYSMVLFAGIAAEALIYG-E-AEGGENDENLFR----SICVLLQPP------------------------ 333 (389)
Q Consensus 284 ~g~lT~~~L~~~i~VlLAGrAAEeLvfG-e-atGgsnDL~~ar----~m~~~lG~~------------------------ 333 (389)
+.+|++++.+.++++|||||||+++|| + ++|++||+++++ .|++++|.+
T Consensus 453 -~l~sk~~l~~~i~~~lgGRaAEel~~g~e~ttGa~~D~~~at~~ar~mVt~~Gms~~lG~v~~~~~~~~flg~~~~~~~ 531 (596)
T COG0465 453 -YLMSKEELLDRIDVLLGGRAAEELIFGYEITTGASNDLEKATDLARAMVTEYGMSAKLGPVAYEQVEGVFLGRYQKAKN 531 (596)
T ss_pred -ccccHHHHHHHHHHHhCCcHhhhhhhcccccccchhhHHHHHHHHHHhhhhcCcchhhCceehhhcccccccccccccC
Confidence 567999999999999999999999999 7 469999999875 555555531
Q ss_pred cc---HHHHHHHH----HHHHHHHHHHHHHcHHHHHHHHHHHHhcCcHH
Q 016454 334 LS---MAQMSNQA----RWAVLQSYNLLKWHKHAHLEAVKALESGSSLS 375 (389)
Q Consensus 334 ~s---~~~id~~v----r~A~~rA~~LLrehr~aLe~LAeaLle~ETL~ 375 (389)
+| .+.||+++ ..+|.++++||.+|++.++.++++|+++||++
T Consensus 532 ~Se~ta~~ID~evk~ii~~~y~~a~~il~~~~~~l~~~~~~Lle~Eti~ 580 (596)
T COG0465 532 YSEETAQEIDREVKDIIDEAYERAKELLNENKDALETLAEMLLEKETID 580 (596)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhccC
Confidence 33 24466655 45999999999999999999999999999973
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=99.92 E-value=2.4e-24 Score=222.32 Aligned_cols=157 Identities=22% Similarity=0.235 Sum_probs=126.2
Q ss_pred HHHHHHHhCcccccccCCCChhhhHHHHHHHHhHHHHHHHhC--CCcceEEecchhhhhcCccccccceecchhhhhhhh
Q 016454 206 ALVDAIFLGGVCLAQISSYWPPYKRRILVHEAGHLLIAYLMG--CPIRGVILDPIVAMQMGIQGQAGTQFWDEKMNNELA 283 (389)
Q Consensus 206 ~aiD~V~~Gg~~~~~l~~ls~~ekrRIAyHEAGHALVAyLLg--~PV~kvTIiP~~a~rrG~~gagGt~f~~p~~e~~l~ 283 (389)
.+++++.+|.... -..+++++|+++||||||||||+++++ .|++++||.| +|. .+|+++..|..+
T Consensus 290 ~a~~~~~~~~~~~--~~~~~~~~~~~~A~hEaGhAlv~~~l~~~~~v~~vsi~p-----rg~--~~G~~~~~~~~~---- 356 (495)
T TIGR01241 290 EAIDRVIAGPEKK--SRVISEKEKKLVAYHEAGHALVGLLLKDADPVHKVTIIP-----RGQ--ALGYTQFLPEED---- 356 (495)
T ss_pred HHHHHHhcccccc--cccccHHHHHHHHHHHHhHHHHHHhcCCCCceEEEEEee-----cCC--ccceEEecCccc----
Confidence 4688998887532 224679999999999999999999995 7999999999 674 556676666433
Q ss_pred ccCCCHHHHHHHHHHHchHHHHHHHHhCCC-cchHhHHHHHHHH----HHHhCCC-------------------------
Q 016454 284 EGRLSGTAFDRYSMVLFAGIAAEALIYGEA-EGGENDENLFRSI----CVLLQPP------------------------- 333 (389)
Q Consensus 284 ~g~lT~~~L~~~i~VlLAGrAAEeLvfGea-tGgsnDL~~ar~m----~~~lG~~------------------------- 333 (389)
.+..|+++++++++|+|||||||+++||+. +|+++|+++|+++ +..+|+.
T Consensus 357 ~~~~t~~~l~~~i~v~LaGraAE~~~~G~~s~Ga~~Dl~~At~lA~~mv~~~Gm~~~~g~~~~~~~~~~~~l~~~~~~~~ 436 (495)
T TIGR01241 357 KYLYTKSQLLAQIAVLLGGRAAEEIIFGEVTTGASNDIKQATNIARAMVTEWGMSDKLGPVAYGSDGGDVFLGRGFAKAK 436 (495)
T ss_pred cccCCHHHHHHHHHHHhhHHHHHHHHhcCCCCCchHHHHHHHHHHHHHHHHhCCCcccCceeeccCcccccccccccccc
Confidence 246799999999999999999999999986 5999999999755 3334420
Q ss_pred -cc---H----HHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHhcCcHH
Q 016454 334 -LS---M----AQMSNQARWAVLQSYNLLKWHKHAHLEAVKALESGSSLS 375 (389)
Q Consensus 334 -~s---~----~~id~~vr~A~~rA~~LLrehr~aLe~LAeaLle~ETL~ 375 (389)
++ . .++++.++++|.+|++||++|++++++||++|+++|+|+
T Consensus 437 ~~s~~~~~~id~~v~~lL~~a~~ra~~lL~~~~~~l~~la~~Ll~~e~L~ 486 (495)
T TIGR01241 437 EYSEETAREIDEEVKRIIEEAYKRAKQILTENRDELELLAKALLEKETIT 486 (495)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCeeC
Confidence 11 1 223455679999999999999999999999999999984
No 7
>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.88 E-value=1.2e-22 Score=218.23 Aligned_cols=163 Identities=20% Similarity=0.259 Sum_probs=134.2
Q ss_pred HHHHHHHhCcccccccCCCChhhhHHHHHHHHhHHHHHHHhC--CCcceEEecchhhhhcCccccccceecchhhhhhhh
Q 016454 206 ALVDAIFLGGVCLAQISSYWPPYKRRILVHEAGHLLIAYLMG--CPIRGVILDPIVAMQMGIQGQAGTQFWDEKMNNELA 283 (389)
Q Consensus 206 ~aiD~V~~Gg~~~~~l~~ls~~ekrRIAyHEAGHALVAyLLg--~PV~kvTIiP~~a~rrG~~gagGt~f~~p~~e~~l~ 283 (389)
-++||++.|.+.. ...+++++++.+|||||||++++++++ +|+.++||+| |. +.|++++.|.++
T Consensus 548 ~a~~Rvi~G~~~~--~~~~~~~~~~~~a~~eagha~~g~~l~~~dpl~kvsIiP------Gq--alG~a~~~P~~~---- 613 (774)
T KOG0731|consen 548 YAIERVIAGMEKK--SRVLSLEEKKTVAYHEAGHAVVGWLLEHADPLLKVSIIP------GQ--ALGYAQYLPTDD---- 613 (774)
T ss_pred HHHHHHhcccccc--chhcCHhhhhhhhhhhccchhhhccccccCcceeEEecc------CC--ccceEEECCccc----
Confidence 3799999997642 235789999999999999999998887 7999999999 53 678888888644
Q ss_pred ccCCCHHHHHHHHHHHchHHHHHHHHhC-C-CcchHhHHHHHHHH----HHHhCC---------------------Cc--
Q 016454 284 EGRLSGTAFDRYSMVLFAGIAAEALIYG-E-AEGGENDENLFRSI----CVLLQP---------------------PL-- 334 (389)
Q Consensus 284 ~g~lT~~~L~~~i~VlLAGrAAEeLvfG-e-atGgsnDL~~ar~m----~~~lG~---------------------~~-- 334 (389)
+.+|+.+|.+++|++|||||||+++|| + ++|++||++++|.| +..+|+ ++
T Consensus 614 -~l~sk~ql~~rm~m~LGGRaAEev~fg~~iTtga~ddl~kvT~~A~~~V~~~Gms~kig~~~~~~~~~~~~~~~~p~s~ 692 (774)
T KOG0731|consen 614 -YLLSKEQLFDRMVMALGGRAAEEVVFGSEITTGAQDDLEKVTKIARAMVASFGMSEKIGPISFQMLLPGDESFRKPYSE 692 (774)
T ss_pred -ccccHHHHHHHHHHHhCcchhhheecCCccCchhhccHHHHHHHHHHHHHHcCcccccCceeccCcccccccccCccch
Confidence 568999999999999999999999998 4 57999999998755 344442 12
Q ss_pred -cHHHHHHHHH----HHHHHHHHHHHHcHHHHHHHHHHHHhcCcH--HHHHHHHHH
Q 016454 335 -SMAQMSNQAR----WAVLQSYNLLKWHKHAHLEAVKALESGSSL--SVVIRRIEE 383 (389)
Q Consensus 335 -s~~~id~~vr----~A~~rA~~LLrehr~aLe~LAeaLle~ETL--~~Ci~~IE~ 383 (389)
+.+.||.+++ .||++|.++|++|++.++.+|+.|+++|++ ++++.++..
T Consensus 693 ~~~~~Id~ev~~lv~~ay~~~~~ll~~n~~~l~~ia~~LLeke~l~~ee~~~ll~~ 748 (774)
T KOG0731|consen 693 KTAQLIDTEVRRLVQKAYERTKELLRTNRDKLDKIAEVLLEKEVLTGEEIIALLGE 748 (774)
T ss_pred hHHHHHHHHHHHHHhhHHHHHHHHHHHhHHHHHHHHHHHHHhhhccHHHHHHHhcc
Confidence 2345776655 499999999999999999999999999997 777777654
No 8
>CHL00206 ycf2 Ycf2; Provisional
Probab=98.79 E-value=7.3e-09 Score=120.76 Aligned_cols=108 Identities=18% Similarity=0.141 Sum_probs=78.1
Q ss_pred HHHHHHHhCcccccccCCCChhhhHHHHHHHHhHHHHHHHhC--CCcceEEecch-hhhhcCccccccceecchhhhhhh
Q 016454 206 ALVDAIFLGGVCLAQISSYWPPYKRRILVHEAGHLLIAYLMG--CPIRGVILDPI-VAMQMGIQGQAGTQFWDEKMNNEL 282 (389)
Q Consensus 206 ~aiD~V~~Gg~~~~~l~~ls~~ekrRIAyHEAGHALVAyLLg--~PV~kvTIiP~-~a~rrG~~gagGt~f~~p~~e~~l 282 (389)
.|+||+++|... +. .+..++ +|||||+|||+|+.++. +||+++||.|- ...++| .+.|++++.|..
T Consensus 1872 ~Al~Rq~~g~~~--~~--~~~~~~-~ia~yEiGhAvvq~~L~~~~pv~kISIy~~~~~~r~~--~~yl~~wyle~~---- 1940 (2281)
T CHL00206 1872 SALHRQTWDLRS--QV--RSVQDH-GILFYQIGRAVAQNVLLSNCPIDPISIYMKKKSCKEG--DSYLYKWYFELG---- 1940 (2281)
T ss_pred HHHHHHHhhhhh--cc--cCcchh-hhhhhHHhHHHHHHhccCCCCcceEEEecCCccccCc--ccceeEeecCCc----
Confidence 479999999752 22 233444 58999999999999986 79999999641 112222 345777777742
Q ss_pred hccCCCHHHHHHHHHHHchHHHHHHHHhCCC--------c-ch-HhHHHHHHHH
Q 016454 283 AEGRLSGTAFDRYSMVLFAGIAAEALIYGEA--------E-GG-ENDENLFRSI 326 (389)
Q Consensus 283 ~~g~lT~~~L~~~i~VlLAGrAAEeLvfGea--------t-Gg-snDL~~ar~m 326 (389)
..+++.++..+++++|||+|||++.|+.. . |- .+|+..+-.+
T Consensus 1941 --~~mkk~tiL~~Il~cLAGraAedlwf~~~~~~~n~It~yg~vEnD~~La~gl 1992 (2281)
T CHL00206 1941 --TSMKKLTILLYLLSCSAGSVAQDLWSLPGPDEKNGITSYGLVENDSDLVHGL 1992 (2281)
T ss_pred --ccCCHHHHHHHHHHHhhhhhhhhhccCcchhhhcCcccccchhhhhHHhHhH
Confidence 46799999999999999999999999632 1 32 5787766544
No 9
>cd06163 S2P-M50_PDZ_RseP-like RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses. Also included in this group are such homologs as Bacillus subtilis YluC, Mycobacterium tuberculosis Rv2869c S2P, and Bordetella bronchiseptica HurP. Rv2869c S2P appears to have a role in the regulation of prokaryotic lipid biosynthesis and membrane composition and YluC of Bacillus has a role in transducing membrane stress. This group includes bacterial and eukaryotic S2P/M50s homologs with either one or two PDZ domains present. PDZ domains are believed to have a regulatory role. The RseP PDZ domain is required for the inhibitory reaction that prevents cleavage of its substrate, RseA.
Probab=96.99 E-value=0.0011 Score=61.62 Aligned_cols=24 Identities=42% Similarity=0.697 Sum_probs=21.3
Q ss_pred HHHHHHHhHHHHHHHhCCCcceEE
Q 016454 231 RILVHEAGHLLIAYLMGCPIRGVI 254 (389)
Q Consensus 231 RIAyHEAGHALVAyLLg~PV~kvT 254 (389)
-|..||.||+++|...|.+|.+++
T Consensus 11 ~v~iHElGH~~~Ar~~Gv~v~~f~ 34 (182)
T cd06163 11 LIFVHELGHFLVAKLFGVKVEEFS 34 (182)
T ss_pred HHHHHHHHHHHHHHHcCCeeeEee
Confidence 378999999999999999998844
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=96.54 E-value=0.0024 Score=61.07 Aligned_cols=60 Identities=23% Similarity=0.321 Sum_probs=44.5
Q ss_pred HHHHHHHhHHHHHHHhCCCcceEEecchhhhhcCccccccceecchhhhhhhhccCCCHHHHHHHHHHHchHHHHHHHHh
Q 016454 231 RILVHEAGHLLIAYLMGCPIRGVILDPIVAMQMGIQGQAGTQFWDEKMNNELAEGRLSGTAFDRYSMVLFAGIAAEALIY 310 (389)
Q Consensus 231 RIAyHEAGHALVAyLLg~PV~kvTIiP~~a~rrG~~gagGt~f~~p~~e~~l~~g~lT~~~L~~~i~VlLAGrAAEeLvf 310 (389)
-+..||.||+++|+.+|.+++++++.|+ ||++..+++. .+ ..+.+.|++||-++.-++.
T Consensus 55 ~v~iHElgH~~~A~~~G~~v~~i~l~p~----------Gg~~~~~~~~--------~~---~~~~~~IalAGPl~Nllla 113 (227)
T cd06164 55 SVLLHELGHSLVARRYGIPVRSITLFLF----------GGVARLEREP--------ET---PGQEFVIAIAGPLVSLVLA 113 (227)
T ss_pred HHHHHHHHHHHHHHHcCCeECeEEEEee----------eEEEEecCCC--------CC---HHHHhhhhhhHHHHHHHHH
Confidence 5789999999999999999999999993 3444443311 12 2345679999999987764
Q ss_pred C
Q 016454 311 G 311 (389)
Q Consensus 311 G 311 (389)
.
T Consensus 114 ~ 114 (227)
T cd06164 114 L 114 (227)
T ss_pred H
Confidence 3
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=96.40 E-value=0.0027 Score=59.68 Aligned_cols=60 Identities=30% Similarity=0.475 Sum_probs=43.3
Q ss_pred HHHHHHHhHHHHHHHhCCCcceEEecchhhhhcCccccccceecchhhhhhhhccCCCHHHHHHHHHHHchHHHHHHHHh
Q 016454 231 RILVHEAGHLLIAYLMGCPIRGVILDPIVAMQMGIQGQAGTQFWDEKMNNELAEGRLSGTAFDRYSMVLFAGIAAEALIY 310 (389)
Q Consensus 231 RIAyHEAGHALVAyLLg~PV~kvTIiP~~a~rrG~~gagGt~f~~p~~e~~l~~g~lT~~~L~~~i~VlLAGrAAEeLvf 310 (389)
-+..||.||+++|+.+|.+++++++.|+ | |....++. . . .-.+.+.|++||-.+.-++.
T Consensus 40 ~v~iHElgH~~~A~~~G~~v~~i~l~p~-----G-----g~~~~~~~-------~--~--~~~~~~lIalAGPl~n~~la 98 (208)
T cd06161 40 SVLLHELGHALVARRYGIRVRSITLLPF-----G-----GVAELEEE-------P--E--TPKEEFVIALAGPLVSLLLA 98 (208)
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEee-----e-----eeeeeccC-------C--C--ChhHheeeeeehHHHHHHHH
Confidence 5789999999999999999999999993 2 32222211 0 1 22345678999999997765
Q ss_pred C
Q 016454 311 G 311 (389)
Q Consensus 311 G 311 (389)
.
T Consensus 99 ~ 99 (208)
T cd06161 99 G 99 (208)
T ss_pred H
Confidence 4
No 12
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=96.19 E-value=0.0046 Score=64.25 Aligned_cols=26 Identities=31% Similarity=0.451 Sum_probs=23.4
Q ss_pred HHHHHHHhHHHHHHHhCCCcceEEec
Q 016454 231 RILVHEAGHLLIAYLMGCPIRGVILD 256 (389)
Q Consensus 231 RIAyHEAGHALVAyLLg~PV~kvTIi 256 (389)
.|.+||.||||+|.++|..|.+++|-
T Consensus 17 li~vHElGHfl~Ar~~gv~V~~FsiG 42 (449)
T PRK10779 17 LITVHEFGHFWVARRCGVRVERFSIG 42 (449)
T ss_pred HHHHHHHHHHHHHHHcCCeeeEEEee
Confidence 58899999999999999999987764
No 13
>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=96.17 E-value=0.0032 Score=56.93 Aligned_cols=75 Identities=21% Similarity=0.106 Sum_probs=42.0
Q ss_pred HHHHHHHhHHHHHHHhCCCcceEEecchhhhhc-----Cc--cccccceecchhhhhhhhccCCCHHHHHHHHHHHchHH
Q 016454 231 RILVHEAGHLLIAYLMGCPIRGVILDPIVAMQM-----GI--QGQAGTQFWDEKMNNELAEGRLSGTAFDRYSMVLFAGI 303 (389)
Q Consensus 231 RIAyHEAGHALVAyLLg~PV~kvTIiP~~a~rr-----G~--~gagGt~f~~p~~e~~l~~g~lT~~~L~~~i~VlLAGr 303 (389)
-+..||.||+++|+..|+++.+.++...-...+ |. ---+|+....+..++. .+..-.+.+.|.+||.
T Consensus 10 ~i~iHE~gH~~~A~~~G~~~~~~~~~~~~~~~~~~~~~~~~~ip~gG~~~~~~~~~~~------~~~~~~~~~~i~laGP 83 (180)
T cd05709 10 SVTVHELGHALVARRLGVKVARFSGGFTLNPLKHGDPYGIILIPLGGYAKPVGENPRA------FKKPRWQRLLVALAGP 83 (180)
T ss_pred HHHHHHHHHHHHHHHcCCCchheeeeEEECCcCCCCEehHHHHhccCeeccCCCChhh------hccchhhhhhhhhhhH
Confidence 368999999999999999776554321000000 00 0023444333321110 0123445667899999
Q ss_pred HHHHHHhC
Q 016454 304 AAEALIYG 311 (389)
Q Consensus 304 AAEeLvfG 311 (389)
.+.-+...
T Consensus 84 l~nllla~ 91 (180)
T cd05709 84 LANLLLAL 91 (180)
T ss_pred HHHHHHHH
Confidence 99987654
No 14
>PF13398 Peptidase_M50B: Peptidase M50B-like
Probab=96.08 E-value=0.0059 Score=57.19 Aligned_cols=27 Identities=44% Similarity=0.753 Sum_probs=25.8
Q ss_pred HHHHHHHhHHHHHHHhCCCcceEEecc
Q 016454 231 RILVHEAGHLLIAYLMGCPIRGVILDP 257 (389)
Q Consensus 231 RIAyHEAGHALVAyLLg~PV~kvTIiP 257 (389)
-+..||.||++++.++|..++++++.|
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 389999999999999999999999999
No 15
>TIGR00054 RIP metalloprotease RseP. A model that detects fragments as well matches a number of members of the PEPTIDASE FAMILY S2C. The region of match appears not to overlap the active site domain.
Probab=95.93 E-value=0.0067 Score=62.66 Aligned_cols=22 Identities=45% Similarity=0.674 Sum_probs=20.1
Q ss_pred HHHHHHHhHHHHHHHhCCCcce
Q 016454 231 RILVHEAGHLLIAYLMGCPIRG 252 (389)
Q Consensus 231 RIAyHEAGHALVAyLLg~PV~k 252 (389)
.|.+||.||+++|.++|..|.+
T Consensus 16 ~v~~HE~gH~~~a~~~g~~v~~ 37 (420)
T TIGR00054 16 LIFVHELGHFLAARLCGIKVER 37 (420)
T ss_pred HHHHHhHHHHHHHHHcCCEEEE
Confidence 5789999999999999998885
No 16
>PF02163 Peptidase_M50: Peptidase family M50; InterPro: IPR008915 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This entry contains metallopeptidases belonging to MEROPS peptidase family M50 (S2P protease family, clan MM). Members of the M50 metallopeptidase family include: mammalian sterol-regulatory element binding protein (SREBP) site 2 protease, Escherichia coli protease EcfE, stage IV sporulation protein FB and various hypothetical bacterial and eukaryotic homologues. A number of proteins are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity.; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3B4R_A 3ID4_A 3ID2_A 2ZPL_B 3ID1_A 2ZPM_A 3ID3_B 2HGA_A.
Probab=95.74 E-value=0.0092 Score=54.23 Aligned_cols=24 Identities=38% Similarity=0.445 Sum_probs=18.0
Q ss_pred HHHHHHhHHHHHHHhCCCcceEEe
Q 016454 232 ILVHEAGHLLIAYLMGCPIRGVIL 255 (389)
Q Consensus 232 IAyHEAGHALVAyLLg~PV~kvTI 255 (389)
+..||.||+++|+..|+++.++++
T Consensus 10 i~~HE~gH~~~a~~~G~~~~~~~~ 33 (192)
T PF02163_consen 10 IVLHELGHALAARLYGDKVPRFEG 33 (192)
T ss_dssp HHHHHHHHHHHHHTTT--B--EEE
T ss_pred cccccccccccccccccccccccc
Confidence 678999999999999999888853
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=94.94 E-value=0.025 Score=56.15 Aligned_cols=67 Identities=15% Similarity=0.024 Sum_probs=43.8
Q ss_pred HHHHHHHhHHHHHHHhCCCcceEEecchhhhhcCccccccceecchhhhhhhhccCCCHHHHHHHHHHHchHHHHHHHHh
Q 016454 231 RILVHEAGHLLIAYLMGCPIRGVILDPIVAMQMGIQGQAGTQFWDEKMNNELAEGRLSGTAFDRYSMVLFAGIAAEALIY 310 (389)
Q Consensus 231 RIAyHEAGHALVAyLLg~PV~kvTIiP~~a~rrG~~gagGt~f~~p~~e~~l~~g~lT~~~L~~~i~VlLAGrAAEeLvf 310 (389)
-+..||-||+++|...|.+|+++.+.++--+ -+|+.-.+++ +. . ..+. .+++.|++||.++.-++-
T Consensus 137 svvvHElgHal~A~~~gi~V~~iGl~l~~~~------pGa~ve~~~e--~~-~--~~~~---~~~l~Ia~AGp~~NlvLa 202 (277)
T cd06162 137 SGVVHEMGHGVAAVREQVRVNGFGIFFFIIY------PGAYVDLFTD--HL-N--LISP---VQQLRIFCAGVWHNFVLG 202 (277)
T ss_pred HHHHHHHHHHHHHHHcCCeeceEEEeeeecc------CeeEEeeccc--cc-c--cCCh---hhhhheehhhHHHHHHHH
Confidence 4689999999999999999999988763111 1333333222 11 1 1222 246689999999988765
Q ss_pred C
Q 016454 311 G 311 (389)
Q Consensus 311 G 311 (389)
.
T Consensus 203 ~ 203 (277)
T cd06162 203 L 203 (277)
T ss_pred H
Confidence 4
No 18
>cd06160 S2P-M50_like_2 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with additional putative N- and C-terminal transmembrane spanning regions, relative to the core protein, and no PDZ domains.
Probab=94.22 E-value=0.038 Score=51.47 Aligned_cols=27 Identities=30% Similarity=0.308 Sum_probs=25.2
Q ss_pred HHHHHHHhHHHHHHHhCCCcceEEecc
Q 016454 231 RILVHEAGHLLIAYLMGCPIRGVILDP 257 (389)
Q Consensus 231 RIAyHEAGHALVAyLLg~PV~kvTIiP 257 (389)
-+..||.||+++|+..|+++.+..+.|
T Consensus 43 ~l~iHElgH~~~A~~~G~~~~~~~l~P 69 (183)
T cd06160 43 ILGIHEMGHYLAARRHGVKASLPYFIP 69 (183)
T ss_pred HHHHHHHHHHHHHHHCCCCccceeeee
Confidence 578999999999999999999999888
No 19
>cd06159 S2P-M50_PDZ_Arch Uncharacterized Archaeal homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group appears to be limited to Archaeal S2P/M50s homologs with additional putative N-terminal transmembrane spanning regions, relative to the core protein, and either one or two PDZ domains present.
Probab=92.31 E-value=0.056 Score=53.16 Aligned_cols=66 Identities=18% Similarity=0.194 Sum_probs=40.3
Q ss_pred HHHHHHHhHHHHHHHhCCCcceEEecchhhhhcCccccccceecchhhhhhhhccCCCHHHHHHHHHHHchHHHHHHHHh
Q 016454 231 RILVHEAGHLLIAYLMGCPIRGVILDPIVAMQMGIQGQAGTQFWDEKMNNELAEGRLSGTAFDRYSMVLFAGIAAEALIY 310 (389)
Q Consensus 231 RIAyHEAGHALVAyLLg~PV~kvTIiP~~a~rrG~~gagGt~f~~p~~e~~l~~g~lT~~~L~~~i~VlLAGrAAEeLvf 310 (389)
-+..||.||+++|...|++|+.+.+.- ... --|| +..|+++.. .+..-.+++.|++||..+.-+..
T Consensus 120 sv~iHElgHa~~Ar~~G~~V~~iGl~l-----~~i-p~Gg--~v~~~~~~~------~~~~~~~~~~Ia~AGP~~Nlvla 185 (263)
T cd06159 120 GVVVHELSHGILARVEGIKVKSGGLLL-----LII-PPGA--FVEPDEEEL------NKADRRIRLRIFAAGVTANFVVA 185 (263)
T ss_pred HHHHHHHHHHHHHHHcCCEECchhHHH-----Hhh-hcEE--EEEecchhh------ccCChhheeeeeeehHHHHHHHH
Confidence 478999999999999999988865421 000 0123 333322211 11223356678999998886654
No 20
>cd06158 S2P-M50_like_1 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with a minimal core protein and no PDZ domains.
Probab=89.39 E-value=0.26 Score=45.61 Aligned_cols=75 Identities=21% Similarity=0.248 Sum_probs=41.1
Q ss_pred HHHHHHhHHHHHHHhCCCcc----eEEecchhhhhc-Ccc----c-cccceecchhhhhhhhccCCCHHHHHHHHHHHch
Q 016454 232 ILVHEAGHLLIAYLMGCPIR----GVILDPIVAMQM-GIQ----G-QAGTQFWDEKMNNELAEGRLSGTAFDRYSMVLFA 301 (389)
Q Consensus 232 IAyHEAGHALVAyLLg~PV~----kvTIiP~~a~rr-G~~----g-agGt~f~~p~~e~~l~~g~lT~~~L~~~i~VlLA 301 (389)
+..||.||+++|+..|++.. ..|+.|+.-..- |.- . ..|..+..|..-+. ... ++.-.+...|++|
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 67899999999999998665 367767311110 100 0 00233333321111 011 2222345679999
Q ss_pred HHHHHHHHh
Q 016454 302 GIAAEALIY 310 (389)
Q Consensus 302 GrAAEeLvf 310 (389)
|-++.-+..
T Consensus 88 GP~~n~~la 96 (181)
T cd06158 88 GPLSNLLLA 96 (181)
T ss_pred hHHHHHHHH
Confidence 999987653
No 21
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=83.16 E-value=0.84 Score=44.05 Aligned_cols=19 Identities=47% Similarity=0.651 Sum_probs=15.1
Q ss_pred HHHHHHHhHHHHHHHhCCCc
Q 016454 231 RILVHEAGHLLIAYLMGCPI 250 (389)
Q Consensus 231 RIAyHEAGHALVAyLLg~PV 250 (389)
-|-|||.||||+..+ +.||
T Consensus 94 ~~l~HE~GHAlI~~~-~lPv 112 (220)
T PF14247_consen 94 FTLYHELGHALIDDL-DLPV 112 (220)
T ss_pred HHHHHHHHHHHHHHh-cCCc
Confidence 588999999999854 4554
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=80.52 E-value=0.81 Score=39.62 Aligned_cols=16 Identities=31% Similarity=0.482 Sum_probs=13.5
Q ss_pred hhhhHHHHHHHHhHHH
Q 016454 226 PPYKRRILVHEAGHLL 241 (389)
Q Consensus 226 ~~ekrRIAyHEAGHAL 241 (389)
..+...|+.||.||+|
T Consensus 102 ~~~~~~v~~HEiGHaL 117 (154)
T PF00413_consen 102 GNDLQSVAIHEIGHAL 117 (154)
T ss_dssp SEEHHHHHHHHHHHHT
T ss_pred hhhhhhhhhhcccccc
Confidence 4567799999999985
No 23
>cd04279 ZnMc_MMP_like_1 Zinc-dependent metalloprotease; MMP_like sub-family 1. A group of bacterial, archaeal, and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=77.30 E-value=1.4 Score=38.88 Aligned_cols=17 Identities=35% Similarity=0.415 Sum_probs=14.1
Q ss_pred hhhhHHHHHHHHhHHHH
Q 016454 226 PPYKRRILVHEAGHLLI 242 (389)
Q Consensus 226 ~~ekrRIAyHEAGHALV 242 (389)
..+...|+.||.||+|=
T Consensus 101 ~~~~~~~~~HEiGHaLG 117 (156)
T cd04279 101 AENLQAIALHELGHALG 117 (156)
T ss_pred chHHHHHHHHHhhhhhc
Confidence 45778999999999863
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=73.64 E-value=2.1 Score=37.54 Aligned_cols=16 Identities=38% Similarity=0.416 Sum_probs=13.6
Q ss_pred hhhhHHHHHHHHhHHH
Q 016454 226 PPYKRRILVHEAGHLL 241 (389)
Q Consensus 226 ~~ekrRIAyHEAGHAL 241 (389)
..+...++.||.||+|
T Consensus 91 ~~~~~~~~~HEiGHaL 106 (165)
T cd04268 91 GARLRNTAEHELGHAL 106 (165)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 3567899999999996
No 25
>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=69.06 E-value=2.2 Score=37.79 Aligned_cols=16 Identities=31% Similarity=0.343 Sum_probs=13.5
Q ss_pred hhhhHHHHHHHHhHHH
Q 016454 226 PPYKRRILVHEAGHLL 241 (389)
Q Consensus 226 ~~ekrRIAyHEAGHAL 241 (389)
..+...|+.||.||+|
T Consensus 104 ~~~~~~~~~HEiGHaL 119 (157)
T cd04278 104 GTDLFSVAAHEIGHAL 119 (157)
T ss_pred cchHHHHHHHHhcccc
Confidence 4567899999999984
No 26
>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=67.23 E-value=3.7 Score=36.92 Aligned_cols=15 Identities=47% Similarity=0.685 Sum_probs=11.6
Q ss_pred hhhHHHHHHHHhHHH
Q 016454 227 PYKRRILVHEAGHLL 241 (389)
Q Consensus 227 ~ekrRIAyHEAGHAL 241 (389)
-+.-||+-||.||.|
T Consensus 75 y~~~RIaaHE~GHiL 89 (132)
T PF02031_consen 75 YNSTRIAAHELGHIL 89 (132)
T ss_dssp S-HHHHHHHHHHHHH
T ss_pred Cccceeeeehhcccc
Confidence 345689999999975
No 27
>cd04277 ZnMc_serralysin_like Zinc-dependent metalloprotease, serralysin_like subfamily. Serralysins and related proteases are important virulence factors in pathogenic bacteria. They may be secreted into the medium via a mechanism found in gram-negative bacteria, that does not require n-terminal signal sequences which are cleaved after the transmembrane translocation. A calcium-binding domain c-terminal to the metalloprotease domain, which contains multiple tandem repeats of a nine-residue motif including the pattern GGxGxD, and which forms a parallel beta roll may be involved in the translocation mechanism and/or substrate binding. Serralysin family members may have a broad spectrum of substrates each, including host immunoglobulins, complement proteins, cell matrix and cytoskeletal proteins, as well as antimicrobial peptides.
Probab=64.96 E-value=4.1 Score=37.05 Aligned_cols=17 Identities=35% Similarity=0.593 Sum_probs=14.1
Q ss_pred hhhhHHHHHHHHhHHHH
Q 016454 226 PPYKRRILVHEAGHLLI 242 (389)
Q Consensus 226 ~~ekrRIAyHEAGHALV 242 (389)
..+...++.||.||+|=
T Consensus 110 g~~~~~t~~HEiGHaLG 126 (186)
T cd04277 110 GSYGYQTIIHEIGHALG 126 (186)
T ss_pred ChhhHHHHHHHHHHHhc
Confidence 35678999999999873
No 28
>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=61.49 E-value=4.2 Score=39.52 Aligned_cols=13 Identities=31% Similarity=0.580 Sum_probs=10.7
Q ss_pred HHHHHHHhHHHHH
Q 016454 231 RILVHEAGHLLIA 243 (389)
Q Consensus 231 RIAyHEAGHALVA 243 (389)
-||-||+|||+=-
T Consensus 91 aVAAHEvGHAiQ~ 103 (222)
T PF04298_consen 91 AVAAHEVGHAIQH 103 (222)
T ss_pred HHHHHHHhHHHhc
Confidence 4899999999743
No 29
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=60.78 E-value=6.6 Score=39.18 Aligned_cols=26 Identities=27% Similarity=0.499 Sum_probs=22.3
Q ss_pred HHHHHHHhHHHHHHHhCCCcceEEec
Q 016454 231 RILVHEAGHLLIAYLMGCPIRGVILD 256 (389)
Q Consensus 231 RIAyHEAGHALVAyLLg~PV~kvTIi 256 (389)
.+..||-||+++++.++..|.+++|.
T Consensus 15 lv~~he~gh~~~a~~~~~~v~~f~ig 40 (375)
T COG0750 15 LVFVHELGHFWVARRCGVKVERFSIG 40 (375)
T ss_pred HHHHHHHhhHHHHHhcCceeEEEEec
Confidence 58899999999999999877777653
No 30
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=59.80 E-value=7 Score=41.22 Aligned_cols=25 Identities=36% Similarity=0.503 Sum_probs=21.2
Q ss_pred HHHHHHhHHHHHHHhCCCcceEEec
Q 016454 232 ILVHEAGHLLIAYLMGCPIRGVILD 256 (389)
Q Consensus 232 IAyHEAGHALVAyLLg~PV~kvTIi 256 (389)
.-+||.||||+|-.-|.+|.++-|-
T Consensus 134 ~vvHElGHalAA~segV~vngfgIf 158 (484)
T KOG2921|consen 134 VVVHELGHALAAASEGVQVNGFGIF 158 (484)
T ss_pred HHHHHhhHHHHHHhcCceeeeeEEE
Confidence 4689999999999999888877543
No 31
>cd04327 ZnMc_MMP_like_3 Zinc-dependent metalloprotease; MMP_like sub-family 3. A group of bacterial and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=58.27 E-value=6.3 Score=36.59 Aligned_cols=17 Identities=35% Similarity=0.401 Sum_probs=13.3
Q ss_pred hhHHHHHHHHhHHHHHH
Q 016454 228 YKRRILVHEAGHLLIAY 244 (389)
Q Consensus 228 ekrRIAyHEAGHALVAy 244 (389)
+...++.||.||||=-+
T Consensus 91 ~~~~~i~HElgHaLG~~ 107 (198)
T cd04327 91 EFSRVVLHEFGHALGFI 107 (198)
T ss_pred hHHHHHHHHHHHHhcCc
Confidence 45679999999997543
No 32
>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=56.74 E-value=5.5 Score=34.34 Aligned_cols=11 Identities=45% Similarity=0.752 Sum_probs=9.9
Q ss_pred HHHHHHHhHHH
Q 016454 231 RILVHEAGHLL 241 (389)
Q Consensus 231 RIAyHEAGHAL 241 (389)
.|+.||.||+|
T Consensus 88 ~~~~HEigHaL 98 (140)
T smart00235 88 GVAAHELGHAL 98 (140)
T ss_pred ccHHHHHHHHh
Confidence 39999999997
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=51.18 E-value=6.8 Score=35.52 Aligned_cols=16 Identities=38% Similarity=0.474 Sum_probs=12.9
Q ss_pred hhhhHHHHHHHHhHHH
Q 016454 226 PPYKRRILVHEAGHLL 241 (389)
Q Consensus 226 ~~ekrRIAyHEAGHAL 241 (389)
+....++..||.||.|
T Consensus 66 ~~~~g~TltHEvGH~L 81 (154)
T PF05572_consen 66 QYNFGKTLTHEVGHWL 81 (154)
T ss_dssp TS-SSHHHHHHHHHHT
T ss_pred ccccccchhhhhhhhh
Confidence 4566799999999987
No 34
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=49.67 E-value=24 Score=22.33 Aligned_cols=28 Identities=21% Similarity=0.476 Sum_probs=25.2
Q ss_pred HHHhhhccchHHHHHHHHHHHHhCCCCC
Q 016454 104 VLDTCLNADDLKLVASAYKFLQNRGFLP 131 (389)
Q Consensus 104 ~l~~~~~~~d~~~v~~~y~~l~~~G~l~ 131 (389)
++++|.+..|.+.+-++++.+++.|.-|
T Consensus 7 ll~a~~~~g~~~~a~~~~~~M~~~gv~P 34 (34)
T PF13812_consen 7 LLRACAKAGDPDAALQLFDEMKEQGVKP 34 (34)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence 6899999999999999999999998644
No 35
>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=46.38 E-value=10 Score=33.05 Aligned_cols=16 Identities=31% Similarity=0.378 Sum_probs=13.2
Q ss_pred hhhHHHHHHHHhHHHH
Q 016454 227 PYKRRILVHEAGHLLI 242 (389)
Q Consensus 227 ~ekrRIAyHEAGHALV 242 (389)
..-..++.||.||+|=
T Consensus 94 ~~~~~~~~HElGH~LG 109 (167)
T cd00203 94 KEGAQTIAHELGHALG 109 (167)
T ss_pred ccchhhHHHHHHHHhC
Confidence 3567899999999985
No 36
>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=44.65 E-value=22 Score=28.53 Aligned_cols=23 Identities=35% Similarity=0.417 Sum_probs=17.5
Q ss_pred CChhhhHHHHHHHHhHHHHHHHh
Q 016454 224 YWPPYKRRILVHEAGHLLIAYLM 246 (389)
Q Consensus 224 ls~~ekrRIAyHEAGHALVAyLL 246 (389)
.++..++=+..||.||.+...--
T Consensus 37 ~~~~~~~f~laHELgH~~~~~~~ 59 (122)
T PF06114_consen 37 LSPERQRFTLAHELGHILLHHGD 59 (122)
T ss_dssp S-HHHHHHHHHHHHHHHHHHH-H
T ss_pred CCHHHHHHHHHHHHHHHHhhhcc
Confidence 56777778999999999987543
No 37
>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1.
Probab=41.36 E-value=97 Score=28.81 Aligned_cols=63 Identities=22% Similarity=0.512 Sum_probs=47.4
Q ss_pred HHHHHHH-HHHHHH----hhhcHHHHHHHhhh-cCCCCCCCccchhhhhcccccccCCccCCCCchhHHHHhhhccchHH
Q 016454 42 RALKEWQ-EYEDAV----KRKDLARALRFLKN-KNDNNPIEPLSDSLMGESNRARLPEFVGGFDRDWEVLDTCLNADDLK 115 (389)
Q Consensus 42 ~~~~~~~-~~~~~~----~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~d~~ 115 (389)
.-|+.-+ .||.-| ..+++..|+||.++ +..+. + |. =.+|+++.+.+|..
T Consensus 83 DMLkRL~~~~~~iievLL~~g~vl~ALr~ar~~~~~~~------------~-----~~--------~~fLeAA~~~~D~~ 137 (167)
T PF07035_consen 83 DMLKRLGTAYEEIIEVLLSKGQVLEALRYARQYHKVDS------------V-----PA--------RKFLEAAANSNDDQ 137 (167)
T ss_pred HHHHHhhhhHHHHHHHHHhCCCHHHHHHHHHHcCCccc------------C-----CH--------HHHHHHHHHcCCHH
Confidence 5566666 666655 58999999999987 33331 1 11 24799999999999
Q ss_pred HHHHHHHHHHhCCC
Q 016454 116 LVASAYKFLQNRGF 129 (389)
Q Consensus 116 ~v~~~y~~l~~~G~ 129 (389)
+...+|.+...++.
T Consensus 138 lf~~V~~ff~~~n~ 151 (167)
T PF07035_consen 138 LFYAVFRFFEERNL 151 (167)
T ss_pred HHHHHHHHHHHhhH
Confidence 99999999999883
No 38
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=35.00 E-value=19 Score=30.12 Aligned_cols=12 Identities=42% Similarity=0.600 Sum_probs=10.4
Q ss_pred HHHHHHHHhHHH
Q 016454 230 RRILVHEAGHLL 241 (389)
Q Consensus 230 rRIAyHEAGHAL 241 (389)
..+..||.||.|
T Consensus 108 ~~~~~HEiGH~l 119 (124)
T PF13582_consen 108 VDTFAHEIGHNL 119 (124)
T ss_dssp TTHHHHHHHHHT
T ss_pred ceEeeehhhHhc
Confidence 389999999986
No 39
>smart00762 Cog4 COG4 transport protein. This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport.
Probab=33.70 E-value=32 Score=34.70 Aligned_cols=21 Identities=33% Similarity=0.645 Sum_probs=19.4
Q ss_pred HHHHHHHHhhhcHHHHHHHhh
Q 016454 47 WQEYEDAVKRKDLARALRFLK 67 (389)
Q Consensus 47 ~~~~~~~~~~~~~~~~~~~~~ 67 (389)
+++|++||+.+|.+...||.|
T Consensus 13 ~~~F~~Av~~~D~~~i~rffk 33 (324)
T smart00762 13 KERFDEAVKAQDVPELTRFFK 33 (324)
T ss_pred HHHHHHHHHcCCHHHHHHHHH
Confidence 579999999999999999876
No 40
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=33.34 E-value=43 Score=27.04 Aligned_cols=23 Identities=26% Similarity=0.409 Sum_probs=18.4
Q ss_pred ChhhhHHHHHHHHhHHHHHHHhC
Q 016454 225 WPPYKRRILVHEAGHLLIAYLMG 247 (389)
Q Consensus 225 s~~ekrRIAyHEAGHALVAyLLg 247 (389)
++..-.++..||.+|.+.....+
T Consensus 21 ~~~~~~~~l~HE~~H~~~~~~~~ 43 (128)
T PF13485_consen 21 DEDWLDRVLAHELAHQWFGNYFG 43 (128)
T ss_pred CHHHHHHHHHHHHHHHHHHHHcC
Confidence 34445699999999999988765
No 41
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=29.69 E-value=89 Score=19.24 Aligned_cols=29 Identities=21% Similarity=0.351 Sum_probs=25.7
Q ss_pred HHHhhhccchHHHHHHHHHHHHhCCCCCC
Q 016454 104 VLDTCLNADDLKLVASAYKFLQNRGFLPS 132 (389)
Q Consensus 104 ~l~~~~~~~d~~~v~~~y~~l~~~G~l~~ 132 (389)
+++++....+....-+.|..+++.|.-|+
T Consensus 6 li~~~~~~~~~~~a~~~~~~M~~~g~~p~ 34 (35)
T TIGR00756 6 LIDGLCKAGRVEEALELFKEMLERGIEPD 34 (35)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence 67889999999999999999999998664
No 42
>PF07998 Peptidase_M54: Peptidase family M54; InterPro: IPR012962 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This entry represents zinc-dependent peptidases belonging to the MEROPS peptidase family M54, more commonly known as the archaemetzincins. The family has a wide taxonomic distribution, being found in archaea, bacteria and eukaryotes. Two human homologues have been characterised []. ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding; PDB: 3LMC_A 2XHQ_A 2X7M_A.
Probab=27.94 E-value=30 Score=32.97 Aligned_cols=11 Identities=55% Similarity=0.884 Sum_probs=9.3
Q ss_pred HHHHHHHhHHH
Q 016454 231 RILVHEAGHLL 241 (389)
Q Consensus 231 RIAyHEAGHAL 241 (389)
+.+.||.||.+
T Consensus 147 Kea~HElGH~~ 157 (194)
T PF07998_consen 147 KEAVHELGHLF 157 (194)
T ss_dssp HHHHHHHHHHT
T ss_pred HHHHHHHHHHc
Confidence 57999999965
No 43
>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=27.70 E-value=33 Score=34.26 Aligned_cols=22 Identities=27% Similarity=0.261 Sum_probs=17.0
Q ss_pred hhhHHHHHHHHhHHHHHHHhCC
Q 016454 227 PYKRRILVHEAGHLLIAYLMGC 248 (389)
Q Consensus 227 ~ekrRIAyHEAGHALVAyLLg~ 248 (389)
-+-=.+..||.||++=..+...
T Consensus 152 ~~~v~tl~HE~GHa~h~~l~~~ 173 (365)
T cd06258 152 HDDINTLFHEFGHAVHFLLIQQ 173 (365)
T ss_pred HHHHHHHHHHHhHHHHHHHhcC
Confidence 3344789999999998887763
No 44
>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=26.77 E-value=32 Score=31.60 Aligned_cols=14 Identities=36% Similarity=0.223 Sum_probs=11.7
Q ss_pred HHHHHHHHhHHHHH
Q 016454 230 RRILVHEAGHLLIA 243 (389)
Q Consensus 230 rRIAyHEAGHALVA 243 (389)
..++.||.||||=-
T Consensus 75 ~g~v~HE~~HalG~ 88 (180)
T cd04280 75 LGTIVHELMHALGF 88 (180)
T ss_pred CchhHHHHHHHhcC
Confidence 58999999999644
No 45
>PF01400 Astacin: Astacin (Peptidase family M12A) This Prosite motif covers only the active site.; InterPro: IPR001506 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M12, subfamily M12A (astacin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. The astacin () family of metalloendopeptidases encompasses a range of proteins found in hydra to humans, in mature and developmental systems []. Their functions include activation of growth factors, degradation of polypeptides, and processing of extracellular proteins []. The proteins are synthesised with N-terminal signal and pro-enzyme sequences, and many contain multiple domains C-terminal to the protease domain. They are either secreted from cells, or are associated with the plasma membrane. The astacin molecule adopts a kidney shape, with a deep active-site cleft between its N- and C-terminal domains []. The zinc ion, which lies at the bottom of the cleft, exhibits a unique penta-coordinated mode of binding, involving 3 histidine residues, a tyrosine and a water molecule (which is also bound to the carboxylate side chain of Glu93) []. The N-terminal domain comprises 2 alpha-helices and a 5-stranded beta-sheet. The overall topology of this domain is shared by the archetypal zinc-endopeptidase thermolysin. Astacin protease domains also share common features with serralysins, matrix metalloendopeptidases, and snake venom proteases; they cleave peptide bonds in polypeptides such as insulin B chain and bradykinin, and in proteins such as casein and gelatin; and they have arylamidase activity [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3LQB_A 3EDH_A 3EDG_A 3EDI_A 1IAE_A 1IAB_A 1IAA_A 1AST_A 1IAC_A 1QJJ_A ....
Probab=26.61 E-value=41 Score=31.19 Aligned_cols=16 Identities=31% Similarity=0.463 Sum_probs=12.1
Q ss_pred hHHHHHHHHhHHHHHH
Q 016454 229 KRRILVHEAGHLLIAY 244 (389)
Q Consensus 229 krRIAyHEAGHALVAy 244 (389)
...++.||.||||=-+
T Consensus 79 ~~~~i~HEl~HaLG~~ 94 (191)
T PF01400_consen 79 SVGTILHELGHALGFW 94 (191)
T ss_dssp SHHHHHHHHHHHHTB-
T ss_pred CccchHHHHHHHHhhh
Confidence 3579999999997433
No 46
>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=25.97 E-value=46 Score=32.24 Aligned_cols=20 Identities=25% Similarity=0.358 Sum_probs=15.8
Q ss_pred CChhhhHHHHHHHHhHHHHH
Q 016454 224 YWPPYKRRILVHEAGHLLIA 243 (389)
Q Consensus 224 ls~~ekrRIAyHEAGHALVA 243 (389)
.+....+.|..||.||.+==
T Consensus 128 ~~~~~~~hvi~HEiGH~IGf 147 (211)
T PF12388_consen 128 YSVNVIEHVITHEIGHCIGF 147 (211)
T ss_pred CchhHHHHHHHHHhhhhccc
Confidence 35567888999999998743
No 47
>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=25.92 E-value=14 Score=37.49 Aligned_cols=17 Identities=18% Similarity=0.169 Sum_probs=13.8
Q ss_pred hhhHHHHHHHHhHHHHH
Q 016454 227 PYKRRILVHEAGHLLIA 243 (389)
Q Consensus 227 ~ekrRIAyHEAGHALVA 243 (389)
.+..---|||.|||||-
T Consensus 92 ~~~~lY~Y~~iGHFWVk 108 (299)
T PF12994_consen 92 EETHLYNYGEIGHFWVK 108 (299)
T ss_pred HHHHHhhccccceeeec
Confidence 55666789999999984
No 48
>COG2738 Predicted Zn-dependent protease [General function prediction only]
Probab=24.07 E-value=40 Score=32.72 Aligned_cols=13 Identities=31% Similarity=0.593 Sum_probs=10.8
Q ss_pred HHHHHHHhHHHHH
Q 016454 231 RILVHEAGHLLIA 243 (389)
Q Consensus 231 RIAyHEAGHALVA 243 (389)
-||-||.|||+=-
T Consensus 94 aVAAHEVGHAiQd 106 (226)
T COG2738 94 AVAAHEVGHAIQD 106 (226)
T ss_pred HHHHHHhhHHHhh
Confidence 4789999999854
No 49
>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=23.99 E-value=38 Score=32.64 Aligned_cols=18 Identities=33% Similarity=0.704 Sum_probs=16.1
Q ss_pred hhhhHHHHHHHHhHHHHHH
Q 016454 226 PPYKRRILVHEAGHLLIAY 244 (389)
Q Consensus 226 ~~ekrRIAyHEAGHALVAy 244 (389)
..||.-+.-||.||+| +|
T Consensus 136 ~~YRqYvINHEVGH~L-Gh 153 (203)
T PF11350_consen 136 ASYRQYVINHEVGHAL-GH 153 (203)
T ss_pred HHHHHHhhhhhhhhhc-cc
Confidence 5899999999999999 55
No 50
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=23.67 E-value=1.1e+02 Score=18.62 Aligned_cols=26 Identities=8% Similarity=0.282 Sum_probs=23.5
Q ss_pred HHHhhhccchHHHHHHHHHHHHhCCC
Q 016454 104 VLDTCLNADDLKLVASAYKFLQNRGF 129 (389)
Q Consensus 104 ~l~~~~~~~d~~~v~~~y~~l~~~G~ 129 (389)
++++|.+..+.+-+-+.|+.+++.|.
T Consensus 6 li~~~~~~~~~~~a~~~~~~M~~~g~ 31 (31)
T PF01535_consen 6 LISGYCKMGQFEEALEVFDEMRERGI 31 (31)
T ss_pred HHHHHHccchHHHHHHHHHHHhHCcC
Confidence 68999999999999999999999884
No 51
>PF10579 Rapsyn_N: Rapsyn N-terminal myristoylation and linker region; InterPro: IPR019568 Neuromuscular junction formation relies upon the clustering of acetylcholine receptors and other proteins in the muscle membrane. Rapsyn is a peripheral membrane protein that is selectively concentrated at the neuromuscular junction and is essential for the formation of synaptic acetylcholine receptor aggregates. Acetylcholine receptors fail to aggregate beneath nerve terminals in mice where rapsyn has been knocked out. The N-terminal six amino acids of rapsyn are its myristoylation site, and myristoylation is necessary for the targeting of the protein to the membrane []. ; GO: 0008270 zinc ion binding, 0033130 acetylcholine receptor binding, 0007268 synaptic transmission, 0005856 cytoskeleton, 0030054 cell junction, 0045211 postsynaptic membrane
Probab=23.05 E-value=77 Score=26.40 Aligned_cols=18 Identities=33% Similarity=0.743 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 016454 38 KYLARALKEWQEYEDAVK 55 (389)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~ 55 (389)
-||..|.-||..|+|+.+
T Consensus 47 G~l~qA~~e~Gkyr~~L~ 64 (80)
T PF10579_consen 47 GYLIQAHMEWGKYREMLA 64 (80)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 377899999999999653
No 52
>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=23.04 E-value=44 Score=31.30 Aligned_cols=16 Identities=38% Similarity=0.395 Sum_probs=12.5
Q ss_pred HHHHHHHHhHHHHHHH
Q 016454 230 RRILVHEAGHLLIAYL 245 (389)
Q Consensus 230 rRIAyHEAGHALVAyL 245 (389)
.-++.||.||||=-+=
T Consensus 78 ~G~i~HEl~HaLG~~H 93 (182)
T cd04283 78 KGIIQHELLHALGFYH 93 (182)
T ss_pred cchHHHHHHHHhCCcc
Confidence 3689999999985543
No 53
>PRK13379 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=22.99 E-value=1.3e+02 Score=26.82 Aligned_cols=33 Identities=15% Similarity=0.434 Sum_probs=26.1
Q ss_pred chhhhHHHH---HHHHHHH---HHHHHHhhhcHHHHHHH
Q 016454 33 KPLRTKYLA---RALKEWQ---EYEDAVKRKDLARALRF 65 (389)
Q Consensus 33 ~~~~~~~~~---~~~~~~~---~~~~~~~~~~~~~~~~~ 65 (389)
..||.+.++ +.+.||. |=.+||+++|..+.+++
T Consensus 38 ~~~RerF~aDe~ay~~~~~Lt~eqk~aV~~RDw~~mi~~ 76 (119)
T PRK13379 38 APWRDRFLQDAEALMQEAGLTEQEKELIRARDWLGLVQY 76 (119)
T ss_pred HHHHHHHHhCHHHHHHHcCCCHHHHHHHHhccHHHHHHc
Confidence 357888877 6778884 66789999999999954
No 54
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=22.37 E-value=44 Score=31.41 Aligned_cols=15 Identities=33% Similarity=0.357 Sum_probs=11.5
Q ss_pred HHHHHHHhHHHHHHH
Q 016454 231 RILVHEAGHLLIAYL 245 (389)
Q Consensus 231 RIAyHEAGHALVAyL 245 (389)
.+..||.||.|=+.=
T Consensus 139 ~~~aHEiGH~lGl~H 153 (206)
T PF13583_consen 139 QTFAHEIGHNLGLRH 153 (206)
T ss_pred hHHHHHHHHHhcCCC
Confidence 568899999876543
No 55
>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=21.91 E-value=47 Score=31.54 Aligned_cols=15 Identities=40% Similarity=0.649 Sum_probs=11.8
Q ss_pred HHHHHHHhHHHHHHH
Q 016454 231 RILVHEAGHLLIAYL 245 (389)
Q Consensus 231 RIAyHEAGHALVAyL 245 (389)
-++.||.||||=-+=
T Consensus 89 Gti~HEl~HaLGf~H 103 (200)
T cd04281 89 GIVVHELGHVIGFWH 103 (200)
T ss_pred chHHHHHHHHhcCcc
Confidence 489999999985443
No 56
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=21.75 E-value=64 Score=30.96 Aligned_cols=25 Identities=20% Similarity=0.178 Sum_probs=20.3
Q ss_pred CCCChhhhHHHHHHHHhHHHHHHHh
Q 016454 222 SSYWPPYKRRILVHEAGHLLIAYLM 246 (389)
Q Consensus 222 ~~ls~~ekrRIAyHEAGHALVAyLL 246 (389)
..++++|-+-|.-||.||..-.+..
T Consensus 150 ~~l~~dEl~aVlaHElgHi~~rd~~ 174 (302)
T COG0501 150 DLLNDDELEAVLAHELGHIKNRHTL 174 (302)
T ss_pred hhCCHHHHHHHHHHHHHHHhcccHH
Confidence 3568999999999999998765543
No 57
>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=21.62 E-value=59 Score=30.82 Aligned_cols=30 Identities=10% Similarity=0.257 Sum_probs=18.7
Q ss_pred ccccccccccccccccchhhhHHHHHHHHHHHHHH
Q 016454 17 QKCCFLFPQTLVQGKLKPLRTKYLARALKEWQEYE 51 (389)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 (389)
+.|.|-+....- +.||+ .+..++++|.++=
T Consensus 8 ~pItyyI~~~~p----~~~r~-aI~~A~~~Wn~~f 37 (197)
T cd04276 8 EPIVYYLDNTFP----EKYRD-AIREGVLYWNKAF 37 (197)
T ss_pred CCEEEEecCCCc----HHHHH-HHHHHHHHHHHHH
Confidence 455555544321 56654 5788999998864
No 58
>PRK13267 archaemetzincin-like protein; Reviewed
Probab=21.40 E-value=52 Score=30.78 Aligned_cols=11 Identities=45% Similarity=0.773 Sum_probs=8.9
Q ss_pred HHHHHHHhHHH
Q 016454 231 RILVHEAGHLL 241 (389)
Q Consensus 231 RIAyHEAGHAL 241 (389)
+.+.||.||.|
T Consensus 127 k~~~HElGH~l 137 (179)
T PRK13267 127 KEVTHELGHTL 137 (179)
T ss_pred HHHHHHHHHHc
Confidence 45999999973
No 59
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=21.16 E-value=96 Score=27.69 Aligned_cols=27 Identities=30% Similarity=0.560 Sum_probs=22.4
Q ss_pred hhHHHHhhhccchHHHHHHHHHHHHhCCC
Q 016454 101 DWEVLDTCLNADDLKLVASAYKFLQNRGF 129 (389)
Q Consensus 101 ~~~~l~~~~~~~d~~~v~~~y~~l~~~G~ 129 (389)
.|. +++-+..|+..|.++|..|++.|.
T Consensus 111 ~W~--~~f~~~~~l~~i~~~y~~L~~~G~ 137 (142)
T cd03569 111 AWA--LAFRNKPQLKYVVDTYQILKAEGH 137 (142)
T ss_pred HHH--HHhCCCcccHHHHHHHHHHHHcCC
Confidence 454 456666799999999999999998
No 60
>COG5549 Predicted Zn-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=21.14 E-value=49 Score=32.42 Aligned_cols=19 Identities=26% Similarity=0.118 Sum_probs=15.4
Q ss_pred CChhhhHHHHHHHHhHHHH
Q 016454 224 YWPPYKRRILVHEAGHLLI 242 (389)
Q Consensus 224 ls~~ekrRIAyHEAGHALV 242 (389)
.+.++..-+|.||-||||=
T Consensus 182 ~~~e~L~~tarhElGhaLg 200 (236)
T COG5549 182 ELRENLNPTARHELGHALG 200 (236)
T ss_pred cchhhhhHHHHHhhcchhe
Confidence 3567777899999999973
No 61
>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=20.80 E-value=15 Score=35.39 Aligned_cols=18 Identities=33% Similarity=0.331 Sum_probs=14.3
Q ss_pred hhhhHHHHHHHHhHHHHH
Q 016454 226 PPYKRRILVHEAGHLLIA 243 (389)
Q Consensus 226 ~~ekrRIAyHEAGHALVA 243 (389)
+...-+++.||.||.|--
T Consensus 134 ~~n~g~t~~HEvGH~lGL 151 (225)
T cd04275 134 PYNLGDTATHEVGHWLGL 151 (225)
T ss_pred cccccceeEEeccceeee
Confidence 456678999999998743
No 62
>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=20.75 E-value=71 Score=29.03 Aligned_cols=24 Identities=21% Similarity=0.250 Sum_probs=19.7
Q ss_pred CChhhhHHHHHHHHhHHHHHHHhC
Q 016454 224 YWPPYKRRILVHEAGHLLIAYLMG 247 (389)
Q Consensus 224 ls~~ekrRIAyHEAGHALVAyLLg 247 (389)
++++|..-|.-||.||..-.+..-
T Consensus 84 ~~~~el~aVlaHElgH~~~~h~~~ 107 (226)
T PF01435_consen 84 LSEDELAAVLAHELGHIKHRHILK 107 (226)
T ss_dssp SSHHHHHHHHHHHHHHHHTTHCCC
T ss_pred ccHHHHHHHHHHHHHHHHcCCcch
Confidence 468999999999999998666543
Done!